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González-Cebrián A, Bradford M, Chis AE, González-Vélez H. Standardised Versioning of Datasets: a FAIR-compliant Proposal. Sci Data 2024; 11:358. [PMID: 38594314 PMCID: PMC11003959 DOI: 10.1038/s41597-024-03153-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/15/2024] [Indexed: 04/11/2024] Open
Abstract
This paper presents a standardised dataset versioning framework for improved reusability, recognition and data version tracking, facilitating comparisons and informed decision-making for data usability and workflow integration. The framework adopts a software engineering-like data versioning nomenclature ("major.minor.patch") and incorporates data schema principles to promote reproducibility and collaboration. To quantify changes in statistical properties over time, the concept of data drift metrics (d) is introduced. Three metrics (dP, dE,PCA, and dE,AE) based on unsupervised Machine Learning techniques (Principal Component Analysis and Autoencoders) are evaluated for dataset creation, update, and deletion. The optimal choice is the dE,PCA metric, combining PCA models with splines. It exhibits efficient computational time, with values below 50 for new dataset batches and values consistent with seasonal or trend variations. Major updates (i.e., values of 100) occur when scaling transformations are applied to over 30% of variables while efficiently handling information loss, yielding values close to 0. This metric achieved a favourable trade-off between interpretability, robustness against information loss, and computation time.
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Affiliation(s)
| | - Michael Bradford
- Cloud Competency Centre, National College of Ireland, Dublin, Ireland
| | - Adriana E Chis
- Cloud Competency Centre, National College of Ireland, Dublin, Ireland
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Ward J, Reynolds RJ, Connell E, Anton W, Kabeel A, Charvat JM, Nartey N, Marotta K, Abukmail A, Buckland DM, Van Baalen M, Antonsen E. Levels of evidence for human system risk evaluation. NPJ Microgravity 2024; 10:33. [PMID: 38509136 PMCID: PMC10954631 DOI: 10.1038/s41526-024-00372-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 02/19/2024] [Indexed: 03/22/2024] Open
Abstract
NASA uses a continuous risk management process to seek out new knowledge of spaceflight-induced risk to human health and performance. The evidence base that informs the risk assessments in this domain is constantly changing as more information is gleaned from a continuous human presence in space and from ongoing research. However, the limitations of this evidence are difficult to characterize because fewer than 700 humans have ever flown in space, and information comes from a variety of sources that span disciplines, including engineering, medicine, food and nutrition, and many other life sciences. The Human System Risk Board (HSRB) at NASA is responsible for assessing risk to astronauts and communicating this risk to agency decision-makers. A critical part of that communication is conveying the uncertainty regarding the understanding of the changes that spaceflight induces in human processes and the complex interactions between humans and the spacecraft. Although the strength of evidence grades is common in the academic literature, these scores are often not useful for the problems of human spaceflight. The HSRB continues to update the processes used to report the levels of evidence. This paper describes recent updates to the methods used to assign the level of evidence scores to the official risk postures and to the causal diagrams used by the HSRB.
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Affiliation(s)
- Jessica Ward
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.
| | | | | | | | | | | | | | - Kristina Marotta
- NASA Pathways Intern, NASA Johnson Space Center, Houston, TX, USA
| | | | | | | | - Erik Antonsen
- Department of Emergency Medicine, Center for Space Medicine, Baylor College of Medicine, Houston, TX, USA
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Antonsen E, Reynolds RJ, Charvat J, Connell E, Monti A, Petersen D, Nartey N, Anton W, Abukmail A, Marotta K, Van Baalen M, Buckland DM. Causal diagramming for assessing human system risk in spaceflight. NPJ Microgravity 2024; 10:32. [PMID: 38503732 PMCID: PMC10951288 DOI: 10.1038/s41526-024-00375-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
For over a decade, the National Aeronautics and Space Administration (NASA) has tracked and configuration-managed approximately 30 risks that affect astronaut health and performance before, during and after spaceflight. The Human System Risk Board (HSRB) at NASA Johnson Space Center is responsible for setting the official risk posture for each of the human system risks and determining-based on evaluation of the available evidence-when that risk posture changes. The ultimate purpose of tracking and researching these risks is to find ways to reduce spaceflight-induced risk to astronauts. The adverse effects of spaceflight begin at launch and continue throughout the duration of the mission, and in some cases, across the lifetime of the astronaut. Historically, research has been conducted in individual risk "silos" to characterize risk, however, astronauts are exposed to all risks simultaneously. In January of 2020, the HSRB at NASA began assessing the potential value of causal diagramming as a tool to facilitate understanding of the complex causes and effects that contribute to spaceflight-induced human system risk. Causal diagrams in the form of directed acyclic graphs (DAGs) are used to provide HSRB stakeholders with a shared mental model of the causal flow of risk. While primarily improving communication among those stakeholders, DAGs also allow a composite risk network to be created that can be tracked and configuration managed. This paper outlines the HSRB's pilot process for this effort, the lessons learned, and future goals for data-driven risk management approaches.
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Affiliation(s)
- Erik Antonsen
- Center for Space Medicine, Department of Emergency Medicine, Baylor College of Medicine, Houston, TX, USA.
| | | | | | | | | | | | | | | | | | | | | | - Daniel M Buckland
- NASA Johnson Space Center, Houston, TX, USA
- Duke University, Durham, NC, USA
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Ritto AP, de Araujo AL, de Carvalho CRR, De Souza HP, Favaretto PMES, Saboya VRB, Garcia ML, Kulikowski LD, Kallás EG, Pereira AJR, Cobello Junior V, Silva KR, Abdalla ERF, Segurado AAC, Sabino EC, Ribeiro Junior U, Francisco RPV, Miethke-Morais A, Levin ASS, Sawamura MVY, Ferreira JC, Silva CA, Mauad T, Gouveia NDC, Letaif LSH, Bego MA, Battistella LR, Duarte AJDS, Seelaender MCL, Marchini J, Forlenza OV, Rocha VG, Mendes-Correa MC, Costa SF, Cerri GG, Bonfá ESDDO, Chammas R, de Barros Filho TEP, Busatto Filho G. Data-driven, cross-disciplinary collaboration: lessons learned at the largest academic health center in Latin America during the COVID-19 pandemic. Front Public Health 2024; 12:1369129. [PMID: 38476486 PMCID: PMC10927964 DOI: 10.3389/fpubh.2024.1369129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/13/2024] [Indexed: 03/14/2024] Open
Abstract
Introduction The COVID-19 pandemic has prompted global research efforts to reduce infection impact, highlighting the potential of cross-disciplinary collaboration to enhance research quality and efficiency. Methods At the FMUSP-HC academic health system, we implemented innovative flow management routines for collecting, organizing and analyzing demographic data, COVID-related data and biological materials from over 4,500 patients with confirmed SARS-CoV-2 infection hospitalized from 2020 to 2022. This strategy was mainly planned in three areas: organizing a database with data from the hospitalizations; setting-up a multidisciplinary taskforce to conduct follow-up assessments after discharge; and organizing a biobank. Additionally, a COVID-19 curated collection was created within the institutional digital library of academic papers to map the research output. Results Over the course of the experience, the possible benefits and challenges of this type of research support approach were identified and discussed, leading to a set of recommended strategies to enhance collaboration within the research institution. Demographic and clinical data from COVID-19 hospitalizations were compiled in a database including adults and a minority of children and adolescents with laboratory confirmed COVID-19, covering 2020-2022, with approximately 350 fields per patient. To date, this database has been used in 16 published studies. Additionally, we assessed 700 adults 6 to 11 months after hospitalization through comprehensive, multidisciplinary in-person evaluations; this database, comprising around 2000 fields per subject, was used in 15 publications. Furthermore, thousands of blood samples collected during the acute phase and follow-up assessments remain stored for future investigations. To date, more than 3,700 aliquots have been used in ongoing research investigating various aspects of COVID-19. Lastly, the mapping of the overall research output revealed that between 2020 and 2022 our academic system produced 1,394 scientific articles on COVID-19. Discussion Research is a crucial component of an effective epidemic response, and the preparation process should include a well-defined plan for organizing and sharing resources. The initiatives described in the present paper were successful in our aim to foster large-scale research in our institution. Although a single model may not be appropriate for all contexts, cross-disciplinary collaboration and open data sharing should make health research systems more efficient to generate the best evidence.
