检索结果-内蒙古大学图书馆

SSRN 2022年

作者： Clark, Eliza I. Stahlke, Amanda R. Gaskin, John F. Bean, Dan W. Hohenlohe, Paul A. Hufbauer, Ruth A. Bitume, Ellyn V. Graduate Degree Program in Ecology Department of Agricultural Biology Colorado State University 1177 Campus Delivery Fort CollinsCO80523 United States Initiative for Bioinformatics and Evolutionary Studies Department of Biological Sciences University of Idaho MoscowID United States Colorado Department of Agriculture PalisadeCO United States Institute of Pacific Islands Forestry Pacific Southwest Research Station USDA Forest Service Hilo HI United States U.S. Department of Agriculture Agricultural Research Service SidneyMT United States

Releasing several biotypes or species of biological control agent is common in many biological control programs. However, the consequences of hybridization for fitness and host use of the resulting hybrids are difficult to predict, especially for hybrids between more than two species and with varying levels of introgression. Hybridization of biocontrol agents may increase or decrease fitness, with consequences for control efficacy. Additionally, hybridization may lead to changes in host use patterns that may put non-target host species at increased risk. We collected genomic data to determine ancestry of individuals from ten locations across a hybrid zone of Diorhabda spp., the biological control agent of Tamarix spp. in North America. We paired genomic data with phenotypic data on fitness proxies of body size and early fecundity and host use for individuals from three of those sites. We found two originally released pure species and a wide range of introgression in hybrids between three Diorhabda species. Body size and early fecundity were similar in pure species and hybrids, indicating hybridization is not detrimental to insect fitness or the biocontrol program and may provide variation that allows populations to become locally adapted. Host use of hybrids was very similar to that of pure species, although some hybrid individuals had increased preference for Frankenia salina , a native non-target species. We find that hybridization has likely not been detrimental to the efficacy and safety of the Diorhabda biocontrol program, but possible impacts on F. salina should be monitored, considering ongoing hybridization and evolution in the field. © 2022, The Authors. All rights reserved.

关键词： Anthropometry

来源：评论

学校读者我要写书评

暂无评论

The dynamic immune behavior of primary and metastatic ovarian carcinoma

引用

npj Precision Oncology 2025年第1期9卷 1-12页

作者： Stur, Elaine Peng, Fuduan Teng, Pang-Ning Bayraktar, Emine Hu, Min Corvigno, Sara Brown, David J. Lee, Sanghoon Moore, Kathleen N. Bateman, Nicholas W. Darcy, Kathleen M. Maxwell, George L. P. Conrads, Thomas Sahni, Nidhi Vázquez-García, Ignacio Shah, Sohrab P. Celestino, Joseph D. Fleming, Nicole Navin, Nicholas E. Wang, Linghua Sood, Anil K. Department of Gynecologic Oncology and Reproductive Medicine The University of Texas MD Anderson Cancer Center Houston TX United States Department of Genomic Medicine The University of Texas MD Anderson Cancer Center Houston TX United States Gynecologic Cancer Center of Excellence The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc. Walter Reed National Military Medical Center Bethesda 20889 MD United States Department of Gynecologic Surgery and Obstetrics Uniformed Services University of the Health Sciences Walter Reed National Military Medical Center Bethesda MD United States Department of Genetics The University of Texas MD Anderson Cancer Center Houston TX United States Obstetrics and Gynecology Stephenson Cancer Center Stephenson Cancer Center at the University of Oklahoma Health Sciences Center/Sarah Cannon Research Institute Oklahoma City OK United States Women’s Health Integrated Research Center Women’s Service Line Inova Health System Falls Church VA United States Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Baylor College of Medicine Houston TX United States Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston TX United States Quantitative and Computational Biosciences Program Baylor College of Medicine Houston TX United States Computational Oncology Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY United States The Halvorsen Center for Computational Oncology Memorial Sloan Kettering Cancer Center Boston MA United States Irving Institute for Cancer Dynamics Columbia University Cambridge 10027 MA United States Department of Systems Biology The University of Texas MD Anderson Cancer Center Houston MA United States The James P. Allison Institute The University of Texas MD Anderson Cancer Center Houston 77030 TX United States The Institute for Data Sc

