@article{Meng2019, doi = {10.1038/s41467-019-11126-8}, url = {https://doi.org/10.1038/s41467-019-11126-8}, year = {2019}, month = jul, publisher = {Springer Science and Business Media LLC}, volume = {10}, number = {1}, author = {Ran Meng and Mengqiu Jiang and Zhicheng Cui and Jeng-Yih Chang and Kailu Yang and Joanita Jakana and Xinzhe Yu and Zhao Wang and Bo Hu and Junjie Zhang}, title = {Structural basis for the adsorption of a single-stranded RNA bacteriophage}, journal = {Nature Communications} } @article{Salem2020, doi = {10.1186/s13293-020-00327-2}, url = {https://doi.org/10.1186/s13293-020-00327-2}, year = {2020}, month = sep, publisher = {Springer Science and Business Media LLC}, volume = {11}, number = {1}, author = {Nihal A. Salem and Amanda H. Mahnke and Alan B. Wells and Alexander M. Tseng and Lyubov Yevtushok and Natalya Zymak-Zakutnya and Wladimir Wertlecki and Christina D. Chambers and Rajesh C. Miranda and}, title = {Association between fetal sex and maternal plasma microRNA responses to prenatal alcohol exposure: evidence from a birth outcome-stratified cohort}, journal = {Biology of Sex Differences} } @article{Hwang2020, doi = {10.1073/pnas.2005899117}, url = {https://doi.org/10.1073/pnas.2005899117}, year = {2020}, month = aug, publisher = {Proceedings of the National Academy of Sciences}, volume = {117}, number = {35}, pages = {21336--21345}, author = {Wonmuk Hwang and Robert J. Mallis and Matthew J. Lang and Ellis L. Reinherz}, title = {TheαβTCR mechanosensor exploits dynamic ectodomain allostery to optimize its ligand recognition site}, journal = {Proceedings of the National Academy of Sciences} } @article{Krieger2020, doi = {10.1016/j.jmb.2020.06.013}, url = {https://doi.org/10.1016/j.jmb.2020.06.013}, year = {2020}, month = jul, publisher = {Elsevier BV}, volume = {432}, number = {16}, pages = {4623--4636}, author = {Inna V. Krieger and Vladimir Kuznetsov and Jeng-Yih Chang and Junjie Zhang and Samir H. Moussa and Ryland F. Young and James C. Sacchettini}, title = {The Structural Basis of T4 Phage Lysis Control: DNA as the Signal for Lysis Inhibition}, journal = {Journal of Molecular Biology} } @article{Shi2020, doi = {10.1016/j.bpj.2020.03.026}, url = {https://doi.org/10.1016/j.bpj.2020.03.026}, year = {2020}, month = may, publisher = {Elsevier {BV}}, volume = {118}, number = {10}, pages = {2502--2512}, author = {Jie Shi and Qingliang Shen and Jae-Hyun Cho and Wonmuk Hwang}, title = {Entropy Hotspots for the Binding of Intrinsically Disordered Ligands to a Receptor Domain}, journal = {Biophysical Journal} } @article{Xing2020, doi = {10.3389/fgene.2020.00082}, url = {https://doi.org/10.3389/fgene.2020.00082}, year = {2020}, month = feb, publisher = {Frontiers Media SA}, volume = {11}, author = {Yue Xing and Alan R. Dabney and Xiao Li and Guosong Wang and Clare A. Gill and Claudio Casola}, title = {SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference Genomes}, journal = {Frontiers in Genetics} } @article{Mateos2019, doi = {10.1002/ece3.4874}, url = {https://doi.org/10.1002/ece3.4874}, year = {2019}, month = jan, publisher = {Wiley}, volume = {9}, number = {4}, pages = {1845--1857}, author = {Mariana Mateos and Omar Domínguez-Domínguez and Alejandro Varela-Romero}, title = {A multilocus phylogeny of the fish Poeciliopsis: Solving taxonomic uncertainties and preliminary evidence of reticulation}, journal = {Ecology and Evolution} } @article{Eggleston2020, doi = {10.1186/s12864-020-06981-5}, url = {https://doi.org/10.1186/s12864-020-06981-5}, year = {2020}, month = aug, publisher = {Springer Science and Business Media LLC}, volume = {21}, number = {1}, author = {Heather Eggleston and Zach N. Adelman}, title = {Transcriptomic analyses of Aedes aegypti cultured cells and ex vivo midguts in response to an excess or deficiency of heme: a quest for transcriptionally-regulated heme transporters}, journal = {BMC Genomics} } @article{Yang2020, doi = {10.1186/s12934-020-01463-5}, url = {https://doi.org/10.1186/s12934-020-01463-5}, year = {2020}, month = nov, publisher = {Springer Science and Business Media LLC}, volume = {19}, number = {1}, author = {Fang Yang and Jennifer A. A. DeLuca and Rani Menon and Erika Garcia-Vilarato and Evelyn Callaway and Kerstin K. Landrock and Kyongbum Lee and Stephen H. Safe and Robert S. Chapkin and Clinton D. Allred and Arul Jayaraman}, title = {Effect of diet and intestinal AhR expression on fecal microbiome and metabolomic profiles}, journal = {Microbial Cell Factories} } @article{Dadaneh2020, doi = {10.1186/s12864-020-06938-8}, url = {https://doi.org/10.1186/s12864-020-06938-8}, year = {2020}, month = sep, publisher = {Springer Science and Business Media LLC}, volume = {21}, number = {S9}, author = {Siamak Zamani Dadaneh and Paul de Figueiredo and Sing-Hoi Sze and Mingyuan Zhou and Xiaoning Qian}, title = {Bayesian gamma-negative binomial modeling of single-cell RNA sequencing data}, journal = {BMC Genomics} } @article{Orr2020, doi = {10.1016/j.compchemeng.2020.107063}, url = {https://doi.org/10.1016/j.compchemeng.2020.107063}, year = {2020}, month = dec, publisher = {Elsevier BV}, volume = {143}, pages = {107063}, author = {Asuka A. Orr and Shujun He and Meichen Wang and Alicia Goodall and Sara E. Hearon and Timothy D. Phillips and Phanourios Tamamis}, title = {Insights into the interactions of bisphenol and phthalate compounds with unamended and carnitine-amended montmorillonite clays}, journal = {Computers & Chemical Engineering} } @article{Khan2020, doi = {10.7554/elife.57081}, url = {https://doi.org/10.7554/elife.57081}, year = {2020}, month = aug, publisher = {eLife Sciences Publications, Ltd}, volume = {9}, author = {Danish Khan and Dongju Lee and Gulcin Gulten and Anup Aggarwal and Joshua Wofford and Inna Krieger and Ashutosh Tripathi and John W Patrick and Debra M Eckert and Arthur Laganowsky and James Sacchettini and Paul Lindahl and Vytas A Bankaitis}, title = {A Sec14-like phosphatidylinositol transfer protein paralog defines a novel class of heme-binding proteins}, journal = {eLife} } @article{Jing2020, doi = {10.1126/sciadv.aba7880}, url = {https://doi.org/10.1126/sciadv.aba7880}, year = {2020}, month = jul, publisher = {American Association for the Advancement of Science (AAAS)}, volume = {6}, number = {31}, author = {Zhao Jing and Shengpeng Wang and Lixin Wu and Ping Chang and Qiuying Zhang and Bingrong Sun and Xiaohui Ma and Bo Qiu and Justing Small and Fei-Fei Jin and Zhaohui Chen and Bolan Gan and Yun Yang and Haiyuan Yang and Xiuquan Wan}, title = {Maintenance of mid-latitude oceanic fronts by mesoscale eddies}, journal = {Science Advances} } @article{Karimi2020, doi = {10.1093/bioinformatics/btaa317}, url = {https://doi.org/10.1093/bioinformatics/btaa317}, year = {2020}, month = jul, publisher = {Oxford University Press (OUP)}, volume = {36}, number = {Supplement_1}, pages = {i445--i454}, author = {Mostafa Karimi and Arman Hasanzadeh and Yang Shen}, title = {Network-principled deep generative models for designing drug combinations as graph sets}, journal = {Bioinformatics} } @article{Cao2020, doi = {10.1021/acs.jctc.0c00476}, url = {https://doi.org/10.1021/acs.jctc.0c00476}, year = {2020}, month = jun, publisher = {American Chemical Society ACS)}, volume = {16}, number = {8}, pages = {5334--5347}, author = {Yue Cao and Yang Shen}, title = {Bayesian Active Learning for Optimization and Uncertainty Quantification in Protein Docking}, journal = {Journal of Chemical Theory and Computation} } @article{Dalaijamts2020, doi = {10.1016/j.taap.2020.115069}, url = {https://doi.org/10.1016/j.taap.2020.115069}, year = {2020}, month = aug, publisher = {Elsevier BV}, volume = {400}, pages = {115069}, author = {Chimeddulam Dalaijamts and Joseph A. Cichocki and Yu-Syuan Luo and Ivan Rusyn and Weihsueh A. Chiu}, title = {PBPK modeling of impact of nonalcoholic fatty liver disease on toxicokinetics of perchloroethylene in mice}, journal = {Toxicology and Applied Pharmacology} } @article{Ogunka2020, doi = {10.3390/biomimetics5010009}, url = {https://doi.org/10.3390/biomimetics5010009}, year = {2020}, month = mar, publisher = {MDPI AG}, volume = {5}, number = {1}, pages = {9}, author = {Uchenna E. Ogunka and Mohsen Daghooghi and Amir M. Akbarzadeh and Iman Borazjani}, title = {The Ground Effect in Anguilliform Swimming}, journal = {Biomimetics} } @article{Kawaguchi2020, doi = {10.1074/jbc.ra119.010252}, url = {https://doi.org/10.1074/jbc.ra119.010252}, year = {2020}, month = feb, publisher = {Elsevier BV}, volume = {295}, number = {9}, pages = {2640--2649}, author = {Madoka Kawaguchi and Nurmaa Dashzeveg and Yue Cao and Yuzhi Jia and Xia Liu and Yang Shen and Huiping Liu}, title = {Extracellular Domains I and II of cell-surface glycoprotein CD44 mediate its trans-homophilic dimerization and tumor cluster aggregation}, journal = {Journal of Biological Chemistry} } @article{Orr2020, doi = {10.1016/j.bpj.2019.11.3382}, url = {https://doi.org/10.1016/j.bpj.2019.11.3382}, year = {2020}, month = jan, publisher = {Elsevier BV}, volume = {118}, number = {2}, pages = {492--504}, author = {Asuka A. Orr and Jingyun Yang and Nitesh Sule and Ravi Chawla and Kenneth G. Hull and Mingzhao Zhu and Daniel Romo and Pushkar P. Lele and Arul Jayaraman and Michael D. Manson and Phanourios Tamamis}, title = {Molecular Mechanism for Attractant Signaling to DHMA by E.coli Tsr}, journal = {Biophysical Journal} } @article{Hu2019, doi = {10.1038/s41467-019-12452-7}, url = {https://doi.org/10.1038/s41467-019-12452-7}, year = {2019}, month = oct, publisher = {Springer Science and Business Media LLC}, volume = {10}, number = {1}, author = {Yong-Jie Hu and Ge Zhao and Baiyu Zhang and Chaoming Yang and Mingfei Zhang and Zi-Kui Liu and Xiaofeng Qian and Liang Qi}, title = {Local electronic descriptors for solute-defect interactions in bcc refractory metals}, journal = {Nature Communications} } @article{Wang2019, doi = {10.1126/sciadv.aav9743}, url = {https://doi.org/10.1126/sciadv.aav9743}, year = {2019}, month = aug, publisher = {American Association for the Advancement of Science (AAAS)}, volume = {5}, number = {8}, author = {Hua Wang and Xiaofeng Qian}, title = {Ferroicity-driven nonlinear photocurrent switching in time-reversal invariant ferroic materials}, journal = {Science Advances} } @article{Boluki2019, doi = {10.1186/s12859-019-2832-3}, url = {https://doi.org/10.1186/s12859-019-2832-3}, year = {2019}, month = jun, publisher = {Springer Science and Business Media LLC}, volume = {20}, number = {S12}, author = {Shahin Boluki and Siamak Zamani Dadaneh and Xiaoning Qian and Edward R. Dougherty}, title = {Optimal clustering with missing values}, journal = {BMC Bioinformatics} } @article{Hajiramezanali2019, doi = {10.1186/s12864-019-5720-3}, url = {https://doi.org/10.1186/s12864-019-5720-3}, year = {2019}, month = jun, publisher = {Springer Science and Business Media LLC}, volume = {20}, number = {S6}, author = {Ehsan Hajiramezanali and Mahdi Imani and Ulisses Braga-Neto and Xiaoning Qian and Edward R. Dougherty}, title = {Scalable optimal Bayesian classification of single-cell trajectories under regulatory model uncertainty}, journal = {BMC Genomics} } @article{Zapletal2020, doi = {10.1098/rstb.2019.0804}, url = {https://doi.org/10.1098/rstb.2019.0804}, year = {2020}, month = dec, publisher = {The Royal Society}, volume = {376}, number = {1818}, pages = {20190804}, author = {Josef Zapletal and Neda Najmitabrizi and Madhav Erraguntla and Mark A. Lawley and Kevin M. Myles and Zach N. Adelman}, title = {Making gene drive biodegradable}, journal = {Philosophical Transactions of the Royal Society B: Biological Sciences} } @article{Chiu2020, doi = {10.1038/s41562-020-00969-7}, url = {https://doi.org/10.1038/s41562-020-00969-7}, year = {2020}, month = oct, publisher = {Springer Science and Business Media LLC}, volume = {4}, number = {10}, pages = {1080--1090}, author = {Weihsueh A. Chiu and Rebecca Fischer and Martial L. Ndeffo-Mbah}, title = {State-level needs for social distancing and contact tracing to contain COVID-19 in the United States}, journal = {Nature Human Behaviour} } @article{SHIN2022101618, title = {On simulating impact fracture in high-strength concrete using GraFEA}, journal = {Extreme Mechanics Letters}, volume = {52}, pages = {101618}, year = {2022}, issn = {2352-4316}, doi = {https://doi.org/10.1016/j.eml.2022.101618}, url = {https://www.sciencedirect.com/science/article/pii/S2352431622000086}, author = {H.Y. Shin and P. Thamburaja and A. Srinivasa and J.N. Reddy}, keywords = {Concrete, Constitutive theory, Graph-based FEA, Non-local fracture, Impact prediction}, abstract = {In this work, we use a recently-formulated Graph-based Finite-Element Analysis (GraFEA) framework developed for modeling deformation and non-local fracture in quasi-brittle materials to simulate the fracture response of high-strength concrete (HSC) samples under impact loads. By fitting the material parameters in the theory to match a macroscopic force–displacement response obtained from a three-point bending experiment conducted under quasi-static conditions, we show that the GraFEA computational method is able to independently validate the experimentally-determined impulse response, obtained from impact experiments conducted under various initial impact speeds imposed by a drop-weight on HSC samples that are 6 to 7 orders of magnitude higher than the quasistatic tests. Furthermore, the GraFEA-based FEM simulations are also able to reproduce experimental crack propagation speeds in a HSC sample under different initial impact speeds to good accord.} } @article{YANG2022122639, title = {Deep convolutional autoencoder augmented CFD thermal analysis of bearings with inter pad groove mixing}, journal = {International Journal of Heat and Mass Transfer}, volume = {188}, pages = {122639}, year = {2022}, issn = {0017-9310}, doi = {https://doi.org/10.1016/j.ijheatmasstransfer.2022.122639}, url = {https://www.sciencedirect.com/science/article/pii/S0017931022001211}, author = {Jongin Yang and Alan Palazzolo}, keywords = {Thermal analysis, Rotor-bearing heat transfer, Deep learning, Groove mixing}, abstract = {The treatment of thermal mixing in inter pad grooves of a fluid film bearing is essential due to its influence on the heat transfer with the rotating shaft and stationary bearing. Lower fidelity models that either neglect or over approximate thermal groove mixing may lead to premature bearing or machinery failure, most commonly from babbitt thermally induced fatigue. Conventional models rely on bulk flow and thermal analyses yielding a single temperature at the groove outlet into the pad inlet. The high uncertainty of this approach carries over into downstream predictions for bearing life, stiffness and damping, and machinery vibration predictions. Contrary to a uniform temperature, CFD-Conjugate heat transfer studies reveal large gradient temperature distributions varying in both the radial and axial directions at the groove outlet, especially with jet lubrication implemented with multiple nozzles. These distributions vary continuously with time as the spinning shaft and bearing pads vibrate. A direct CFD simulation thus becomes computationally prohibitive. The present work introduces a novel approach which yields highly detailed lubricant temperature distributions at the pad inlets in a computationally economical manner. This is implemented with a surrogate groove model via a deep convolutional autoencoder neural network based on CFD (Computational Fluid Dynamics) data. The trained Convolutional Neural Network (CNN) shows excellent prediction capability for 2D temperature distribution at a circumferential groove outlet. The trained CNN is combined with a rotor-bearing model, and the combined model is verified by full CFD results and experimental data. In addition, this approach is expanded to include various oil injection types, illustrating their detailed heat transfer to the rotating shaft and bearing.} } @article{Li2021, doi = {10.3389/fgene.2021.661440}, url = {https://doi.org/10.3389/fgene.2021.661440}, year = {2021}, month = may, publisher = {Frontiers Media SA}, volume = {12}, author = {Jingjia Li and Jason B. West and Alexander Hart and Jill L. Wegrzyn and Matthew A. Smith and Jean-Christophe Domec and Carol A. Loopstra and Claudio Casola}, title = {Extensive Variation in Drought-Induced Gene Expression Changes Between Loblolly Pine Genotypes}, journal = {Frontiers in Genetics} } @article{Muthusamy2021, doi = {10.1016/j.buildenv.2021.108280}, url = {https://doi.org/10.1016/j.buildenv.2021.108280}, year = {2021}, month = dec, publisher = {Elsevier BV}, volume = {206}, pages = {108280}, author = {Jayaveera Muthusamy and Syed Haq and Saad Akhtar and Mahmoud A. Alzoubi and Tariq Shamim and Jorge Alvarado}, title = {Implication of coughing dynamics on safe social distancing in an indoor environment. A numerical perspective}, journal = {Building and Environment} } @article{Chu2021, doi = {10.1038/s41598-021-96870-y}, url = {https://doi.org/10.1038/s41598-021-96870-y}, year = {2021}, month = aug, publisher = {Springer Science and Business Media LLC}, volume = {11}, number = {1}, author = {Candice P. Chu and Shiguang Liu and Wenping Song and Ethan Y. Xu and Mary B. Nabity}, title = {Small RNA sequencing evaluation of renal microRNA biomarkers in dogs with X-linked hereditary nephropathy}, journal = {Scientific Reports} } @article{Salem2021, doi = {10.1016/j.isci.2021.102439}, url = {https://doi.org/10.1016/j.isci.2021.102439}, year = {2021}, month = may, publisher = {Elsevier BV}, volume = {24}, number = {5}, pages = {102439}, author = {Nihal A. Salem and Amanda H. Mahnke and Kranti Konganti and Andrew E. Hillhouse and Rajesh C. Miranda}, title = {Cell-type and fetal-sex-specific targets of prenatal alcohol exposure in developing mouse cerebral cortex}, journal = {iScience} } @article{Aviv2021, doi = {10.3390/ijms22179634}, url = {https://doi.org/10.3390/ijms22179634}, year = {2021}, month = sep, publisher = {MDPI AG}, volume = {22}, number = {17}, pages = {9634}, author = {Moran Aviv and Dana Cohen-Gerassi and Asuka A. Orr and Rajkumar Misra and Zohar A. Arnon and Linda J. W. Shimon and Yosi Shacham-Diamand and Phanourios Tamamis and Lihi Adler-Abramovich}, title = {Modification of a Single Atom Affects the Physical Properties of Double Fluorinated Fmoc-Phe Derivatives}, journal = {International Journal of Molecular Sciences} } @article{Taftaf2021, doi = {10.1038/s41467-021-25189-z}, url = {https://doi.org/10.1038/s41467-021-25189-z}, year = {2021}, month = aug, publisher = {Springer Science and Business Media LLC}, volume = {12}, number = {1}, author = {Rokana Taftaf and Xia Liu and Salendra Singh and Yuzhi Jia and Nurmaa K. Dashzeveg and Andrew D. Hoffmann and Lamiaa El-Shennawy and Erika K. Ramos and Valery Adorno-Cruz and Emma J. Schuster and David Scholten and Dhwani Patel and Youbin Zhang and Andrew A. Davis and Carolina Reduzzi and Yue Cao and Paolo D'Amico and Yang Shen and Massimo Cristofanilli and William A. Muller and Vinay Varadan and Huiping Liu}, title = {ICAM1 initiates CTC cluster formation and trans-endothelial migration in lung metastasis of breast cancer}, journal = {Nature Communications} } @article{Foquet2021, doi = {10.1038/s41598-021-91317-w}, url = {https://doi.org/10.1038/s41598-021-91317-w}, year = {2021}, month = jun, publisher = {Springer Science and Business Media LLC}, volume = {11}, number = {1}, author = {Bert Foquet and Adrian A. Castellanos and Hojun Song}, title = {Comparative analysis of phenotypic plasticity sheds light on the evolution and molecular underpinnings of locust phase polyphenism}, journal = {Scientific Reports} } @article{Yan2021, doi = {10.1038/s41597-021-01010-w}, url = {https://doi.org/10.1038/s41597-021-01010-w}, year = {2021}, month = sep, publisher = {Springer Science and Business Media LLC}, volume = {8}, number = {1}, author = {Yechao Yan and Yangyang Xu and Shuping Yue}, title = {A high-spatial-resolution dataset of human thermal stress indices over South and East Asia}, journal = {Scientific Data} } @article{Arora2021, doi = {10.1038/s41598-021-93796-3}, url = {https://doi.org/10.1038/s41598-021-93796-3}, year = {2021}, month = jul, publisher = {Springer Science and Business Media LLC}, volume = {11}, number = {1}, author = {Akhil Arora and M. M. Faruque Hasan}, title = {Flexible oxygen concentrators for medical applications}, journal = {Scientific Reports} } @article{Grimes2021, doi = {10.1038/s41598-021-90540-9}, url = {https://doi.org/10.1038/s41598-021-90540-9}, year = {2021}, month = may, publisher = {Springer Science and Business Media {LLC}}, volume = {11}, number = {1}, author = {C. J. Grimes and L. H. Petersen and A. Schulze}, title = {Differential gene expression indicates modulated responses to chronic and intermittent hypoxia in corallivorous fireworms (Hermodice carunculata)}, journal = {Scientific Reports} } @article{Orr2021, doi = {10.1021/acsomega.1c00481}, url = {https://doi.org/10.1021/acsomega.1c00481}, year = {2021}, month = may, publisher = {American Chemical Society (ACS)}, volume = {6}, number = {22}, pages = {14090--14103}, author = {Asuka A. Orr and Meichen Wang and Burcu Beykal and Hari S. Ganesh and Sara E. Hearon and Efstratios N. Pistikopoulos and Timothy D. Phillips and Phanourios Tamamis}, title = {Combining Experimental Isotherms, Minimalistic Simulations, and a Model to Understand and Predict Chemical Adsorption onto Montmorillonite Clays}, journal = {ACS Omega} } @article{Kim2021, doi = {10.21037/qims-20-745}, url = {https://doi.org/10.21037/qims-20-745}, year = {2021}, month = may, publisher = {AME Publishing Company}, volume = {11}, number = {5}, pages = {1763--1781}, author = {Taeouk Kim and Mohammadali Hedayat and Veronica V. Vaitkus and Marek Belohlavek and Vinayak Krishnamurthy and Iman Borazjani}, title = {Automatic segmentation of the left ventricle in echocardiographic images using convolutional neural networks}, journal = {Quantitative Imaging in Medicine and Surgery} } @article{Herath2021, doi = {10.3390/ijms22062837}, url = {https://doi.org/10.3390/ijms22062837}, year = {2021}, month = mar, publisher = {MDPI AG}, volume = {22}, number = {6}, pages = {2837}, author = {Venura Herath and Jeanmarie Verchot}, title = {Transcriptional Regulatory Networks Associate with Early Stages of Potato Virus X Infection of Solanum tuberosum}, journal = {International Journal of Molecular Sciences} } @article{Ravirala2021, doi = {10.1016/j.omto.2021.10.006}, url = {https://doi.org/10.1016/j.omto.2021.10.006}, year = {2021}, month = dec, publisher = {Elsevier BV}, volume = {23}, pages = {330--341}, author = {Divya Ravirala and Guangsheng Pei and Zhongming Zhao and Xiaoliu Zhang}, title = {Single-cell RNA sequencing reveals a strong connection between Gadd45g upregulation and oncolytic HSV infection in tumor tissue}, journal = {Molecular Therapy - Oncolytics} } @article{Morris2022, doi = {10.1128/spectrum.00764-21}, url = {https://doi.org/10.1128/spectrum.00764-21}, year = {2022}, month = jan, publisher = {American Society for Microbiology}, author = {Ellen Ruth A. Morris and Jing Wu and Angela I. Bordin and Sara D. Lawhon and Noah D. Cohen}, editor = {Cheryl P. Andam}, title = {Differences in the Accessory Genomes and Methylomes of Strains of Streptococcus equi subsp. equi and of Streptococcus equi subsp. zooepidemicus Obtained from the Respiratory Tract of Horses from Texas}, journal = {Microbiology Spectrum} } @article{Bernard2021, doi = {10.1093/texcom/tgab050}, url = {https://doi.org/10.1093/texcom/tgab050}, year = {2021}, month = jan, publisher = {Oxford University Press (OUP)}, volume = {2}, number = {3}, author = {Jessica A Bernard and Hannah K Ballard and Trevor Bryan Jackson}, title = {Cerebellar Dentate Connectivity across Adulthood: A Large-Scale Resting State Functional Connectivity Investigation}, journal = {Cerebral Cortex Communications} } @article{Karki2021, doi = {10.3390/cancers13112682}, url = {https://doi.org/10.3390/cancers13112682}, year = {2021}, month = may, publisher = {MDPI AG}, volume = {13}, number = {11}, pages = {2682}, author = {Keshav Karki and Kumaravel Mohankumar and Abigail Schoeller and Gregory Martin and Rupesh Shrestha and Stephen Safe}, title = {NR4A1 Ligands as Potent Inhibitors of Breast Cancer Cell and Tumor Growth}, journal = {Cancers} } @article{Lee2016, doi = {10.1105/tpc.16.00408}, url = {https://doi.org/10.1105/tpc.16.00408}, year = {2016}, month = sep, publisher = {Oxford University Press OUP}, volume = {28}, number = {9}, pages = {2212--2224}, author = {Jung Ro Lee and Xiaoyuan Xie and Kailu Yang and Junjie Zhang and Sang Yeol Lee and Dorothy E. Shippen}, title = {Dynamic Interactions of Arabidopsis TEN1: Stabilizing Telomeres in Response to Heat Stress}, journal = {The Plant Cell} } @article{Khan2016, doi = {10.1194/jlr.m066381}, url = {https://doi.org/10.1194/jlr.m066381}, year = {2016}, month = apr, publisher = {Elsevier BV}, volume = {57}, number = {4}, pages = {650--662}, author = {Danish Khan and Kaitlyn R. McGrath and Oleksandra Dorosheva and Vytas A. Bankaitis and Ashutosh Tripathi}, title = {Structural elements that govern Sec14-like PITP sensitivities to potent small molecule inhibitors}, journal = {Journal of Lipid Research} } @article{Fernando2017, doi = {10.1186/s13104-017-2685-7}, url = {https://doi.org/10.1186/s13104-017-2685-7}, year = {2017}, month = jul, publisher = {Springer Science and Business Media LLC}, volume = {10}, number = {1}, author = {Sandun Fernando and Teshan Fernando}, title = {Antivirals for allosteric inhibition of Zika virus using a homology model and experimentally determined structure of envelope protein}, journal = {BMC Research Notes} } @article{Thyparambil2017, doi = {10.3390/toxins9120395}, url = {https://doi.org/10.3390/toxins9120395}, year = {2017}, month = dec, publisher = {MDPI AG}, volume = {9}, number = {12}, pages = {395}, author = {Aby Thyparambil and Ingrid Bazin and Anthony Guiseppi-Elie}, title = {Molecular Modeling and Simulation Tools in the Development of Peptide-Based Biosensors for Mycotoxin Detection: Example of Ochratoxin}, journal = {Toxins} } @article{Mukherjee2017, doi = {10.3762/bjoc.13.246}, url = {https://doi.org/10.3762/bjoc.13.246}, year = {2017}, month = nov, publisher = {Beilstein Institut}, volume = {13}, pages = {2486--2501}, author = {Tathagata Mukherjee and Soumik Biswas and Andreas Ehnbom and Subrata K Ghosh and Ibrahim El-Zoghbi and Nattamai Bhuvanesh and Hassan S Bazzi and John A Gladysz}, title = {Syntheses, structures, and stabilities of aliphatic and aromatic fluorous iodine(I) and iodine(III) compounds: the role of iodine Lewis basicity}, journal = {Beilstein Journal of Organic Chemistry} } @article{Weaver2017, doi = {10.1038/ncomms15934}, url = {https://doi.org/10.1038/ncomms15934}, year = {2017}, month = jun, publisher = {Springer Science and Business Media LLC}, volume = {8}, number = {1}, author = {Jeremy Weaver and Mengqiu Jiang and Andrew Roth and Jason Puchalla and Junjie Zhang and Hays S. Rye}, title = {GroEL actively stimulates folding of the endogenous substrate protein PepQ}, journal = {Nature Communications} } @article{Thyparambil2017, doi = {10.3390/toxins9050164}, url = {https://doi.org/10.3390/toxins9050164}, year = {2017}, month = may, publisher = {MDPI AG}, volume = {9}, number = {5}, pages = {164}, author = {Aby A. Thyparambil and Ingrid Bazin and Anthony Guiseppi-Elie}, title = {Evaluation of Ochratoxin Recognition by Peptides Using Explicit Solvent Molecular Dynamics}, journal = {Toxins} } @article{A2018, doi = {10.16966/2575-0305.106}, url = {https://doi.org/10.16966/2575-0305.106}, year = {2018}, publisher = {Sci Forschen, Inc.}, volume = {2}, number = {1}, author = {Tripathi A and Bankaitis VA}, title = {Molecular Docking: From Lock and Key to Combination Lock}, journal = {Journal of Molecular Medicine and Clinical Applications} } @article{Zheng2017, doi = {10.1534/g3.117.300120}, url = {https://doi.org/10.1534/g3.117.300120}, year = {2017}, month = dec, publisher = {Oxford University Press (OUP)}, volume = {7}, number = {12}, pages = {3849--3856}, author = {Qi Zheng}, title = {rSalvador: An R Package for the Fluctuation Experiment}, journal = {G3 Genes|Genomes|Genetics} } @article{Yang2017, doi = {10.1093/nar/gkx785}, url = {https://doi.org/10.1093/nar/gkx785}, year = {2017}, month = sep, publisher = {Oxford University Press (OUP)}, volume = {45}, number = {18}, pages = {10884--10894}, author = {Kailu Yang and Jeng-Yih Chang and Zhicheng Cui and Xiaojun Li and Ran Meng and Lijun Duan and Jirapat Thongchol and Joanita Jakana and Christoph M. Huwe and James C. Sacchettini and Junjie Zhang}, title = {Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis}, journal = {Nucleic Acids Research} } @article{Yoo2017, doi = {10.1038/s41467-017-00431-9}, url = {https://doi.org/10.1038/s41467-017-00431-9}, year = {2017}, month = aug, publisher = {Springer Science and Business Media LLC}, volume = {8}, number = {1}, author = {Hyun Deog Yoo and Yanliang Liang and Hui Dong and Junhao Lin and Hua Wang and Yisheng Liu and Lu Ma and Tianpin Wu and Yifei Li and Qiang Ru and Yan Jing and Qinyou An and Wu Zhou and Jinghua Guo and Jun Lu and Sokrates T. Pantelides and Xiaofeng Qian and Yan Yao}, title = {Fast kinetics of magnesium monochloride cations in interlayer-expanded titanium disulfide for magnesium rechargeable batteries}, journal = {Nature Communications} } @article{Grabon2017, doi = {10.1074/jbc.m117.791467}, url = {https://doi.org/10.1074/jbc.m117.791467}, year = 2017, month = sep, publisher = {Elsevier BV}, volume = 292, number = 35, pages = {14438--14455}, author = {Aby Grabon and A Adam Orłowski and Ashutosh Tripathi and Joni Vuorio and Matti Javanainen and Tomasz Róg and Max Lönnfors and Mark I. McDermott and Garland Siebert and Pentti Somerharju and Ilpo Vattulainen and Vytas A. Bankaitis}, title = {Dynamics and energetics of the mammalian phosphatidylinositol transfer protein phospholipid exchange cycle}, journal = {Journal of Biological Chemistry} } @article{Chen2017, doi = {10.1126/sciadv.aao2710}, url = {https://doi.org/10.1126/sciadv.aao2710}, year = {2017}, month = nov, publisher = {American Association for the Advancement of Science (AAAS)}, volume = {3}, number = {11}, author = {Di Chen and Nan Li and Dina Yuryev and J. Kevin Baldwin and Yongqiang Wang and Michael J. Demkowicz}, title = {Self-organization of helium precipitates into elongated channels within metal nanolayers}, journal = {Science Advances} } @article{Fanning2018, doi = {10.7554/elife.37161}, url = {https://doi.org/10.7554/elife.37161}, year = {2018}, month = nov, publisher = {eLife Sciences Publications, Ltd}, volume = {7}, author = {Sean W Fanning and Rinath Jeselsohn and Venkatasubramanian Dharmarajan and Christopher G Mayne and Mostafa Karimi and Gilles Buchwalter and René Houtman and Weiyi Toy and Colin E Fowler and Ross Han and Muriel Lainé and Kathryn E Carlson and Teresa A Martin and Jason Nowak and Jerome C Nwachukwu and David J Hosfield and Sarat Chandarlapaty and Emad Tajkhorshid and Kendall W Nettles and Patrick R Griffin and Yang Shen and John A Katzenellenbogen and Myles Brown and Geoffrey L Greene}, title = {The SERM/SERD bazedoxifene disrupts ESR1 helix 12 to overcome acquired hormone resistance in breast cancer cells}, journal = {eLife} } @article{Zhao2018, doi = {10.1038/s41598-018-34426-3}, url = {https://doi.org/10.1038/s41598-018-34426-3}, year = {2018}, month = nov, publisher = {Springer Science and Business Media LLC}, volume = {8}, number = {1}, author = {Wei L. Z. Zhao and Konstantin S. Tikhonov and Alexander M. Finkel'stein}, title = {Flexural phonons in supported graphene: from pinning to localization}, journal = {Scientific Reports} } @article{Su2018, doi = {10.1038/s41598-018-23426-y}, url = {https://doi.org/10.1038/s41598-018-23426-y}, year = {2018}, month = mar, publisher = {Springer Science and Business Media LLC}, volume = {8}, number = {1}, author = {Qing Su and Hepeng Ding and Lloyd Price and Lin Shao and Jonathan A. Hinks and Graeme Greaves and Stephen E. Donnelly and Michael J. Demkowicz and Michael Nastasi}, title = {Rapid and damage-free outgassing of implanted helium from amorphous silicon oxycarbide}, journal = {Scientific Reports} } @article{Dehghannasiri2018, doi = {10.1186/s12918-018-0649-8}, url = {https://doi.org/10.1186/s12918-018-0649-8}, year = {2018}, month = dec, publisher = {Springer Science and Business Media LLC}, volume = {12}, number = {S8}, author = {Roozbeh Dehghannasiri and Mohammad Shahrokh Esfahani and Edward R. Dougherty}, title = {An experimental design framework for Markovian gene regulatory networks under stationary control policy}, journal = {BMC Systems Biology} } @article{Li2018, doi = {10.1021/acscatal.8b03146}, url = {https://doi.org/10.1021/acscatal.8b03146}, year = {2018}, month = oct, publisher = {American Chemical Society (ACS)}, volume = {8}, number = {11}, pages = {10606--10618}, author = {Haixia Li and Jennifer V. Obligacion and Paul J. Chirik and Michael B. Hall}, title = {Cobalt Pincer Complexes in Catalytic C-H Borylation: The Pincer Ligand Flips Rather Than Dearomatizes}, journal = {ACS Catalysis} } @article{Cheng2018, doi = {10.3390/mi9100479}, url = {https://doi.org/10.3390/mi9100479}, year = {2018}, month = sep, publisher = {MDPI AG}, volume = {9}, number = {10}, pages = {479}, author = {Way Cheng and Celal Erbay and Reza Sadr and Arum Han}, title = {Dynamic Flow Characteristics and Design Principles of Laminar Flow Microbial Fuel Cells}, journal = {Micromachines} } @article{Leon2018, doi = {10.1128/aem.02829-17}, url = {https://doi.org/10.1128/aem.02829-17}, year = {2018}, month = jul, publisher = {American Society for Microbiology}, volume = {84}, number = {13}, author = {I. M. Leon and S. D. Lawhon and K. N. Norman and D. S. Threadgill and N. Ohta and J. Vinasco and H. M. Scott}, editor = {Eric V. Stabb}, title = {Serotype Diversity and Antimicrobial Resistance among Salmonella enterica Isolates from Patients at an Equine Referral Hospital}, journal = {Applied and Environmental Microbiology} } @article{Dalaijamts2018, doi = {10.1016/j.taap.2018.05.033}, url = {https://doi.org/10.1016/j.taap.2018.05.033}, year = {2018}, month = aug, publisher = {Elsevier BV}, volume = {352}, pages = {142--152}, author = {Chimeddulam Dalaijamts and Joseph A. Cichocki and Yu-Syuan Luo and Ivan Rusyn and Weihsueh A. Chiu}, title = {Incorporation of the glutathione conjugation pathway in an updated physiologically-based pharmacokinetic model for perchloroethylene in mice}, journal = {Toxicology and Applied Pharmacology} } @article{Nsouglo2018, doi = {10.1098/rspa.2017.0575}, url = {https://doi.org/10.1098/rspa.2017.0575}, year = {2018}, month = mar, publisher = {The Royal Society}, volume = {474}, number = {2211}, pages = {20170575}, author = {K. E. N'souglo and A. Srivastava and S. Osovski and J. A. Rodríguez-Martínez}, title = {Random distributions of initial porosity trigger regular necking patterns at high strain rates}, journal = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences} } @article{Orr2018, doi = {10.1016/j.compchemeng.2018.02.013}, url = {https://doi.org/10.1016/j.compchemeng.2018.02.013}, year = {2018}, month = aug, publisher = {Elsevier BV}, volume = {116}, pages = {322--332}, author = {Asuka A. Orr and Hamed Shaykhalishahi and Ewa A. Mirecka and Sai Vamshi R. Jonnalagadda and Wolfgang Hoyer and Phanourios Tamamis}, title = {Elucidating the multi-targeted anti-amyloid activity and enhanced islet amyloid polypeptide binding of β-wrapins}, journal = {Computers & Chemical Engineering} } @article{Pries2018, doi = {10.1016/j.chembiol.2017.12.007}, url = {https://doi.org/10.1016/j.chembiol.2017.12.007}, year = {2018}, month = mar, publisher = {Elsevier BV}, volume = {25}, number = {3}, pages = {279--290.e7}, author = {Verena Pries and Christina Nöcker and Danish Khan and Philipp Johnen and Zebin Hong and Ashutosh Tripathi and Anna-Lena Keller and Michael Fitz and Francesca Perruccio and Ireos Filipuzzi and Sasikala Thavam and Thomas Aust and Ralph Riedl and Slava Ziegler and Fulvia Bono and Gabriel Schaaf and Vytas A. Bankaitis and Herbert Waldmann and Dominic Hoepfner}, title = {Target Identification and Mechanism of Action of Picolinamide and Benzamide Chemotypes with Antifungal Properties}, journal = {Cell Chemical Biology} } @article{Beykal2018, doi = {10.1016/j.compchemeng.2018.02.017}, url = {https://doi.org/10.1016/j.compchemeng.2018.02.017}, year = {2018}, month = aug, publisher = {Elsevier BV}, volume = {116}, pages = {488--502}, author = {Burcu Beykal and Fani Boukouvala and Christodoulos A. Floudas and Efstratios N. Pistikopoulos}, title = {Optimal design of energy systems using constrained grey-box multi-objective optimization}, journal = {Computers & Chemical Engineering} } @article{Karimi2018, doi = {10.1093/bioinformatics/bty564}, url = {https://doi.org/10.1093/bioinformatics/bty564}, year = {2018}, month = sep, publisher = {Oxford University Press (OUP)}, volume = {34}, number = {17}, pages = {i811--i820}, author = {Mostafa Karimi and Yang Shen}, title = {iCFN: an efficient exact algorithm for multistate protein design}, journal = {Bioinformatics} } @article{Jakubowski2020, doi = {10.1021/acs.jcim.0c00784}, url = {https://doi.org/10.1021/acs.jcim.0c00784}, year = {2020}, month = jul, publisher = {American Chemical Society (ACS)}, volume = {60}, number = {8}, pages = {4108--4108}, author = {Joseph M. Jakubowski and Asuka A. Orr and Doan A. Le and Phanourios Tamamis}, title = {Correction to "Interactions between Curcumin Derivatives and Amyloid-β Fibrils: Insights from Molecular Dynamics Simulations"}, journal = {Journal of Chemical Information and Modeling} } @article{Bi2020, doi = {10.1021/acs.iecr.0c02657}, url = {https://doi.org/10.1021/acs.iecr.0c02657}, year = {2020}, month = aug, publisher = {American Chemical Society (ACS)}, volume = {59}, number = {37}, pages = {16357--16367}, author = {Kexin Bi and Burcu Beykal and Styliani Avraamidou and Iosif Pappas and Efstratios N. Pistikopoulos and Tong Qiu}, title = {Integrated Modeling of Transfer Learning and Intelligent Heuristic Optimization for a Steam Cracking Process}, journal = {Industrial & Engineering Chemistry Research} } @article{Cho2020, doi = {10.1073/pnas.1920582117}, url = {https://doi.org/10.1073/pnas.1920582117}, year = {2020}, month = mar, publisher = {Proceedings of the National Academy of Sciences}, volume = {117}, number = {12}, pages = {6550--6558}, author = {Jae-Hyun Cho and Baoyu Zhao and Jie Shi and Nowlan Savage and Qingliang Shen and James Byrnes and Lin Yang and Wonmuk Hwang and Pingwei Li}, title = {Molecular recognition of a host protein by NS1 of pandemic and seasonal influenza A viruses}, journal = {Proceedings of the National Academy of Sciences} } @article{Kokotidou2019, doi = {10.3390/biom10010007}, url = {https://doi.org/10.3390/biom10010007}, year = {2019}, month = dec, publisher = {MDPI AG}, volume = {10}, number = {1}, pages = {7}, author = {Chrysoula Kokotidou and Sai Vamshi R. Jonnalagadda and Asuka A. Orr and George Vrentzos and Androniki Kretsovali and Phanourios Tamamis and Anna Mitraki}, title = {Designer Amyloid Cell-Penetrating Peptides for Potential Use as Gene Transfer Vehicles}, journal = {Biomolecules} } @article{Shi2019, doi = {10.3390/ijms20235855}, url = {https://doi.org/10.3390/ijms20235855}, year = {2019}, month = nov, publisher = {MDPI AG}, volume = {20}, number = {23}, pages = {5855}, author = {Tianran Shi and Vijay Joshi and Madhumita Joshi and Stanislav Vitha and Holly Gibbs and Kehua Wang and Sakiko Okumoto}, title = {Broad-Spectrum Amino Acid Transporters ClAAP3 and ClAAP6 Expressed in Watermelon Fruits}, journal = {International Journal of Molecular Sciences} } @inproceedings{7966097, author={Jin, Yingyezhe and Li, Peng}, booktitle={2017 International Joint Conference on Neural Networks (IJCNN)}, title={Calcium-modulated supervised spike-timing-dependent plasticity for readout training and sparsification of the liquid state machine}, year={2017}, volume={}, number={}, pages={2007-2014}, doi={10.1109/IJCNN.2017.7966097} } @article{VERDONKIDD2017123, title = {A comparative study of historical droughts over Texas, USA and Murray-Darling Basin, Australia: Factors influencing initialization and cessation}, journal = {Global and Planetary Change}, volume = {149}, pages = {123-138}, year = {2017}, issn = {0921-8181}, doi = {https://doi.org/10.1016/j.gloplacha.2017.01.001}, url = {https://www.sciencedirect.com/science/article/pii/S0921818116301382}, author = {Danielle C. Verdon-Kidd and Bridget R. Scanlon and Tong Ren and D. Nelun Fernando}, keywords = {Drought, Texas, Murray Darling Basin, El Nino/Southern Oscillation (ENSO), Pacific Decadal Oscillation (PDO), Interdecadal Pacific Oscillation (IPO), Atlantic Multidecadal Oscillation (AMO), Indian Ocean Dipole (IOD)}, } @article{SOLEYMANIHA2016166, title = {Design of a heated micro-cantilever optimized for thermo-capillary driven printing of molten polymer nanostructures}, journal = {International Journal of Heat and Mass Transfer}, volume = {101}, pages = {166-174}, year = {2016}, issn = {0017-9310}, doi = {https://doi.org/10.1016/j.ijheatmasstransfer.2016.04.063}, url = {https://www.sciencedirect.com/science/article/pii/S0017931016302733}, author = {Mohammadreza Soleymaniha and Jonathan R. Felts}, keywords = {Atomic force microscope (AFM), Micro-cantilever, Microchannel, Thermocapillary flow, Thermal dip-pen nanolithography (tDPN), Polymer nanostructure}, } @article { IstheAwarenessoftheAerosolStateUsefulinPredictingEnhancedLightningforLightningProducingStormsoverNorthernAlabama, author = {Tong Ren and Anita D. Rapp and Shaima L. Nasiri and John R. Mecikalski and Jason Apke}, title = "Is the Awareness of the Aerosol State Useful in Predicting Enhanced Lightning for Lightning-Producing Storms over Northern Alabama?", journal = "Journal of Applied Meteorology and Climatology", year = "2018", publisher = "American Meteorological Society", address = "Boston MA, USA", volume = "57", number = "8", doi = "10.1175/JAMC-D-17-0182.1", pages= "1663 - 1681", url = "https://journals.ametsoc.org/view/journals/apme/57/8/jamc-d-17-0182.1.xml" } @article{TENG20181791, title = {Effect of Methylation on Local Mechanics and Hydration Structure of DNA}, journal = {Biophysical Journal}, volume = {114}, number = {8}, pages = {1791-1803}, year = {2018}, issn = {0006-3495}, doi = {https://doi.org/10.1016/j.bpj.2018.03.022}, url = {https://www.sciencedirect.com/science/article/pii/S0006349518303898}, author = {Xiaojing Teng and Wonmuk Hwang}, abstract = {Cytosine methylation affects mechanical properties of DNA and potentially alters the hydration fingerprint for recognition by proteins. The atomistic origin for these effects is not well understood, and we address this via all-atom molecular dynamics simulations. We find that the stiffness of the methylated dinucleotide step changes marginally, whereas the neighboring steps become stiffer. Stiffening is further enhanced for consecutively methylated steps, providing a mechanistic origin for the effect of hypermethylation. Steric interactions between the added methyl groups and the nonpolar groups of the neighboring nucleotides are responsible for the stiffening in most cases. By constructing hydration maps, we found that methylation also alters the surface hydration structure in distinct ways. Its resistance to deformation may contribute to the stiffening of DNA for deformational modes lacking steric interactions. These results highlight the sequence- and deformational-mode-dependent effects of cytosine methylation.} } @article { ForcingoftheUpperTroposphericMonsoonAnticyclones, author = {Leong Wai Siu and Kenneth P. Bowman}, title = "Forcing of the Upper-Tropospheric Monsoon Anticyclones", journal = "Journal of the Atmospheric Sciences", year = "2019", publisher = "American Meteorological Society", address = "Boston MA, USA", volume = "76", number = "7", doi = "10.1175/JAS-D-18-0340.1", pages= "1937 - 1954", url = "https://journals.ametsoc.org/view/journals/atsc/76/7/jas-d-18-0340.1.xml" } @article{REN2020106694, title = {Improved δ-Eddington approximation for optically thin clouds}, journal = {Journal of Quantitative Spectroscopy and Radiative Transfer}, volume = {240}, pages = {106694}, year = {2020}, issn = {0022-4073}, doi = {https://doi.org/10.1016/j.jqsrt.2019.106694}, url = {https://www.sciencedirect.com/science/article/pii/S0022407319304212}, author = {Tong Ren and Ping Yang and Guanglin Tang and Xianglei Huang and Eli Mlawer}, keywords = {-Eddington approximation, Forward fraction of scattering, The asymmetry factor}, abstract = {The δ-Eddington simulations of broadband shortwave net radiation fluxes at the top of the atmosphere (FTOA) and the surface (FSURF) are evaluated with different parameterizations of the forward fraction of scattering (f), including the square of the asymmetry factor (f = g2), the fraction of the forward single-scattered intensity over the total single-scattered intensity (f = fp), and the cube of the asymmetry factor (f = g3). g2 and g3 are respectively the 2nd and 3rd moments of the Henyey–Greenstein (HG) phase function and hence approximate measures of the variance and skewness of the phase function. The factor fp for spherical droplets is estimated using a truncation angle, which separates the forward peak and diffusive portions of a highly anisotropic phase function. The results show that the simulations of FTOA and FSURF are not improved, if the conventional approach f = g2 is replaced by f = fp in the δ-Eddington approximation for an atmosphere in the presence of liquid clouds. For the optically thick conditions, multiple scattering plays a dominant role in determining the reflectance (R) and transmittance (T) of the cloudy layer; the conventional parameterization f = g2 is most accurate among the three parameterizations. For the optically thin conditions, single scattering dominates over multiple scattering and thus f = g2 results in biased FTOA and FSURF calculations, particularly with low solar elevations. For such cases, f = g3 shows most accurate FTOA and FSURF results for both liquid and ice clouds, though f = g3 also results in smaller cloud layer heating rates in general.} } @article{https://doi.org/10.1029/2019JD031544, author = {Ren, Tong and Rapp, Anita D. and Mecikalski, John R. and Apke, Jason}, title = {Lightning and Associated Convection Features in the Presence of Absorbing Aerosols Over Northern Alabama}, journal = {Journal of Geophysical Research: Atmospheres}, volume = {124}, number = {23}, pages = {13375-13396}, doi = {https://doi.org/10.1029/2019JD031544}, url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019JD031544}, eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2019JD031544}, abstract = {Abstract Many of the previous aerosol-convection/lightning enhancement studies are based on convective storms that occur in the presence of absorbing aerosols; such aerosols may impact deep convection through their microphysical and radiative effects. In this study, lightning flash rates (FRs) are analyzed together with aerosol optical depth (AOD) retrievals from the Moderate Resolution Imaging Spectroradiometer for summer storms during 2002–2015. Aerosol index retrievals from the Ozone Monitoring Instrument are used to separate nonabsorbing and absorbing aerosol cases. Statistical analyses are performed to test for significant sample differences and linear relationships between the AOD of case studies and the FRs, convective available potential energy, planetary boundary layer height, and low-level vertical wind shear to identify if evidence of regulation of storms by absorbing aerosols exists. Overall, AOD and FR do not show any significant linear relationship. When just observing absorbing aerosols, however, AOD and FR show a stronger (but still very weak) positive correlation. The weak correlation may be related to the absorbing aerosols' impact on convective available potential energy, which has a moderate linear correlation to AOD particularly when the instability is low, which implies some kind of convection or convective environment modification by absorbing aerosols. Although the planetary boundary layer height tends to decrease with increasing amount of absorbing aerosols, it is found that low-level vertical wind shear does not correlate with AOD for either absorbing or nonabsorbing aerosols. This result suggests little influence of the interaction between absorbing aerosols and turbulent mixing on storms.}, year = {2019} } @article{PhysRevLett.124.180601, title = {Operator L'evy Flight: Light Cones in Chaotic Long-Range Interacting Systems}, author = {Zhou, Tianci and Xu, Shenglong and Chen, Xiao and Guo, Andrew and Swingle, Brian}, journal = {Phys. Rev. Lett.}, volume = {124}, issue = {18}, pages = {180601}, numpages = {6}, year = {2020}, month = {May}, publisher = {American Physical Society}, doi = {10.1103/PhysRevLett.124.180601}, url = {https://link.aps.org/doi/10.1103/PhysRevLett.124.180601} } @article{https://doi.org/10.1029/2020GL087776, author = {Arcomano, Troy and Szunyogh, Istvan and Pathak, Jaideep and Wikner, Alexander and Hunt, Brian R. and Ott, Edward}, title = {A Machine Learning-Based Global Atmospheric Forecast Model}, journal = {Geophysical Research Letters}, volume = {47}, number = {9}, pages = {e2020GL087776}, doi = {https://doi.org/10.1029/2020GL087776}, url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020GL087776}, eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2020GL087776}, note = {e2020GL087776 10.1029/2020GL087776}, abstract = {Abstract The paper investigates the applicability of machine learning (ML) to weather prediction by building a reservoir computing-based, low-resolution, global prediction model. The model is designed to take advantage of the massively parallel architecture of a modern supercomputer. The forecast performance of the model is assessed by comparing it to that of daily climatology, persistence, and a numerical (physics-based) model of identical prognostic state variables and resolution. Hourly resolution 20-day forecasts with the model predict realistic values of the atmospheric state variables at all forecast times for the entire globe. The ML model outperforms both climatology and persistence for the first three forecast days in the midlatitudes, but not in the tropics. Compared to the numerical model, the ML model performs best for the state variables most affected by parameterized processes in the numerical model.}, year = {2020} } @article{https://doi.org/10.1111/vde.12885, author = {Older, Caitlin E. and Diesel, Alison B. and Starks, Jill M. and Lawhon, Sara D. and Rodrigues Hoffmann, Aline}, title = {Characterization of staphylococcal communities on healthy and allergic feline skin}, journal = {Veterinary Dermatology}, volume = {32}, number = {1}, pages = {61-e10}, doi = {https://doi.org/10.1111/vde.12885}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/vde.12885}, eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/vde.12885}, abstract = {Various Staphylococcus species have been demonstrated to play important roles on the skin, including causing disease and protecting the host from pathogens. Although culture-based studies have isolated various Staphylococcus spp. from feline skin, very little is known regarding the species-level communities on the host. To describe the species-level staphylococcal communities inhabiting the skin of healthy cats and cats with allergic dermatitis. Skin swabs from the ear canal and groin of 11 healthy and 10 allergic (nonlesional) cats were obtained. DNA was extracted from the skin swabs and used for next-generation sequencing targeting the V1–3 region of the 16S rRNA gene. Following a standard microbiota analysis of the sequencing data, species-level assignment for the staphylococcal sequences were obtained using a staphylococci-specific database. Staphylococcus spp. had similar relative abundance in healthy and allergic samples. The most abundant staphylococcal species were S. epidermidis in healthy samples, and S. felis and S. capitis in allergic samples. The composition of staphylococcal communities, as well as relative abundance of Staphylococcus spp., was variable between body sites and individual cats sampled. These results demonstrate that diverse staphylococcal communities inhabit the skin of healthy and allergic cats, and provide a starting point for further research into the importance of Staphylococcus spp. in feline allergic skin disease.}, year = {2021} } @Article{pathogens9080638, AUTHOR = {Older, Caitlin E. and Rodrigues Hoffmann, Aline and Hoover, Kathleen and Banovic, Frane}, TITLE = {Characterization of Cutaneous Bacterial Microbiota from Superficial Pyoderma Forms in Atopic Dogs}, JOURNAL = {Pathogens}, VOLUME = {9}, YEAR = {2020}, NUMBER = {8}, ARTICLE-NUMBER = {638}, URL = {https://www.mdpi.com/2076-0817/9/8/638}, PubMedID = {32781634}, pages = {1-12}, ISSN = {2076-0817}, ABSTRACT = {Although Staphylococcus pseudintermedius is considered the major pathogen associated with superficial canine pyoderma, no study has investigated the entire bacterial community in these lesions with molecular techniques. The objectives of this study were to characterize the bacterial microbiota in two forms of superficial canine pyoderma lesions, superficial bacterial folliculitis (SBF) and epidermal collarette (EC), especially in terms of the staphylococcal community. Swabs from 12 SBF and 9 EC lesions were obtained from eight and six atopic dogs, respectively. Eight samples from the axilla and groin of four healthy dogs served as controls. DNA was extracted for 16S rRNA gene sequencing and quantitative polymerase chain reaction of Staphylococcus spp. and S. pseudintermedius. Healthy skin samples harbored significantly more diverse bacterial communities than pyoderma samples. Healthy samples had communities that were more similar to each other, and were distinct from pyoderma samples. Staphylococcus spp. abundance was increased in pyoderma samples, especially those from EC samples. Although determining species-level identities of staphylococcal sequences revealed many species, S. pseudintermedius was the primary staphylococcal species found in all sample types. As expected, there are many differences in the microbiota when comparing healthy and canine pyoderma lesions samples. These lesions do not seem to be associated with a change in the relative abundance of specific Staphylococcus species, but simply an overall increase in Staphylococcus spp. abundance. The results of this study provide a starting point for future studies investigating how antimicrobial treatments may further change the microbiota associated with these lesions.}, DOI = {10.3390/pathogens9080638} } @Article{pathogens9050383, AUTHOR = {Older, Caitlin E. and Gomes, Márcia de Oliveira Sampaio and Hoffmann, Aline Rodrigues and Policano, Mariel Dalmédico and Reis, Camila Aparecida Cruz dos and Carregaro, Adriano Bonfim and Ambrósio, Carlos Eduardo and Carregaro, Valéria Maria Lara}, TITLE = {Influence of the FIV Status and Chronic Gingivitis on Feline Oral Microbiota}, JOURNAL = {Pathogens}, VOLUME = {9}, YEAR = {2020}, pages = {1-11}, NUMBER = {5}, ARTICLE-NUMBER = {383}, URL = {https://www.mdpi.com/2076-0817/9/5/383}, PubMedID = {32429494}, ISSN = {2076-0817}, ABSTRACT = {Feline chronic gingivostomatitis (FCGS) has an unclear pathogenesis with the oral microbiome and viral infections, such as feline immunodeficiency virus (FIV), thought to contribute. Although the relationship between the FIV status and FCGS is not clear, one theory is FIV-induced immune dysregulation could contribute to oral dysbiosis, promoting FCGS development. To further understand the relationship between FCGS, FIV infection, and the oral microbiome, oral cavities of forty cats fitting within 4 groups (FIV- without gingivitis, FIV+ without gingivitis, FIV- with gingivitis, FIV+ with gingivitis) were swabbed. Next generation sequencing targeting the V4 region of the 16s rRNA gene was performed for bacterial community profiling. No differences in diversity were observed, however, analysis of the data in terms of gingivitis revealed differences in the relative abundance of taxa and predicted functional output. Odoribacter spp., a bacteria associated with oral disease, was found in higher relative abundances in cats with the highest gingivitis grade. Cats with gingivitis were also found to harbor communities more involved in production of short-chain fatty acids, which have been connected with oral disease. Significant findings associated with the FIV status were few and of low impact, suggesting any connection between the FIV status and FCGS is likely not related to the oral microbiota.}, DOI = {10.3390/pathogens9050383} } @article{10.1371/journal.pone.0220463, doi = {10.1371/journal.pone.0220463}, author = {Older, Caitlin E. AND Diesel, Alison B. AND Lawhon, Sara D. AND Queiroz, Cintia R. R. AND Henker, Luan C. AND Rodrigues Hoffmann, Aline}, journal = {PLOS ONE}, publisher = {Public Library of Science}, title = {The feline cutaneous and oral microbiota are influenced by breed and environment}, year = {2019}, month = {07}, volume = {14}, url = {https://doi.org/10.1371/journal.pone.0220463}, pages = {1-19}, abstract = {Previous research revealed the feline skin bacterial microbiota to be site-specific and the fungal microbiota to be individual-specific. The effect of other factors, such as genotype and environment, have not yet been studied in cats, but have been shown to be potentially important in shaping the cutaneous microbiota of other animals. Therefore, the objectives of this study were to evaluate the effect of these factors on the bacterial and fungal microbiota of feline skin and oral cavity. The influence of genotype was assessed through the analysis of different cat breeds, and the influence of environment through comparison of indoor and outdoor cats. DNA was extracted from skin and oral swabs, and bacterial and fungal next-generation sequencing were performed. Analysis of the skin microbiota of different cat breeds revealed significant differences in alpha diversity, with Sphynx and Bengal cats having the most diverse communities. Many taxa were found to be differentially abundant between cat breeds, including Veillonellaceae and Malassezia spp. Outdoor environment exposure had considerable influence on beta diversity, especially in the oral cavity, and resulted in numerous differentially abundant taxa. Our findings indicate that the oral bacterial microbiota and both fungal and bacterial microbiota of feline skin are influenced by breed, and to a lesser degree, environment.}, number = {7}, } @article{https://doi.org/10.1029/2020JD032591, author = {Ren, Tong and Yang, Ping and Schumacher, Courtney and Huang, Xianglei and Lin, Wuyin}, title = {Impact of Cloud Longwave Scattering on Radiative Fluxes Associated With the Madden-Julian Oscillation in the Indian Ocean and Maritime Continent}, journal = {Journal of Geophysical Research: Atmospheres}, volume = {125}, number = {13}, pages = {e2020JD032591}, doi = {https://doi.org/10.1029/2020JD032591}, url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020JD032591}, eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2020JD032591}, note = {e2020JD032591 2020JD032591}, abstract = {Abstract Previous studies suggested that cloud longwave radiation contributes to the development and maintenance of the Madden-Julian Oscillation (MJO) and model-based convection is highly sensitive to the radiation scheme. However, currently used radiation schemes do not take cloud longwave scattering into account, resulting in an overestimation of the outgoing longwave radiation (OLR) and an underestimation of the downward longwave flux at the surface. We use combined active and passive satellite cloud property retrievals to quantify the one-layer cloud OLR and heating rate (HR) biases introduced by neglecting cloud longwave scattering in the Indian Ocean and Maritime Continent in the context of MJO, with a focus on its phases 3, 5, and 6. The results show that the satellite-detected one-layer cloud area consists primarily of ice clouds, particularly during the boreal winter in the 4-year study period. An increased ice cloud area fraction of one-layer cloud groups is present up to 5 days before the onset of MJO events. If longwave scattering is neglected, the composite mean OLR overestimation over the one-layer ice cloud area from 5 days before to 4 days after the MJO passage is approximately 3.5 to 5.0 W m−2. Neglecting longwave scattering also leads to a HR underestimation at cloud base and an overestimation at cloud top, making the base-to-top heating gradient less sharp at the cloud-resolving scale.}, year = {2020} } @article{doi:10.1080/02786826.2017.1322174, author = {Huan Li and William B. Faulkner and John S. Haglund and Ronald E. Lacey}, title = {Effect of convergence angle on impactor performance}, journal = {Aerosol Science and Technology}, volume = {51}, number = {8}, pages = {981-987}, year = {2017}, publisher = {Taylor & Francis}, doi = {10.1080/02786826.2017.1322174}, URL = {https://doi.org/10.1080/02786826.2017.1322174}, eprint = {https://doi.org/10.1080/02786826.2017.1322174} } @article{guerrero_raw_2021, title = {Raw pacific biosciences and illumina sequencing reads and assembled genome data for the cattle ticks Rhipicephalus microplus and Rhipicephalus annulatus}, volume = {35}, issn = {2352-3409}, url = {https://www.sciencedirect.com/science/article/pii/S2352340921001360}, doi = {10.1016/j.dib.2021.106852}, abstract = {Ticks from the genus Rhipicephalus have enormous global economic impact as ectoparasites of cattle. Rhipicephalus microplus and Rhipicephalus annulatus are known to harbor infectious pathogens such as Babesia bovis, Babesia bigemina, and Anaplasma marginale. Having reference quality genomes of these ticks would advance research to identify druggable targets for chemical entities with acaricidal activity and refine anti-tick vaccine approaches. We sequenced and assembled the genomes of R. microplus and R. annulatus, using Pacific Biosciences and HiSeq 4000 technologies on very high molecular weight genomic DNA. We used 22 and 29 SMRT cells on the Pacific Biosciences Sequel for R. microplus and R. annulatus, respectively, and 3 lanes of the Illumina HiSeq 4000 platform for each tick. The PacBio sequence yields for R. microplus and R. annulatus were 21.0 and 27.9 million subreads, respectively, which were assembled with Canu v. 1.7. The final Canu assemblies consisted of 92,167 and 57,796 contigs with an average contig length of 39,249 and 69,055 bp for R. microplus and R. annulatus, respectively. Annotated genome quality was assessed by BUSCO analysis to provide quantitative measures for each assembled genome. Over 82\% and 92\% of the 1066 member BUSCO gene set was found in the assembled genomes of R. microplus and R. annulatus, respectively. For R. microplus, only 189 of the 1066 BUSCO genes were missing and only 140 were present in a fragmented condition. For R. annulatus, only 75 of the BUSCO genes were missing and only 109 were present in a fragmented condition. The raw sequencing reads and the assembled contigs/scaffolds are archived at the National Center for Biotechnology Information.}, language = {en}, urldate = {2021-05-06}, journal = {Data in Brief}, author = {Guerrero, Felix D. and Ghaffari, Noushin and Bendele, Kylie G. and Metz, Richard P. and Dickens, C. Michael and Blood, Philip D. and Tidwell, Jason and Miller, Robert J. and de León, Adalberto A. Pérez and Teel, Pete D. and Johnson, Charles D.}, month = apr, year = {2021}, keywords = {Canu assembler, Cattle tick, Large genome assembly, PacBio genome sequencing, Rhipicephalus annulatus, Rhipicephalus microplus}, pages = {106852}, file = {ScienceDirect Full Text PDF:/home/cmdickens/Zotero/storage/RWIDP3Q3/Guerrero et al. - 2021 - Raw pacific biosciences and illumina sequencing re.pdf:application/pdf;ScienceDirect Snapshot:/home/cmdickens/Zotero/storage/F5XG6RYB/S2352340921001360.html:text/html}, } @article{couperthwaite_materials_2020, title = {Materials Design Through Batch Bayesian Optimization with Multisource Information Fusion}, volume = {72}, issn = {1543-1851}, url = {https://doi.org/10.1007/s11837-020-04396-x}, doi = {10.1007/s11837-020-04396-x}, abstract = {Integrated computational materials engineering (ICME) calls for the integration of simulation tools and experiments to accelerate the development of materials. ICME approaches tend to be computationally costly, and recently, Bayesian optimization (BO) has been proposed as a way to make ICME more resource efficient. Conventional BO, however, is sequential (i.e., one-at-a-time) in nature, which makes it very time-consuming when the evaluation of a materials design choice is costly. While conventional high-throughput approaches enable the synthesis and characterization (or simulation) of materials in a parallel manner, they tend to be “open loop” and are unable to provide recommendations of what to try next once the parallel experiment/simulation has been carried out and analyzed. Here, we address this problem by introducing a batch BO framework that enables the exploration of the material’s design space in a parallel fashion. We augment this approach by incorporating information fusion frameworks capable of integrating multiple information sources. Demonstrating the proposed approach in the computational design of dual-phase steel, we show that batch BO can result in a significant reduction in the time and resources needed to carry out the design task. The proposed approach has wider applicability, well beyond the ICME example used to demonstrate it.}, language = {en}, number = {12}, urldate = {2021-05-06}, journal = {JOM}, author = {Couperthwaite, Richard and Molkeri, Abhilash and Khatamsaz, Danial and Srivastava, Ankit and Allaire, Douglas and Arròyave, Raymundo}, month = dec, year = {2020}, pages = {4431-4443}, file = {Springer Full Text PDF:/home/cmdickens/Zotero/storage/WSAH4IEZ/Couperthwaite et al. - 2020 - Materials Design Through Batch Bayesian Optimizati.pdf:application/pdf}, } @article{https://doi.org/10.1111/eva.13238, author = {Raszick, Tyler J. and Dickens, C. Michael and Perkin, Lindsey C. and Tessnow, Ashley E. and Suh, Charles P.-C. and Ruiz-Arce, Raul and Boratynski, Theodore N. and Falco, Marcelo R. and Johnston, J. Spencer and Sword, Gregory A.