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Affiliation(s)
- Ana Paula Ritto
- Faculdade de Medicina, Hospital das Clínicas HC-FMUSP, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Heraldo Possolo De Souza
- Departamento de Emergências Médicas, Faculdade de Medicina, Hospital das Clínicas HC-FMUSP, Universidade de São Paulo, São Paulo, Brazil
| | - Patricia Manga e Silva Favaretto
- Diretoria Executiva dos Laboratórios de Investigação Médica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Vivian Renata Boldrim Saboya
- Diretoria Executiva dos Laboratórios de Investigação Médica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Michelle Louvaes Garcia
- Faculdade de Medicina, Instituto do Coração, Hospital das Clínicas HC-FMUSP, Universidade de São Paulo, São Paulo, Brazil
| | | | - Esper Georges Kallás
- Departamento de Moléstias Infecciosas e Parasitárias, Hospital das Clínicas HC-FMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | - Vilson Cobello Junior
- Núcleo Especializado em Tecnologia da Informação, Hospital das Clínicas HC-FMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Katia Regina Silva
- Faculdade de Medicina, Instituto do Coração, Hospital das Clínicas HC-FMUSP, Universidade de São Paulo, São Paulo, Brazil
| | - Eidi Raquel Franco Abdalla
- Divisão de Biblioteca e Documentação, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Aluisio Augusto Cotrim Segurado
- Departamento de Moléstias Infecciosas e Parasitárias, Hospital das Clínicas HC-FMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ester Cerdeira Sabino
- Departamento de Moléstias Infecciosas e Parasitárias, Hospital das Clínicas HC-FMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ulysses Ribeiro Junior
- Departamento de Gastroenterologia, Hospital das Clínicas HC-FMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Rossana Pulcineli Vieira Francisco
- Departamento de Obstetrícia e Ginecologia, Hospital das Clínicas HC-FMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Anna Miethke-Morais
- Diretoria Clínica, Hospital das Clínicas HC-FMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Anna Sara Shafferman Levin
- Departamento de Moléstias Infecciosas e Parasitárias, Hospital das Clínicas HC-FMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Marcio Valente Yamada Sawamura
- Faculdade de Medicina, Instituto de Radiologia, Hospital das Clínicas HC-FMUSP, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Juliana Carvalho Ferreira
- Faculdade de Medicina, Instituto do Coração, Hospital das Clínicas HC-FMUSP, Universidade de São Paulo, São Paulo, Brazil
| | - Clovis Artur Silva
- Instituto da Criança e do Adolescente, Hospital das Clínicas HC-FMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Thais Mauad
- Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Nelson da Cruz Gouveia
- Departamento de Medicina Preventiva, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Leila Suemi Harima Letaif
- Diretoria Clínica, Hospital das Clínicas HC-FMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Marco Antonio Bego
- Faculdade de Medicina, Instituto de Radiologia, Hospital das Clínicas HC-FMUSP, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Linamara Rizzo Battistella
- Instituto de Medicina Física e Reabilitação, Hospital das Clínicas HC-FMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Alberto José da Silva Duarte
- Divisão de Laboratório Central, Hospital das Clínicas HC-FMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | - Julio Marchini
- Departamento de Emergências Médicas, Faculdade de Medicina, Hospital das Clínicas HC-FMUSP, Universidade de São Paulo, São Paulo, Brazil
| | - Orestes Vicente Forlenza
- Departamento e Instituto de Psiquiatria, Hospital das Clínicas HC-FMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Vanderson Geraldo Rocha
- Departamento de Clínica Médica, Hospital das Clínicas HC-FMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Cassia Mendes-Correa
- Departamento de Moléstias Infecciosas e Parasitárias, Hospital das Clínicas HC-FMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Silvia Figueiredo Costa
- Departamento de Moléstias Infecciosas e Parasitárias, Hospital das Clínicas HC-FMUSP, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Giovanni Guido Cerri
- Faculdade de Medicina, Instituto de Radiologia, Hospital das Clínicas HC-FMUSP, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | - Roger Chammas
- Departamento de Radiologia e Oncologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | - Geraldo Busatto Filho
- Departamento e Instituto de Psiquiatria, Hospital das Clínicas HC-FMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
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Cheng C, Messerschmidt L, Bravo I, Waldbauer M, Bhavikatti R, Schenk C, Grujic V, Model T, Kubinec R, Barceló J. A General Primer for Data Harmonization. Sci Data 2024; 11:152. [PMID: 38297013 PMCID: PMC10831085 DOI: 10.1038/s41597-024-02956-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Affiliation(s)
- Cindy Cheng
- Hochschule für Politik, Technical University of Munich, Richard-Wagner Str. 1, Munich, 80333, Bavaria, Germany.
| | - Luca Messerschmidt
- Hochschule für Politik, Technical University of Munich, Richard-Wagner Str. 1, Munich, 80333, Bavaria, Germany
| | - Isaac Bravo
- Hochschule für Politik, Technical University of Munich, Richard-Wagner Str. 1, Munich, 80333, Bavaria, Germany
| | - Marco Waldbauer
- Hochschule für Politik, Technical University of Munich, Richard-Wagner Str. 1, Munich, 80333, Bavaria, Germany
| | | | - Caress Schenk
- School of Humanities and Social Sciences, Nazarbayev University, Kabanbay Batry Ave., 53, Astana, 010000, Kazakhstan
| | - Vanja Grujic
- Faculty of Law, University of Brasilia, Campus Universitário Darcy Ribeiro Asa Norte, Brasília, 10587, Brazil
| | - Tim Model
- Delve, 2225 3rd St, San Francisco, 94107, California, USA
| | - Robert Kubinec
- Division of Social Science, New York University Abu Dhabi, Social Science Building (A5), Abu Dhabi, 129188, United Arab Emirates
| | - Joan Barceló
- Division of Social Science, New York University Abu Dhabi, Social Science Building (A5), Abu Dhabi, 129188, United Arab Emirates
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Shorinola O, Marks R, Emmrich P, Jones C, Odeny D, Chapman MA. Integrative and inclusive genomics to promote the use of underutilised crops. Nat Commun 2024; 15:320. [PMID: 38191605 PMCID: PMC10774273 DOI: 10.1038/s41467-023-44535-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/14/2023] [Indexed: 01/10/2024] Open
Abstract
Underutilised crops or orphan crops are important for diversifying our food systems towards food and nutrition security. Here, the authors discuss how the development of underutilised crop genomic resource should align with their breeding and capacity building strategies, and leverage advances made in major crops.
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Affiliation(s)
- Oluwaseyi Shorinola
- International Livestock Research Institute, Naivasha Road, Nairobi, Kenya.
- School of Bioscience, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Rose Marks
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - Peter Emmrich
- Norwich Institute for Sustainable Development, School of Global Development, University of East Anglia, England, NR4 7TJ, UK
| | - Chris Jones
- International Livestock Research Institute, Naivasha Road, Nairobi, Kenya
| | - Damaris Odeny
- Center of Excellence in Genomics and Systems Biology, ICRISAT, Patancheru, 502324, Telangana, India
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
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Schilder BM, Murphy AE, Skene NG. rworkflows: automating reproducible practices for the R community. Nat Commun 2024; 15:149. [PMID: 38167858 PMCID: PMC10761765 DOI: 10.1038/s41467-023-44484-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Despite calls to improve reproducibility in research, achieving this goal remains elusive even within computational fields. Currently, >50% of R packages are distributed exclusively through GitHub. While the trend towards sharing open-source software has been revolutionary, GitHub does not have any default built-in checks for minimal coding standards or software usability. This makes it difficult to assess the current quality R packages, or to consistently use them over time and across platforms. While GitHub-native solutions are technically possible, they require considerable time and expertise for each developer to write, implement, and maintain. To address this, we develop rworkflows; a suite of tools to make robust continuous integration and deployment ( https://github.com/neurogenomics/rworkflows ). rworkflows can be implemented by developers of all skill levels using a one-time R function call which has both sensible defaults and extensive options for customisation. Once implemented, any updates to the GitHub repository automatically trigger parallel workflows that install all software dependencies, run code checks, generate a dedicated documentation website, and deploy a publicly accessible containerised environment. By making the rworkflows suite free, automated, and simple to use, we aim to promote widespread adoption of reproducible practices across a continually growing R community.
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Affiliation(s)
- Brian M Schilder
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, W12 0BZ, UK.
- UK Dementia Research Institute at Imperial College London, London, W12 0BZ, UK.
| | - Alan E Murphy
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, W12 0BZ, UK
- UK Dementia Research Institute at Imperial College London, London, W12 0BZ, UK
| | - Nathan G Skene
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, W12 0BZ, UK.
- UK Dementia Research Institute at Imperial College London, London, W12 0BZ, UK.
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Muhlestein WE, Chang KWC, Justice D, Johnson S, Brown S, Popadich M. Developing interdisciplinary research teams in neurosurgery: key elements to success in brachial plexus and peripheral nerve surgery. J Neurosurg 2023; 139:1552-1559. [PMID: 37178028 DOI: 10.3171/2023.4.jns222254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/07/2023] [Indexed: 05/15/2023]
Abstract
The highest-impact medical literature is increasingly produced by interdisciplinary teams. The field of neurosurgery, which involves complex pathologies and recoveries, is particularly amenable to interdisciplinary research approaches. However, research in the medical context regarding the characteristics of effective teams, as well as how to develop and maintain interdisciplinary teams, remains lacking. Here, the authors used the business literature to identify the characteristics of effective teams. They then used the University of Michigan Brachial Plexus and Peripheral Nerve Program, founded under the leadership of the late Dr. Lynda Yang, as a case study for how these principles can be applied to build and operationalize a successful interdisciplinary team. They suggest that these same techniques can be used to create interdisciplinary research groups in other areas of neurosurgery.
