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1.
J Undergrad Neurosci Educ ; 22(3): R1-R5, 2024.
Article in English | MEDLINE | ID: mdl-39355665

ABSTRACT

Foundational textbooks for neuroscience courses can be cost-prohibitive for students and may omit recent advances in the field. Therefore, an Open Educational Resource (OER) repository was curated using existing OER materials for use in behavioral neuroscience and physiology courses. The Behavioral Research and Interdisciplinary Neuroscience Open Educational Repository (BRAINOER) contains 9 modules that include the following foundational topics: (1) The Brain and Nervous System, (2) Neurons, (3) The Endocrine System, (4) Neurotransmitters and Psychopharmacology, (5) Motor Processing, (6) Advanced Brain Functions, (7) Sensation and Perception, (8) Genetics and Evolution, (9) Research, Design, and Methods. Each module contains learning objectives in a checklist format, and modules are divided into basic and advanced content where appropriate. Because the repository is divided into content modules, the materials can be used as a full-curriculum or assigned on a module-by-module basis.

2.
J Contam Hydrol ; 267: 104417, 2024 Aug 26.
Article in English | MEDLINE | ID: mdl-39265306

ABSTRACT

In order to assess sites for a deep geological repository for storing high-level nuclear waste safely in Germany, various numerical models and tools will be in use. For their interaction within one workflow, their reproducibility, and reliability version-controlled open-source solutions and careful documentation of model setups, results and verifications are of special value. However, spatially fully resolved models including all relevant physical and chemical processes are neither computationally feasible for large domains nor is the data typically available to parameterize such models. Thus, simplified models are crucial for the pre-assessment of possible sites to narrow down the list of suitable candidates for which detailed site investigations and fully resolved models will be done at a later stage. Still, the accuracy of these simplified models is of importance as the pre-assessment of suitable sites will be based on them. In this study, we compare the modelling capabilities of TransPyREnd, a one-dimensional transport code based on finite differences, specifically developed for the fast estimation of radionuclide transport by the German federal company for radioactive waste disposal (BGE), with OpenGeoSys, which is a modelling platform based on finite elements in up to three spatial dimensions. Both codes are used in the site selection procedure for the German nuclear waste repository. The comparison of the model results of TransPyREnd and OpenGeoSys is augmented by comparisons with an analytical solution for a homogeneous material. For the purpose of numerical benchmarking, we consider a geological profile located in southern Germany as an example where the hypothetical repository is located in a clay-stone formation. TransPyREnd and OpenGeoSys yield overall similar results. However, both codes use different discretizations which impact is the highest for strongly sorbing compounds, while the difference gets negligible for less sorbing and more diffusive compounds as higher diffusion tends to blur the initial conditions. Overall, the OpenGeoSys model is more exact whereas the TransPyREnd model has considerable faster run times. We found in our example, that significant substance amounts are only leaving the host rock formation, if apparent diffusion is high, for which case both codes give similar results, while relative differences are considerable for strongly sorbing compounds. However, in the latter case no significant substance amount of radionuclides leaves the host-rock formation, thus deeming the differences in the model results minor for the overall safety assessments of sites.

3.
Stud Health Technol Inform ; 317: 129-137, 2024 Aug 30.
Article in English | MEDLINE | ID: mdl-39234715

ABSTRACT

INTRODUCTION: The German Central Health Study Hub is a service that was initially developed at short notice during the COVID-19 pandemic. Since then, it has been expanded in scope, content, active users and functionality. The service is aimed at two main audiences: data provider and data consumers. The former want to share research data from clinical, public health and epidemiological studies and related documents according to the FAIR criteria for research data, and the latter want to find and ultimately reuse relevant research data in the above areas. METHODS: The service connects both groups via graphical and programmatic interfaces. A sophisticated information model is employed to describe and publish various research data objects while obeying data protection and fulfilling FAIR requirements. The service is being developed in a demand-driven manner with extensive user interaction. RESULTS: A free-to-use service, built on open-source software (Dataverse, MICA, Keycloak), accessible via a web-browser. In close collaboration with users several features (ranging from collection to group items to combined data capture via API and UI) were created. The adoption of the service increases continuously and results in over 1,970 research data objects in June 2024. CONCLUSION: The service fills a marked gap and connects both user groups, yet it still needs to be improved in various dimensions (features, content, usage). The impact on the community needs to be further assessed. Despite recent legislative changes (GDNG, EHDS), the system improves the findability of sensitive data, provides a blueprint for similar systems and shows how to create a useful and user-friendly service together with users.


