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arXiv 2022年

作者： Shan, Siyuan Baskaran, Vishal Athreya Yi, Haidong Ranek, Jolene Stanley, Natalie Oliva, Junier B. Department of Computer Science UNC Chapel Hill United States Computational Medicine Program Curriculum in Bioinformatics and Computational Biology UNC Chapel Hill United States Computational Medicine Program Department of Computer Science UNC Chapel Hill United States

Modern single-cell flow and mass cytometry technologies measure the expression of several proteins of the individual cells within a blood or tissue sample. Each profiled biological sample is thus represented by a set of hundreds of thousands of multidimensional cell feature vectors, which incurs a high computational cost to predict each biological sample’s associated phenotype with machine learning models. Such a large set cardinality also limits the interpretability of machine learning models due to the difficulty in tracking how each individual cell influences the ultimate prediction. We propose using Kernel Mean Embedding to encode the cellular landscape of each profiled biological sample. Although our foremost goal is to make a more transparent model, we find that our method achieves comparable or better accuracies than the state-of-the-art gating-free methods through a simple linear classifier. As a result, our model contains few parameters but still performs similarly to deep learning models with millions of parameters. In contrast with deep learning approaches, the linearity and sub-selection step of our model makes it easy to interpret classification results. Analysis further shows that our method admits rich biological interpretability for linking cellular heterogeneity to clinical phenotype. © 2022, CC0.

关键词： Forecasting

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Repurposing transfer learning strategy of computer vision for owl sound classification

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Procedia Computer Science 2023年 216卷 424-430页

作者： Kevin William Gunawan Alam Ahmad Hidayat Tjeng Wawan Cenggoro Bens Pardamean Computer Science Department BINUS Graduate Program – Master of Computer Science Bina Nusantara University Jakarta 11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta 11480 Indonesia

Accurately predicting an owl species based on its sound can be helpful for owl conservation. To build an accurate model for owl sound classification, deep learning is currently the most preferred algorithm, due to its excellent performance for modeling audio data. However, deep learning is generally underperformed for a small dataset, which is the case for recognizing scops owl sound. To overcome the issue, we proposed a transfer learning strategy, which is common for computer vision tasks, that can alleviate overfitting in a deep learning model for the owl sound classification. In our approach, we propose a neural network architecture consisting of the backbone of a EfficientNet model pre-trained on the massive ImageNet database. The model takes the sound input that has been converted as two image representations: Spectrogram and Mel Frequency Cepstral Coefficients. Our strategy enables the use of a relatively small size of pre-trained image classification model, which is widely available, for transfer learning in owl sound classification. Deploying the lightweight model in an automatic sound classifier provides a fast and accurate tool for various owl conservation purposes.

关键词： acoustics deep learning bird sound species detection transfer learning

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Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice

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Plant Communications 2022年第3期3卷 59-71页

作者： Haidong Yan David C.Haak Song Li Linkai Huang Aureliano Bombarely School of Plant and Environmental Sciences Virginia TechBlacksburgVA 24061USA Graduate Program in Genetics Bioinformatics and Computational Biology(GBCB)Virginia TechBlacksburgVA 24061USA Department of Grassland Science Animal Science and Technology CollegeSichuan Agricultural UniversityChengdu 611130China Department of Bioscience Universita degli Studi di Milano(UNIMI)20133 MilanoItaly Instituto de Biologıa Molecular y Celular de Plantas(IBMCP) UPV-CSIC46022 ValenciaSpain

Transposable elements(TEs)are a major force in the production of new alleles during domestication;nevertheless,their use in association studies has been limited because of their *** have developed a TE genotyping pipeline(TEmarker)and applied it to whole-genome genome-wide association study(GWAS)data from 176 Oryza sativa *** accessions to identify genetic elements associated with specific agronomic *** markers recovered a large proportion(69%)of single-nucleotide polymorphism(SNP)-based GWAS peaks,and these TE peaks retained ca.25%of the *** use of TEs in GWASs may reduce false positives associated with linkage disequilibrium(LD)among SNP markers.A genome scan revealed positive selection on TEs associated with agronomic *** found several cases of insertion and deletion variants that potentially resulted from the direct action of TEs,including an allele of LOC_Os11g08410 associated with plant height and panicle length ***,these findings reveal the utility of TE markers for connecting genotype to phenotype and suggest a potential role for TEs in influencing phenotypic variations in rice that impact agronomic traits.

