cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18368326
title: Context Engineering for AI Agents in Open-Source Software (Supplementary Material)

description: GenAI-based coding assistants have disrupted software development. The next generation of these tools is agent-based, operating with more autonomy and potentially without human oversight. Like human developers, AI agents require contextual information to develop solutions that are in line with the standards, policies, and workflows of the software projects they operate in.  Vendors of popular agentic tools (e.g., Claude Code) recommend maintaining version-controlled Markdown files that describe aspects such as the project structure, code style, or building and testing. The content of these files is then automatically added to each prompt. Recently, AGENTS.md has emerged as a potential standard that consolidates existing tool-specific formats. However, little is known about whether and how developers adopt this format. Therefore, in this paper, we present the results of a preliminary study investigating the adoption of AI context files in 466 open-source software projects. We analyze the information that developers provide in AGENTS.md files, how they present that information, and how the files evolve over time. Our findings indicate that there is no established content structure yet and that there is a lot of variation in terms of how context is provided (descriptive, prescriptive, prohibitive, explanatory, conditional). Our commit-level analysis provides first insights into the evolution of the provided context. AI context files provide a unique opportunity to study real-world context engineering. In particular, we see great potential in studying which structural or presentational modifications can positively affect the quality of the generated content.We thank Levi Böhme for allowing us to use his repository ranking appraoch in our study.
DOI: 10.5281/zenodo.17428770
title: Context Engineering for AI Agents in Open-Source Software (Supplementary Material)

description: GenAI-based coding assistants have disrupted software development. The next generation of these tools is agent-based, operating with more autonomy and potentially without human oversight. Like human developers, AI agents require contextual information to develop solutions that are in line with the standards, policies, and workflows of the software projects they operate in.  Vendors of popular agentic tools (e.g., Claude Code) recommend maintaining version-controlled Markdown files that describe aspects such as the project structure, code style, or building and testing. The content of these files is then automatically added to each prompt. Recently, AGENTS.md has emerged as a potential standard that consolidates existing tool-specific formats. However, little is known about whether and how developers adopt this format. Therefore, in this paper, we present the results of a preliminary study investigating the adoption of AI context files in 466 open-source software projects. We analyze the information that developers provide in AGENTS.md files, how they present that information, and how the files evolve over time. Our findings indicate that there is no established content structure yet and that there is a lot of variation in terms of how context is provided (descriptive, prescriptive, prohibitive, explanatory, conditional). Our commit-level analysis provides first insights into the evolution of the provided context. AI context files provide a unique opportunity to study real-world context engineering. In particular, we see great potential in studying which structural or presentational modifications can positively affect the quality of the generated content.We thank Levi Böhme for allowing us to use his repository ranking appraoch in our study.
DOI: 10.5061/dryad.cz8w9gj8q
title: Birth and death dates for individuals of twelve Rhododendron species

description: Birth (planting) date, depart date, and depart type (C = censored (not
 dead), D = dead), for individuals of twelve Rhododendron species planted
 at the Royal Botanic Garden Edinburgh.
description: # RhododendronRBGE
 [https://doi.org/10.5061/dryad.cz8w9gj8q](https://doi.org/10.5061/dryad.cz8w9gj8q) The dataset contains birth (planting) date, depart date, and depart type (C = censored (not dead), D = dead), for individuals of twelve Rhododendron species planted at the Royal Botanic Garden Edinburgh. It was used to assess mortality trajectories. ## Description of the data and file structure The data file consists of four columns, "Species.Name" (a text string of the scientific name of the species), "Birth.Date" (a date: the date of planting), Depart.Date (a date: when the individual was no longer recorded), and "Depart.Type" ("D" means the individual was observed dead at the "depart date", "C" means it was censored, i.e. either still alive at the end of the study, or it was removed from the garden before dying. Rows represent individuals. ## Sharing/Access information Data was derived from the Royal Botanic Garden Edinburgh's electronic records and complemented with data from hand written index cards.
DOI: 10.15468/dl.a4w5eb
title: Occurrence Download

description: A dataset containing 97 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Anthidium psoraleae"
 ]
}

 The dataset includes 97 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003692-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c2umn4
title: Occurrence Download

description: A dataset containing 134540 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Manchester Museum, University of Manchester, Botany Collection"
 ]
}

