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PloS One 2024Making data FAIR-findable, accessible, interoperable, reproducible-has become the recurring theme behind many research data management efforts. dtool is a lightweight...
Making data FAIR-findable, accessible, interoperable, reproducible-has become the recurring theme behind many research data management efforts. dtool is a lightweight data management tool that packages metadata with immutable data to promote accessibility, interoperability, and reproducibility. Each dataset is self-contained and does not require metadata to be stored in a centralised system. This decentralised approach means that finding datasets can be difficult. dtool's lookup server, short dserver, as defined by a REST API, makes dtool datasets findable, hence rendering the dtool ecosystem fit for a FAIR data management world. Its simplicity, modularity, accessibility and standardisation via API distinguish dtool and dserver from other solutions and enable it to serve as a common denominator for cross-disciplinary research data management. The dtool ecosystem bridges the gap between standardisation-free data management by individuals and FAIR platform solutions with rigid metadata requirements.
Topics: Software; Data Management; Metadata; Ecosystem; Reproducibility of Results; Internet
PubMed: 38917182
DOI: 10.1371/journal.pone.0306100 -
PloS One 2024This study aims to develop a digital retrieval system for art museums to solve the problems of inaccurate information and low retrieval efficiency in the digital...
This study aims to develop a digital retrieval system for art museums to solve the problems of inaccurate information and low retrieval efficiency in the digital management of cultural heritage. By introducing an improved Genetic Algorithm (GA), digital management and access efficiency are enhanced, to bring substantial optimization and innovation to the digital management of cultural heritage. Based on the collection of art museums, this study first integrates the collection's images, texts, and metadata with multi-source intelligent information to achieve a more accurate and comprehensive description of digital content. Second, a GA is introduced, and a GA 2 Convolutional Neural Network (GA2CNN) optimization model combining domain knowledge is proposed. Moreover, the convergence speed of traditional GA is improved to adapt to the characteristics of cultural heritage data. Lastly, the Convolutional Neural Network (CNN), GA, and GA2CNN are compared to verify the proposed system's superiority. The results show that in all models, the sample output results' actual value is 2.62, which represents the real data observation results. For sample number 5, compared with the actual value of 2.62, the predicted values of the GA2CNN and GA models are 2.6177 and 2.6313, and their errors are 0.0023 and 0.0113. The CNN model's predicted value is 2.6237, with an error of 0.0037. It can be found that the network fitting accuracy after optimization of the GA2CNN model is high, and the predicted value is very close to the actual value. The digital retrieval system integrated with the GA2CNN model has a good performance in enhancing retrieval efficiency and accuracy. This study provides technical support for the digital organization and display of cultural heritage and offers valuable references for innovative exploration of museum information management in the digital era.
Topics: Museums; Algorithms; Neural Networks, Computer; Information Storage and Retrieval; Art; Humans
PubMed: 38917118
DOI: 10.1371/journal.pone.0305690 -
BioRxiv : the Preprint Server For... Jun 2024Mice are able to navigate an odor plume with a complex spatiotemporal structure in the dark to find the source of odorants. We developed a protocol to monitor behavior...
UNLABELLED
Mice are able to navigate an odor plume with a complex spatiotemporal structure in the dark to find the source of odorants. We developed a protocol to monitor behavior and record Ca transients in dorsal CA1 stratum pyramidale neurons at the hippocampus (dCA1) in mice navigating an odor plume in a 50 cm x 50 cm x 25 cm odor arena. Ca transients were imaged by an epifluorescence miniscope focused through a GRIN lens on dCA1 neurons expressing the calcium sensor GCaMP6f in Thy1-GCaMP6f mice. We describe the behavioral protocol to train the mice to perform this odor plume navigation task in an automated odor arena. We provide the step-by-step procedure for the surgery for GRIN lens implantation and baseplate placement for imaging GCaMP6f in CA1. We provide information on real time tracking of the mouse position to automate the start of the trials and delivery of a sugar water reward. In addition, we provide information on the use of an Intan board to synchronize metadata describing the automation of the odor navigation task and frame times for the miniscope and a FLIR camera tracking mouse position. Moreover, we delineate the pipeline used to process GCaMP6f fluorescence movies by motion correction using NorMCorre followed by identification of regions of interest (ROIs) with EXTRACT. Finally, we describe use of artificial neural network (ANN) machine learning to decode spatial paths from CA1 neural ensemble activity to predict mouse navigation of the odor plume.