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Bailo D, Paciello R, Michalek J, Cocco M, Freda C, Jeffery K, Atakan K. The EPOS multi-disciplinary Data Portal for integrated access to solid Earth science datasets. Sci Data 2023; 10:784. [PMID: 37938570 PMCID: PMC10632364 DOI: 10.1038/s41597-023-02697-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
The European Plate Observing System (EPOS) is a long-term initiative aimed at integrating research infrastructures for solid Earth science in Europe. EPOS provides a sustainable, multidisciplinary user-oriented platform - the EPOS Data Portal - that facilitates data integration, access, use, and re-use, while adhering to the FAIR principles. The paper describes the key governance, community building, and technical aspects for achieving multidisciplinary data integration through the portal. It also outlines the key portal features for aggregating approximately 250 data sources from more than ten different scientific communities. The main architectural concepts underpinning the portal, namely the rich-metadata, the service-driven data provision, and the usage of semantics, are outlined. The paper discusses the challenges encountered during the creation of the portal, describes the community engagement process, and highlights the benefits to the scientific community and society. Future work includes expanding portal functionalities to include data analysis, processing, and visualization and releasing the portal as an open-source software package.
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Affiliation(s)
- Daniele Bailo
- Istituto Nazionale di Geofisica e Vulcanologia, Rome, Italy.
| | | | - Jan Michalek
- Universitetet i Bergen (UiB), 5020, Bergen, Norway
| | - Massimo Cocco
- Istituto Nazionale di Geofisica e Vulcanologia, Rome, Italy
| | - Carmela Freda
- European Plate Observing System, EPOS ERIC, Rome, Italy
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Smith JG, Laver S. 'Jumping through hoops': A metaphor for early career nurse researchers' experiences and resilience building as international collaborators. J Adv Nurs 2023; 79:4238-4244. [PMID: 37626469 DOI: 10.1111/jan.15836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023]
Abstract
AIM To present and discuss our experiences of learning how to establish and maintain an international collaboration as early career nurse researchers residing in the United States and Australia. BACKGROUND International research collaborations require additional startup time given the complexities of navigating cultural differences, obtaining ethics committee approvals in different countries and collecting human subject data. International collaborations may be daunting for early career researchers given their inexperience and pragmatic focus on research projects that lead to outputs achievable on short timelines for career advancement. DESIGN Discussion paper. DATA SOURCES Evidence from international literature about global collaborations across numerous disciplines, including potential factors that could facilitate or constrain early career researcher efforts to engage in international collaborations, were combined with authors' lived experiences as early career researchers. DISCUSSION Our collaboration began in July 2022 through a professional introduction spurred by a call for applications to fund global nursing education collaborations. Interpersonal, logistical and organizational factors played a role in our lived experiences of beginning an international collaboration. Our experiences are consistent with published literature about the time and complexity involved in conducting international research. CONCLUSION Investing time building interpersonal relationships strengthens international research and supports collaborative learning and intercultural understanding. These professional relationships can be built over time to develop significant bodies of research with international impact. Early career researchers need to be resilient, persistent and tenacious as they 'jump through hoops' to establish international research collaborations. IMPACT Building relationships during international research collaborations supports collaborative learning for intercultural understanding and strengthens research to address emerging global problems. International nursing research collaborations could encourage greater curiosity, innovative ideas and solutions to international problems that could not be achieved in isolation. PATIENT OR PUBLIC CONTRIBUTION There was no patient or public involvement in the design and development of this paper.
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Affiliation(s)
- Jessica G Smith
- College of Nursing and Health Innovation, University of Texas at Arlington, Arlington, Texas, USA
| | - Sharon Laver
- School of Nursing, Paramedicine and Healthcare Sciences, Charles Sturt University, Bathurst, New South Wales, Australia
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Howell LL, Bateman T. Extending research impact by sharing maker information. Nat Commun 2023; 14:6170. [PMID: 37794043 PMCID: PMC10550907 DOI: 10.1038/s41467-023-41886-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/22/2023] [Indexed: 10/06/2023] Open
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Brockhoven F, Raphael M, Currier J, Jäderholm C, Mody P, Shannon J, Starling B, Turner-Uaandja H, Pashayan N, Arteaga I. REPRESENT recommendations: improving inclusion and trust in cancer early detection research. Br J Cancer 2023; 129:1195-1208. [PMID: 37689805 PMCID: PMC10575902 DOI: 10.1038/s41416-023-02414-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 08/01/2023] [Accepted: 08/21/2023] [Indexed: 09/11/2023] Open
Abstract
Detecting cancer early is essential to improving cancer outcomes. Minoritized groups remain underrepresented in early detection cancer research, which means that findings and interventions are not generalisable across the population, thus exacerbating disparities in cancer outcomes. In light of these challenges, this paper sets out twelve recommendations to build relations of trust and include minoritized groups in ED cancer research. The Recommendations were formulated by a range of stakeholders at the 2022 REPRESENT consensus-building workshop and are based on empirical data, including a systematic literature review and two ethnographic case studies in the US and the UK. The recommendations focus on: Long-term relationships that build trust; Sharing available resources; Inclusive and accessible communication; Harnessing community expertise; Unique risks and benefits; Compensation and support; Representative samples; Demographic data; Post-research support; Sharing results; Research training; Diversifying research teams. For each recommendation, the paper outlines the rationale, specifications for how different stakeholders may implement it, and advice for best practices. Instead of isolated recruitment, public involvement and engagement activities, the recommendations here aim to advance mutually beneficial and trusting relationships between researchers and research participants embedded in ED cancer research institutions.
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Grants
- EICEDAAP\100011 Cancer Research UK
- Cancer Research UK (CRUK)
- The International Alliance for Cancer Early Detection, an alliance between Cancer Research UK [EICEDAAP\100011], Canary Center at Stanford University, the University of Cambridge, OHSU Knight Cancer Institute, University College London and the University of Manchester.
- This work was supported by the International Alliance for Cancer Early Detection, an alliance between Cancer Research UK [EICEDAAP\100011], Canary Center at Stanford University, the University of Cambridge, OHSU Knight Cancer Institute, University College London and the University of Manchester.
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Affiliation(s)
| | - Maya Raphael
- Department of Social Anthropology, University of Cambridge, Cambridge, UK
| | - Jessica Currier
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Christina Jäderholm
- School of Public Health, Oregon Health & Science University-Portland State University, Portland, OR, USA
| | - Perveez Mody
- Department of Social Anthropology, University of Cambridge, Cambridge, UK
| | - Jackilen Shannon
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Bella Starling
- Vocal, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - Nora Pashayan
- Department of Applied Health Research, University College London, London, UK
| | - Ignacia Arteaga
- Department of Social Anthropology, University of Cambridge, Cambridge, UK.
- Early Cancer Institute, University of Cambridge, Cambridge, UK.
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13
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Antonsen EL, Connell E, Anton W, Reynolds RJ, Buckland DM, Van Baalen M. Updates to the NASA human system risk management process for space exploration. NPJ Microgravity 2023; 9:72. [PMID: 37679359 PMCID: PMC10485075 DOI: 10.1038/s41526-023-00305-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 07/06/2023] [Indexed: 09/09/2023] Open
Abstract
This paper describes updates to NASA's approach for assessing and mitigating spaceflight-induced risks to human health and performance. This approach continues to evolve to meet dynamically changing risk environments: lunar missions are currently being designed and the ultimate destination will be Mars. Understanding the risks that astronauts will face during a Mars mission will depend on building an evidence base that informs not only how the humans respond to the challenges of the spaceflight environment, but also how systems and vehicles can be designed to support human capabilities and limitations. This publication documents updates to the risk management process used by the Human System Risk Board at NASA and includes changes to the likelihood and consequence matrix used by the board, the design reference mission categories and parameters, and the standardized evaluation of the levels of evidence that the board accepts when setting risk posture. Causal diagramming, using directed acyclic graphs, provides all stakeholders with the current understanding of how each risk proceeds from a spaceflight hazard to a mission-level outcome. This standardized approach enables improved communication among stakeholders and delineates how and where more knowledge can improve perspective of human system risks and which countermeasures can best mitigate these risks.