关键词： transposable element marker agronomic trait rice GWAS

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Connecting polymer collapse and the onset of jamming

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Physical Review E 2024年第3期109卷 034406-034406页

作者： Alex T. Grigas Aliza Fisher Mark D. Shattuck Corey S. O'Hern Graduate Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut 06520 USA Department of Mechanical Engineering and Materials Science Yale University New Haven Connecticut 06520 USA Benjamin Levich Institute and Physics Department The City College of New York New York New York 10031 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA

Previous studies have shown that the interiors of proteins are densely packed, reaching packing fractions that are as large as those found for static packings of individual amino-acid-shaped particles. How can the interiors of proteins take on such high packing fractions given that amino acids are connected by peptide bonds and many amino acids are hydrophobic with attractive interactions? We investigate this question by comparing the structural and mechanical properties of collapsed attractive disk-shaped bead-spring polymers to those of three reference systems: static packings of repulsive disks, of attractive disks, and of repulsive disk-shaped bead-spring polymers. We show that the attractive systems quenched to temperatures below the glass transition T≪Tg and static packings of both repulsive disks and bead-spring polymers possess similar interior packing fractions. Previous studies have shown that static packings of repulsive disks are isostatic at jamming onset, i.e., the number of interparticle contacts Nc matches the number of degrees of freedom, which strongly influences their mechanical properties. We find that repulsive polymer packings are hypostatic at jamming onset (i.e., with fewer contacts than degrees of freedom) but are effectively isostatic when including stabilizing quartic modes, which give rise to quartic scaling of the potential energy with displacements along these modes. While attractive disk and polymer packings are often considered hyperstatic with excess contacts over the isostatic number, we identify a definition for interparticle contacts for which they can also be considered as effectively isostatic. As a result, we show that the mechanical properties (e.g., scaling of the potential energy with excess contact number and low-frequency contribution to the density of vibrational modes) of weakly attractive disk and polymer packings are similar to those of isostatic repulsive disk and polymer packings. Our results demonstrate that static

关键词： Jamming Polymer folding Protein folding Single polymer chains

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Influence of conformational change of chain unit on the intrinsic negative thermal expansion of polymers

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Chinese Chemical Letters 2021年第4期32卷 1515-1518页

作者： Qiangsheng Sun Ke Jin Yuhui Huang Jia Guo Thanyada Rungrotmongkol Phornphimon Maitarad Changchun Wang State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science Fudan UniversityShanghai 200433.China Biocatalyst and Environmental Biotechnology Research Unit Department of BiochemistryFaculty of Science and Program in Bioinformatics and Computational BiologyGraduate SchoolChulalongkom UniversityBangkok 10330Thailand Research Center of Nano Science and Technology Shanghai UniversityShanghai 200444China

Negative thermal expansion(NTE) behavior has roused wide interest for the control of thermomechanical properties of functional *** NTE behaviors have been found in kinds of compounds,it remains challenging for polymers to achieve intrinsic NTE *** this work,we systematically studied the conformational change of dibenzocyclooctadiene(DBCOD) derivatives between chair(C) and twist-boat(TB) forms based on density-functional theo ry(DFT) calculations,and found clear evidence of the relationship between the structure of DBCOD units and the thermal contraction behavior of the related *** order to obtain the polymer with NTE property,two conditions should be met for the thermal contracting DBCOD related units as follows:(i) the TB conformation can turn into C conformation as the temperature increases,and(ii) the volume of C conformation is smaller than that of TB *** rule should offer a guidance to exploration of the new intrinsic NTE polymers in the future.

关键词： Negative thermal expansion Conformational change Polyarylamides Density-functional theory Dibenzocyclooctadiene

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Correction: Diversity of sulfur cycling halophiles within the Salton Sea, California's largest lake

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BMC microbiology 2025年第1期25卷 225页

作者： Linton Freund Caroline Hung Talyssa M Topacio Charles Diamond Alyson Fresquez Timothy W Lyons Emma L Aronson Genetics Genomics and Bioinformatics Program University of California Riverside 900 University Ave Riverside CA 92521 USA. lintonfreund@***. Department of Microbiology and Plant Pathology University of California Riverside 900 University Ave Riverside CA 92521 USA. Department of Earth and Planetary Sciences University of California Riverside 900 University Ave Riverside CA 92521 USA.