 The dataset includes 134540 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003658-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.n5tb2rc26
title: Partial migration in Magellanic penguins

description: We study the migration of Magellanic penguins at the southern tip of the
 breeding distribution. We found for the first time for this species
 evidence of partial migration within the same colony. Forty-three percent
 of the penguins studied stayed within ~290 km from the colony (residents),
 while others went northwards as far as 2000 km. All penguins spent the
 same amount of time at sea and traveled similar total distances, but
 residents experienced colder waters (2 °C less) and lower
 chlorophyll-a habitats than migrants. The two habitats are inhabited by
 different prey items, consequently giving the penguins different
 possibilities of prey items. We have shown individual strategies with high
 variability in the non-breeding dispersion behavior of Magellanic
 penguins, nonetheless, further research is required to understand the
 proximate and ultimate causes and the consequences of this behavior.
description: We tracked 14 Magellanic penguins from the colony Cabo Vírgenes
 in 2020 and 2021. We used geolocators that were analyzed following the
 methods in Lisovski et al. (2020) and Barrionuevo et al. (2023).
description: # Partial migration in Magellanic penguins
 [https://doi.org/10.5061/dryad.n5tb2rc26](https://doi.org/10.5061/dryad.n5tb2rc26) Data of tracked Magellanic penguins during their migration. This is a data set of 14 trips recorded during 2020 and 2021 of females and males from Cabo Vírgenes colony (52°21´S, 68°23´W). This data was recorded with MK3 and MK4 geolocators (Lotek, UK). ## Description of the data and file structure Excel file, Barrionuevo&Frere, has the time of the locations of the migration trips. Longitude and latitude are presented as mean and sd positions (in decimal degrees). Also, de 2.5 and 97.5 % of the distributions of the locations are shown. This allows us to set the error of the GLS. * anio = year of the trips * colonia = is the breeding colony of the penguins. In this case only Cabo Vírgenes. * especie = study species, in this case, Magellanic penguins *Spheniscus magellanicus.* * sexo= is a two-level factor with the sex of the penguins. hembra: female; macho: male. * gls= is the id og the gls. * id= is a unique random number for each track. * anillo= is a unique identifier for each penguin. This is the real number of the rings of the penguins. The CSV file, envMcmcTracks2.csv, has also the oceanographic variables for each location. * id=is a unique random number for each trip * date=is the date and hour of the positions. * x=the longitud, decimals degrees * y=the latitud, decimals degrees * SST=sea surface temperature, in degrees Celsius * depth=batymetry, in meters * Slope= slope of the bathymetry, in meters * ChlA= chlorophyll a concentrations, in mg/L * salinity= salinity, in psu
DOI: 10.5061/dryad.b5mkkwhk8
title: Data from: Acetylcholine waves and dopamine release in the striatum

description: Striatal dopamine encodes reward, with recent work showing that dopamine
 release occurs in spatiotemporal waves. However, the mechanism of dopamine
 waves is unknown. Here we report that acetylcholine release in mouse
 striatum also exhibits wave activity, and that the spatial scale of
 striatal dopamine release is extended by nicotinic acetylcholine
 receptors. Based on these findings, and on our demonstration that single
 cholinergic interneurons can induce dopamine release, we hypothesized that
 the local reciprocal interaction between cholinergic interneurons and
 dopamine axons suffices to drive endogenous traveling waves. We show that
 the morphological and physiological properties of cholinergic interneuron
 – dopamine axon interactions can be modeled as a reaction-diffusion system
 that gives rise to traveling waves. Analytically-tractable versions of the
 model show that the structure and the nature of propagation of
 acetylcholine and dopamine traveling waves depend on their coupling, and
 that traveling waves can give rise to empirically observed correlations
 between these signals. Thus, our study provides evidence for striatal
 acetylcholine waves in vivo, and proposes a testable theoretical framework
 that predicts that the observed dopamine and acetylcholine waves are
 strongly coupled phenomena.
description: # Raw data accompanying manuscript entitled "Acetylcholine waves and
 dopamine release in the striatum"
 [https://doi.org/10.5061/dryad.b5mkkwhk8](https://doi.org/10.5061/dryad.b5mkkwhk8) The dataset includes all the raw data belonging to Figures 1-3 in the main text and Supplementary Figs. 1-2. These include movies of the Acetylcholine indicators in the dorsal striatum (Figure 1 & Supplementary Fig. 1), and the two-photon laser scanning microscopy in conjunction with electrophysiological data regarding dopamine and acetylcholine release in acute striatal slices (Figs 2-3 and Supplementary Fig. 2). Each dataset includes it's own README files.
DOI: 10.13140/rg.2.2.35825.13928
title: Supplementary_Material_MCQ_Clinical_Critical_Thinking_Al_Shawki
DOI: 10.60593/ur.d.31129234
title: "Developmental exposure to a PFAS mixture impairs the anamnestic response to influenza A virus infection in mice": CD4 transcription factor panel FCS files.

