ORCID Profile
0000-0002-8990-1985
Current Organisations
Research Software Alliance
,
Australian Research Data Commons
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Publisher: Center for Open Science
Date: 11-06-2022
Abstract: The biological sciences community is increasingly recognizing the value of open, reproducible, and transparent research practices for science and society at large. Despite this recognition, many researchers remain reluctant to share their data and code publicly. This hesitation may arise from knowledge barriers about how to archive data and code, concerns about its re-use, and misaligned career incentives. Here, we define, categorise, and discuss barriers to data and code sharing that are relevant to many research fields. We explore how real and perceived barriers might be overcome or reframed in light of the benefits relative to costs. By elucidating these barriers and the contexts in which they arise, we can take steps to mitigate them and align our actions with the goals of open science, both as in idual scientists and as a scientific community.
Publisher: Pensoft Publishers
Date: 12-10-2022
DOI: 10.3897/RIO.8.E95724
Abstract: In academic research virtually every field has increased its use of digital and computational technology, leading to new scientific discoveries, and this trend is likely to continue. Reliable and efficient scholarly research requires researchers to be able to validate and extend previously generated research results. In the digital era, this implies that digital objectsKahn and Wilensky 2006 used in research should be Findable, Accessible, Interoperable and Reusable (FAIR). These objects include (but are not limited to) data, software, models (for ex le, machine learning), representations of physical objects, virtual research environments, workflows, etc. Leaving any of these digital objects out of the FAIR process may result in a loss of academic rigor and may have severe consequences in the long term for the field, such as a reproducibility crisis. In this extended abstract, we focus on research software as a FAIR digital object (FDO). The FDO framework De Smedt et al. 2020 describes FDOs as being actionable units of knowledge, which can be aggregated, analyzed, and processed by different types of algorithms. Such algorithms must be implemented by software in one form or another. The framework also describes large software stacks supporting FDOs enabling responsible data science and increasing reproducibility. This implies that software is a key ingredient of the FDO framework, and should adhere to the FAIR principles. Software plays multiple roles: it is a DO itself, it is responsible for creating new FDOs (e.g., data) and it helps to make them available to the public (e.g., via repositories and registries). However there is a need to specify in more detail how non-data DOs, in particular software, fit in this framework. Different classes of digital objects have different intrinsic properties and ways to relate to other DOs. This means that while they, in principle, are subject to the high-level FAIR principles, there are also differences depending on their type and properties, requiring an adaptation so FAIR implementations are more aligned to the digital object itself. This holds true in particular to software. Software has intrinsic properties (executability, composite nature, development practices, continuous evolution and versioning, and packaging and distribution) and specific needs that must be considered by the FDO framework. For ex le, open source software is typically developed in the open on social coding platforms, where releases are distributed through package management systems, unlike data that is typically published in archival repositories. These social coding platforms do not provide long term archiving, permanent identifiers, or metadata, and package management systems, while somewhat better, similarly do not make a commitment to long term archiving, do not use identifiers that fit the scholarly publication system well, and provide metadata that may be missing key elements. The FAIR for research software (FAIR4RS, Chue Hong et al. 2021) working group has dedicated significant effort in building a community consensus around developing FAIR principles that are customized for research software, providing methods for researchers to understand and address these gaps. In this presentation we will highlight the importance of software for the FAIR landscape and why different (but related) FAIR principles are needed for software (vs those originally developed for data). Our goal here is to contribute to building an FDO landscape together, where we consider all different types of digital objects that are essential in today's research, and we are enthusiastic about contributing our expertise on research software in helping shape this landscape.
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 05-2023
DOI: 10.1161/HYPERTENSIONAHA.122.20515
Abstract: Aldosterone-producing adenoma (APA) is a benign adrenal tumor with autonomous aldosterone production which causes hypertension and excess cardiovascular risk. Protein phosphorylation regulates aldosterone secretion from adrenal cortical cells, but how signaling networks are remodeled in APA remains unknown. We performed an integrated proteomic and phosphoproteomic profiling of 15 APA and 10 matched nonfunctioning adrenocortical tumors (NFAT) based on the 4-dimensional label-free technique. We further validated our main findings in enlarged APA s les, mice, and adrenocortical cell line. The proteomic and phosphoproteomic profiling of APA and NFAT quantified 5989 proteins and 9011 phosphopeptides. We highlighted differentially expressed and phosphorylated proteins which modulated aldosterone synthesis and secretion from APA. As intracellular calcium is the central signal for aldosterone synthesis, our integrated calcium signaling network implicated wolframin in the control of calcium influx and CYP11B2 (aldosterone synthase) activation in APA (ratio of wolframin expression in APA to NFAT: 6.411, P .001). Among 97 APA cases for validation, a higher expression level of wolframin was associated with a higher plasma aldosterone concentration postcaptopril challenge test and a higher systolic blood pressure. In vitro, the secretion of aldosterone was enhanced by wolframin overexpression, while aldosterone secretion in response to potassium or angiotensin II was inhibited by the knockdown of wolframin. Further in vivo and in vitro data demonstrated the wolframin-calcium axis as an important regulator of CYP11B2 expression and aldosterone production. Wolframin is a regulatory protein in aldosterone hypersecretion. Remodeled calcium transportation and mitochondrial function are involved in wolframin-related aldosterone secretion.