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Affiliation(s)
- Erik L Antonsen
- Center for Space Medicine, Department of Emergency Medicine, Baylor College of Medicine, Houston, TX, USA.
| | | | | | | | - Daniel M Buckland
- Duke University, Durham, NC, USA
- NASA Johnson Space Center, Houston, TX, USA
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14
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Huerta EA, Blaiszik B, Brinson LC, Bouchard KE, Diaz D, Doglioni C, Duarte JM, Emani M, Foster I, Fox G, Harris P, Heinrich L, Jha S, Katz DS, Kindratenko V, Kirkpatrick CR, Lassila-Perini K, Madduri RK, Neubauer MS, Psomopoulos FE, Roy A, Rübel O, Zhao Z, Zhu R. FAIR for AI: An interdisciplinary and international community building perspective. Sci Data 2023; 10:487. [PMID: 37495591 PMCID: PMC10372139 DOI: 10.1038/s41597-023-02298-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 06/09/2023] [Indexed: 07/28/2023] Open
Affiliation(s)
- E A Huerta
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois, 60439, USA.
- Department of Computer Science, University of Chicago, Chicago, Illinois, 60637, USA.
| | - Ben Blaiszik
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois, 60439, USA
- Globus, University of Chicago, Chicago, Illinois, 60637, USA
| | - L Catherine Brinson
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, 27708, USA
| | - Kristofer E Bouchard
- Scientific Data Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems & Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California, 94720, USA
| | - Daniel Diaz
- Department of Physics, University of California San Diego, La Jolla, California, 92093, USA
| | - Caterina Doglioni
- Lund University, Department of Physics, Box 118, 221 00, Lund, Sweden
- School of Physics & Astronomy, The University of Manchester, Manchester, M13 9PL, UK
| | - Javier M Duarte
- Department of Physics, University of California San Diego, La Jolla, California, 92093, USA
| | - Murali Emani
- Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois, 60439, USA
| | - Ian Foster
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois, 60439, USA
- Department of Computer Science, University of Chicago, Chicago, Illinois, 60637, USA
| | - Geoffrey Fox
- Biocomplexity Institute and Department of Computer Science, University of Virginia, Charlottesville, Virginia, 22904, USA
| | - Philip Harris
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Lukas Heinrich
- Technical University Munich, Arcisstraβe 21, 80333, München, Germany
| | - Shantenu Jha
- Computational Science Initiative Brookhaven National Laboratory Upton, New York, 11973, USA
- Electrical and Computer Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Daniel S Katz
- National Center for Supercomputing Applications, University of Illinois, Urbana-Champaign, Urbana, Illinois, 61801, USA
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- Department of Electrical & Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- School of Information Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Volodymyr Kindratenko
- National Center for Supercomputing Applications, University of Illinois, Urbana-Champaign, Urbana, Illinois, 61801, USA
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- Department of Electrical & Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Christine R Kirkpatrick
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California, 92093, USA
| | - Kati Lassila-Perini
- Helsinki Institute of Physics, University of Helsinki, P.O. Box 64, Helsinki, 00014, Finland
| | - Ravi K Madduri
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois, 60439, USA
| | - Mark S Neubauer
- National Center for Supercomputing Applications, University of Illinois, Urbana-Champaign, Urbana, Illinois, 61801, USA
- Department of Electrical & Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Fotis E Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Avik Roy
- National Center for Supercomputing Applications, University of Illinois, Urbana-Champaign, Urbana, Illinois, 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Oliver Rübel
- Scientific Data Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Zhizhen Zhao
- National Center for Supercomputing Applications, University of Illinois, Urbana-Champaign, Urbana, Illinois, 61801, USA
- Department of Electrical & Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Ruike Zhu
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
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15
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Kerfant C, Ruiz-Pérez J, García-Granero JJ, Lancelotti C, Madella M, Karoune E. A dataset for assessing phytolith data for implementation of the FAIR data principles. Sci Data 2023; 10:479. [PMID: 37479711 PMCID: PMC10361956 DOI: 10.1038/s41597-023-02296-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 06/07/2023] [Indexed: 07/23/2023] Open
Abstract
Phytolith research contributes to our understanding of plant-related studies such as plant use in archaeological contexts and past landscapes in palaeoecology. This multi-disciplinarity combined with the specificities of phytoliths themselves (multiplicity, redundancy, naming issues) produces a wide variety of methodologies. Combined with a lack of data sharing and transparency in published studies, it means data are hard to find and understand, and therefore difficult to reuse. This situation is challenging for phytolith researchers to collaborate from the same and different disciplines for improving methodologies and conducting meta-analyses. Implementing The FAIR Data principles (Findable, Accessible, Interoperable and Reusable) would improve transparency and accessibility for greater research data sustainability and reuse. This paper sets out the method used to conduct a FAIR assessment of existing phytolith data. We sampled and assessed 100 articles of phytolith research (2016-2020) in terms of the FAIR principles. The end goal of this project is to use the findings from this dataset to propose FAIR guidance for more sustainable publishing of data and research in phytolith studies.
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Affiliation(s)
- Céline Kerfant
- Universitat Pompeu Fabra, Department of Humanities, Barcelona, 08005, Spain.
| | - Javier Ruiz-Pérez
- Texas A&M University, Department of Ecology and Conservation Biology, College Station, TX 77843, Texas, USA
| | | | - Carla Lancelotti
- Universitat Pompeu Fabra, Department of Humanities, Barcelona, 08005, Spain
- ICREA, Catalan Institution for Research and Advanced Studies, Barcelona, 08010, Spain
| | - Marco Madella
- Universitat Pompeu Fabra, Department of Humanities, Barcelona, 08005, Spain
- ICREA, Catalan Institution for Research and Advanced Studies, Barcelona, 08010, Spain
| | - Emma Karoune
- Historic England, Investigative Science Team, Portsmouth, PO4 9LD, England
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16
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Fu Z, Liu X, Zhao S, Yuan Y, Jiang M. Reducing Clinical Trial Monitoring Resources and Costs With Remote Monitoring: Retrospective Study Comparing On-Site Versus Hybrid Monitoring. J Med Internet Res 2023; 25:e42175. [PMID: 37368468 DOI: 10.2196/42175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/02/2022] [Accepted: 06/07/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Clinical research associates (CRAs) monitor the progress of a trial, verify the data collected, and ensure that the trial is carried out and reported in accordance with the trial protocol, standard operating procedures, and relevant laws and regulations. In response to monitoring challenges during the COVID-19 pandemic, Peking University Cancer Hospital launched a remote monitoring system and established a monitoring model, combining on-site and remote monitoring of clinical trials. Considering the increasing digitization of clinical trials, it is important to determine the optimal monitoring model for the general benefit of centers conducting clinical trials worldwide. OBJECTIVE We sought to summarize our practical experience of a hybrid model of remote and on-site monitoring of clinical trials and provide guidance for clinical trial monitoring management. METHODS We evaluated 201 trials conducted by our hospital that used on-site monitoring alone or a hybrid monitoring model, of which 91 trials used on-site monitoring alone (arm A) and 110 used a hybrid model of remote and on-site monitoring (arm B). We reviewed trial monitoring reports from June 20, 2021, to June 20, 2022, and used a customized questionnaire to collect and compare the following information: monitoring cost of trials in the 2 models as a sum of the CRAs' transportation (eg, taxi fare and air fare), accommodation, and meal costs; differences in monitoring frequency; the number of monitored documents; and monitoring duration. RESULTS From June 20, 2021, to June 20, 2022, a total of 320 CRAs representing 201 sponsors used the remote monitoring system for source data review and the verification of data from 3299 patients in 320 trials. Arm A trials were monitored 728 times and arm B trials were monitored 849 times. The hybrid model in arm B had 52.9% (449/849) remote visits and 48.1% (409/849) on-site visits. The number of patients' visits that could be reviewed in the hybrid monitoring model increased by 34% (4.70/13.80; P=.004) compared with that in the traditional model, whereas the duration of monitoring decreased by 13.8% (3.96/28.61; P=.03) and the total cost of monitoring decreased by 46.2% (CNY ¥188.74/408.80; P<.001). These differences were shown by nonparametric testing to be statistically significant (P<.05). CONCLUSIONS The hybrid monitoring model can ensure timely detection of monitoring issues, improve monitoring efficiency, and reduce the cost of clinical trials and should therefore be applied more broadly in future clinical studies.
