open science

开放科学
  • 文章类型: Journal Article
    Open science (OS) awareness and skills are increasingly becoming an essential part of everyday scientific work as e.g., many journals require authors to share data. However, following an OS workflow can seem challenging at first. Thus, instructions by journals and other guidelines are important. But how comprehensive are they in the field of ecology and evolutionary biology (Ecol Evol)? To find this out, we reviewed 20 published OS guideline articles aimed for ecologists or evolutionary biologists, together with the data policies of 17 Ecol Evol journals to chart the current landscape of OS guidelines in the field, find potential gaps, identify field-specific barriers for OS and discuss solutions to overcome these challenges. We found that many of the guideline articles covered similar topics, despite being written for a narrow field or specific target audience. Likewise, many of the guideline articles mentioned similar obstacles that could hinder or postpone a transition to open data sharing. Thus, there could be a need for a more widely known, general OS guideline for Ecol Evol. Following the same guideline could also enhance the uniformity of the OS practices carried on in the field. However, some topics, like long-term experiments and physical samples, were mentioned surprisingly seldom, although they are typical issues in Ecol Evol. Of the journals, 15 out of 17 expected or at least encouraged data sharing either for all articles or under specific conditions, e.g. for registered reports and 10 of those required data sharing at the submission phase. The coverage of journal data policies varied greatly between journals, from practically non-existing to very extensive. As journals can contribute greatly by leading the way and making open data useful, we recommend that the publishers and journals would invest in clear and comprehensive data policies and instructions for authors.
    Avoimen tieteen ymmärrys ja taitojen hallinta on yhä tärkeämpi osa tutkijan arkea, sillä esimerkiksi monet tieteelliset lehdet odottavat aineiston avointa jakamista. Avoimen tieteen työtapojen noudattaminen voi kuitenkin tuntua alkuun haastavalta, minkä vuoksi esimerkiksi tieteellisten lehtien ja muiden tahojen laatimat ohjeet ovat tärkeitä. Mutta kuinka kattavia ne ovat ekologian ja evoluutiobiologian alalla? Kävimme läpi 20 julkaistua ekologeille tai evoluutiobiologeille suunnattua avoimen tieteen ohjeistusta sekä 17 ekologian ja evoluutiobiologian tieteellisen lehden datakäytännöt, tarkoituksenamme kartoittaa alojen avoimen tieteen ohjeiden nykytilaa, löytää mahdollisia puutteita, tunnistaa alakohtaisia esteitä avoimen tieteen käytäntöjen toteutumiselle sekä keskustella ratkaisuista, joilla nämä haasteet voitaisiin ratkaista. Havaitsimme, että monet ohjeistukset käsittelivät samankaltaisia aiheita, vaikka ne oli tarkoitettu kapealle erityisalalle tai suunnattu hyvin rajoitetulle kohderyhmälle. Samoin monissa ohjeistuksissa mainittiin samankaltaisia aineistojen avoimen jakamisen hidastamista tai estämistä aiheuttavia haasteita. Toiset aiheet, kuten pitkäaikaiskokeet ja fyysiset näytteet, sen sijaan mainittiin yllättävän harvoin, vaikka niissä on tyypillisiä ekologian ja evoluutiobiologian alojen haasteita. Tieteellisistä lehdistä 15:ssä 17:sta vaadittiin tai vähintään kannustettiin jakamaan aineisto avoimesti joko kaikkien artikkelien osalta tai tietyin edellytyksin, esim. rekisteröityjen tutkimusraporttien osalta. Lisäksi 10 näistä lehdistä edellytti aineiston avointa jakamista jo submittointivaiheessa. Tieteellisten lehtien aineisto‐ohjeiden kattavuus vaihteli suuresti lehtien välillä, käytännössä olemattomasta hyvin laajaan. Koska tieteellisillä lehdillä on suuri vaikutusvalta avoimen tieteen käytäntöjen edistämiseen, suosittelemme kustantajia ja lehtiä panostamaan selkeisiin ja kattaviin aineistolinjauksiin ja ohjeistuksiin.