description: Each folder contains flow cytometry standard (FCS) files to identify Th1, Th2, Th17, and T regulatory cells on days 0, 9, 70, 75, and 77 relative to primary influenza A virus infection. In the publication, the data from these files is presented in Table S7 and S8.
DOI: 10.60593/ur.d.31129234.v1
title: "Developmental exposure to a PFAS mixture impairs the anamnestic response to influenza A virus infection in mice": CD4 transcription factor panel FCS files.

description: Each folder contains flow cytometry standard (FCS) files to identify Th1, Th2, Th17, and T regulatory cells on days 0, 9, 70, 75, and 77 relative to primary influenza A virus infection. In the publication, the data from these files is presented in Table S7 and S8.
DOI: 10.58053/mapbiomas/6szrdu
title: MapBiomas General “Handbook” - Algorithm Theoretical Basis Document (ATBD) - Collection 10 - Pantanal - Appendix

description: This document details the theoretical basis, justification, and methods applied to produce annual maps of land cover and land use (LCLU) specifically for the Pantanal biome from 1985 to 2024 as part of MapBiomas Collection 10. Additionally, the document presents historical context and background information, a general description of the satellite imagery datasets, feature inputs, and details about the accuracy assessment method applied.
DOI: 10.5061/dryad.7pvmcvf0p
title: Data from: Hypoxia blunts angiogenic signaling and upregulates the antioxidant system in elephant seal endothelial cells

description: Background Elephant seals exhibit extreme hypoxemic tolerance derived from
 repetitive hypoxia/reoxygenation episodes they experience during diving
 bouts. Real-time assessment of the molecular changes underlying protection
 against hypoxic injury in seals remains restricted by their at-sea
 inaccessibility. Hence, we developed a proliferative arterial endothelial
 cell culture model from elephant seals and used RNA-seq, functional
 assays, and confocal microscopy to assess the molecular response to
 prolonged hypoxia. Results Seal and human endothelial cells exposed to 1%
 O2 for up to 6 h respond differently to acute and prolonged hypoxia. Seal
 cells decouple stabilization of the hypoxia-sensitive transcriptional
 regulator HIF-1α from angiogenic signaling. Rapid upregulation of genes
 involved in glutathione (GSH) metabolism supports the maintenance of GSH
 pools, and intracellular succinate increases in seal but not human cells.
 High maximal and spare respiratory capacity in seal cells after hypoxia
 exposure occurs in concert with increasing mitochondrial branch length and
 independent from major changes in extracellular acidification rate,
 suggesting that seal cells recover oxidative metabolism without
 significant glycolytic dependency after hypoxia exposure. Conclusions We
 found that the glutathione antioxidant system is upregulated in seal cells
 during hypoxia, while this system remains static in comparable human
 cells. Furthermore, we found that in contrast to human cells, hypoxia
 exposure rapidly activates HIF-1 in seal cells, but this response is
 decoupled from the canonical HIF-angiogenesis pathway. These results
 highlight the unique mechanisms that confer extraordinary tolerance to
 limited oxygen availability in a champion diving mammal.
description: # Data from: Hypoxia blunts angiogenic signaling and upregulates the
 antioxidant system in elephant seal endothelial cells
 [https://doi.org/10.5061/dryad.7pvmcvf0p](https://doi.org/10.5061/dryad.7pvmcvf0p) Code for RNAseq data associated with "Hypoxia blunts angiogenic signaling and upregulates the antioxidant system in elephant seal endothelial cells." bioRxiv manuscript doi: 10.1101/2023.07.01.547248 SRA BioProjects: PRJNA1017894 and PRJNA1017895 ## Code and files **config files are separated into seal and human data** seal_config.json human_config.json **compare_config files are separated into seal and human data** *compare_config files were used to determine differential gene expression at each time point vs control, and pairwise between timepoints using EBSeq* seal_compare_config.json human_compare_config.json **Snakefile** provides snakemake pipeline **code.R** **contains code for cluster analysis and pathway enrichment for both species, using the following files:** ma_genes_results.results rsem output ma_genes.txt rsem output with sample names modified to fit R hs_genes_results.txt rsem output hs_genes.txt rsem output with sample names modified to fit R
DOI: 10.5061/dryad.m63xsj47v
title: In-situ relative humidity and air temperature urban microclimate data