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Affiliation(s)
- Zhiying Fu
- Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiaohong Liu
- Peking University Cancer Hospital & Institute, Beijing, China
| | - Shuhua Zhao
- Peking University Cancer Hospital & Institute, Beijing, China
| | - Yannan Yuan
- Peking University Cancer Hospital & Institute, Beijing, China
| | - Min Jiang
- Peking University Cancer Hospital & Institute, Beijing, China
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17
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Graykowski A, Lambert RA, Marchis F, Cazeneuve D, Dalba PA, Esposito TM, O'Conner Peluso D, Sgro LA, Blaclard G, Borot A, Malvache A, Marfisi L, Powell TM, Huet P, Limagne M, Payet B, Clarke C, Murabana S, Owen DC, Wasilwa R, Fukui K, Goto T, Guillet B, Huth P, Ishiyama S, Kukita R, Mitchell M, Primm M, Randolph J, Rivett DA, Ryno M, Shimizu M, Toullec JP, Will S, Yue WC, Camilleri M, Graykowski K, Janetzke R, Janke D, Kardel S, Loose M, Pickering JW, Smith BA, Transom IM. Light curves and colours of the ejecta from Dimorphos after the DART impact. Nature 2023; 616:461-464. [PMID: 36858076 PMCID: PMC10115630 DOI: 10.1038/s41586-023-05852-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 02/15/2023] [Indexed: 03/03/2023]
Abstract
On 26 September 2022, the Double Asteroid Redirection Test (DART) spacecraft struck Dimorphos, a satellite of the asteroid 65803 Didymos1. Because it is a binary system, it is possible to determine how much the orbit of the satellite changed, as part of a test of what is necessary to deflect an asteroid that might threaten Earth with an impact. In nominal cases, pre-impact predictions of the orbital period reduction ranged from roughly 8.8 to 17 min (refs. 2,3). Here we report optical observations of Dimorphos before, during and after the impact, from a network of citizen scientists' telescopes across the world. We find a maximum brightening of 2.29 ± 0.14 mag on impact. Didymos fades back to its pre-impact brightness over the course of 23.7 ± 0.7 days. We estimate lower limits on the mass contained in the ejecta, which was 0.3-0.5% Dimorphos's mass depending on the dust size. We also observe a reddening of the ejecta on impact.
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Affiliation(s)
| | - Ryan A Lambert
- SETI Institute, Carl Sagan Center, Mountain View, CA, USA
| | - Franck Marchis
- SETI Institute, Carl Sagan Center, Mountain View, CA, USA
- Unistellar, Marseille, France
| | | | - Paul A Dalba
- SETI Institute, Carl Sagan Center, Mountain View, CA, USA
- Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA, USA
- Heising-Simons 51 Pegasi b Postdoctoral Fellow, New York City, NY, USA
| | - Thomas M Esposito
- SETI Institute, Carl Sagan Center, Mountain View, CA, USA
- Unistellar, Marseille, France
- Astronomy Department, University of California, Berkeley, CA, USA
| | - Daniel O'Conner Peluso
- SETI Institute, Carl Sagan Center, Mountain View, CA, USA
- Centre for Astrophysics, University of Southern Queensland, Toowoomba, Queensland, Australia
| | - Lauren A Sgro
- SETI Institute, Carl Sagan Center, Mountain View, CA, USA
- Unistellar, Marseille, France
| | | | | | | | | | - Tyler M Powell
- Department of Earth, Planetary, and Space Sciences, University of California, Los Angeles, CA, USA
| | | | | | - Bruno Payet
- Unistellar Citizen Scientist, La Rivière, Réunion
| | - Colin Clarke
- Armagh Observatory and Planetarium, College Hill, Armagh, UK
- The Travelling Telescope, Nairobi Planetarium, Nairobi, Kenya
- Unistellar Citizen Scientist, College Hill, UK
| | - Susan Murabana
- The Travelling Telescope, Nairobi Planetarium, Nairobi, Kenya
- Unistellar Citizen Scientist, Nairobi, Kenya
| | - Daniel Chu Owen
- The Travelling Telescope, Nairobi Planetarium, Nairobi, Kenya
- Unistellar Citizen Scientist, Nairobi, Kenya
| | - Ronald Wasilwa
- The Travelling Telescope, Nairobi Planetarium, Nairobi, Kenya
- Unistellar Citizen Scientist, Nairobi, Kenya
| | | | | | | | - Patrick Huth
- Community College of Allegheny County, Pittsburgh, PA, USA
- Unistellar Citizen Scientist, Schenley, PA, USA
| | | | | | - Mike Mitchell
- Unistellar Citizen Scientist, Oklahoma City, OK, USA
| | | | | | - Darren A Rivett
- Unistellar Citizen Scientist, Lake Macquarie, New South Wales, Australia
| | - Matthew Ryno
- Unistellar Citizen Scientist, Milwaukee, WI, USA
| | | | | | - Stefan Will
- Unistellar Citizen Scientist, Raleigh, NC, USA
| | | | | | | | - Ron Janetzke
- Unistellar Citizen Scientist, San Antonio, TX, USA
| | - Des Janke
- Unistellar Citizen Scientist, Toowoomba, Queensland, Australia
| | - Scott Kardel
- Palomar Community College, San Marcos, CA, USA
- Unistellar Citizen Scientist, San Marcos, CA, USA
| | | | - John W Pickering
- Department of Medicine, University of Otago, Christchurch, New Zealand
- Emergency Care Foundation, Christchurch Hospital, Christchurch, New Zealand
- Unistellar Citizen Scientist, Christchurch, New Zealand
| | | | - Ian M Transom
- Hamilton Astronomical Society Observatory, Hamilton, New Zealand
- Unistellar Citizen Scientist, Cambridge, New Zealand
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18
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Corrie PG. Revitalising cancer clinical trials: definitely time for patient-centred reform. Br J Cancer 2023;:1-2. [PMID: 36882481 DOI: 10.1038/s41416-023-02198-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 03/09/2023] Open
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19
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Gong H, He J, Zhang X, Duan L, Tian Z, Zhao W, Gong F, Liu T, Wang Z, Zhao H, Jia W, Zhang L, Jiang X, Chen W, Liu S, Xiu H, Yang W, Wan J. A repository for the publication and sharing of heterogeneous materials data. Sci Data 2022; 9:787. [PMID: 36575234 DOI: 10.1038/s41597-022-01897-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022] Open
Abstract
National Materials Data Management and Service platform (NMDMS) is a materials data repository for the publication and sharing of heterogeneous materials scientific data and follows the FAIR principles: Findable, Accessible, Interoperable, and Reusable. To ensure data are 'Interoperable, NMDMS uses a user-friendly semi-structured scientific data model, named dynamic container', to define, exchange, and store heterogeneous scientific data. Then, a personalized yet standardized data submission subsystem, a rigorous project data review and publication subsystem, and a multi-granularity data query and retrieval subsystem collaboratively make data 'Reusable', 'Findable', and 'Accessible'. Finally, China's "National Key R&D Program: Material Genetic Engineering Key Special Project" has adopted NMDMS to publish and share its project data. There are 12,251,040 pieces of data published in NMDMS since 2018, under 87 categories and 1,912 user-defined schemas from 45 projects. The platform has been accessed 908875 times, and 2403,208 pieces of data have been downloaded. In short, NMDMS effectively accelerates the publication and sharing of material project data in China.
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20
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Abstract
The development and approval of new treatments generates large volumes of results, such as summaries of efficacy and safety. However, it is commonly overlooked that analyzing clinical study data also produces data in the form of results. For example, descriptive statistics and model predictions are data. Although integrating and putting findings into context is a cornerstone of scientific work, analysis results are often neglected as a data source. Results end up stored as "data products" such as PDF documents that are not machine readable or amenable to future analyses. We propose a solution to "calculate once, use many times" by combining analysis results standards with a common data model. This analysis results data model re-frames the target of analyses from static representations of the results (e.g., tables and figures) to a data model with applications in various contexts, including knowledge discovery. Further, we provide a working proof of concept detailing how to approach standardization and construct a schema to store and query analysis results.
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Affiliation(s)
- Joana M Barros
- Analytics, Novartis Pharma AG, Basel, Switzerland.
- Department of Biometry, Idorsia Pharmaceuticals, Allschwil, Switzerland.
| | | | - Mark Baillie
- Analytics, Novartis Pharma AG, Basel, Switzerland.
| | - Simon Wandel
- Analytics, Novartis Pharma AG, Basel, Switzerland
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21
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Melo AM, Oliveira S, Oliveira JS, Martin CS, Leite RB. Making European performance and impact assessment frameworks for research infrastructures glocal. F1000Res 2022; 11:ELIXIR-278. [PMID: 36016992 PMCID: PMC9372636 DOI: 10.12688/f1000research.108804.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/29/2022] [Indexed: 11/23/2022] Open
Abstract
Sustainability of research infrastructures (RIs) is a big challenge for funders, stakeholders and operators, and the development and adoption of adequate management tools is a major concern, namely tools for monitoring and evaluating their performance and impact. BioData.pt is the Portuguese Infrastructure of Biological data and the Portuguese node of the European Strategy Forum on Research Infrastructures "Landmark" ELIXIR. The foundations of this national research infrastructure were laid under the "Building BioData.pt" project, for four years. During this period, performance and impact indicators were collected and analysed under the light of international guidelines for assessing the performance and impact of European research infrastructures produced by the European Strategy Forum on Research Infrastructures, the Organisation for Economic Co-operation and Development and the EU-funded RI-PATHS project. The exercise shared herein showed that these frameworks can be adopted by national RIs, with the necessary adaptations, namely to reflect the national landscape and specificity of activities, and can be powerful tools in supporting the management of RIs. "Not everything that counts can be counted, and not everything that can be counted, counts". (Attributed to William Bruce Cameron).