Patients with high-grade serous ovarian carcinoma (HGSC) are usually diagnosed with advanced-stage disease, and the tumors often have immunosuppressive characteristics. Together, these factors are important for disease progression, drug resistance, and mortality. In this study, we used a combination of single-cell sequencing and spatial transcriptomics to identify the molecular mechanisms that lead to immunosuppression in HGSC. Primary tumors consistently showed a more active immune microenvironment than did omental tumors. In addition, we found that untreated primary tumors were mostly populated by dysfunctional CD4 and CD8 T cells in later stages of differentiation;this, in turn, was correlated with expression changes in the interferon α and γ pathways in epithelial cells, showing that cross-communication between the epithelial and immune compartments is important for immune suppression in HGSC. These findings could have implications for the design of clinical trials with immune-modulating drugs. © The Author(s) 2025.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Tessellated granular metamaterials with tunable elastic moduli

arXiv

引用

arXiv 2023年

作者： Pashine, Nidhi Wang, Dong Zhang, Jerry Patiballa, Sree Kalyan Witthaus, Sven Shattuck, Mark D. O’Hern, Corey S. Kramer-Bottiglio, Rebecca Department of Mechanical Engineering & Materials Science Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States Graduate Program in Computational Biology & Bioinformatics Yale University New HavenCT06520 United States Benjamin Levich Institute Physics Department The City College of the City University of New York New YorkNY10031 United States

Most granular packings possess shear moduli (G) that increase with the applied external pressure, and bulk moduli (B) that increase or remain constant with pressure. This paper presents "tessellated" granular metamaterials for which both G and the ratio G/B decrease with increasing pressure. The granular metamaterials are made from flexible tessellations forming a ring of closed cells, each containing a small number of solid particles. For under-constrained tessellations, the dominant contributions to G and B are the particle-particle and particle-cell interactions. With specific particle configurations in the cells, we limit the number of possible particle rearrangements to achieve decreasing G as we increase the pressure difference between the inside and outside of the tessellation, leading to G/B 1 at large pressures. We further study tessellated granular metamaterials with cells containing a single particle and many particles to determine the variables that control the mechanical response of particle-filled tessellations as a function of pressure. © 2023, CC BY.

关键词： Metamaterials

来源：评论

学校读者我要写书评

暂无评论

Glycans on influenza hemagglutinin affect receptor binding and immune response

引用

Proceedings of the National Academy of Sciences of the United States of America 2009年第43期106卷 18137-18142页

作者： Wang, Cheng-Chi Chen, Juine-Ruey Tseng, Yung-Chieh Hsu, Che-Hsiung Hung, Yu-Fu Chen, Shih-Wei Chen, Chin-Mei Khoo, Kay-Hooi Cheng, Ting-Jen Cheng, Yih-Shyun E. Jan, Jia-Tsrong Wu, Chung-Yi Ma, Che Wong, Chi-Huey Genomics Research Center Taipei 115 Taiwan Institute of Biochemical Sciences National Taiwan University Taipei 106 Taiwan Institute of Biochemistry and Molecular Biology National Yang-Ming University Taipei 112 Taiwan Chemical Biology and Molecular Biophysics Taiwan International Graduate Program Taipei 115 Taiwan Institute of Bioinformatics and Structural Biology National Tsing Hua University Hsinchu 300 Taiwan Institute of Biological Chemistry Academia Sinica Taipei 115 Taiwan

Recent cases of avian influenza H5N1 and the swine-origin 2009 H1N1 have caused a great concern that a global disaster like the 1918 influenza pandemic may occur again. Viral transmission begins with a critical interaction between hemagglutinin (HA) glycoprotein, which is on the viral coat of influenza, and sialic acid (SA) containing glycans, which are on the host cell surface. To elucidate the role of HA glycosylation in this important interaction, various defined HA glycoforms were prepared, and their binding affinity and specificity were studied by using a synthetic SA microarray. Truncation of the N-glycan structures on HA increased SA binding affinities while decreasing specificity toward disparate SA ligands. The contribution of each monosaccharide and sulfate group within SA ligand structures to HA binding energy was quantitatively dissected. It was found that the sulfate group adds nearly 100-fold (2.04 kcal/mol) in binding energy to fully glycosylated HA, and so does the biantennary glycan to the monoglycosylated HA glycoform. Antibodies raised against HA protein bearing only a single N-linked GlcNAc at each glycosylation site showed better binding affinity and neutralization activity against influenza subtypes than the fully glycosylated HAs elicited. Thus, removal of structurally nonessential glycans on viral surface glycoproteins may be a very effective and general approach for vaccine design against influenza and other human viruses.

