arXiv - QuanBio - Other Quantitative Biology最新文献

Opportunities and challenges of mRNA technologies in development of Dengue Virus Vaccine mRNA 技术在登革热病毒疫苗开发中的机遇与挑战

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-09-17 DOI: arxiv-2409.10805

Xiaoyang Liu, Daniel Salmon

引用次数: 0

Compatibility studies of loquat scions with loquat and quince rootstocks 枇杷接穗与枇杷和榅桲砧木的兼容性研究

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-09-17 DOI: arxiv-2409.11451

Rasul Rafiq Aziz, Fakhraddin Mustafa Hama Salih, Ibrahim Maaroof Noori

{"title":"Compatibility studies of loquat scions with loquat and quince rootstocks","authors":"Rasul Rafiq Aziz, Fakhraddin Mustafa Hama Salih, Ibrahim Maaroof Noori","doi":"arxiv-2409.11451","DOIUrl":"https://doi.org/arxiv-2409.11451","url":null,"abstract":"Experiment 1. Rooting of quince hardwood cuttings: Rooting success was\u0000influenced by both the concentrations of IBA and the selection of rooting\u0000media. However, the control group (without IBA) notably enhanced rooting when\u0000compared to the various IBA concentrations. Cuttings in the control group\u0000(without IBA) and those planted in river sand exhibited notably high\u0000percentages of successful rooting, underscoring the importance of the selected\u0000planting medium. Experiment 2. Bench grafting of loquat: The success of\u0000grafting loquat cutting stocks varied based on grafting dates, types of\u0000cuttings, and concentrations of IBA. However, IBA at different concentrations\u0000did not have a significant impact. Notably, certain interactions such as\u0000grafting on February 20 with loquat stock cuttings, yielded higher percentages\u0000of successful graft bud sprouting. Experiment 3. Performance of grafting\u0000loquats onto different rootstocks: Grafting success was notably influenced by\u0000the selection of rootstock, with loquat rootstock demonstrating superior\u0000performance compared to quince. The highest significant levels of successful\u0000grafting were attained on February 20, underscoring the crucial role of\u0000grafting dates. Experiment 4. Impact of tree stock types on grafting success:\u0000Grafting success percentage was higher in loquat tree stock when compared to\u0000quince. The consistency of grafting success percentages across three dates\u0000underscores the significant influence of rootstock type. Experiment 5. Bench\u0000grafting of loquat cutting stocks: Graft bud sprout percentages exhibited\u0000variations, with loquat stock cuttings surpassing quince. Grafting success\u0000demonstrated a consistent increase from February 20 to March 30, underscoring\u0000the importance of selecting appropriate grafting dates.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142261166","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

Analysis of Potential Biases and Validity of Studies Using Multiverse Approaches to Assess the Impacts of Government Responses to Epidemics 使用多元宇宙方法评估政府应对流行病影响的研究的潜在偏差和有效性分析

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-09-11 DOI: arxiv-2409.06930

Jeremy D. Goldhaber-Fiebert

{"title":"Analysis of Potential Biases and Validity of Studies Using Multiverse Approaches to Assess the Impacts of Government Responses to Epidemics","authors":"Jeremy D. Goldhaber-Fiebert","doi":"arxiv-2409.06930","DOIUrl":"https://doi.org/arxiv-2409.06930","url":null,"abstract":"We analyze the methodological approach and validity of interpretation of\u0000using national-level time-series regression analyses relating epidemic outcomes\u0000to policies that estimate many models involving permutations of analytic\u0000choices (i.e., a \"multiverse\" approach). Specifically, we evaluate the possible\u0000biases and pitfalls of interpretation of a multiverse approach to the context\u0000of government responses to epidemics using the example of COVID-19 and a\u0000recently published peer-reviewed paper by Bendavid and Patel (2024) along with\u0000the subsequent commentary that the two authors published discussing and\u0000interpreting the implications of their work. While we identify multiple\u0000potential errors and sources of biases in how the specific analyses were\u0000undertaken that are also relevant for other studies employing similar\u0000approaches, our most important finding involves constructing a counterexample\u0000showing that causal model specification-agnostic multiverse analyses can be\u0000incorrectly used to suggest that no consistent effect can be discovered in data\u0000especially in cases where most specifications estimated with the data are far\u0000from causally valid. Finally, we suggest an alternative approach involving\u0000hypothesis-drive specifications that explicitly account for infectiousness\u0000across jurisdictions in the analysis as well as the interconnected ways that\u0000policies and behavioral responses may evolve within and across these\u0000jurisdictions.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"48 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142189274","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

Advances in Nanoparticle-Based Targeted Drug Delivery Systems for Colorectal Cancer Therapy: A Review 基于纳米粒子的结直肠癌靶向给药系统的研究进展：综述

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-09-08 DOI: arxiv-2409.05222

Mahadi Hasan, Camryn Grace Evett, Jack Burton

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Unveiling Parkinson's Disease-like Changes Triggered by Spaceflight 揭示太空飞行引发的帕金森病样变化

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-08-25 DOI: arxiv-2408.15021

Nilufar Ali, Afshin Beheshti, Greg Hampikian

引用次数: 0

Comment on Miscalibration of the Honeybee Odometer 关于蜜蜂里程表误判的评论

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-08-21 DOI: arxiv-2408.11520

Mandyam Srinivasan, Juergen Tautz, Geoffrey W Stuart

引用次数: 0

biorecap: an R package for summarizing bioRxiv preprints with a local LLM biorecap：用本地 LLM 总结 bioRxiv 预印本的 R 软件包

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-08-21 DOI: arxiv-2408.11707

