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arXiv 2020年

作者： Tuckman, Philip J. VanderWerf, Kyle Yuan, Ye Zhang, Shiyun Zhang, Jerry Shattuck, Mark D. O’Hern, Corey S. Department of Physics Yale University New HavenCT06520 United States Department of Mechanics and Engineering Science College of Engineering Peking University Beijing100871 China Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Benjamin Levich Institute and Physics Department City College of New York New YorkNY10031 United States Department of Physics Yale University Department of Applied New HavenCT06520 United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States

We investigate the mechanical response of packings of purely repulsive, frictionless disks to quasistatic deformations. The deformations include simple shear strain at constant packing fraction and at constant pressure, "polydispersity" strain (in which we change the particle size distribution) at constant packing fraction and at constant pressure, and isotropic compression. For each deformation, we show that there are two classes of changes in the interparticle contact networks: jump changes and point changes. Jump changes occur when a contact network becomes mechanically unstable, particles "rearrange", and the potential energy (when the strain is applied at constant packing fraction) or enthalpy (when the strain is applied at constant pressure) and all derivatives are discontinuous. During point changes, a single contact is either added to or removed from the contact network. For repulsive linear spring interactions, second- and higher-order derivatives of the potential energy/enthalpy are discontinuous at a point change, while for Hertzian interactions, third- and higher-order derivatives of the potential energy/enthalpy are discontinuous. We illustrate the importance of point changes by studying the transition from a hexagonal crystal to a disordered crystal induced by applying polydispersity strain. During this transition, the system only undergoes point changes, with no jump changes. We emphasize that one must understand point changes, as well as jump changes, to predict the mechanical properties of jammed packings. Copyright © 2020, The Authors. All rights reserved.

关键词： Potential energy

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Metagenomic analysis reveals the roles of Actinobacteria in plasticizer-contaminated landfills and aids in identifying key degraders

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Scientific reports 2025年第1期15卷 18157页

作者： Adisan Rungsihiranrut Chanokporn Muangchinda Onruthai Pinyakong International Postgraduate Programs in Hazardous Substance and Environmental Management Graduate School Chulalongkorn University Bangkok 10330 Thailand. Center of Excellence in Microbial Technology for Marine Pollution Treatment (MiTMaPT) Department of Microbiology Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. Center of Excellence in Microbial Technology for Marine Pollution Treatment (MiTMaPT) Department of Microbiology Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. onruthai.p@chula.ac.th. Research Program on Remediation Technologies for Petroleum Contamination Center of Excellence on Hazardous Substance Management (HSM) Bangkok 10330 Thailand. onruthai.p@chula.ac.th. Omics Sciences and Bioinformatics Center Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. onruthai.p@chula.ac.th. Department of Microbiology Faculty of Science Chulalongkorn University Bangkok 10330 Thailand. onruthai.p@chula.ac.th.

Phthalate ester (PAE) contamination, particularly from dibutyl phthalate (DBP) and di-2-ethylhexyl phthalate (DEHP), originating from landfills and released into the environment, poses a significant concern. Understanding PAE biodegradation is crucial for developing bioremediation strategies. This study used cover material from a 1-month-old landfill for soil microcosms. Indigenous microbes effectively removed 300 mg kg of DBP and DEHP as individual and mixed substrates, achieving complete DBP removal and 70% DEHP removal at room temperature (27-30 °C) and 37 °C. Actinobacteria were dominant, indicating potential active PAE-degraders. Shotgun metagenomic analysis revealed an increased abundance of potential PAE catabolic genes, such as those encoding esterase, lipase, and dioxygenase, under all conditions, mainly associated with Streptomyces, Saccharopolyspora, Nocardia, Nocardioides, and Amycolatopsis. The genes associated with Saccharopolyspora were abundant at 37 °C, while those related to Nocardia and Actinomadura were prevalent at room temperature, suggesting temperature preferences. The genera Saccharopolyspora and Actinomadura have not been linked to PAE degradation, indicating potential novel PAE degraders. Furthermore, PAE-degrading bacteria were isolated using media designed from metagenomic data and were categorized into Streptomyces, Amycolatopsis, and Nocardia. This work highlights the roles of rare taxa and provides insights into potential novel PAE degraders, emphasizing the need for further research into these organisms.