}, title = {Population genomics and phylogeography of the boll weevil, Anthonomus grandis Boheman (Coleoptera: Curculionidae), in the United States, northern Mexico, and Argentina}, journal = {Evolutionary Applications}, volume = {n/a}, number = {n/a}, pages = {1-16}, keywords = {boll weevil, ddRADseq, phylogenetics, phylogeography, population genetics, population genomics}, doi = {https://doi.org/10.1111/eva.13238}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.13238}, eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.13238}, abstract = {Abstract The boll weevil, Anthonomus grandis Boheman (Coleoptera: Curculionidae), is an important pest of commercial cotton across the Americas. In the United States, eradication of this species is complicated by re-infestations of areas where eradication has been previously successful and by the existence of morphologically similar variants that can confound identification efforts. To date, no study has applied a high-throughput sequencing approach to better understand the population genetic structure of the boll weevil. Furthermore, only a single study has investigated genetic relationships between populations in North and South America. We used double digest restriction site-associated DNA sequencing (ddRADseq) to resolve the population genomic structure of the boll weevil in the southern United States, northern Mexico, and Argentina. Additionally, we assembled the first complete mitochondrial genome for this species and generated a preliminary whole genome assembly, both of which were used to improve the identification of informative loci. Downstream analyses revealed two main lineages—one consisting of populations found geographically west of the Sierra Madre Occidental mountain range and the second consisting of populations found to the east—were revealed, and both were sub-structured. Population geographic structure was consistent with the isolation by distance model, indicating that geogrpahic distance is likely a primary mechanism driving divergence in this species. Boll weevil populations from Argentina were found to be more closely related to the eastern lineage, suggesting a recent colonization of South America by the eastern lineage, but additional sampling across Mexico, Central America and South America is needed to further clarify their origin. Finally, we uncovered an instance of population turnover or replacement, highlighting the temporal instability of population structure.}, year = {2021}, } @article{https://doi.org/10.1002/ps.5518, author = {Raszick, Tyler J and Suh, Charles P-C and Dickens, Charles Michael and Sword, Gregory A}, title = {Genome-wide markers reveal temporal instability of local population genetic structure in the cotton fleahopper, Pseudatomoscelis seriatus (Hemiptera: Miridae)}, journal = {Pest Management Science}, volume = {76}, number = {1}, pages = {324-332}, keywords = {cotton fleahopper, population genomics, resistance management, refuge}, doi = {https://doi.org/10.1002/ps.5518}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ps.5518}, eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/ps.5518}, abstract = {Abstract BACKGROUND The cotton fleahopper, Pseudatomoscelis seriatus (Reuter) (Hemiptera: Miridae), is a pest of upland cotton, Gossypium hirsutum L. (Malvales: Malvaceae), that attacks pre-floral buds (squares), leading to abscission and yield losses. In the Brazos Valley cotton production area of Texas (USA), P. seriatus exhibits a seasonal pattern of host use. In spring, eggs hatch from stems of the overwintering host, woolly croton, Croton capitatus Michx. (Malpighiales: Euphorbiaceae). During the growing season, individuals feed on a variety of host plants, including cotton. Adults return to woolly croton at season end to oviposit. We investigated if genetic differentiation exists between populations infesting cotton and those infesting alternative hosts, and whether woolly croton serves as a year-end site of admixture that could be suitable as a natural refuge for the purposes of insect resistance management. We combined high-throughput DNA sequencing with fine-scale spatio-temporal sampling to test (i) whether a population genomic approach would recover patterns of genetic variation consistent with earlier studies and (ii) if local genetic population structure was robust to seasonal changes in local habitat over time. RESULTS We found high gene flow among populations of P. seriatus collected from different host plants in the Brazos Valley. We also identified temporal instability of the local population genetic structure, including the near complete loss of a genotypic group that had been previously abundant. CONCLUSION We support the status of woolly croton as a natural refuge that promotes year-end gene flow between genotypes infesting cotton and those infesting alternative hosts. © 2019 Society of Chemical Industry}, year = {2020} } @article {Wahl617241, author = {Wahl, Nancy J. and Murray, Seth C. and Zhang, Hong-Bin and Zhang, Meiping and Dickens, C. Michael and Isakeit, Thomas S.}, title = {Maize Kernel Development Stage the Primary Factor in Differential Gene Expression in Response to Two Methods of Field Inoculation with Aspergillus flavus}, elocation-id = {617241}, year = {2019}, pages = {1-47}, doi = {10.1101/617241}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Background Aflatoxins, produced by the fungus Aspergillus flavus, often contaminate preharvest maize (Zea mays L.) grain under heat and drought stresses, posing serious health hazards to humans and livestock, and resulting in significant costs to identify and dispose of contaminated grain. This study was designed to investigate the changes in differential gene expression during seed morphogenesis and maturation in the {\textquotedblleft}aflatoxin resistant{\textquotedblright} Argentinian inbred line Tx772 when challenged by the introduction of A. flavus through two different methods of ear inoculation; non-wounding (silk channel, used to select Tx772), wounding (side needle) and a non-inoculated control.Method and Findings Grain maturity had the largest effect on overall RNA-Seq differential gene expression (DGE) as measured by edgeR of the Bioconductor platform. However, within each stage of development, ranging from blister to dent, similar up-regulation in expression of many maize genes following inoculation with either method was observed; a total of 16 genes previously associated with resistance to pathogens were identified among the transcripts differentially expressed (DE) at p <= .05, FDR <= .10, and fold change >= 2.0 over all stages. The side needle technique produced a larger effect of infection as evidenced by 6,324 fungal reads versus 518 in silk channel and a higher level of aflatoxin. Correlations between approximately 7,000 fungal reads and the number of maize DE genes for each of the eight treatment groups was 0.56 (p = .152) and was 0.65 (p < .001) with levels of aflatoxin ranging from 0 to 137 ng g-1.Conclusion These correlations provided an internal measure of effectiveness of inoculation methods that were associated with the mostly up-regulation of defense-related genes in response to the presence of Aspergillus flavus in a unique maize genetic background.}, url = {https://www.biorxiv.org/content/early/2019/05/09/617241}, eprint = {https://www.biorxiv.org/content/early/2019/05/09/617241.full.pdf}, journal = {bioRxiv} } @article{10.1115/1.4041123, author = {Wu, Tingcheng and San Andrés, Luis}, title = "{Leakage and Dynamic Force Coefficients for Two Labyrinth Gas Seals: Teeth-on-Stator and Interlocking Teeth Configurations. A Computational Fluid Dynamics Approach to Their Performance}", journal = {Journal of Engineering for Gas Turbines and Power}, volume = {141}, number = {4}, pages = {1-12}, year = {2018}, month = {10}, abstract = "{Labyrinth gas seals (LSs) commonly used in turbomachines reduce secondary flow leakage. Conventional see-through labyrinth seal designs include either all teeth-on-stator (TOS) or all teeth-on-rotor (TOR). Experience shows that an interlocking labyrinth seal (ILS), with teeth on both stator and rotor, reduces gas leakage by up to 30\\% compared to the conventional see-through designs. However, field data for ILS rotordynamic characteristics are still vague and scarce in the literature. This work presents flow predictions for an ILS and a TOS LS, both seals share identical design features, namely radial clearance Cr = 0.2 mm, rotor diameter D = 150 mm, tooth pitch Li = 3.75 mm, and tooth height B = 3 mm. Air enters the seal at supply pressure Pin = 3.8, 6.9 bar (absolute) and temperature of 25 °C. The ratio of gas exit pressure to supply pressure ranges from 0.5 to 0.8, and the rotor speed is fixed at 10 krpm (surface speed of 79 m/s). The analysis implements a computational fluid dynamics (CFD) method with a multi-frequency-orbit rotor whirl model. The CFD predicted mass flow rate for the ILS is ∼ 21\\% lower than that of the TOS LS, thus making the ILS a more efficient choice. Integration of the dynamic pressure fields in the seal cavities, obtained for excitation frequency (ω) ranging from 12\\% to 168\\% of rotor speed (sub and super synchronous whirl), allows an accurate estimation of the seal dynamic force coefficients. For all the considered operating conditions, at low frequency range, the TOS LS shows a negative direct stiffness (K < 0), frequency independent; whereas the ILS has K > 0 that increases with both frequency and supply pressure. For both seals, the magnitude of K decreases when the exit pressure/inlet pressure ratio increases. On the other hand, the cross-coupled stiffness (k) from both seals is frequency dependent, its magnitude increases with gas supply pressure, and k for the ILS is more sensitive to a change in the exit/inlet pressure ratio. Notably, k turns negative for subsynchronous frequencies below rotor speed (Ω) for both the TOS LS and the ILS. The direct damping (C) for the TOS LS remains constant for ω > ½ Ω and has a larger magnitude than the damping for the ILS over the frequency range up to 1.5 Ω. An increase in exit/inlet pressure ratio decreases the direct damping for both seals. The effective damping coefficient, Ceff = (C-k/ω), whenever positive aids to damp vibrations, whereas Ceff < 0 is a potential source for an instability. For frequencies ω/Ω < 1.3, Ceff for the TOS LS is higher in magnitude than that for the ILS. From a rotordynamics point of view, the ILS is not a sound selection albeit it reduces leakage. Comparison of the CFD predicted force coefficients against those from a bulk flow model demonstrates that the later simple model delivers poor results, often contradictory and largely indifferent to the type of seal, ILS or TOS LS. In addition, CFD model predictions are benchmarked against experimental dynamic force coefficients for two TOS LSs published by Ertas et al. (2012, “Rotordynamic Force Coefficients for Three Types of Annular Gas Seals With Inlet Preswirl and High Differential Pressure Ratio,” ASME J. Eng. Gas Turbines Power, 134(4), pp. 04250301–04250312) and Vannini et al. (2014, “Labyrinth Seal and Pocket Damper Seal High Pressure Rotordynamic Test Data,” ASME J. Eng. Gas Turbines Power, 136(2), pp. 022501–022509.)}", issn = {0742-4795}, doi = {10.1115/1.4041123}, url = {https://doi.org/10.1115/1.4041123}, note = {042501}, eprint = {https://asmedigitalcollection.asme.org/gasturbinespower/article-pdf/141/4/042501/6183430/gtp\_141\_04\_042501.pdf}, } @article{10.1115/1.4040742, author = {Yang, Jing and San Andrés, Luis}, title = "{On the Influence of the Entrance Section on the Rotordynamic Performance of a Pump Seal With Uniform Clearance: A Sharp Edge Versus A Round Inlet}", journal = {Journal of Engineering for Gas Turbines and Power}, volume = {141}, number = {3}, year = {2018}, pages = {1-9}, month = {12}, abstract = "{Secondary flows through annular seals in pumps must be minimized to improve their mechanical efficiency. Annular seals, in particular balance piston seals, also produce rotordynamic force coefficients, which easily control the placement of rotor critical speeds and determine system stability. A uniform clearance annular seal produces a direct (centering) static stiffness as a result of the sudden entrance pressure drop at its inlet plane when the fluid flow accelerates from an upstream (stagnant) flow region into a narrow film land. This so-called Lomakin effect equates the entrance pressure drop to the dynamic flow head through an empirical entrance pressure loss coefficient. Most seal designs regard the inlet as a sharp edge or square corner. In actuality, a customary manufacturing process could produce a rounded corner at the seal inlet. Furthermore, after a long period of operation, a sharp corner may wear out into a round section. Notice that to this date, bulk-flow model (BFM) analyses rely on a hitherto unknown entrance pressure coefficient to deliver accurate predictions for seal force coefficients. This paper establishes the ground to quantify the influence of an inlet round corner on the performance of a water lubricated seal reproducing a configuration tested by Marquette et al. (1997). The smooth surface seal has clearance Cr = 0.11 mm, length L = 35 mm, and diameter D = 76 mm (L/D = 0.46). The test case considers design operation at 10.2 krpm and 6.9 MPa pressure drop. Computational fluid dynamics (CFD) simulations apply to a seal with either a sharp edge or an inlet section with curvature rc varying from ¼Cr to 5Cr. Note the largest radius (rc) is just 1.6\\% of the overall seal length L. Going from a sharp edge inlet plane to one with a small curvature rc = ¼Cr produces a ∼20\\% decrease on the inlet pressure loss coefficient (ξ). A further reduction occurs with a larger circular corner; ξ drops from 0.43 to 0.17. That is, the entrance pressure loss will be lesser in a seal with a curved inlet. This can occur easily if the inlet edge wears due to solid particles eroding the seal inlet section. Further CFD simulations show that operating conditions in rotor speed and pressure drop do not affect the inlet loss coefficient, while the inlet circumferential swirl velocity does. In addition, further CFD results for a shorter (half) length seal produce a very similar entrance loss coefficient, whereas an enlarged (double) clearance seal leads to an increase in the entrance pressure loss parameter as the inlet section becomes less round. CFD predictions for most rotordynamic coefficients are within 10\\% relative to published test data, except for the direct damping coefficient C. For the seal with a rounded edge (rc = 5 Cr) at the inlet plane, both the direct stiffness K and direct damping C decrease about 10\\% compared against the coefficients for the seal with a sharp inlet edge. The other force coefficients, namely cross-coupled stiffness and added mass, are unaffected by the inlet edge geometry. The same result holds for seal leakage, as expected. A BFM incorporates the CFD derived entrance pressure loss coefficients and produces rotordynamic coefficients for the same operating conditions. The CFD and BFM predictions are in good agreement, though there is still ∼10\\% discrepancy for the direct stiffnesses delivered by the two methods. In the end, the analysis of the CFD results quantifies the pressure loss coefficient as a function of the inlet geometry for ready use in engineering BFM tools.}", issn = {0742-4795}, doi = {10.1115/1.4040742}, url = {https://doi.org/10.1115/1.4040742}, note = {031029}, eprint = {https://asmedigitalcollection.asme.org/gasturbinespower/article-pdf/141/3/031029/6181659/gtp\_141\_03\_031029.pdf}, } @article{10.1115/1.4040766, author = {San Andrés, Luis and Yang, Jing and Lu, Xueliang}, title = "{On the Leakage, Torque, and Dynamic Force Coefficients of Air in Oil (Wet) Annular Seal: A Computational Fluid Dynamics Analysis Anchored to Test Data}", journal = {Journal of Engineering for Gas Turbines and Power}, volume = {141}, number = {2}, year = {2018}, pages = {1-11}, month = {09}, abstract = "{Subsea pumps and compressors must withstand multiphase flows whose gas volume fraction (GVF) or liquid volume fraction (LVF) varies over a wide range. Gas or liquid content as a dispersed phase in the primary stream affects the leakage, drag torque, and dynamic forced performance of secondary flow components, namely seals, thus affecting the process efficiency and mechanical reliability of pumping/compressing systems, in particular during transient events with sudden changes in gas (or liquid) content. This paper, complementing a parallel experimental program, presents a computational fluid dynamics (CFD) analysis to predict the leakage, drag power, and dynamic force coefficients of a smooth surface, uniform clearance annular seal supplied with air in oil mixture whose inlet GVF varies discretely from 0.0 to 0.9, i.e., from a pure liquid stream to a nearly all-gas content mixture. The test seal has uniform radial clearance Cr = 0.203 mm, diameter D = 127 mm, and length L = 0.36 D. The tests were conducted with an inlet pressure/exit pressure ratio equal to 2.5 and a rotor surface speed of 23.3 m/s (3.5 krpm), similar to conditions in a pump neck wear ring seal. The CFD two-phase flow model, first to be anchored to test data, uses an Euler–Euler formulation and delivers information on the precise evolution of the GVF and the gas and liquid streams' velocity fields. Recreating the test data, the CFD seal mass leakage and drag power decrease steadily as the GVF increases. A multiple-frequency shaft whirl orbit method aids in the calculation of seal reaction force components, and from which dynamic force coefficients, frequency-dependent, follow. For operation with a pure liquid, the CFD results and test data produce a constant cross-coupled stiffness, damping, and added mass coefficients, while also verifying predictive formulas typical of a laminar flow. The injection of air in the oil stream, small or large in gas volume, immediately produces force coefficients that are frequency-dependent; in particular the direct dynamic stiffness which hardens with excitation frequency. The effect is most remarkable for small GVFs, as low as 0.2. The seal test direct damping and cross-coupled dynamic stiffness continuously drop with an increase in GVF. CFD predictions, along with results from a bulk-flow model (BFM), reproduce the test force coefficients with great fidelity. Incidentally, early engineering practice points out to air injection as a remedy to cure persistent (self-excited) vibration problems in vertical pumps, submersible and large size hydraulic. Presently, the model predictions, supported by the test data, demonstrate that even a small content of gas in the liquid stream significantly raises the seal direct stiffness, thus displacing the system critical speed away to safety. The sound speed of a gas in liquid mixture is a small fraction of those speeds for either the pure oil or the gas, hence amplifying the fluid compressibility that produces the stiffness hardening. The CFD model and a dedicated test rig, predictions and test data complementing each other, enable engineered seals for extreme applications.}", issn = {0742-4795}, doi = {10.1115/1.4040766}, url = {https://doi.org/10.1115/1.4040766}, note = {021008}, eprint = {https://asmedigitalcollection.asme.org/gasturbinespower/article-pdf/141/2/021008/6184351/gtp\_141\_02\_021008.pdf}, } @article{Wang_2017, doi = {10.1088/2053-1583/4/1/015042}, url = {https://doi.org/10.1088/2053-1583/4/1/015042}, year = 2017, month = {jan}, publisher = {IOP Publishing}, volume = {4}, number = {1}, pages = {015042}, author = {Hua Wang and Xiaofeng Qian}, title = {Two-dimensional multiferroics in monolayer group IV monochalcogenides}, journal = {2D Materials}, } @article{abdoelatef_mesoscale_2019, title = {Mesoscale Modeling of High Burn-Up Structure Formation and Evolution in UO2}, volume = {71}, issn = {1543-1851}, url = {https://doi.org/10.1007/s11837-019-03830-z}, doi = {10.1007/s11837-019-03830-z}, number = {12}, journal = {JOM}, author = {Abdoelatef, M. Gomaa and Badry, Fergany and Schwen, Daniel and Permann, Cody and Zhang, Yongfeng and Ahmed, Karim}, month = dec, year = {2019}, pages = {4817-4828}, } @article {Gerth2020.06.23.165548, author = {Gerth, Michael and Martinez-Montoya, Humberto and Ramirez, Paulino and Masson, Florent and Griffin, Joanne S. and Aramayo, Rodolfo and Siozios, Stefanos and Lemaitre, Bruno and Mateos, Mariana and Hurst, Gregory D.D.}, title = {Rapid molecular evolution of Spiroplasma symbionts of Drosophila}, elocation-id = {2020.06.23.165548}, year = {2020}, pages = {1-40}, doi = {10.1101/2020.06.23.165548}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Spiroplasma are a group of Mollicutes whose members include plant pathogens, insect pathogens, and endosymbionts of animals. Spiroplasma phenotypes have been repeatedly observed to be spontaneously lost in Drosophila cultures, and several studies have documented a high genomic turnover in Spiroplasma symbionts and plant pathogens. These observations suggest that Spiroplasma evolves quickly in comparison to other insect symbionts. Here, we systematically assess evolutionary rates and patterns of Spiroplasma poulsonii, a natural symbiont of Drosophila. We analysed genomic evolution of sHy within flies, and sMel within in vitro culture over several years. We observed that S. poulsonii substitution rates are among the highest reported for any bacteria, and around two orders of magnitude higher compared with other inherited arthropod endosymbionts. The absence of mismatch repair loci mutS and mutL is conserved across Spiroplasma and likely contributes to elevated substitution rates. Further, the closely related strains sMel and sHy (>99.5\% sequence identity in shared loci) show extensive structural genomic differences, which potentially indicates a higher degree of host adaptation in sHy, a protective symbiont of Drosophila hydei. Finally, comparison across diverse Spiroplasma lineages confirms previous reports of dynamic evolution of toxins, and identifies loci similar to the male-killing toxin Spaid in several Spiroplasma lineages and other endosymbionts. Overall, our results highlight the peculiar nature of Spiroplasma genome evolution, which may explain unusual features of its evolutionary ecology.Competing Interest StatementThe authors have declared no competing interest.}, url = {https://www.biorxiv.org/content/early/2020/11/30/2020.06.23.165548}, eprint = {https://www.biorxiv.org/content/early/2020/11/30/2020.06.23.165548.full.pdf}, journal = {bioRxiv} } @article {10.7554/eLife.53127, article_type = {journal}, title = {Translational control of one-carbon metabolism underpins ribosomal protein phenotypes in cell division and longevity}, author = {Maitra, Nairita and He, Chong and Blank, Heidi M and Tsuchiya, Mitsuhiro and Schilling, Birgit and Kaeberlein, Matt and Aramayo, Rodolfo and Kennedy, Brian K and Polymenis, Michael}, editor = {Smith, Jeff and Tyler, Jessica K and Smith, Jeff}, volume = 9, year = 2020, month = {may}, pub_date = {2020-05-20}, pages = {e53127}, citation = {eLife 2020;9:e53127}, doi = {10.7554/eLife.53127}, url = {https://doi.org/10.7554/eLife.53127}, abstract = {A long-standing problem is how cells that lack one of the highly similar ribosomal proteins (RPs) often display distinct phenotypes. Yeast and other organisms live longer when they lack specific ribosomal proteins, especially of the large 60S subunit of the ribosome. However, longevity is neither associated with the generation time of RP deletion mutants nor with bulk inhibition of protein synthesis. Here, we queried actively dividing RP mutants through the cell cycle. Our data link transcriptional, translational, and metabolic changes to phenotypes associated with the loss of paralogous RPs. We uncovered translational control of transcripts encoding enzymes of methionine and serine metabolism, which are part of one-carbon (1C) pathways. Cells lacking Rpl22Ap, which are long-lived, have lower levels of metabolites associated with 1C metabolism. Loss of 1C enzymes increased the longevity of wild type cells. 1C pathways exist in all organisms and targeting the relevant enzymes could represent longevity interventions.}, keywords = {ribosomal, translation, one-carbon, cell cycle, longevity, Rpl22}, journal = {eLife}, issn = {2050-084X}, publisher = {eLife Sciences Publications, Ltd}, } @article{mateos_effect_2019, title = {Effect of heritable symbionts on maternally-derived embryo transcripts}, volume = {9}, issn = {2045-2322}, url = {https://doi.org/10.1038/s41598-019-45371-0}, doi = {10.1038/s41598-019-45371-0}, abstract = {Maternally-transmitted endosymbiotic bacteria are ubiquitous in insects. Among other influential phenotypes, many heritable symbionts of arthropods are notorious for manipulating host reproduction through one of four reproductive syndromes, which are generally exerted during early developmental stages of the host: male feminization; parthenogenesis induction; male killing; and cytoplasmic incompatibility (CI). Major advances have been achieved in understanding mechanisms and identifying symbiont factors involved in reproductive manipulation, particularly male killing and cytoplasmic incompatibility. Nonetheless, whether cytoplasmically-transmitted bacteria influence the maternally-loaded components of the egg or early embryo has not been examined. In the present study, we investigated whether heritable endosymbionts that cause different reproductive phenotypes in Drosophila melanogaster influence the mRNA transcriptome of early embryos. We used mRNA-seq to evaluate differential expression in Drosophila embryos lacking endosymbionts (control) to those harbouring the male-killing Spiroplasma poulsonii strain MSRO-Br, the CI-inducing Wolbachia strain wMel, or Spiroplasma poulsonii strain Hyd1; a strain that lacks a reproductive phenotype and is naturally associated with Drosophila hydei. We found no consistent evidence of influence of symbiont on mRNA composition of early embryos, suggesting that the reproductive manipulation mechanism does not involve alteration of maternally-loaded transcripts. In addition, we capitalized on several available mRNA-seq datasets derived from Spiroplasma-infected Drosophila melanogaster embryos, to search for signals of depurination of rRNA, consistent with the activity of Ribosome Inactivating Proteins (RIPs) encoded by Spiroplasma poulsonii. We found small but statistically significant signals of depurination of Drosophila rRNA in the Spiroplasma treatments (both strains), but not in the symbiont-free control or Wolbachia treatment, consistent with the action of RIPs. The depurination signal was slightly stronger in the treatment with the male-killing strain. This result supports a recent report that RIP-induced damage contributes to male embryo death.}, number = {1}, journal = {Scientific Reports}, author = {Mateos, Mariana and Silva, Nadisha O. and Ramirez, Paulino and Higareda-Alvear, Victor M. and Aramayo, Rodolfo and Erickson, James W.}, month = jun, year = {2019}, pages = {8847}, } @article{stavrianakou_draft_2017, title = {Draft de novo transcriptome assembly and proteome characterization of the electric lobe of {Tetronarce} californica: a molecular tool for the study of cholinergic neurotransmission in the electric organ}, volume = {18}, issn = {1471-2164}, url = {https://doi.org/10.1186/s12864-017-3890-4}, doi = {10.1186/s12864-017-3890-4}, abstract = {The electric organ of Tetronarce californica (an electric ray formerly known as Torpedo californica) is a classic preparation for biochemical studies of cholinergic neurotransmission. To broaden the usefulness of this preparation, we have performed a transcriptome assembly of the presynaptic component of the electric organ (the electric lobe). We combined our assembled transcriptome with a previous transcriptome of the postsynaptic electric organ, to define a MetaProteome containing pre- and post-synaptic components of the electric organ.}, number = {1}, journal = {BMC Genomics}, author = {Stavrianakou, Maria and Perez, Ricardo and Wu, Cheng and Sachs, Matthew S. and Aramayo, Rodolfo and Harlow, Mark}, month = aug, year = {2017}, pages = {611}, } @article{aramayo_ribosome_2017, title = {Ribosome profiling the cell cycle: lessons and challenges}, volume = {63}, issn = {1432-0983}, url = {https://doi.org/10.1007/s00294-017-0698-3}, doi = {10.1007/s00294-017-0698-3}, abstract = {Understanding the causes and consequences of dynamic changes in the abundance and activity of cellular components during cell division is what most cell cycle studies are about. Here we focus on control of gene expression in the cell cycle at the level of translation. The advent of deep sequencing methodologies led to technologies that quantify the levels of all mRNAs that are bound by ribosomes and engaged in translation in the cell (Ingolia et al. Science 324:218–223, 2009). This approach has been applied recently to synchronous cell populations to find transcripts under translational control at different cell cycle phases (Blank et al. EMBO J 36:487–502, 2017; Stumpf et al. Mol Cell 52:574–582, 2013; Tanenbaum et al. Elife 4:e07957, 2015). These studies revealed new biology, but they also have limitations, pointing to challenges that need to be addressed in the future.}, number = {6}, journal = {Current Genetics}, author = {Aramayo, Rodolfo and Polymenis, Michael}, month = dec, year = {2017}, pages = {959-964}, } @article{clanton_control_2017, title = {Control of seizures by ketogenic diet-induced modulation of metabolic pathways}, volume = {49}, issn = {1438-2199}, url = {https://doi.org/10.1007/s00726-016-2336-7}, doi = {10.1007/s00726-016-2336-7}, abstract = {Epilepsy is too complex to be considered as a disease; it is more of a syndrome, characterized by seizures, which can be caused by a diverse array of afflictions. As such, drug interventions that target a single biological pathway will only help the specific individuals where that drug’s mechanism of action is relevant to their disorder. Most likely, this will not alleviate all forms of epilepsy nor the potential biological pathways causing the seizures, such as glucose/amino acid transport, mitochondrial dysfunction, or neuronal myelination. Considering our current inability to test every individual effectively for the true causes of their epilepsy and the alarming number of misdiagnoses observed, we propose the use of the ketogenic diet (KD) as an effective and efficient preliminary/long-term treatment. The KD mimics fasting by altering substrate metabolism from carbohydrates to fatty acids and ketone bodies (KBs). Here, we underscore the need to understand the underlying cellular mechanisms governing the KD’s modulation of various forms of epilepsy and how a diverse array of metabolites including soluble fibers, specific fatty acids, and functional amino acids (e.g., leucine, d-serine, glycine, arginine metabolites, and N-acetyl-cysteine) may potentially enhance the KD’s ability to treat and reverse, not mask, these neurological disorders that lead to epilepsy.}, number = {1}, journal = {Amino Acids}, author = {Clanton, Ryan M. and Wu, Guoyao and Akabani, Gamal and Aramayo, Rodolfo}, month = jan, year = {2017}, pages = {1-20}, } @article{https://doi.org/10.15252/embj.201695050, author = {Blank, Heidi M and Perez, Ricardo and He, Chong and Maitra, Nairita and Metz, Richard and Hill, Joshua and Lin, Yuhong and Johnson, Charles D and Bankaitis, Vytas A and Kennedy, Brian K and Aramayo, Rodolfo and Polymenis, Michael}, title = {Translational control of lipogenic enzymes in the cell cycle of synchronous, growing yeast cells}, journal = {The EMBO Journal}, volume = {36}, number = {4}, pages = {487-502}, keywords = {ACC1, cell size, mitosis, translation, upstream open reading frame}, doi = {https://doi.org/10.15252/embj.201695050}, url = {https://www.embopress.org/doi/abs/10.15252/embj.201695050}, eprint = {https://www.embopress.org/doi/pdf/10.15252/embj.201695050}, abstract = {Abstract Translational control during cell division determines when cells start a new cell cycle, how fast they complete it, the number of successive divisions, and how cells coordinate proliferation with available nutrients. The translational efficiencies of mRNAs in cells progressing synchronously through the mitotic cell cycle, while preserving the coupling of cell division with cell growth, remain uninvestigated. We now report comprehensive ribosome profiling of a yeast cell size series from the time of cell birth, to identify mRNAs under periodic translational control. The data reveal coordinate translational activation of mRNAs encoding lipogenic enzymes late in the cell cycle including Acc1p, the rate-limiting enzyme acetyl-CoA carboxylase. An upstream open reading frame (uORF) confers the translational control of ACC1 and adjusts Acc1p protein levels in different nutrients. The ACC1 uORF is relevant for cell division because its ablation delays cell cycle progression, reduces cell size, and suppresses the replicative longevity of cells lacking the Sch9p protein kinase regulator of ribosome biogenesis. These findings establish an unexpected relationship between lipogenesis and protein synthesis in mitotic cell divisions.}, year = {2017} } @article{LI201752, title = {Synaptic vesicles isolated from the electric organ of Torpedo californica and from the central nervous system of Mus musculus contain small ribonucleic acids (sRNAs)}, journal = {Genomics Data}, volume = {12}, pages = {52-53}, year = {2017}, issn = {2213-5960}, doi = {https://doi.org/10.1016/j.gdata.2017.02.015}, url = {https://www.sciencedirect.com/science/article/pii/S2213596017300260}, author = {Huinan Li and Cheng Wu and Rodolfo Aramayo and Matthew S. Sachs and Mark L. Harlow}, keywords = {Synaptic vesicle, Micro-RNA, tRNA fragment, , }, abstract = {Synaptic vesicles (SVs) are presynaptic organelles that load and release small molecule neurotransmitters at chemical synapses. In addition to classic neurotransmitters, we have demonstrated that SVs isolated from the Peripheral Nervous Systems (PNS) of the electric organ of Torpedo californica, a model cholinergic synapse, and SVs isolated from the Central Nervous System (CNS) of Mus musculus (mouse) contain small ribonucleic acids (sRNAs; ≤50 nucleotides) (Scientific Reports, 5:1–14(14918) Li et al. (2015) [1]). Our previous publication provided the five most abundant sequences associated with the T. californica SVs, and the ten most abundant sequences associated with the mouse SVs, representing 59% and 39% of the total sRNA reads sequenced, respectively). We provide here a full repository of the SV sRNAs sequenced from T. californica and the mouse deposited in the NCBI as biosamples. Three data studies are included: SVs isolated from the electric organ of T. californica using standard techniques, SVs isolated from the electric organ of T. californica using standard techniques with an additional affinity purification step, and finally, SVs isolated from the CNS of mouse. The three biosamples are available at https://www.ncbi.nlm.nih.gov/biosample/ SRS1523467, SRS1523466, and SRS1523472 respectively.