Stephen D. Turner

{"title":"biorecap: an R package for summarizing bioRxiv preprints with a local LLM","authors":"Stephen D. Turner","doi":"arxiv-2408.11707","DOIUrl":"https://doi.org/arxiv-2408.11707","url":null,"abstract":"The establishment of bioRxiv facilitated the rapid adoption of preprints in\u0000the life sciences, accelerating the dissemination of new research findings.\u0000However, the sheer volume of preprints published daily can be overwhelming,\u0000making it challenging for researchers to stay updated on the latest\u0000developments. Here, I introduce biorecap, an R package that retrieves and\u0000summarizes bioRxiv preprints using a large language model (LLM) running locally\u0000on nearly any commodity laptop. biorecap leverages the ollamar package to\u0000interface with the Ollama server and API endpoints, allowing users to prompt\u0000any local LLM available through Ollama. The package follows tidyverse\u0000conventions, enabling users to pipe the output of one function as input to\u0000another. Additionally, biorecap provides a single wrapper function that\u0000generates a timestamped CSV file and HTML report containing short summaries of\u0000recent preprints published in user-configurable subject areas. By combining the\u0000strengths of LLMs with the flexibility and security of local execution,\u0000biorecap represents an advancement in the tools available for managing the\u0000information overload in modern scientific research. The biorecap R package is\u0000available on GitHub at https://github.com/stephenturner/biorecap under an\u0000open-source (MIT) license.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142189272","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

Effect of IBA concentration and water soaking on rooting hardwood cuttings of black mulberry (Morus nigra L.) IBA 浓度和水浸对黑桑硬木插条生根的影响

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-08-20 DOI: arxiv-2408.11083

Rasul Rafiq Aziz, Aram Akram Mohammed, Faraydwn Karim Ahmad, Ari Jamil Ali

引用次数: 0

Patterns of Transposable Element Distribution Around Chromatin Ligation Points Revealed by Micro-C Data Analysis 通过 Micro-C 数据分析揭示染色质连接点周围转座元件的分布模式

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-08-20 DOI: arxiv-2408.11079

Alexandr V. Vikhorev, Michael M. Rempel, Oksana O. Polesskaya, Ivan V. Savelev, Max V. Myakishev-Rempel

{"title":"Patterns of Transposable Element Distribution Around Chromatin Ligation Points Revealed by Micro-C Data Analysis","authors":"Alexandr V. Vikhorev, Michael M. Rempel, Oksana O. Polesskaya, Ivan V. Savelev, Max V. Myakishev-Rempel","doi":"arxiv-2408.11079","DOIUrl":"https://doi.org/arxiv-2408.11079","url":null,"abstract":"Transposable elements (TEs) constitute a significant portion of eukaryotic\u0000genomes, yet their role in chromatin organization remains poorly understood.\u0000This study investigates the distribution patterns of TEs around chromatin\u0000ligation points (LPs) identified through Micro-C experiments in human cells. We\u0000analyzed the density of various TE families within a 100kb window centered on\u0000LPs, focusing on major families such as Alu and LINE-1 (L1) elements. Our\u0000findings reveal distinct, non-random distribution patterns that differ between\u0000TE families and exhibit consistent strand-specific biases. These patterns were\u0000reproducible across two independent datasets and showed marked differences from\u0000random genomic distributions. Notably, we observed family-specific variations\u0000in TE density near LPs, with some families showing depletion at LPs followed by\u0000periodic fluctuations in density. The consistency of these patterns across TE\u0000families and their orientation relative to chromosome arms suggest a\u0000fundamental relationship between TEs and higher-order chromatin structure. Our\u0000results provide new insights into the potential role of TEs in genome\u0000organization and challenge the notion of TEs as passive genomic components.\u0000This study lays the groundwork for future investigations into the functional\u0000implications of TE distribution in chromatin architecture and gene regulation.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142224563","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

GitHub is an effective platform for collaborative and reproducible laboratory research GitHub 是实验室合作研究和可重现性研究的有效平台

arXiv - QuanBio - Other Quantitative Biology Pub Date : 2024-08-18 DOI: arxiv-2408.09344

Katharine Y. Chen, Maria Toro-Moreno, Arvind Rasi Subramaniam

{"title":"GitHub is an effective platform for collaborative and reproducible laboratory research","authors":"Katharine Y. Chen, Maria Toro-Moreno, Arvind Rasi Subramaniam","doi":"arxiv-2408.09344","DOIUrl":"https://doi.org/arxiv-2408.09344","url":null,"abstract":"Laboratory research is a complex, collaborative process that involves several\u0000stages, including hypothesis formulation, experimental design, data generation\u0000and analysis, and manuscript writing. Although reproducibility and data sharing\u0000are increasingly prioritized at the publication stage, integrating these\u0000principles at earlier stages of laboratory research has been hampered by the\u0000lack of broadly applicable solutions. Here, we propose that the workflow used\u0000in modern software development offers a robust framework for enhancing\u0000reproducibility and collaboration in laboratory research. In particular, we\u0000show that GitHub, a platform widely used for collaborative software projects,\u0000can be effectively adapted to organize and document all aspects of a research\u0000project's lifecycle in a molecular biology laboratory. We outline a three-step\u0000approach for incorporating the GitHub ecosystem into laboratory research\u0000workflows: 1. designing and organizing experiments using issues and project\u0000boards, 2. documenting experiments and data analyses with a version control\u0000system, and 3. ensuring reproducible software environments for data analyses\u0000and writing tasks with containerized packages. The versatility, scalability,\u0000and affordability of this approach make it suitable for various scenarios,\u0000ranging from small research groups to large, cross-institutional\u0000collaborations. Adopting this framework from a project's outset can increase\u0000the efficiency and fidelity of knowledge transfer within and across research\u0000laboratories. An example GitHub repository based on the above approach is\u0000available at https://github.com/rasilab/github_demo.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142189329","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