关键词： Bioremediation PAE biodegradation pathway Plasticizer Shotgun sequencing Soil microcosm

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Comparing the Efficacy and Safety of Treating Chronic Hepatitis B Infection during Pregnancy with Lamivudine,Telbivudine,and Tenofovir:A Meta-analysis

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Journal of Clinical and Translational Hepatology 2019年第3期7卷 197-212页

作者： Shahnaz Sali Mohammad Darvishi Mojtaba GhasemiAdl Meisam Akhlaghdoust Azin Mirzazadeh Somayeh Elikaei Behjati Hossein Sheikh-Zeinolabedini Shervin Shokouhi Soheil Tavakolpour Infectious Diseases and Tropical Medicine Research Center Shahid Beheshti University of Medical SciencesTehranIran Department of Aerospace and Subaquatic Medicine Infectious Diseases and Tropical Medicine Research Center(IDTMRC)AJA University of Medical SciencesTehranIran Pharmaceutical Sciences Research Center Tehran University of Medical SciencesTehranIran Pars Advanced and Minimally Invasive Medical Manners Research Center Pars HospitalIran University of Medical SciencesTehranIran Joint Bioinformatics Graduate Program University of Arkansas Little Rock and University of Arkansas for Medical SciencesLittle RockARUSA The Genetics Department at Islamic Azad University Science and Research BranchTehranIran Infectious Diseases and Tropical Medicine Research Center Shahid Beheshti University of Medical SciencesTehran 198396-3113Iran

Background and Aims:The perinatal transmission of hepatitis B virus(HBV)remains an important global health ***,a systematic review and meta-analysis were conducted to evaluate the evidence regarding the efficacy and maternal/fetal safety of treating pregnant women with lamivudine,telbivudine(LdT),and tenofovir(TDF).Methods:A PubMed and Scopus search resulted in 1,076 records,which were reduced to 36,containing 7,717 pregnant women with chronic HBV infection and 7467 infants meeting the inclusion *** latest search was in August ***:Treatment with LdT,but not lamivudine and TDF,could significantly reduce the hepatitis B virus surface antigen-positive rate(odds ratio(OR)=0.37)in infants;it also led to higher rates of hepatitis B e antigen loss(OR=12.14),hepatitis B e antigen seroconversion(OR=8.93),and alanine aminotransferase normalization in mothers(OR=1.49).Each of these treatments was able to significantly reduce HBV DNA positivity at birth(total OR=0.19)and mother-to-child-transmission of HBV(total OR=0.15),and to cause higher rates of HBV DNA suppression in mothers(total OR=25.53).However,nucleos(t)ide analogues might also be involved in creatine kinase elevation(total OR=7.48).In contrast,no significant association was found between nucleos(t)ide analogue therapy and preterm/premature births,congenital malformation,low birth weight,and abortion or fetal/infant *** results suggested LdT's high capability of preventing ***,TDF failed to show significant associations to a reduced risk of mother-to-child-transmission,probably due to the low number of patients ***:Although using either lamivudine,LdT,orTDF could lead to more favorable maternal/fetal outcomes,LdT seemed to show more potential in resolving certain infant-and maternal-related *** studies on the safety profile of such treatments are required.

关键词： Hepatitis B virus Antiviral therapy Tenofovir Telbivudine Lamivudine Nucleos(t)ide analogues Pregnancy

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Pinned, locked, pushed, and pulled traveling waves in structured environments

arXiv

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arXiv 2018年

作者： Wang, Ching-Hao Matin, Sakib George, Ashish B. Korolev, Kirill S. Department of Physics Boston University BostonMA02215 United States Department of Physics and Graduate Program in Bioinformatics Boston University BostonMA02215

Traveling fronts describe the transition between two alternative states in a great number of physical and biological systems. Examples include the spread of beneficial mutations, chemical reactions, and the invasions by foreign species. In homogeneous environments, the alternative states are separated by a smooth front moving at a constant velocity. This simple picture can break down in structured environments such as tissues, patchy landscapes, and microfluidic devices. Habitat fragmentation can pin the front at a particular location or lock invasion velocities into specific values. Locked velocities are not sensitive to moderate changes in dispersal or growth and are determined by the spatial and temporal periodicity of the environment. The synchronization with the environment results in discontinuous fronts that propagate as periodic pulses. We characterize the transition from continuous to locked invasions and show that it is controlled by positive density-dependence in dispersal or growth. We also demonstrate that velocity locking is robust to demographic and environmental fluctuations and examine stochastic dynamics and evolution in locked invasions. Copyright © 2018, The Authors. All rights reserved.

