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
    最近发布的干细胞研究中的ISSCR标准推荐人多能干细胞系(hPSC)的注册。注册对于建立干细胞来源和将细胞系与源自这些细胞系的数据连接至关重要。在这项研究中,我们试图通过与48个澳大利亚干细胞利益相关者进行访谈来了解注册的常见障碍,包括研究人员,临床医生,和行业专业人士。澳大利亚干细胞研究人员通常不会注册他们的细胞系,国际注册局捕获的澳大利亚线路中只有三分之一完全完成了注册过程。大多数注册的澳大利亚细胞系缺乏有关其伦理来源或关键多能性特征的完整信息。不完整的注册与注册管理机构建立的开放科学的目标不相称。用户还对提供给资源的不完整信息的质量表示关切。注册被认为是负面的,例如作为出版的障碍或障碍,这影响了用户对注册有用性的看法,并降低了他们与注册管理机构合作寻找资源的可能性。期刊更广泛地采用注册,干细胞协会的持续倡导,将是意识和参与注册的重要杠杆。尽管澳大利亚社区只占潜在注册用户的一小部分,这项研究的结果为期刊提供了方法,登记册,资助者,和国际干细胞界提高注册合规性。
    The recently issued ISSCR standards in stem cell research recommend registration of human pluripotent stem cell lines (hPSCs). Registration is critical to establishing stem cell provenance and connecting cell lines to data derived on those lines. In this study, we sought to understand common barriers to registration by conducting interviews with forty-eight Australian stem cell stakeholders, including researchers, clinicians, and industry professionals. Australian stem cell researchers do not routinely register their lines, and only a third of those Australian lines captured by an international registry have fully completed the registration process. Most registered Australian cell lines lack complete information about their ethical provenance or key pluripotency characteristics. Incomplete registration is poorly aligned with the goals of open science on which registries are founded. Users also expressed concerns about the quality of the incomplete information provided to the resource. Registration was considered negatively, for instance as a hurdle or barrier to publication, which impacted on user perceptions of usefulness of registration and lowered the likelihood that they would engage with registries to find resources. Broader adoption of registration by journals, and continued advocacy by stem cell societies, will be important levers for awareness and engagement with registration. Although the Australian community represents a small fraction of potential registry users, the results of this study suggest ways for journals, registries, funders, and the international stem cell community to improve registration compliance.
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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
    EMOKINE是一个软件包和数据集创建套件,用于实验心理学中的情感全身运动研究,情感神经科学,计算机视觉。一个计算框架,全面的指示,一个试点数据集,观察者评级,提供了运动学特征提取代码,以促进未来大规模的数据集创建。此外,EMOKINE框架概述了复杂的运动序列如何促进情绪研究。传统上,在这样的研究中经常使用基于情绪的“行动”刺激,像挥手或走路动作。在这里,相反,一个试点数据集提供了短舞蹈编舞,舞者重复了几次,每次重复都表达了不同的情感意图:愤怒,满足,恐惧,joy,中立,和悲伤。数据集同时是专业拍摄的,并使用XSENS®运动捕捉技术(17个传感器,240帧/秒)。离线提取了12个运动学特征的32个统计数据,第一次在一个单一的数据集中:速度,加速度,角速度,角加速度,肢体收缩,到质心的距离,运动量,无量纲冲击(积分),头部角度(相对于垂直轴和背部),和空间(凸包2D和3D)。Average,中位数绝对偏差(MAD),和最大值是根据适用情况计算的。EMOKINE软件适用于其他运动捕捉系统,并可在Zenodo存储库中公开使用。GitHub上的版本包括:(i)提取32个统计数据的代码,(ii)用于将MVNX文件转换为Blender格式(MVNX=输出文件XSENS®系统)的Python索具插件,和(iii)Python脚本支持的自定义软件,以帮助模糊面孔;后两个在GPLv3许可证下。
    EMOKINE is a software package and dataset creation suite for emotional full-body movement research in experimental psychology, affective neuroscience, and computer vision. A computational framework, comprehensive instructions, a pilot dataset, observer ratings, and kinematic feature extraction code are provided to facilitate future dataset creations at scale. In addition, the EMOKINE framework outlines how complex sequences of movements may advance emotion research. Traditionally, often emotional-\'action\'-based stimuli are used in such research, like hand-waving or walking motions. Here instead, a pilot dataset is provided with short dance choreographies, repeated several times by a dancer who expressed different emotional intentions at each repetition: anger, contentment, fear, joy, neutrality, and sadness. The dataset was simultaneously filmed professionally, and recorded using XSENS® motion capture technology (17 sensors, 240 frames/second). Thirty-two statistics from 12 kinematic features were extracted offline, for the first time in one single dataset: speed, acceleration, angular speed, angular acceleration, limb contraction, distance to center of mass, quantity of motion, dimensionless jerk (integral), head angle (with regards to vertical axis and to back), and space (convex hull 2D and 3D). Average, median absolute deviation (MAD), and maximum value were computed as applicable. The EMOKINE software is appliable to other motion-capture systems and is openly available on the Zenodo Repository. Releases on GitHub include: (i) the code to extract the 32 statistics, (ii) a rigging plugin for Python for MVNX file-conversion to Blender format (MVNX=output file XSENS® system), and (iii) a Python-script-powered custom software to assist with blurring faces; latter two under GPLv3 licenses.
