arXiv - QuanBio - Other Quantitative Biology最新文献_第8页

Ten simple rules for collaborating with wet lab researchers for computational researchers 计算研究人员与湿实验室研究人员合作的十条简单规则

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-02-27 DOI: arxiv-2402.18348

Mark D. Robinson, Peiying Cai, Martin Emons, Reto Gerber, Pierre-Luc Germain, Samuel Gunz, Siyuan Luo, Giulia Moro, Emanuel Sonder, Anthony Sonrel, Jiayi Wang, David Wissel, Izaskun Mallona

引用次数: 0

RAM-EHR: Retrieval Augmentation Meets Clinical Predictions on Electronic Health Records RAM-EHR：检索增强满足电子健康记录的临床预测

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-02-25 DOI: arxiv-2403.00815

Ran Xu, Wenqi Shi, Yue Yu, Yuchen Zhuang, Bowen Jin, May D. Wang, Joyce C. Ho, Carl Yang

引用次数: 0

Implications of self-identified race, ethnicity, and genetic ancestry on genetic association studies in biobanks within health systems 自我认定的种族、民族和遗传祖先对卫生系统内生物库遗传关联研究的影响

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-02-24 DOI: arxiv-2402.15696

Ruth Johnson, Bogdan Pasaniuc

{"title":"Implications of self-identified race, ethnicity, and genetic ancestry on genetic association studies in biobanks within health systems","authors":"Ruth Johnson, Bogdan Pasaniuc","doi":"arxiv-2402.15696","DOIUrl":"https://doi.org/arxiv-2402.15696","url":null,"abstract":"Precision medicine aims to create biomedical solutions tailored to specific\u0000factors that affect disease risk and treatment responses within the population.\u0000The success of the genomics era and recent widespread availability of\u0000electronic health records (EHR) has ushered in a new wave of genomic biobanks\u0000connected to EHR databases (EHR-linked biobanks). This perspective aims to\u0000discuss how race, ethnicity, and genetic ancestry are currently utilized to\u0000study common disease variation through genetic association studies. Although\u0000genetic ancestry plays a significant role in shaping the genetic landscape\u0000underlying disease risk in humans, the overall risk of a disease is caused by a\u0000complex combination of environmental, sociocultural, and genetic factors. When\u0000using EHR-linked biobanks to interrogate underlying disease etiology, it is\u0000also important to be aware of how the biases associated with commonly used\u0000descent-associated concepts such as race and ethnicity can propagate to\u0000downstream analyses. We intend for this resource to support researchers who\u0000perform or analyze genetic association studies in the EHR-linked biobank\u0000setting such as those involved in consortium-wide biobanking efforts. We\u0000provide background on how race, ethnicity, and genetic ancestry play a role in\u0000current association studies, highlight considerations where there is no\u0000consensus about best practices, and provide transparency about the current\u0000shortcomings.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139979259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Evolution of Raw Data Archiving and the Growth of Its Importance in Crystallography 原始数据存档的演变及其在晶体学中重要性的提升

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-02-23 DOI: arxiv-2402.16652

John R. Helliwell, James R. Hester, Loes Kroon-Batenburg, Brian McMahon, Selina L. S. Storm

引用次数: 0

Effect of Rootstock on Some Aspects of Pistachio (Pistacia vera L.): A Review 砧木对楷树某些方面的影响：综述

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-02-22 DOI: arxiv-2402.14896

Aram Akram Mohammed, Fakhraddin Mustafa Hama Salih

引用次数: 0

The affinity-efficacy problem: an essential part of pharmacology education 亲和力-效能问题：药理学教育的重要组成部分

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-02-21 DOI: arxiv-2402.14617

James P Higham, David Colquhoun

引用次数: 0

Gradients of brain organization: Smooth sailing from methods development to user community 大脑组织的梯度：从方法开发到用户社区的顺利进行

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-02-16 DOI: arxiv-2402.11055

Jessica Royer, Casey Paquola, Sofie L. Valk, Matthias Kirschner, Seok-Jun Hong, Bo-yong Park, Richard A. I. Bethlehem, Robert Leech, B. T. Thomas Yeo, Elizabeth Jefferies, Jonathan Smallwood, Daniel Margulies, Boris C. Bernhardt