关键词： Velocity

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An Improved Version of Texture-based Foreground Segmentation: Block-based Adaptive Segmenter 3

An Improved Version of Texture-based Foreground Segmentation...

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3rd International Conference on Computer Science and Computational Intelligence, ICCSCI 2018

作者： Muchtar, Kahlil Rahman, Faris Cenggoro, Tjeng Wawan Budiarto, Arif Pardamean, Bens Nodeflux Inc. Jakarta Indonesia Syiah Kuala University Aceh Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia

Foreground segmentation is one of moving object detection techniques of computer vision applications. To date, modern moving object detection methods require complex background modeling and thresholds tuning to confront illumination changes. This paper proposes an adaptive approach based on non-overlapping block texture representation. It aims to design a computationally light and efficient solution to improve the robustness of detection. We evaluate our proposed method on internal and public sequences and provide the quantitative and qualitative measurements. Experimental results show that the proposed method can improve the results of previous method and suitable for real-time challenges. © 2018 The Authors. Published by Elsevier Ltd.

关键词： Textures

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Glycyrrhizic acid conjugates with amino acid methyl esters target the main protease, exhibiting antiviral activity against wild-type and nirmatrelvir-resistant SARS-CoV-2 variants

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Antiviral research 2024年 227卷 105920页

作者： Uyen Nguyen Phuong Le Yu-Jen Chang Chih-Hao Lu Yeh Chen Wen-Chi Su Shao-Ting Chao Lia A Baltina Svetlana F Petrova Sin-Rong Li Mien-Chie Hung Michael M C Lai Lidia A Baltina Cheng-Wen Lin Graduate Institute of Biological Science and Technology China Medical University Taichung Taiwan Department of Medical Laboratory Science and Biotechnology China Medical University Taichung Taiwan. The Ph.D. Program of Biotechnology and Biomedical Industry China Medical University Taichung Taiwan. The Ph.D. Program of Biotechnology and Biomedical Industry China Medical University Taichung Taiwan Institute of Bioinformatics and Systems Biology National Yang Ming Chiao Tung University Hsinchu Taiwan Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu Taiwan. Department of Food Science and Biotechnology National Chung Hsing University Taichung 402 Taiwan. Graduate Institute of Biomedical Sciences China Medical University Taichung Taiwan. Ufa Institute of Chemistry Ufa Federal Research Center of the Russian Academy of Sciences Russia. Department of Laboratory Medicine China Medical University Hospital Taichung 404327 Taiwan. Research Center for Cancer Biology China Medical University Taichung 404327 Taiwan Center for Molecular Medicine China Medical University Hospital Taichung 404327 Taiwan. Institute of Molecular Biology Academia Sinica Taipei 115201 Taiwan. Ufa Institute of Chemistry Ufa Federal Research Center of the Russian Academy of Sciences Russia. Electronic address: baltina@anrb.ru. Department of Medical Laboratory Science and Biotechnology China Medical University Taichung Taiwan Graduate Institute of Biomedical Sciences China Medical University Taichung Taiwan Department of Medical Laboratory Science and Biotechnology Asia University Taichung Taiwan. Electronic address: cwlin@mail.cmu.edu.tw.

