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
Computational biologists are frequently engaged in collaborative data analysis with wet lab researchers. These interdisciplinary projects, as necessary as they are to the scientific endeavour, can be surprisingly challenging due to cultural differences in operations and values. In these Ten Simple Rules guide we aim to help dry lab researchers identify sources of friction; and provide actionable tools to facilitate respectful, open, transparent and rewarding collaborations.
{"title":"Ten simple rules for collaborating with wet lab researchers for computational researchers","authors":"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","doi":"arxiv-2402.18348","DOIUrl":"https://doi.org/arxiv-2402.18348","url":null,"abstract":"Computational biologists are frequently engaged in collaborative data\u0000analysis with wet lab researchers. These interdisciplinary projects, as\u0000necessary as they are to the scientific endeavour, can be surprisingly\u0000challenging due to cultural differences in operations and values. In these Ten\u0000Simple Rules guide we aim to help dry lab researchers identify sources of\u0000friction; and provide actionable tools to facilitate respectful, open,\u0000transparent and rewarding collaborations.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"29 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140003523","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}
Ran Xu, Wenqi Shi, Yue Yu, Yuchen Zhuang, Bowen Jin, May D. Wang, Joyce C. Ho, Carl Yang
We present RAM-EHR, a Retrieval AugMentation pipeline to improve clinical predictions on Electronic Health Records (EHRs). RAM-EHR first collects multiple knowledge sources, converts them into text format, and uses dense retrieval to obtain information related to medical concepts. This strategy addresses the difficulties associated with complex names for the concepts. RAM-EHR then augments the local EHR predictive model co-trained with consistency regularization to capture complementary information from patient visits and summarized knowledge. Experiments on two EHR datasets show the efficacy of RAM-EHR over previous knowledge-enhanced baselines (3.4% gain in AUROC and 7.2% gain in AUPR), emphasizing the effectiveness of the summarized knowledge from RAM-EHR for clinical prediction tasks. The code will be published at url{https://github.com/ritaranx/RAM-EHR}.
{"title":"RAM-EHR: Retrieval Augmentation Meets Clinical Predictions on Electronic Health Records","authors":"Ran Xu, Wenqi Shi, Yue Yu, Yuchen Zhuang, Bowen Jin, May D. Wang, Joyce C. Ho, Carl Yang","doi":"arxiv-2403.00815","DOIUrl":"https://doi.org/arxiv-2403.00815","url":null,"abstract":"We present RAM-EHR, a Retrieval AugMentation pipeline to improve clinical\u0000predictions on Electronic Health Records (EHRs). RAM-EHR first collects\u0000multiple knowledge sources, converts them into text format, and uses dense\u0000retrieval to obtain information related to medical concepts. This strategy\u0000addresses the difficulties associated with complex names for the concepts.\u0000RAM-EHR then augments the local EHR predictive model co-trained with\u0000consistency regularization to capture complementary information from patient\u0000visits and summarized knowledge. Experiments on two EHR datasets show the\u0000efficacy of RAM-EHR over previous knowledge-enhanced baselines (3.4% gain in\u0000AUROC and 7.2% gain in AUPR), emphasizing the effectiveness of the summarized\u0000knowledge from RAM-EHR for clinical prediction tasks. The code will be\u0000published at url{https://github.com/ritaranx/RAM-EHR}.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"48 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140046930","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}
Precision medicine aims to create biomedical solutions tailored to specific factors that affect disease risk and treatment responses within the population. The success of the genomics era and recent widespread availability of electronic health records (EHR) has ushered in a new wave of genomic biobanks connected to EHR databases (EHR-linked biobanks). This perspective aims to discuss how race, ethnicity, and genetic ancestry are currently utilized to study common disease variation through genetic association studies. Although genetic ancestry plays a significant role in shaping the genetic landscape underlying disease risk in humans, the overall risk of a disease is caused by a complex combination of environmental, sociocultural, and genetic factors. When using EHR-linked biobanks to interrogate underlying disease etiology, it is also important to be aware of how the biases associated with commonly used descent-associated concepts such as race and ethnicity can propagate to downstream analyses. We intend for this resource to support researchers who perform or analyze genetic association studies in the EHR-linked biobank setting such as those involved in consortium-wide biobanking efforts. We provide background on how race, ethnicity, and genetic ancestry play a role in current association studies, highlight considerations where there is no consensus about best practices, and provide transparency about the current shortcomings.