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Construction and validation of a mouse model for studying severe human adenovirus infections

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Virologica Sinica 2024年第6期39卷 963-973页

作者： Dingbin Chen Yuqian Yan Ting Mei Peipei Yang Siqi Deng Yiqiang Li Tie Zhao Ning Xin Biyan Duan Weifeng Liang Yuemei Yang Wei Zhao Donald Seto Junxian Ou Qiwei Zhang Institute of Medical Microbiology Department of Immunology and MicrobiologyCollege of Life Science and TechnologyJinan UniversityGuangzhou510632China BSL-3 Laboratory(Guangdong) Guangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical UniversityGuangzhou510515China Department of Clinical Laboratory Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhou510620China South Yunnan Central Hospital(Honghe First People's Hospital) MengziYunnan661100China Bioinformatics and Computational Biology Program School of Systems BiologyGeorge Mason UniversityManassasVA20110USA The Affiliated Guangdong Second Provincial General Hospital of Jinan University Guangzhou510310China Key Laboratory of Viral Pathogenesis&Infection Prevention and Control(Jinan University) Ministry of EducationGuangzhou510632China

Human adenoviruses(HAdVs)are highly contagious pathogens with various genotypes implicated in acute respiratory disease(ARD)and linked to fatality,especially in immunosuppressed patients,young children,and military ***,no vaccines or specific drugs are approved for clinical *** hosts of adenoviruses are strictly species-specific,which strongly limits the development of vaccines and drugs against *** this study,immunocompetent BALB/c mice were challenged with different doses of human adenovirus type 5(HAdV-5)via tail intravenous injection(i.v.).All mice challenged with a high dose of HAdV-5(3.21010 TCID50/kg)died within 3–5 days,while those receiving a low dose of HAdV-5(8109 or 4109 TCID50/kg)***,among the mice receiving a medium dose of HAdV-5(1.61010 TCID50/kg),60%(n¼3/5)of male mice died,while all female mice *** suggests that male mice may be more susceptible to HAdV-5 infection than female mice,consistent with clinical findings in ***-5 DNA was mainly distributed in the liver,followed by the spleen and *** changes were observed in the lung,liver,and spleen,with severity increasing in correlation with the virus challenge *** and qPCR analyses of the liver indicated that the down-regulated expression of the H2-Aa,H2-Ea-ps,CD74,and H2-Eb1 genes in male mice,as well as the AHR gene in female mice,may contribute to the observed higher mortality rates in male ***,this effective,feasible,and costefficient mouse model could serve as a candidate for evaluating HAdV vaccines and anti-adenovirus therapeutics.

关键词： Human adenovirus type 5(HAdV-5) Animal model BALB/c mice Severe human adenovirus infections

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Diffusion curvature for estimating local curvature in high dimensional data 22

Diffusion curvature for estimating local curvature in high d...

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Proceedings of the 36th International Conference on Neural Information Processing Systems

作者： Dhananjay Bhaskar Kincaid MacDonald Oluwadamilola Fasina Dawson Thomas Bastian Rieck Ian Adelstein Smita Krishnaswamy Department of Genetics Yale University Department of Mathematics Yale University Applied Mathematics Program Yale University Department of Mathematics Department of Physics Yale University Institute of AI for Health Helmholtz Pioneer Campus Helmholtz Munich Department of Computer Science Department of Genetics Applied Mathematics Program Program for Computational Biology and Bioinformatics Yale University

ISBN: (纸本)9781713871088

We introduce a new intrinsic measure of local curvature on point-cloud data called diffusion curvature. Our measure uses the framework of diffusion maps, including the data diffusion operator, to structure point cloud data and define local curvature based on the laziness of a random walk starting at a point or region of the data. We show that this laziness directly relates to volume comparison results from Riemannian geometry. We then extend this scalar curvature notion to an entire quadratic form using neural network estimations based on the diffusion map of point-cloud data. We show applications of both estimations on toy data, single-cell data and on estimating local Hessian matrices of neural network loss landscapes.