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  • 文章类型: Journal Article
    科学外交与开放科学在当今世界的相关性是不可否认的。科学外交使各国能够共同应对紧迫的全球挑战,比如气候变化,大流行,和粮食安全。开放科学,促进可访问和透明的研究,在这方面起着举足轻重的作用。然而,开放程度视具体情况而定,取决于不同的因素,包括当地的知识和资源。拉丁美洲不仅处于开创性的开放获取战略的最前沿,使它成为一个有趣的案例来研究,但它也对使用科学外交表现出了切实的兴趣。我们的研究采用了混合方法,纳入涉及50个组织和倡议的定量调查,致力于促进拉丁美洲的开放科学,以及两项定性焦点小组研究。我们的主要目标是评估这些实体是否以及如何使用科学外交来实现其目标。非政策实体由于其在该区域的机构稳定而被列为优先事项。我们强调成功的战略,并深入研究阻碍全面实施开放科学原则的现有障碍。我们的研究旨在通过提供一系列建议来加强这些组织与政策和决策者之间的合作。通过揭示拉丁美洲开放科学的现状和动态,我们渴望专注于科学外交,促进知情决策,制定进一步推动该地区走上开放道路的政策,合作,和科研创新。
    The relevance of science diplomacy and open science in today\'s world is undeniable. Science diplomacy enables countries to jointly address pressing global challenges, such as climate change, pandemics, and food security. Open science, promoting accessible and transparent research, plays a pivotal role in this context. Nevertheless, the degree of openness is subject to specific circumstances, contingent upon varying factors, including local knowledge and resources. Latin America has not only been at the forefront of pioneering open access strategies, making it an interesting case to study, but it has also shown a tangible interest in using science diplomacy. Our research employs a mixed-methods approach, incorporating a quantitative survey involving 50 organizations and initiatives dedicated to promoting open science in Latin America, along with two qualitative focus group studies. Our primary objective is to assess if and how these entities use science diplomacy to achieve their objectives. Non-policy entities were prioritized due to their institutional stability in the region. We highlight successful strategies and delve into the existing barriers hindering the full implementation of open science principles. Our research aims to enhance collaboration between these organizations and policy and decision-makers by providing a set of recommendations in that direction. By shedding light on the current landscape and dynamics of open science in Latin America, we aspire to focus on science diplomacy, facilitate informed decision-making, and formulate policies that further propel the region along the path of openness, collaboration, and innovation in scientific research.
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  • 文章类型: Journal Article
    图书馆员通过促进开放科学和开放数据实践来支持研究人员。本文探讨了支持和促进开放科学实践的五种免费工具。开放科学框架为项目管理提供了一个平台,数据共享,和数据存储。OpenRefine清理和格式化数据。DMPTool具有用于数据管理和共享计划的模板,这些模板符合资助者的要求。NIH通用数据元素是标准化数据元素的存储库,最后,NLM洗涤器是用于对临床文本数据进行去识别的工具。信息专业人员可以将这些工具添加到他们的曲目中,并与他们所在机构的研究人员分享。
    Librarians support researchers by promoting open science and open data practices. This article explores five freely available tools that support and facilitate open science practices. Open Science Framework provides a platform for project management, data sharing, and data storage. OpenRefine cleans and formats data. DMPTool has templates for data management and sharing plans that comply with funder mandates. The NIH Common Data Elements is a repository for standardized data elements, and finally, the NLM Scrubber is a tool for de-identifying clinical text data. Information professionals can add these tools to their repertoire and share them with researchers at their institution.