Publisher: Zenodo
Date: 2021
Publisher: Open Science Framework
Date: 2019
Publisher: IEEE
Date: 10-2018
Publisher: Zenodo
Date: 2022
Publisher: Zenodo
Date: 2021
Publisher: Zenodo
Date: 2021
Publisher: Zenodo
Date: 2022
Publisher: Springer Science and Business Media LLC
Date: 14-10-2022
DOI: 10.1038/S41597-022-01710-X
Abstract: Research software is a fundamental and vital part of research, yet significant challenges to discoverability, productivity, quality, reproducibility, and sustainability exist. Improving the practice of scholarship is a common goal of the open science, open source, and FAIR (Findable, Accessible, Interoperable and Reusable) communities and research software is now being understood as a type of digital object to which FAIR should be applied. This emergence reflects a maturation of the research community to better understand the crucial role of FAIR research software in maximising research value. The FAIR for Research Software (FAIR4RS) Working Group has adapted the FAIR Guiding Principles to create the FAIR Principles for Research Software (FAIR4RS Principles). The contents and context of the FAIR4RS Principles are summarised here to provide the basis for discussion of their adoption. Ex les of implementation by organisations are provided to share information on how to maximise the value of research outputs, and to encourage others to lify the importance and impact of this work.
Publisher: Zenodo
Date: 2019
Publisher: Zenodo
Date: 2018
Publisher: Pensoft Publishers
Date: 02-07-2019
DOI: 10.3897/BISS.3.37677
Abstract: ELIXIR (ELIXIR Europe 2019a) is an intergovernmental organization that brings together life science resources across Europe. These resources include databases, software tools, training materials, cloud storage, and supercomputers. One of the goals of ELIXIR is to coordinate these resources so that they form a single infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. ELIXIR's activities are ided into the following five areas: Data, Tools, Interoperability, Compute and Training, each known as “platform”. The ELIXIR Tools Platform works to improve the discovery, quality and sustainability of software resources. The Software Development Best Practices task of the Tools Platform aims to raise the quality and sustainability of research software by producing, adopting, and promoting information standards and best practices relevant to the software development life cycle. We have published four (4OSS) simple recommendations to encourage best practices in research software (Jiménez et al. 2017) and the Top 10 metrics for recommended life science software practices (Artaza et al. 2016). The 4OSS simple recommendations are as follows: Develop a publicly accessible open source code from day one. Make software easy to discover by providing software metadata via a popular community registry. Adopt a license and comply with the licenses of third-party dependencies. Have clear and transparent contribution, governance and communication processes. Develop a publicly accessible open source code from day one. Make software easy to discover by providing software metadata via a popular community registry. Adopt a license and comply with the licenses of third-party dependencies. Have clear and transparent contribution, governance and communication processes. In order to encourage researchers and developers to adopt the 4OSS recommendations and build FAIR (Findable, Accessible, Interoperable and Reusable) software, the best practices group, in partnership with the ELIXIR Training platform, The Carpentries (Carpentries 2019, ELIXIR Europe 2019b), and other communities, are creating a collection of training materials (Kuzak et al. 2019). The next step is to adopt, promote, and recognise these information standards and best practices. The group will address this by (i) developing comprehensive guidelines for software curation, (ii) through training researchers and developers towards the adoption of software best practices and (iii) improvement of the usability of Tools Platform products. Additionally, a direct outcome of this task will be a software management plan template, connected to a concise description of the guidelines for open research software and production of a white paper for the software development management plan for ELIXIR, which can be consequently used to produce training materials. We will work with the newly formed ReSA (Research Software Alliance) to facilitate the adoption of this plan for the broader community.
