cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kd51c5bhv
title: Earth history and trait innovation drive the global radiation of modern toads

description: The distributions of species radiations reflect environmental changes
 driven by both Earth history (geological processes) and the evolution of
 biological traits (critical to survival and adaptation), which profoundly
 drive biodiversity yet are rarely studied together. Modern toads
 (Bufonidae, Amphibia), an iconic radiation with global distribution and
 high phenotypic diversity, are an ideal group for exploring these
 dynamics. Using phylogenomic data from 124 species
 across six continents, we reconstruct their evolutionary history.
 Biogeographic analyses suggest modern toads originated in South America ~
 61 million years ago, later dispersing to Africa and Asia, thereby
 challenging hypotheses of dispersal via North America. Species
 diversification rates increased after leaving South America, linked to
 Cenozoic geological events and key innovations like toxic parotoid glands
 for predator defense. The emergence of parotoid glands coincided
 with the South American dispersal,
 promoting diversification and enabling toads to
 dominate both Old and New Worlds. In contrast, the evolution of other
 traits, despite being crucial to adaptation, did not promote species
 diversification (e.g., large body size) or were ambiguously associated
 with expansion into the Old World (e.g., developmental modes). These
 findings highlight the adaptability of modern toads and reveal the
 interplay between Earth's history and phenotypic innovation in
 shaping biodiversity.
description: We used Anchored Hybridization Enrichment (AHE) to select 150
 conserved orthologous gene loci from the genome of Bufo bufo and designed
 9,807 probes. Additionally, based on the mitochondrial genome of Bufo
 gargarizans, we selected 13 mitochondrial gene loci for probe design. We
 then conducted AHE sequencing on 124 species of Bufonidae and 7 outgroup
 species.
description: # Earth history and trait innovation drive the global radiation of modern
 toads Dataset DOI: [10.5061/dryad.kd51c5bhv](10.5061/dryad.kd51c5bhv) ##
 Description of the data and file structure ### Files and variables ####
 File: tree_files.zip **Description:** Tree files include the ML tree
 constructed using only the 150 AHE genes, as well as the combined dataset
 with the 14 additional genes. Additionally, the species tree was inferred
 using ASTRAL software, and the time-calibrated tree was generated using
 treePL. The 95% confidence intervals were derived from summarizing 100
 bootstrap ML trees. #### File: Data.zip **Description:** Sequence files
 for each locus are included, comprising 150 AHE genes and 14 genes from
 previously published studies, with an overlap of nine genes (five nuclear,
 four mitochondrial). The concatenated sequence file is provided in PHYLIP
 format, containing both the 150 AHE genes alone and the combined dataset
 with the 14 genes from published sources.
DOI: 10.5061/dryad.c866t1gj0
title: Columbia Suicide Severity Rating Scale Screen scores in adults with Chiari malformation Type 1

description: Adult Chiari malformation Type 1 is a neurological condition characterized
 by high levels of chronic pain, disability, and psychological distress,
 yet self-harming behaviors have not previously been studied in this
 patient group. The purpose of this study was to determine the prevalence
 of elevated suicide risk scores among adults with Chiari malformation Type
 I using the Columbia Suicide Severity Rating Scale – Screen and examine
 the association between risk scores and pain, disability, and
 psychological distress. A web-based, anonymous survey was administered,
 comprised of validated scales and demographic questions. Suicide
 risk (Columbia Screen score) was dichotomized as Low or High-Risk, and
 both crude and adjusted odds ratios were calculated to determine
 statistical associations with pain, disability, and psychological
 measures. Overall, 44% of 372 respondents scored in the High-Risk
 group. Depression at the moderate level or above, age younger than 30
 years, and severe or complete neck-related disability were each
 significant predictors of High-Risk scoring. This study suggests that
 suicidal ideation is a potentially serious morbidity associated with
 Chiari malformation Type 1 and should be investigated further.
description: # Columbia Suicide Severity Rating Scale Screen scores in adults with
 Chiari malformation Type 1
 [https://doi.org/10.5061/dryad.c866t1gj0](https://doi.org/10.5061/dryad.c866t1gj0) ## Description of the data and file structure An anonymous, web-based survey was administered to adults (18+) with a self-reported physician diagnosis of Chiari malformation Type 1. The dataset includes 372 respondents who completed the survey. Participants were recruited through Conquer Chiari's (a patient organization) website, social media platforms, and email contact list. ### Files and variables #### File: Suicide_Risk_in_Adults_with_Chiari_malformation_Type_I.xlsx **Description:** An Excel file with 372 data rows and 14 columns. Note that one subject contains missing data for Gender and Age, which is entered as 'n/a'. ##### Variables * ID - Unique identifier * Gender - Not defined to protect human subjects' anonymity * Age (years) * Surgery - history of Chiari decompression surgery (Yes=1) * CSSRS Screen - Risk category from Columbia Suicide Severity Rating Scale - Screen * Suicide HiRisk - CSSRS risk category dichotomized (0-1 = 0; 2-3 = 1) * UCLA - Total score from the UCLA Loneliness scale * SFMPQ - Total pain score from McGill Short Form Pain Questionnaire - 2 * IES - Total score from Impact of Event Scale - Revised * DASSD - Depression subscale score from the DASS-21 * DASSA - Anxiety subscale score from the DASS-21 * NDI - Total Neck Disability Index score (doubled) * Covid - Total score from the Covid Impact Scale * PCS - Total score from the Pain Catastrophizing Scale ## Code/software Any spreadsheet software ## Access information NA
DOI: 10.15468/dl.fx7gxs
title: Occurrence Download