SUMMARY
This protocol describes how to investigate the brain-behavior relationship in hippocampal CA1 in mice navigating an odor plume. We provide a step-by-step protocol including the surgery to access imaging of the hippocampus, behavioral training, miniscope GCaMP6f recording and processing of the brain and behavioral data to decode the mouse position from ROI neural activity.
PubMed: 38915584
DOI: 10.1101/2024.06.12.598681 -
Genomics, Proteomics & Bioinformatics Jun 2024The rapid advancement of sequencing technologies poses challenges in managing the large volume and exponential growth of sequence data efficiently and on time. To...
The rapid advancement of sequencing technologies poses challenges in managing the large volume and exponential growth of sequence data efficiently and on time. To address this issue, we present GenBase (https://ngdc.cncb.ac.cn/genbase), an open-access data repository that follows the International Nucleotide Sequence Database Collaboration (INSDC) data standards and structures, for efficient nucleotide sequence archiving, searching, and sharing. As a core resource within the National Genomics Data Center (NGDC), of the China National Center for Bioinformation (CNCB; https://ngdc.cncb.ac.cn), GenBase offers bilingual submission pipeline and services, as well as local submission assistance in China. GenBase also provides a unique Excel format for metadata description and feature annotation of nucleotide sequences, along with a real-time data validation system to streamline sequence submissions. As of April 23, 2024, GenBase received 68,251 nucleotide sequences and 689,574 annotated protein sequences across 414 species from 2319 submissions. Out of these, 63,614 (93%) nucleotide sequences and 620,640 (90%) annotated protein sequences have been released and are publicly accessible through GenBase's web search system, File Transfer Protocol (FTP), and Application Programming Interface (API). Additionally, in collaboration with INSDC, GenBase has constructed an effective data exchange mechanism with GenBank and started sharing released nucleotide sequences. Furthermore, GenBase integrates all sequences from GenBank with daily updates, demonstrating its commitment to actively contributing to global sequence data management and sharing.
PubMed: 38913867
DOI: 10.1093/gpbjnl/qzae047 -
Journal of Visualized Experiments : JoVE Jun 2024Coral reefs are facing a crisis as the frequency of bleaching events caused by ocean warming increases, resulting in the death of corals on reefs around the world. The...
Coral reefs are facing a crisis as the frequency of bleaching events caused by ocean warming increases, resulting in the death of corals on reefs around the world. The subsequent loss of genetic diversity and biodiversity can diminish the ability of coral to adapt to the changing climate, so efforts to preserve existing diversity are essential to maximize the resources available for reef restoration now and in the future. The most effective approach to secure genetics long-term is cryopreservation and biobanking, which permits the frozen storage of living samples at cryogenic temperatures in liquid nitrogen indefinitely. Cryopreservation of coral sperm has been possible since 2012, but the seasonal nature of coral reproduction means that biobanking activities are restricted to just a few nights per year when spawning occurs. Improving the efficiency of coral sperm processing and cryopreservation workflows is therefore essential to maximizing these limited biobanking opportunities. To this end, we set out to optimize cryopreservation processing pathways for coral sperm by building on existing technologies and creating a semi-automated approach to streamline the assessment, handling, and cryopreservation of coral sperm. The process, which combines computer-assisted sperm analysis, barcoded cryovials, and a series of linked auto-datasheets for simultaneous editing by multiple users, improves the efficiency of both sample processing and metadata management in the field. Through integration with cross-cutting research programs such as the Reef Restoration and Adaptation Program in Australia, cryopreservation can play a crucial role in large-scale reef restoration programs by facilitating the genetic management of aquaculture populations, supporting research to enhance thermal tolerance, and preventing the extinction of coral species. The described procedures will be utilized for coral cryopreservation and biobanking practitioners on reefs worldwide and will provide a model for the transition of cryopreservation technologies from research laboratories to large-scale applications.
Topics: Anthozoa; Cryopreservation; Animals; Male; Biological Specimen Banks; Aquaculture; Spermatozoa; Workflow; Semen Preservation; Coral Reefs
PubMed: 38912771
DOI: 10.3791/66233 -
Journal of the Medical Library... Jan 2024By defining search strategies and related database exports as code/scripts and data, librarians and information professionals can expand the mandate of research data...