{"title":"Gradients of brain organization: Smooth sailing from methods development to user community","authors":"Jessica Royer, Casey Paquola, Sofie L. Valk, Matthias Kirschner, Seok-Jun Hong, Bo-yong Park, Richard A. I. Bethlehem, Robert Leech, B. T. Thomas Yeo, Elizabeth Jefferies, Jonathan Smallwood, Daniel Margulies, Boris C. Bernhardt","doi":"arxiv-2402.11055","DOIUrl":"https://doi.org/arxiv-2402.11055","url":null,"abstract":"Multimodal neuroimaging grants a powerful in vivo window into the structure\u0000and function of the human brain. Recent methodological and conceptual advances\u0000have enabled investigations of the interplay between large-scale spatial\u0000trends, or gradients, in brain structure and function, offering a framework to\u0000unify principles of brain organization across multiple scales. Strong community\u0000enthusiasm for these techniques has been instrumental in their widespread\u0000adoption and implementation to answer key questions in neuroscience. Following\u0000a brief review of current literature on this framework, this perspective paper\u0000will highlight how pragmatic steps aiming to make gradient methods more\u0000accessible to the community propelled these techniques to the forefront of\u0000neuroscientific inquiry. More specifically, we will emphasize how interest for\u0000gradient methods was catalyzed by data sharing, open-source software\u0000development, as well as the organization of dedicated workshops led by a\u0000diverse team of early career researchers. To this end, we argue that the\u0000growing excitement for brain gradients is the result of coordinated and\u0000consistent efforts to build an inclusive community and can serve as a case in\u0000point for future innovations and conceptual advances in neuroinformatics. We\u0000close this perspective paper by discussing challenges for the continuous\u0000refinement of neuroscientific theory, methodological innovation, and real-world\u0000translation to maintain our collective progress towards integrated models of\u0000brain organization.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139910540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Brief overview on Bacteriophage therapy; Alternative to Antibiotics 噬菌体疗法简介；抗生素的替代疗法

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-02-15 DOI: arxiv-2402.10245

Rameen Atique, Hafiza Arshi Saeed, Bushra Anwar, Tehreem Rana, Ayesha Haidar, Ayesha Muazzam, Areesha Naveed, Javeria Sharif, Aqsa Perveen, Hafiza Rida Fatima, Abdul Samad

{"title":"Brief overview on Bacteriophage therapy; Alternative to Antibiotics","authors":"Rameen Atique, Hafiza Arshi Saeed, Bushra Anwar, Tehreem Rana, Ayesha Haidar, Ayesha Muazzam, Areesha Naveed, Javeria Sharif, Aqsa Perveen, Hafiza Rida Fatima, Abdul Samad","doi":"arxiv-2402.10245","DOIUrl":"https://doi.org/arxiv-2402.10245","url":null,"abstract":"The term bacteriophage means killer or eater of bacteria. They were initially\u0000discovered by F.W. Twort and later on, Felix d'Herelle unveiled them to the\u0000world in 1910. Phage therapy has arisen as a favorable option to conventional\u0000antibiotics by reducing the multinational problem of increasing antibacterial\u0000resistance. These virulent viruses particularly prey on and contaminate\u0000bacterial strains and aid in fighting bacterial diseases. Researchers are\u0000performing various clinical trials on the bacteriophage to tackle pathogenic\u0000bacterial infections, varying from typical illnesses to highly invulnerable\u0000biofilms that cannot be treated with antibiotics. The primary experiments\u0000demonstrated that phage therapy has fewer consequences than traditional\u0000antimicrobial drugs. It is safer to use and show results within a few days.\u0000Although phage therapy has a wide range of promising results, but it also\u0000encounters diverse obstacles. One is that they are host-specific and can merely\u0000be used for personalized therapy. As thousands of bacteria can cause disease,\u0000clinicians have to construct a library of phage viruses. For successful\u0000treatment, an analysis of versatility, stability, and immune interference\u0000related to bacteriophage is necessary. Phage therapy is an excellent substitute\u0000for antibiotics as it illustrates a living base for the treatment of infections\u0000and it is climate-friendly. It only targets the pathogenic cells and has less\u0000influence on the normal microbiota. Regardless of the challenges and problems,\u0000phage therapy is approved as a beneficial approach to combating contagious\u0000infections.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"44 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139902707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development of an updated, comprehensive food composition database for Australian-grown horticultural commodities 为澳大利亚种植的园艺产品开发最新的综合食品成分数据库

