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Utilizing Machine Learning and causal graph approaches to Address Confounding Factors in Health Science Research: A Scoping Review. 利用机器学习和因果图方法解决健康科学研究中的混淆因素:范围综述。
F1000Research Pub Date : 2025-09-10 eCollection Date: 2025-01-01 DOI: 10.12688/f1000research.159632.2
Ahmed Hossain
{"title":"Utilizing Machine Learning and causal graph approaches to Address Confounding Factors in Health Science Research: A Scoping Review.","authors":"Ahmed Hossain","doi":"10.12688/f1000research.159632.2","DOIUrl":"10.12688/f1000research.159632.2","url":null,"abstract":"<p><p>Confounding can significantly distort the findings of studies examining cause-and-effect relationships, especially in etiological research. To mitigate this issue, researchers must carefully assess potential confounding variables that may relate to both the exposure and outcome but are not directly influenced by the exposure itself. It is essential that these variables truly impact the outcome rather than simply being correlated with the exposure to avoid false associations. Strengthening confidence in the actual relationship between exposure and outcome requires an understanding of biological mechanisms and the application of various methods to adjust for confounders. The oversight of confounding often arises from inappropriate statistical tests and the aggregation of data across multiple studies. This scoping review article discusses the challenges posed by confounding and presents machine learning approaches for effective control in health science research. Directed acyclic graphs (DAGs) serve as causal graph tools to identify potential confounding variables in health research. By mapping presumed relationships between variables, DAGs enable researchers to estimate causal effects more accurately. While traditional methods such as randomization, matching, and stratification remain effective for controlling confounding, newer techniques like latent variable modeling with negative controls and machine learning methods such as LASSO, Ridge regression, and random forests offer enhanced flexibility and adaptability.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"14 ","pages":"129"},"PeriodicalIF":0.0,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12457880/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145148114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A libraries reproducibility hackathon: connecting students to university research and testing the longevity of published code. 图书馆再现性黑客马拉松:将学生与大学研究联系起来,并测试已发布代码的寿命。
F1000Research Pub Date : 2025-09-09 eCollection Date: 2024-01-01 DOI: 10.12688/f1000research.156917.2
Chasz Griego, Kristen Scotti, Elizabeth Terveen, Joseph Chan, Daisy Sheng, Alfredo González-Espinoza, Christopher Warren
{"title":"A libraries reproducibility hackathon: connecting students to university research and testing the longevity of published code.","authors":"Chasz Griego, Kristen Scotti, Elizabeth Terveen, Joseph Chan, Daisy Sheng, Alfredo González-Espinoza, Christopher Warren","doi":"10.12688/f1000research.156917.2","DOIUrl":"10.12688/f1000research.156917.2","url":null,"abstract":"<p><strong>Background: </strong>Reproducibility is a basis of scientific integrity, yet it remains a significant challenge across disciplines in computational science. This reproducibility crisis is now being met with an Open Science movement, which has risen to prominence within the scientific community and academic libraries especially. At the Carnegie Mellon University Libraries, the Open Science and Data Collaborations (OSDC) Program promotes Open Science practices with resources, services, and events. Hosting hackathons in academic libraries may show promise for furthering such efforts.</p><p><strong>Methods: </strong>To address the need for reproducible computational research and promote Open Science within the community, members of the OSDC Program organized a single-day hackathon centered around reproducibility. Partnering with a faculty researcher in English and Digital Humanities, we invited community members to reuse Python code and data from a research publication deposited to Harvard Dataverse. We also published these materials as a compute capsule in Code Ocean that participants could also access. Additionally, we investigated ways to use ChatGPT to troubleshoot errors from rerunning this code.