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  • 文章类型: Journal Article
    呼吸测定法是了解整个动物能量和水平衡与环境关系的重要工具。因此,在过去十年中,使用呼吸测量法的研究越来越多,因此需要可靠的报告和数据共享,以进行有效的传播和研究综合。我们提供了五个关键部分的清单指南,以促进透明度,再现性,呼吸测定研究的可重复性:1)材料,设置,管道,2)主题条件/维护,3)测量条件,4)数据处理,5)数据报告和统计,每个都有解释和例子研究。报告和数据可用性的透明度在多个方面都有好处。作者可以使用这个清单来设计和报告他们的研究,审稿人和编辑可以使用清单来评估他们审稿的报告质量。改进的报告标准将提高初级研究的价值,并将极大地促进开展更高质量的研究综合以解决生态和进化理论的能力。
    Respirometry is an important tool for understanding whole-animal energy and water balance in relation to the environment. Consequently, the growing number of studies using respirometry over the last decade warrants reliable reporting and data sharing for effective dissemination and research synthesis. We provide a checklist guideline on five key sections to facilitate the transparency, reproducibility, and replicability of respirometry studies: 1) materials, set up, plumbing, 2) subject conditions/maintenance, 3) measurement conditions, 4) data processing, and 5) data reporting and statistics, each with explanations and example studies. Transparency in reporting and data availability has benefits on multiple fronts. Authors can use this checklist to design and report on their study, and reviewers and editors can use the checklist to assess the reporting quality of the manuscripts they review. Improved standards for reporting will enhance the value of primary studies and will greatly facilitate the ability to carry out higher quality research syntheses to address ecological and evolutionary theories.
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  • 文章类型: Journal Article
    最近发布的南非卫生研究伦理指南草案:原则,国家卫生研究伦理委员会的过程和结构(指南草案)承认开放数据,并在南非卫生研究的背景下为此提供指导原则。虽然它的纳入是一个积极的发展,还有改进的余地。尽管指南草案利用了国家数据和云政策草案,它缺乏其他相关政府政策的整合,特别是国家开放科学政策草案,并且未能充分详细说明开放科学和开放获取的原则。这种有限的范围和缺乏全面的定义和详细的指导给研究人员在南非进行道德和负责任的健康研究带来了挑战。它限制了准则草案与国家要务完全一致和促进以非洲为中心的方法。为了解决这些问题,建议准则草案纳入更广泛的政策和原则,通过全面的定义提高清晰度,提供有关开放访问的详细指导,并推广以非洲为中心的方法。实施这些解决方案将加强准则草案,使它们与开放科学的国家愿景保持一致,从而利用南非多样化科学界的全部潜力推进健康研究。
    The recently released draft South African Ethics in Health Research Guidelines: Principles, Processes and Structures (Draft Guidelines) by the National Health Research Ethics Council recognize open data and provide guiding principles for this in the context of health research in South Africa. While its inclusion is a positive development, there is room for improvement. Although the Draft Guidelines leverage the Draft National Policy on Data and Cloud, it lacks incorporation of other relevant government policies, notably the Draft National Open Science Policy, and fails to sufficiently detail the principles of open science and open access. This limited scope and lack of comprehensive definition and detailed guidance present challenges for researchers in conducting ethical and responsible health research in South Africa. It constrains the Draft Guidelines from fully aligning with national imperatives and from fostering African-centric approaches. To address these issues, it is recommended that the Draft Guidelines integrate broader policies and principles, enhance clarity through comprehensive definitions, provide detailed guidance on open access, and promote African-centric approaches. Implementing these solutions will strengthen the Draft Guidelines, aligning them with national visions of open science, and thereby harnessing the full potential of South Africa\'s diverse scientific community in advancing health research.