Subject(s)
COVID-19 , Germany , COVID-19/epidemiology , Humans , SARS-CoV-2 , Information Dissemination , Software , Public Health
4.
Clinicoecon Outcomes Res ; 16: 647-656, 2024.
Article in English | MEDLINE | ID: mdl-39257454

ABSTRACT

Purpose: To investigate the effect of StrataGraft (bioengineered allogeneic cellularized construct [BACC]) treatment on inpatient length of stay (LOS) as an indicator of hospital resource utilization. Patients and Methods: Data from the single-arm StrataCAT trial for adult patients with deep partial-thickness (DPT) burns who received BACC were compared with data from a matched external control arm comprising patients who received autografting for burn treatment from the National Burn Repository (NBR) during the same time period as StrataCAT. A matching, quasi-experimental approach was used to investigate the cause-and-effect relationship between BACC treatment and LOS (days). Matching factors included sex, age, ethnicity, race, burn causes, %TBSA burned (third-degree), %TBSA burned (second- and third-degrees), inhalation injury, diabetes mellitus, and hypertension. Balance was assessed between the cohorts for each confounder by standardized mean differences (SMD). Outcome was reported as average treatment effect on the treated. Results: The BACC and NBR Autograft cohorts included 47 and 2641 patients, respectively. Following matching, the Autograft cohort had 137 patients and was weighted to 47 patients. Patients in the BACC and final (matched) Autograft cohorts were similar in all demographic and clinical covariate categories after matching (ie, the absolute SMD were < 0.1). Treatment with BACC reduced the inpatient LOS by an average of 4.84 days (P = 0.0127) relative to the comparable (matched) Autograft cohort. An ad hoc analysis revealed that mean [SD] LOS for BACC and the weighted Autograft cohorts were 17.68 [12.75] and 22.51 [19.75] days, respectively, and were 1.39 [0.94] and 1.88 [1.31] days per %TBSA burned, respectively. Conclusion: The significantly reduced inpatient LOS observed with BACC compared to Autograft in adults with DPT burns may translate into reduced burden on the healthcare system, reduced costs for inpatient burn treatment, and clinical benefits for patients.

5.
JMIR Form Res ; 8: e52120, 2024 Sep 03.
Article in English | MEDLINE | ID: mdl-39226547

ABSTRACT

BACKGROUND: The COVID-19 pandemic sparked a surge of research publications spanning epidemiology, basic science, and clinical science. Thanks to the digital revolution, large data sets are now accessible, which also enables real-time epidemic tracking. However, despite this, academic faculty and their trainees have been struggling to access comprehensive clinical data. To tackle this issue, we have devised a clinical data repository that streamlines research processes and promotes interdisciplinary collaboration. OBJECTIVE: This study aimed to present an easily accessible up-to-date database that promotes access to local COVID-19 clinical data, thereby increasing efficiency, streamlining, and democratizing the research enterprise. By providing a robust database, a broad range of researchers (faculty and trainees) and clinicians from different areas of medicine are encouraged to explore and collaborate on novel clinically relevant research questions. METHODS: A research platform, called the Yale Department of Medicine COVID-19 Explorer and Repository (DOM-CovX), was constructed to house cleaned, highly granular, deidentified, and continually updated data from over 18,000 patients hospitalized with COVID-19 from January 2020 to January 2023, across the Yale New Haven Health System. Data across several key domains were extracted including demographics, past medical history, laboratory values during hospitalization, vital signs, medications, imaging, procedures, and outcomes. Given the time-varying nature of several data domains, summary statistics were constructed to limit the computational size of the database and provide a reasonable data file that the broader research community could use for basic statistical analyses. The initiative also included a front-end user interface, the DOM-CovX Explorer, for simple data visualization of aggregate data. The detailed clinical data sets were made available for researchers after a review board process. RESULTS: As of January 2023, the DOM-CovX Explorer has received 38 requests from different groups of scientists at Yale and the repository has expanded research capability to a diverse group of stakeholders including clinical and research-based faculty and trainees within 15 different surgical and nonsurgical specialties. A dedicated DOM-CovX team guides access and use of the database, which has enhanced interdepartmental collaborations, resulting in the publication of 16 peer-reviewed papers, 2 projects available in preprint servers, and 8 presentations in scientific conferences. Currently, the DOM-CovX Explorer continues to expand and improve its interface. The repository includes up to 3997 variables across 7 different clinical domains, with continued growth in response to researchers' requests and data availability. CONCLUSIONS: The DOM-CovX Data Explorer and Repository is a user-friendly tool for analyzing data and accessing a consistently updated, standardized, and large-scale database. Its innovative approach fosters collaboration, diversity of scholarly pursuits, and expands medical education. In addition, it can be applied to other diseases beyond COVID-19.