BACKGROUND
By defining search strategies and related database exports as code/scripts and data, librarians and information professionals can expand the mandate of research data management (RDM) infrastructure to include this work. This new initiative aimed to create a space in McGill University's institutional data repository for our librarians to deposit and share their search strategies for knowledge syntheses (KS).
CASE PRESENTATION
The authors, a health sciences librarian and an RDM specialist, created a repository collection of librarian-authored knowledge synthesis (KS) searches in McGill University's Borealis Dataverse collection. We developed and hosted a half-day "Dataverse-a-thon" where we worked with a team of health sciences librarians to develop a standardized KS data management plan (DMP), search reporting documentation, Dataverse software training, and howto guidance for the repository.
CONCLUSION
In addition to better documentation and tracking of KS searches at our institution, the KS Dataverse collection enables sharing of searches among colleagues with discoverable metadata fields for searching within deposited searches. While the initial creation of the DMP and documentation took about six hours, the subsequent deposit of search strategies into the institutional data repository requires minimal effort (e.g., 5-10 minutes on average per deposit). The Dataverse collection also empowers librarians to retain intellectual ownership over search strategies as valuable stand-alone research outputs and raise the visibility of their labor. Overall, institutional data repositories provide specific benefits in facilitating compliance both with PRISMA-S guidance and with RDM best practices.
Topics: Humans; Information Storage and Retrieval; Information Dissemination; Data Management; Libraries, Medical; Librarians
PubMed: 38911529
DOI: 10.5195/jmla.2024.1791 -
Gynecology and Minimally Invasive... 2024High-intensity focused ultrasound (HIFU) is commonly used to treat uterine fibroids and adenomyosis, but there is no evidence using metadata to compare fertility... (Review)
Review
High-intensity Focused Ultrasound is a Better Choice for Women with Fertility Desire: A Systematic Review and Meta-analysis of the Comparison between High-intensity Focused Ultrasound and Laparoscopic Treatment of Uterine Fibroids.
High-intensity focused ultrasound (HIFU) is commonly used to treat uterine fibroids and adenomyosis, but there is no evidence using metadata to compare fertility outcomes between conventional laparoscopic procedures and HIFU. The purpose of this study analysis is that evidence-based fertility outcomes may provide better treatment options for clinicians and patients considering fertility. The literature on fertility data for HIFU surgery versus laparoscopic myomectomy was searched in seven English language databases from January 1, 2010, to November 23, 2022. A total of 1375 articles were received in the literature, 14 of which were selected. We found that women who underwent HIFU surgery had higher rates of spontaneous pregnancy, higher rates of spontaneous delivery, and higher rates of full-term delivery but may have higher rates of miscarriage or postpartum complications than women who underwent laparoscopic myomectomy. Looking forward to future studies, it is hoped that the literature will examine endometrial differences in women who undergo HIFU and laparoscopic myomectomy to demonstrate the ability of endometrial repair. The location of fibroids in the sample should also be counted to allow for attribution statistics on the cause of miscarriage.
PubMed: 38911304
DOI: 10.4103/gmit.gmit_23_23 -
World Journal of Microbiology &... Jun 2024Genetic diversity in Sclerotium rolfsii is useful for understanding its population structure, identifying different mycelial compatibility groups (MCGs), and developing...
Genetic diversity in Sclerotium rolfsii is useful for understanding its population structure, identifying different mycelial compatibility groups (MCGs), and developing targeted strategies for disease management in affected crops. In our study, a comprehensive genetic analysis was conducted on 50 isolates of S. rolfsii, collected from various geographic regions and host plants. Two specific genes, TEF1α and RPB2, were utilized to assess the genetic diversity and relationships among these isolates. Notably, out of 1225 pairings examined, only 154 exhibited a compatible reaction, while the majority displayed antagonistic reactions, resulting in the formation of a barrier zone. The isolates were grouped into 10 distinct MCGs. These MCGs were further characterized using genetic sequencing. TEF1α sequences distinguished the isolates into 17 distinct clusters, and RPB2 sequences classified them into 20 clusters. Some MCGs shared identical gene sequences within each gene, while others exhibited unique sequences. Intriguingly, when both TEF1α and RPB2 sequences were combined, all 10 MCGs were effectively differentiated, even those that appeared identical with single-gene analysis. This combined approach provided a comprehensive understanding of the genetic diversity and relationships among the S. rolfsii isolates, allowing for precise discrimination between different MCGs. The results shed light on the population structure and genetic variability within this plant pathogenic fungus, providing valuable insights for disease management and control strategies. This study highlights the significance of comprehending the varied virulence characteristics within S. rolfsii isolates, categorizing them into specific virulence groups based on disease severity index (DSI) values. The association with MCGs provides additional insights into the genetic underpinnings of virulence in this pathogen. Furthermore, the identification of geographical patterns in virulence implies the influence of region-specific factors, with potential implications for disease control and crop protection strategies.Please confirm if the author names are presented accurately and in the correct sequence (given name, middle name/initial, family name). Author 1 Given name: [G. M. Sandeep] Last name [Kumar]. Author 2 Given name: [Praveen Kumar] Last name [Singh]. Also, kindly confirm the details in the metadata are correct.I confirm that the given names are accurate and presented in the correct sequence.