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-02-09 DOI: arxiv-2402.06169

Eleanor Dunlop, Judy Cunningham, Paul Adorno, Shari Fatupaito, Stuart K Johnson, Lucinda J Black

{"title":"Development of an updated, comprehensive food composition database for Australian-grown horticultural commodities","authors":"Eleanor Dunlop, Judy Cunningham, Paul Adorno, Shari Fatupaito, Stuart K Johnson, Lucinda J Black","doi":"arxiv-2402.06169","DOIUrl":"https://doi.org/arxiv-2402.06169","url":null,"abstract":"Australian agriculture supplies many horticultural commodities to domestic\u0000and international markets; however, food composition data for many commodities\u0000are outdated or unavailable. We produced an up-to-date, nationally\u0000representative dataset of up to 148 nutrients and related components in 92\u0000Australian-grown fruit (fresh n=39, dried n=6), vegetables (n=43) and nuts\u0000(n=4) by replacing outdated data (pre-2000), confirming concentrations of\u0000important nutrients and retaining relevant existing data. Primary samples (n =\u0000902) were purchased during peak growing season in Sydney, Melbourne and Perth\u0000between June 2021 and May 2022. While new data reflect current growing\u0000practices, varieties, climate and analytical methods, few notable differences\u0000were found between old and new data where methods of analysis are comparable.\u0000The new data will be incorporated into the Australian Food Composition\u0000Database, allowing free online access to stakeholders. The approach used could\u0000serve as a model for cost-effective updates of national food composition\u0000databases worldwide.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139760943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Use of a Golden Gate plasmid set enabling scarless MoClo-compatible transcription unit assembly 使用 "金门 "质粒组，实现与 MoClo 兼容的无痕转录单元组装

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-02-05 DOI: arxiv-2402.03410

Stijn T. de Vries, Laura Kley, Daniel Schindler

{"title":"Use of a Golden Gate plasmid set enabling scarless MoClo-compatible transcription unit assembly","authors":"Stijn T. de Vries, Laura Kley, Daniel Schindler","doi":"arxiv-2402.03410","DOIUrl":"https://doi.org/arxiv-2402.03410","url":null,"abstract":"Golden Gate cloning has become a powerful and widely used DNA assembly\u0000method. Its modular nature and the reusability of standardized parts allow\u0000rapid construction of transcription units and multi-gene constructs.\u0000Importantly, its modular structure makes it compatible with laboratory\u0000automation, allowing for systematic and highly complex DNA assembly. Golden\u0000Gate cloning relies on Type IIS enzymes that cleave an adjacent undefined\u0000sequence motif at a defined distance from the directed enzyme recognition\u0000motif. This feature has been used to define hierarchical Golden Gate assembly\u0000standards with defined overhangs (\"fusion sites\") for defined part libraries.\u0000The simplest Golden Gate standard would consist of three part libraries, namely\u0000promoter, coding and terminator sequences, respectively. Each library would\u0000have defined fusion sites, allowing a hierarchical Golden Gate assembly to\u0000generate transcription units. Typically, Type IIS enzymes are used, which\u0000generate four nucleotide overhangs. This results in small scar sequences in\u0000hierarchical DNA assemblies, which can affect the functionality of\u0000transcription units. However, there are enzymes that generate three nucleotide\u0000overhangs, such as SapI. Here we provide a step-by-step protocol on how to use\u0000SapI to assemble transcription units using the start and stop codon for\u0000scarless transcription unit assembly. The protocol also provides guidance on\u0000how to perform multi-gene Golden Gate assemblies with the resulting\u0000transcription units using the Modular Cloning standard. The transcription units\u0000expressing fluorophores are used as an example.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"102 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139760957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0