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Affiliation(s)
- Ana M.P. Melo
- BioData.pt - Portuguese Infrastructure of Biological Data, Oeiras, Portugal
- INESC ID - Instituto Nacional de Engenharias de Sistemas e Computadores - Investigação e Desenvolvimento, Lisboa, Portugal
| | - Sofia Oliveira
- BioData.pt - Portuguese Infrastructure of Biological Data, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Jorge S. Oliveira
- BioData.pt - Portuguese Infrastructure of Biological Data, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Corinne S. Martin
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ricardo B. Leite
- BioData.pt - Portuguese Infrastructure of Biological Data, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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22
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Melo AM, Oliveira S, Oliveira JS, Martin CS, Leite RB. Making European performance and impact assessment frameworks glocal. F1000Res 2022; 11:ELIXIR-278. [PMID: 36016992 PMCID: PMC9372636 DOI: 10.12688/f1000research.108804.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/16/2022] [Indexed: 01/30/2024] Open
Abstract
Sustainability of research infrastructures (RIs) is a big challenge for funders, stakeholders and operators, and the development and adoption of adequate management tools is a major concern, namely tools for monitoring and evaluating their performance and impact. BioData.pt is the Portuguese Infrastructure of Biological and Portuguese node of the European Strategy Forum on Research Infrastructures "Landmark" ELIXIR. The foundations of this national research infrastructure were laid under the "Building BioData.pt" project, for four years. During this period, performance and impact indicators were collected and analysed under the light of international guidelines for assessing the performance and impact of European research infrastructures produced by the European Strategy Forum on Research Infrastructures, the Organisation for Economic Co-operation and Development and the EU-funded RI-PATHS project. The exercise shared herein showed that these frameworks can be adopted by national RIs, with the necessary adaptations, namely to reflect the national landscape and specificity of activities, and can be powerful tools in supporting the management of RIs. "Not everything that counts can be counted, and not everything that can be counted, counts". Albert Einstein, Theoretical physicist and Nobel Prize winner.
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Affiliation(s)
- Ana M.P. Melo
- BioData.pt - Portuguese Infrastructure of Biological Data, Oeiras, Portugal
- INESC ID - Instituto Nacional de Engenharias de Sistemas e Computadores - Investigação e Desenvolvimento, Lisboa, Portugal
| | - Sofia Oliveira
- BioData.pt - Portuguese Infrastructure of Biological Data, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Jorge S. Oliveira
- BioData.pt - Portuguese Infrastructure of Biological Data, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Corinne S. Martin
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ricardo B. Leite
- BioData.pt - Portuguese Infrastructure of Biological Data, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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23
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Balconi M, Bove M, Bossola M, Angioletti L, Fronda G, Crivelli D. Monitoring Strategies and Intervention Policies for the Enhancement and Protection of Advanced Neuroscientific Research Post COVID-19 in Italy: Preliminary Evidence. Front Public Health 2021; 9:748223. [PMID: 34900899 PMCID: PMC8655842 DOI: 10.3389/fpubh.2021.748223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/08/2021] [Indexed: 12/03/2022] Open
Affiliation(s)
- Michela Balconi
- International Research Center for Cognitive Applied Neuroscience (IrcCAN), Università Cattolica del Sacro Cuore, Milan, Italy.,Research Unit in Affective and Social Neuroscience, Department of Psychology, Università Cattolica del Sacro Cuore, Milan, Italy
| | - Marco Bove
- Section of Human Physiology, Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy
| | - Maurizio Bossola
- Dyalisis Service, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Laura Angioletti
- International Research Center for Cognitive Applied Neuroscience (IrcCAN), Università Cattolica del Sacro Cuore, Milan, Italy.,Research Unit in Affective and Social Neuroscience, Department of Psychology, Università Cattolica del Sacro Cuore, Milan, Italy
| | - Giulia Fronda
- International Research Center for Cognitive Applied Neuroscience (IrcCAN), Università Cattolica del Sacro Cuore, Milan, Italy.,Research Unit in Affective and Social Neuroscience, Department of Psychology, Università Cattolica del Sacro Cuore, Milan, Italy
| | - Davide Crivelli
- International Research Center for Cognitive Applied Neuroscience (IrcCAN), Università Cattolica del Sacro Cuore, Milan, Italy.,Research Unit in Affective and Social Neuroscience, Department of Psychology, Università Cattolica del Sacro Cuore, Milan, Italy
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24
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Schnog JJB, Samson MJ, Gans ROB, Duits AJ. An urgent call to raise the bar in oncology. Br J Cancer 2021; 125:1477-1485. [PMID: 34400802 PMCID: PMC8365561 DOI: 10.1038/s41416-021-01495-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 06/09/2021] [Accepted: 07/09/2021] [Indexed: 02/07/2023] Open
Abstract
Important breakthroughs in medical treatments have improved outcomes for patients suffering from several types of cancer. However, many oncological treatments approved by regulatory agencies are of low value and do not contribute significantly to cancer mortality reduction, but lead to unrealistic patient expectations and push even affluent societies to unsustainable health care costs. Several factors that contribute to approvals of low-value oncology treatments are addressed, including issues with clinical trials, bias in reporting, regulatory agency shortcomings and drug pricing. With the COVID-19 pandemic enforcing the elimination of low-value interventions in all fields of medicine, efforts should urgently be made by all involved in cancer care to select only high-value and sustainable interventions. Transformation of medical education, improvement in clinical trial design, quality, conduct and reporting, strict adherence to scientific norms by regulatory agencies and use of value-based scales can all contribute to raising the bar for oncology drug approvals and influence drug pricing and availability.
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Affiliation(s)
- John-John B. Schnog
- Department of Hematology-Medical Oncology, Curaçao Medical Center, Willemstad, Curaçao ,Curaçao Biomedical and Health Research Institute, Willemstad, Curaçao
| | - Michael J. Samson
- Department of Radiation Oncology, Curaçao Medical Center, Willemstad, Curaçao
| | - Rijk O. B. Gans
- grid.4494.d0000 0000 9558 4598Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ashley J. Duits
- Curaçao Biomedical and Health Research Institute, Willemstad, Curaçao ,grid.4494.d0000 0000 9558 4598Institute for Medical Education, University Medical Center Groningen, Groningen, The Netherlands ,Red Cross Blood Bank Foundation, Willemstad, Curaçao
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25
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Sandhu A, Hany R, Hirohata A, Hishita S, Kimlicka K, Naito M, Nishimura C. Global snapshot of the effects of the COVID-19 pandemic on the research activities of materials scientists between Spring and Autumn 2020. Sci Technol Adv Mater 2021; 22:173-184. [PMID: 33967627 PMCID: PMC8079126 DOI: 10.1080/14686996.2021.1894756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We conducted a global survey on the effects of the COVID-19 pandemic on the research activities of materials scientists by distributing a questionnaire on 9 October 2020 with a response deadline of 23 October 2020. The questions covered issues such as access to labs, effectiveness of online conferences, and effects on doctoral students for the period covering the first lockdowns until the relaxation of restrictions in late September 2020 in many countries. The survey also included online interviews with eminent materials scientists who shared their local experiences during this period. The interviews were compiled as a series of audio conversations for The STAM Podcast that is freely available worldwide. Our findings included that the majority of institutes were not prepared for such a crisis; researchers in China, Japan, and Singapore were able to resume research much quicker - for example after approximately one month in Japan - than their counterparts in the US and Europe after the first lockdowns; researchers adapted to using virtual teleconferencing to maintain contact with colleagues; and doctoral students were the hardest hit by the pandemic with deep concerns about completing their research and career prospects. We hope that the analysis from this survey will enable the global materials science community to learn from each other's experiences and move forward from the unprecedented circumstances created by the pandemic.