description: A dataset containing 1106197 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Engraulis",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 1106197 records from 116 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004253-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dv41ns28r
title: Presence of tertiary lymphoid structures and exhausted tissue-resident T cells determines clinical response to PD-1 blockade in renal cell carcinoma

description: Immune checkpoint inhibitors (ICI) targeting the PD-1 pathway have
 transformed treatment of advanced renal cell carcinoma (RCC), but
 mechanisms underlying therapeutic response remain largely unknown. Herein,
 we perform transcriptomic analysis on RCC biospecimens from 102 patients
 enrolled in a phase II clinical trial of frontline nivolumab (NCT03117309)
 to investigate determinants of response to anti-PD1 monotherapy. Through
 bulk analysis, we identify an enrichment of genes associated with tertiary
 lymphoid structures (TLS) in responding patients. Using single-cell
 transcriptomics and external cohort validation, we identify a population
 of tissue-resident (ZNF683+ SLAMF7+) exhausted CD8+ T cells enriched in
 patients with poor clinical outcomes. Integrating these findings, we find
 tumors with high TLS and low tissue-resident exhausted CD8+ T cells have
 superior clinical outcomes with nivolumab. Altogether, these analyses
 contribute to a growing understanding of how the tumor microenvironment
 drives ICI- resistance and propose possible therapeutic targets to
 rationally overcome resistance to anti-PD1 monotherapy.
description: # **Presence of tertiary lymphoid structures and exhausted tissue-resident
 T cells determines clinical response to PD-1 blockade in renal cell
 carcinoma**
 [https://doi.org/10.5061/dryad.dv41ns28r](https://doi.org/10.5061/dryad.dv41ns28r) ## Description of the data and file structure This dataset contains single-cell RNA sequencing (scRNA-seq) data from 19 samples from 17 renal cell carcinoma (RCC) patients, including 2 sets of paired pre- and post-treatment (aPD-1) samples. Each dataset is provided as a zip file, corresponding to one patient. The data was processed using the 10x Genomics Chromium platform and is provided in the standard sparse matrix format. Each zip file contains the following three files: * **barcodes.tsv** – A list of cell barcodes. * **features.tsv** – A list of gene identifiers. * **matrix.mtx** – A sparse matrix storing gene expression counts. **File Naming Conventions** The files are named using the following format: * **260-1XXX_BL_filtered_feature_bc_matrix.zip** – Data from the **baseline sequencing** time point. * **260-1XXX_PR_filtered_feature_bc_matrix.zip** – Data from the **progression sequencing** time point. where XXX is a unique patient identifier. ### Files and variables #### File: Data\_S1.zip **Description:** Lists all filtered single cell feature-barcode matrices.  ## Code/software Where relevant, R v4.1 and packages within Bioconductor v3.13 were implemented. Filtered single cell feature-barcode matrices were loaded into R using DropletUtils and used to construct a SingleCellExperiment object (SingleCellExperiment v1.14.1).
DOI: 10.15468/dl.zh3r7b
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aspersentis johni",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004262-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j6q573nrc
title: Learning realistic lip motions for humanoid face robots