} } @article{https://doi.org/10.1002/2016JD026080, author = {Saito, Masanori and Iwabuchi, Hironobu and Yang, Ping and Tang, Guanglin and King, Michael D. and Sekiguchi, Miho}, title = {Ice particle morphology and microphysical properties of cirrus clouds inferred from combined CALIOP-IIR measurements}, journal = {Journal of Geophysical Research: Atmospheres}, volume = {122}, number = {8}, pages = {4440-4462}, keywords = {cirrus clouds, remote sensing, oriented plates, lidar ratio}, doi = {https://doi.org/10.1002/2016JD026080}, url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2016JD026080}, eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1002/2016JD026080}, abstract = {Abstract Ice particle morphology and microphysical properties of cirrus clouds are essential for assessing radiative forcing associated with these clouds. We develop an optimal estimation-based algorithm to infer cirrus cloud optical thickness (COT), cloud effective radius (CER), plate fraction including quasi-horizontally oriented plates (HOPs), and the degree of surface roughness from the Cloud Aerosol Lidar with Orthogonal Polarization (CALIOP) and the Infrared Imaging Radiometer (IIR) on the Cloud Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) platform. A simple but realistic ice particle model is used, and the relevant bulk optical properties are computed using state-of-the-art light-scattering computational capabilities. Rigorous estimation of uncertainties related to surface properties, atmospheric gases, and cloud heterogeneity is performed. The results based on the present method show that COTs are quite consistent with other satellite products and CERs essentially agree with the other counterparts. A 1 month global analysis for April 2007, in which CALIPSO off-nadir angle is 0.3°, shows that the HOP has significant temperature-dependence and is critical to the lidar ratio when cloud temperature is warmer than −40°C. The lidar ratio is calculated from the bulk optical properties based on the inferred parameters, showing robust temperature dependence. The median lidar ratio of cirrus clouds is 27–31 sr over the globe.}, year = {2017} } @article{saito_yang_ding_liu_2021, title={A Comprehensive Database of the Optical Properties of Irregular Aerosol Particles for Radiative Transfer Simulations}, url={https://journals.ametsoc.org/view/journals/atsc/aop/JAS-D-20-0338.1/JAS-D-20-0338.1.xml}, journal={AMETSOC}, publisher={American Meteorological Society}, author={Saito, Masanori and Yang, Ping and Ding, Jiachen and Liu, Xu}, pages = {2089-2111}, doi = {https://doi.org/10.1175/JAS-D-20-0338.1}, keywords = {Radiative transfer; Databases; Aerosol optical properties}, year={2021}, month={Jul} } @article{saito_yang_2019, title={Oriented Ice Crystals: A Single-Scattering Property Database for Applications to Lidar and Optical Phenomenon Simulations}, url={https://journals.ametsoc.org/view/journals/atsc/76/9/jas-d-19-0031.1.xml}, journal={AMETSOC}, publisher={American Meteorological Society}, author={Saito, Masanori and Yang, Ping}, pages = {2635-2652}, doi = {https://doi.org/10.1175/JAS-D-19-0031.1}, keywords = {Cloud microphysics; Radiative transfer; Databases; Remote sensing}, year={2019}, month={Sep} } @article{saito_yang_loeb_kato_2019, title={A Novel Parameterization of Snow Albedo Based on a Two-Layer Snow Model with a Mixture of Grain Habits}, url={https://journals.ametsoc.org/view/journals/atsc/76/5/jas-d-18-0308.1.xml}, journal={AMETSOC}, publisher={American Meteorological Society}, author={Saito, Masanori and Yang, Ping and Loeb, Norman G. and Kato, Seiji}, pages = {1419-1436}, doi = {https://doi.org/10.1175/JAS-D-18-0308.1}, keywords = {Snow; Albedo; Ice particles; Radiative transfer; Snow cover; Parameterization}, year={2019}, month={May} } @Article{rs13142754, AUTHOR = {Wang, Yi and Yang, Ping and King, Michael D. and Baum, Bryan A.}, TITLE = {Optical Property Model for Cirrus Clouds Based on Airborne Multi-Angle Polarization Observations}, JOURNAL = {Remote Sensing}, VOLUME = {13}, YEAR = {2021}, NUMBER = {14}, ARTICLE-NUMBER = {2754}, URL = {https://www.mdpi.com/2072-4292/13/14/2754}, ISSN = {2072-4292}, PAGES = {1-18}, ABSTRACT = {We present an improved remote sensing technique to infer an optimal habit/shape model for ice particles in cirrus clouds using multi-angle polarimetric measurements at 865 nm made by the Airborne Multi-angle SpectroPolarimeter Imager (AirMSPI) instrument. The common method of ice model inference is based on intensity (total reflectivity) measurements, which is generally not applicable to optically thin ice clouds (i.e., cirrus clouds) where single scattering dominates. The new approach is able to infer an ice model in clouds with optical thicknesses smaller than 5. The improvement is made by first assuming the optical thickness retrieved using total reflectivity. Subsequently, the polarized reflectivity is calculated based on look-up tables generated from simulated polarized reflectances computed for cirrus clouds in conjunction with eight ice particle models. The ice particle model that leads to the closest fit to the measurements is regarded as the optimal ice particle model. Additionally, an alternative method is applied that does not consider polarized reflectivity. These two methods are applied to a data sample as a proof-of-concept study where AirMSPI observed a single cirrus layer. In this case study, the hexagonal column aggregate model works for most pixels both with and without considering polarized reflectivities. The retrieval cost function is high when the camera pairs with large zenith angles are included in the retrievals. This result suggests that further studies will be necessary to have a better understanding of all eight selected ice particle models at scattering angles smaller than 100°.}, DOI = {10.3390/rs13142754} } @Article{rs10121981, AUTHOR = {Wang, Yi and Hioki, Souichiro and Yang, Ping and King, Michael D. and Di Girolamo, Larry and Fu, Dongwei and Baum, Bryan A.}, TITLE = {Inference of an Optimal Ice Particle Model through Latitudinal Analysis of MISR and MODIS Data}, JOURNAL = {Remote Sensing}, VOLUME = {10}, YEAR = {2018}, NUMBER = {12}, ARTICLE-NUMBER = {1981}, PAGES = {1-17}, URL = {https://www.mdpi.com/2072-4292/10/12/1981}, ISSN = {2072-4292}, ABSTRACT = {The inference of ice cloud properties from remote sensing data depends on the assumed forward ice particle model, as they are used in the radiative transfer simulations that are part of the retrieval process. The Moderate Resolution Imaging Spectroradiometer (MODIS) Collection 6 (MC6) ice cloud property retrievals are produced in conjunction with a single-habit ice particle model with a fixed degree of ice particle surface roughness (the MC6 model). In this study, we examine the MC6 model and five other ice models with either smoother or rougher surface textures to determine an optimal model to reproduce the angular variation of the radiation field sampled by the Multi-angle Imaging Spectroradiometer (MISR) as a function of latitude. The spherical albedo difference (SAD) method is used to infer an optimal ice particle model. The method is applied to collocated MISR and MODIS data over ocean for clouds with temperatures ≤233 K during December solstice from 2012–2015. The range of solar zenith angles covered by the MISR cameras is broader at the solstices than at other times of the year, with fewer scattering angles associated with sun glint during the December solstice than the June solstice. The results suggest a latitudinal dependence in an optimal ice particle model, and an additional dependence on the solar zenith angle (SZA) at the time of the observations. The MC6 model is one of the most optimal models on the global scale. In further analysis, the results are filtered by a cloud heterogeneity index to investigate cloudy scenarios that are less susceptible to potential 3D effects. Compared to results for global data, the consistency between measurements and a given model can be distinguished in both the tropics and extra-tropics. The SAD analysis suggests that the optimal model for thick homogeneous clouds corresponds to more roughened ice particles in the tropics than in the extra-tropics. While the MC6 model is one of the models most consistent with the global data, it may not be the most optimal model for the tropics.}, DOI = {10.3390/rs10121981} } @article{https://doi.org/10.1029/2019JD030457, author = {Wang, Yi and Yang, Ping and Hioki, Souichiro and King, Michael D. and Baum, Bryan A. and Di Girolamo, Larry and Fu, Dongwei}, title = {Ice Cloud Optical Thickness, Effective Radius, And Ice Water Path Inferred From Fused MISR and MODIS Measurements Based on a Pixel-Level Optimal Ice Particle Roughness Model}, journal = {Journal of Geophysical Research: Atmospheres}, volume = {124}, number = {22}, pages = {12126-12140}, keywords = {ice clouds, MISR, MODIS, optical thickness, effective radius, ice particle model}, doi = {https://doi.org/10.1029/2019JD030457}, url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019JD030457}, eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2019JD030457}, abstract = {Abstract The Multi-angle Imaging SpectroRadiometer (MISR) provides measurements over a wider scattering-angle range for a given location than a cross-track scanning sensor such as the MODerate resolution Imaging Spectroradiometer (MODIS). Based on a full year (2013) of fused MISR-MODIS datasets, we develop a variable surface roughness model for ice particles with the goal of identifying the optimal degree of roughness in the ice model for a given pixel containing single-layer ice clouds. For the MISR-MODIS observations over oceans, severe roughness values are often selected for a pixel when optical thickness (τ) and particle effective radius (Reff) are large in conjunction with larger cloud heterogeneity index (Hσ) or a warmer cloud top temperature. Furthermore, τ, Reff, and ice water path are retrieved with the optimal model and compared to operational MODIS Collection 6 (MC6) products that assume a constant roughness. In general, the retrievals based on the present optimal model lead to greater consistency with MISR measurements, and result in larger median τ by 10.1\% and smaller median Reff by 6.5\% but almost identical ice water path in comparison with the MC6 counterparts. The higher average τ value is caused by a slightly larger number of large τ cases, but the smaller average Reff value is due to the shifting of the retrieved Reff value toward smaller values by approximately 2–4 μm in comparison to the MC6 distribution over all seasons. Both τ retrievals have similar regional and monthly variations, but a larger annual cycle of Reff is associated with the optimal model.}, year = {2019} } @article{ren_li_muller_yang_2021, title={Sensitivity of radiative flux simulations to ice cloud parameterization over the equatorial western Pacific Ocean region}, DOI={10.1175/jas-d-21-0017.1}, author={Ren, Tong and Li, Dongchen and Muller, Jake and Yang, Ping}, journal={Journal of the Atmospheric Sciences}, pages = {2549-2571}, volume = {78}, number = {8}, year={2021}, month = jul, doi = {https://doi.org/10.1175/JAS-D-21-0017.1}, url = {https://journals.ametsoc.org/view/journals/atsc/aop/JAS-D-21-0017.1/JAS-D-21-0017.1.xml} } @article{https://doi.org/10.1029/2020JD033968, author = {Gu, Boyan and Ren, Tong and Kuo, Chia-Pang and Yang, Ping and Bowman, Kenneth}, title = {Global Impact of Cloud Longwave Scattering in an Atmosphere-Only General Circulation Model Simulation}, journal = {Journal of Geophysical Research: Atmospheres}, volume = {126}, number = {3}, pages = {e2020JD033968}, doi = {https://doi.org/10.1029/2020JD033968}, url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020JD033968}, eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2020JD033968}, note = {e2020JD033968 2020JD033968}, abstract = {Abstract Most general circulation models (GCMs) neglect cloud longwave scattering in pursuit of computational efficiency. This study implements the 2-/4-stream (2/4S) method, a relatively fast cloud longwave scattering treatment, in Community Atmospheric Model version 5 (CAM5) to analyze the impact of cloud longwave scattering on the large-scale circulation. Two 45-years-long integrations are performed with prescribed sea surface temperature (SST). In the experiment run, cloud longwave scattering is included using the 2/4S method; in the control run, clouds only absorb in the longwave. The results show that cloud longwave scattering acts to enhance the cloud longwave (greenhouse) effect by reducing outgoing longwave radiation (OLR) and enhancing downward longwave irradiance at the surface. The OLR reduction is most significant over the tropics, where surface temperatures and cloud elevations are high. The surface downward irradiance increase is most significant over polar areas and the Tibetan Plateau, where cloud elevations are low and the air below clouds is dry. Inclusion of cloud longwave scattering enhances the Walker circulation, suggestive of the importance of diabatic radiative heating in the tropical circulation. Inclusion of cloud longwave scattering also appears to shift the eddy-driven jet poleward in the austral summer in the Southern Hemisphere, suggesting that the cloud longwave effect plays a role in shaping the jet position. Persistent equatorward jet biases in GCMs may be reduced if cloud longwave scattering is considered.}, year = {2021} } @article{BI201693, title = {Tunneling effects in electromagnetic wave scattering by nonspherical particles: A comparison of the Debye series and physical-geometric optics approximations}, journal = {Journal of Quantitative Spectroscopy and Radiative Transfer}, volume = {178}, pages = {93-107}, year = {2016}, note = {Electromagnetic and light scattering by nonspherical particles XV: Celebrating 150 years of Maxwell's electromagnetics}, issn = {0022-4073}, doi = {https://doi.org/10.1016/j.jqsrt.2015.11.022}, url = {https://www.sciencedirect.com/science/article/pii/S002240731530100X}, author = {Lei Bi and Ping Yang}, keywords = {Debye series, Diffraction, Reflection, Tunneling}, abstract = {The accuracy of the physical-geometric optics (PG-O) approximation is examined for the simulation of electromagnetic scattering by nonspherical dielectric particles. This study seeks a better understanding of the tunneling effect on the phase matrix by employing the invariant imbedding method to rigorously compute the zeroth-order Debye series, from which the tunneling efficiency and the phase matrix corresponding to the diffraction and external reflection are obtained. The tunneling efficiency is shown to be a factor quantifying the relative importance of the tunneling effect over the Fraunhofer diffraction near the forward scattering direction. Due to the tunneling effect, different geometries with the same projected cross section might have different diffraction patterns, which are traditionally assumed to be identical according to the Babinet principle. For particles with a fixed orientation, the PG-O approximation yields the external reflection pattern with reasonable accuracy, but ordinarily fails to predict the locations of peaks and minima in the diffraction pattern. The larger the tunneling efficiency, the worse the PG-O accuracy is at scattering angles less than 90°. If the particles are assumed to be randomly oriented, the PG-O approximation yields the phase matrix close to the rigorous counterpart, primarily due to error cancellations in the orientation-average process. Furthermore, the PG-O approximation based on an electric field volume-integral equation is shown to usually be much more accurate than the Kirchhoff surface integral equation at side-scattering angles, particularly when the modulus of the complex refractive index is close to unity. Finally, tunneling efficiencies are tabulated for representative faceted particles.} } @article{Hioki2016, doi = {10.5194/acp-16-7545-2016}, url = {https://doi.org/10.5194/acp-16-7545-2016}, year = {2016}, month = jun, publisher = {Copernicus {GmbH}}, volume = {16}, number = {12}, pages = {7545-7558}, author = {Souichiro Hioki and Ping Yang and Bryan A. Baum and Steven Platnick and Kerry G. Meyer and Michael D. King and Jerome Riedi}, title = {Degree of ice particle surface roughness inferred from polarimetric observations}, journal = {Atmospheric Chemistry and Physics} } @article{SUN2016154, title = {Radiance and polarization in the diffusion region with an arbitrary scattering phase matrix}, journal = {Journal of Quantitative Spectroscopy and Radiative Transfer}, volume = {183}, pages = {154-161}, year = {2016}, note = {Viktor V. Sobolev and His Scientific Legacy}, issn = {0022-4073}, doi = {https://doi.org/10.1016/j.jqsrt.2016.06.021}, url = {https://www.sciencedirect.com/science/article/pii/S0022407316302928}, author = {Bingqiang Sun and George W. Kattawar and Ping Yang}, keywords = {Radiative transfer, Diffusion region, Polarization, Generalized spherical functions}, abstract = {Radiance and polarization patterns in an optically deep region, the so-called diffusion region or asymptotic region, of a homogeneous atmosphere or ocean, depend mainly on the scattering phase matrix and the single-scattering albedo of the medium. The radiance and polarization properties in the diffusion region for an arbitrary scattering phase matrix can be obtained in terms of a series of the generalized spherical functions. The number of terms is closely related to the single-scattering albedo of the medium. If the medium is conservative, the radiance is isotropic in conjunction with no polarization. If the single-scattering albedo is close to 1, several terms are sufficient to obtain the patterns, in which the degree of polarization feature is less than 1%. If the medium is highly absorptive, more expansion terms are required to obtain the diffusion patterns. The examples of simulated radiance and polarization patterns for Rayleigh scattering, Henyey–Greenstein–Rayleigh scattering, and haze L and cloud C1 scattering, defined by Deirmendjian, are calculated.} } @article{SUN20161, title = {Rigorous 3-D vectorial complex ray model applied to light scattering by an arbitrary spheroid}, journal = {Journal of Quantitative Spectroscopy and Radiative Transfer}, volume = {179}, pages = {1-10}, year = {2016}, issn = {0022-4073}, doi = {https://doi.org/10.1016/j.jqsrt.2016.03.010}, url = {https://www.sciencedirect.com/science/article/pii/S0022407315303228}, author = {Bingqiang Sun and George W. Kattawar and Ping Yang and Kuan Fang Ren}, keywords = {Light scattering, Vectorial complex ray-tracing, Spheroid}, abstract = {After a ray bundle passes a curved surface, the equal-phase wavefront associated with the refracted rays will be distorted. Consequently, the cross-section of a ray bundle with a curved wavefront during propagation in a homogeneous medium will vary with the ray-bundle propagation distance. Moreover, the phase of a ray bundle with convergent wavefront will undergo a phase shift of π/2 with each passage of a focal line. The contribution to the scattering amplitude by a ray bundle after passing a scatterer is determined by three elements: the cross-section variation of its wavefront, the total phase, and the refraction coefficients determined by Fresnel equations. In the geometric optics regime, the aforesaid three elements caused by a curved surface can be systematically quantified in terms of the vectorial complex ray-tracing technique. In this study, rigorous vectorial complex ray-tracing calculations are conducted for light scattering by a general spheroid and the results are validated in comparison with the benchmarks provided by the rigorous T-matrix method.} } @article{SUN2016390, title = {Simulation of the scattering properties of a chain-forming triangular prism oceanic diatom}, journal = {Journal of Quantitative Spectroscopy and Radiative Transfer}, volume = {178}, pages = {390-399}, year = {2016}, note = {Electromagnetic and light scattering by nonspherical particles XV: Celebrating 150 years of Maxwell's electromagnetics}, issn = {0022-4073}, doi = {https://doi.org/10.1016/j.jqsrt.2016.02.035}, url = {https://www.sciencedirect.com/science/article/pii/S0022407315301278}, author = {Bingqiang Sun and George W. Kattawar and Ping Yang and Michael S. Twardowski and James M. Sullivan}, keywords = {Optical properties, Diatom chains, Many-body iterative T-matrix, Ray-by-ray geometric optics method}, abstract = {The optical properties of diatom chains in the ocean are studied based on a combination of the many-body iterative T-matrix (MBIT) method and an improved implementation of the ray-by-ray (RBR) geometric optics method. The MBIT, a numerically accurate method, is advantageous for scatterers with linear cells. In contrast to other popular geometric optics methods, the RBR, an approximate method, considers the interference of all outgoing rays. The two methods are verified in comparison with benchmark simulations. The simulation results of diatom chains in a wide size range can be obtained with either or both methods, and each can be applied to any optically soft particle, i.e., in the case when relative refractive index approaches unity.} } @article{TANG2016416, title = {Sensitivity study of ice crystal optical properties in the 874GHz submillimeter band}, journal = {Journal of Quantitative Spectroscopy and Radiative Transfer}, volume = {178}, pages = {416-421}, year = {2016}, note = {Electromagnetic and light scattering by nonspherical particles XV: Celebrating 150 years of Maxwell's electromagnetics}, issn = {0022-4073}, doi = {https://doi.org/10.1016/j.jqsrt.2015.12.008}, url = {https://www.sciencedirect.com/science/article/pii/S002240731530131X}, author = {Guanglin Tang and Ping Yang and Dong L. Wu}, keywords = {Ice crystals, Optical properties, 874GHz, Submillimeter}, abstract = {Testing of an 874GHz submillimeter radiometer on meteorological satellites is being planned to improve ice water content retrievals. In this paper we study the optical properties of ice cloud particles in the 874GHz band. The results show that the bulk scattering and absorption coefficients of an ensemble of ice cloud particles are sensitive to the particle shape and effective diameter, whereas the latter is also sensitive to temperature. The co-polar back scattering cross-section is not sensitive to particle shape, temperature, and the effective diameter in the range of 50–200μm.} } ~ @article{TANG201670, title = {Enhancement of the computational efficiency of the near-to-far field mapping in the finite-difference method and ray-by-ray method with the fast multi-pole plane wave expansion approach}, journal = {Journal of Quantitative Spectroscopy and Radiative Transfer}, volume = {176}, pages = {70-81}, year = {2016}, issn = {0022-4073}, doi = {https://doi.org/10.1016/j.jqsrt.2016.02.027}, url = {https://www.sciencedirect.com/science/article/pii/S0022407316300061}, author = {Guanglin Tang and Ping Yang and Bingqiang Sun and R. Lee Panetta and George W. Kattawar}, keywords = {Fast multi-pole, Plane wave expansion, Finite-difference time-domain, Ray-by-ray, Near-to-far field mapping}, abstract = {The finite-difference time-domain (FDTD) and ray-by-ray (RBR) methods are techniques used to calculate the optical properties of nonspherical particles for small-to-moderate and large size parameters, respectively. The former is a rigorous method, and the latter is an approximate geometric–physical optics-hybrid method that takes advantage of both high efficiency of the geometric optics approach and high accuracy of the physical optics approach. In these two methods, the far field is calculated by mapping the near field to the far field with consideration of the phase interference. The mapping computation is more time-consuming than the near-field simulation when multiple scattering directions are involved, particularly in the case of the RBR implementation. To overcome the difficulty, in this study the fast multi-pole method is applied to both FDTD and RBR towards accelerating the far-field calculation, without degrading the accuracy of the simulation results.} } @article{https://doi.org/10.1002/2016JD025207, author = {Yi, Bingqi and Yang, Ping and Liu, Quanhua and van Delst, Paul and Boukabara, Sid-Ahmed and Weng, Fuzhong}, title = {Improvements on the ice cloud modeling capabilities of the Community Radiative Transfer Model}, journal = {Journal of Geophysical Research: Atmospheres}, volume = {121}, number = {22}, pages = {13,577-13,590}, keywords = {CRTM, ice cloud, radiative transfer, optical properties}, doi = {https://doi.org/10.1002/2016JD025207}, url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2016JD025207}, eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1002/2016JD025207}, abstract = {Abstract Noticeable improvements on the ice cloud modeling capabilities of the Community Radiative Transfer Model (CRTM) are reported, which are based on the most recent advances in understanding ice cloud microphysical (particularly, ice particle habit/shape characteristics) and optical properties. The new CRTM ice cloud model is derived from the Moderate Resolution Imaging Spectroradiometer (MODIS) collection 6 ice cloud habit model, which represents ice particles as severely roughened hexagonal ice column aggregates with a gamma size distribution. The single-scattering properties of the new ice particle model are derived from a state-of-the-art ice optical property library and are constructed as look-up tables for rapid CRTM computations. Various sensitivity studies concerning instrument-specific applications and simulations are performed to validate CRTM against satellite observations. In particular, radiances in a spectral region covering the infrared wavelengths are simulated. Comparisons of brightness temperatures between CRTM simulations and observations (from MODIS, the Atmospheric Infrared Sounder, and the Advanced Microwave Sounding Unit) show that the new ice cloud optical property look-up table substantially enhances the performance of the CRTM under ice cloud conditions.}, year = {2016} } @article{ZHANG2016325, title = {Optical scattering simulation of ice particles with surface roughness modeled using the Edwards-Wilkinson equation}, journal = {Journal of Quantitative Spectroscopy and Radiative Transfer}, volume = {178}, pages = {325-335}, year = {2016}, note = {Electromagnetic and light scattering by nonspherical particles XV: Celebrating 150 years of Maxwell's electromagnetics}, issn = {0022-4073}, doi = {https://doi.org/10.1016/j.jqsrt.2016.02.013}, url = {https://www.sciencedirect.com/science/article/pii/S0022407315301321}, author = {Jianing Zhang and Lei Bi and Jianping Liu and R. Lee Panetta and Ping Yang and George W. Kattawar}, keywords = {Particle surface roughness, Light scattering, Edwards-Wilkinson equation, Discrete differential geometry}, abstract = {Constructing an appropriate particle morphology model is essential for realistic simulation of optical properties of atmospheric particles. This paper presents a model for generating surface roughness based on a combination of methods from discrete differential geometry combined with a stochastic partial differential equation for surface evolution introduced by Edwards and Wilkinson. Scattering of light by roughened particles is simulated using the Invariant Imbedding T-Matrix (II-TM) method. The effects of surface roughness on the single-scattering properties, namely, the phase matrix, asymmetry factor, and extinction efficiency, are investigated for a single wavelength in the visible range and for a range of size parameters up to x=50. Three different smooth shapes are considered: spherical, spheroidal, and hexagonal, the latter two in just the “compact particle” case of unit aspect ratio. It is shown that roughness has negligible effects on the optical scattering properties for size parameters less than 20. For size parameters ranging from 20 to 50, the phase matrix elements are more sensitive to the surface roughness than are two important integral optical properties, the extinction efficiency and asymmetry factor. As has been seen in studies using other forms of roughening, the phase function is progressively smoothed as roughness increases. The effect on extinction efficiency is to increase it, and on asymmetry factor is to decrease it. Each of these effects is relatively modest in the size range considered, but the trend of results suggests that greater effects will be seen for size parameters larger than ones considered here.} } @article{https://doi.org/10.1002/2017MS001117, author = {Kuo, Chia-Pang and Yang, Ping and Huang, Xianglei and Feldman, Daniel and Flanner, Mark and Kuo, Chaincy and Mlawer, Eli J.}, title = {Impact of Multiple Scattering on Longwave Radiative Transfer Involving Clouds}, journal = {Journal of Advances in Modeling Earth Systems}, volume = {9}, number = {8}, pages = {3082-3098}, keywords = {longwave scattering, radiative effect of clouds, radiative transfer, doubling CO2, outgoing longwave radiation, simulation biases}, doi = {https://doi.org/10.1002/2017MS001117}, url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2017MS001117}, eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1002/2017MS001117}, abstract = {Abstract General circulation models (GCMs) are extensively used to estimate the influence of clouds on the global energy budget and other aspects of climate. Because radiative transfer computations involved in GCMs are costly, it is typical to consider only absorption but not scattering by clouds in longwave (LW) spectral bands. In this study, the flux and heating rate biases due to neglecting the scattering of LW radiation by clouds are quantified by using advanced cloud optical property models, and satellite data from Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO), CloudSat, Clouds and the Earth's Radiant Energy System (CERES), and Moderate Resolution Imaging Spectrometer (MODIS) merged products (CCCM). From the products, information about the atmosphere and clouds (microphysical and buck optical properties, and top and base heights) is used to simulate fluxes and heating rates. One-year global simulations for 2010 show that the LW scattering decreases top-of-atmosphere (TOA) upward flux and increases surface downward flux by 2.6 and 1.2 W/m2, respectively, or approximately 10\% and 5\% of the TOA and surface LW cloud radiative effect, respectively. Regional TOA upward flux biases are as much as 5\% of global averaged outgoing longwave radiation (OLR). LW scattering causes approximately 0.018 K/d cooling at the tropopause and about 0.028 K/d heating at the surface. Furthermore, over 40\% of the total OLR bias for ice clouds is observed in 350–500 cm−1. Overall, the radiative effects associated with neglecting LW scattering are comparable to the counterpart due to doubling atmospheric CO2 under clear-sky conditions.}, year = {2017} } @article{Sun2017, doi = {10.1175/jas-d-16-0278.1}, url = {https://doi.org/10.1175/jas-d-16-0278.1}, year = {2017}, month = {may}, publisher = {American Meteorological Society}, volume = {74}, number = {6}, pages = {1959-1987}, keywords = {Albedo; Atmosphere-land interaction; Clouds; Planetary atmospheres; Radiances; Radiative transfer}, author = {Bingqiang Sun and George W. Kattawar and Ping Yang and Eli Mlawer}, title = {An Improved Small-Angle Approximation for Forward Scattering and Its Use in a Fast Two-Component Radiative Transfer Method}, journal = {Journal of the Atmospheric Sciences} } @article{Sun:17, author = {Bingqiang Sun and Ping Yang and George W. Kattawar and Xiaodong Zhang}, journal = {Opt. Express}, keywords = {Scattering; Scattering, particles; Effective refractive index; Forward scattering; Geometric optics; Particle scattering; Physical optics; Refractive index}, number = {20}, pages = {24044-24060}, publisher = {OSA}, title = {Physical-geometric optics method for large size faceted particles}, volume = {25}, month = {Oct}, year = {2017}, url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-25-20-24044}, doi = {10.1364/OE.25.024044}, abstract = {A new physical-geometric optics method is developed to compute the single-scattering properties of faceted particles. It incorporates a general absorption vector to accurately account for inhomogeneous wave effects, and subsequently yields the relevant analytical formulas effective and computationally efficient for absorptive scattering particles. A bundle of rays incident on a certain facet can be traced as a single beam. For a beam incident on multiple facets, a systematic beam-splitting technique based on computer graphics is used to split the original beam into several sub-beams so that each sub-beam is incident only on an individual facet. The new beam-splitting technique significantly reduces the computational burden. The present physical-geometric optics method can be generalized to arbitrary faceted particles with either convex or concave shapes and with a homogeneous or an inhomogeneous (e.g., a particle with a core) composition. The single-scattering properties of irregular convex homogeneous and inhomogeneous hexahedra are simulated and compared to their counterparts from two other methods including a numerically rigorous method.