cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/absjsd
title: Systematics of three pan-Amazonian antwren lineages (Aves: Passeriformes: Thamnophilidae: Myrmotherula and Isleria)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Isler, Morton L., Chesser, R. Terry, Stryjewski, Katherine Faust, Whitney, Bret M. (2025): Systematics of three pan-Amazonian antwren lineages (Aves: Passeriformes: Thamnophilidae: Myrmotherula and Isleria). Zootaxa 5722 (1): 45-78, DOI: 10.11646/zootaxa.5722.1.2, URL: https://doi.org/10.11646/zootaxa.5722.1.2AbstractWorking within the framework of a companion phylogenetic analysis, we reexamined species limits within three lineages of antwrens (two species and one species complex) widely distributed across the Amazon Basin. Diagnostic differences in vocal and plumage characters provided the basis for the following taxonomic revisions. Myrmotherula longipennis is found to comprise three species: (1) M. longipennis (sensu stricto), which is confined to the region north of the Amazon; (2) M. garbei, which is elevated from subspecies status and includes the subspecies zimmeri; and (3) M. paraensis, which is also elevated from subspecies status and includes subspecies transitiva and ochrogyna. Myrmotherula menetriesii also comprises three species: (1) M. menetriesii (sensu stricto), which occurs in the southwest quadrant of Amazonia and includes the subspecies berlepschi; (2) M. cinereiventris, which is elevated from subspecies status and includes the subspecies pallida; and (3) M. omissa, which is monotypic and is also elevated from subspecies status. We maintain two species in the Isleria complex, I. guttata and I. hauxwelli. Isleria guttata remains monotypic, but the subspecies of I. hauxwelli are revised. Isleria h. hellmayri is preserved as currently defined, but I. h. suffusa is synonymized with the nominate form, the geographic range of which is restricted to western Amazonia. A fourth subspecies, I. h. clarior, is resurrected; this subspecies occupies the major part of the range previously assigned to I. h. hauxwelli.
DOI: 10.15468/dl.vv724c
title: Occurrence Download

description: A dataset containing 284 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "OccurrenceStatus is Present",
 "TaxonKey is Loxosceles laeta"
 ]
}

 The dataset includes 284 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003884-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.qfttdz0qp
title: Data from: Heat stress conditions affect the social network structure of free‐ranging sheep

description: Extreme weather conditions, like heatwave events, are becoming more
 frequent with climate change. Animals often modify their behaviour to cope
 with environmental changes and extremes. During heat stress conditions,
 individuals change their spatial behaviour and increase the use of shaded
 areas to assist with thermoregulation. Here, we suggest that for social
 species, these behavioural changes and ambient conditions have the
 potential to influence an individual's position in its social
 network, and the social network structure as a whole. We investigated
 whether heat stress conditions (quantified through the temperature
 humidity index) and the resulting use of shaded areas, influence the
 social network structure and an individual's connectivity in it. We
 studied this in free‐ranging sheep in the arid zone of Australia,
 GPS‐tracking all 48 individuals in a flock. When heat stress conditions
 worsened, individuals spent more time in the shade and the network was
 more connected (higher density) and less structured (lower modularity).
 Furthermore, we then identified the behavioural change that drove the
 altered network structure and showed that an individual's shade use
 behaviour affected its social connectivity. Interestingly, individuals
 with intermediate shade use were most strongly connected (degree,
 strength, betweenness), indicating their importance for the connectivity
 of the social network during heat stress conditions. Heat stress
 conditions, which are predicted to increase in severity and frequency due
 to climate change, influence resource use within the ecological
 environment. Importantly, our study shows that these heat stress
 conditions also affect the animal's social environment through the
 changed social network structure. Ultimately, this could have further flow
 on effects for social foraging and individual health since social
 structure drives information and disease transmission.
description: # Data from: Heat stress conditions affect the social network structure of
 free‐ranging sheep article
 by Borthwick, Z., Quiring, K., Griffith, S. C., & Leu, S. T. published
 in Ecology and Evolution For questions, contact Zachary Borthwick
 () or Stephan Leu
 (). (A) global_net.csv contains the
 data to investigate the network on the global level. Variables in the
 file: study.day --- number of each study day, which were numbered
 consecutively mean.THI --- mean Temperature Humidity Index network.density
 --- network density modularity --- network modularity CV.edgeweight ---
 coefficient of variation of edge weights (B) node_net.csv contains the
 data to investigate the network on the individual level. Variables in the
 file: study.day --- number of each study day, which were numbered
 consecutively ID --- ID number of each individual sheep degree --- node
 degree strength --- node strength betweenness --- betweenness centrality
 shade.use --- describes how long the individual sheep spent in the shade
 during the 3-hour midday period (in minutes)
DOI: 10.5061/dryad.wdbrv15wb
title: Ecological niche modelling to project past, current and future distributional shift of black ebony tree (Diospyros melanoxylon Roxb.) in India