基因组学时代的成功和最近电子健康记录（EHR）的普及，带来了与 EHR 数据库相连接的基因组生物库（EHR-linked biobanks）的新浪潮。本视角旨在讨论目前如何通过遗传关联研究利用种族、民族和遗传祖先来研究常见疾病的变异。虽然遗传血统在形成人类疾病风险的遗传景观方面起着重要作用，但疾病的总体风险是由环境、社会文化和遗传因素的复杂组合造成的。在使用与电子病历相关联的生物库研究潜在的疾病病因学时，同样重要的是要意识到与常用的世系相关概念（如种族和民族）相关的偏差会如何传播到下游分析中。我们希望该资源能为那些在与电子病历相关的生物库中进行或分析遗传关联研究的研究人员提供支持，例如那些参与全联盟生物库工作的研究人员。我们将提供有关种族、民族和遗传祖先如何在当前关联研究中发挥作用的背景资料，强调在最佳实践方面尚未达成共识的注意事项，并提供有关当前趋势的透明度。
{"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}
John R. Helliwell, James R. Hester, Loes Kroon-Batenburg, Brian McMahon, Selina L. S. Storm
The hardware for data archiving has expanded capacities for digital storage enormously in the past decade or more. This article charts the efforts of IUCr to facilitate discussions and plans relating to raw data archiving and reuse within the various communities of crystallography, diffraction, and scattering.
{"title":"The Evolution of Raw Data Archiving and the Growth of Its Importance in Crystallography","authors":"John R. Helliwell, James R. Hester, Loes Kroon-Batenburg, Brian McMahon, Selina L. S. Storm","doi":"arxiv-2402.16652","DOIUrl":"https://doi.org/arxiv-2402.16652","url":null,"abstract":"The hardware for data archiving has expanded capacities for digital storage\u0000enormously in the past decade or more. This article charts the efforts of IUCr\u0000to facilitate discussions and plans relating to raw data archiving and reuse\u0000within the various communities of crystallography, diffraction, and scattering.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"295 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139979381","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}
Aram Akram Mohammed, Fakhraddin Mustafa Hama Salih
Budding and grafting are the strategies employed to combat unfavorable environmental conditions and improve some physiological defects in the Pistacia vera tree. Drought and salinity stresses are the most prominent adverse conditions encountered in pistachio production. It has been observed in different studies that various pistachio rootstocks can be used to ameliorate the effect of those two stresses. Besides, rootstock has a role in some physiological performances of pistachios such as nutrient uptake and photosynthesis. Furthermore, nut blank, unsplit nut, and alternate bearing are three physiological disorders found in pistachio. Relationships have been found between the degree of these physiological disorders and the rootstock effect. The impact of rootstock on drought and salinity stresses, physiological performances, and physiological disorders in P. vera will be discussed in this review.
{"title":"Effect of Rootstock on Some Aspects of Pistachio (Pistacia vera L.): A Review","authors":"Aram Akram Mohammed, Fakhraddin Mustafa Hama Salih","doi":"arxiv-2402.14896","DOIUrl":"https://doi.org/arxiv-2402.14896","url":null,"abstract":"Budding and grafting are the strategies employed to combat unfavorable\u0000environmental conditions and improve some physiological defects in the Pistacia\u0000vera tree. Drought and salinity stresses are the most prominent adverse\u0000conditions encountered in pistachio production. It has been observed in\u0000different studies that various pistachio rootstocks can be used to ameliorate\u0000the effect of those two stresses. Besides, rootstock has a role in some\u0000physiological performances of pistachios such as nutrient uptake and\u0000photosynthesis. Furthermore, nut blank, unsplit nut, and alternate bearing are\u0000three physiological disorders found in pistachio. Relationships have been found\u0000between the degree of these physiological disorders and the rootstock effect.\u0000The impact of rootstock on drought and salinity stresses, physiological\u0000performances, and physiological disorders in P. vera will be discussed in this\u0000review.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139968908","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 fundamental mistake in receptor theory has led to an enduring misunderstanding of how to estimate the affinity and efficacy of an agonist. These properties are inextricably linked and cannot be easily separated in any case where the binding of a ligand induces a conformation change in its receptor. Consequently, binding curves and concentration-response relationships for receptor agonists have no straightforward interpretation. This problem, the affinity-efficacy problem, remains overlooked and misunderstood despite it being recognised in 1987. To avoid the further propagation of this misunderstanding, we propose that the affinity-efficacy problem should be included in the core curricula for pharmacology undergraduates proposed by the British Pharmacological Society and IUPHAR.