}, } @article{Sun:17, author = {Bingqiang Sun and Ping Yang and George W. Kattawar and Michael I. Mishchenko}, journal = {Opt. Lett.}, keywords = {Diffraction; Diffractive optics; Scattering, particles; Scattering theory ; Diffraction; Far field diffraction; Huygens Fresnel principle; Light scattering; Ptychography; Refractive index}, number = {23}, pages = {5026-5029}, publisher = {OSA}, title = {On Babinet's principle and diffraction associated with an arbitrary particle}, volume = {42}, month = {Dec}, year = {2017}, url = {http://ol.osa.org/abstract.cfm?URI=ol-42-23-5026}, doi = {10.1364/OL.42.005026}, abstract = {Babinet's principle is widely used to compute the diffraction by a particle. However, the diffraction by a 3-D object is not totally the same as that simulated with Babinet's principle. This Letter uses a surface integral equation to exactly formulate the diffraction by an arbitrary particle and illustrate the condition for the applicability of Babinet's principle. The present results may serve to close the debate on the diffraction formalism.}, } @ARTICLE{8002644, author={Tang, Guanglin and Yang, Ping and Stegmann, Patrick G. and Lee Panetta, R. and Tsang, Leung and Johnson, Benjamin}, journal={IEEE Transactions on Geoscience and Remote Sensing}, title={Effect of Particle Shape, Density, and Inhomogeneity on the Microwave Optical Properties of Graupel and Hailstones}, year={2017}, volume={55}, number={11}, pages={6366-6378}, doi={10.1109/TGRS.2017.2726994} } @article{Xu:17, author = {Guanglang Xu and Patrick G. Stegmann and Sarah D. Brooks and Ping Yang}, journal = {Opt. Express}, keywords = {Atmospheric and oceanic optics ; Remote sensing and sensors ; Scattering; Effective medium theory; Light properties; Multiple scattering; Optical depth; Particle scattering; Radiative transfer}, number = {24}, pages = {A990-A1008}, publisher = {OSA}, title = {Modeling the single and multiple scattering properties of soot-laden mineral dust aerosols}, volume = {25}, month = {Nov}, year = {2017}, url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-25-24-A990}, doi = {10.1364/OE.25.00A990}, abstract = {Fractal particle morphologies are employed to study the light scattering properties of soot-laden mineral dust aerosols. The applicability of these models is assessed in comparison with measurements and other numerical studies. To quantify the dust-soot mixing effects on the single and multiple scattering properties, a parameterization of the effective bulk properties is developed. Based on the parameterized bulk properties, polarized one-dimensional radiative transfer simulations are performed. The results indicate that small uncertainties in conjunction with soot contamination parameters may lead to large uncertainties in both forward and inverse modeling involving mineral dust contaminated with soot.}, } @article{XU201730, title = {Modeling the inherent optical properties of aquatic particles using an irregular hexahedral ensemble}, journal = {Journal of Quantitative Spectroscopy and Radiative Transfer}, volume = {191}, pages = {30-39}, year = {2017}, issn = {0022-4073}, doi = {https://doi.org/10.1016/j.jqsrt.2017.01.020}, url = {https://www.sciencedirect.com/science/article/pii/S0022407316306598}, author = {Guanglang Xu and Bingqiang Sun and Sarah D. Brooks and Ping Yang and George W. Kattawar and Xiaodong Zhang}, keywords = {Inherent optical properties, Aquatic particles, Lorenz-Mie theory, Nonspherical effects, Hexahedral ensemble, Backscattering properties, Polarimetric properties}, abstract = {A statistical approach in defining particle morphology in terms of an ensemble of hexahedra of distorted shapes is employed for modeling the Inherent Optical Properties (IOPs) of aquatic particles. The approach is inspired by the rich variability in shapes of real aquatic particles that cannot be represented by one particular shape. Two methods, the Invariant Imbedding T-matrix (II-TM) and Physical Geometric Optics Hybrid (PGOH) method, are combined to simulate the IOPs for aquatic particles of sizes ranging from the Rayleigh scattering to geometric optics regimes. Nonspherical effects on the IOPs are examined by comparing the results with predictions based on the Lorenz-Mie theory to explore the limitations of assuming the particles to be spherical. We pay special attention to backscattering-related and polarimetric scattering properties, particularly the backscattering ratio, Gordon parameter, backscattering volume scattering function and the degree of linear polarization. The simulated IOPs are compared with the in-situ measurements to assess the feasibility of using a hexahedral ensemble in modeling the IOPs of the aquatic particles.} } @article{Loeb2018, doi = {10.1175/jcli-d-17-0426.1}, url = {https://doi.org/10.1175/jcli-d-17-0426.1}, year = {2018}, month = mar, publisher = {American Meteorological Society}, volume = {31}, number = {5}, pages = {1851-1864}, author = {Norman G. Loeb and Ping Yang and Fred G. Rose and Gang Hong and Sunny Sun-Mack and Patrick Minnis and Seiji Kato and Seung-Hee Ham and William L. Smith and Souichiro Hioki and Guanglin Tang}, title = {Impact of Ice Cloud Microphysics on Satellite Cloud Retrievals and Broadband Flux Radiative Transfer Model Calculations}, journal = {Journal of Climate} } @article{STEGMANN20189, title = {A stochastic model for density-dependent microwave Snow- and Graupel scattering coefficients of the NOAA JCSDA community radiative transfer model}, journal = {Journal of Quantitative Spectroscopy and Radiative Transfer}, volume = {211}, pages = {9-24}, year = {2018}, issn = {0022-4073}, doi = {https://doi.org/10.1016/j.jqsrt.2018.02.026}, url = {https://www.sciencedirect.com/science/article/pii/S0022407317305782}, author = {Patrick G. Stegmann and Guanglin Tang and Ping Yang and Benjamin T. Johnson}, keywords = {Snow, Graupel, CRTM, FDTD, Bicontinuous random medium}, abstract = {A structural model is developed for the single-scattering properties of snow and graupel particles with a strongly heterogeneous morphology and an arbitrary variable mass density. This effort is aimed to provide a mechanism to consider particle mass density variation in the microwave scattering coefficients implemented in the Community Radiative Transfer Model (CRTM). The stochastic model applies a bicontinuous random medium algorithm to a simple base shape and uses the Finite-Difference-Time-Domain (FDTD) method to compute the single-scattering properties of the resulting complex morphology.} } @article{Tang2018, doi = {10.1175/jas-d-18-0014.1}, url = {https://doi.org/10.1175/jas-d-18-0014.1}, year = {2018}, month = jun, publisher = {American Meteorological Society}, volume = {75}, number = {7}, pages = {2217-2233}, author = {Guanglin Tang and Ping Yang and George W. Kattawar and Xianglei Huang and Eli J. Mlawer and Bryan A. Baum and Michael D. King}, title = {Improvement of the Simulation of Cloud Longwave Scattering in Broadband Radiative Transfer Models}, journal = {Journal of the Atmospheric Sciences} } @article{STEGMANN20191, title = {Study of the effects of phytoplankton morphology and vertical profile on lidar attenuated backscatter and depolarization ratio}, journal = {Journal of Quantitative Spectroscopy and Radiative Transfer}, volume = {225}, pages = {1-15}, year = {2019}, issn = {0022-4073}, doi = {https://doi.org/10.1016/j.jqsrt.2018.12.009}, url = {https://www.sciencedirect.com/science/article/pii/S0022407318306022}, author = {Patrick G. Stegmann and Bingqiang Sun and Jiachen Ding and Ping Yang and Xiaodong Zhang}, keywords = {Monte Carlo, Radiative transfer, Ocean optics, Phytoplankton, Lidar, Net primary production, Remote sensing}, abstract = {Propagation of a lidar beam in a coupled atmosphere-ocean model consisting of multiple atmospheric and upper oceanic layers and a rough ocean surface is studied by using a vectorized Monte Carlo radiative transfer solver optimized specifically for lidar-based remote sensing applications. The effects of assumed phytoplankton morphology variations and its vertical distribution on the lidar attenuated backscatter and depolarization ratio are studied. In this study, a phytoplankton particle is assumed to be a sphere, a sphere with a core, or a randomly distorted hexahedron with or without a core. The single-scattering properties of the nonspherical/inhomogeneous particles are computed using appropriate state-of-the-art light-scattering computational capabilities. Vertical variation of the phytoplankton distribution is derived explicitly using a PAR (photosynthetically active radiation) limited carbon biomass balance equation that is subsequently coupled with the Monte Carlo solver.} } ~ @article{Zhai:19, author = {Siyao Zhai and R. Lee Panetta and Ping Yang}, journal = {Opt. Express}, keywords = {Atmospheric ice crystals; Atmospheric optics; Electric fields; Light scattering; Radiative transfer; Remote sensing}, number = {20}, pages = {A1441-A1457}, publisher = {OSA}, title = {Improvements in the computational efficiency and convergence of the Invariant Imbedding T-matrix method for spheroids and hexagonal prisms}, volume = {27}, month = {Sep}, year = {2019}, url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-27-20-A1441}, doi = {10.1364/OE.27.0A1441}, abstract = {The invariant-imbedding T-matrix (II-TM) method is a numerical method for accurately computing the single-scattering properties of dielectric particles. Because of the linearity of Maxwell&\#x2019;s equations, the incident electric field and the scattered electric field can be related through a transition matrix (T-Matrix). The II-TM method computes the T-matrix through a matrix recurrence formula which stems from an electromagnetic volume integral equation. The recurrence starts with an inscribed sphere within the particle and ends with the circumscribed sphere of the particle. For each iteration, a matrix known as the U-matrix is computed with the Gauss Legendre (GL) quadrature, and matrix inversion is subsequently performed to obtain the T-matrix corresponding to the portion of the particle enclosed by the spherical shell. We modify a commonly used scheme to avoid applying the quadrature scheme to discontinuities. Moreover, we apply a new scheme to generate nodes and weights in conjunction with the GL quadrature. This leads to a considerable improvement on convergence and computational efficiency in the cases of hexagonal prisms and spheroids. The basic shapes of ice crystals in the atmosphere are hexagonal columns and plates. The single-scattering properties of hexagonal ice prisms are important to atmospheric optics, radiative transfer, and remote sensing. We demonstrate that the present approach can significantly accelerate the convergence in simulating light scattering by hexagonal ice crystals.}, } @article{KUO2020106683, title = {Assessing the accuracy and efficiency of longwave radiative transfer models involving scattering effect with cloud optical property parameterizations}, journal = {Journal of Quantitative Spectroscopy and Radiative Transfer}, volume = {240}, pages = {106683}, year = {2020}, issn = {0022-4073}, doi = {https://doi.org/10.1016/j.jqsrt.2019.106683}, url = {https://www.sciencedirect.com/science/article/pii/S0022407319305606}, author = {Chia-Pang Kuo and Ping Yang and Xianglei Huang and Yi-Hsuan Chen and Guosheng Liu}, keywords = {Radiative transfer, Water cloud parameterization, Ice cloud parameterization}, abstract = {A radiative transfer model (RTM) that accurately and explicitly accounts for both absorbing and scattering effects requires a substantial amount of computational effort. In the longwave (LW) spectral regime, the atmosphere is optically opaque and absorbs a large portion of terrestrial thermal radiation. To alleviate the computational burden, clouds are assumed to be only absorptive in most general circulation models (GCMs) and their scattering effects are neglected. Using parameterizations of cloud bulk single-scattering properties derived from the latest cloud optical property models for satellite remote sensing, this study analyzes the numerical accuracy and efficiency of a variety of LW RTMs . The approaches considered in this study include the absorption approximation (AA), the absorption approximation with scattering parameterization (ASA), the two-stream approximation (2S), a hybrid two- and four-stream approximation (2/4S), and the discrete ordinate radiative transfer (DISORT) with multiple streams. These approximations are benchmarked against 128-stream DISORT calculation. After evaluating the full ranges of ice and water cloud optical and microphysical properties using these RTMs, we find that neglecting LW scattering effect causes simulation errors as large as ±15% by using the AA method. Among these RTMs, the 2/4S method provides an optimal balance between computational efficiency and accuracy, leading to the maximum cloud emissivity errors within ±5%, 25th to 75th percentile errors about ±1%, and almost zero net bias. Therefore, the 2/4S approximation is computationally accurate and yet affordable option for incorporating cloud longwave scattering effect into the radiation schemes used in weather and climate models.} } @article{10.1371/journal.pntd.0009334, doi = {10.1371/journal.pntd.0009334}, author = {Tsujimoto, Hitoshi and Anderson, Michelle A. E. and Eggleston, Heather and Myles, Kevin M. and Adelman, Zach N.}, journal = {PLOS Neglected Tropical Diseases}, publisher = {Public Library of Science}, title = {Aedes aegypti dyspepsia encodes a novel member of the SLC16 family of transporters and is critical for reproductive fitness}, year = {2021}, month = {04}, volume = {15}, url = {https://doi.org/10.1371/journal.pntd.0009334}, pages = {1-19}, abstract = {As a key vector for major arthropod-borne viruses (arboviruses) such as dengue, Zika and chikungunya, control of Aedes aegypti represents a major challenge in public health. Bloodmeal acquisition is necessary for the reproduction of vector mosquitoes and pathogen transmission. Blood contains potentially toxic amounts of iron while it provides nutrients for mosquito offspring; disruption of iron homeostasis in the mosquito may therefore lead to novel control strategies. We previously described a potential iron exporter in Ae. aegypti after a targeted functional screen of ZIP (zinc-regulated transporter/Iron-regulated transporter-like) and ZnT (zinc transporter) family genes. In this study, we performed an RNAseq-based screen in an Ae. aegypti cell line cultured under iron-deficient and iron-excess conditions. A subset of differentially expressed genes were analyzed via a cytosolic iron-sensitive dual-luciferase reporter assay with several gene candidates potentially involved in iron transport. In vivo gene silencing resulted in significant reduction of fecundity (egg number) and fertility (hatch rate) for one gene, termed dyspepsia. Silencing of dyspepsia reduced the induction of ferritin expression in the midgut and also resulted in delayed/impaired excretion and digestion. Further characterization of this gene, including a more direct confirmation of its substrate (iron or otherwise), could inform vector control strategies as well as to contribute to the field of metal biology.}, number = {4}, } @article{ZHENG2020138924, title = {Structural and microstructural influence on deformation and fracture of dual-phase steels}, journal = {Materials Science and Engineering: A}, volume = {774}, pages = {138924}, year = {2020}, issn = {0921-5093}, doi = {https://doi.org/10.1016/j.msea.2020.138924}, url = {https://www.sciencedirect.com/science/article/pii/S0921509320300162}, author = {Xinzhu Zheng and Hassan Ghassemi-Armaki and Ankit Srivastava}, keywords = {Characterization, Finite element analysis, In situ tension test, Digital image correlation, Plasticity, Fracture behavior}, abstract = {The objective of this work is to demonstrate that the mechanical response of multiphase materials is fundamentally different in an imposed deformation field that is homogeneous, versus in an imposed deformation field that is heterogeneous, at a length-scale greater than the microstructural length-scale. To this end, we focus on two dual-phase steels with significantly different nominal chemical composition and microstructure. The mechanical response of the steels is characterized by in-situ SEM tensile tests of flat dog-bone and single-edge notch specimens. The experimental results show that the dog-bone specimens of the two steels exhibit very similar mechanical response but the mechanical response of their single-edge notch specimens differs significantly. This is in contrast to any classical analysis that will predict the same mechanical response in the presence of a notch for two materials that give the same mechanical response under uniaxial tension. The high resolution in-situ tests coupled with microstructure-based digital image correlation and finite element analysis are then used to elucidate how the interlacing of imposed heterogeneous deformation field and material microstructure affects the mechanical response of these steels. Our results clearly highlight that a mechanistic analysis of multiphase materials under imposed heterogeneous deformation field must involve explicit consideration of the length-scales associated with the material microstructure.} } @article{Chen_2021, doi = {10.3847/1538-4357/ac178d}, url = {https://doi.org/10.3847/1538-4357/ac178d}, year = 2021, month = {nov}, publisher = {American Astronomical Society}, volume = {922}, number = {1}, pages = {15}, author = {Xingzhuo Chen and Lei Hu and Lifan Wang}, title = {Constraining Type Ia Supernova Delay Time with Spatially Resolved Star Formation Histories}, journal = {The Astrophysical Journal}, abstract = {We present the delay time distribution (DTD) estimates of Type Ia supernovae (SNe Ia) using spatially resolved SN Ia host galaxy spectra from MUSE and MaNGA. By employing a grouping algorithm based on k-means and earth mover’s distances (EMDs), we separated the host galaxy stellar population age distributions (SPADs) into spatially distinct regions and used maximum likelihood method to constrain the DTD of SN Ia progenitors. When a power-law model of the form DTD(t) ∝ t s (t > τ) is used, we find an SN rate decay slope and a delay time . Moreover, we tested other DTD models, such as a broken power-law model and a two-component power-law model, and found no statistically significant support for these alternative models.} } @article{Chen_2020, doi = {10.3847/1538-4365/ab9a3b}, url = {https://doi.org/10.3847/1538-4365/ab9a3b}, year = 2020, month = {sep}, publisher = {American Astronomical Society}, volume = {250}, number = {1}, pages = {12}, author = {Xingzhuo Chen and Lei Hu and Lifan Wang}, title = {Artificial Intelligence-Assisted Inversion (AIAI) of Synthetic Type Ia Supernova Spectra}, journal = {The Astrophysical Journal Supplement Series}, abstract = {We generate ∼100,000 model spectra of Type 1a supernovae (SNe Ia) to form a spectral library for the purpose of building an artificial intelligence–assisted inversion (AIAI) algorithm for theoretical models. As a first attempt, we restrict our studies to the time around B-band maximum and compute theoretical spectra with a broad spectral wavelength coverage from 2000 to 10000 Å using the code TARDIS. Based on the library of theoretically calculated spectra, we construct the AIAI algorithm with a multiresidual convolutional neural network to retrieve the contributions of different ionic species to the heavily blended spectral profiles of the theoretical spectra. The AIAI is found to be very powerful in distinguishing spectral patterns due to coupled atomic transitions and has the capacity to quantitatively measure the contributions from different ionic species. By applying the AIAI algorithm to a set of well-observed SN Ia spectra, we demonstrate that the model can yield powerful constraints on the chemical structures of these SNe Ia. Using the chemical structures deduced from AIAI, we successfully reconstructed the observed data, thus confirming the validity of the method. We show that the light-curve decline rate of SNe Ia is correlated with the amount of 56Ni above the photosphere in the ejecta. We detect a clear decrease of 56Ni mass with time that can be attributed to its radioactive decay. Our code and model spectra are available on the website https://github.com/GeronimoChen/AIAI-Supernova.} } @inproceedings{musick2021numerical, url = {https://meetings.aps.org/Meeting/DFD21/Session/F25.2}, pages = { F25 }, number = { 17 }, volume = { 66 }, year = { 2021 }, title = { Numerical Simulations of High Speed, Reacting, Multiphase Flows }, booktitle = { 74th Annual Meeting of the APS Division of Fluid Dynamics }, author = { Musick and Paudel and McFarland and Ramaprabhu and Tarey }, abstract = {While gaseous detonations are well studied and documented by the scientific community, detonations propagating through liquid fogs and sprays of fuel are less understood. Multiphase detonations develop characteristics that are more complicated to predict than single phase reactions. Newer technologies such as Pulse and Rotating Detonation Engines (PDE and RDE) aim to utilize common liquid propellants and drive a need to understand the multiphase detonation process better. This presentation will focus on the numerical results of liquid spray detonations with a primary focus on n-dodecane as a fuel. The effects of droplet sizes, distributions, evaporation, and breakup will be discussed in detail. The multiphase results will be compared to data from idealized, single phase simulations and results from other simulation codes. The software used to generate this data is the FLASH code, in part developed by the Flash Center at the University of Chicago, and modified for this problem to include an induction parameter model for single step reactions and active, Lagrangian particles using the Particle-in-Cell (PIC) method.}, } @article{holt2020hydrogel, doi = {10.1002/marc.202000287}, url = {https://pubmed.ncbi.nlm.nih.gov/32515861}, title={Hydrogel Synthesis and Stabilization via Tetrazine Click-Induced Secondary Interactions}, author={Holt, Samantha E and Rakoski, Amanda and Jivan, Faraz and Perez, Lisa M and Alge, Daniel L}, journal={Macromolecular Rapid Communications}, volume={41}, number={14}, pages={2000287}, year={2020}, publisher={Wiley Online Library} } @inproceedings{gardner2019streamlining, title={Streamlining Simulation and Data Transfer in a Heterogeneous Environment}, url={https://dl.acm.org/doi/10.1145/3332186.3335199}, author={Gardner, Matthew C and Luo, Ping and Johnson, Matthew and Toliyat, Hamid A}, booktitle={Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning)}, pages={1-3}, year={2019} } @inproceedings{zainab2020distributed, url={https://ieeexplore.ieee.org/document/9039899}, title={Distributed computing for smart meter data management for electrical utility applications}, author={Zainab, Ameema and Refaat, Shady S and Abu-Rub, Haitham and Bouhali, Othmane}, booktitle={2020 Cybernetics & Informatics (K&I)}, pages={1--6}, year={2020}, organization={IEEE} } @article{jochum2019host, url={https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0225933}, title={Host-mediated microbiome engineering (HMME) of drought tolerance in the wheat rhizosphere}, author={Jochum, Michael D and McWilliams, Kelsey L and Pierson, Elizabeth A and Jo, Young-Ki}, journal={Plos one}, volume={14}, number={12}, pages={e0225933}, year={2019}, publisher={Public Library of Science San Francisco, CA USA} } @conference{jufinding, url={https://hprc.tamu.edu/files/events/conferences/sc2014/Poster.Yang_Liu.Finding_Vertex_Cover_Acceleration_via_CUDA.pdf}, title={Finding Vertex Cover: Acceleration via CUDA}, pages={1}, year={2014}, author={Liu, Yang and Ju, Jinbin and Rodriguez, Derek} } @article{lim2018neutron, url={https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.121.062701}, title={Neutron star tidal deformabilities constrained by nuclear theory and experiment}, author={Lim, Yeunhwan and Holt, Jeremy W}, journal={Physical review letters}, volume={121}, number={6}, pages={062701}, year={2018}, publisher={APS} } @conference{duongmolecular, url={https://hprc.tamu.edu/files/events/conferences/sc2020/poster.Duong.TD_HPRC20.pdf}, title={Molecular dynamics simulation of high strain rate nanoindentation}, author={Duong, T and Demkowicz, MJ}, pages={1}, year={2020}, } @article{mortazavi2018prediction, url={https://asmedigitalcollection.asme.org/vibrationacoustics/article/140/3/031002/392590/Prediction-of-Rotordynamic-Performance-of-Smooth}, title={Prediction of rotordynamic performance of smooth stator-grooved rotor liquid annular seals utilizing computational fluid dynamics}, author={Mortazavi, Farzam and Palazzolo, Alan}, journal={Journal of Vibration and Acoustics}, volume={140}, number={3}, pages={031002}, year={2018}, publisher={American Society of Mechanical Engineers} } @article{liu2018improved, url={https://arxiv.org/pdf/1807.00202.pdf}, title={Improved techniques for learning to dehaze and beyond: A collective study}, author={Liu, Yu and Zhao, Guanlong and Gong, Boyuan and Li, Yang and Raj, Ritu and Goel, Niraj and Kesav, Satya and Gottimukkala, Sandeep and Wang, Zhangyang and Ren, Wenqi and others}, pages={1-6}, journal={arXiv preprint arXiv:1807.00202}, year={2018} } @article{fernando2016approach, url={https://link.springer.com/article/10.1007%2Fs12033-016-9979-1}, title={An approach for Zika virus inhibition using homology structure of the envelope protein}, author={Fernando, Sandun and Fernando, Teshan and Stefanik, Michal and Eyer, Ludek and Ruzek, Daniel}, journal={Molecular biotechnology}, volume={58}, number={12}, pages={801--806}, year={2016}, publisher={Springer} } @article{beykal2020data, url={https://aiche.onlinelibrary.wiley.com/doi/full/10.1002/aic.16657}, title={A data-driven optimization algorithm for differential algebraic equations with numerical infeasibilities}, author={Beykal, Burcu and Onel, Melis and Onel, Onur and Pistikopoulos, Efstratios N}, journal={AIChE Journal}, volume={66}, number={10}, pages={e16657}, year={2020}, publisher={Wiley Online Library} } @inproceedings{al2018performance, url={https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=8604682}, title={The Performance of Suction Caissons for Floating Offshore Wind Turbines under Inclined Cyclic Survival Loads}, author={Al-Ramthan, Ahmed Qasim Obaid and Aubeny, Charles P}, booktitle={OCEANS 2018 MTS/IEEE Charleston}, pages={1--5}, year={2018}, organization={IEEE} } @article{brady2021normalizing, doi={https://doi.org/10.1103/PhysRevLett.127.062701}, url={https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.127.062701}, title={Normalizing Flows for Microscopic Many-Body Calculations: An Application to the Nuclear Equation of State}, author={Brady, Jack and Wen, Pengsheng and Holt, Jeremy W}, journal={Physical Review Letters}, volume={127}, number={6}, pages={062701}, year={2021}, publisher={APS} } @article{hajiramezanali2018bayesian, url={https://arxiv.org/abs/1810.09433}, title={Bayesian multi-domain learning for cancer subtype discovery from next-generation sequencing count data}, author={Hajiramezanali, Ehsan and Dadaneh, Siamak Zamani and Karbalayghareh, Alireza and Zhou, Mingyuan and Qian, Xiaoning}, pages={1-13}, journal={arXiv preprint arXiv:1810.09433}, year={2018} } @inproceedings{davis2019write, url={https://ieeexplore.ieee.org/document/8916550}, title={Write quick, run fast: Sparse deep neural network in 20 minutes of development time via SuiteSparse: GraphBLAS}, author={Davis, Timothy A and Aznaveh, Mohsen and Kolodziej, Scott}, booktitle={2019 IEEE High Performance Extreme Computing Conference (HPEC)}, pages={1--6}, year={2019}, organization={IEEE} } @inproceedings{garza2019bit, url={https://par.nsf.gov/servlets/purl/10126754}, title={Bit-level perceptron prediction for indirect branches}, author={Garza, Elba and Mirbagher-Ajorpaz, Samira and Khan, Tahsin Ahmad and Jimenez, Daniel A}, booktitle={2019 ACM/IEEE 46th Annual International Symposium on Computer Architecture (ISCA)}, pages={27--38}, year={2019}, organization={IEEE} } @article{seguin2016stacking, url={https://pubmed.ncbi.nlm.nih.gov/27860103}, title={Stacking and Electrostatic Interactions Drive the Stereoselectivity of Silylium-Ion Asymmetric Counteranion-Directed Catalysis}, author={Seguin, Trevor J and Wheeler, Steven E}, journal={Angewandte Chemie International Edition}, volume={55}, number={51}, pages={15889--15893}, year={2016}, publisher={Wiley Online Library} } @phdthesis{shah2020accurate, url={https://oaktrust.library.tamu.edu/bitstream/handle/1969.1/188418/SHAH-FINALTHESIS-2021.pdf}, title={Accurate Identification of Traffic Signs Using Radar and Camera Fusion}, author={Shah, Shrey}, year={2020} } @article{nimmagadda2017enantioselective, url={https://onlinelibrary.wiley.com/doi/full/10.1002/anie.201611602}, title={Enantioselective synthesis of chiral oxime ethers: Desymmetrization and dynamic kinetic resolution of substituted cyclohexanones}, author={Nimmagadda, Sri Krishna and Mallojjala, Sharath Chandra and Woztas, Lukasz and Wheeler, Steven E and Antilla, Jon C}, journal={Angewandte Chemie International Edition}, volume={56}, number={9}, pages={2454--2458}, year={2017}, publisher={Wiley Online Library} } @article{zaheer2020reversible, goi={https://pubs.acs.org/doi/10.1021/acsenergylett.0c01328}, title={Reversible Room-Temperature Fluoride-Ion Insertion in a Tunnel-Structured Transition Metal Oxide Host}, author={Zaheer, Wasif and Andrews, Justin L and Parija, Abhishek and Hyler, Forrest P and Jaye, Cherno and Weiland, Conan and Yu, Young-Sang and Shapiro, David A and Fischer, Daniel A and Guo, Jinghua and others}, journal={ACS Energy Letters}, volume={5}, number={8}, pages={2520--2526}, year={2020}, publisher={ACS Publications} } @article{brdar2021axionlike, url={https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.126.201801}, doi = {https://doi.org/10.1103/PhysRevLett.126.201801}, title={Axionlike Particles at Future Neutrino Experiments: Closing the Cosmological Triangle}, author={Brdar, Vedran and Dutta, Bhaskar and Jang, Wooyoung and Kim, Doojin and Shoemaker, Ian M and Tabrizi, Zahra and Thompson, Adrian and Yu, Jaehoon}, journal={Physical Review Letters}, volume={126}, number={20}, pages={201801}, year={2021}, publisher={APS} } @inproceedings{tiugli2018case, url={https://www.scientific.net/MSF.915.185.pdf}, title={A case study on metal-ceramic interfaces: wetting of alumina by molten aluminum}, author={Tigli, Ahmet and Cagin, Tahir}, booktitle={Materials Science Forum}, volume={915}, pages={185--189}, year={2018}, organization={Trans Tech Publ} } @article{liang2020perovskite, url={https://onlinelibrary.wiley.com/doi/full/10.1002/adma.202004111}, title={Perovskite-Derivative Valleytronics}, author={Liang, Jia and Fang, Qiyi and Wang, Hua and Xu, Rui and Jia, Shuai and Guan, Yuxuan and Ai, Qing and Gao, Guanhui and Guo, Hua and Shen, Kaijun and others}, journal={Advanced Materials}, volume={32}, number={48}, pages={2004111}, year={2020}, publisher={Wiley Online Library} } @inproceedings{aslan2018influence, url={https://www.scientific.net/MSF.915.224}, title={Influence of H-Content on Thermo-Mechanical Properties of NiAl Alloys}, author={Aslan, Ugur and Cagin, Tahir}, booktitle={Materials Science Forum}, volume={915}, pages={224--228}, year={2018}, organization={Trans Tech Publ} } @inproceedings{bhatia2019perceptron, url={https://ieeexplore.ieee.org/document/8980306}, title={Perceptron-based prefetch filtering}, author={Bhatia, Eshan and Chacon, Gino and Pugsley, Seth and Teran, Elvira and Gratz, Paul V and Jimenez, Daniel A}, booktitle={2019 ACM/IEEE 46th Annual International Symposium on Computer Architecture (ISCA)}, pages={1--13}, year={2019}, organization={IEEE} } @techreport{shayit2021vacuum, url={https://oaktrust.library.tamu.edu/handle/1969.1/194332}, title={Vacuum energy density and pressure inside a soft wall}, author={Shayit, Agam and Fulling, SA and Settlemyre, TE and Merritt, Joseph}, journal={arXiv preprint arXiv:2107.10439}, year={2021} } @article{kordell2020first, url={https://arxiv.org/abs/2009.03512}, title={First results from Hybrid Hadronization in small and large systems}, pages={1--5}, author={Kordell II, Michael and Angerami, A and Bass, SA and Cao, S and Chen, Y and Coleman, J and Cunqueiro, L and Dai, T and Du, L and Ehlers, R and others}, journal={arXiv preprint arXiv:2009.03512}, year={2020} } @article{rossi2018light, url={https://pubs.acs.org/doi/10.1021/acsnano.8b06649}, title={Light-induced activation of forbidden exciton transition in strongly confined perovskite quantum dots}, author={Rossi, Daniel and Wang, Hua and Dong, Yitong and Qiao, Tian and Qian, Xiaofeng and Son, Dong Hee}, journal={ACS nano}, volume={12}, number={12}, pages={12436--12443}, year={2018}, publisher={ACS Publications} } @article{gober2020temporal, url={https://research.ece.ncsu.edu/ipc/wp-content/uploads/2020/05/tap_final.pdf}, title={Temporal ancestry prefetcher}, pages={1--5}, author={Gober, Nathan and Chacon, Gino and Jimenez, DA and Gratz, P}, journal={The 1st Instruction Prefetching Championship (IPC1)}, year={2020} } @article{bedre2019genfam, url={https://pubmed.ncbi.nlm.nih.gov/31844835/}, title={GenFam: A web application and database for gene family-based classification and functional enrichment analysis}, author={Bedre, Renesh and Mandadi, Kranthi}, journal={Plant direct}, volume={3}, number={12}, pages={e00191}, year={2019}, publisher={Wiley Online Library} } @article{hiokiinfluence, url={https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&ved=2ahUKEwj32JeMxK_1AhWEZd8KHakTC1AQFnoECAsQAQ&url=https%3A%2F%2Fams.confex.com%2Fams%2F96Annual%2Fwebprogram%2FManuscript%2FPaper290825%2Fams_2016spring_extended_abstract_v06.pdf&usg=AOvVaw0PN4rZpW5rLR8_5U5Fs2Qm}, title={The Influence of Spatial Resolution on the Inference of Ice Cloud Particle Morphological Parameters from Multi-angle Satellite Observations}, pages={1-3}, author={Hioki, Souichiro and Yang, Ping}, year={2016}, } @article{shan2020surface, url={https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2019GL086050}, title={Surface heat flux induced by mesoscale eddies cools the Kuroshio-Oyashio Extension region}, author={Shan, Xuan and Jing, Zhao and Gan, Bolan and Wu, Lixin and Chang, Ping and Ma, Xiaohui and Wang, Shengpeng and Chen, Zhaohui and Yang, Haiyuan}, journal={Geophysical Research Letters}, volume={47}, number={1}, pages={e2019GL086050}, year={2020}, publisher={Wiley Online Library} } @article{murray2020macrolide, url={https://pubmed.ncbi.nlm.nih.gov/31883125}, title={Macrolide-susceptible probiotic Enterococcus faecium ST296 exhibits faecal-environmental-oral microbial community cycling among beef cattle in feedlots}, author={Murray, SA and Holbert, AC and Norman, KN and Lawhon, Sara D and Sawyer, JE and Scott, HM}, journal={Letters in applied microbiology}, volume={70}, number={4}, pages={274--281}, year={2020}, publisher={Wiley Online Library} } @article{pi2020convolutional, url={https://www.sciencedirect.com/science/article/pii/S1474034619305828}, title={Convolutional neural networks for object detection in aerial imagery for disaster response and recovery}, author={Pi, Yalong and Nath, Nipun D and Behzadan, Amir H}, journal={Advanced Engineering Informatics}, volume={43}, pages={101009}, year={2020}, publisher={Elsevier} } @article{jin2018hybrid, url={https://arxiv.org/abs/1805.07866}, title={Hybrid macro/micro level backpropagation for training deep spiking neural networks}, pages={1-12}, author={Jin, Yingyezhe and Zhang, Wenrui and Li, Peng}, journal={arXiv preprint arXiv:1805.07866}, year={2018} } @article{jochum2019bioprospecting, url={https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6747002}, title={Bioprospecting plant growth-promoting rhizobacteria that mitigate drought stress in grasses}, author={Jochum, Michael D and McWilliams, Kelsey L and Borrego, Eli J and Kolomiets, Mike V and Niu, Genhua and Pierson, Elizabeth A and Jo, Young-Ki}, journal={Frontiers in microbiology}, volume={10}, pages={2106}, year={2019}, publisher={Frontiers} } @article{https://doi.org/10.1002/anie.202105830, url = {https://pubmed.ncbi.nlm.nih.gov/34014019}, author = {Chen, Yu and Yang, Yuqin and Orr, Asuka A. and Makam, Pandeeswar and Redko, Boris and Haimov, Elvira and Wang, Yannan and Shimon, Linda J. W. and Rencus-Lazar, Sigal and Ju, Meiting and Tamamis, Phanourios and Dong, Hao and Gazit, Ehud}, title = {Self-Assembled Peptide Nano-Superstructure towards Enzyme Mimicking Hydrolysis}, journal = {Angewandte Chemie International Edition}, volume = {60}, number = {31}, pages = {17164-17170}, keywords = {biocatalysis, nano-superstructure, peptide, self-assembly, supramolecular chemistry}, doi = {https://doi.org/10.1002/anie.202105830}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202105830}, eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.202105830}, abstract = {Abstract The structural arrangement of amino acid residues in native enzymes underlies their remarkable catalytic properties, thus providing a notable point of reference for designing potent yet simple biomimetic catalysts. Herein, we describe a minimalistic approach to construct a dipeptide-based nano-superstructure with enzyme-like activity. The self-assembled biocatalyst comprises one peptide as a single building block, readily synthesized from histidine. Through coordination with zinc ion, the peptide self-assembly procedure allows the formation of supramolecular β-sheet ordered nanocrystals, which can be used as basic units to further construct higher-order superstructure. As a result, remarkable hydrolysis activity and enduring stability are demonstrated. Our work exemplifies the use of a bioinspired supramolecular assembly approach to develop next-generation biocatalysts for biotechnological applications.