Metadata

Natural products exhibit interesting structural features and significant biological activities. The discovery of new bioactive molecules is a complex process that requires high-quality metabolite profiling data to properly target the isolation of compounds of interest and enable their complete structural characterization. The same metabolite profiling data can also be used to better understand chemotaxonomic links between species. This Data Descriptor details a dataset resulting from the untargeted liquid chromatography-mass spectrometry metabolite profiling of 76 natural extracts of the Celastraceae family...

Reports an error in "Digital traces of offline mobilization" by Laura G. E. Smith, Lukasz Piwek, Joanne Hinds, Olivia Brown and Adam Joinson ( Journal of Personality and Social Psychology , 2023[Sep], Vol 125[3], 496-518). The following article is being corrected: https://doi.org/10.1037/pspa0000338. Cangxiong Chen is added as the fifth author in the byline and author note. Cangxiong Chen's ORCID ID is now included in the author note. The CRediT paragraph in the author note now includes Cangxiong Chen's supporting role for the article...

BACKGROUND: Public health policy researchers face a persistent challenge in identifying and integrating relevant data, particularly in the context of the U.S. opioid crisis, where a comprehensive approach is crucial. PURPOSE: To meet this new workforce demand health policy and health economics programs are increasingly introducing data analysis and data visualization skills. Such skills facilitate data integration and discovery by linking multiple resources. Common linking strategies include individual or aggregate level linking (e...

Data collection, curation, and cleaning constitute a crucial phase in Machine Learning (ML) projects. In biomedical ML, it is often desirable to leverage multiple datasets to increase sample size and diversity, but this poses unique challenges, which arise from heterogeneity in study design, data descriptors, file system organization, and metadata. In this study, we present an approach to the integration of multiple brain MRI datasets with a focus on homogenization of their organization and preprocessing for ML...

The Gene Expression Omnibus (GEO) is a major open biomedical research repository for transcriptomics and other omics datasets. It currently contains millions of gene expression samples from tens of thousands of studies collected by many biomedical research laboratories from around the world. While users of the GEO repository can search the metadata describing studies for locating relevant datasets, there are currently no methods or resources that facilitate global search of GEO at the data level. To address this shortcoming, we developed RummaGEO, a webserver application that enables gene expression signature search of a large collection of human and mouse RNA-seq studies deposited into GEO...

Ground truth data (GTD) is used by those in the field of digital forensics (DF) for a variety of purposes including to evaluate the functionality of undocumented, new, or emerging technology and services and the digital traces left behind following their usage. Most accepted and reliable trace interpretations must be derived from an examination of relevant GTD, yet despite the importance of it to the DF community, there is little formal guidance available for supporting those who create it, to do so in a way that ensures any data is of good quality, reliable, and therefore usable...

Multiplexed assays of variant effect (MAVEs) have emerged as a powerful approach for interrogating thousands of genetic variants in a single experiment. The flexibility and widespread adoption of these techniques across diverse disciplines have led to a heterogeneous mix of data formats and descriptions, which complicates the downstream use of the resulting datasets. To address these issues and promote reproducibility and reuse of MAVE data, we define a set of minimum information standards for MAVE data and metadata and outline a controlled vocabulary aligned with established biomedical ontologies for describing these experimental designs...

Through investigating the combined impact of the environmental exposures experienced by an individual throughout their lifetime, exposome research provides opportunities to understand and mitigate negative health outcomes. While current exposome research is driven by epidemiological studies that identify associations between exposures and effects, new frameworks integrating more substantial population-level metadata, including electronic health and administrative records, will shed further light on characterizing environmental exposure risks...

INTRODUCTION: The biology of symptomatic neuromas is poorly understood, particularly the factors causing pain in human neuromas. Pain presence varies among and within individuals, with some having painful and nonpainful neuromas. To bridge these knowledge gaps, our group developed a protocol for assessing neuroma pain and collecting tissue for molecular analysis. This manuscript outlines our workflow and challenges and aims to inspire other centers to share their experiences with these tissues...

This article presents comprehensive data derived from lab-scale batch anaerobic digesters that were subjected to inhibition by various sources of ammonia. To counter this inhibition, zeolite was introduced into selected digesters. The provided dataset offers a detailed depiction of degradation performance dynamics over time, as well as insights into both microbial and metabolic changes during the inhibition. In detail, 10 conditions were tested in triplicate. In a first series of 15 bioreactors ammonia was introduced to achieve a TAN concentration of 8 g/L, utilizing NH3 solution, NH4 Cl salt, (NH4 )2 CO3 salt, or (NH4 )2 PO4 salt as inhibitors...