</p><p><strong>Results: </strong>Three students from the School of Computer Science participated in this hackathon. Accessing materials from Harvard Dataverse, these students found success reproducing most of the data visualizations, but they required some manual setup and modifications to address depreciated libraries used in the code. Alternatively, we found Code Ocean to be a highly accessible option, free from depreciation risk. Last, ChatGPT also aided in finding and addressing the same roadblocks to successfully reproduce the same figures as the participating students.</p><p><strong>Conclusions: </strong>This hackathon allowed several students an opportunity to interact with and evaluate real research outputs, testing the reproducibility of computational data analyses. Partnering with faculty opened opportunities to improve open research materials. This case study outlines one approach for other academic libraries to highlight challenges that face reproducibility in an interactive setting.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"13 ","pages":"1305"},"PeriodicalIF":0.0,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12501581/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145250552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Hesitant Fuzzy Subalgebras, Ideals and Congruences on Autometrized Algebras. 自动机代数上的犹豫模糊子代数、理想与同余。
F1000Research Pub Date : 2025-09-09 eCollection Date: 2025-01-01 DOI: 10.12688/f1000research.161430.2
Gebrie Yeshiwas Tilahun
{"title":"Hesitant Fuzzy Subalgebras, Ideals and Congruences on Autometrized Algebras.","authors":"Gebrie Yeshiwas Tilahun","doi":"10.12688/f1000research.161430.2","DOIUrl":"10.12688/f1000research.161430.2","url":null,"abstract":"<p><p>This paper introduces the study of hesitant fuzzy subalgebras of autometrized algebras, obtains some of their properties, and gives some examples. Next, we introduce the concept of the hesitant fuzzy ideal and examine some of its properties. Finally, we introduce a hesitant fuzzy congruence on autometrized algebras and discuss some of its properties. We also introduce the characteristic equations and level subsets of hesitant fuzzy sets and relations on autometrized algebras.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"14 ","pages":"183"},"PeriodicalIF":0.0,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12441674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145112360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Forecasting in vivo pharmacokinetics of metformin HCl floating beads using Gastroplus® PBPK. 利用Gastroplus®PBPK预测盐酸二甲双胍浮珠的体内药代动力学。
F1000Research Pub Date : 2025-09-09 eCollection Date: 2025-01-01 DOI: 10.12688/f1000research.159438.2
Sura Zuhair Mahmood, Nora Zawar Yousif, Masar Basim Mohsin Mohamed
{"title":"Forecasting <i>in vivo</i> pharmacokinetics of metformin HCl floating beads using Gastroplus® PBPK.","authors":"Sura Zuhair Mahmood, Nora Zawar Yousif, Masar Basim Mohsin Mohamed","doi":"10.12688/f1000research.159438.2","DOIUrl":"10.12688/f1000research.159438.2","url":null,"abstract":"<p><strong>Background: </strong>Diabetes mellitus type II is expected to impact a large population worldwide. Among the available therapeutic options, Metformin hydrochloride is a key medication, particularly for those who cannot effectively manage the condition through changes in diet and lifestyle alone. This research aimed to predict their <i>in vivo</i> parameters from an <i>in vitro</i> release study by developing a physiologically based pharmacokinetic (PBPK) model by using Gastroplus <sup>®</sup> software.</p><p><strong>Methods: </strong>Sodium alginate-based MH floating beads were prepared by dissolving different concentrations of sodium alginate in deionized water, incorporating MH (1 g) and calcium carbonate (1.5 mg) as a gas-forming agent, and mixing at 200 rpm. The air-free dispersion, achieved through 30 minutes of sonication, was dropped into a 5% w/v calcium chloride solution containing 5% v/v isopropyl alcohol via a syringe for cross-linking and bead formation. Beads were cured in the solution for 30 minutes to enhance mechanical strength, then filtered, washed, and air-dried for 24 hours, ensuring uniformity and stability for controlled drug delivery and the prepared beads were evaluated for their entrapment efficiency %, morphology, floating property and <i>in vitro</i> release Ultimately, using Gastroplus <sup>®</sup> software, to predict the pharmacokinetic profile of <i>in vitro</i> release results.</p><p><strong>Results: </strong>Entrapment efficiency exhibited acceptable values, and the beads were smooth, and rounded in shape for all formulations. The beads remained afloat during the release study; the release study revealed that F1 to F5 showed asymptotic slow-release, while F6 and F7 gave shorter release times. The prediction of absorption indicated highest MH absorption was in the jejunum, then the duodenum.</p><p><strong>Conclusion: </strong>The prepared Beads had promising pharmacokinetic parameters and C max was close to MH modified released tablet.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"14 ","pages":"140"},"PeriodicalIF":0.0,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12485330/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Case Report: Pericardial effusion in late onset neonatal Escherichia coli sepsis. 病例报告:迟发性新生儿大肠杆菌败血症心包积液。