COVID-19 pandemic is predominantly caused by SARS-CoV-2, with its main protease, Mpro, playing a pivotal role in viral replication and serving as a potential target for inhibiting different variants. In this study, potent Mpro inhibitors were identified from glycyrrhizic acid (GL) derivatives with amino acid methyl/ethyl esters. Out of the 17 derivatives semisynthesized, Compounds 2, 6, 9, and 15, with methionine methyl esters, D-tyrosine methyl esters, glutamic acid methyl esters, and methionines in the carbohydrate moiety, respectively, significantly inhibited wild-type SARS-CoV-2 Mpro-mediated proteolysis, with IC50 values ranging from 0.06 μM to 0.84 μM. They also demonstrated efficacy in inhibiting trans-cleavage by mutant Mpro variants (Mpro_P132H, Mpro_E166V, Mpro_P168A, Mpro_Q189I), with IC50 values ranging from 0.05 to 0.92 μM, surpassing nirmatrelvir (IC50: 1.17-152.9 μM). Molecular modeling revealed stronger interactions with Valine166 in the structural complex of Mpro_E166V with the compounds compared to nirmatrelvir. Moreover, these compounds efficiently inhibited the post-entry viral processes of wild-type SARS-CoV-2 single-round infectious particles (SRIPs), mitigating viral cytopathic effects and reducing replicon-driven GFP reporter signals, as well as in vitro infectivity of wild-type, Mpro_E166V, and Mpro_Q189I SRIPs, with EC50 values ranging from 0.02 to 0.53 μM. However, nirmatrelvir showed a significant decrease in inhibiting the replication of mutant SARS-CoV-2 SRIPs carrying Mpro_E166V (EC50: >20 μM) and Mpro_Q189I (EC50: 13.2 μM) compared to wild-type SRIPs (EC50: 0.06 μM). Overall, this study identifies four GL derivatives as promising lead compounds for developing treatments against various SARS-CoV-2 strains, including Omicron, and nirmatrelvir-resistant variants.

关键词： Glycyrrhizic acid derivative Inhibitor Mpro Nirmatrelvir-resistant variant Omicron SARS-CoV-2

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Void distributions reveal structural link between jammed packings and protein cores

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Physical Review E 2019年第2期99卷 022416-022416页

作者： John D. Treado Zhe Mei Lynne Regan Corey S. O'Hern Department of Mechanical Engineering & Materials Science Yale University New Haven Connecticut 06520 USA Integrated Graduate Program in Physical & Engineering Biology Yale University New Haven Connecticut 06520 USA Department of Chemistry Yale University New Haven Connecticut 06520 USA Department of Molecular Biophysics & Biochemistry Yale University New Haven Connecticut 06520 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA

Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction ϕ≈0.56, which is the same as dense, random packing of amino-acid-shaped particles. In this article, we compare the structural properties of protein cores and jammed packings of amino-acid-shaped particles in much greater depth by measuring their local and connected void regions. We find that the distributions of surface Voronoi cell volumes and local porosities obey similar statistics in both systems. We also measure the probability that accessible, connected void regions percolate as a function of the size of a spherical probe particle and show that both systems possess the same critical probe size. We measure the critical exponent τ that characterizes the size distribution of connected void clusters at the onset of percolation. We find that the cluster size statistics are similar for void percolation in packings of amino-acid-shaped particles and randomly placed spheres, but different from that for void percolation in jammed sphere packings. We propose that the connected void regions are a defining structural feature of proteins and can be used to differentiate experimentally observed proteins from decoy structures that are generated using computational protein design software. This work emphasizes that jammed packings of amino-acid-shaped particles can serve as structural and mechanical analogs of protein cores, and could therefore be useful in modeling the response of protein cores to cavity-expanding and -reducing mutations.

关键词： Jamming Protein structure Packing & jamming problems Proteins Crystal structures Finite-size scaling Molecular dynamics Percolation theory

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Author Correction: Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease

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Nature communications 2023年第1期14卷 4370页

作者： Matteo D'Antonio Jennifer P Nguyen Timothy D Arthur Hiroko Matsui Agnieszka D'Antonio-Chronowska Kelly A Frazer Department of Pediatrics University of California San Diego La Jolla CA 92093 USA. madantonio@ucsd.edu. Division of Biomedical Informatics University of California San Diego La Jolla CA 92093 USA. madantonio@ucsd.edu. Institute of Genomic Medicine University of California San Diego 9500 Gilman Dr La Jolla CA 92093 USA. madantonio@ucsd.edu. Division of Biomedical Informatics University of California San Diego La Jolla CA 92093 USA. Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA 92093 USA. Biomedical Sciences Graduate Program University of California San Diego La Jolla CA 92093 USA. Institute of Genomic Medicine University of California San Diego 9500 Gilman Dr La Jolla CA 92093 USA. Department of Pediatrics University of California San Diego La Jolla CA 92093 USA. Department of Pediatrics University of California San Diego La Jolla CA 92093 USA. kafrazer@health.ucsd.edu. Institute of Genomic Medicine University of California San Diego 9500 Gilman Dr La Jolla CA 92093 USA. kafrazer@health.ucsd.edu.