}, year = {2021} } @article{D1CC00574J, author ="Kuai, Dacheng and Cheng, Heyong and Kuan, Kai-Yuan and Yan, Xin", title ="Accelerated five-component spiro-pyrrolidine construction at the air–liquid interface", journal ="Chem. Commun.", year ="2021", volume ="57", issue ="31", pages ="3757-3760", publisher ="The Royal Society of Chemistry", doi ="10.1039/D1CC00574J", url ="http://dx.doi.org/10.1039/D1CC00574J", abstract ="Multi-component reactions assemble complex molecules in a highly effective way{,} however{,} they often suffer from long reaction times. We demonstrate that acceleration of a five-component spiro-pyrrolidine construction can be achieved in microdroplets and thin films. The deposition method and mild heating are crucial factors for product formation. Three key intermediates were captured by mass spectrometry to elucidate the tandem reaction mechanism. We also found that hydrogen bonding can significantly flatten the energy barrier at the air–liquid interface." } @article{doi:10.1021/jacs.0c05610, author = {Song, Yue and Yang, Xin and Shen, Yidan and Dong, Mei and Lin, Yen-Nan and Hall, Michael B. and Wooley, Karen L.}, title = {Invoking Side-Chain Functionality for the Mediation of Regioselectivity during Ring-Opening Polymerization of Glucose Carbonates}, journal = {Journal of the American Chemical Society}, volume = {142}, number = {40}, pages = {16974-16981}, year = {2020}, doi = {10.1021/jacs.0c05610}, note ={PMID: 32965109}, url = {https://doi.org/10.1021/jacs.0c05610}, eprint = {https://doi.org/10.1021/jacs.0c05610} } @article{doi:10.1061/ASCEST.1943-541X.0003204, author = {Eric Stoddard and Matthew Yarnold}, title = {Residual Stress and Global Deflection Limits for Future Hot-Rolled Steel Asymmetric I-Beams}, journal = {Journal of Structural Engineering}, volume = {148}, number = {1}, pages = {04021232}, year = {2022}, doi = {10.1061/(ASCE)ST.1943-541X.0003204}, url = {https://ascelibrary.org/doi/abs/10.1061/%28ASCE%29ST.1943-541X.0003204}, eprint = {https://ascelibrary.org/doi/pdf/10.1061/%28ASCE%29ST.1943-541X.0003204}, abstract = { Medium-span to long-span floor systems in residential and commercial construction have commonly used steel–concrete composite construction. These composite floor systems have become more structurally efficient with the use of built-up asymmetric steel beam sections. Although structural efficiency is important, a fast and cost-effective solution is paramount. The research presented herein is being conducted for the AISC on hot-rolled asymmetric I-beams (A-shapes) for potential future addition to the AISC Steel Construction Manual. The aim is to adequately proportion these hot-rolled shapes so they match or improve built-up asymmetric beam structural efficiency while increasing the speed and economy of steel–concrete composite floor systems. The initial focus has been placed on steel behavior as a result of the manufacturing process, where residual stresses and deformations can be an issue due to uneven cooling. A better understanding of residual stresses is critical for accurate calculation of the lateral torsional buckling strength during deck casting and placement. In addition, steel mills have expressed concern regarding global deformation of an asymmetric I-shape. As a result, an extensive thermomechanical finite-element modeling approach, using nonlinear thermomechanical properties of steel, was devised to simulate the cooling process of hot-rolled steel shapes. A single model requires up to 50 h of processing time using the Texas A&M high-performance computing center. The modeling procedure was validated against accepted residual stress experimental test measurements. Proof-of-concept (POC) A-shape beams were also produced by Nucor. The POC beam cooling profiles were used as further validation. Then, a parametric study was executed that individually altered the top flange width and thickness of two different-depth W-shapes. The parametric study identified a maximum flange width-to-thickness ratio to satisfy a reasonable residual compressive stress limit. The study also found that, despite concerns, global deformations are not an issue for realistic proportions of future hot-rolled asymmetric I-beams.} } @article{doi:10.1021/acsomega.0c05519, author = {Grajales, Javier A. and Pérez, Lisa M. and Schwab, A. Paul and Little, Dallas N.}, title = {Quantum Chemical Modeling of the Effects of Hydrated Lime (Calcium Hydroxide) as a Filler in Bituminous Materials}, journal = {ACS Omega}, volume = {6}, number = {4}, pages = {3130-3139}, year = {2021}, doi = {10.1021/acsomega.0c05519}, note ={PMID: 33553929}, url = {https://doi.org/10.1021/acsomega.0c05519}, eprint = {https://doi.org/10.1021/acsomega.0c05519} } @article{doi:10.1021/acsnano.9b10024, author = {Chen, Yu and Orr, Asuka A. and Tao, Kai and Wang, Zhibin and Ruggiero, Antonella and Shimon, Linda J. W. and Schnaider, Lee and Goodall, Alicia and Rencus-Lazar, Sigal and Gilead, Sharon and Slutsky, Inna and Tamamis, Phanourios and Tan, Zhan’ao and Gazit, Ehud}, title = {High-Efficiency Fluorescence through Bioinspired Supramolecular Self-Assembly}, journal = {ACS Nano}, volume = {14}, number = {3}, pages = {2798-2807}, year = {2020}, doi = {10.1021/acsnano.9b10024}, note ={PMID: 32013408}, url = {https://doi.org/10.1021/acsnano.9b10024}, eprint = {https://doi.org/10.1021/acsnano.9b10024} } @inproceedings{hajiramezanali2020variational, url={https://arxiv.org/abs/1908.09710}, title={Variational Graph Recurrent Neural Networks}, author={Ehsan Hajiramezanali and Arman Hasanzadeh and Nick Duffield and Krishna R Narayanan and Mingyuan Zhou and Xiaoning Qian}, year={2020}, pages={1-11}, eprint={1908.09710}, archivePrefix={arXiv}, primaryClass={cs.LG} } @article{nathmulti, url={https://www.semanticscholar.org/paper/MULTI-DIMENSIONAL-SEQUENCE-ALIGNMENT-FOR-HUMAN-OF-Nath-Behzadan/ea912149dc1cd4da2f8fb86300f7024bd3e95e8b}, title={MULTI-DIMENSIONAL SEQUENCE ALIGNMENT FOR CONTEXT-AWARE HUMAN ACTION ANALYSIS OF BODY-SENSOR DATA}, pages={61-68}, year={2019}, author={Nath, Nipun D and Behzadan, Amir H and Shrestha, Prabhat} } @article{yang2021computational, url={https://asmedigitalcollection.asme.org/tribology/article/143/1/011801/1085121/Computational-Fluid-Dynamics-Based-Mixing}, title={Computational fluid dynamics based mixing prediction for tilt pad journal bearing TEHD modeling—Part I: TEHD-CFD model validation and improvements}, author={Yang, Jongin and Palazzolo, Alan}, journal={Journal of Tribology}, volume={143}, number={1}, pages={011801}, year={2021}, publisher={American Society of Mechanical Engineers} } @article{tapia2017bayesian, doi={doi.org/10.1115/1.4035898}, title={Bayesian calibration and uncertainty quantification for a physics-based precipitation model of nickel--titanium shape-memory alloys}, author={Tapia, Gustavo and Johnson, Luke and Franco, Brian and Karayagiz, Kubra and Ma, Ji and Arroyave, Raymundo and Karaman, Ibrahim and Elwany, Alaa}, pages={1-13}, journal={Journal of Manufacturing Science and Engineering}, volume={139}, number={7}, year={2017}, publisher={American Society of Mechanical Engineers Digital Collection} } @article{yang2019three, doi={https://doi.org/10.1115/1.4043350}, title={Three-dimensional thermo-elasto-hydrodynamic computational fluid dynamics model of a tilting pad journal bearing—Part II: Dynamic response}, author={Yang, Jongin and Palazzolo, Alan}, pages={1-16}, journal={Journal of Tribology}, volume={141}, number={6}, year={2019}, publisher={American Society of Mechanical Engineers Digital Collection} } @article{ma2016western, doi={https://doi.org/10.1038/nature18640}, title={Western boundary currents regulated by interaction between ocean eddies and the atmosphere}, author={Ma, Xiaohui and Jing, Zhao and Chang, Ping and Liu, Xue and Montuoro, Raffaele and Small, R Justin and Bryan, Frank O and Greatbatch, Richard J and Brandt, Peter and Wu, Dexing and others}, journal={Nature}, volume={535}, number={7613}, pages={533--537}, year={2016}, publisher={Nature Publishing Group} } @article{wang2017giant, url={https://pubs.acs.org/doi/10.1021/acs.nanolett.7b02268}, title={Giant optical second harmonic generation in two-dimensional multiferroics}, author={Wang, Hua and Qian, Xiaofeng}, journal={Nano letters}, volume={17}, number={8}, pages={5027--5034}, year={2017}, publisher={ACS Publications} } @article{rahmani2020methane, doi={https://doi.org/10.1002/qua.26065}, title={Methane dehydrogenation on Cu and Ni surfaces with low and moderate oxygen coverage}, author={Rahmani Didar, Behnaz and Balbuena, Perla B}, journal={International Journal of Quantum Chemistry}, volume={120}, number={2}, pages={e26065}, year={2020}, publisher={Wiley Online Library} } @inproceedings{szafranski2019studying, doi={https://doi.org/10.1190/segam2019-3216344.1}, title={Studying stress state and fault zone properties of source regions of induced seismicity using dynamic rupture models}, author={Szafranski, Dawid and Duan, Benchun}, pages={2099-2103}, booktitle={SEG International Exposition and Annual Meeting}, year={2019}, organization={OnePetro} } @article{hsieh2018applying, doi={https://doi.org/10.3389/fphar.2018.00588}, title={Applying a global sensitivity analysis workflow to improve the computational efficiencies in physiologically-based pharmacokinetic modeling}, author={Hsieh, Nan-Hung and Reisfeld, Brad and Bois, Frederic Y and Chiu, Weihsueh A}, journal={Frontiers in pharmacology}, volume={9}, pages={588}, year={2018}, publisher={Frontiers} } @inproceedings{gardner2019loss, url={https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=8785369}, title={Loss breakdown of a dual conical rotor permanent magnet motor using grain oriented electrical steel and soft magnetic composites}, author={Gardner, Matthew C and Zhang, Yichi and Talebi, Dorsa and Toliyat, Hamid A and Crapo, Alan and Knauer, Paul and Willis, Harold}, booktitle={2019 IEEE International Electric Machines & Drives Conference (IEMDC)}, pages={1067--1074}, year={2019}, organization={IEEE} } @inproceedings{wu2018deep, url={https://arxiv.org/abs/1806.09228}, title={Deep k-means: Re-training and parameter sharing with harder cluster assignments for compressing deep convolutions}, author={Wu, Junru and Wang, Yue and Wu, Zhenyu and Wang, Zhangyang and Veeraraghavan, Ashok and Lin, Yingyan}, booktitle={International Conference on Machine Learning}, pages={5363--5372}, year={2018}, organization={PMLR} } @inproceedings{hajiramezanali2020semi, url={https://ieeexplore.ieee.org/document/9053491}, title={Semi-implicit stochastic recurrent neural networks}, author={Hajiramezanali, Ehsan and Hasanzadeh, Arman and Duffield, Nick and Narayanan, Krishna and Zhou, Mingyuan and Qian, Xiaoning}, booktitle={ICASSP 2020-2020 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)}, pages={3342-3346}, year={2020}, organization={IEEE} } @inproceedings{lim2016automated, url={https://pubmed.ncbi.nlm.nih.gov/28269722}, title={Automated neurovascular tracing and analysis of the knife-edge scanning microscope rat nissl data set using a computing cluster}, author={Lim, Sungjun and Nowak, Michael R and Choe, Yoonsuck}, booktitle={2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)}, pages={6445--6448}, year={2016}, organization={IEEE} } @inproceedings{syed2019averaging, doi={https://doi.org/10.1109/BigData47090.2019.9006183}, title={Averaging ensembles model for forecasting of short-term load in smart grids}, author={Syed, Dabeeruddin and Refaat, Shady S and Abu-Rub, Haitham and Bouhali, Othmane and Zainab, Ameema and Xie, Le}, booktitle={2019 IEEE International Conference on Big Data (Big Data)}, pages={2931--2938}, year={2019}, organization={IEEE} } @article{praslicka2021review, doi={https://doi.org/10.1109/JESTPE.2021.3053544}, title={Review and analysis of coaxial magnetic gear pole pair count selection effects}, pages={1-10}, author={Praslicka, Bryton and Gardner, Matthew C and Johnson, Matthew and Toliyat, Hamid A}, journal={IEEE Journal of Emerging and Selected Topics in Power Electronics}, year={2021}, publisher={IEEE} } @inproceedings{naghavi2021permanent, url={https://arxiv.org/abs/2108.08346}, title={Permanent Magnet Linear Generator Design for Surface Riding Wave Energy Converters}, author={Naghavi, Farid and Sheshaprasad, Shrikesh and Gardner, Matthew and Meduri, Aghamarshana and Kang, HeonYong and Toliyat, Hamid}, booktitle={2021 IEEE Energy Conversion Congress and Exposition (ECCE)}, pages={4369--4375}, year={2021}, organization={IEEE} } @article{gorzelnik2016asymmetric, doi={https://doi.org/10.1073/pnas.1609482113}, title={Asymmetric cryo-EM structure of the canonical Allolevivirus Qβ reveals a single maturation protein and the genomic ssRNA in situ}, author={Gorzelnik, Karl V and Cui, Zhicheng and Reed, Catrina A and Jakana, Joanita and Young, Ry and Zhang, Junjie}, journal={Proceedings of the National Academy of Sciences}, volume={113}, number={41}, pages={11519--11524}, year={2016}, publisher={National Acad Sciences} } @inproceedings{pi2020disaster, url={https://www.semanticscholar.org/paper/Disaster-Impact-Information-Retrieval-Using-Deep-in-Pi-Nath/cfad820459c1a246e6bce7cf0d72fabba5766f09}, title={Disaster impact information retrieval using deep learning object detection in crowdsourced drone footage}, author={Pi, Yalong and Nath, Nipun D and Behzadan, Amir H}, booktitle={Proc., Int. Workshop on Intelligent Computing in Engineering}, pages={134--143}, year={2020} } @inproceedings{doi:10.1061/9780784483404.023, author = {Junho Lee and Charles P. Aubeny }, title = {Effect of Keying Flaps on a Multiline Ring Anchor in Soft Clay}, booktitle = {IFCEE 2021}, year = {2021}, chapter = {}, pages = {249-256}, doi = {10.1061/9780784483404.023}, url = {https://ascelibrary.org/doi/abs/10.1061/9780784483404.023}, eprint = {https://ascelibrary.org/doi/pdf/10.1061/9780784483404.023}, abstract = { The multiline ring anchor (MRA) was devised as a cost-effective means for securing floating offshore wind turbines (FOWTs) to the seabed. FOWTs occurring in arrays create the possibility for attaching mooring lines from multiple units to a single anchor. Additionally, the deep embedment of the MRA into relatively strong soil permits high load capacity to be achievable with a small and lighter anchor, thereby reducing anchor material, transport, and installation costs. However, since the MRA is shorter than a conventional caisson, features such as wing plates and keying flaps are needed to achieve parity in load capacity with a caisson having a comparable diameter. Preliminary studies show that attaching wing plates to MRA in soft clay is highly effective in enhancing its horizontal load capacity, but only marginally effective in improving vertical load capacity. This motivated the current study investigating the use of keying flaps to further enhance vertical load capacity. Two-dimensional finite element analyses were conducted to understand how keying flaps impact the failure mechanism of the stiffeners and provide reliable evaluations of the uplift resistance of the MRA. The results show that the thickness of the stiffener, flap length, and flap angle can affect the failure mechanism and bearing factors. For the optimal design of the stiffener, a comparative study was carried out to compare the effects of keying flaps and thickness of the stiffener. The studies show that introducing keying flaps can have comparable load capacity with thicker stiffeners and that it can be an economical solution for achieving high vertical load capacity while containing material and fabrication costs. } } @inproceedings{hasanpour2021design, doi={https://doi.org/10.1109/SDEMPED51010.2021.9605546}, title={Design and Control of a Fault Tolerant Permanent Magnet Motor with Independently Optimized Phase and Pole Counts}, author={Hasanpour, Shima and Sheshaprasad, Shrikesh and Gardner, Matthew C and Johnson, Matthew and Praslicka, Bryton and Toliyat, Hamid A}, booktitle={2021 IEEE 13th International Symposium on Diagnostics for Electrical Machines, Power Electronics and Drives (SDEMPED)}, volume={1}, pages={58--64}, year={2021}, organization={IEEE} } @article{zhou2018modelling, doi={https://doi.org/10.1080/17452759.2018.1442681}, title={Modelling and estimation of tensile behaviour of polylactic acid parts manufactured by fused deposition modelling using finite element analysis and knowledge-based library}, author={Zhou, Xunfei and Hsieh, Sheng-Jen and Ting, Chen-Ching}, journal={Virtual and Physical Prototyping}, volume={13}, number={3}, pages={177--190}, year={2018}, publisher={Taylor & Francis} } @article{blanchette2020bayesian, doi={https://doi.org/10.1093/toxsci/kfaa151}, title={A bayesian method for population-wide cardiotoxicity hazard and risk characterization using an in vitro human model}, author={Blanchette, Alexander D and Burnett, Sarah D and Grimm, Fabian A and Rusyn, Ivan and Chiu, Weihsueh A}, journal={Toxicological Sciences}, volume={178}, number={2}, pages={391--403}, year={2020}, publisher={Oxford University Press} } @article{mulgaonkar2020bcr, url={https://www.biorxiv.org/content/biorxiv/early/2020/08/18/2020.06.18.158196.full.pdf}, title={Bcr-Abl tyrosine kinase inhibitor imatinib as a potential drug for COVID-19}, author={Mulgaonkar, Nirmitee Sanjay and Wang, Haoqi and Mallawarachchi, Samavath and Ruzek, Daniel and Martina, Byron and Fernando, Sandun}, pages={1--15}, journal={bioRxiv}, year={2020}, publisher={Cold Spring Harbor Laboratory} } @article{hasanzadeh2019semi, url={https://arxiv.org/abs/1908.07078}, title={Semi-implicit graph variational auto-encoders}, pages={1-12}, author={Hasanzadeh, Arman and Hajiramezanali, Ehsan and Duffield, Nick and Narayanan, Krishna R and Zhou, Mingyuan and Qian, Xiaoning}, journal={arXiv preprint arXiv:1908.07078}, year={2019} } @inproceedings{ardywibowo2020nads, url={https://arxiv.org/abs/2006.06646}, title={Nads: Neural architecture distribution search for uncertainty awareness}, author={Ardywibowo, Randy and Boluki, Shahin and Gong, Xinyu and Wang, Zhangyang and Qian, Xiaoning}, booktitle={International Conference on Machine Learning}, pages={356--366}, year={2020}, organization={PMLR} } @article{nath2020deep, doi={https://doi.org/10.3389/fbuil.2020.00097}, title={Deep convolutional networks for construction object detection under different visual conditions}, author={Nath, Nipun D and Behzadan, Amir H}, journal={Frontiers in Built Environment}, volume={6}, pages={97}, year={2020}, publisher={Frontiers} } @article{iino2020optimizing, doi={https://doi.org/10.2118/190304-PA}, title={Optimizing CO2-and field-gas-injection EOR in unconventional reservoirs using the fast-marching method}, author={Iino, Atsushi and Onishi, Tsubasa and Datta-Gupta, Akhil}, journal={SPE Reservoir Evaluation & Engineering}, volume={23}, number={01}, pages={261--281}, year={2020}, publisher={OnePetro} } @article{vashisth2019mechanical, doi={https://doi.org/10.1039/C9NR00958B}, title={Mechanical size effects of amorphous polymer-derived ceramics at the nanoscale: experiments and ReaxFF simulations}, author={Vashisth, Aniruddh and Khatri, Sumit and Hahn, Seung Ho and Zhang, Weiwei and Van Duin, Adri CT and Naraghi, Mohammad}, journal={Nanoscale}, volume={11}, number={15}, pages={7447--7456}, year={2019}, publisher={Royal Society of Chemistry} } @inproceedings{syed2020performance, doi={https://doi.org/10.1109/KI48306.2020.9039797}, title={Performance evaluation of distributed machine learning for load forecasting in smart grids}, author={Syed, Dabeeruddin and Refaat, Shady S and Abu-Rub, Haitham}, booktitle={2020 Cybernetics & Informatics (K&I)}, pages={1--6}, year={2020}, organization={IEEE} } @article{tao2021edta, doi={https://doi.org/10.1039/D1TA03985G}, title={EDTA-mimicking amino acid--metal ion coordination for multifunctional packings}, author={Tao, Kai and Orr, Asuka A and Hu, Wen and Makam, Pandeeswar and Zhang, Jiahao and Geng, Qiang and Li, Boxin and Jakubowski, Joseph M and Wang, Yancheng and Tamamis, Phanourios and others}, journal={Journal of Materials Chemistry A}, volume={9}, number={36}, pages={20385--20394}, year={2021}, publisher={Royal Society of Chemistry} } @article{tao2020enhanced, doi={https://doi.org/10.1002/adfm.201909614}, title={Enhanced Fluorescence for Bioassembly by Environment-Switching Doping of Metal Ions}, author={Tao, Kai and Chen, Yu and Orr, Asuka A and Tian, Zhen and Makam, Pandeeswar and Gilead, Sharon and Si, Mingsu and Rencus-Lazar, Sigal and Qu, Songnan and Zhang, Mingjun and others}, journal={Advanced functional materials}, volume={30}, number={10}, pages={1909614}, year={2020}, publisher={Wiley Online Library} } @inproceedings{praslicka2021practical, doi={https://doi.org/10.1109/IEMDC47953.2021.9449504}, title={Practical Analysis and Design of a 50: 1 Cycloidal Magnetic Gear with Balanced Off-Axis Moments and a High Specific Torque for Lunar Robots}, author={Praslicka, Bryton and Johnson, Matthew and Zamarron, Daniel and Marshall, Avery and Hasanpour, Shima and Gardner, Matthew C and Nguyen, Alex and Goodarzi, Abas and Bauk, Enzo and Toliyat, Hamid A}, booktitle={2021 IEEE International Electric Machines & Drives Conference (IEMDC)}, pages={1--8}, year={2021}, organization={IEEE} } @article{demirhan2019sustainable, doi={https://doi.org/10.1002/aic.16498}, title={Sustainable ammonia production through process synthesis and global optimization}, author={Demirhan, C Doga and Tso, William W and Powell, Joseph B and Pistikopoulos, Efstratios N}, journal={AIChE Journal}, volume={65}, number={7}, pages={e16498}, year={2019}, publisher={Wiley Online Library} } @article{yang2021computational, doi={https://doi.org/10.1115/1.4047751}, title={Computational fluid dynamics based mixing prediction for tilt pad journal bearing TEHD modeling—Part II: Implementation with machine learning}, author={Yang, Jongin and Palazzolo, Alan}, journal={Journal of Tribology}, volume={143}, number={1}, pages={011802}, year={2021}, publisher={American Society of Mechanical Engineers} } @inproceedings{haq2019effectiveness, url={https://dl.astfe.org/conferences/tfec2019,482783b20ce88b27,4c5489b33ebe9605.html}, title={Effectiveness of Micro-Droplet Train and Micro-Jet Impingement in Surface Cooling}, author={Haq, Syed and Muthusamy, Jayaveera Pandian and Zhang, Taolue and Alvarado, Jorge L}, pages={1}, booktitle={ASTFE Digital Library}, year={2019}, organization={Begel House Inc.} } @inproceedings{nath2020deep, url={https://ascelibrary.org/doi/10.1061/9780784482865.020}, title={Deep Learning Detection of Personal Protective Equipment to Maintain Safety Compliance on Construction Sites}, author={Nath, Nipun D and Behzadan, Amir H}, booktitle={Construction Research Congress 2020: Computer Applications}, pages={181--190}, year={2020}, organization={American Society of Civil Engineers Reston, VA} } @article{chandelia2018fem, url={https://www.proquest.com/docview/2281302726?pq-origsite=gscholar&fromopenview=true}, title={FEM modeling on scratch behavior of multiphase polymeric systems}, author={Chandelia, Vijay Kisan and Sue, Hung-Jue and Hossain, Mohammad Motaher}, journal={Tribology Letters}, volume={66}, number={2}, pages={1--16}, year={2018}, publisher={Springer} } @inproceedings{talebi2021electromagnetic, doi={https://doi.org/10.1109/IEMDC47953.2021.9449611}, title={Electromagnetic Design Characterization of a Dual Rotor Axial Flux Motor for Electric Aircraft}, author={Talebi, Dorsa and Gardner, Matthew C and Sankarraman, Sri Vignesh and Daniar, Ahmad and Toliyat, Hamid A}, booktitle={2021 IEEE International Electric Machines & Drives Conference (IEMDC)}, pages={1--8}, year={2021}, organization={IEEE} } @article{yruegas2021nickel, doi={https://doi.org/10.1021/acs.inorgchem.1c01845}, title={Nickel--Borolide Complexes and Their Complex Electronic Structure}, author={Yruegas, Sam and Tang, Hao and Bornovski, Gayle Z and Su, Xiaojun and Sung, Siyoung and Hall, Michael B and Nippe, Michael and Martin, Caleb D}, journal={Inorganic Chemistry}, volume={60}, number={21}, pages={16160--16167}, year={2021}, publisher={ACS Publications} } @article{foquet2020there, doi={https://doi.org/10.7717/peerj.9618}, title={There is no magic bullet: the importance of testing reference gene stability in RT-qPCR experiments across multiple closely related species}, author={Foquet, Bert and Song, Hojun}, journal={PeerJ}, volume={8}, pages={e9618}, year={2020}, publisher={PeerJ Inc.} } @article{xing2018simulatecnvs, doi={https://doi.org/10.1101/407486}, title={SimulateCNVs: a novel software application for simulating CNVs in WES and WGS data}, author={Xing, Yue and Dabney, Alan R and Li, Xiao and Casola, Claudio}, journal={BioRxiv}, pages={407486}, year={2018}, publisher={Cold Spring Harbor Laboratory} } @article{https://doi.org/10.1111/mice.12658, author = {Cheng, Chih-Shen and Behzadan, Amir H. and Noshadravan, Arash}, title = {Deep learning for post-hurricane aerial damage assessment of buildings}, journal = {Computer-Aided Civil and Infrastructure Engineering}, volume = {36}, number = {6}, pages = {695-710}, doi = {https://doi.org/10.1111/mice.12658}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mice.12658}, eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/mice.12658}, abstract = {Abstract This study aims to improve post-disaster preliminary damage assessment (PDA) using artificial intelligence (AI) and unmanned aerial vehicle (UAV) imagery. In particular, a stacked convolutional neural network (CNN) architecture is introduced and trained on an in-house visual dataset from Hurricane Dorian. To account for the ordinality of damage level classes, the cross-entropy classification loss function is replaced with the square of earth mover's distance (EMD2) loss. The trained model achieves 65.6\% building localization precision and 61\% (90\% considering ±1 class deviation from ground-truth) classification accuracy. It also exhibits a positive accuracy–confidence correlation, which is valuable for model assessment in situations where ground-truth information is not readily available. Finally, the outcome of damage assessment is compared with the literature by examining the relationship between building size and number of stories, and severity of induced disaster damage.}, year = {2021} } @article{dadaneh2018bayesian, doi={https://doi.org/10.1093/bioinformatics/bty808}, title={Bayesian negative binomial regression for differential expression with confounding factors}, author={Dadaneh, Siamak Zamani and Zhou, Mingyuan and Qian, Xiaoning}, journal={Bioinformatics}, volume={34}, number={19}, pages={3349--3356}, year={2018}, publisher={Oxford University Press} } @article{taghizadeh2020turbulence, url={https://iopscience.iop.org/article/10.1088/1367-2630/abadb3}, title={Turbulence closure modeling with data-driven techniques: physical compatibility and consistency considerations}, author={Taghizadeh, Salar and Witherden, Freddie D and Girimaji, Sharath S}, journal={New Journal of Physics}, volume={22}, number={9}, pages={093023}, year={2020}, publisher={IOP Publishing} } @article{chu2017rna, url={https://www.nature.com/articles/s41598-017-16603-y}, title={RNA-seq of serial kidney biopsies obtained during progression of chronic kidney disease from dogs with X-linked hereditary nephropathy}, author={Chu, Candice P and Hokamp, Jessica A and Cianciolo, Rachel E and Dabney, Alan R and Brinkmeyer-Langford, Candice and Lees, George E and Nabity, Mary B}, journal={Scientific reports}, volume={7}, number={1}, pages={1--14}, year={2017}, publisher={Nature Publishing Group} } @article{kiani2018fatigue, doi={https://doi.org/10.1111/ffe.12697}, title={Fatigue analysis of railway wheel using a multiaxial strain-based critical-plane index}, author={Kiani, M and Fry, GT}, journal={Fatigue & Fracture of Engineering Materials & Structures}, volume={41}, number={2}, pages={412--424}, year={2018}, publisher={Wiley Online Library} } @article{morris2021differences, doi={https://doi.org/10.1371/journal.pone.0252804}, title={Differences in the genome, methylome, and 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institution={DEVCOM Army Research Laboratory} } @article{beykal2020domino, url={https://link.springer.com/article/10.1007/s10898-020-00890-3}, title={Domino: Data-driven optimization of bi-level mixed-integer nonlinear problems}, author={Beykal, Burcu and Avraamidou, Styliani and Pistikopoulos, Ioannis PE and Onel, Melis and Pistikopoulos, Efstratios N}, journal={Journal of Global Optimization}, volume={78}, number={1}, pages={1--36}, year={2020}, publisher={Springer} } @inproceedings{hara2019high, doi={https://doi.org/10.2514/6.2019-4249}, title={High-energy ion generation due to the plasma wave driven by current-carrying instabilities}, author={Hara, Kentaro}, booktitle={AIAA Propulsion and Energy 2019 Forum}, pages={4249}, year={2019} } @article{guan2018aaron, doi={https://doi.org/10.1021/acs.jctc.8b00578}, title={AARON: an automated reaction optimizer for new catalysts}, author={Guan, Yanfei and Ingman, Victoria M and Rooks, Benjamin J and Wheeler, Steven E}, journal={Journal of chemical theory and computation}, volume={14}, number={10}, pages={5249--5261}, year={2018}, publisher={ACS Publications} } @article{hollenbach2019bayesian, doi={https://doi.org/10.1017/psrm.2018.15}, title={Bayesian versus maximum likelihood estimation of treatment effects in bivariate probit instrumental variable models}, author={Hollenbach, Florian M and Montgomery, Jacob M and Crespo-Tenorio, Adriana}, journal={Political Science Research and Methods}, volume={7}, number={3}, pages={651--659}, year={2019}, publisher={Cambridge University Press} } @article{pandey2021genetic, url={https://www.nature.com/articles/s41598-021-87284-x}, title={Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA}, author={Pandey, Jeewan and Scheuring, Douglas C and Koym, Jeffrey W and Coombs, Joseph and Novy, Richard G and Thompson, Asunta L and Holm, David G and Douches, David S and Miller, J Creighton and Vales, M Isabel}, journal={Scientific reports}, volume={11}, number={1}, pages={1--18}, year={2021}, publisher={Nature Publishing Group} } @inproceedings{muthusamy2019numerical, url={https://oaktrust.library.tamu.edu/handle/1969.1/173760}, title={NUMERICAL AND EXPERIMENTAL STUDY OF HYDRODYNAMICS OF MULTIPLE DROPLET STREAM IMPINGEMENT FOR ATOMIZATION}, pages={1-192}, author={Muthusamy, Jayaveera Pandian and Zhang, Taolue and Alvarado, Jorge L}, booktitle={ASTFE Digital Library}, year={2019}, organization={Begel House Inc.