{"title":"The affinity-efficacy problem: an essential part of pharmacology education","authors":"James P Higham, David Colquhoun","doi":"arxiv-2402.14617","DOIUrl":"https://doi.org/arxiv-2402.14617","url":null,"abstract":"A fundamental mistake in receptor theory has led to an enduring\u0000misunderstanding of how to estimate the affinity and efficacy of an agonist.\u0000These properties are inextricably linked and cannot be easily separated in any\u0000case where the binding of a ligand induces a conformation change in its\u0000receptor. Consequently, binding curves and concentration-response relationships\u0000for receptor agonists have no straightforward interpretation. This problem, the\u0000affinity-efficacy problem, remains overlooked and misunderstood despite it\u0000being recognised in 1987. To avoid the further propagation of this\u0000misunderstanding, we propose that the affinity-efficacy problem should be\u0000included in the core curricula for pharmacology undergraduates proposed by the\u0000British Pharmacological Society and IUPHAR.","PeriodicalId":501219,"journal":{"name":"arXiv - QuanBio - Other Quantitative Biology","volume":"77 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139952152","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}
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
Multimodal neuroimaging grants a powerful in vivo window into the structure and function of the human brain. Recent methodological and conceptual advances have enabled investigations of the interplay between large-scale spatial trends, or gradients, in brain structure and function, offering a framework to unify principles of brain organization across multiple scales. Strong community enthusiasm for these techniques has been instrumental in their widespread adoption and implementation to answer key questions in neuroscience. Following a brief review of current literature on this framework, this perspective paper will highlight how pragmatic steps aiming to make gradient methods more accessible to the community propelled these techniques to the forefront of neuroscientific inquiry. More specifically, we will emphasize how interest for gradient methods was catalyzed by data sharing, open-source software development, as well as the organization of dedicated workshops led by a diverse team of early career researchers. To this end, we argue that the growing excitement for brain gradients is the result of coordinated and consistent efforts to build an inclusive community and can serve as a case in point for future innovations and conceptual advances in neuroinformatics. We close this perspective paper by discussing challenges for the continuous refinement of neuroscientific theory, methodological innovation, and real-world translation to maintain our collective progress towards integrated models of brain organization.
{"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}
The term bacteriophage means killer or eater of bacteria. They were initially discovered by F.W. Twort and later on, Felix d'Herelle unveiled them to the world in 1910. Phage therapy has arisen as a favorable option to conventional antibiotics by reducing the multinational problem of increasing antibacterial resistance. These virulent viruses particularly prey on and contaminate bacterial strains and aid in fighting bacterial diseases. Researchers are performing various clinical trials on the bacteriophage to tackle pathogenic bacterial infections, varying from typical illnesses to highly invulnerable biofilms that cannot be treated with antibiotics. The primary experiments demonstrated that phage therapy has fewer consequences than traditional antimicrobial drugs. It is safer to use and show results within a few days. Although phage therapy has a wide range of promising results, but it also encounters diverse obstacles. One is that they are host-specific and can merely be used for personalized therapy. As thousands of bacteria can cause disease, clinicians have to construct a library of phage viruses. For successful treatment, an analysis of versatility, stability, and immune interference related to bacteriophage is necessary. Phage therapy is an excellent substitute for antibiotics as it illustrates a living base for the treatment of infections and it is climate-friendly. It only targets the pathogenic cells and has less influence on the normal microbiota. Regardless of the challenges and problems, phage therapy is approved as a beneficial approach to combating contagious infections.