Subject(s)
COVID-19 , Fellowships and Scholarships , Humans , Connecticut/epidemiology , Cooperative Behavior , COVID-19/epidemiology , Databases, Factual , Pandemics , Schools, Medical/organization & administration
6.
Brain Sci ; 14(9)2024 Sep 14.
Article in English | MEDLINE | ID: mdl-39335416

ABSTRACT

STUDY OBJECTIVES: The Federal Interagency Traumatic Brain Injury Research (FITBIR) Informatics System contains individual-patient-level traumatic brain injury (TBI) data, which when combined, allows for the examination of rates and outcomes for key subpopulations at risk for developing sleep disturbance. METHODS: This proof-of-concept study creates a model system for harmonizing data (i.e., combining and standardizing data) across FITBIR studies for participants with and without a history of TBI to estimate rates of sleep disturbance and identify risk factors. RESULTS: Three studies were eligible for harmonization (N = 1753). Sleep disturbance was common among those with a history of mild TBI (63%). Individuals with mild TBI were two to four times more likely to have sleep disturbance compared to those with no history of TBI. CONCLUSIONS: This study established methods, harmonization code, and meta-databases that are publicly available on the FITBIR website. We demonstrated how the harmonization of FITBIR studies can answer TBI research questions, showing that associations between TBI and sleep disturbance may be influenced by demographic factors.

7.
Stud Health Technol Inform ; 318: 182-183, 2024 Sep 24.
Article in English | MEDLINE | ID: mdl-39320207

ABSTRACT

The research community in Australia is building a national infrastructure to facilitate access to and sharing of data from health studies. A federation of nine nodes representing 72 health research organisations provides coordination across their partners to establish systems, processes and relationships promoting FAIR approaches to clinical trial data. This paper describes this initiative.


Subject(s)
Biomedical Research , Australia , Information Dissemination , Humans , Clinical Trials as Topic
8.
JMIR Med Inform ; 12: e60293, 2024 Sep 30.
Article in English | MEDLINE | ID: mdl-39348178

ABSTRACT

BACKGROUND: Data element repositories facilitate high-quality medical data sharing by standardizing data and enhancing semantic interoperability. However, the application of repositories is confined to specific projects and institutions. OBJECTIVE: This study aims to explore potential issues and promote broader application of data element repositories within the medical field by evaluating and analyzing typical repositories. METHODS: Following the inclusion of 5 data element repositories through a literature review, a novel analysis framework consisting of 7 dimensions and 36 secondary indicators was constructed and used for evaluation and analysis. RESULTS: The study's results delineate the unique characteristics of different repositories and uncover specific issues in their construction. These issues include the absence of data reuse protocols and insufficient information regarding the application scenarios and efficacy of data elements. The repositories fully comply with only 45% (9/20) of the subprinciples for Findable and Reusable in the FAIR principle, while achieving a 90% (19/20 subprinciples) compliance rate for Accessible and 67% (10/15 subprinciples) for Interoperable. CONCLUSIONS: The recommendations proposed in this study address the issues to improve the construction and application of repositories, offering valuable insights to data managers, computer experts, and other pertinent stakeholders.