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  • 文章类型: Journal Article
    N-of-1试验是在一个人的时间内完成的多个交叉试验;它们也可以与一系列个体一起完成。与大多数标准临床试验相比,他们对个体作为分析单位的关注保持了统计能力,同时适应了患者之间更大的差异。这使得它们在罕见疾病中特别有用,同时也适用于许多健康状况和人群。最佳做法建议使用报告指南以标准化和透明的方式发布研究。N-of-1试验具有N-of-1方案的SPIRIT扩展(SPENT)和N-of-1试验的CONSORT扩展(CENT)。开放科学是最近的一项运动,旨在使任何人都能充分获得科学知识。加强合作,分享科学努力。开放的科学目标增加了研究的透明度,严谨,和再现性,减少研究浪费。许多组织和文章关注开放科学的特定方面,例如,开放访问发布。在整个研究轨迹(想法,发展,进行审判,分析,出版物,传播,知识翻译/反思),许多开放的科学理想都是通过N-of-1试验的以个人为中心的性质来解决的,包括研究开发中的患者观点等问题,个性化,和出版物,从更广泛的纳入标准中提高公平性,和更容易的远程试验选项。然而,N-of-1试验还帮助我们了解谨慎的领域,例如监测事后分析和开放数据共享中罕见疾病保密的细微差别。N-of-1报告指南鼓励研究轨迹关键方面的N-of-1考虑的严谨性和透明度。
    N-of-1 trials are multiple crossover trials done over time within a single person; they can also be done with a series of individuals. Their focus on the individual as the unit of analysis maintains statistical power while accommodating greater differences between patients than most standard clinical trials. This makes them particularly useful in rare diseases, while also being applicable across many health conditions and populations. Best practices recommend the use of reporting guidelines to publish research in a standardized and transparent fashion. N-of-1 trials have the SPIRIT extension for N-of-1 protocols (SPENT) and the CONSORT extension for N-of-1 trials (CENT). Open science is a recent movement focused on making scientific knowledge fully available to anyone, increasing collaboration, and sharing of scientific efforts. Open science goals increase research transparency, rigor, and reproducibility, and reduce research waste. Many organizations and articles focus on specific aspects of open science, for example, open access publishing. Throughout the trajectory of research (idea, development, running a trial, analysis, publication, dissemination, knowledge translation/reflection), many open science ideals are addressed by the individual-focused nature of N-of-1 trials, including issues such as patient perspectives in research development, personalization, and publications, enhanced equity from the broader inclusion criteria possible, and easier remote trials options. However, N-of-1 trials also help us understand areas of caution, such as monitoring of post hoc analyses and the nuances of confidentiality for rare diseases in open data sharing. The N-of-1 reporting guidelines encourage rigor and transparency of N-of-1 considerations for key aspects of the research trajectory.
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  • 文章类型: Journal Article
    过去十年的研究对迷幻药治疗精神障碍的临床潜力表示相当乐观。这种乐观反映在研究论文的增加上,制药公司的投资,专利,媒体报道,以及政治和立法变革。然而,迷幻科学正面临着严峻的挑战,这些挑战威胁到核心研究结果的有效性,并引起对临床疗效和安全性的怀疑。在本文中,我们介绍了10个最紧迫的挑战,分为简单,中度,和棘手的问题。我们展示了这些问题如何威胁内部有效性(治疗效果是由于与治疗无关的因素),外部有效性(缺乏泛化性),结构效度(工作机制不明确),或统计结论有效性(结论不遵循数据和方法)。这些问题往往在迷幻研究中共同出现,关于迷幻药治疗的安全性和有效性的限制性结论。我们提供了应对这些挑战的路线图,并分享了一份清单,记者,资助者,政策制定者,和其他利益相关者可以用来评估迷幻科学的质量。解决今天的问题是必要的,以找出对迷幻药的治疗潜力的乐观态度是否得到保证,并避免历史重演。
    Research in the last decade has expressed considerable optimism about the clinical potential of psychedelics for the treatment of mental disorders. This optimism is reflected in an increase in research papers, investments by pharmaceutical companies, patents, media coverage, as well as political and legislative changes. However, psychedelic science is facing serious challenges that threaten the validity of core findings and raise doubt regarding clinical efficacy and safety. In this paper, we introduce the 10 most pressing challenges, grouped into easy, moderate, and hard problems. We show how these problems threaten internal validity (treatment effects are due to factors unrelated to the treatment), external validity (lack of generalizability), construct validity (unclear working mechanism), or statistical conclusion validity (conclusions do not follow from the data and methods). These problems tend to co-occur in psychedelic studies, limiting conclusions that can be drawn about the safety and efficacy of psychedelic therapy. We provide a roadmap for tackling these challenges and share a checklist that researchers, journalists, funders, policymakers, and other stakeholders can use to assess the quality of psychedelic science. Addressing today\'s problems is necessary to find out whether the optimism regarding the therapeutic potential of psychedelics has been warranted and to avoid history repeating itself.