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Affiliation(s)
- Adarsh Sandhu
- Department of Engineering Science, Graduate School of Information and Engineering, University of Electro-Communications, Tokyo, Japan
| | - Roland Hany
- Lab for Functional Polymers, Empa, Dübendorf, Switzerland
| | | | - Shunichi Hishita
- Materials Data Platform Center, Publishing Team, Research and Services Division of Materials Data and Integrated System, NIMS, Tsukuba, Japan
| | - Ken Kimlicka
- Global Head of Portfolio, Taylor & Francis, Tokyo, Japan
| | - Masanobu Naito
- Data-driven Polymer Design Group, Research and Services Division of Materials Data and Integrated System, NIMS, Tsukuba, Japan
| | - Chikashi Nishimura
- Materials Data Platform Center, Publishing Team, Research and Services Division of Materials Data and Integrated System, NIMS, Tsukuba, Japan
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26
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Slade M. Management of a High-Performing Mental Health Recovery Research Group. Int J Environ Res Public Health 2021; 18:4007. [PMID: 33920382 PMCID: PMC8070016 DOI: 10.3390/ijerph18084007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022]
Abstract
A personal perspective is given on the processes involved in managing and sustaining a high-performing mental health recovery research group. The broader context of scholarship in the United Kingdom is outlined, in which academic productivity is commodified specifically in relation to peer-reviewed journal papers. Four leadership choices in developing a high-performing research group are discussed: optimal group size; sharing the workload; maintaining a programmatic focus; and performance expectations. Approaches to maximising innovation are identified, including emotional and intellectual engagement of team members, working with diverse stakeholders and convening communities of practice. We use a highly managed approach to publications from inception to acceptance, which is described in detail. The use of these approaches is illustrated in relation to the Recovery Research Team which was formed in 2009. Specific recovery-related issues covered include demonstrating the ability to develop a significant recovery research portfolio (our four current large [>UK£2 m] studies relate to recovery narratives, global mental health peer support work, digital interventions and Recovery Colleges); the positive implications of actively recruiting researchers with mental health lived experience; how performance issues are managed; our approach to involving lived experience co-authors in papers; and our decision to conduct mixed-methods rather than solely qualitative studies.
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Affiliation(s)
- Mike Slade
- School of Health Sciences, Institute of Mental Health, University of Nottingham, Triumph Road, Nottingham NG7 2TU, UK
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27
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Abstract
Analyses of the impacts of climate change on fish species have primarily considered dynamic oceanographic variables that are the output of predictive models, yet fish species distributions are determined by much more than just variables such as ocean temperature. Functionally diverse species are differentially influenced by oceanographic as well as physiographic variables such as bottom substrate, thereby influencing their ability to shift distributions. Here, we show that fish species distributions that are more associated with bottom substrate than other dynamic environmental variables have shifted significantly less over the last 30 years than species whose distributions are associated with bottom salinity. Correspondingly, species whose distributions are primarily determined by bottom temperature or ocean salinity have shifted their mean centroid and southern and northern range boundaries significantly more than species whose distributions are determined by substrate or depth. The influence of oceanographic versus static variables differs by species functional group, as benthic species distributions are more associated with substrate and they have shifted significantly less than pelagic species whose distributions are primarily associated with ocean temperatures. In conclusion, benthic fish, that are more influenced by substrate, may prove much less likely to shift distributions under future climate change.
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Affiliation(s)
- Sarah M Roberts
- Marine Geospatial Ecology Lab, Nicholas School of the Environment and Earth Sciences, Duke University, Durham, NC, 27708, USA.
| | - Andre M Boustany
- Monterey Bay Aquarium, 886 Cannery Row, Monterey, CA, 93940, USA
| | - Patrick N Halpin
- Marine Geospatial Ecology Lab, Nicholas School of the Environment and Earth Sciences, Duke University, Durham, NC, 27708, USA
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28
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Abstract
Disease surveillance systems worldwide face increasing pressure to maintain and distribute data in usable formats supplemented with effective visualizations to enable actionable policy and programming responses. Annual reports and interactive portals provide access to surveillance data and visualizations depicting temporal trends and seasonal patterns of diseases. Analyses and visuals are typically limited to reporting the annual time series and the month with the highest number of cases per year. Yet, detecting potential disease outbreaks and supporting public health interventions requires detailed spatiotemporal comparisons to characterize spatiotemporal patterns of illness across diseases and locations. The Centers for Disease Control and Prevention's (CDC) FoodNet Fast provides population-based foodborne-disease surveillance records and visualizations for select counties across the US. We offer suggestions on how current FoodNet Fast data organization and visual analytics can be improved to facilitate data interpretation, decision-making, and communication of features related to trend and seasonality. The resulting compilation, or analecta, of 436 visualizations of records and codes are openly available online.
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Affiliation(s)
- Ryan B Simpson
- Tufts University Friedman School of Nutrition Science and Policy, Boston, USA
| | - Bingjie Zhou
- Tufts University Friedman School of Nutrition Science and Policy, Boston, USA
| | | | - Elena N Naumova
- Tufts University Friedman School of Nutrition Science and Policy, Boston, USA.
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29
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Huber SP, Zoupanos S, Uhrin M, Talirz L, Kahle L, Häuselmann R, Gresch D, Müller T, Yakutovich AV, Andersen CW, Ramirez FF, Adorf CS, Gargiulo F, Kumbhar S, Passaro E, Johnston C, Merkys A, Cepellotti A, Mounet N, Marzari N, Kozinsky B, Pizzi G. AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance. Sci Data 2020; 7:300. [PMID: 32901044 PMCID: PMC7479590 DOI: 10.1038/s41597-020-00638-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/19/2020] [Indexed: 12/02/2022] Open
Abstract
The ever-growing availability of computing power and the sustained development of advanced computational methods have contributed much to recent scientific progress. These developments present new challenges driven by the sheer amount of calculations and data to manage. Next-generation exascale supercomputers will harden these challenges, such that automated and scalable solutions become crucial. In recent years, we have been developing AiiDA (aiida.net), a robust open-source high-throughput infrastructure addressing the challenges arising from the needs of automated workflow management and data provenance recording. Here, we introduce developments and capabilities required to reach sustained performance, with AiiDA supporting throughputs of tens of thousands processes/hour, while automatically preserving and storing the full data provenance in a relational database making it queryable and traversable, thus enabling high-performance data analytics. AiiDA's workflow language provides advanced automation, error handling features and a flexible plugin model to allow interfacing with external simulation software. The associated plugin registry enables seamless sharing of extensions, empowering a vibrant user community dedicated to making simulations more robust, user-friendly and reproducible.
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Affiliation(s)
- Sebastiaan P Huber
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
| | - Spyros Zoupanos
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Martin Uhrin
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Leopold Talirz
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Rue de l'Industrie 17, Sion, CH-1951, Valais, Switzerland
| | - Leonid Kahle
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Rico Häuselmann
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Dominik Gresch
- Microsoft Station Q, University of California, Santa Barbara, California, 93106-6105, USA
| | - Tiziano Müller
- Department of Chemistry, University of Zürich, Zürich, Switzerland
| | - Aliaksandr V Yakutovich
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), Rue de l'Industrie 17, Sion, CH-1951, Valais, Switzerland
| | - Casper W Andersen
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Francisco F Ramirez
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Carl S Adorf
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Fernando Gargiulo
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Snehal Kumbhar
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Elsa Passaro
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Conrad Johnston
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Andrius Merkys
- Vilnius University Institute of Biotechnology, Saulėtekio al. 7, LT-10257, Vilnius, Lithuania
| | - Andrea Cepellotti
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Nicolas Mounet
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Nicola Marzari
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Boris Kozinsky
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, 02138, United States
- Robert Bosch LLC, Research and Technology Center North America, 255 Main St, Cambridge, Massachusetts, 02142, USA
| | - Giovanni Pizzi
- National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
- Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
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30
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Abstract
There is a broad agreement that psychology is facing a replication crisis. Even some seemingly well-established findings have failed to replicate. Numerous causes of the crisis have been identified, such as underpowered studies, publication bias, imprecise theories, and inadequate statistical procedures. The replication crisis is real, but it is less clear how it should be resolved. Here we examine potential solutions by modeling a scientific community under various different replication regimes. In one regime, all findings are replicated before publication to guard against subsequent replication failures. In an alternative regime, individual studies are published and are replicated after publication, but only if they attract the community's interest. We find that the publication of potentially non-replicable studies minimizes cost and maximizes efficiency of knowledge gain for the scientific community under a variety of assumptions. Provided it is properly managed, our findings suggest that low replicability can support robust and efficient science.
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Affiliation(s)
- Stephan Lewandowsky
- School of Psychological Science, University of Bristol, 12A, Priory Road, Bristol, BS8 1TU, UK.
- School of Psychological Science, University of Western Australia, Perth, WA, Australia.
| | - Klaus Oberauer
- Department of Psychology, University of Zurich, Zurich, Switzerland
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31
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Fryirs KA, Brierley GJ, Dixon T. Engaging with research impact assessment for an environmental science case study. Nat Commun 2019; 10:4542. [PMID: 31586044 PMCID: PMC6778146 DOI: 10.1038/s41467-019-12020-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 08/15/2019] [Indexed: 11/08/2022] Open
Abstract
Impact assessment is embedded in many national and international research rating systems. Most applications use the Research Impact Pathway to track inputs, activities, outputs and outcomes of an invention or initiative to assess impact beyond scholarly contributions to an academic research field (i.e., benefits to environment, society, economy and culture). Existing approaches emphasise easy to attribute 'hard' impacts, and fail to include a range of 'soft' impacts that are less easy to attribute, yet are often a dominant part of the impact mix. Here, we develop an inclusive 3-part impact mapping approach. We demonstrate its application using an environmental initiative.
