Dengue virus (DENV) is a mosquito-borne virus with a significant human health concern. With 390 million infections annually and 96 million showing clinical symptoms, severe dengue can lead to life-threatening conditions like dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). The only FDA-approved vaccine, Dengvaxia, has limitations due to antibody-dependent enhancement (ADE), necessitating careful administration. The recent pre-approval of TAK-003 by WHO in 2024 highlights ongoing efforts to improve vaccine options. This review explores recent advancements in dengue vaccine development, emphasizing potential utility of mRNA-based vaccines. By examining current clinical trial data and innovations, we aim to identify promising strategies to address the limitations of existing vaccines and enhance global dengue prevention efforts.
{"title":"Opportunities and challenges of mRNA technologies in development of Dengue Virus Vaccine","authors":"Xiaoyang Liu, Daniel Salmon","doi":"arxiv-2409.10805","DOIUrl":"https://doi.org/arxiv-2409.10805","url":null,"abstract":"Dengue virus (DENV) is a mosquito-borne virus with a significant human health\u0000concern. With 390 million infections annually and 96 million showing clinical\u0000symptoms, severe dengue can lead to life-threatening conditions like dengue\u0000hemorrhagic fever (DHF) and dengue shock syndrome (DSS). The only FDA-approved\u0000vaccine, Dengvaxia, has limitations due to antibody-dependent enhancement\u0000(ADE), necessitating careful administration. The recent pre-approval of TAK-003\u0000by WHO in 2024 highlights ongoing efforts to improve vaccine options. This\u0000review explores recent advancements in dengue vaccine development, emphasizing\u0000potential utility of mRNA-based vaccines. By examining current clinical trial\u0000data and innovations, we aim to identify promising strategies to address the\u0000limitations of existing vaccines and enhance global dengue prevention efforts.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142261164","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}
Rasul Rafiq Aziz, Fakhraddin Mustafa Hama Salih, Ibrahim Maaroof Noori
Experiment 1. Rooting of quince hardwood cuttings: Rooting success was influenced by both the concentrations of IBA and the selection of rooting media. However, the control group (without IBA) notably enhanced rooting when compared to the various IBA concentrations. Cuttings in the control group (without IBA) and those planted in river sand exhibited notably high percentages of successful rooting, underscoring the importance of the selected planting medium. Experiment 2. Bench grafting of loquat: The success of grafting loquat cutting stocks varied based on grafting dates, types of cuttings, and concentrations of IBA. However, IBA at different concentrations did not have a significant impact. Notably, certain interactions such as grafting on February 20 with loquat stock cuttings, yielded higher percentages of successful graft bud sprouting. Experiment 3. Performance of grafting loquats onto different rootstocks: Grafting success was notably influenced by the selection of rootstock, with loquat rootstock demonstrating superior performance compared to quince. The highest significant levels of successful grafting were attained on February 20, underscoring the crucial role of grafting dates. Experiment 4. Impact of tree stock types on grafting success: Grafting success percentage was higher in loquat tree stock when compared to quince. The consistency of grafting success percentages across three dates underscores the significant influence of rootstock type. Experiment 5. Bench grafting of loquat cutting stocks: Graft bud sprout percentages exhibited variations, with loquat stock cuttings surpassing quince. Grafting success demonstrated a consistent increase from February 20 to March 30, underscoring the importance of selecting appropriate grafting dates.