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  • 文章类型: Journal Article
    青少年大脑与认知发育(ABCD)研究,涉及11,000多名青年及其家人,是一个开创性的项目,研究影响大脑和认知发展的各种因素。尽管产生了数百种出版物并且数量不断增加,该研究缺乏一个集中的帮助平台,以协助研究人员在导航和分析广泛的ABCD数据集。为了支持ABCD研究社区,我们创建了NowIKnowMyABCD,第一个集中的文档和通信资源公开提供给研究人员使用ABCD研究数据。它由两个核心要素组成:以用户为中心的网站和主持的讨论板。该网站充当了与ABCD相关的资源的存储库,教程,以及来自社交媒体网站的相关更新和查询的实时提要。讨论委员会为研究人员提供了一个寻求指导的平台,解决问题,并与同龄人互动。我们的目标是让NowIKnowMyABCD在ABCD研究界的参与下成长,促进透明度,合作,坚持开放的科学原则。
    The Adolescent Brain and Cognitive Development (ABCD) Study, involving over 11,000 youth and their families, is a groundbreaking project examining various factors impacting brain and cognitive development. Despite yielding hundreds of publications and counting, the ABCD Study has lacked a centralized help platform to assist researchers in navigating and analyzing the extensive ABCD dataset. To support the ABCD research community, we created NowIKnowMyABCD, the first centralized documentation and communication resource publicly available to researchers using ABCD Study data. It consists of two core elements: a user-focused website and a moderated discussion board. The website serves as a repository for ABCD-related resources, tutorials, and a live feed of relevant updates and queries sourced from social media websites. The discussion board offers a platform for researchers to seek guidance, troubleshoot issues, and engage with peers. Our aim is for NowIKnowMyABCD to grow with participation from the ABCD research community, fostering transparency, collaboration, and adherence to open science principles.
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  • 文章类型: Journal Article
    在一系列开放科学(OS)政策之后,现在有一波举措来监测其采用情况。然而,与开放科学相关的理解和活动的多样性使得监测非常具有挑战性。有一个危险,通过专注于可以容易观察到的内容(例如出版物),许多其他操作系统活动被忽略(例如参与),随着操作系统范围的潜在缩小,路灯效果,以及与OS值的偏差。由于开放科学可以理解为研究体系的系统性转变,我们借鉴了旨在评估社会技术转型的转型创新政策框架中的概念。根据操作系统作为系统转换的观点,我们建议新的监测工作应转向:(i)考虑与操作系统有关的各种行动的系统观点,包括策略和输出(例如数据集),但也包括过程(例如参与式事件),结果(例如公民对科学的兴趣)和预期的影响(例如对解决社会问题的更好的科学贡献);(ii)将监测作为反身学习(而不是问责制或基准)实施;(iii)绘制活动的方向性以及与方向选择相关的价值观。总之,操作系统的监控框架需要对传统的监控实践进行深刻的改变。范围应从当前对输出(例如出版物)的关注扩展到使科学“开放”的连接过程(用法,共同创造和对话),以及对结果(实践的变化)和反映OS的价值观和规范承诺的长期影响。
    Following a flurry of policies for Open Science (OS), there is now a wave of initiatives to monitor its adoption. However, the great diversity of understandings and activities related to Open Science makes monitoring very challenging. There is a danger that by focusing on what can be readily observed (e.g. publications) many other OS activities are overlooked (e.g. participation), with a potential narrowing of OS scope, streetlight effects, and deviation from the values of OS. Since Open Science can be understood as a systemic transformation of the research system, we have borrowed concepts from Transformative Innovation Policies frameworks which aim at evaluating socio-technical transitions. In accordance with this view of OS as a systemic transformation, we propose that the new monitoring efforts should shift towards: (i) systemic perspectives which considers the various actions related to OS, including policies and outputs (e.g. datasets) but also processes (e.g. participatory events), outcomes (e.g. citizen interest in science) and expected impacts (e.g. better scientific contributions to addressing societal problems); (ii) implementation of monitoring as reflexive learning (rather than accountability or benchmarking); (iii) mapping the directionality of the activities and the values associated with the choices in directions. In summary, a monitoring framework for OS requires a profound change in conventional monitoring practices. The scope should broaden from current focus on outputs (such as publications) towards the processes of connection that make science \'open\' (usage, co-creation and dialogue), as well as towards outcomes (changes in practices) and the longer-term impacts that reflect the values and normative commitments of OS.