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Affiliation(s)
- Kirstie A Fryirs
- Department of Environmental Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
| | - Gary J Brierley
- School of Environment, University of Auckland, Auckland, 1010, New Zealand
| | - Thom Dixon
- Research Services, Macquarie University, Sydney, NSW, 2109, Australia
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32
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Tang M, Joensuu H, Simes RJ, Price TJ, Yip S, Hague W, Sjoquist KM, Zalcberg J. Challenges of international oncology trial collaboration-a call to action. Br J Cancer 2019; 121:515-521. [PMID: 31378784 PMCID: PMC6889481 DOI: 10.1038/s41416-019-0532-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/30/2019] [Accepted: 07/04/2019] [Indexed: 11/25/2022] Open
Abstract
International collaboration in oncology trials has the potential to enhance clinical trial activity by expediting the recruitment of large patient populations, testing treatments in diverse populations and facilitating the study of rare tumours or specific molecular subtypes. However, a number of challenges continue to hinder the efficient and productive conduct of both commercial and non-commercial international clinical trials. These challenges include complex and burdensome regulatory requirements, the high cost of conducting trials, and logistical challenges associated with ethics review, drug supply and biospecimen collection and management. We propose solutions to promote oncology trial collaboration, such as regulatory reform, harmonisation of trial initiation and management processes and greater recognition and funding of academic (non-commercial) clinical trials. It is only through coordinated effort and leadership from researchers, regulators and those responsible for health systems that the full potential of international trial collaboration can be realised.
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Affiliation(s)
- Monica Tang
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia.
| | - Heikki Joensuu
- Department of Oncology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Robert J Simes
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Timothy J Price
- The Queen Elizabeth Hospital and University of Adelaide, Adelaide, SA, Australia
| | - Sonia Yip
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Wendy Hague
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Katrin M Sjoquist
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - John Zalcberg
- Alfred Health and the School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
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33
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Pernet CR, Appelhoff S, Gorgolewski KJ, Flandin G, Phillips C, Delorme A, Oostenveld R. EEG-BIDS, an extension to the brain imaging data structure for electroencephalography. Sci Data 2019; 6:103. [PMID: 31239435 PMCID: PMC6592877 DOI: 10.1038/s41597-019-0104-8] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/07/2019] [Indexed: 11/25/2022] Open
Abstract
The Brain Imaging Data Structure (BIDS) project is a rapidly evolving effort in the human brain imaging research community to create standards allowing researchers to readily organize and share study data within and between laboratories. Here we present an extension to BIDS for electroencephalography (EEG) data, EEG-BIDS, along with tools and references to a series of public EEG datasets organized using this new standard.
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Affiliation(s)
- Cyril R Pernet
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, Scotland.
| | - Stefan Appelhoff
- Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin, Germany.
| | | | | | | | - Arnaud Delorme
- Swart Center for Computational Neuroscience, University of California San Diego, San Diego, California, USA
- CerCo, CNRS/Université Paul Sabatier, Toulouse, France
| | - Robert Oostenveld
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands.
- NatMEG, Karolinska Institutet, Stockholm, Sweden.
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34
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Abstract
BACKGROUND While the burden of disease in Africa is high, health research emanating from the continent is low. Building human capacity and research infrastructure to close the gap between research and disease is thus of great imporatance. OBJECTIVE In order to improve research outputs and postgraduate training in the Faculty of Health Sciences, University of the Witwatersrand, the Health Sciences Research Office put in place a series of strategic initiatives over time. METHODS A range of strategic activities, for both postgraduate students and academic staff, were developed in parallel and sequentially over a period of approximately nine years (2008-2016). The latter years were a time of consolidation of the programmes. Outcomes of these activities were 'measured' by increases in publications, decreases in time to graduation and enrichment of the research environment. RESULTS A doubling of research publications and an increase in citations occurred over the period under review. In addition, there was a decrease in the time postgraduate students took to graduate. CONCLUSIONS A varied, but structured research management plan may be of value in African and other developing health sciences institutions to enable the increase in research outputs and capacity development, desperately needed to close the barrier between disease and health.
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Affiliation(s)
- Beverley Kramer
- a Health Sciences Research Office , University of the Witwatersrand , Johannesburg , South Africa.,b School of Anatomical Sciences, Faculty of Health Sciences , University of the Witwatersrand , Johannesburg , South Africa
| | - Elena Libhaber
- a Health Sciences Research Office , University of the Witwatersrand , Johannesburg , South Africa
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Abstract
Resources for data management, discovery and (re)use are numerous and diverse, and more specifically we need data resources that enable the FAIR principles1 of Findability, Accessibility, Interoperability and Reusability of data.
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Affiliation(s)
- Susanna-Assunta Sansone
- University of Oxford, Oxford e-Research Centre, Department of Engineering Sciences, Oxford OX1 1TQ, UK
| | | | - Mark Thorley
- STFC Rutherford Appleton Laboratory, Scientific Computing, Harwell Campus, Didcot OX11 0QX, UK
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McCauley LK. The Future of Dental Schools in Research Universities and Academic Health Centers. J Dent Educ 2017; 81:eS91-eS96. [PMID: 28864809 DOI: 10.21815/jde.017.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/09/2017] [Indexed: 11/20/2022]
Abstract
As a profession, dentistry is at a point of discernible challenge as well as incredible opportunity in a landscape of evolving changes to health care, higher education, and evidence-based decision making. Respecting the past yet driving forward, a well-mapped future course is critical. Orchestrating this course in a collaborative manner is essential for the visibility, well-being, and potentially the existence of the dental profession. The research performed in dental institutions needs to be contemporary, aligned with biomedical science in general, and united with other disciplines. Dentistry is at risk of attrition in the quality of its research and discovery mission if participation with bioscience colleagues in the collaborative generation of new knowledge is underoptimized. A fundamental opportunity dentistry has is to contribute via its position in academic health centers. Rigorous research as to the impact of interprofessional education and collaborative care on population health outcomes provides significant potential for the dental profession to participate and/or lead such evidence-centered efforts. It is imperative that academic dental institutions are part of interdisciplinary and transdisciplinary organizations that move health care into its new day. Strategizing diversity by bringing together people who have different ways of seeing problems to share perspectives, heuristics, interpretations, technologies, and predictive models across disciplines will lead to impactful progress. Academic dental institutions are a natural part of an emphasis on translational research and acceleration of implementing new scientific discoveries. Dentistry needs to remain an essential and integrated component of higher education in the health professions; doing so necessitates deliberate, respectful, and committed change. This article was written as part of the project "Advancing Dental Education in the 21st Century."
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Affiliation(s)
- Laurie K McCauley
- Dr. McCauley is Dean and William K. and May Anne Najjar Professor of Dentistry, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry and Professor, Department of Pathology, University of Michigan Medical School.
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Affiliation(s)
- Michael Skwarski
- Cancer Research UK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Geoff S Higgins
- Cancer Research UK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
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39
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Sjöström J, von Essen L, Grönqvist H. The Origin and Impact of Ideals in eHealth Research: Experiences From the U-CARE Research Environment. JMIR Res Protoc 2014; 3:e28. [PMID: 24860071 PMCID: PMC4051743 DOI: 10.2196/resprot.3202] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/14/2014] [Accepted: 04/13/2014] [Indexed: 11/25/2022] Open
Abstract
Background The prevalence of information technology (IT) in society is a foundation for new modes of interaction between patients and health specialists. IT plays an important role in the renewal of care. Several countries have incorporated eHealth plans into their national health strategies. Part of the eHealth evolution concerns Internet psychological treatment and psychosocial care. These interventions are complex to design and evaluate due to legal, ethical, organizational, technical, and methodological challenges. Objective The objective of our study was to seek to make explicit contributions to the understanding of ideals in eHealth research, and illuminate their implications for establishing an effective research environment. Our analysis draws from three years of experience in establishing an eHealth research environment, and the literature. Methods We worked inductively to characterize challenging research ideals, and their origins, in our environment. Thereafter, we made a selective search of the literature to scrutinize and illuminate each ideal and it’s implications. Results In this work, we propose a structured approach to address ideals in eHealth research. The scrutinized ideals are accountability, innovation, rigor, relevance, and sustainability. The approach supports researchers to systematically understand the ideals, their origin, and to manage their implications within an eHealth research environment. Conclusions The complexity of eHealth research causes a need for sustainable, multi-disciplinary research environments. There is a need for a structured approach to organize eHealth research. The proposed approach helps to systematically scrutinize ideals, thus promoting high quality research.
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Affiliation(s)
- Jonas Sjöström
- U-CARE, Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden.
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