实验 1.榅桲硬木插条的生根：生根成功率受 IBA 浓度和生根介质选择的影响。然而，与不同浓度的 IBA 相比，对照组（不含 IBA）的生根率明显提高。对照组（不含 IBA）和种植在河沙中的插条的生根成功率明显较高，这突出表明了所选种植介质的重要性。实验 2.枇杷的台式嫁接：根据嫁接日期、插条类型和 IBA 浓度的不同，枇杷插条的嫁接成功率也不同。然而，不同浓度的 IBA 并没有显著影响。值得注意的是，某些交互作用，如在 2 月 20 日嫁接枇杷扦插苗，嫁接芽萌发的成功率较高。实验 3.将枇杷嫁接到不同砧木上的效果：砧木的选择对嫁接成功率有显著影响，枇杷砧木的表现优于榅桲砧木。2 月 20 日的嫁接成功率最高，这说明嫁接日期的关键作用。实验 4.树种对嫁接成功率的影响：与榅桲相比，枇杷树种的嫁接成功率更高。三个日期的嫁接成功率一致，说明砧木类型对嫁接的影响很大。实验 5.枇杷砧木的基准嫁接：嫁接芽萌发率出现了变化，枇杷扦插苗超过了榅桲。从 2 月 20 日到 3 月 30 日，嫁接成功率持续上升，这说明选择适当嫁接日期的重要性。
{"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}
We analyze the methodological approach and validity of interpretation of using national-level time-series regression analyses relating epidemic outcomes to policies that estimate many models involving permutations of analytic choices (i.e., a "multiverse" approach). Specifically, we evaluate the possible biases and pitfalls of interpretation of a multiverse approach to the context of government responses to epidemics using the example of COVID-19 and a recently published peer-reviewed paper by Bendavid and Patel (2024) along with the subsequent commentary that the two authors published discussing and interpreting the implications of their work. While we identify multiple potential errors and sources of biases in how the specific analyses were undertaken that are also relevant for other studies employing similar approaches, our most important finding involves constructing a counterexample showing that causal model specification-agnostic multiverse analyses can be incorrectly used to suggest that no consistent effect can be discovered in data especially in cases where most specifications estimated with the data are far from causally valid. Finally, we suggest an alternative approach involving hypothesis-drive specifications that explicitly account for infectiousness across jurisdictions in the analysis as well as the interconnected ways that policies and behavioral responses may evolve within and across these jurisdictions.
{"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}
Colorectal cancer (CRC) continues to be a significant global health burden, prompting the need for more effective and targeted therapeutic strategies. Nanoparticle-based drug delivery systems have emerged as a promising approach to address the limitations of conventional chemotherapy, offering enhanced specificity, reduced systemic toxicity, and improved therapeutic outcomes. This paper provides an in-depth review of the current advancements in the application of nanoparticles as vehicles for targeted drug delivery in CRC therapy. It covers a variety of nanoparticle types, including liposomes, polymeric nanoparticles, dendrimers, and mesoporous silica nanoparticles (MSNs), with a focus on their design, functionalization, and mechanisms of action. This review also examines the challenges associated with the clinical translation of these technologies and explores future directions, emphasizing the potential of nanoparticle-based systems to revolutionize CRC treatment.
{"title":"Advances in Nanoparticle-Based Targeted Drug Delivery Systems for Colorectal Cancer Therapy: A Review","authors":"Mahadi Hasan, Camryn Grace Evett, Jack Burton","doi":"arxiv-2409.05222","DOIUrl":"https://doi.org/arxiv-2409.05222","url":null,"abstract":"Colorectal cancer (CRC) continues to be a significant global health burden,\u0000prompting the need for more effective and targeted therapeutic strategies.\u0000Nanoparticle-based drug delivery systems have emerged as a promising approach\u0000to address the limitations of conventional chemotherapy, offering enhanced\u0000specificity, reduced systemic toxicity, and improved therapeutic outcomes. This\u0000paper provides an in-depth review of the current advancements in the\u0000application of nanoparticles as vehicles for targeted drug delivery in CRC\u0000therapy. It covers a variety of nanoparticle types, including liposomes,\u0000polymeric nanoparticles, dendrimers, and mesoporous silica nanoparticles\u0000(MSNs), with a focus on their design, functionalization, and mechanisms of\u0000action. This review also examines the challenges associated with the clinical\u0000translation of these technologies and explores future directions, emphasizing\u0000the potential of nanoparticle-based systems to revolutionize CRC treatment.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142189218","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}