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Juntas Contra el Virus del Papiloma Humano: protocol for a pilot randomized controlled trial of an HPV self-sampling intervention for underscreened Latinas

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Pilot and feasibility studies 2025年第1期11卷 65页

作者： Carolyn Y Fang Marisol Cora-Cruz Pratistha Koirala Sophia Perez Minzi Li Brian L Egleston Yuku Chen Gina Mantia-Smaldone Omar Martinez Cancer Prevention and Control Program Fox Chase Cancer Center 333 Cottman Ave. Philadelphia PA 19111 USA. carolyn.fang@fccc.edu. Cancer Prevention and Control Program Fox Chase Cancer Center 333 Cottman Ave. Philadelphia PA 19111 USA. Department of Gynecologic Oncology Fox Chase Cancer Center Philadelphia PA USA. Biostatistics and Bioinformatics Facility Fox Chase Cancer Center Philadelphia PA USA. College of Medicine University of Central Florida Orlando FL USA.

BACKGROUND:Rates of cervical cancer incidence and mortality are persistently higher among Latina women in the continental United States (US) and women in Puerto Rico (a US territory) compared with non-Hispanic White (NHW) women. Multiple factors contribute to low participation in cancer screening, including structural barriers (e.g., low access to healthcare services, racism/discrimination, lack of culturally and linguistically adequate information), cultural concerns, and low perceived risk and awareness of cervical cancer. Although community-based education and navigation support can be effective in overcoming some barriers to screening, structural barriers and limited access remain formidable challenges to overcome. Emerging technologies supporting self-sampling for high-risk human papillomavirus (HPV) testing may offer a valuable evidence-based strategy for empowering Latina women to engage in cervical cancer screening. Thus, the objective of this study is to assess the feasibility and acceptability of a novel HPV self-sampling intervention for underscreened Latina women. METHODS:The study will be a randomized controlled feasibility trial involving 100 Latina women who have not received cervical cancer screening within the recommended guidelines. Participants will be randomly assigned to the intervention condition, which includes a synchronous three-session group cervical cancer educational program delivered virtually along with a mailed HPV self-sampling kit (to obtain self-collected cervical samples for HPV testing), or to a comparison condition that involves receipt of the mailed HPV self-sampling kit with written information about cervical cancer screening and nearby clinics. Study assessments will be obtained at baseline (i.e., study entry) and 1-month post-program. The primary outcome of feasibility will be measured through study enrollment and intervention completion. In addition, acceptability of study materials and the self-sampling procedures will be a

关键词： Cervical cancer Human papillomavirus (HPV) Latinas Screening Self-sampling

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Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events

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Signal Transduction and Targeted Therapy 2022年第5期7卷 1808-1816页

作者： Junxian Ou Wendong Lan Xiaowei Wu Tie Zhao Biyan Duan Peipei Yang Yi Ren Lulu Quan Wei Zhao Donald Seto James Chodosh Zhen Luo Jianguo Wu Qiwei Zhang Guangdong Provincial Key Laboratory of Virology Institute of Medical MicrobiologyJinan University510632 GuangzhouChina BSL-3 Laboratory(Guangdong) Guangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical University510515 GuangzhouChina Bioinformatics and Computational Biology Program School of Systems BiologyGeorge Mason UniversityManassasVA 20110USA Department of Ophthalmology Howe Laboratory Massachusetts Eye and EarHarvard Medical SchoolBostonMA 02114USA Foshan Institute of Medical Microbiology 528315 FoshanChina

The current pandemic of COVID-19 is fueled by more infectious emergent Omicron *** concerns of emergent variants include possible recombinants,as genome recombination is an important evolutionary mechanism for the emergence and re-emergence of human viral *** this study,we identified diverse recombination events between two Omicron major subvariants(BA.1 and BA.2)and other variants of concern(VOCs)and variants of interest(VOIs),suggesting that co-infection and subsequent genome recombination play important roles in the ongoing evolution of *** scanning high-quality completed Omicron spike gene sequences.

关键词： subsequent diverse recombination

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