F1000Research Pub Date : 2025-09-09 eCollection Date: 2025-01-01 DOI: 10.12688/f1000research.167697.2
N Missaoui, Rania Ben Rabeh, Azza Hedhili, Salem Yahiaoui, Sofien Atitallah, Olfa Bouyahia, Sonia Mazigh Mrad, Samir Boukthir
{"title":"Case Report: Pericardial effusion in late onset neonatal Escherichia coli sepsis.","authors":"N Missaoui, Rania Ben Rabeh, Azza Hedhili, Salem Yahiaoui, Sofien Atitallah, Olfa Bouyahia, Sonia Mazigh Mrad, Samir Boukthir","doi":"10.12688/f1000research.167697.2","DOIUrl":"10.12688/f1000research.167697.2","url":null,"abstract":"<p><strong>Background: </strong>Pericardial effusion (PE) is a rare condition in neonates and usually due to central venous catheters. Infective pericarditis is an extremely rare condition in neonates.</p><p><strong>Methods: </strong>We describe a case of a preterm neonate with <i>Escherichia coli</i> pericarditis.</p><p><strong>Results: </strong>A preterm female neonate born at 34 weeks of gestation with a birth weight of 1600 grams was admitted because of respiratory distress. The patient was managed using a high-flow nasal cannula. She did not receive a central venous catheter or antibiotics. The outcome was good and the patient was discharged on day 14 of life. On day 18, she was readmitted because of fever and shortness of breath. Blood sample culture was positive for <i>Escherichia coli</i>. On day 21, the patient presented signs of heart failure. Chest radiography showed cardiomegaly. Cardiac ultrasound showed pre tamponade. Our patient was managed with pericardial drainage and cefotaxime administration. The outcome was good and further follow-up was unremarkable.</p><p><strong>Conclusions: </strong>Even though rare, infective pericarditis with effusion should be suspected in neonates who show deterioration in respiratory and hemodynamic status even if they do not have central venous catheter.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"14 ","pages":"770"},"PeriodicalIF":0.0,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12441665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145085624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Assessing Knowledge and Awareness of Occupational Hazards and Preventive Measures among Dentists and Final-year Students in Two Dentistry Hospitals, Kabul, Afghanistan. 评估阿富汗喀布尔两所牙科医院牙医和最后一年级学生对职业危害和预防措施的知识和意识。
F1000Research Pub Date : 2025-09-09 eCollection Date: 2025-01-01 DOI: 10.12688/f1000research.166053.3
Fariha Kamal, Abdurrahman Anwari, Farahnaz Ghazanfari, Ahmad Anas Khairzad, Nematullah Sharifi, Fariha Omarzad
{"title":"Assessing Knowledge and Awareness of Occupational Hazards and Preventive Measures among Dentists and Final-year Students in Two Dentistry Hospitals, Kabul, Afghanistan.","authors":"Fariha Kamal, Abdurrahman Anwari, Farahnaz Ghazanfari, Ahmad Anas Khairzad, Nematullah Sharifi, Fariha Omarzad","doi":"10.12688/f1000research.166053.3","DOIUrl":"10.12688/f1000research.166053.3","url":null,"abstract":"<p><strong>Introduction: </strong>This study aimed to evaluate the knowledge and awareness of occupational hazards and preventive measures among dentists and final-year students in two dentistry hospitals in Kabul, Afghanistan.</p><p><strong>Methods: </strong>A cross-sectional descriptive study design was used in this research, which was distributed to 198 dental professionals, with Part A dealing with sociodemographic data, Part B focusing on awareness of occupational hazards, and Part C on preventive measures. Responses were analyzed to assess the level of awareness using a five-point scale. The data were also compared using Mann-Whitney U tests to examine the differences between male and female respondents and between final-year dental students and practicing dentists.