A meta-analysis of spaceflight data from both mouse and human flights reveals a striking overlap with Parkinson's disease (PD). Parallels include: changes in gait, loss of dopamine, sustained changes in the basal ganglia, loss of tyrosine hydroxylase in the substantia nigra, and systemic mitochondrial dysfunction. We identified specific Parkinson's genes differentially expressed post-spaceflight. These evidences indicate that spaceflight stressor-induced changes in the brain may become permanent during deep space exploration, posing a risk of PD in astronauts
{"title":"Unveiling Parkinson's Disease-like Changes Triggered by Spaceflight","authors":"Nilufar Ali, Afshin Beheshti, Greg Hampikian","doi":"arxiv-2408.15021","DOIUrl":"https://doi.org/arxiv-2408.15021","url":null,"abstract":"A meta-analysis of spaceflight data from both mouse and human flights reveals\u0000a striking overlap with Parkinson's disease (PD). Parallels include: changes in\u0000gait, loss of dopamine, sustained changes in the basal ganglia, loss of\u0000tyrosine hydroxylase in the substantia nigra, and systemic mitochondrial\u0000dysfunction. We identified specific Parkinson's genes differentially expressed\u0000post-spaceflight. These evidences indicate that spaceflight stressor-induced\u0000changes in the brain may become permanent during deep space exploration, posing\u0000a risk of PD in astronauts","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142189271","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}
Mandyam Srinivasan, Juergen Tautz, Geoffrey W Stuart
This is a point-by-point response to a non-peer-reviewed document titled The Miscalibration of the Honeybee Odometer [arXiv:2405.12998], authored by L. Luebbert and L. Pachter, that was published on arXiv on 8 May 2024 and subsequently publicised via social and mainstream media. The authors never contacted Srinivasan or Tautz personally with their queries, nor did they seek clarification. They do not work in this research area, and they have drawn several unjustified conclusions that reflect a limited understanding of the data they have examined.
本文是对L.Luebbert和L.Pachter撰写的题为《蜜蜂里程表的误差》（TheMiscalibration of the Honeybee Odometer）[arXiv:2405.12998]的非同行评审文件的逐点回应，该文件于2024年5月8日发表在arXiv上，随后通过社交媒体和主流媒体进行了宣传。作者从未亲自联系斯里尼瓦桑或陶兹提出疑问，也没有寻求澄清。他们并不从事这一研究领域的工作，而且得出了许多不合理的结论，反映出他们对所研究数据的理解有限。
{"title":"Comment on Miscalibration of the Honeybee Odometer","authors":"Mandyam Srinivasan, Juergen Tautz, Geoffrey W Stuart","doi":"arxiv-2408.11520","DOIUrl":"https://doi.org/arxiv-2408.11520","url":null,"abstract":"This is a point-by-point response to a non-peer-reviewed document titled The\u0000Miscalibration of the Honeybee Odometer [arXiv:2405.12998], authored by L.\u0000Luebbert and L. Pachter, that was published on arXiv on 8 May 2024 and\u0000subsequently publicised via social and mainstream media. The authors never\u0000contacted Srinivasan or Tautz personally with their queries, nor did they seek\u0000clarification. They do not work in this research area, and they have drawn\u0000several unjustified conclusions that reflect a limited understanding of the\u0000data they have examined.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142189273","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}
The establishment of bioRxiv facilitated the rapid adoption of preprints in the life sciences, accelerating the dissemination of new research findings. However, the sheer volume of preprints published daily can be overwhelming, making it challenging for researchers to stay updated on the latest developments. Here, I introduce biorecap, an R package that retrieves and summarizes bioRxiv preprints using a large language model (LLM) running locally on nearly any commodity laptop. biorecap leverages the ollamar package to interface with the Ollama server and API endpoints, allowing users to prompt any local LLM available through Ollama. The package follows tidyverse conventions, enabling users to pipe the output of one function as input to another. Additionally, biorecap provides a single wrapper function that generates a timestamped CSV file and HTML report containing short summaries of recent preprints published in user-configurable subject areas. By combining the strengths of LLMs with the flexibility and security of local execution, biorecap represents an advancement in the tools available for managing the information overload in modern scientific research. The biorecap R package is available on GitHub at https://github.com/stephenturner/biorecap under an open-source (MIT) license.