description: Lip motion represents outsized importance in human communication,
 capturing nearly half of our visual attention during conversation. Yet
 anthropomorphic robots often fail to achieve lip-audio synchronization,
 resulting in clumsy and lifeless lip behaviors. Two fundamental barriers
 underlay this challenge. First, robotic lips typically lack the mechanical
 complexity required to reproduce nuanced human mouth movements; second,
 existing synchronization methods depend on manually predefined movements
 and rules, restricting adaptability and realism. Here, we present a
 humanoid robot face designed to overcome these limitations, featuring soft
 silicone lips actuated by a ten-degree-of-freedom (10-DoF) mechanism. To
 achieve lip synchronization without predefined movements, we use a
 self-supervised learning pipeline based on a Variational Autoencoder (VAE)
 combined with a Facial Action Transformer, enabling the robot to
 autonomously infer more realistic lip trajectories directly from speech
 audio. Our experimental results suggest that this method outperforms
 simple heuristics like amplitude-based baselines in achieving more
 visually coherent lip-audio synchronization. Furthermore, the learned
 synchronization successfully generalizes across multiple linguistic
 contexts, enabling robot speech articulation in ten languages unseen
 during training.
description: # Learning realistic lip motions for humanoid face robots
 [https://doi.org/10.5061/dryad.j6q573nrc](https://doi.org/10.5061/dryad.j6q573nrc) ## Description of the data and file structure This repository contains datasets used in the experiments and evaluations presented in the paper. ### 1. `real_data.zip` This archive contains **real robot data collected during experiments**. * **Actions**: Robot action commands or control signals executed during data collection. * **Images**: Corresponding visual observations captured by the robot (e.g., RGB images). These data are used to train the FAT model in our work. --- ### 2. `synthesized_data.zip` This archive contains **synthesized videos of the robot performing lip-sync motions**. * The videos are generated to simulate realistic robot facial movements synchronized with speech. * These synthesized lip-sync videos are used **as input to the FAT (Facial Action Transformer) model**. --- ### 3. `synthesized_videos_for_eval.zip` This archive contains fully synthesized robot video samples used for the evaluations reported in the paper. * All visual and audio content in these videos is generated entirely by software. * No real human subjects, human recordings, or human-derived audiovisual data are included. * The videos were presented to participants during evaluation as synthetic stimuli to assess perceptual quality and motion realism, not to analyze or collect human subject data.
DOI: 10.5061/dryad.b5mkkwhq2
title: Comparative chloroplast genome and phylogenetic analysis of Central Asian Tulips

description: Tulipa is a genus that comprises species highly valued as ornamentals
 throughout the world. So far, only a few Tulipa plastid genomes have been
 reported, and there are many taxonomically controversial species. In this
 study, we sequenced the chloroplast genomes (CP) of nineteen species
 collected from Uzbekistan and Kyrgyzstan and conducted comparative
 analysis. In all CP, 136 genes were annotated, of which 114 were unique,
 including 80 protein-coding, 30 tRNA, and 4 rRNA genes. Polymorphic SSRs
 effective for discrimination between species and populations were
 identified. Additionally, comparative Pi diversity analysis of both
 protein coding genes and whole plastomes revealed that the ndhE, ndhF,
 psaC, rpl32 and ycf1 genes and the regions rps16–trnQ-UUG, psbM–psbD,
 trnT-UGU–trnL-UAA, petA–psbJ, rpl33–rps18, petD–rpoA, rpl36–rpl14,
 rpl32–ccsA have higher variability than others. Further, phylogenetic
 reconstruction including 37 species of Tulipa and 3 outgroups based on 76
 shared coding sequences (CDS) and ycf1 genes were made. Both phylogenetic
 trees divided the species into three major clades, and they had almost the
 same topology, confirming that ycf1can be used as a marker for
 phylogenetic relationships. However, the currently recognized sections
 appear non-monophyletic. Insights into the taxonomic classification of
 several species of Tulipa, based on several morphologic,
 phytogeographic, and molecular data are discussed.
description: The data was collected from herbarium, natural habitats and GBIF.
 Phylogenetic trees were built using MrBayes software.
description: # Comparative chloroplast genome and phylogenetic analysis of Central
 Asian Tulips
 [https://doi.org/10.5061/dryad.b5mkkwhq2](https://doi.org/10.5061/dryad.b5mkkwhq2) ## Description of the data and file structure Dataset for the manuscript ID NJB-04460 ### Files and variables #### File: ycf1bayes1.txt **Description:** Bayesian tree built on ycf1 genes #### File: coordinates.zip **Description:** Coordinates of the studied species #### File: TulipCDS\_bayes.txt **Description:** Bayesian tree for protein coding sequences #### File: ycf1\_alignment.fas **Description:** Alignments of ycf1 genes
DOI: 10.5061/dryad.5tb2rbpdw
title: Puma camera trap dataset in Patagonia National Park, Chile