</p><p><strong>Results: </strong>The overall mean proportion of correct answers was 0.71 (71%), indicating moderately high awareness. Part B had a mean of 0.73 (high), and Part C had a mean of 0.69 (medium). High awareness was found in areas such as radiation safety (93.4%), infection control (97.5%) and ergonomics (85.9%). However, gaps were identified in knowledge of lead protective gowns (15.2%) and the inverse square law (8.1%). In Part C, high awareness was noted regarding safety guidelines for electrical devices (85.9%) and protective eyewear (93.4%), but low awareness was found regarding safety boxes for sharp instruments (19.7%) and the scoop technique (31.8%). Mann-Whitney U tests revealed significant differences between male and female respondents (p < 0.001), with females showing higher awareness, although the effect size was small (r = -0.247). No significant difference was observed between the final-year students and practicing dentists (p = 0.575).</p><p><strong>Conclusions: </strong>Although dental professionals exhibit a relatively high level of awareness regarding occupational hazards and preventive measures, specific knowledge gaps persist. Addressing these deficiencies through structured educational interventions and continuous professional training is essential to enhance the occupational safety and improve the overall well-being of dental practitioners.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"14 ","pages":"639"},"PeriodicalIF":0.0,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12457895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145148111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Establishing the ELIXIR Microbiome Community. 建立ELIXIR微生物群落。
F1000Research Pub Date : 2025-09-08 eCollection Date: 2024-01-01 DOI: 10.12688/f1000research.144515.2
Robert D Finn, Bachir Balech, Josephine Burgin, Physilia Chua, Erwan Corre, Cymon J Cox, Claudio Donati, Vitor Martins Dos Santos, Bruno Fosso, John Hancock, Katharina F Heil, Naveed Ishaque, Varsha Kale, Benoit J Kunath, Claudine Médigue, Teresa Nogueira, Evangelos Pafilis, Graziano Pesole, Lorna Richardson, Monica Santamaria, Nikolaos Strepis, Tim Van Den Bossche, Juan Antonio Vizcaíno, Haris Zafeiropoulos, Nils P Willassen, Eric Pelletier, Bérénice Batut
{"title":"Establishing the ELIXIR Microbiome Community.","authors":"Robert D Finn, Bachir Balech, Josephine Burgin, Physilia Chua, Erwan Corre, Cymon J Cox, Claudio Donati, Vitor Martins Dos Santos, Bruno Fosso, John Hancock, Katharina F Heil, Naveed Ishaque, Varsha Kale, Benoit J Kunath, Claudine Médigue, Teresa Nogueira, Evangelos Pafilis, Graziano Pesole, Lorna Richardson, Monica Santamaria, Nikolaos Strepis, Tim Van Den Bossche, Juan Antonio Vizcaíno, Haris Zafeiropoulos, Nils P Willassen, Eric Pelletier, Bérénice Batut","doi":"10.12688/f1000research.144515.2","DOIUrl":"10.12688/f1000research.144515.2","url":null,"abstract":"<p><p>Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples. In particular, experimental approaches such as metagenomics, metabarcoding, metatranscriptomics and metaproteomics have provided profound insights into the vast, hitherto unknown, microbial biodiversity. The ELIXIR Marine Metagenomics Community, initiated amongst researchers focusing on marine microbiomes, has concentrated on promoting standards around microbiome-derived sequence analysis, as well as understanding the gaps in methods and reference databases, and identifying solutions to the computational overheads of performing such analyses. Nevertheless, the methods used and the challenges faced are not confined to marine microbiome studies, but are broadly applicable to other biomes. Thus, expanding this Marine Metagenomics Community to a more inclusive ELIXIR Microbiome Community will enable it to encompass a broader range of biomes and link expertise across 'omics technologies. Furthermore, engaging with a large number of researchers will improve the efficiency and sustainability of bioinformatics infrastructure and resources for microbiome research (standards, data, tools, workflows, training), which will enable a deeper understanding of the function and taxonomic composition of the different microbial communities.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"13 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12441670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145085606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Impact of Green Supply Chain Management on Sustainable Performance: A Dual Mediated-moderated Analysis of Green Technology Innovation And Big Data Analytics Capability Powered by Artificial Intelligence. 绿色供应链管理对可持续绩效的影响:绿色技术创新和人工智能驱动的大数据分析能力的双重中介调节分析
F1000Research Pub Date : 2025-09-08 eCollection Date: 2024-01-01 DOI: 10.12688/f1000research.154615.2
Quswah Makhdoom, Ikramuddin Junejo, Jan Muhammad Sohu, Syed Mir Muhammad Shah, Belal Mahmoud Alwadi, Faisal Ejaz, Md Billal Hossain