关键词： Flu vaccine Glycan binding Glycosylation

来源：评论

学校读者我要写书评

暂无评论

Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain

引用

细胞研究（英文版） 2022年第11期32卷 1008-1021页

作者： Yanxiao Zhang Maria Luisa Amaral Chenxu Zhu Steven Francis Grieco Xiaomeng Hou Lin Lin Justin Buchanan Liqi Tong Sebastian Preissl Xiangmin Xu Bing Ren Ludwig Institute for Cancer Research La JollaCAUSA School of Life Sciences Westlake UniversityHangzhouChina Bioinformatics and Systems Biology Graduate Program University of California San DiegoLa JollaCAUSA Ludwig Institute for Cancer Research La JollaCAUSA Department of Anatomy and Neurobiology School of MedicineUniversity of CaliforniaIrvineCAUSA Center for Epigenomics University of California San DiegoLa JollaCAUSA.6Institute of Experimental and Clinical Pharmacology and ToxicologyFaculty of MedicineUniversity of FreiburgFreiburgGermany Center for Epigenomics University of California San DiegoLa JollaCAUSA.6Institute of Experimental and Clinical Pharmacology and ToxicologyFaculty of MedicineUniversity of FreiburgFreiburgGermany The Center for Neural Circuit Mapping University of CaliforniaIrvineCAUSA Department of Anatomy and Neurobiology School of MedicineUniversity of CaliforniaIrvineCAUSA Department of Cellular and Molecular Medicine University of California San Diego School of MedicineLa JollaCAUSA Ludwig Institute for Cancer Research La JollaCAUSA Center for Epigenomics University of California San DiegoLa JollaCAUSA.6Institute of Experimental and Clinical Pharmacology and ToxicologyFaculty of MedicineUniversity of FreiburgFreiburgGermany institute for Genomic Medicine University of California San DiegoLa JollaCAUSA

Loss of heterochromatin has been implicated as a cause of pre-mature aging and age-associated decline in organ functions in mammals;however,the specific cell types and gene loci affected by this type of epigenetic change have remained *** address this knowledge gap,we probed chromatin accessibility at single-cell resolution in the brains,hearts,skeletal muscles,and bone marrows from young,middle-aged,and old mice,and assessed age-associated changes at 353,126 candidate cis-regulatory elements(cCREs)across 32 major cell ***,we detected increased chromatin accessibility within specific heterochromatin domains in old mouse excitatory *** gain of chromatin accessibility at these genomic loci was accompanied by the cell-type-specific loss of heterochromatin and activation of LINE1 *** further confirmed the loss of the heterochromatin mark H3K9me3 in the excitatory neurons but not in inhibitory neurons or glial *** results reveal the cell-type-specific changes in chromatin landscapes in old mice and shed light on the scope of heterochromatin loss in mammalian aging.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Array-Based High-Throughput Screening UNIT 5C.3 in Mouse Embryonic Stem Cells with shRNAs

引用

Current Protocols in Stem Cell Biology 2013年第SUPPL.26期1卷 5C.3.1-5C.3.19页

作者： Wang, Chia-Hui Ma, Nianhan Lin, Yu-Tsen Wu, Cheng-Chung Wu, Hong-Jin Yu, Ching-Chia Hsiao, Michael Lu, Frank Leigh Schuyler, Scott C. Lu, Jean Genomics Research Center Academia Sinica Taipei Taiwan Institute of Systems Biology and Bioinformatics National Central University Taoyuan Taiwan Graduate Institute of Life Sciences National Defense Medical Center Taipei Taiwan Department of Pediatrics National Taiwan University Hospital and National Taiwan University Medical College Taipei Taiwan Department of Biomedical Sciences College of Medicine Chang Gung University Taoyuan County Taiwan Genomics and System Biology Program College of Life Science National Taiwan University Taipei Taiwan National Core Facility Program for Biotechnology National RNAi Platform Taipei Taiwan