bioRxiv的建立促进了预印本在生命科学领域的快速应用，加速了新研究成果的传播。然而，每天发表的预印本数量之大可能会让人应接不暇，这使得研究人员难以及时了解最新进展。在这里，我将介绍 biorecap，它是一个 R 软件包，可以使用在几乎所有商品笔记本电脑上本地运行的大型语言模型（LLM）检索和汇总 bioRxiv 预印本。biorecap 利用 ollamar 软件包与 Ollama 服务器和 API 端点接口，允许用户通过 Ollama 提示任何可用的本地 LLM。该软件包遵循 tidyverseconventions，使用户能够将一个函数的输出作为另一个函数的输入。此外，biorecap 还提供了一个封装函数，可生成带有时间戳的 CSV 文件和 HTML 报告，其中包含用户可配置的主题领域中近期发表的预印本的简短摘要。通过将 LLM 的优势与本地执行的灵活性和安全性相结合，biorecap 代表了现代科学研究中信息过载管理工具的一大进步。biorecap R 软件包可在 GitHub https://github.com/stephenturner/biorecap 上获取，采用开源（MIT）许可。
{"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}
Rasul Rafiq Aziz, Aram Akram Mohammed, Faraydwn Karim Ahmad, Ari Jamil Ali
The research was conducted at the College of Agricultural Sciences Engineering/University of Sulaimani/ Kurdistan Region-Iraqi to investigate effects of different concentrations of IBA (0, 3000, 4000 and 5000 ppm) and soaking in water for 24 hours on propagation black mulberry (Morus nigra L.) by hardwood cuttings. In this research the parameters of rooting percentage, root number, root length, sprout bud number, shoot length and shoot diameter were measured. Effect of individual factors showed that the highest rooting percentage (15%) was achieved in cuttings soaked in water for 24 hours, as well as improving other traits. Also, the best (23.33%) rooting was found in cuttings dipped in 4000 ppm IBA. Interaction effects of the two factors showed that cuttings treated with 4000 ppm IBA and soaked in water for 24 hours gave the highest (40%) rooting, and the highest other root and shoot traits were achieved in the same interaction as well.
这项研究是在伊拉克库尔德斯坦地区苏莱曼尼大学农业科学工程学院进行的，目的是研究不同浓度的 IBA（0、3000、4000 和 5000 ppm）和在水中浸泡 24 小时对硬木扦插繁殖黑桑（Morus nigra L.）的影响。本研究测定了生根率、根数、根长、萌芽数、芽长和芽直径等参数。各因素的影响表明，在水中浸泡 24 小时的插条生根率最高（15%），其他性状也有所改善。此外，浸泡在 4000 ppm IBA 中的插条生根率最高（23.33%）。两个因素的交互效应表明，用 4000 ppm IBA 处理并在水中浸泡 24 小时的插条生根率最高（40%），在相同的交互效应下，根和芽的其他性状也最高。
{"title":"Effect of IBA concentration and water soaking on rooting hardwood cuttings of black mulberry (Morus nigra L.)","authors":"Rasul Rafiq Aziz, Aram Akram Mohammed, Faraydwn Karim Ahmad, Ari Jamil Ali","doi":"arxiv-2408.11083","DOIUrl":"https://doi.org/arxiv-2408.11083","url":null,"abstract":"The research was conducted at the College of Agricultural Sciences\u0000Engineering/University of Sulaimani/ Kurdistan Region-Iraqi to investigate\u0000effects of different concentrations of IBA (0, 3000, 4000 and 5000 ppm) and\u0000soaking in water for 24 hours on propagation black mulberry (Morus nigra L.) by\u0000hardwood cuttings. In this research the parameters of rooting percentage, root\u0000number, root length, sprout bud number, shoot length and shoot diameter were\u0000measured. Effect of individual factors showed that the highest rooting\u0000percentage (15%) was achieved in cuttings soaked in water for 24 hours, as well\u0000as improving other traits. Also, the best (23.33%) rooting was found in\u0000cuttings dipped in 4000 ppm IBA. Interaction effects of the two factors showed\u0000that cuttings treated with 4000 ppm IBA and soaked in water for 24 hours gave\u0000the highest (40%) rooting, and the highest other root and shoot traits were\u0000achieved in the same interaction as well.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142189284","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}
Alexandr V. Vikhorev, Michael M. Rempel, Oksana O. Polesskaya, Ivan V. Savelev, Max V. Myakishev-Rempel