description: The present study utilized an ensemble modelling approach to predict the
 distribution of D. melanoxylon under present, past (Last Glacial Maximum,
 ~22,000 cal yr BP, Middle Holocene ~6000 cal yr BP) and future climate
 change scenarios (RCP 2.6 and 8.5 for 2050s and 2070s). The annual mean
 temperature, mean temperature of the wettest quarter and annual
 precipitations were the most critical parameters that chiefly influence
 the distribution of D. melanoxylon. The ensemble model rendered high
 accuracy with AUC=0.93, TSS=0.74, and Kappa=0.71. Past projections of D.
 melanoxylon indicated a widespread distribution during the Last Glacial
 Maximum and Middle Holocene suggesting its adaptability to semi-dry as
 well as warm and humid climates, respectively. The presence of fossil
 pollen evidence of D. melanoxylon in the suitable habitats
 derived through past projections in this study complements the model
 results and marks occurrences of the species during the Last Glacial
 Maximum and Middle Holocene. By 2050s and 2070s (RCP 8.5), there would be
 a decline in the distribution by only 0.4% (13622 km2) and 0.2% (6842 km2)
 of the extremely habitat suitable, respectively. The main factor leading
 to reduced habitat suitability is the anticipated rise in temperature and
 variations in seasonal precipitation patterns. Our findings, help in
 identifying the parts of the country which would be severely affected by
 future climate change scenarios and plan conservation strategies for this
 commercially important species to facilitate its growth in suitable
 habitats which are likely to sustain under future climatic conditions.
description: # Ecological niche modelling to project past, current and future
 distributional shift of black ebony tree (Diospyros melanoxylon Roxb.) in
 India ## Description of
 the data and file structure Species occurrence data was compiled from
 India Biodiversity Portal (IBP), Global biodiversity information facility
 (GBIF), field surveys, and herbarium records. All the occurrence data was
 combined and rarified. File name ‘Final_output_rarefied_points’ lists the
 species occurrence data points used for the model runs. Model output files
 (.asc) for Current, Middle Holocene, LGM, and future climate change
 scenarios are also uploaded. ## Sharing/Access information Links to other
 publicly accessible locations of the data are already given in the
 manuscript: * Secondary occurrence data points for the *D. melanoxylon* 
 were extracted from online databases, i.e. Global Biodiversity Information
 Facility (GBIF) from the website   and Indian
 Biodiversity Portal from the website
 Bioclimatic Data was derived from
 the following sources: * Past, current and future bioclimatic variables
 data were extracted from the website
DOI: 10.5061/dryad.00000009r
title: Data from: Rapoport’s rule explains the range size distribution of butterflies along the Eastern Himalayan elevation gradient

description: Understanding elevational range size distribution of organisms can provide
 valuable insights on biogeographic pattern of species and their
 conservation. Rapoport’s rule posits that the elevational range size of
 species increases with increasing elevation. However, the validity of this
 rule is often questioned due to variations in methodologies across studies
 and inconsistencies among different groups of organisms. In this study we
 examined the elevational range size distribution of butterflies in the
 Eastern Himalaya, and assessed the applicability of Rapoport’s rule using
 different approaches, which perhaps is the first of its kind in the
 Himalaya. We sampled butterflies along the elevational gradient of 16
 elevational bands (300 – 3,300 m) using point count method along the
 transect. The sampled butterflies were grouped into various sub-groups
 based on family, biogeographic affinity, and larval feeding pattern. We
 found that the majority of the butterfly species (total as well as
 sub-groups) had small range sizes, and their elevational range
 distribution showed support for the Rapoport’s rule. Increase in variation
 in temperature as measured by temperature seasonality and mean annual
 temperature range were the most important predictors of range size
 distribution pattern of the overall butterfly community. However, the
 relationship between range size and climatic variability differed among
 various sub-groups implying that the perceived pattern may vary even
 within the species of the same taxon.
description: All details have been provided in the Manuscript published in
 Biotropica.
description: # Data from: Rapoport’s rule explains the range size distribution of
 butterflies along the Eastern Himalayan elevation gradient
 [https://doi.org/10.5061/dryad.00000009r](https://doi.org/10.5061/dryad.00000009r) These datasets provides all the data used in the preparation of the Manuscript published in Biotropica. The datasets are provided in two formats. One in .pdf format and the other in .xls format The .pdf files corresponding to the supplementary files, labeled as Appendix 1, have been submitted to the journal. The data are presented in Table S1.1 and Table S1.2. The .xls contains two datasets. One site data (corresponding to Table S1.1 in the appendix) and Species data( corresponding to Table S1.1 in the appendix). Geospatial coordinates and environmental data have been incorporated into the site data for the convenience of those interested in utilizing the information. The methodology for extracting environmental data is detailed in the Methodology section of the article. Additionally, a second abstract (written in Nepali Language) is also provided Additional tables and figures to support our findings are also provided in the attached appendices
DOI: 10.15468/dl.tamb99
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "CatalogNumber" : [
 "is one of (CHR 234555, CHR 369147, CHR 369158, CHR 37078, CHR 49937, CHR 49938)"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003886-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13140/rg.2.2.23753.40804
title: Primes as probe to excite intrinsic geometry spectrum
DOI: 10.5061/dryad.7h44j101z
title: Barcoding of episodic memories in the hippocampus of a food-caching bird