description: This dataset contains information on each photograph in which a puma
 appears, captured by camera traps installed in Patagonia National Park,
 Chile. The data were collected as part of an ecological monitoring effort
 to study puma presence along tourist trails in the park. Camera traps were
 deployed at various locations and recorded the presence of different
 species between August 2020 and March 2022. Each entry in the dataset
 corresponds to a single photograph and includes metadata such as date,
 time, and camera location.
description: # Puma Camera Trap Dataset WLB-2024-01396
 [https://doi.org/10.5061/dryad.5tb2rbpdw](https://doi.org/10.5061/dryad.5tb2rbpdw) ## Description of the data and file structure This dataset contains information extracted from photographic records of *Puma concolor*, captured by camera traps placed along trails inPatagonia National Park between 2020 and 2022. Each record includes: * Period: Sampling period defined by battery replacement and data collection intervals. * Site: Camera trap monitoring location. * Species: The species detected, in this case, *Puma concolor*. * Date and Time: Year, month, day, hour, minute, and second of the photograph. * Number of Individuals (num): The count of pumas present in the image. ### Files and variables #### File: Puma\_Camera\_Trap\_Dataset\_WLB-2024-01396.xlsx **Description:** ##### Variables * **Camera site**: Unique identifier for the camera trap location where the photograph was taken. * **Date**: Date when the photograph was captured (YYYY-MM-DD format). * **Time**: Time when the photograph was captured (HH:MM:SS format). ## Code/software The dataset can be viewed and processed using spreadsheet software (e.g., Microsoft Excel, Google Sheets) or data analysis tools such as R or Python. For data processing and analysis, we used **RStudio** (Version [your version, e.g., 2023.09.1+494]) and the following R packages: * **[camtrapR](cran.r-project.org/web/packages/camtrapR/index.html)**: Used for managing and analyzing camera trap data, including processing image metadata. * **[tidyr](cran.r-project.org/web/packages/tidyr/tidyr.pdf)**: Used for cleaning and restructuring the dataset, including modifying column formats. ### **Workflow** 1. **Data Import**: The raw metadata from the camera traps was loaded into R. 2. **Data Cleaning & Formatting**: Using the tidyr package, column names were adjusted, and date/time formats were standardized. 3. **Metadata Processing**: The camtrapR package was used to extract and structure key metadata from the images. 4. **Analysis & Results**: The temporal activity of pumas and tourists was analyzed to compare them. ## Access information This dataset is original and was collected as part of an ecological monitoring effort in Patagonia National Park, Chile. There are no external sources or publicly accessible links for additional data.
DOI: 10.15468/dl.cevn56
title: Occurrence Download

description: A dataset containing 597 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-54.73016 -1.53387,-49.47145 -1.53387,-49.47145 4.53207,-54.73016 4.53207,-54.73016 -1.53387))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Testudines"
 ]
}

 The dataset includes 597 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004264-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dfgqnj
title: Occurrence Download

description: A dataset containing 196 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation)",
 "Country is Russian Federation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Panthera tigris altaica"
 ]
}

 The dataset includes 196 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004265-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3b26rr
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bolbosoma capitatum",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 10 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004266-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.99bkgv
title: Occurrence Download

description: A dataset containing 558 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Engraulis australis",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 558 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004267-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uwd2h6
title: Occurrence Download

description: A dataset containing 309 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation)",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Phocoena sinus"
 ]
}

 The dataset includes 309 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004269-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4j0zpc8pg
title: Segregation data of maize populations exposed to water-deficit and defoliation stress

description: Meiosis and recombination lead to gametes with novel combinations of genes
 as key processes in evolution and plant breeding. Numerous extrinsic
 factors have been reported to affect meiotic recombination of plants. The
 goal of this research was to identify simple, low-cost and effective
 treatments that affect recombination in maize (Zea mays L.). The
 treatments, water-deficit stress and defoliation, were separately applied
 to two F1-generation genotypes, B73/Mo17 and Mo17/H99. The F1 plants were
 backcrossed to an inbred line to produce the backcross populations that
 were genotyped at microsatellite loci on chromosomes 1 and 10. Overall,
 1,271 crossovers were observed in the progeny of the water-stressed plants
 while 1,092 were observed in the progeny of the non-stressed plants. The
 water-deficit treatment may have increased the rates of recombination in
 both F1-genotypes while the defoliation treatment was ineffective.
description: # Segregation data of maize populations exposed to water-deficit and
 defoliation stress
 [https://doi.org/10.5061/dryad.4j0zpc8pg](https://doi.org/10.5061/dryad.4j0zpc8pg) ## Description of the data and file structure The file contains all raw data and information necessary to support the research findings. The file contains all segregation data collected from all populations described in the manuscript. The file format lists the individual number (1-93) per chromosome of each population along the top, horizontally. On the left side of each of the tables, the first column contains names of the micro satellite loci. The segregation data is represented with letters 'H' or 'B'. Each tab's name describes the Chromosome number, population, stress, and germplasm name, e.g. (Chr1 pop1 WS b73mo17 - chromosome1, population 1, Water Stress, germplasm is B73/Mo17) ### Files and variables #### File: Supplementary\_Information\_file\_S1-S30.zip **Description:** The file contains data and distribution of crossovers on chromosome 1 and 10 of 3 maize populations. The populations were exposed to water-deficit and defoliation stress with a control population also included. Regions with crossovers are highlighted in yellow.  ## Access information Other publicly accessible locations of the data: * [https://dr.lib.iastate.edu/handle/20.500.12876/67500](https://dr.lib.iastate.edu/handle/20.500.12876/67500)