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CollaboNet: Collaboration of deep neural networks for biomedical named entity recognition

arXiv

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arXiv 2018年

作者： Yoon, Wonjin So, Chan Ho Lee, Jinhyuk Kang, Jaewoo Department of Computer Science and Engineering Korea University Seoul02841 Korea Republic of Interdisciplinary Graduate Program in Bioinformatics Korea University Seoul02841 Korea Republic of

Background: Finding biomedical named entities is one of the most essential tasks in biomedical text mining. Recently, deep learning-based approaches have been applied to biomedical named entity recognition (BioNER) and showed promising results. However, as deep learning approaches need an abundant amount of training data, a lack of data can hinder performance. BioNER datasets are scarce resources and each dataset covers only a small subset of entity types. Furthermore, many bio entities are polysemous, which is one of the major obstacles in named entity recognition. Results: To address the lack of data and the entity type misclassification problem, we propose CollaboNet which utilizes a combination of multiple NER models. In CollaboNet, models trained on a different dataset are connected to each other so that a target model obtains information from other collaborator models to reduce false positives. Every model is an expert on their target entity type and takes turns serving as a target and a collaborator model during training time. The experimental results show that CollaboNet can be used to greatly reduce the number of false positives and misclassified entities including polysemous words. CollaboNet achieved state-of-the-art performance in terms of precision, recall and F1 score. Conclusions: We demonstrated the benefits of combining multiple models for BioNER. Our model has successfully reduced the number of misclassified entities and improved the performance by leveraging multiple datasets annotated for different entity types. Given the state-of-the-art performance of our model, we believe that CollaboNet can improve the accuracy of downstream biomedical text mining applications such as bio-entity relation extraction. Copyright © 2018, The Authors. All rights reserved.

关键词： Deep neural networks

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Characterization and expression of the microtubule associated protein tau gene isoforms and their impact on clinical outcomes in glioma patients

Computational and Structural Biotechnology Reports

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Computational and Structural Biotechnology Reports 2024年 1卷

作者： Axel M. Hidalgo Vipin Singh Thenral Mangadu Deblina Guha Enrique I. Ramos Chandrima Das Shrikanth S. Gadad Bioinformatics Program The University of Texas at El Paso USA Center of Emphasis in Cancer Department of Molecular and Translational Medicine Texas Tech University Health Sciences Center El Paso 130 Rick Francis st. El Paso TX 79905 USA Biophysics and Structural Genomics Division Saha Institute of Nuclear Physics 1/AF Bidhannagar Kolkata 700064 India Minority AIDS Research Center Department of Health Sciences The University of Texas at El Paso TX 79968 USA The University of Texas at El Paso TX 79968 USA HomiBhaba National Institute Mumbai 400094 India L. Frederick Francis Graduate School of Biomedical Sciences Texas Tech University Health Sciences Center El Paso 130 Rick Francis st. El Paso TX 79905 USA Mays Cancer Center UT Health San Antonio MD Anderson Cancer Center San Antonio TX 78229 USA

Gliomas are the most common tumors found in the central nervous system. They are classified based on their histopathological malignancy. Low-grade gliomas (LGG) can turn into glioblastomas (GBM), the most aggressive form of brain cancer with the worst prognosis. Previous studies have shown that microtubule-associated protein tau ( MAPT ) is increased in GBM and that reducing it can improve survival in animal models. On the other hand, elevated MAPT expression has been linked to increased survival in LGG, indicating its potential as a survival biomarker. However, previous studies have primarily focused on the canonical protein-coding transcripts and gene-level expression of MAPT , disregarding the diversity of its many isoforms. Many diseases in almost every tissue have been associated with a dysregulation of alternative splicing, either through an altered ratio of the expressed isoforms or by expressing aberrant transcripts with different alternative transcription start and termination sites. This study investigates the association of specific MAPT transcripts with survival in LGG and GBM using publicly available genomic datasets and performing statistical analyses. The results of the study indicated coding and several non-coding isoforms associated with overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI). After including the relevant predictors as covariates, it was observed that among the protein-coding isoforms, MAPT-205 and MAPT-201 were significantly associated with clinical survival endpoints, but with opposite trends. These findings highlight the importance of studying the role of MAPT isoforms in glioma cellular phenotypes, aggressiveness, and patient survival.

关键词： Transcription Gene expression Differential exon usage Isoforms

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