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  • 文章类型: Journal Article
    透明和开放促进(TOP)指南提供了一个框架,以帮助期刊制定开放的科学政策。行为改变的理论可以指导人们理解为什么期刊(不)实施开放的科学政策以及制定干预措施以改善这些政策。在这项研究中,我们使用理论领域框架调查了88位期刊编辑的能力,实施TOP的机会和动力。李克特量表的问题评估了编辑对TOP的支持,以及实施TOP的推动者和障碍。一个定性的问题要求编辑对他们的评级进行反思。大多数参与编辑支持在其期刊上采用TOP(71%),并认为其学科中的其他编辑支持采用TOP(57%)。大多数编辑(93%)同意他们的角色包括维护反映当前最佳实践的政策。然而,与其他编辑职责相比,大多数编辑(74%)没有将实施TOP视为优先事项。定性回答表达了实施TOP的结构性障碍(例如,缺乏时间,实施变更的资源和权限)以及根据研究类型对TOP的不同支持,开放科学标准,和执行水平。我们讨论了这些发现如何为理论上指导的干预措施的发展提供信息,以增加开放的科学政策,程序和实践。
    The Transparency and Openness Promotion (TOP) Guidelines provide a framework to help journals develop open science policies. Theories of behaviour change can guide understanding of why journals do (not) implement open science policies and the development of interventions to improve these policies. In this study, we used the Theoretical Domains Framework to survey 88 journal editors on their capability, opportunity and motivation to implement TOP. Likert-scale questions assessed editor support for TOP, and enablers and barriers to implementing TOP. A qualitative question asked editors to provide reflections on their ratings. Most participating editors supported adopting TOP at their journal (71%) and perceived other editors in their discipline to support adopting TOP (57%). Most editors (93%) agreed their roles include maintaining policies that reflect current best practices. However, most editors (74%) did not see implementing TOP as a high priority compared with other editorial responsibilities. Qualitative responses expressed structural barriers to implementing TOP (e.g. lack of time, resources and authority to implement changes) and varying support for TOP depending on study type, open science standard, and level of implementation. We discuss how these findings could inform the development of theoretically guided interventions to increase open science policies, procedures and practices.
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  • 文章类型: Journal Article
    开放数据有望提高研究的严谨性并使知识生产民主化。但它也提出了实际的,理论,尤其是对定性研究人员的伦理考虑。定性社会心理学中关于开放数据的讨论早于复制危机。然而,这种正在进行的讨论的细微差别尚未转化为当前关于开放数据的期刊指南。在这篇文章中,我们从定性的角度总结了正在进行的关于开放数据的辩论,通过对261种期刊的内容分析,我们建立了社会心理学领域开放数据的期刊政策现状。我们批判性地讨论当前对开放数据的共同期望可能不足以建立定性的严谨性。会带来道德挑战,并可能使那些希望使用定性方法的人在同行评审和出版过程中处于不利地位。我们建议,未来的开放数据指南应旨在反映定性研究中围绕数据共享的争论的细微差别。并摆脱普遍的“一刀切”的数据共享方法。这篇文章概述了过去,present,以及社会心理学期刊开放数据指南的潜在未来。最后,我们为期刊如何更包容地考虑在定性方法中使用开放数据提供了建议,在认识到并为不同的观点留出空间的同时,需要,以及各种形式的社会心理学研究的背景。
    Opening data promises to improve research rigour and democratize knowledge production. But it also presents practical, theoretical, and ethical considerations for qualitative researchers in particular. Discussion about open data in qualitative social psychology predates the replication crisis. However, the nuances of this ongoing discussion have not been translated into current journal guidelines on open data. In this article, we summarize ongoing debates about open data from qualitative perspectives, and through a content analysis of 261 journals we establish the state of current journal policies for open data in the domain of social psychology. We critically discuss how current common expectations for open data may not be adequate for establishing qualitative rigour, can introduce ethical challenges, and may place those who wish to use qualitative approaches at a disadvantage in peer review and publication processes. We advise that future open data guidelines should aim to reflect the nuance of arguments surrounding data sharing in qualitative research, and move away from a universal \"one-size-fits-all\" approach to data sharing. This article outlines the past, present, and the potential future of open data guidelines in social-psychological journals. We conclude by offering recommendations for how journals might more inclusively consider the use of open data in qualitative methods, whilst recognizing and allowing space for the diverse perspectives, needs, and contexts of all forms of social-psychological research.