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  • 文章类型: Journal Article
    Aurignacian是第一个分配给智人的欧洲技术综合体,在广泛的地理范围内得到认可。尽管考古学家主要通过研究石头和骨工具的技术类型变化来确定Aurignacian内部明显的时间文化变化,解开推动这些变化的潜在过程仍然是一个重大的科学挑战。学者们有,例如,假设CampanianIgnimbrite(CI)的超级喷发和与Heinrich事件4的发生相关的气候恶化对欧洲觅食群体产生了重大影响。从Protoaurignacian到早期Aurignacian的技术转变被认为是适应不断变化的环境的考古表现。然而,用于测试这些方案的一些最关键的区域和地层序列被忽视了。在这项研究中,我们深入研究了意大利南部GrottadiCastelcivita的高分辨率地层序列。这里,Uluzzian后面是三个Aurignacian层,由CI的喷发单位密封。采用全面的定量方法-包括属性分析,三维模型分析,和几何形态计量学-我们证明了通常与早期奥里格纳克相关的关键技术特征在CItephra沉积之前就已经发展了。因此,我们的研究提供了第一个直接证据,表明火山超级喷发在这一文化过程中没有任何作用。此外,我们表明,当地的古环境代理与已确定的文化连续性和非连续性模式无关。因此,我们提出了替代研究路径,以探索人口学和区域轨迹在上旧石器时代发展中的作用。
    The Aurignacian is the first European technocomplex assigned to Homo sapiens recognized across a wide geographic extent. Although archaeologists have identified marked chrono-cultural shifts within the Aurignacian mostly by examining the techno-typological variations of stone and osseous tools, unraveling the underlying processes driving these changes remains a significant scientific challenge. Scholars have, for instance, hypothesized that the Campanian Ignimbrite (CI) super-eruption and the climatic deterioration associated with the onset of Heinrich Event 4 had a substantial impact on European foraging groups. The technological shift from the Protoaurignacian to the Early Aurignacian is regarded as an archaeological manifestation of adaptation to changing environments. However, some of the most crucial regions and stratigraphic sequences for testing these scenarios have been overlooked. In this study, we delve into the high-resolution stratigraphic sequence of Grotta di Castelcivita in southern Italy. Here, the Uluzzian is followed by three Aurignacian layers, sealed by the eruptive units of the CI. Employing a comprehensive range of quantitative methods-encompassing attribute analysis, 3D model analysis, and geometric morphometrics-we demonstrate that the key technological feature commonly associated with the Early Aurignacian developed well before the deposition of the CI tephra. Our study provides thus the first direct evidence that the volcanic super-eruption played no role in this cultural process. Furthermore, we show that local paleo-environmental proxies do not correlate with the identified patterns of cultural continuity and discontinuity. Consequently, we propose alternative research paths to explore the role of demography and regional trajectories in the development of the Upper Paleolithic.
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  • 文章类型: Journal Article
    元研究,也被称为“研究中的研究”是一个研究方法的研究领域,reporting,再现性,评估,以及研究连续过程中的激励措施。元研究素养必须确保高质量,透明和可重复的原始数据或元研究产品。在这篇评论中,我们建议对早期职业研究人员进行元研究培训,以此作为对研究过程的更深入理解和评估研究文献和设计高质量原创研究的能力的基础,不管他们选择的研究领域。我们从早期职业培训生的角度讨论元研究和开放科学的重要性,强调增长的重要领域和可能遇到的障碍。
    Meta-research, also known as \"research on research\" is a field of study that investigates the methods, reporting, reproducibility, evaluation, and incentives along the research continuum. Meta-research literacy is imperative to ensure high quality, transparent and reproducible primary data or meta-research products. In this commentary, we propose that early career researchers should be trained in meta-research as a foundation to develop a deeper understanding of the research process and ability to appraise the research literature and design high-quality original studies, irrespective of their chosen field of study. We discuss the importance of meta-research and open science from the perspective of an early career trainee, highlighting essential areas for growth and obstacles one may encounter.
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