Subject(s)
Semantics , Humans , Information Storage and Retrieval/methods , Information Storage and Retrieval/standards , Information Dissemination/methods
9.
Mamm Genome ; 2024 Sep 20.
Article in English | MEDLINE | ID: mdl-39304538

ABSTRACT

Now in its 25th year, the Mutant Mouse Resource and Research Center (MMRRC) consortium continues to serve the United States and international biomedical scientific community as a public repository and distribution archive of laboratory mouse models of human disease for research. Supported by the National Institutes of Health (NIH), the MMRRC consists of 4 regionally distributed and dedicated vivaria, offices, and specialized laboratory facilities and an Informatics Coordination and Service Center (ICSC). The overarching purpose of the MMRRC is to facilitate groundbreaking biomedical research by offering an extensive repertoire of mutant mice that are essential for advancing the understanding of human physiology and disease. The function of the MMRRC is to identify, acquire, evaluate, characterize, cryopreserve, and distribute mutant mouse strains to qualified biomedical investigators around the nation and the globe. Mouse strains accepted from the research community are held to the highest scientific standards to optimize reproducibility and enhance scientific rigor and transparency. All submitted strains are thoroughly reviewed, documented, and validated using extensive scientific quality control measures. In addition, the MMRRC conducts resource-related research on cryopreservation, mouse genetics, environmental conditions, and other topics that enhance operations of the MMRRC. Today, the MMRRC maintains an archive of mice, cryopreserved embryos and sperm, embryonic stem (ES) cell lines, and murine hybridomas for nearly 65,000 alleles. Since its inception, the MMRRC has fulfilled more than 20,000 orders from 13,651 scientists at 8441 institutions worldwide. The MMRRC also provides numerous services to assist researchers, including scientific consultation, technical assistance, genetic assays, microbiome analysis, analytical phenotyping, pathology, cryorecovery, husbandry, breeding and colony management, infectious disease surveillance, and disease modeling. The ICSC coordinates MMRRC operations, interacts with researchers, and manages the website (mmrrc.org) and online catalogue. Researchers benefit from an expansive list of well-defined mouse models of disease that meet the highest scientific standards while submitting investigators benefit by having their mouse strains cryopreserved, protected, and distributed in compliance with NIH policies.

10.
Micro Nano Eng ; 242024 Sep.
Article in English | MEDLINE | ID: mdl-39157761

ABSTRACT

Aquatic germplasm repositories can play a pivotal role in securing the genetic diversity of natural populations and agriculturally important aquatic species. However, existing technologies for repository development and operation face challenges in terms of accuracy, precision, efficiency, and cost-effectiveness, especially for microdevices used in gamete quality evaluation. Quality management is critical throughout genetic resource protection processes from sample collection to final usage. In this study, we examined the potential of using three-dimensional (3-D) stereolithography resin printing to address these challenges and evaluated the overall capabilities and limitations of a representative industrial 3-D resin printer with a price of US$18,000, a consumer-level printer with a price

12.
Best Pract Res Clin Haematol ; 37(2): 101551, 2024 Jun.
Article in English | MEDLINE | ID: mdl-39098795

ABSTRACT

Biobanking provides benefit for future generations by facilitating medical research and subsequent translation and application of research findings. Long-term storage and research involving biological material and associated data necessitate the proper implementation of ethical and legal standards. A key principle includes recognizing informed consent as a crucial element for legitimizing the collection of biological material and data. Furthermore, any collected material and data must be employed exclusively for the research framework that aligns with the explicit consent provided by the participants. Last but not least, data privacy and security are essential in biobanking. This review elucidates chances and limitations of biobanking in the field of allogeneic hematopoietic cell transplantation. We discuss the practical implementation of the requirements, illustrated by the Collaborative Biobank, a collaborative research platform for research in blood cancer.