} } @article{brazzolotto2018tuning, doi={https://doi.org/10.1021/acscatal.8b02830}, title={Tuning reactivity of bioinspired [NiFe]-hydrogenase models by ligand design and modeling the CO inhibition process}, author={Brazzolotto, Deborah and Wang, Lianke and Tang, Hao and Gennari, Marcello and Queyriaux, Nicolas and Philouze, Christian and Demeshko, Serhiy and Meyer, Franc and Orio, Maylis and Artero, Vincent and others}, journal={ACS Catalysis}, volume={8}, number={11}, pages={10658--10667}, year={2018}, publisher={ACS Publications} } @article{karimi2019deepaffinity, url={https://arxiv.org/ct?url=https%3A%2F%2Fdx.doi.org%2F10.1093%2Fbioinformatics%2Fbtz111&v=e3d4316d}, title={DeepAffinity: interpretable deep learning of compound--protein affinity through unified recurrent and convolutional neural networks}, author={Karimi, Mostafa and Wu, Di and Wang, Zhangyang and Shen, Yang}, journal={Bioinformatics}, volume={35}, number={18}, pages={3329--3338}, year={2019}, publisher={Oxford University Press} } @article{mohan2018virtual, doi={https://dx.doi.org/10.1021%2Facsomega.8b00606}, title={Virtual screening of chemical compounds for discovery of complement C3 ligands}, author={Mohan, Rohith R and Wilson, Mark and Gorham Jr, Ronald D and Harrison, Reed ES and Morikis, Vasilios A and Kieslich, Chris A and Orr, Asuka A and Coley, Alexis V and Tamamis, Phanourios and Morikis, Dimitrios}, journal={ACS omega}, volume={3}, number={6}, pages={6427--6438}, year={2018}, publisher={ACS Publications} } @article{choi2020study, doi={https://doi.org/10.1021/acs.est.0c02958}, title={Study of Secondary Organic Aerosol Formation from Chlorine Radical-Initiated Oxidation of Volatile Organic Compounds in a Polluted Atmosphere Using a 3D Chemical Transport Model}, author={Choi, Min Su and Qiu, Xionghui and Zhang, Jie and Wang, Shuxiao and Li, Xinghua and Sun, Yele and Chen, Jianmin and Ying, Qi}, journal={Environmental science & technology}, volume={54}, number={21}, pages={13409--13418}, year={2020}, publisher={ACS Publications} } @phdthesis{sakuru2016qr, url={https://oaktrust.library.tamu.edu/handle/1969.1/157785}, title={QR Decomposition Framework for Efficient Implementation of Linear Support Vector Machines Using Dual Ascent}, author={Sakuru, Venkata Naga Sai Prithvi}, year={2016} } @inproceedings{ghoreyshi2017numerical, doi={https://doi.org/10.1115/GT2017-65029}, title={Numerical simulation of the multistage ultra-high efficiency gas turbine engine, UHEGT}, author={Ghoreyshi, Seyed M and Schobeiri, Meinhard T}, booktitle={Turbo Expo: Power for Land, Sea, and Air}, volume={50831}, pages={V003T06A034}, year={2017}, organization={American Society of Mechanical Engineers} } @article{yang2021leakage, doi={https://doi.org/10.1115/1.4048459}, title={On the Leakage and Dynamic Force Coefficients of a Novel Stepped Shaft Pocket Damper Seal: Experimental and Numerical Verification}, author={Yang, Jing and San Andrés, Luis and Lu, Xueliang}, journal={Journal of Engineering for Gas Turbines and Power}, volume={143}, number={3}, pages={031002}, year={2021}, publisher={American Society of Mechanical Engineers} } @article{koosha2019effect, doi={https://doi.org/10.1115/1.4045278}, title={Effect of pad and liner material properties on the static load performance of a tilting pad thrust bearing}, author={Koosha, Rasool and San Andrés, Luis}, journal={Journal of Engineering for Gas Turbines and Power}, volume={141}, number={12}, pages={121007}, year={2019}, publisher={American Society of Mechanical Engineers} } @inproceedings{johnson2021analysis, url={https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=9595788}, title={Analysis and Benchmarking of Radial Flux Cycloidal Magnetic Gears with Reduced Permanent Magnet Piece Count Using Consequent Poles}, author={Johnson, Matthew and Hasanpour, Shima and Gardner, Matthew C and Toliyat, Hamid A}, booktitle={2021 IEEE Energy Conversion Congress and Exposition (ECCE)}, pages={4334--4341}, year={2021}, organization={IEEE} } @article{borazjani2021sharp, doi={https://doi.org/10.2514/1.J059626}, title={Sharp-Interface Immersed-Boundary Method for Compressible Flows with Shock--Particle Interaction}, author={Borazjani, Iman}, journal={AIAA Journal}, volume={59}, number={4}, pages={1169--1183}, year={2021}, publisher={American Institute of Aeronautics and Astronautics} } @article{chen2014openfoam, url={https://www.ams.org/notices/201404/rnoti-p354.pdf}, title={OpenFOAM for computational fluid dynamics}, author={Chen, Goong and Xiong, Qingang and Morris, Philip J and Paterson, Eric G and Sergeev, Alexey and Wang, Y}, journal={Not. AMS}, volume={61}, number={4}, pages={354--363}, year={2014} } @article{hollenbach2017re, doi={https://doi.org/10.1177%2F2053168017730687}, title={A re-assessment of reporting bias in event-based violence data with respect to cell phone coverage}, author={Hollenbach, Florian M and Pierskalla, Jan H}, journal={Research & Politics}, volume={4}, number={3}, pages={2053168017730687}, year={2017}, publisher={SAGE Publications Sage UK: London, England} } @article{selis2019dendrite, doi={https://doi.org/10.1039/C9RA05067A}, title={Dendrite formation in Li-metal anodes: an atomistic molecular dynamics study}, author={Selis, Luis A and Seminario, Jorge M}, journal={RSC advances}, volume={9}, number={48}, pages={27835--27848}, year={2019}, publisher={Royal Society of Chemistry} } @article{hall2017reactive, url={https://deepblue.lib.umich.edu/bitstream/handle/2027.42/136450/pola28519.pdf}, title={Reactive ligand influence on initiation in phenylene catalyst-transfer polymerization}, author={Hall, Ariana O and Lee, Se Ryeon and Bootsma, Andrea N and Bloom, Jacob WG and Wheeler, Steven E and McNeil, Anne J}, journal={Journal of Polymer Science Part A: Polymer Chemistry}, volume={55}, number={9}, pages={1530--1535}, year={2017}, publisher={Wiley Online Library} } @article{wei2021improved, doi={https://doi.org/10.1029/2020JC016958}, title={An improved ocean surface albedo computational scheme: Structure and Performance}, author={Wei, Jian and Ren, Tong and Yang, Ping and DiMarco, Steven F and Mlawer, Eli}, journal={Journal of Geophysical Research: Oceans}, volume={126}, number={8}, pages={e2020JC016958}, year={2021}, publisher={Wiley Online Library} } @article{Bedre2021, doi = {10.1038/s41598-021-98124-3}, url = {https://doi.org/10.1038/s41598-021-98124-3}, year = {2021}, month = sep, publisher = {Springer Science and Business Media LLC}, volume = {11}, number = {1}, author = {Renesh Bedre and Carlos Avila and Kranthi Mandadi}, title = {HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis}, journal = {Scientific Reports} } @article{selis2018dendrite, doi={https://doi.org/10.1039/C7RA12690E}, title={Dendrite formation in silicon anodes of lithium-ion batteries}, author={Selis, Luis A and Seminario, Jorge M}, journal={RSC advances}, volume={8}, number={10}, pages={5255--5267}, year={2018}, publisher={Royal Society of Chemistry} } @article{harding2020importance, doi={https://doi.org/10.26434/chemrxiv.9936473.v1}, title={Importance of model size in quantum mechanical studies of DNA intercalation}, author={Harding, Drew P and Kingsley, Laura J and Spraggon, Glen and Wheeler, Steven E}, journal={Journal of computational chemistry}, volume={41}, number={12}, pages={1175--1184}, year={2020}, publisher={Wiley Online Library} } @article{langlett2021rainbow, url={https://www.semanticscholar.org/paper/Rainbow-Scars%3A-From-Area-to-Volume-Law-Langlett-Yang/498a1abd49ba3f1d22aefdab4063b0f2c0f37b34}, title={Rainbow Scars: From Area to Volume Law}, author={Langlett, Christopher M and Yang, Zhi-Cheng and Wildeboer, Julia and Gorshkov, Alexey V and Iadecola, Thomas and Xu, Shenglong}, pages={1--12}, journal={arXiv preprint arXiv:2107.03416}, year={2021} } @article{silvestri2019development, doi={https://doi.org/10.1177%2F0361198119845898}, title={Development of a new manual for assessing safety hardware TL-3 low-profile portable concrete barrier for high-speed applications}, author={Silvestri Dobrovolny, Chiara and Shi, Shengyi and Kovar, James and Bligh, Roger P and Hurlebaus, Stefan}, journal={Transportation research record}, volume={2673}, number={7}, pages={630--640}, year={2019}, publisher={SAGE Publications Sage CA: Los Angeles, CA} } @article{lin2019interaction, doi={https://doi.org/10.5194/acp-19-8003-2019}, title={Interaction between succinic acid and sulfuric acid--base clusters}, author={Lin, Yun and Ji, Yuemeng and Li, Yixin and Secrest, Jeremiah and Xu, Wen and Xu, Fei and Wang, Yuan and An, Taicheng and Zhang, Renyi}, journal={Atmospheric Chemistry and Physics}, volume={19}, number={12}, pages={8003--8019}, year={2019}, publisher={Copernicus GmbH} } @article{wang2019numerical, doi={https://doi.org/10.1002/nag.3001}, title={Numerical study on the effect of rigid inclusions on existing railroads}, author={Wang, Dong and S{\'a}nchez, Marcelo and Briaud, Jean-Louis}, journal={International Journal for Numerical and Analytical Methods in Geomechanics}, volume={43}, number={18}, pages={2772--2796}, year={2019}, publisher={Wiley Online Library} } @article{doi:10.1021/acsanm.1c03860, author = {Kaynan, Ozge and Pérez, Lisa M. and Asadi, Amir}, title = {Cellulose Nanocrystal-Enabled Tailoring of the Interface in Carbon Nanotube- and Graphene Nanoplatelet-Carbon Fiber Polymer Composites: Implications for Structural Applications}, journal = {ACS Applied Nano Materials}, volume = {0}, number = {0}, pages = {null}, year = {2022}, doi = {10.1021/acsanm.1c03860}, url = {https://doi.org/10.1021/acsanm.1c03860}, eprint = {https://doi.org/10.1021/acsanm.1c03860} } @ARTICLE{10.3389/fpls.2022.916231, AUTHOR={Lau, Jeekin and Young, Ellen L. and Collins, Sara and Windham, Mark T. and Klein, Patricia E. and Byrne, David H. and Riera-Lizarazu, Oscar}, TITLE={Rose Rosette Disease Resistance Loci Detected in Two Interconnected Tetraploid Garden Rose Populations}, JOURNAL={Frontiers in Plant Science}, PAGES = {1}, VOLUME={13}, YEAR={2022}, URL={https://www.frontiersin.org/articles/10.3389/fpls.2022.916231}, DOI={10.3389/fpls.2022.916231}, ISSN={1664-462X}, ABSTRACT={Rose rosette disease (RRD), caused by the Rose rosette emaravirus (RRV), is a major threat to the garden rose industry in the United States. There has been limited work on the genetics of host plant resistance to RRV. Two interconnected tetraploid garden rose F₁ biparental mapping populations were created to develop high-quality tetraploid rose linkage maps that allowed the discovery of RRD resistance quantitative trait loci (QTLs) on linkage groups (LGs) 5, 6, and 7. These QTLs individually accounted for around 18–40% of the phenotypic variance. The locus with the greatest effect on partial resistance was found in LG 5. Most individuals with the LG 5 QTL were in the simplex configuration; however, two individuals were duplex (likely due to double reduction). Identification of resistant individuals and regions of interest can help the development of diagnostic markers for marker-assisted selection in a breeding program.} } @article{https://doi.org/10.1002/smll.202202216, author = {Aramfard, Mohammad and Kaynan, Ozge and Hosseini, Ehsan and Zakertabrizi, Mohammad and Pérez, Lisa M. and Asadi, Amir}, title = {Aqueous Dispersion of Carbon Nanomaterials with Cellulose Nanocrystals: An Investigation of Molecular Interactions}, journal = {Small}, volume = {n/a}, number = {n/a}, year = {2022}, pages = {2202216}, keywords = {aqueous dispersion, carbon nanotubes, cellulose nanocrystals, density functional theory, graphene nanoplatelets}, doi = {https://doi.org/10.1002/smll.202202216}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/smll.202202216}, eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/smll.202202216}, abstract = {Abstract Dispersing carbon nanomaterials in solvents is effective in transferring their significant mechanical and functional properties to polymers and nanocomposites. However, poor dispersion of carbon nanomaterials impedes exploiting their full potential in nanocomposites. Cellulose nanocrystals (CNCs) are promising for dispersing and stabilizing pristine carbon nanotubes (pCNTs) and graphene nanoplatelets (pGnP) in protic media without functionalization. Here, the underlying mechanisms at the molecular level are investigated between CNC and pCNT/pGnP that stabilize their dispersion in polar solvents. Based on the spectroscopy and microscopy characterization of CNC-pCNT/pGnP and density functional theory (DFT) calculations, an additional intermolecular mechanism is proposed between CNC and pCNT/pGnP that forms carbon-oxygen covalent bonds between hydroxyl end groups of CNCs and the defected sites of pCNTs/pGnPs preventing re-agglomeration in polar solvents. This work's findings indicate that the CNC-assisted process enables new capabilities in harnessing nanostructures at the molecular level and tailoring the performance of nanocomposites at higher length scales.} } @article { AMicrophysicsSchemeConsistentSnowOpticalParameterizationfortheCommunityRadiativeTransferModel, author = {Tong Ren and Ping Yang and Kevin Garrett and Yingtao Ma and Jiachen Ding and James Coy}, title = "A Microphysics-Scheme-Consistent Snow Optical Parameterization for the Community Radiative Transfer Model", journal = "Monthly Weather Review", year = "2023", publisher = "American Meteorological Society", address = "Boston MA, USA", volume = "151", number = "2", doi = "10.1175/MWR-D-22-0145.1", pages= "383 - 402", url = "https://journals.ametsoc.org/view/journals/mwre/151/2/MWR-D-22-0145.1.xml" } @article{https://doi.org/10.1029/2021MS002754, author = {Ren, Tong and Yang, Ping and Wei, Jian and Huang, Xianglei and Sang, Huiyan}, title = {Performance of Cloud 3D Solvers in Ice Cloud Shortwave Radiation Closure Over the Equatorial Western Pacific Ocean}, journal = {Journal of Advances in Modeling Earth Systems}, volume = {14}, number = {2}, pages = {e2021MS002754}, keywords = {cloud 3D effect, cloud top variability, cloud vertical extent}, doi = {https://doi.org/10.1029/2021MS002754}, url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2021MS002754}, eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2021MS002754}, note = {e2021MS002754 2021MS002754}, abstract = {Abstract For retrieving cloud optical properties from satellite images or computing these properties from climate model output, computationally efficient treatments of cloud horizontal inhomogeneity include the Monte Carlo Independent Column Approximation (McICA) and the Tripleclouds method. Computationally efficient treatment of cloud horizontal radiation exchanges includes the SPeedy Algorithm for Radiative TrAnsfer through CloUd Sides (SPARTACUS). As a test to derive properties from satellite images, we collocate Moderate Resolution Imaging Spectroradiometer (MODIS) cloud retrievals with near-nadir Cloud and the Earth's Radiant Energy System (CERES) footprints in July 2008 over an equatorial western Pacific Ocean region to compare the performance of the McICA, Tripleclouds, and SPARTACUS solvers to the conventional plane-parallel homogeneous (PPH) treatment. PPH overestimates cloud albedo, and the three solvers effectively reduce overestimation with root mean square error of shortwave upwelling irradiance decreasing between 15.72 and 18.53 W m−2, or about 22\%–25\%. Although cloud top variability does not get fed into the simulations, all three solvers also reduce the effect of cloud top variability on cloud albedo. Entrapment (energy reflected downward from clouds) and horizontal radiation transfer have opposite effects on the SPARTACUS cloud albedo simulation. The net effect depends on the cloud vertical extent, the unawareness of which limits the performance of the SPARTACUS solver.}, year = {2022} } @article{LI2023100092, title = {Plastic collapse analysis in multiaxially loaded defective pipe specimens at different temperatures}, journal = {Journal of Pipeline Science and Engineering}, volume = {3}, number = {1}, pages = {100092}, year = {2023}, issn = {2667-1433}, doi = {https://doi.org/10.1016/j.jpse.2022.100092}, url = {https://www.sciencedirect.com/science/article/pii/S2667143322000646}, author = {Y. Li and C. Sakonder and M. Paredes}, keywords = {Multiaxial loads, Cracked pipes, Ductile fracture, Martensite kinetic phase transformation}, abstract = {A comprehensive numerical investigation is carried out using a newly developed constitutive model to describe failure at low temperatures in multiaxially loaded cracked pipes made of 316L stainless steel. The kinetic phase transformation and the temperature-dependent fracture criterion are implemented to accurately capture the mechanical response at different temperature levels. Although experimental observations of these simulations were not available, their results were quite consistent with some already published results obtained on similar materials and loading conditions at room temperature. The results indicate that the existing multiaxial plastic collapse failure criterion, including shearing, still provides a fail-safe design margin for low temperature loading conditions, including internal pressure. Moreover, martensite kinetic phase transformation plays an important role, especially during straining at low temperatures.} } @article{RANAIEFAR2022110328, title = {A differential evaporation model to predict chemistry change of additively manufactured metals}, journal = {Materials & Design}, volume = {213}, pages = {110328}, year = {2022}, issn = {0264-1275}, doi = {https://doi.org/10.1016/j.matdes.2021.110328}, url = {https://www.sciencedirect.com/science/article/pii/S0264127521008832}, author = {Meelad Ranaiefar and Pejman Honarmandi and Lei Xue and Chen Zhang and Alaa Elwany and Ibrahim Karaman and Edwin J. Schwalbach and Raymundo Arroyave}, keywords = {Additive manufacturing, Markov chain Monte Carlo, Differential evaporation, NiTi, Shape memory alloys, Bayesian calibration, 4D printing}, abstract = {The desire for increased performance and functionality has introduced additional complexities to the design and fabrication of additively manufactured (AM) parts. However, addressing these needs would require improved control over local properties using in-line feedback from fast-acting low-fidelity models during the fabrication process. In this regard, differential evaporation is an inherent characteristic in metal AM processes, directly influencing local chemistry, material properties, functionality, and performance. In the present work, a differential evaporation model (DEM) is presented for laser powder bed fusion (LPBF) AM to predict and control the effect of evaporation on chemistry and properties on local and part-wide scales. The DEM model is coupled with an analytical thermal model that is calibrated against 51.2 Ni [at%] nickel titanium shape memory alloy (NiTi SMA) single-track experiments and a multi-layer model that accounts for the AM part’s multi-layer design and the inherent melt pool overlap and chemistry propagation. The combined hierarchical model, consisting of the thermal, evaporation, and multi-layer components, is used to predict location-specific chemistry for LBPF AM fabrication of Ni50.8Ti49.2 [at%] SMAs. Model predictions are validated with values obtained from multi-layer experiments on a commercial LPBF system, resulting in a root mean square error (RMSE) of 0.25 Ni [at%] for predicted Ni content. Additionally, martensitic transformation temperature, Ms, is calculated and compared with empirical data, resulting in an RMSE of 18.6 K. A practical account of the cumulative and propagative thermal-induced evaporation effect on location-specific chemistry is made through this linkage of models. Fundamentally, this model chain has also provided a solution to the forward modeling problem, enabling steps to be taken towards resolving the inverse design problem of determining processing parameters based on desired location-specific properties.} } @article{HONARMANDI2021102300, title = {A rigorous test and improvement of the Eagar-Tsai model for melt pool characteristics in laser powder bed fusion additive manufacturing}, journal = {Additive Manufacturing}, volume = {47}, pages = {102300}, year = {2021}, issn = {2214-8604}, doi = {https://doi.org/10.1016/j.addma.2021.102300}, url = {https://www.sciencedirect.com/science/article/pii/S2214860421004590}, author = {P. Honarmandi and R. Seede and L. Xue and D. Shoukr and P. Morcos and B. Zhang and C. Zhang and A. Elwany and I. Karaman and R. Arroyave}, keywords = {Additive manufacturing, Bayesian inference, Markov Chain Monte Carlo, Uncertainty quantification, Uncertainty propagation}, abstract = {The accurate prediction of the thermal histories and melt pool characteristics during additive manufacturing (AM) is necessary to understand the factors responsible for the quality and integrity of the manufactured part. More importantly, the determination of optimal process windows and even feed-forward and in-line feedback control of the manufacturing process require computationally cheap, fast-acting, quantitative models connecting (local) processing parameters to melt and solidification conditions. Initially developed in the context of welding, the Eagar-Tsai (E-T) model stands out among the most widely used computationally cheap models to predict melt pool characteristics during AM. Despite its widespread use, its statistical validity in the context of AM has yet to be thoroughly verified. In this work, we study the E-T model in a systematic manner, from an uncertainty quantification/propagation (UQ/UP) perspective. E-T model parameters are calibrated against high quality single-track experimental data on the melt pool geometries of several materials through Markov Chain Monte Carlo (MCMC) sampling. Posterior distributions of the model parameter values are then propagated. We find that there are considerable discrepancies between predicted and measured melt pool depths when process conditions correspond to keyholing. We then apply a physics-based correction and find that it is possible to achieve much better agreement with experiments without increasing significantly the complexity of the E-T model. Although there might be some uncertainties due to the missing physics and assumptions in the model, the model accuracy and trend are satisfactory for the purpose of accelerated product design under uncertainty.} } @inproceedings{Gaonkar2022, author={Gaonkar, Cheetan, and Campbell, Lisa}, title={Transcriptome Analysis Reveals Potential Markers for Species Delineation in Dinophysis}, journal={BMC Genomics}, year={2022}, month={Oct}, day={26}, pages={1}, abstract={Species within the genus Dinophysis can produce okadiac acid, dinophysistoxins, and/or pectenotoxins, which inhibit protein phosphatase, leading to diarrhetic shellfish poisoning (DSP). The potential of these species to close aquaculture harvesting when toxin concentrations exceed recommended levels can lead to economic crises, which highlights the significance of studying this group.}, issn={2022-10}, url={https://neiwpcc.org/wp-content/uploads/2022/09/Chetan_Gaonkar.pdf} } @inproceedings{10.1145/3491418.3530772, author = {Nasari, Abhinand and Le, Hieu and Lawrence, Richard and He, Zhenhua and Yang, Xin and Krell, Mario and Tsyplikhin, Alex and Tatineni, Mahidhar and Cockerill, Tim and Perez, Lisa and Chakravorty, Dhruva and Liu, Honggao}, title = {Benchmarking the Performance of Accelerators on National Cyberinfrastructure Resources for Artificial Intelligence / Machine Learning Workloads}, year = {2022}, isbn = {9781450391610}, publisher = {Association for Computing Machinery}, address = {New York, NY, USA}, url = {https://doi.org/10.1145/3491418.3530772}, doi = {10.1145/3491418.3530772}, abstract = {Upcoming regional and National Science Foundation (NSF)-funded Cyberinfrastructure (CI) resources will give researchers opportunities to run their artificial intelligence / machine learning (AI/ML) workflows on accelerators. To effectively leverage this burgeoning CI-rich landscape, researchers need extensive benchmark data to maximize performance gains and map their workflows to appropriate architectures. This data will further assist CI administrators, NSF program officers, and CI allocation-reviewers make informed determinations on CI-resource allocations. Here, we compare the performance of two very different architectures: the commonly used Graphical Processing Units (GPUs) and the new generation of Intelligence Processing Units (IPUs), by running training benchmarks of common AI/ML models. We leverage the maturity of software stacks, and the ease of migration among these platforms to learn that performance and scaling are similar for both architectures. Exploring training parameters, such as batch size, however finds that owing to memory processing structures, IPUs run efficiently with smaller batch sizes, while GPUs benefit from large batch sizes to extract sufficient parallelism in neural network training and inference. This comes with different advantages and disadvantages as discussed in this paper.As such considerations of inference latency, inherent parallelism and model accuracy will play a role in researcher selection of these architectures. The impact of these choices on a representative image compression model system is discussed.}, booktitle = {Practice and Experience in Advanced Research Computing}, articleno = {19}, numpages = {9}, keywords = {Frontera, Graphics Processing Unit, ResNet50, LoneStar6, Convolution Neural Network, Intelligence Processing Unit, Expanse, Optimization, ACES (Accelerating Computing for Emerging Sciences), Classification, PopVision}, location = {Boston, MA, USA}, series = {PEARC '22} } @inproceedings{10.1145/3491418.3535182, author = {Pham, Duy and Hsu, Kyle and Pennings, Marinus and Pham, Tri and Au, Phi}, title = {Extending Functionalities on a Web-Based Portal for Research Computing}, year = {2022}, isbn = {9781450391610}, publisher = {Association for Computing Machinery}, address = {New York, NY, USA}, url = {https://doi.org/10.1145/3491418.3535182}, doi = {10.1145/3491418.3535182}, abstract = {This paper introduces a research computing portal built as an extension to the OpenOnDemand (OOD) framework. Students 100% implemented the portal at Texas A&M University's (TAMU) High Performance Research Computing (HPRC) facility. It offers an intuitive way for researchers to see all their research computing information on a single web page. This information includes billing accounts, file quotas, recently completed jobs, and currently running jobs. A researcher will also be able to view detailed job information, both for running and completed jobs. The dashboard also provides a 100% visual interface for creating jobs and “offloading” user codes to the cluster and functionality to manage accounts and request quota increases and software installations,}, booktitle = {Practice and Experience in Advanced Research Computing}, articleno = {37}, numpages = {4}, keywords = {dashboard, Open OnDemand, portal, HPC, gateway}, location = {Boston, MA, USA}, series = {PEARC '22} } @inproceedings{10.1145/3437359.3465602, author = {Lau, Michael and Trivedi, Stuti and He, Zhenhua and Pham, Tri and Perez, Lisa and Chakravorty, Dhruva}, title = {Research Cloud Bazaar: A Software Defined Cloud Workflow Cost Management Tool}, year = {2021}, isbn = {9781450382922}, publisher = {Association for Computing Machinery}, address = {New York, NY, USA}, url = {https://doi.org/10.1145/3437359.3465602}, doi = {10.1145/3437359.3465602}, abstract = {Research workflows will benefit from a hybrid computing environment that offers seamless integration between on-campus and off-campus cloud resources. Commercial and Federal and commercial clouds provide researchers a rich set of computing platforms that allow opportunities to improve workflows and reduce the time to research. The large number of cloud offerings, however, makes cost management, and workflow transitions to appropriate platforms challenging. Successfully mapping workflows from on-campus resources to the cloud and leveraging the available cost structures to find economical cost models are critical steps to enabling researcher access to this vast resource. To address these concerns, here we introduce the Research Computing Bazaar (RCB) software application for resource mapping and cost estimation. RCB is a software-as-a-service platform that is an elastic, scalable, and fault tolerant system. It is developed using actual data from research computing workloads and can be easily configured to be used by users or system administrators in computing environments that use Slurm. In this pilot, we inform researchers about opportunities offered by RCB to leverage flexible workload orchestration in managing cloud costs on a major cloud service provider. An extension into predictive capacities with machine learning mechanisms is being developed.}, booktitle = {Practice and Experience in Advanced Research Computing}, articleno = {27}, numpages = {4}, keywords = {Classification, Cloud, Slurm, Cloud Cost Management, Workflow Orchestration, Flask, Docker, Machine Learning, Resource Mapping, API-led integration, Apache Superset}, location = {Boston, MA, USA}, series = {PEARC '21} } @article{jocse-10-1-7, author={Dhruva K. Chakravorty and Marinus "Maikel" Pennings and Honggao Liu and Zengyu "Sheldon" Wei and Dylan M. Rodriguez and Levi T. Jordan and Donald "Rick" McMullen and Noushin Ghaffari and Shaina D. Le}, title={Effectively Extending Computational Training Using Informal Means at Larger Institutions}, journal={The Journal of Computational Science Education}, year=2019, month=jan, volume=10, issue=1, pages={40--47}, doi={https://doi.org/10.22369/issn.2153-4136/10/1/7} } @article{Luo2019-rt, title={TAMU HPRC Portal: Leveraging Open OnDemand for Research and Education}, author={Ping Luo and Donale McMullen and T. Mark Huang and Shaowen Mao and C. Michael Dickens and Marinus Pennings and Yang Liu}, abstract={The Texas A&M University High Performance Research Computing (TAMU HPRC) Portal is a local installation and adaptation of Open OnDemand (OOD) on the HPRC clusters. The Portal provides an advanced cyberinfrastructure that enables HPRC users to utilize the High Performance Computing (HPC) resources for their research. It also serves as an educational platform for faculty and staff for teaching and training.}, url={https://osf.io/2qj5m}, pages={1-4}, year=2019 } @article{YU2023106282, title = {Artificial intelligence-based HDX (AI-HDX) prediction reveals fundamental characteristics to protein dynamics: Mechanisms on SARS-CoV-2 immune escape}, journal = {iScience}, volume = {26}, number = {4}, pages = {106282}, year = {2023}, issn = {2589-0042}, doi = {https://doi.org/10.1016/j.isci.2023.106282}, url = {https://www.sciencedirect.com/science/article/pii/S2589004223003590}, author = {Jiali Yu and Ugur Uzuner and Bin Long and Zachary Wang and Joshua S. Yuan and Susie Y. Dai}, keywords = {Immunology, Virology}, abstract = {Summary Three-dimensional structure and dynamics are essential for protein function. Advancements in hydrogen-deuterium exchange (HDX) techniques enable probing protein dynamic information in physiologically relevant conditions. HDX-coupled mass spectrometry (HDX-MS) has been broadly applied in pharmaceutical industries. However, it is challenging to obtain dynamics information at the single amino acid resolution and time consuming to perform the experiments and process the data. Here, we demonstrate the first deep learning model, artificial intelligence-based HDX (AI-HDX), that predicts intrinsic protein dynamics based on the protein sequence. It uncovers the protein structural dynamics by combining deep learning, experimental HDX, sequence alignment, and protein structure prediction. AI-HDX can be broadly applied to drug discovery, protein engineering, and biomedical studies. As a demonstration, we elucidated receptor-binding domain structural dynamics as a potential mechanism of anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody efficacy and immune escape. AI-HDX fundamentally differs from the current AI tools for protein analysis and may transform protein design for various applications.