噬菌体一词的意思是细菌的杀手或食者。噬菌体最初是由 F.W. Twort 发现的，后来 Felix d'Herelle 于 1910 年将其公诸于世。噬菌体疗法的出现减少了抗菌药耐药性不断增强的跨国问题，是传统抗生素的有利选择。噬菌体病毒尤其能捕食和污染细菌菌株，帮助对抗细菌性疾病。研究人员正在对噬菌体进行各种临床试验，以应对病原性细菌感染，包括从典型疾病到无法用抗生素治疗的高致病性生物膜。主要实验证明，噬菌体疗法比传统抗菌药物的后果更少。虽然噬菌体疗法取得了一系列令人鼓舞的成果，但它也遇到了各种各样的障碍。其一，噬菌体具有宿主特异性，只能用于个性化治疗。由于可以致病的细菌成千上万，临床医生必须构建一个噬菌体病毒库。为了成功治疗，有必要对噬菌体的多功能性、稳定性和免疫干扰进行分析。噬菌体疗法是抗生素的绝佳替代品，因为它为治疗感染提供了一个有生命的基础，而且对气候无害。它只针对病原细胞，对正常微生物群的影响较小。无论存在哪些挑战和问题，噬菌体疗法都被认为是抗击传染性感染的有益方法。
{"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}
Eleanor Dunlop, Judy Cunningham, Paul Adorno, Shari Fatupaito, Stuart K Johnson, Lucinda J Black
Australian agriculture supplies many horticultural commodities to domestic and international markets; however, food composition data for many commodities are outdated or unavailable. We produced an up-to-date, nationally representative dataset of up to 148 nutrients and related components in 92 Australian-grown fruit (fresh n=39, dried n=6), vegetables (n=43) and nuts (n=4) by replacing outdated data (pre-2000), confirming concentrations of important nutrients and retaining relevant existing data. Primary samples (n = 902) were purchased during peak growing season in Sydney, Melbourne and Perth between June 2021 and May 2022. While new data reflect current growing practices, varieties, climate and analytical methods, few notable differences were found between old and new data where methods of analysis are comparable. The new data will be incorporated into the Australian Food Composition Database, allowing free online access to stakeholders. The approach used could serve as a model for cost-effective updates of national food composition databases worldwide.
{"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}
Golden Gate cloning has become a powerful and widely used DNA assembly method. Its modular nature and the reusability of standardized parts allow rapid construction of transcription units and multi-gene constructs. Importantly, its modular structure makes it compatible with laboratory automation, allowing for systematic and highly complex DNA assembly. Golden Gate cloning relies on Type IIS enzymes that cleave an adjacent undefined sequence motif at a defined distance from the directed enzyme recognition motif. This feature has been used to define hierarchical Golden Gate assembly standards with defined overhangs ("fusion sites") for defined part libraries. The simplest Golden Gate standard would consist of three part libraries, namely promoter, coding and terminator sequences, respectively. Each library would have defined fusion sites, allowing a hierarchical Golden Gate assembly to generate transcription units. Typically, Type IIS enzymes are used, which generate four nucleotide overhangs. This results in small scar sequences in hierarchical DNA assemblies, which can affect the functionality of transcription units. However, there are enzymes that generate three nucleotide overhangs, such as SapI. Here we provide a step-by-step protocol on how to use SapI to assemble transcription units using the start and stop codon for scarless transcription unit assembly. The protocol also provides guidance on how to perform multi-gene Golden Gate assemblies with the resulting transcription units using the Modular Cloning standard. The transcription units expressing fluorophores are used as an example.
金门克隆已成为一种功能强大、应用广泛的 DNA 组装方法。重要的是，它的模块化结构使其与实验室自动化兼容，可以进行系统化和高度复杂的 DNA 组装。GoldenGate 克隆依靠的是 IIS 型酶，这种酶可以在与定向酶识别基元之间的确定距离上裂解相邻的未定义序列基元。最简单的金门标准由三个部分库组成，分别是启动子序列、编码序列和终止子序列。最简单的金门标准由三个部分库组成，分别是启动子序列、编码序列和终止子序列。每个部分库都有确定的融合位点，允许分级金门组装以生成转录单元。通常使用 IIS 型酶，它能产生四个核苷酸的悬垂。这会导致分层 DNA 组装中出现小的疤痕序列，从而影响转录单元的功能。不过，也有一些酶能产生三个核苷酸的悬垂，如 SapI。在此，我们提供了一个分步方案，说明如何使用 SapI 利用起始密码子和终止密码子组装转录单位，以实现无痕转录单位组装。该方案还提供了如何使用模块化克隆标准对得到的转录单位进行多基因金门组装的指导。以表达荧光团的转录单位为例。
{"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}
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