description: The hippocampus is critical for episodic memory. Although hippocampal
 activity represents place and other behaviorally relevant variables, it is
 unclear how it encodes numerous memories of specific events in life. To
 study episodic coding, we leveraged the specialized behavior of chickadees
 – food-caching birds that form memories at well-defined moments in time
 whenever they cache food for subsequent retrieval. Our recordings during
 caching revealed very sparse, transient barcode-like patterns of firing
 across hippocampal neurons. Each “barcode” uniquely represented a caching
 event and transiently reactivated during the retrieval of that specific
 cache. Barcodes co-occurred with the conventional activity of place cells,
 but were uncorrelated even for nearby cache locations that had similar
 place codes. We propose that animals recall episodic memories by
 reactivating hippocampal barcodes. Similarly to computer hash codes, these
 patterns assign unique identifiers to different events and could be a
 mechanism for rapid formation and storage of many non-interfering
 memories.
description: Raw electrophysiological, calcium imaging, and behavioral video
 recordings during food caching behavior in chickadee hippocampus were
 collected and pre-processed as described in the associated
 manuscript. 
description: # Barcoding of episodic memories in the hippocampus of a food-caching bird
 [https://doi.org/10.5061/dryad.7h44j101z](https://doi.org/10.5061/dryad.7h44j101z) This repository contains all data used in the accompanying paper. This includes behavioral tracking and annotation of food caching behavior, electrophysiology, and calcium imaging data. Further details on the experiments, data and methods are available in the paper, published in Cell (April 11, 2024) and available as a free pre-print at: [https://www.biorxiv.org/content/10.1101/2023.05.27.542597v2](https://www.biorxiv.org/content/10.1101/2023.05.27.542597v2) ## Description of the data and file structure Electrophysiology experiments in the grid arena are in `Grid Caching Data` with documentation in a README.m file (provided outside of the zipped archive), and imaging experiments in the circular arena are in `Circular Arena Data` with documentation in a Word doc ('Calcium imaging documentation' - also outside the zipped archive). The `Figure Scripts` file in the associated Zenodo repository contains additional information about the analysis and data underlying the figures in the paper, Matlab figure files containing the underlying data, and includes code to regenerate plots from intermediate pre-computed results, with description and documentation in RUNME.m Documentation is located in a zip file along with the associated dataset. Additionally, documentation files are provided as standalone files to permit examination without downloading the full dataset.  Matlab 2019b and 2022a were used for all analyses.
DOI: 10.15468/dl.jha4xr
title: Occurrence Download

description: A dataset containing 2643 records in GBIF matching the query:
SELECT
 '483' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 46.479780028101516
 AND decimalLatitude &lt;= 51.21395264452012
 AND decimalLongitude &gt;= 69.23837900975829
 AND decimalLongitude &lt;= 80.17725619669127
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 2643 records were derived from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003878-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m0cfxppb7
title: Post-transcriptional splicing can occur in a slow-moving zone around the gene

description: Splicing is the stepwise molecular process by which introns are removed
 from pre-mRNA and exons are joined together to form mature mRNA sequences.
 The ordering and spatial distribution of these steps remains
 controversial, with opposing models suggesting splicing occurs either
 during or after transcription. We used single-molecule RNA FISH, expansion
 microscopy, and live-cell imaging to reveal the spatiotemporal
 distribution of nascent transcripts in mammalian cells. At
 super-resolution levels, we found that pre-mRNA formed clouds around the
 transcription site. These clouds indicate the existence of a transcription
 site proximal zone through which RNA moves more slowly than in the
 nucleoplasm. Full-length pre-mRNA undergoes continuous splicing as they
 move through this zone following transcription, suggesting a model in
 which splicing can occur post-transcriptionally but still within the
 proximity of the transcription site, thus seeming co-transcriptional by
 most assays. These results may unify conflicting reports of
 co-transcriptional versus post-transcriptional splicing.
description: # Post-transcriptional splicing can occur in a slow-moving zone around the
 gene
 [https://doi.org/10.5061/dryad.m0cfxppb7](https://doi.org/10.5061/dryad.m0cfxppb7) ## Description of the data and file structure Matlab scripts in the **extraction_scripts** folder were used to generate data in the **extracted_data** and **extracted_images** folders. This data was analyzed by R and Matlab scripts in the **analysis_scripts** folder. Analyzed data was plotted into figure graphs using the R scripts in the **plot_scripts** folder. ### Folder structure: #### Cote\_eLife\_scripts * /analysis_scripts: R and .m files * /extracted_data: CSV files with information about genes, etc., and .tif images, STORM density maps * /extracted_images: organized .tif files * /extraction_scripts: .m scripts * /plot_scripts: R scripts for plots #### Cote\_eLife\_raw\_data\_1 - Cote\_eLife\_raw\_data\_6 These folders contain .tif images of cells, and some contain matlab files with the corresponding data. ## Sharing/Access information Sequencing data generated for this paper can be found on GEO under accession number **GSE254859**. ## Code/Software Image analysis requires the RajLabImageTools pipeline, found at the GitHub link in the Related Works section.
DOI: 10.5061/dryad.tht76hf63
title: Beyond mutations: accounting for selection and self-organization in the analysis of protein evolution