Topics: Genetic Variation; Plant Diseases; Multilocus Sequence Typing; Phylogeny; Basidiomycota; Mycelium; Fungal Proteins; DNA, Fungal; Crops, Agricultural
PubMed: 38910228
DOI: 10.1007/s11274-024-04049-0 -
Oral and Maxillofacial Surgery Jun 2024This study aims to conduct a thorough analysis, both quantitative and qualitative, of bibliometric parameters related to preemptive analgesia (PA) in oral surgical... (Review)
Review
Mapping trends in preemptive analgesia related to oral surgery with the use of Ibuprofen: a comprehensive quantitative and qualitative analysis of bibliometric parameters.
PURPOSE
This study aims to conduct a thorough analysis, both quantitative and qualitative, of bibliometric parameters related to preemptive analgesia (PA) in oral surgical procedures (OSP).
METHODS
Research trends on PA in OSP using ibuprofen were reviewed through bibliometric analysis of 68 journal articles published from 1991 to 2022 in the Web of Science database. Bibliometric indicators were applied to analyze the journal article data, including the annual distribution of publications and literature growth, document types, citation indicators to measure qualitative research performance, and keyword mapping to identify research trends. The results were imported into RStudio, and the Bibliometrix package was used to prepare and analyze the metadata.
RESULTS
The 68 included articles received a total of 900 citations, ranging from 1 source to 72 citations with some fluctuations. The papers on PA in OSP using ibuprofen had an average of 16.85 citations per paper. These publications were originated from 25 countries, with the highest contributions from Brazil (n = 17), the USA (n = 13), and Turkey (n = 8). The top five major contributing journals were the International Journal of Oral and Maxillofacial Surgery, Journal of Oral and Maxillofacial Surgery, Journal of Cranio-Maxillo-Facial Surgery, Journal of Periodontology, and Acta Odontologica Scandinavica, representing more than half of all selected papers.
CONCLUSION
Papers focused on PA in OSP received numerous citations. The citation per article correlated with the number of publications at the affiliation, author, country, and journal levels. However, there is still a scarcity of studies in this field.
PubMed: 38910211
DOI: 10.1007/s10006-024-01274-7 -
Scientific Data Jun 2024The development of platforms for distributed analytics has been driven by a growing need to comply with various governance-related or legal constraints. Among these...
The development of platforms for distributed analytics has been driven by a growing need to comply with various governance-related or legal constraints. Among these platforms, the so-called Personal Health Train (PHT) is one representative that has emerged over the recent years. However, in projects that require data from sites featuring different PHT infrastructures, institutions are facing challenges emerging from the combination of multiple PHT ecosystems, including data governance, regulatory compliance, or the modification of existing workflows. In these scenarios, the interoperability of the platforms is preferable. In this work, we introduce a conceptual framework for the technical interoperability of the PHT covering five essential requirements: Data integration, unified station identifiers, mutual metadata, aligned security protocols, and business logic. We evaluated our concept in a feasibility study that involves two distinct PHT infrastructures: PHT-meDIC and PADME. We analyzed data on leukodystrophy from patients in the University Hospitals of Tübingen and Leipzig, and patients with differential diagnoses at the University Hospital Aachen. The results of our study demonstrate the technical interoperability between these two PHT infrastructures, allowing researchers to perform analyses across the participating institutions. Our method is more space-efficient compared to the multi-homing strategy, and it shows only a minimal time overhead.
Topics: Humans; Data Analysis; Hereditary Central Nervous System Demyelinating Diseases; Health Information Interoperability
PubMed: 38909050
DOI: 10.1038/s41597-024-03450-6