{"title":"Impact of Green Supply Chain Management on Sustainable Performance: A Dual Mediated-moderated Analysis of Green Technology Innovation And Big Data Analytics Capability Powered by Artificial Intelligence.","authors":"Quswah Makhdoom, Ikramuddin Junejo, Jan Muhammad Sohu, Syed Mir Muhammad Shah, Belal Mahmoud Alwadi, Faisal Ejaz, Md Billal Hossain","doi":"10.12688/f1000research.154615.2","DOIUrl":"10.12688/f1000research.154615.2","url":null,"abstract":"<p><strong>Background: </strong>This study aims to empirically test a comprehensive interrelationship between green supply chain management (GSCM), green technology innovation (GTI), waste management (WM), big data analytics capability powered by artificial intelligence (BDAC-AI), and their collective impact on sustainable performance (SP) in organizational contexts.</p><p><strong>Methods: </strong>This study was conducted in Pakistan's food processing sector. The respondents included 495 managers working in the food processing industry. A structural equation modelling (SEM) approach is used to examine direct and indirect relationships between the variables. The originality of this study lies in integration of the technology acceptance model (TAM) and dynamic capability theory (DCT) to understand sustainable practices in the context of the provided model.</p><p><strong>Results: </strong>This study highlights that GSCM, GTI, WM, and BDAC-AI have positive, strong, and direct impacts on SP. Furthermore, GTI and WM only partially mediate the link between GSCM and SP, whereas the two moderate the link. In addition, BDAC-AI had a moderating effect on the relationship between GTI and SP. This study has managerial implications, including strategies that involve the use of theoretical frameworks for technological acceptance and dynamic capabilities to support sustainable initiatives. However, it is worth noting that the findings provide a practical contingency for managers and businesses interested in implementing green studies effectively, improving technologies, and strengthening sustainable performance capabilities.</p><p><strong>Conclusions: </strong>The study extends the literature by establishing a model for operationalizing GSCM in the food processing sector. Furthermore, it adds value in that it first integrates TAM and DCT to explain sustainable operations and their impact on organizations. Furthermore, it extends the existing literature by establishing a relationship between GSCM and SC. It offers a model through which GSCM can be operationalized in the context of the FS sector.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"13 ","pages":"1140"},"PeriodicalIF":0.0,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12504947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Foundational Competencies and Responsibilities of a Research Software Engineer: Current State and Suggestions for Future Directions. 研究软件工程师的基本能力和责任。
F1000Research Pub Date : 2025-09-08 eCollection Date: 2024-01-01 DOI: 10.12688/f1000research.157778.2
Florian Goth, Renato Alves, Matthias Braun, Leyla Jael Castro, Gerasimos Chourdakis, Simon Christ, Jeremy Cohen, Stephan Druskat, Fredo Erxleben, Jean-Noël Grad, Magnus Hagdorn, Toby Hodges, Guido Juckeland, Dominic Kempf, Anna-Lena Lamprecht, Jan Linxweiler, Frank Löffler, Michele Martone, Moritz Schwarzmeier, Heidi Seibold, Jan Philipp Thiele, Harald von Waldow, Samantha Wittke
{"title":"Foundational Competencies and Responsibilities of a Research Software Engineer: Current State and Suggestions for Future Directions.","authors":"Florian Goth, Renato Alves, Matthias Braun, Leyla Jael Castro, Gerasimos Chourdakis, Simon Christ, Jeremy Cohen, Stephan Druskat, Fredo Erxleben, Jean-Noël Grad, Magnus Hagdorn, Toby Hodges, Guido Juckeland, Dominic Kempf, Anna-Lena Lamprecht, Jan Linxweiler, Frank Löffler, Michele Martone, Moritz Schwarzmeier, Heidi Seibold, Jan Philipp Thiele, Harald von Waldow, Samantha Wittke","doi":"10.12688/f1000research.157778.2","DOIUrl":"10.12688/f1000research.157778.2","url":null,"abstract":"<p><p>The term Research Software Engineer, or RSE, emerged a little over 10 years ago as a way to represent individuals working in the research community but focusing on software development. The term has been widely adopted and there are a number of high-level definitions of what an RSE is. However, the roles of RSEs vary depending on the institutional context they work in. At one end of the spectrum, RSE roles may look similar to a traditional research role. At the other extreme, they resemble that of a software engineer in industry. Most RSE roles inhabit the space between these two extremes. Therefore, providing a straightforward, comprehensive definition of what