High-throughput short-hairpin RNA (shRNA) lentivirus screening is a powerful tool for identifying multiple functional regulators in embryonic stem cells (ESCs). shRNA libraries can efficiently down-regulate target genes persistently with high efficiency. The concurrent measurement of relative cell number by alamarBlue (AB) assay and undifferentiated ESC markers via an alkaline phosphatase (ALP) activity assay in the same cell culture well provides an efficient and economical way to pinpoint factors crucial for ESC pluripotency and/or expansion. Most of the renewal pathways affect ALP activity. Thus, multiple positive and negative regulators can be identified by this method. In addition, morphological changes and/or the expression levels of specific pluripotency or differentiation markers examined by immunofluorescence can be used as secondary screens for target-gene selection. In summary, we describe an efficient way to identify multiple regulators of ESC renewal using shRNAs. © 2013 by John Wiley & Sons, Inc.

关键词： Embryonic stem cells High-throughput screening RNA interference Short-hairpin RNA

来源：评论

学校读者我要写书评

暂无评论

Dynamic Hierarchical Skeleton-Based Network for Human Action Recognition in Video Content

SSRN

引用

SSRN 2024年

作者： Yang, Hualin Li, Xiying Chen, Calvin Yu-Chian Artificial Intelligence Medical Research Center School of Intelligent Systems Engineering Shenzhen Campus of Sun Yat-sen University Guangdong Shenzhen518107 China - Preferred Program Peking University Shenzhen Graduate School Guangdong Shenzhen518055 China School of Electronic and Computer Engineering Peking University Shenzhen Graduate School Guangdong Shenzhen518055 China Department of Medical Research China Medical University Hospital Taichung40447 Taiwan Department of Bioinformatics and Medical Engineering Asia University Taichung41354 Taiwan Guangdong Provincial Key Laboratory of Intelligent Transportation System Sun Yat-sen University Guangzhou China School of Intelligent Systems Engineering Sun Yat-sen University Guangdong Shenzhen518107 China

Human skeleton-based action recognition represents a pivotal field of study, capturing the intricate interplay between physical dynamics and intentional actions. Current research primarily focuses on extracting structural and temporal information from static skeleton-based graphs, but they grapple with a myriad of challenges. These include 1) an absence of hierarchical structure in encoding the skeleton-based graphs;2) A requirement for substantial prior knowledge to interpret the diverse spatial dynamics within singular action labels;3) An intricate task of representing the multifaceted temporal dynamics of individual actions. To counter this issue, we propose DHS-Net, an innovative dynamic hierarchical skeleton-based network in video content. The proposed DHS-Net incorporates the DHS Block as a central element, effectively facilitating information exchange through node concentration and diffusion across both structural and temporal dimensions. Through this architectural design, DHS-Net extracts hierarchical representations, enhancing the comprehensive understanding of spatio-temporal dynamics and marking a significant advancement in human action recognition. Our rigorous experimental evaluations further substantiate DHS-Net's supremacy, outperforming several state-of-the-art benchmarks in skeleton-based action recognition and achieving remarkable prediction accuracy. © 2024, The Authors. All rights reserved.

关键词： Dynamics

来源：评论

学校读者我要写书评

暂无评论

Analyses of protein cores reveal fundamental differences between solution and crystal structures

arXiv

引用

arXiv 2019年

作者： Mei, Zhe Treado, John D. Grigas, Alex T. Levine, Zachary A. Regan, Lynne O'Hern, Corey S. Integrated Graduate Program in Physical & Engineering Biology Yale University New HavenCT06520 United States Department of Chemistry Yale University New HavenCT06520 United States Department of Mechanical Engineering & Materials Science Yale University New HavenCT06520 United States Graduate Program in Computational Biology & Bioinformatics Yale University New HavenCT06520 United States Department of Pathology Yale University New HavenCT06520 United States Department of Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States Institute of Quantitative Biology Biochemistry and Biotechnology Center for Synthetic and Systems Biology School of Biological Sciences University of Edinburgh Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality protein structures solved by both methods. We also find significant differences between NMR and crystal structures|in the root-mean-square deviations of the Cα atomic positions, identities of core amino acids, backbone and sidechain dihedral angles, and packing fraction of core residues. In contrast to prior studies, we identify the physical basis for these differences by modelling protein cores as jammed packings of amino-acid-shaped particles. We find that we can tune the jammed packing fraction by varying the degree of thermalization used to generate the packings. For an athermal protocol, we find that the average jammed packing fraction is identical to that observed in the cores of protein structures solved by x-ray crystallography. In contrast, highly thermalized packing-generation protocols yield jammed packing fractions that are even higher than those observed in NMR structures. These results indicate that thermalized systems can pack more densely than athermal systems, which suggests a physical basis for the structural differences between protein structures solved by NMR and x-ray crystallography. Copyright © 2019, The Authors. All rights reserved.