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  • 文章类型: Journal Article
    使用原始加速度或机器学习等新颖分析方法(“新颖方法”)分析加速度计数据的方法的激增超过了其在实践中的实现。这可能是由于缺乏可访问性,要么是因为作者没有提供他们开发的模型,要么是因为这些模型在作为补充材料包含时很难找到。此外,当提供对模型的访问时,作者可能不包括如何使用模型的示例数据或说明。这进一步阻碍了其他研究人员的使用,特别是那些不是统计或编写计算机代码的专家。目标:我们创建了一个分析加速度计数据的新方法库,用于估算能量消耗和/或身体活动强度,以及一个框架和报告指南,以指导未来的工作。方法:方法是从最近的范围审查中确定的。可用代码,模型,样本数据,和指令被编译或创建。主要结果:63种方法托管在存储库中,在学龄前儿童中(n=6),儿童/青少年(n=20),和成年人(n=42),使用髋关节(n=45),手腕(n=25),大腿(n=4),胸部(n=4),脚踝(n=6),其他(n=4),或监测磨损位置的组合(n=9)。在R中实现了15个模型,虽然提供了48个作为切入点,方程,或决策树。意义:开发的工具应有助于使用和开发分析加速度计数据的新方法,从而提高研究之间的数据一致性和一致性。未来的进步可能涉及包括作者未链接到原始发表的文章或识别活动类型的模型。
    The proliferation of approaches for analyzing accelerometer data using raw acceleration or novel analytic approaches like machine learning (\'novel methods\') outpaces their implementation in practice. This may be due to lack of accessibility, either because authors do not provide their developed models or because these models are difficult to find when included as supplementary material. Additionally, when access to a model is provided, authors may not include example data or instructions on how to use the model. This further hinders use by other researchers, particularly those who are not experts in statistics or writing computer code.Objective: We created a repository of novel methods of analyzing accelerometer data for the estimation of energy expenditure and/or physical activity intensity and a framework and reporting guidelines to guide future work.Approach: Methods were identified from a recent scoping review. Available code, models, sample data, and instructions were compiled or created.Main Results: Sixty-three methods are hosted in the repository, in preschoolers (n = 6), children/adolescents (n = 20), and adults (n = 42), using hip (n = 45), wrist (n = 25), thigh (n = 4), chest (n = 4), ankle (n = 6), other (n = 4), or a combination of monitor wear locations (n = 9). Fifteen models are implemented in R, while 48 are provided as cut-points, equations, or decision trees.Significance: The developed tools should facilitate the use and development of novel methods for analyzing accelerometer data, thus improving data harmonization and consistency across studies. Future advances may involve including models that authors did not link to the original published article or those which identify activity type.
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  • 文章类型: Journal Article
    光声成像(PAI)是一种新兴的模式,已显示出在一系列应用中改善患者管理的希望。不幸的是,当前PAI数据格式缺乏统一性,损害了用户间的数据交换和比较,这阻碍了:技术进步;有效的研究合作;以及提供多中心临床试验的努力。为了克服这一挑战,国际光声标准化联盟(IPASC)建立了具有定义的共识元数据结构的数据格式,并开发了开源软件应用程序编程接口(API),以实现从专有文件格式到IPASC格式的转换。该格式基于分层数据格式5(HDF5)并且被设计为存储光声原始时间序列数据。包括内部质量控制机制,以确保转换数据的完整性和一致性。通过将各种专有数据和元数据定义统一为共识格式,IPASC希望促进PAI数据的交换和比较。
    Photoacoustic imaging (PAI) is an emerging modality that has shown promise for improving patient management in a range of applications. Unfortunately, the current lack of uniformity in PAI data formats compromises inter-user data exchange and comparison, which impedes: technological progress; effective research collaboration; and efforts to deliver multi-centre clinical trials. To overcome this challenge, the International Photoacoustic Standardisation Consortium (IPASC) has established a data format with a defined consensus metadata structure and developed an open-source software application programming interface (API) to enable conversion from proprietary file formats into the IPASC format. The format is based on Hierarchical Data Format 5 (HDF5) and designed to store photoacoustic raw time series data. Internal quality control mechanisms are included to ensure completeness and consistency of the converted data. By unifying the variety of proprietary data and metadata definitions into a consensus format, IPASC hopes to facilitate the exchange and comparison of PAI data.
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  • 文章类型: Journal Article
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