Subject(s)
Biological Specimen Banks , Hematopoietic Stem Cell Transplantation , Humans , Tissue Donors , Informed Consent , Allografts
13.
Ecol Evol ; 14(8): e70129, 2024 Aug.
Article in English | MEDLINE | ID: mdl-39139913

ABSTRACT

The open science movement produces vast quantities of openly published data connected to journal articles, creating an enormous resource for educators to engage students in current topics and analyses. However, educators face challenges using these materials to meet course objectives. I present a case study using open science (published articles and corresponding datasets) and open educational practices in a capstone course. While engaging in current topics of conservation, students trace connections in the research process, learn statistical analyses, and recreate analyses using the programming language R. I assessed the presence of best practices in open articles and datasets, examined student selection in the open grading policy, surveyed students on their perceived learning gains, and conducted a thematic analysis on student reflections. First, articles and datasets met just over half of the assessed fairness practices, which increased with the publication date. There was a marginal difference in how assessment categories were weighted by students, with reflections highlighting appreciation for student agency. In course content, students reported the greatest learning gains in describing variables, while collaborative activities (e.g., interacting with peers and instructor) were the most effective support. The most effective tasks to facilitate these learning gains included coding exercises and team-led assignments. Autocoding of student reflections identified 16 themes, and positive sentiments were written nearly 4x more often than negative sentiments. Students positively reflected on their growth in statistical analyses, and negative sentiments focused on how limited prior experience with statistics and coding made them feel nervous. As a group, we encountered several challenges and opportunities in using open science materials. I present key recommendations, based on student experiences, for scientists to consider when publishing open data to provide additional educational benefits to the open science community.

14.
Chemosphere ; 364: 143007, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39098347

ABSTRACT

High-level radioactive waste needs to be safely stored for a long time in a deep geological repository by using a multi-barrier system. In this system, suitable barrier materials are selected that ideally show long-term stability to prevent early radionuclide release into the biosphere. In this study, different container matals (copper and cast iron) and pore water compositions (Opalinus Clay pore water and saline cap rock solution) were combined with Bavarian bentonite in static batch experiments to investigate microbial-influenced corrosion. The increasing concentration of iron and copper in the solution as well as detected corrosion products on the metal surface are indicative of anaerobic corrosion of the respective metals during an incubation of 400 days at 37 °C. However, although the intrinsic microbial bentonite community was stimulated with either lactate or H2, an acceleration of cast iron- and copper corrosion did not occur. Furthermore, neither corrosive bacteria nor conventional bacterial corrosion products, such as metal sulfides, were detected in any of the analyzed samples. The analyses of geochemical parameters (e.g. ferrous iron-, iron-, copper- and potassium concentrations as well as redox potentials) showed significant changes in some cast iron- and copper-containing setups, but these changes did not correlate with the microbial community structure in the respective microcosms, as confirmed by statistical analyses. Hence, the analyzed Bavarian bentonite (type B25) showed no significant contribution to cast iron and copper corrosion under the applied conditions after 400 days of incubation. From this perspective, bentonite B25 could be a suitable candidate as a geotechnical barrier in future repositories.


Subject(s)
Bentonite , Copper , Iron , Bentonite/chemistry , Corrosion , Copper/chemistry , Iron/chemistry , Bacteria/metabolism , Radioactive Waste
15.
Expert Opin Drug Metab Toxicol ; 20(9): 923-938, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39167118

ABSTRACT

BACKGROUND: Considerable interindividual variability for the pharmacokinetics of caffeine in preterm infants has been demonstrated, emphasizing the importance of personalized dosing. This study aimed to develop and apply a repository of currently published population pharmacokinetic (PopPK) models of caffeine in preterm infants to facilitate model-informed precision dosing (MIPD). RESEARCH DESIGN AND METHODS: Literature search was conducted using PubMed, Embase, Scopus, and Web of Science databases. Relevant publications were screened, and their quality was assessed. PopPK models were reestablished to develop the model repository. Covariate effects were evaluated and the concentration-time profiles were simulated. An online simulation and calculation tool was developed as an instance. RESULTS: Twelve PopPK models were finally included in the repository. Preterm infants' age and body size, especially the postnatal age and current weight, were identified as the most clinically critical covariates. Simulated blood concentration-time profiles across these models were comparable. Caffeine citrate-dose regimen should be adjusted according to the age and body size of preterm infants. The developed online tool can be used to facilitate clinical decision-making. CONCLUSIONS: The first developed repository of PopPK models for caffeine in preterm infants has a wide range of potential applications in the MIPD of caffeine.