description: Molecular phylogenetic research has relied on the analysis of the coding
 sequences by genes or of the amino acid sequences by the encoded proteins.
 Enumerating the numbers of mismatches, being indicators of mutation, has
 been central to pertinent algorithms. However, the constraining forces of
 selection and self-organization have been unaccounted for in conventional
 approaches, possibly causing available models to fall short of
 representing the actual evolutionary history. Specific amino acids possess
 quantifiable characteristics that enable the conversion from “words”
 (strings of letters denoting amino acids or bases) to “waves” (strings of
 quantitative values representing the physico-chemical properties) or to
 matrices (coordinates representing the positions in a comprehensive
 property space). The application of such numerical representations to
 evolutionary analysis takes into account not only mutation but also
 selection/self-organization as influences that drive speciation, because
 selective pressures favor certain mutations over others, and this
 predilection is represented in the characteristics of the incorporated
 amino acids (it is not born out solely by the mismatches). Besides being
 more discriminating sources for treegenerating algorithms than
 match/mismatch, the number strings can be examined for overall similarity
 with average mutual information, autocorrelation, and fractal dimension.
 Bivariate wavelet analysis aids in distinguishing hypermutable versus
 conserved domains of the protein. Further, the matrix depiction is readily
 subjected to comparisons of distances (Euclidean distance, Frobenius
 distance), and it allows the generation of heat maps or graphs. These
 analytical algorithms have been automated in R and are applicable to
 various processes that are describable in matrix format.
description: # Beyond Mutations: Accounting for Selection and Self-Organization in the
 Analysis of Protein Evolution
 [https://doi.org/10.5061/dryad.tht76hf63](https://doi.org/10.5061/dryad.tht76hf63) ## Description of the data and file structure Publicly accessible sequences were collected from the NCBI landmark model organisms and then sought to add representatives of diverse clades from NCBI nucleotide. ## Sharing/Access information Data was derived from the following sources: * NCBI ## Code/Software NA
DOI: 10.15468/dl.byh8ak
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Alien Species in Poland - Plants"
 ]
}

 The dataset includes 61 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003887-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6073/pasta/a3e3050469c1e6660a782c1612746324
title: North Temperate Lakes LTER: High Frequency Meteorological and Dissolved Oxygen Data - Trout Lake Buoy 2004 - current

description: The instrumented buoy on Trout Lake is equipped with a dissolved oxygen sensor, a thermistor chain, and meteorological sensors that provide fundamental information on lake thermal structure, weather conditions, and lake metabolism. Data are usually collected every 10 minutes with occasional periods of 2 minute data for short periods to answer specific questions. The D-Opto dissolved oxygen sensor is 0.5m from the lake surface. Meteorological sensors measure wind speed, wind direction, relative humidity, air temperature, photosynthetically active radiation (PAR), and barometric pressure. Starting in 2005, thermistors were placed every 0.5-1m from the surface through 14m and every 2 to 4m from 14m to the bottom of the water column at 31m. In July 2006, a new thermistor chain was deployed with thermistors placed every meter from the surface through a depth of 19 meters. After correcting for flux to or from the atmosphere and vertical mixing within the water column, high frequency measurements of dissolved gases such as carbon dioxide and oxygen can be used to estimate gross primary productivity, respiration, and net ecosystem productivity, the basic components of whole lake metabolism. Data are averaged to daily values from one minute samples for years 2005 - 2006. Daily values are computed from high resolution data starting in year 2007. Data are averaged to hourly values from one minute samples for years 2005 - 2008, Hourly values are computed from high resolution data starting in year 2009. Hourly and daily values may not be current with high resolution data in the current year. Sampling Frequency: varies for instantaneous sample. averaged to hourly and daily values from one minute samples. Times are Central Standard Time (CST). Number of sites: 1