PURPOSE: A preprint is a version of a research manuscript posted to a preprint server prior to peer review. Preprints enable authors to quickly and openly share research, afford opportunities for expedient feedback, and enable immediate listing of research on grant and promotion applications. In medical education, most journals welcome preprints, which suggests preprints play a role in the field's discourse. Yet, little is known about medical education preprints, including author characteristics, preprint use, and ultimate publication status...

Many data resources generate, process, store, or provide kidney related molecular, pathological, and clinical data. Reference ontologies offer an opportunity to support knowledge and data integration. The Kidney Precision Medicine Project (KPMP) team contributed to the representation and addition of 329 kidney phenotype terms to the Human Phenotype Ontology (HPO), and identified many subcategories of acute kidney injury (AKI) or chronic kidney disease (CKD). The Kidney Tissue Atlas Ontology (KTAO) imports and integrates kidney-related terms from existing ontologies (e...

BACKGROUND: Regular quality-assured whole-genome sequencing linked to antimicrobial resistance (AMR) and patient metadata is imperative to elucidate the shifting gonorrhoea epidemiology, both nationally and internationally. We aimed to examine the gonococcal population in the European Economic Area (EEA) in 2020, elucidate emerging and disappearing gonococcal lineages associated with AMR and patient metadata, compare with 2013 and 2018 whole-genome sequencing data, and explain changes in gonococcal AMR and gonorrhoea epidemiology...

The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the management, display, annotation and manipulation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 6 introduces a modernized and completely rewritten user interface, together with numerous new features. A new dataset type has been introduced (colored/labeled ranges), greatly upgrading the functionality of the previous simple colored range annotation function. Additional annotation options have been implemented for several existing dataset types...

The growing availability of smart meter data has facilitated the development of energy-saving services like demand response, personalized energy feedback, and non-intrusive-load-monitoring applications, all of which heavily rely on advanced machine learning algorithms trained on energy consumption datasets. To ensure the accuracy and reliability of these services, real-world smart meter data collection is crucial. The Plegma dataset described in this paper addresses this need bfy providing whole- house aggregate loads and appliance-level consumption measurements at 10-second intervals from 13 different households over a period of one year...

BACKGROUND: Distributional data on planktonic, benthic and sympagic copepods collected in the framework of the XXXIVth Expeditions of the Italian National Antarctic Programme (PNRA) to the Ross Sea sector from 2018-2019 are here provided. These occurrences correspond to specimens collected from the 25 μm filters used in the desalination plant of the Italian research station "Mario Zucchelli" (MZS), located in the Terra Nova Bay area (TNB; Ross Sea, Antarctica). This dataset is a contribution to the Antarctic Biodiversity Portal, the thematic Antarctic node for both the Ocean Biogeographic Information System (AntOBIS) and the Global Biodiversity Information Facility Antarctic Biodiversity Information Facility (ANTABIF)...

Globally, there is a concerning decline in many insect populations, and this trend likely extends to all arthropods, potentially impacting unique island biota. Native non-endemic and endemic species on islands are under threat due to habitat destruction, with the introduction of exotic, and potentially invasive, species, further contributing to this decline. While long-term studies of plants and vertebrate fauna are available, long-term arthropod datasets are limited, hindering comparisons with better-studied taxa...

The United States has one of the largest incarcerated populations per capita. Prisons are dangerous environments, with high in-prison and postrelease mortality. The Death in Custody Reporting Acts (DCRAs) of 2000 and 2013 require deaths of people in correctional custody or caused by law enforcement to be reported to the Bureau of Justice Assistance. These deaths must be reported within 3 months of the death and include 10 required fields (eg, age, cause of death). There is no public reporting requirement. Our Third City Mortality project tracks near-real-time data about individual deaths released publicly and prison system metadata, including data completeness and release speed, across (N = 54) US state, federal (N = 2; Bureau of Prisons, Immigration and Customs Enforcement), Washington, District of Columbia, and Puerto Rico prison systems...

COVID-19 dashboards with geospatial data visualization have become ubiquitous. There is a growing sense of responsibility to report public health data pushing governments and community organizations to develop and share web-based dashboards. While a substantial body of literature exists on how these GIS technologies and urban analytics approaches support COVID-19 monitoring, their level of social embeddedness, quality and accessibility of user interface, and overall decision-making capabilities has not been rigorously assessed...

Microbial endophytes are microorganisms that live inside plants, and some of them play important yet understudied roles in plant health, growth, and adaptation to environmental conditions. Their diversity within plants has traditionally been underestimated due to the limitations of culture-dependent techniques. Metagenomic profiling provides a culture-independent approach to characterize entire microbial communities. The argan tree ( Argania spinosa ) is ecologically and economically important in Morocco, yet its seed endophyte microbiome remains unexplored...