} } @Article{jof9040418, AUTHOR = {Yu, Jiali and Lai, Jingru and Neal, Brian M. and White, Bert J. and Banik, Mark T. and Dai, Susie Y.}, TITLE = {Genomic Diversity and Phenotypic Variation in Fungal Decomposers Involved in Bioremediation of Persistent Organic Pollutants}, JOURNAL = {Journal of Fungi}, VOLUME = {9}, YEAR = {2023}, NUMBER = {4}, ARTICLE-NUMBER = {418}, URL = {https://www.mdpi.com/2309-608X/9/4/418}, ISSN = {2309-608X}, ABSTRACT = {Fungi work as decomposers to break down organic carbon, deposit recalcitrant carbon, and transform other elements such as nitrogen. The decomposition of biomass is a key function of wood-decaying basidiomycetes and ascomycetes, which have the potential for the bioremediation of hazardous chemicals present in the environment. Due to their adaptation to different environments, fungal strains have a diverse set of phenotypic traits. This study evaluated 320 basidiomycetes isolates across 74 species for their rate and efficiency of degrading organic dye. We found that dye-decolorization capacity varies among and within species. Among the top rapid dye-decolorizing fungi isolates, we further performed genome-wide gene family analysis and investigated the genomic mechanism for their most capable dye-degradation capacity. Class II peroxidase and DyP-type peroxidase were enriched in the fast-decomposer genomes. Gene families including lignin decomposition genes, reduction-oxidation genes, hydrophobin, and secreted peptidases were expanded in the fast-decomposer species. This work provides new insights into persistent organic pollutant removal by fungal isolates at both phenotypic and genotypic levels.}, DOI = {10.3390/jof9040418} } @inproceedings{ han2023mlpinit, doi={https://doi.org/10.48550/arXiv.2210.00102}, title={MLPInit: Embarrassingly Simple GNN Training Acceleration with MLP Initialization}, author={Xiaotian Han and Tong Zhao and Yozen Liu and Xia Hu and Neil Shah}, booktitle={The Eleventh International Conference on Learning Representations }, year={2023}, url={https://openreview.net/forum?id=P8YIphWNEGO} } @article{doi:10.1021/acsami.3c01307, author = {Carrola, Mia and Fallahi, Hamed and Koerner, Hilmar and Pérez, Lisa M. and Asadi, Amir}, title = {Fundamentals of Crystalline Evolution and Properties of Carbon Nanotube-Reinforced Polyether Ether Ketone Nanocomposites in Fused Filament Fabrication}, journal = {ACS Applied Materials \& Interfaces}, volume = {15}, number = {18}, pages = {22506-22523}, year = {2023}, doi = {10.1021/acsami.3c01307}, note ={PMID: 37099604}, URL = {https://doi.org/10.1021/acsami.3c01307}, eprint = {https://doi.org/10.1021/acsami.3c01307} } @article{AYYILDIZ2023786, title = {Research on pinhole accidental gas release in pipelines: Statistical modeling, real gas CFD simulation, and validation}, journal = {Process Safety and Environmental Protection}, volume = {176}, pages = {786-796}, year = {2023}, issn = {0957-5820}, doi = {https://doi.org/10.1016/j.psep.2023.06.041}, url = {https://www.sciencedirect.com/science/article/pii/S0957582023005281}, author = {Burak Ayyildiz and M. Ziyan Sheriff and Mohammad Azizur Rahman and Adolfo Delgado and Ibrahim Hassan and Hazem Nounou and Mohamed Nounou}, keywords = {CFD simulation, Chronic leak detection, NG pipeline leakage, Real gas simulation, Generalized Likelihood Ratio (GLR), Numerical investigation}, abstract = {The successful risk mitigation of Natural Gas (NG) leakage to reduce its environmental and economic impact depends chiefly on timely detection leaks and predicting the amount of gas release. In the present study, we investigated pinhole leaks and predicted the gas release rate for various leak to pipe diameter ratios and operating pressures ranging from 2 bar to 110 bar. We first set up a laboratory-scale experiment. The generalized likelihood ratio (GLR) is used as an advanced statistical hypothesis testing technique to detect any shifts in the mean and variance of the process measurements in real-time. These results improved the understanding of several leak detection systems and contributed to a reduction in false alarms in these systems. The presence of a leak was flagged almost immediately after it occurred, indicating the speed and efficiency of statistical techniques in detecting microleaks. The present computational fluid dynamics (CFD) study provides details on the entire leak flow field that are not possible to obtain with experimental methods. CFD is a critical tool in process safety management, helping to identify, analyze, and mitigate potential risks in natural gas pipeline. The CFD study proposes new correlations to predict the nominal leak volume flow rate by investigating the influence of leak size, pipe diameter, and pipe pressure for wide ranges of pressures. The correlations were derived from three-dimensional transient detachable eddy simulation model in a commercial CFD code (ANSYS Fluent R3). The correlations enhance the conventional models by incorporating the gas compressibility effect for high-pressure conditions. The percentage of error between the results of the CFD and delivered correlation fluctuated between 4% and − 5%, demonstrating the high accuracy of the new correlation.} } @ARTICLE{10.3389/fpls.2023.1209445, AUTHOR={Lau, Jeekin and Gill, Haramrit and Taniguti, Cristiane H. and Young, Ellen L. and Klein, Patricia E. and Byrne, David H. and Riera-Lizarazu, Oscar}, TITLE={QTL discovery for resistance to black spot and cercospora leaf spot, and defoliation in two interconnected F1 bi-parental tetraploid garden rose populations}, JOURNAL={Frontiers in Plant Science}, VOLUME={14}, YEAR={2023}, URL={https://www.frontiersin.org/articles/10.3389/fpls.2023.1209445}, DOI={10.3389/fpls.2023.1209445}, ISSN={1664-462X}, ABSTRACT={Garden roses are an economically important horticultural crop worldwide, and two major fungal pathogens, black spot (Diplocarpon rosae F.A. Wolf) and cercospora leaf spot of rose (Rosisphaerella rosicola Pass.), affect both the health and ornamental value of the plant. Most studies on black spot disease resistance have focused on diploid germplasm, and little work has been performed on cercospora leaf spot resistance. With the use of newly developed software tools for autopolyploid genetics, two interconnected tetraploid garden rose F₁ populations (phenotyped over the course of 3 years) were used for quantitative trait locus (QTL) analysis of black spot and cercospora leaf spot resistance as well as plant defoliation. QTLs for black spot resistance were mapped to linkage groups (LGs) 1–6. QTLs for cercospora resistance and susceptibility were found in LGs 1, 4, and 5 and for defoliation in LGs 1, 3, and 5. The major locus on LG 5 for black spot resistance coincides with the previously discovered Rdr4 locus inherited from Rosa L. ‘Radbrite’ (Brite Eyes™), the common parent used in these mapping populations. This work is the first report of any QTL for cercospora resistance/susceptibility in tetraploid rose germplasm and the first report of defoliation QTL in roses. A major QTL for cercospora susceptibility coincides with the black spot resistance QTL on LG 5 (Rdr4). A major cercospora resistance QTL was found on LG 1. These populations provide a genetic resource that will further the knowledge base of rose genetics as more traits are studied. Studying more traits from these populations will allow for the stacking of various QTLs for desirable traits.} } @article{LIU2023154741, title = {Effect of free surfaces on localized plastic deformation in single-crystal nickel containing helium bubbles and radiation-induced self-interstitial atom clusters}, journal = {Journal of Nuclear Materials}, volume = {587}, pages = {154741}, year = {2023}, issn = {0022-3115}, doi = {https://doi.org/10.1016/j.jnucmat.2023.154741}, url = {https://www.sciencedirect.com/science/article/pii/S0022311523005081}, author = {Tung Yan Liu and Michael J. Demkowicz}, keywords = {Molecular dynamics, nickel, slip band, nanotwin, Helium bubble, free surface}, abstract = {This paper presents molecular dynamics (MD) simulations of plastic deformation in single-crystal Ni models containing internal distributions of helium (He) bubbles and self-interstitial atom (SIA) clusters corresponding to experimental characterization of ex-service Inconel X-750 components. We simulate single crystals with and without free surfaces at room temperature and 588K, the latter temperature corresponding to the Inconel X-750 service conditions. Both models are deformed under multiple slip to a maximum deviatoric strain of ∼10 %. A dislocation slip band forms in the model without free surfaces, but not in the model with free surfaces. However, the latter exhibits nano-twin nucleation from surfaces. Helium (He) bubbles that overlap with a slip band or a nano-twinned region deform more severely than other bubbles in the model. Nevertheless, the bubbles do not link up and do not form configurations that resemble incipient cracks.} } @article{https://doi.org/10.1029/2023JD038747, author = {Ren, Tong and Yang, Ping and Loeb, Norman G. and Smith Jr., William L. and Minnis, Patrick}, title = {On the Consistency of Ice Cloud Optical Models for Spaceborne Remote Sensing Applications and Broadband Radiative Transfer Simulations}, journal = {Journal of Geophysical Research: Atmospheres}, volume = {128}, number = {20}, pages = {e2023JD038747}, doi = {https://doi.org/10.1029/2023JD038747}, url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2023JD038747}, eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2023JD038747}, note = {e2023JD038747 2023JD038747}, abstract = {Abstract Aqua satellite Moderate Resolution Imaging Spectroradiometer (MODIS) 1-km observations are collocated with Clouds and the Earth's Radiant Energy System (CERES) fields of view taken during July 2008 afternoon satellite passes over the equatorial western Pacific Ocean. Radiation simulations are compared with collocated CERES observations to better understand the sensitivity of computed fluxes to two ice cloud broadband radiation parameterization schemes and inferred ice cloud characteristics. In particular, the radiation computational schemes and ice cloud property retrievals are based on two respective ice particle models, the MODIS Collection 6 (MC6) aggregate model and a more microphysically consistent two-habit model (THM). The simulation results show that both MC6 and THM overestimate the shortwave (SW) and longwave (LW) cloud radiative effects at the top of the atmosphere, as compared to the CERES observations; the difference between the MC6 and THM-based ice cloud retrievals is too small to compensate for the differences between the two model-based radiation schemes. Therefore, the present finding suggests that broadband radiative simulations are more sensitive to the radiation parameterization scheme than to the input cloud properties retrieved using the corresponding ice cloud particle optical property model.}, year = {2023} } @article{https://doi.org/10.1111/acel.13968, author = {Yang, Wanbao and Kim, Da Mi and Jiang, Wen and Ai, Weiqi and Pan, Quan and Rahman, Shahina and Cai, James J. and Brashear, Wesley A. and Sun, Yuxiang and Guo, Shaodong}, title = {Suppression of FOXO1 attenuates inflamm-aging and improves liver function during aging}, journal = {Aging Cell}, volume = {22}, number = {10}, pages = {e13968}, keywords = {aging, FOXO1, inflamm-aging, inflammation, Kupffer cell, liver function, monocyte-derived macrophage}, doi = {https://doi.org/10.1111/acel.13968}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/acel.13968}, eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/acel.13968}, note = {e13968 ACE-23-0446}, abstract = {Abstract The liver is a key metabolic organ that maintains whole-body nutrient homeostasis. Aging-induced liver function alterations contribute to systemic susceptibility to aging-related diseases. However, the molecular mechanisms of liver aging remain insufficiently understood. In this study, we performed bulk RNA-Seq and single-cell RNA-Seq analyses to investigate the underlying mechanisms of the aging-induced liver function changes. We found that liver inflammation, glucose intolerance, and liver fat deposition were aggravated in old mice. Aging significantly increased pro-inflammation in hepatic macrophages. Furthermore, we found that Kupffer cells (KCs) were the major driver to induce pro-inflammation in hepatic macrophages during aging. In KCs, aging significantly increased pro-inflammatory levels; in monocyte-derived macrophages (MDMs), aging had a limited effect on pro-inflammation but led to a functional quiescence in antigen presentation and phagosome process. In addition, we identified an aging-responsive KC-specific (ARKC) gene set that potentially mediates aging-induced pro-inflammation in KCs. Interestingly, FOXO1 activity was significantly increased in the liver of old mice. FOXO1 inhibition by AS1842856 significantly alleviated glucose intolerance, hepatic steatosis, and systemic inflammation in old mice. FOXO1 inhibition significantly attenuated aging-induced pro-inflammation in KCs partially through downregulation of ARKC genes. However, FOXO1 inhibition had a limited effect on aging-induced functional quiescence in MDMs. These results indicate that aging induces pro-inflammation in liver mainly through targeting KCs and FOXO1 is a key player in aging-induced pro-inflammation in KCs. Thus, FOXO1 could be a potential therapeutic target for the treatment of age-associated chronic diseases.}, year = {2023} } @article{li2023machine, title={Machine Learning for Mechanistic Models of Metapopulation Dynamics}, author={Jifan Li and Edward L. Ionides and Aaron A. King and Mercedes Pascual and Ning Ning}, year={2023}, doi={https://doi.org/10.48550/arXiv.2311.06702}, eprint={2311.06702}, archivePrefix={arXiv}, primaryClass={stat.AP} } @article{https://doi.org/10.1029/2023GL106076, author = {Ren, Tong and Yang, Ping and Huang, Xianglei and Chen, Xiuhong and Shen, Zhaoyi}, title = {Enhanced Cloud Top Longwave Radiative Cooling Due To the Effect of Horizontal Radiative Transfer in the Stratocumulus to Trade Cumulus Transition Regime}, journal = {Geophysical Research Letters}, volume = {50}, number = {22}, pages = {e2023GL106076}, doi = {https://doi.org/10.1029/2023GL106076}, url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2023GL106076}, eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2023GL106076}, note = {e2023GL106076 2023GL106076}, abstract = {Abstract Recent studies develop the SPeedy Algorithm for Radiative TrAnsfer through CloUd Sides (SPARTACUS) to handle the influence of horizontal RT on vertical radiative fluxes within an atmospheric column. The present study applies SPARTACUS to large eddy simulation (LES)-generated cloud fields across the stratocumulus to trade cumulus transition (STCT) regime with coarse and fine vertical resolutions. The results show that, as the vertical resolution increases, radiation simulations show increasingly stronger cloud-top longwave (LW) radiative cooling. Consequently, the sharp radiative heating gradient across the cloud layer in the LES-like resolution simulations cannot be resolved with the coarse resolution simulations. Including the horizontal RT typically enhances cloud LW radiative cooling rate by less than 10\% for all the cloud fields but more significantly in the cloud fields during the STCT. The enhanced cloud LW radiative cooling also occurs in the lower cloud layer in the decoupled cumulus cloud regime.}, year = {2023} } @ARTICLE{10286268, author={Rajabioun, Ramin and Afshar, Mojtaba and Mete, Mutlu and Atan, Özkan and Akin, Bilal}, journal={IEEE Journal of Emerging and Selected Topics in Industrial Electronics}, title={Distributed Bearing Fault Classification of Induction Motors Using 2-D Deep Learning Model}, year={2024}, volume={5}, number={1}, pages={115-125}, keywords={Feature extraction;Induction motors;Fault diagnosis;Vibrations;DC motors;Brushless DC motors;Indexes;Deep learning (DL);distributed bearing fault detection;distributed fault detection;2-D convolutional neural network (CNN)}, doi={10.1109/JESTIE.2023.3323253}} @conference{hong2024dpopt, title={DP-OPT: Make Large Language Model Your Privacy-Preserving Prompt Engineer}, author={Junyuan Hong and Jiachen T. Wang and Chenhui Zhang and Zhangheng Li and Bo Li and Zhangyang Wang}, year={2024}, eprint={2312.03724}, archivePrefix={arXiv}, primaryClass={cs.CL} } @article{LIU2024155030, title = {Effect of grain boundaries and rigid inclusions on plasticity in nickel bicrystals containing helium bubbles and radiation-induced self-interstitial atom clusters}, journal = {Journal of Nuclear Materials}, volume = {594}, pages = {155030}, year = {2024}, issn = {0022-3115}, doi = {https://doi.org/10.1016/j.jnucmat.2024.155030}, url = {https://www.sciencedirect.com/science/article/pii/S0022311524001338}, author = {Tung Yan Liu and Michael J. Demkowicz}, keywords = {Grain boundary, Inclusion, Nickel, Helium bubble, Molecular dynamics, Radiation}, abstract = {We use molecular dynamics to assess the effect of grain boundaries and rigid intergranular inclusions on plastic deformation in nickel (Ni) containing helium (He) bubbles and self-interstitial atom clusters. Our simulations show that plasticity in Ni bicrystals is relatively uniform, with no localized slip bands or nano-twins. We attribute this behavior to grain boundaries, which block dislocations and favor activation of new sources over persistent slip along a single plane. While there is no initiation of intergranular cracks, He bubbles at matrix/inclusion interfaces elongate along the tensile axis and migrate towards regions of high tension, potentially setting the conditions for formation of crack-like flaws via bubble coalescence. We discuss the implications of our work for understanding degradation of mechanical properties in Ni-base alloys in nuclear reactors.} } @article{SHEU2024120002, title = {Permeation of niobium through grain boundaries in copper}, journal = {Acta Materialia}, volume = {274}, pages = {120002}, year = {2024}, issn = {1359-6454}, doi = {https://doi.org/10.1016/j.actamat.2024.120002}, url = {https://www.sciencedirect.com/science/article/pii/S1359645424003549}, author = {Emmeline Sheu and Tung Yan Liu and Darrick J. Williams and Jon K. Baldwin and Michael J. Demkowicz}, keywords = {Copper, Interdiffusion, Grain boundary, Transmission Kikuchi diffraction, Molecular dynamics}, abstract = {Low mutual solubility is expected to avert interdiffusion in layered composites of phase-separating metals. However, we show that Nb diffuses through polycrystalline Cu—despite the minimal bulk solubility of these elements—due to short circuit transport of Nb along certain grain boundaries in Cu. Atomistic modeling demonstrates that Nb-permeable Cu grain boundaries exhibit negative enthalpy of mixing of Nb, resulting in an enthalpically-stabilized solution of highly mobile Nb atoms that easily diffuse through the boundary. By contrast, Mo, which also has minimal solubility with Cu, has positive enthalpy of mixing at Nb-permeable Cu grain boundaries and does not diffuse through them. Our findings suggest material selection and grain boundary engineering as pathways for designing improved diffusion barriers and thermally stable laminate composites.} } @article{Galvez-Aranda_2022, doi = {10.1149/1945-7111/ac55c8}, url = {https://dx.doi.org/10.1149/1945-7111/ac55c8}, year = {2022}, month = {mar}, publisher = {IOP Publishing}, volume = {169}, number = {3}, pages = {030502}, author = {Diego E. Galvez-Aranda and Jorge M. Seminario}, title = {Li-Metal Anode in a Conventional Li-Ion Battery Electrolyte: Solid Electrolyte Interphase Formation using Ab Initio Molecular Dynamics}, journal = {Journal of The Electrochemical Society}, abstract = {Ab initio molecular dynamics simulations were performed for Li+ conducting electrolytes based on 1M lithium hexafluorophosphate (Li+ ) in ethylene carbonate (EC)-ethylmethyl carbonate (EMC) (3:7wt) with 5 wt% vinylene carbonate (VC) in contact with Li-metal (electrode), finding a variety of products due to dissociations of all electrolyte components. The formed solid electrolyte interphase from electrolyte degradation arranges in an outer layer composed of denser materials (sitting over the anode surface) such as Li2(CH2O)2 from EC, Li2CO3, Li2C2H2 and Li2CO2 from VC, and Li2C3H5O2 and LiCH3O from EMC dissociations. Then follows an inner layer made of Li-binary compounds, Li3CO, Li2O and Li3C from EC, Li2O, Li2C2 and LiH from VC, and LiF and Li3P from dissociations. We calculated electron affinities of electrolyte molecules during their decomposition using a polarizable continuum model to consider solvent effects molecules degradation. has the highest first and second electron affinities, despite explicit Coulomb repulsion, which eventually dissociates the molecule right after capturing an electron from the metal-anode; therefore, is also the fastest to dissociate. EMC has the lowest first and second electron affinities, thus it is the least prone to accept electrons and the least likely to dissociate at the Li-metal interface.} } @article{BORGESMARTINEZ2022120740, title = {Fullerene binding effects in Al(III)/Zn(II) Porphyrin/Phthalocyanine photophysical properties and charge transport}, journal = {Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy}, volume = {269}, pages = {120740}, year = {2022}, issn = {1386-1425}, doi = {https://doi.org/10.1016/j.saa.2021.120740}, url = {https://www.sciencedirect.com/science/article/pii/S1386142521013172}, author = {Merlys Borges-Martínez and Nicolás Montenegro-Pohlhammer and Xiance Zhang and Diego E. Galvez-Aranda and Victor Ponce and Jorge M. Seminario and Gloria Cárdenas-Jirón}, keywords = {Fullerene, Phthalocyanine, Porphyrin, Charge transport, Solar cells}, abstract = {We evaluate the fullerene C60 binding effect; through the metal (Al) and through the ligand (Pc,TPP), on the photophysical and charge transport properties of M−porphyrin(TPP)/phthalocyanine(Pc) (M = Al(III), Zn(II)). We perform density functional theory (DFT) and time-dependent DFT calculations for the macrocycle-C60 dyads, showing that all systems studied are thermodynamically favorable. The C60 binding effect on the absorption spectrum is a red-shift of the Q and Soret (B) bands of TPPs and Pcs. The Pc-dyads show longer λ for Q bands (673 nm) than those with TPP (568 nm). AlTPP-C60 and ZnTPP-C60 show a more favorable electron injection to TiO2 than the analogs Pcs, and the regeneration of the dye is preferred in AlTPP-C60 and AlPc-C60. Zero-bias conductance is computed (10-4–10-7 G0) for the dyads using molecular junctions with Au(111)-based electrodes. When a bias voltage of around 0.6 V up to 1 V is applied, an increase in current is obtained for AlTPP-C60 (10-7 A), ZnTPP-C60 (10-7 A), and AlPc-C60 (10-8 A). Although there is not a unique trend in the behavior of the dyads, Pcs have better photophysical properties than TPPs and the latter are better in the charge transport. We conclude that AlTPP(ZnTPP)-C60 dyads are an excellent alternative for designing new materials for dye-sensitized solar cells or optoelectronic devices.} } @article{Ye2024_1, doi = {10.1007/s41324-023-00553-x}, url = {https://doi.org/10.1007/s41324-023-00553-x}, year = {2024}, month = apr, publisher = {Springer Science and Business Media B.V.}, volume = {32}, number = {2}, pages = {195-206}, author = {Ye, X., Lian, X., Xu, H., Du, J., & Bao, S.}, title = {An integrated space–time framework for linkage discovery of big survey data}, journal = {Spatial Information Research} } @article{YE2024105223, title = {Enhancing population data granularity: A comprehensive approach using LiDAR, POI, and quadratic programming}, journal = {Cities}, volume = {152}, pages = {105223}, year = {2024}, month = jun, publisher = {Elsevier BV}, issn = {0264-2751}, doi = {https://doi.org/10.1016/j.cities.2024.105223}, url = {https://www.sciencedirect.com/science/article/pii/S0264275124004372}, author = {Xinyue Ye and Weishan Bai and Wenyu Wang and Xiao Huang}, keywords = {Population downscaling, LiDAR remote sensing, Microsoft building footprint, Quadratic programming, Monte Carlo simulation}, } @article{doi:10.1177/23998083231175681, author = {Ge Gao and Xinyue Ye and Shoujia Li and Xiao Huang and Huan Ning and David Retchless and Zhenlong Li}, title ={Exploring flood mitigation governance by estimating first-floor elevation via deep learning and google street view in coastal Texas}, journal = {Environment and Planning B: Urban Analytics and City Science}, volume = {51}, number = {2}, pages = {296-313}, year = {2024}, month = may, publisher = {Sage Publications}, doi = {10.1177/23998083231175681}, URL = {https://doi.org/10.1177/23998083231175681}, eprint = {https://doi.org/10.1177/23998083231175681}, } @article{HAN2024104953, title = {Retreat from flood zones: Simulating land use changes in response to compound flood risk in coastal communities}, journal = {Cities}, volume = {149}, pages = {104953}, year = {2024}, month = mar, issn = {0264-2751}, publisher = {Elsevier BV}, doi = {https://doi.org/10.1016/j.cities.2024.104953}, url = {https://www.sciencedirect.com/science/article/pii/S0264275124001677}, author = {Yu Han and Xinyue Ye and Kayode Atoba and Pallab Mozumder and Changjie Chen and Bastian {van den Bout} and Cees {van Westen}}, keywords = {Managed retreat, Land use simulation, Population growth, Sea level rise, Gradient boost machine}, abstract = {Coastal communities are increasingly vulnerable due to sea level rise and population growth. Managed retreat is commonly recognized as a strategy that yields multifaced benefits in community adaptation. However, limited studies have explored the cumulative effects of sea level rise, population migration, and managed retreat on the community resilience. This study presents a parcel-level land use change model to analysis land-based flood mitigation strategies in Galveston County, Texas. The developed model integrates a Gradient Boosting Decision Tree with a flood risk model and diverse datasets. Our model results reveal the spatial patterns of urban development in Galveston under different relocation policies and the compounding impacts of sea level rise and population growth. Our findings illustrate that elevating the first floors of buildings can significantly mitigate flood risks and associated relocation costs. The private adaptation measure, together with government-led buyout policies, could foster a shift toward more resilient urban development and yield a more affordable relocation strategy. Our findings emphasize the need for a multidisciplinary approach in building resilient coastal communities, particularly in the face of escalating climate risks in local communities.} } @inproceedings{10.1145/3557916.3567822, author = {Du, Jiaxin and Ye, Xinyue and Newman, Galen and Retchless, David}, title = {Network science-based urban forecast dashboard}, year = {2022}, month = nov, isbn = {9781450395304}, publisher = {Association for Computing Machinery}, address = {New York, NY, USA}, url = {https://doi.org/10.1145/3557916.3567822}, doi = {10.1145/3557916.3567822}, abstract = {The urban environment is a highly dynamic and complex system. Urban dynamics in this complex system is largely reflected by the movement of people to and from Places of Interest (POIs) in the urban area. To better understand and plan for the city's various scenarios, there is a need to forecast urban dynamic conditions in terms of the possible movements of people across POIs. However, such predictions are not easy because an interdependent and living system is hard to forecast. In addition, the commuting and shopping of individuals in urban environments will show distinct patterns at various stages of disasters as compared to normal situations.This paper presents a network science-based urban forecast dashboard, in order to monitor urban events and identify the interdependencies that characterize urban dynamics. Behind the dashboard is a deep learning model that incorporates the network dynamics between POIs. The dashboard powers the prediction of urban dynamics from a network science perspective. This research calls for a unified framework to model the flow and network in the city. The dashboard visualizes how network science and urban science can mutually benefit from each other.}, booktitle = {Proceedings of the 5th ACM SIGSPATIAL International Workshop on Advances in Resilient and Intelligent Cities}, pages = {7–10}, numpages = {4}, keywords = {dashboard, events, network science, resilience, urban forecast}, location = {Seattle, Washington}, series = {ARIC '22} } @article{doi:10.1177/23998083211064624, author = {Yang Song and Huan Ning and Xinyue Ye and Divya Chandana and Shaohua Wang}, title = {Analyze the usage of urban greenways through social media images and computer vision}, journal = {Environment and Planning B: Urban Analytics and City Science}, publisher = {Sage Publications}, volume = {49}, number = {6}, pages = {1682-1696}, year = {2022}, month = {jan}, doi = {10.1177/23998083211064624}, url = {https://doi.org/10.1177/23998083211064624}, } @article{Shaikh2024, author={Shaikh, Razeen and Larson, Nissa J. and Kam, Jayden and Hanjaya-Putra, Donny and Zartman, Jeremiah and Umulis, David M. and Li, Linlin and Reeves, Gregory T.}, title={Optimal performance objectives in the highly conserved bone morphogenetic protein signaling pathway}, journal={npj Systems Biology and Applications}, year={2024}, month={Sep}, day={14}, doi={https://doi.org/10.1038/s41540-024-00430-9}, } @article{https://doi.org/10.1029/2024GL110469, author = {Ren, Tong and Yang, Ping and Huang, Xianglei and Iwabuchi, Hironobu}, title = {Light Transfers Through a Koch Shape Cloud}, journal = {Geophysical Research Letters}, volume = {51}, number = {17}, pages = {e2024GL110469}, doi = {https://doi.org/10.1029/2024GL110469}, eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2024GL110469}, note = {e2024GL110469 2024GL110469}, abstract = {Abstract Modeling radiative transfer in a 3D cloudy atmosphere is critical to climate projections. A recently developed fast 3D radiation parameterization scheme gains some success in quantifying horizontal radiative transfer through cloud sides using cloud area fraction. Based on 3D Monte Carlo simulations of radiative transfer through an idealized single-layer cloud with Koch-shaped fractal geometry edges, here we show that radiative energy transport through cloud sides correlates more significantly with cloud area fraction than with cloud perimeter length. The results exemplify the importance of accounting for the horizontal radiative energy exchanges between cloud-free and cloudy regions with cloud area fraction. Results from additional sensitivity simulations show that increased cloud vertical extent often enhances cloud-side sunlight leak more significantly than cloud-side sunlight interception. At low sun elevations, cloud-side sunlight interception is enhanced more than cloud-side sunlight leak does with the increase of cloud mass.}, year = {2024} } @article{42f56f853eb84e4b89cd202d26864afb, title = "Factors influencing long-term city park visitations for mid-sized US cities: A big data study using smartphone user mobility", keywords = "Behavior monitoring, Health improvement, Long-term study, Mid-sized city, Mobility, Park visitation, Public health, Smartphone data", author = {Yang Song and Galen Newman and Xinke Huang and Xinyue Ye}, note = "Publisher Copyright: {textcopyright} 2022 Elsevier Ltd", year = "2022", month = may, doi = {10.1016/j.scs.2022.103815}, language = "English (US)", volume = "80", journal = "Sustainable Cities and Society", issn = "2210-6707", publisher = "Elsevier BV", } @article{10.1145/3618393, author = {Paliwal, Avinash and Nguyen, Brandon G. and Tsarov, Andrii and Kalantari, Nima Khademi}, title = {ReShader: View-Dependent Highlights for Single Image View-Synthesis}, year = {2023}, issue_date = {December 2023}, publisher = {Association for Computing Machinery}, address = {New York, NY, USA}, volume = {42}, number = {6}, issn = {0730-0301}, url = {https://doi.org/10.1145/3618393}, doi = {10.1145/3618393}, journal = {ACM Trans. Graph.}, month = dec, articleno = {216}, numpages = {9}, keywords = {neural network, relocation, reshading, view synthesis} } @article{MottadeCastro2024, author={Motta de Castro, Emile and Tabei, Ali and Cline, Daren B H and Haque, Ejaz and Chambers, Lindsay B and Song, Kenan and Perez, Lisa and Kalaitzidou, Kyriaki and Asadi, Amir}, title={New insights in understanding the fiber-matrix interface and its reinforcement behavior using single fiber fragmentation data}, journal={Advanced Composites and Hybrid Materials}, year={2024}, doi={10.1007/s42114-024-01054-7}, } @Article{atmos16010048, AUTHOR = {Wei, Shijin and Shores, Kyle and Xu, Yangyang}, TITLE = {A Comparison of Machine Learning-Based Approaches in Estimating Surface PM2.5 Concentrations Focusing on Artificial Neural Networks and High Pollution Events}, JOURNAL = {Atmosphere}, VOLUME = {16}, YEAR = {2025}, NUMBER = {1}, ARTICLE-NUMBER = {48}, URL = {https://www.mdpi.com/2073-4433/16/1/48}, ISSN = {2073-4433}, DOI = {10.3390/atmos16010048} }