关键词： X ray crystallography

来源：评论

学校读者我要写书评

暂无评论

Assessment of scoring functions for computational models of protein-protein interfaces

arXiv

引用

arXiv 2024年

作者： Sumner, Jacob Meng, Grace Brandt, Naomi Grigas, Alex T. Córdoba, Andrés Shattuck, Mark D. O’Hern, Corey S. Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Department of Chemistry Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States Department of Chemistry Duke University DurhamNC27708 United States Department of Physics Duke University DurhamNC27708 United States Benjamin Levich Institute Physics Department City College of New York New YorkNY10031 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

A goal of computational studies of protein-protein interfaces (PPIs) is to predict the binding site between two monomers that form a heterodimer. The simplest version of this problem is to rigidly re-dock the bound forms of the monomers, which involves generating computational models of the heterodimer and then scoring them to determine the most native-like models. Scoring functions have been assessed previously using rank- and classification-based metrics, however, these methods are sensitive to the number and quality of models in the scoring function training set. We assess the accuracy of seven PPI scoring functions by comparing their scores to a measure of structural similarity to the x-ray crystal structure (i.e. the DockQ score) for a non-redundant set of heterodimers from the Protein Data Bank. For each heterodimer, we generate re-docked models uniformly sampled over DockQ and calculate the Spearman correlation between the PPI scores and DockQ. For some targets, the scores and DockQ are highly correlated;however, for many targets, there are weak correlations. Several physical features can explain the difference between difficult- and easy-to-score targets. For example, strong correlations exist between the score and DockQ for targets with highly intertwined monomers and many interface contacts. We also develop a new score based on only three physical features that matches or exceeds the performance of current PPI scoring functions. These results emphasize that PPI prediction can be improved by focusing on correlations between the PPI score and DockQ and incorporating more discriminating physical features into PPI scoring functions. © 2024, CC BY.

关键词： Monomers

来源：评论

学校读者我要写书评

暂无评论

Using physical features of protein core packing to distinguish real proteins from decoys

arXiv

引用

arXiv 2020年

作者： Grigas, Alex T. Mei, Zhe Treado, John D. Levine, Zachary A. Regan, Lynne O'Hern, Corey S. Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Department of Chemistry Yale University New HavenCT06520 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Pathology Yale University New HavenCT06520 United States Department of Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States Institute of Quantitative Biology Biochemistry and Biotechnology Centre for Synthetic and Systems Biology School of Biological Sciences University of Edinburgh Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical features that specify a real protein. For example, it has long been appreciated that the hydrophobic cores of proteins contribute signifficantly to their stability. As a dataset of decoys to compare with real protein structures, we studied submissions to the bi-annual CASP competition (speciffically CASP11, 12, and 13), in which researchers attempt to predict the structure of a protein only knowing its amino acid sequence. Our analysis reveals that many of the submissions possess cores that do not recapitulate the features that define real proteins. In particular, the model structures appear more densely packed (because of energetically unfavorable atomic overlaps), contain too few residues in the core, and have improper distributions of hydrophobic residues throughout the structure. Based on these observations, we developed a deep learning method, which incorporates key physical features of protein cores, to predict how well a computational model recapitulates the real protein structure without knowledge of the structure of the target sequence. By identifying the important features of protein structure, our method is able to rank decoys from the CASP competitions equally well, if not better than, state-of-the-art methods that incorporate many additional features. Copyright © 2020, The Authors. All rights reserved.

关键词： Proteins

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：