Subject(s)
Caffeine , Dose-Response Relationship, Drug , Infant, Premature , Models, Biological , Humans , Caffeine/administration & dosage , Caffeine/pharmacokinetics , Infant, Newborn , Central Nervous System Stimulants/pharmacokinetics , Central Nervous System Stimulants/administration & dosage , Age Factors , Precision Medicine/methods , Computer Simulation , Citrates
16.
Expert Opin Drug Deliv ; 21(8): 1263-1278, 2024 Aug.
Article in English | MEDLINE | ID: mdl-39210626

ABSTRACT

BACKGROUND: The administration of repository corticotropin injection (Acthar Gel) via a single-dose prefilled injector (SelfJect) is intended to provide a simple, ergonomic alternative to traditional injection. Iterative human factors (HF) studies were conducted to identify potential use deviations and ensure appropriate device use. RESEARCH DESIGN AND METHODS: This article presents seven formative studies, a validation study (with prior pilot validation studies), and a supplemental validation study with participants including lay users, patients, caregivers, and healthcare providers. Participant interactions with SelfJect and the user interface were assessed. Use deviations, user preferences, and participants' ability to successfully complete tasks were evaluated to generate modifications to the device and user interface. RESULTS: In the validation study, 91% of participants successfully administered their first injection. Use errors were rare with simulated-use (6.9%) and knowledge-based (1.6%) testing. Use deviations were commonly attributed to experimental artifact or information oversight, and device warming had the most use errors (49% of participants), even with extensive testing and adjustments to the user interface. CONCLUSIONS: SelfJect was able to be used in a safe and effective manner by the intended users. Iterative HF studies informed the mitigation of use-related risks to reduce the occurrence of use deviations during simulated use.


Subject(s)
Adrenocorticotropic Hormone , Disposable Equipment , Gels , Humans , Injections, Subcutaneous/instrumentation , Male , Adult , Female , Adrenocorticotropic Hormone/administration & dosage , Middle Aged , Ergonomics , Self Administration , Young Adult , Equipment Design , Health Personnel , Drug Delivery Systems/instrumentation
17.
HGG Adv ; 5(4): 100346, 2024 Oct 10.
Article in English | MEDLINE | ID: mdl-39183478

ABSTRACT

Research participants report interest in receiving genetic research results. How best to return results remains unclear. In this randomized pilot study, we sought to assess the feasibility of returning actionable research results through a two-step process including a patient-centered digital intervention as compared with a genetic counselor (GC) in the Penn Medicine biobank. In Step 1, participants with an actionable result and procedural controls (no actionable result) were invited to digital pre-disclosure education and provided options for opting out of results. In Step 2, those with actionable results who had not opted out were randomized to receive results via a digital disclosure intervention or with a GC. Five participants (2%) opted out of results after Step 1. After both steps, 52 of 113 (46.0%) eligible cases received results, 5 (4.4%) actively declined results, 34 (30.1%) passively declined, and 22 (19.5%) could not be reached. Receiving results was associated with younger age (p < 0.001), completing pre-disclosure education (p < 0.001), and being in the GC arm (p = 0.06). Being older, female, and of Black race were associated with being unable to reach. Older age and Black race were associated with passively declining. Forty-seven percent of those who received results did not have personal or family history to suggest the mutation, and 55.1% completed clinical confirmation testing. The use of digital tools may be acceptable to participants and could reduce costs of returning results. Low uptake, disparities in uptake, and barriers to confirmation testing will be important to address to realize the benefit of returning actionable research results.


Subject(s)
Biological Specimen Banks , Humans , Female , Male , Middle Aged , Adult , Genetic Research , Aged , Disclosure , Pilot Projects , Genetic Counseling
18.
World J Microbiol Biotechnol ; 40(9): 264, 2024 Jul 11.
Article in English | MEDLINE | ID: mdl-38990244