Publisher: The Royal Society
Date: 23-11-2022
Abstract: The biological sciences community is increasingly recognizing the value of open, reproducible and transparent research practices for science and society at large. Despite this recognition, many researchers fail to share their data and code publicly. This pattern may arise from knowledge barriers about how to archive data and code, concerns about its reuse, and misaligned career incentives. Here, we define, categorize and discuss barriers to data and code sharing that are relevant to many research fields. We explore how real and perceived barriers might be overcome or reframed in the light of the benefits relative to costs. By elucidating these barriers and the contexts in which they arise, we can take steps to mitigate them and align our actions with the goals of open science, both as in idual scientists and as a scientific community.
Publisher: Zenodo
Date: 2021
Publisher: figshare
Date: 2021
Publisher: Zenodo
Date: 2019
Publisher: Zenodo
Date: 2022
Publisher: Zenodo
Date: 2021
Publisher: American Association for Cancer Research (AACR)
Date: 02-06-2022
DOI: 10.1158/1055-9965.EPI-22-0234
Abstract: Mechanisms for how Helicobacter pylori infection affects risk of gastroesophageal reflux disease (GERD) and Barrett's esophagus are incompletely understood and might differ by sex. In a case–control study nested in the Melbourne Collaborative Cohort Study with 425 GERD cases and 169 Barrett's esophagus cases (identified at 2007–2010 follow-up), we estimated sex-specific odds ratios for participants who were H. pylori seronegative versus seropositive at baseline (1990–1994). To explore possible mechanisms, we (i) compared patterns of H. pylori-induced gastritis by sex using serum pepsinogen-I and gastrin-17 data and (ii) quantified the effect of H. pylori seronegativity on Barrett's esophagus mediated by GERD using causal mediation analysis. For men, H. pylori seronegativity was associated with 1.69-fold [95% confidence interval (CI), 1.03–2.75] and 2.28-fold (95% CI, 1.27–4.12) higher odds of GERD and Barrett's esophagus, respectively. No association was observed for women. H. pylori-induced atrophic antral gastritis was more common in men (68%) than in women (56% P = 0.015). For men, 5 of the 15 per 1,000 excess Barrett's esophagus risk from being seronegative were mediated by GERD. Men, but not women, who were H. pylori seronegative had increased risks of GERD and Barrett's esophagus. A possible explanation might be sex differences in patterns of H. pylori-induced atrophic antral gastritis, which could lead to less erosive reflux for men. Evidence of GERD mediating the effect of H. pylori on Barrett's esophagus risk among men supports this proposed mechanism. The findings highlight the importance of investigating sex differences in the effect of H. pylori on risk of GERD and Barrett's esophagus in future studies.
Publisher: Zenodo
Date: 2020
Publisher: Zenodo
Date: 2021
Publisher: Zenodo
Date: 2020
Publisher: Zenodo
Date: 2019
Publisher: Zenodo
Date: 2019
Publisher: Center for Open Science
Date: 07-12-2021
Abstract: Sharing of research code would greatly benefit neuroscience, but this practice is h ered by a collective action problem. Since the development of the internet, conditional pledge platforms (e.g., Kickstarter) have increasingly been used to solve globally-dispersed collective action problems (Hallam, 2016). However, this strategy has yet to be implemented within academia. In this brief paper, we introduce a general purpose conditional pledge platform for the research community: Project Free Our Knowledge. We highlight a new conditional pledge c aign that was initiated at Brainhack 2021 and aims to motivate a critical mass of neuroscientists to share their research code. Crucially, this commitment activates only when a user-defined threshold of support is reached. We conclude by sharing our vision for how the research community could use collective action c aigns to create a sustained, evidence-based movement for social change in academia.
Publisher: Zenodo
Date: 2022
Publisher: Zenodo
Date: 2022
Publisher: Zenodo
Date: 2022
Publisher: Zenodo
Date: 2022
Publisher: Zenodo
Date: 2022
Publisher: Zenodo
Date: 2021
Publisher: F1000 Research Limited
Date: 2018
Publisher: Zenodo
Date: 2022
Publisher: Zenodo
Date: 2019
Publisher: Zenodo
Date: 2022
Publisher: Zenodo
Date: 2018
Publisher: Zenodo
Date: 2018
Publisher: IOS Press
Date: 12-06-2020
DOI: 10.3233/DS-190026
Publisher: Software Sustainability Institute: Collaborations Workshop
Date: 2021
Publisher: Zenodo
Date: 2018
Publisher: Public Library of Science (PLoS)
Date: 23-07-2020
Publisher: figshare
Date: 2020
Location: Australia
No related grants have been discovered for Paula Andrea Martinez.