Transposable elements (TEs) constitute a significant portion of eukaryotic genomes, yet their role in chromatin organization remains poorly understood. This study investigates the distribution patterns of TEs around chromatin ligation points (LPs) identified through Micro-C experiments in human cells. We analyzed the density of various TE families within a 100kb window centered on LPs, focusing on major families such as Alu and LINE-1 (L1) elements. Our findings reveal distinct, non-random distribution patterns that differ between TE families and exhibit consistent strand-specific biases. These patterns were reproducible across two independent datasets and showed marked differences from random genomic distributions. Notably, we observed family-specific variations in TE density near LPs, with some families showing depletion at LPs followed by periodic fluctuations in density. The consistency of these patterns across TE families and their orientation relative to chromosome arms suggest a fundamental relationship between TEs and higher-order chromatin structure. Our results provide new insights into the potential role of TEs in genome organization and challenge the notion of TEs as passive genomic components. This study lays the groundwork for future investigations into the functional implications of TE distribution in chromatin architecture and gene regulation.
可转座元件（Transposable elements，TEs）在真核基因组中占很大比例，但它们在染色质组织中的作用却鲜为人知。本研究调查了通过人类细胞中的Micro-C实验确定的染色质连接点（LPs）周围TEs的分布模式。我们分析了以 LPs 为中心的 100kb 窗口内各种 TE 家族的密度，重点分析了 Alu 和 LINE-1 (L1) 元件等主要家族。我们的发现揭示了不同 TE 族之间不同的、非随机的分布模式，并表现出一致的链特异性偏倚。这些模式在两个独立的数据集上都可以重现，并显示出与随机基因组分布的明显差异。值得注意的是，我们观察到了LPs附近TE密度的家族特异性变化，一些家族在LPs处显示出耗竭，随后密度出现周期性波动。这些模式在TE家族间的一致性以及它们相对于染色体臂的取向表明，TE与高阶染色质结构之间存在基本关系。我们的研究结果为TEs在基因组组织中的潜在作用提供了新的见解，并对TEs作为被动基因组元件的概念提出了挑战。这项研究为今后研究TE在染色质结构和基因调控中的分布的功能含义奠定了基础。
{"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}
Katharine Y. Chen, Maria Toro-Moreno, Arvind Rasi Subramaniam
Laboratory research is a complex, collaborative process that involves several stages, including hypothesis formulation, experimental design, data generation and analysis, and manuscript writing. Although reproducibility and data sharing are increasingly prioritized at the publication stage, integrating these principles at earlier stages of laboratory research has been hampered by the lack of broadly applicable solutions. Here, we propose that the workflow used in modern software development offers a robust framework for enhancing reproducibility and collaboration in laboratory research. In particular, we show that GitHub, a platform widely used for collaborative software projects, can be effectively adapted to organize and document all aspects of a research project's lifecycle in a molecular biology laboratory. We outline a three-step approach for incorporating the GitHub ecosystem into laboratory research workflows: 1. designing and organizing experiments using issues and project boards, 2. documenting experiments and data analyses with a version control system, and 3. ensuring reproducible software environments for data analyses and writing tasks with containerized packages. The versatility, scalability, and affordability of this approach make it suitable for various scenarios, ranging from small research groups to large, cross-institutional collaborations. Adopting this framework from a project's outset can increase the efficiency and fidelity of knowledge transfer within and across research laboratories. An example GitHub repository based on the above approach is available at https://github.com/rasilab/github_demo.
{"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}
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