an RSE does and what experience, skills and competencies are required to become one is challenging. In this community paper we define the broad notion of what an RSE is, explore the different types of work they undertake, and define a list of foundational competencies as well as values that outline the general profile of an RSE. These foundational skills are encountered to a large extent within the skill sets of current RSEs in Germany and beyond, and we propose them as a starting point for aspiring RSEs to shape their technical profile. Further research and training can build upon this foundation of skills and focus on various aspects in greater detail. We expect that graduates and practitioners will have a larger and more diverse set of skills than outlined here. On this basis, we elaborate on the progression of these skills along different dimensions. We look at specific types of RSE roles, propose recommendations for organisations, give examples of future specialisations, and detail how existing curricula fit into this framework.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"13 ","pages":"1429"},"PeriodicalIF":0.0,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12426816/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145063806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Engaging Sustainable Reforestation and Forest Protection in the Wallacea Line, Indonesia. 参与印尼瓦拉科线的可持续再造林和森林保护。
F1000Research Pub Date : 2025-09-08 eCollection Date: 2025-01-01 DOI: 10.12688/f1000research.159731.3
Yohanis Ngongo, Gerson N Njurumana, Markus Kudeng Sallata, Merryana Kiding Allo, Nurhaedah Muin, Wahyudi Isnan, Nardy Noerman Najib, Achmad Rizal Hak Bisjoe, Indra A S L P Putri, Hariany Siappa, Ronald T P Hutapea, Yelin Adalina, Suhartati Suhartati, Yohanes Leki Seran, Agustinus Panusunan Tampubolon
{"title":"Engaging Sustainable Reforestation and Forest Protection in the Wallacea Line, Indonesia.","authors":"Yohanis Ngongo, Gerson N Njurumana, Markus Kudeng Sallata, Merryana Kiding Allo, Nurhaedah Muin, Wahyudi Isnan, Nardy Noerman Najib, Achmad Rizal Hak Bisjoe, Indra A S L P Putri, Hariany Siappa, Ronald T P Hutapea, Yelin Adalina, Suhartati Suhartati, Yohanes Leki Seran, Agustinus Panusunan Tampubolon","doi":"10.12688/f1000research.159731.3","DOIUrl":"10.12688/f1000research.159731.3","url":null,"abstract":"<p><p>The Wallacea region of Indonesia has high biodiversity and highly unique and endangered species. Its terrestrial ecosystems have unique flora and fauna found nowhere else. Nevertheless, the strategy for protecting and conserving the Wallacea ecosystem is like that in other parts of Indonesia, since it refers to the national forest and environmental regulations. The uniqueness of the Wallacea ecosystem does not reflect the extraordinary efforts of protecting and conserving the region's pristine ecosystem. The continuing decline of the forestland and expansions of agricultural lands have indicated the need for a more fundamental and integrative approach to conserving and protecting the Wallacea ecosystem, particularly forestlands. We use the actor-centered power (ACP) approach or ideas and use the Wallacea Line to highlight how this idea is contested and confronted with the dynamics of complex societies and ecosystems. The ACP approach is the most widely used one in the implementation of the community forest (CF) program in Indonesia. The CF program is one of Indonesia's community-based forest management schemes that empowers local communities to manage state forests sustainably. We chose two national parks established in the Wallacea region, Mutis on Timor Island and Matalawa on Sumba Island, to elaborate further on the development, conservation, and changes that occurred within that landscape. The ACP approach, in line with the spirit of the decentralization era, has mixed consequences for forest management and the biodiversity of the Wallacea region. Regarding the specific characteristics of the Wallacea region and lessons learned from the ACP approach implementation in the CF program, we then propose a sustainable model of reforestation and forest protection that applies the principle of \"unity in diversity,\" where all actors involved have space for the growth of creativity and positive contributions to sustainable forest protection.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"14 ","pages":"165"},"PeriodicalIF":0.0,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12498518/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145244050","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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