description: Monitoring and understanding the variability of heat within cities is
 important for urban planning and public health, and there has been a
 growth in the number of studies measuring intra-urban temperature
 variability. Recognizing that the physiological effects of heat depend on
 humidity as well as temperature, some of these measurement campaigns have
 included measurements of relative humidity alongside temperature. Reported
 analyses, however, have not reported whether spatial structure in
 humidity, independent from temperature, contributes significantly to
 intra-urban heat variability. Here we use summer temperature and humidity
 from networks of stationary sensors in multiple cities in the USA to
 examine this issue. It is shown that although there are spatial variations
 in relative humidity there are only very weak spatial variations in the
 absolute humidity within these cities.  This variability in
 absolute humidity plays an insignificant role in the spatial variability
 of the heat index and humidex, and the spatial variability of the heat
 metrics is dominated by temperature variability. A practical consequence
 of this is that a network of sensors that only measure temperature is
 sufficient to quantify the spatial variability of heat across these cities
 when combined with humidity measured at a single location, allowing for
 lower-cost heat monitoring networks.
description: Data was collected on Thermocron iButtons placed at 2 m height
 within trees in each of the cities.
description: # Relative Humidity and Air Temperature for Eight U.S. Cities
 [https://doi.org/10.5061/dryad.m63xsj47v](https://doi.org/10.5061/dryad.m63xsj47v) Dataset include spreadsheets of in-situ relative humidity and air temperature at 80-100 microsites located in eight U.S cities (Baltimore, Denver, Las Vegas, Los Angeles, Miami, Phoenix, Portland, Tucson).Microclimate was recorded for every hour over three months during 2017-2019. A metadata excel sheet includes the geolocations and ID numbers for each sensor, as well as the NDVI at each location. ## Description of the data and file structure Relative humidity and air temperature data is provided in .csv's for each city. In each .csv the columns provide the Date and Hour of data recording and the SensorID of a specific sensor. Each row is one hour's recording of microclimate within that city. The metadata excel spreadsheet includes the geolocation for each sensorID. This data can be used to map out the relative humidity and air temperature within the eight United States cities (Baltimore, Denver, Las Vegas, Los Angeles, Miami, Phoenix, Portland, Tucson). All data is associate with a specific iButton sensor which was hung inside the crown of a tree. All locations are geo referenced and time stamped to the hour and date. .
DOI: 10.82294/dvnlglmm1
title: Replication Data for: Categorías y códigos. Una visión del fenómeno educativo, social y cultural de la educación artística
title: Categorías implementadas en el proyecto de formación en educación artñistica y cultural

description: La construcción de las categorías y códigos de esta propuesta educativa e investigativa se sustentan gracias a autores que han desarrollado propuestas e investigaciones sobre estudios curriculares recientes, retomando nombres como William Pinar, Ivor Goodson, Juny Montoya, Jimeno Sacritán, Kerry Freedman, Ritta Irwin, Jhon Biggs, entre otros. Por ende, la propuesta acá desarrollada le apuesta a la comprensión de la educación como un fenómeno social, cultural y educativo, promueve la comprensión curricular y el tránsito de los currículos por reproducción hacia los currículos por interpretación, y fomentan un cambio paradigmático de las prácticas educativas, artísticas y culturales.
DOI: 10.60593/ur.d.31129336
title: "Developmental exposure to a PFAS mixture impairs the anamnestic response to influenza A virus infection in mice": Sample code for FCS files.

description: This file contains the sample code for the samples collected on each day relative to primary infection (day 0, 9, 14, 70, 75, 77). Each day is on a separate tab. Each tab contains a table listing the sample number and the sample identifiers: dam ID, treatment, sex, and the number of MLN cells harvested from each animal. This information is necessary to analyze the accompanying flow cytometry data.
DOI: 10.60593/ur.d.31129336.v1
title: "Developmental exposure to a PFAS mixture impairs the anamnestic response to influenza A virus infection in mice": Sample code for FCS files.

description: This file contains the sample code for the samples collected on each day relative to primary infection (day 0, 9, 14, 70, 75, 77). Each day is on a separate tab. Each tab contains a table listing the sample number and the sample identifiers: dam ID, treatment, sex, and the number of MLN cells harvested from each animal. This information is necessary to analyze the accompanying flow cytometry data.
DOI: 10.15468/dl.5wjacv
title: Occurrence Download

description: A dataset containing 673 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tetrapturus angustirostris",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 673 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025419-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.enqjtn
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Garra tana)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025420-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15315610
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by C. Novoa Sepúlveda, https://orcid.org/0000-0001-6113-9725. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
DOI: 10.5281/zenodo.15346894
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by C. Novoa Sepúlveda, https://orcid.org/0000-0001-6113-9725. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
DOI: 10.5281/zenodo.15580096
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by C. Novoa Sepúlveda, https://orcid.org/0000-0001-6113-9725. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
DOI: 10.15468/dl.wrcjt2
title: Occurrence Download

description: A dataset containing 9488 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Fistularia commersonii Rüppell, 1838"
 ]
}

 The dataset includes 9488 records from 200 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016468-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.