ABSTRACT

Bentonite is an integral part of the engineered barrier system (EBS) in deep geological repositories (DGR) for nuclear waste, but its indigenous microorganisms may jeopardize long-term EBS integrity. To predict microbial activity in DGRs, it is essential to understand microbial reactions to the early hot phase of DGR evolution. Two bentonites (BCV and MX-80) with varied bentonite/water ratios and saturation levels (compacted to 1600 kg.m- 3 dry density/powder/suspension), were subjected to heat (90-150 °C) and irradiation (0.4 Gy.h- 1) in the long-term experiments (up to 18 months). Molecular-genetic, microscopic, and cultivation-based techniques assessed microbial survivability. Exposure to 90 °C and 150 °C notably diminished microbial viability, irrespective of bentonite form, with negligible impacts from irradiation or sample type compared to temperature. Bentonite powder samples exhibited microbial recovery after 90 °C heating for up to 6 months but not 12 months in most cases; exposure to 150 °C had an even stronger effect. Further long-term experiments at additional temperatures combined with the mathematical prediction of temperature evolution in DGR are recommended to validate the possible evolution and spatial distribution of microbially depleted zones in bentonite buffer around the waste canisters and refine predictions of microbial effects over time in the DGR.


Subject(s)
Bacteria , Bentonite , Gamma Rays , Hot Temperature , Microbial Viability , Bentonite/chemistry , Microbial Viability/radiation effects , Bacteria/classification , Bacteria/radiation effects , Bacteria/genetics , Bacteria/growth & development , Radioactive Waste/analysis , Soil Microbiology
19.
Article in English | MEDLINE | ID: mdl-38862433

ABSTRACT

During the last decade, the generation and accumulation of petabase-scale high-throughput sequencing data have resulted in great challenges, including access to human data, as well as transfer, storage, and sharing of enormous amounts of data. To promote data-driven biological research, the Korean government announced that all biological data generated from government-funded research projects should be deposited at the Korea BioData Station (K-BDS), which consists of multiple databases for individual data types. Here, we introduce the Korean Nucleotide Archive (KoNA), a repository of nucleotide sequence data. As of July 2022, the Korean Read Archive in KoNA has collected over 477 TB of raw next-generation sequencing data from national genome projects. To ensure data quality and prepare for international alignment, a standard operating procedure was adopted, which is similar to that of the International Nucleotide Sequence Database Collaboration. The standard operating procedure includes quality control processes for submitted data and metadata using an automated pipeline, followed by manual examination. To ensure fast and stable data transfer, a high-speed transmission system called GBox is used in KoNA. Furthermore, the data uploaded to or downloaded from KoNA through GBox can be readily processed using a cloud computing service called Bio-Express. This seamless coupling of KoNA, GBox, and Bio-Express enhances the data experience, including submission, access, and analysis of raw nucleotide sequences. KoNA not only satisfies the unmet needs for a national sequence repository in Korea but also provides datasets to researchers globally and contributes to advances in genomics. The KoNA is available at https://www.kobic.re.kr/kona/.


Subject(s)
Databases, Nucleic Acid , Republic of Korea , Humans , High-Throughput Nucleotide Sequencing/methods
20.
JMIR Med Inform ; 12: e50194, 2024 Jun 24.
Article in English | MEDLINE | ID: mdl-38915177

ABSTRACT

Background: Biomedical data warehouses (BDWs) have become an essential tool to facilitate the reuse of health data for both research and decisional applications. Beyond technical issues, the implementation of BDWs requires strong institutional data governance and operational knowledge of the European and national legal framework for the management of research data access and use. Objective: In this paper, we describe the compound process of implementation and the contents of a regional university hospital BDW. Methods: We present the actions and challenges regarding organizational changes, technical architecture, and shared governance that took place to develop the Nantes BDW. We describe the process to access clinical contents, give details about patient data protection, and use examples to illustrate merging clinical insights. Unlabelled: More than 68 million textual documents and 543 million pieces of coded information concerning approximately 1.5 million patients admitted to CHUN between 2002 and 2022 can be queried and transformed to be made available to investigators. Since its creation in 2018, 269 projects have benefited from the Nantes BDW. Access to data is organized according to data use and regulatory requirements. Conclusions: Data use is entirely determined by the scientific question posed. It is the vector of legitimacy of data access for secondary use. Enabling access to a BDW is a game changer for research and all operational situations in need of data. Finally, data governance must prevail over technical issues in institution data strategy vis-à-vis care professionals and patients alike.

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