cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25909/5bdaa4431a941
title: Laboratory contamination over time during low-biomass sample analysis

description: Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (<i>e.g.</i> skin swabs, tissue biopsies, ice, water, degraded forensic samples, or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high-throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no-template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over five years to characterize long-term contaminant diversity. We additionally compared the contaminant content within a homemade silica-based extraction method, commonly used to analyse low-endogenous samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to the modern molecular biology laboratories, and changed over time according to researchers, month, and season. The commercial kit contained higher microbial diversity and several human-associated taxa in comparison to the homemade silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low-biomass metagenomic studies: 1) extraction blank controls should be included and sequenced with every batch of extractions and 2) the contributions of laboratory contamination should be assessed and reported in each high-throughput metagenomic study.<b> </b>
DOI: 10.25909/5be500cf5f0c4
title: Data for Ecomorphological diversity of Australian tadpoles

description: Landmark and semilandmark coordinate data (2-dimensional) for tadpole body shape of 187 species of Australian frogs, and 17 species of worldwide frogs. To accompany: Sherratt, Anstis and Keogh 2018 Ecomorphological diversity of Australian tadpoles, <i>Ecology & Evolution.</i> <br><b>File List</b>17spp_World_raw_coords_unbent.tps17spp_World_raw_coords.tps187spp_Australia_raw_coords_unbent.tps187spp_Australia_raw_coords.tpsCurve_sliding_for_GPA.csvUnbend_tadpole_tail_eye.nts<br><b>Details</b>Data are provided as raw landmark coordinates, and after unbending using the quadratic approach in tpsUtil v.1.74 (unbent using the landmarks identified in "Unbend_tadpole_tail_eye.nts"). Sliding semilandmarks can be done during generalized Procrustes superimposition using the landmarks identified in "Curve_sliding_for_GPA.csv" - for use with R package geomorph.<br><b>e.g.,</b>library(geomorph)# Read in datatadpoles # PAUSE: Negative landmark coordinates have been identified. Should they be considered as NAs? (y/n) n # Perform GPA with minimising bending energy curve.sliding tad.gpa <br><b>Landmarks and semilandmarks</b> defined as: 1, centre of the eye; 2, centre of the external nares; 3, point where the upper labium contacts the head/body in lateral view; 4, point where the lower labium contacts the head/body in lateral view; 5, intersection of the head/body and tail on the ventral side, anterior to the vent; 6, intersection of the ventral edge if the tail muscle and the head/body; 7, intersection of the dorsal edge if the tail muscle and the head/body; 8, tip of the tail; 9, point on the dorsal fin closest to landmark 7 (superficially denotes the intersection of the head/body and tail regions); 10–17, equally-spaced semilandmarks marking the curve of the dorsal aspect of the head/body when viewed laterally; 18–27, equally-spaced semilandmarks marking the curve of the dorsal aspect of the tail fin when viewed laterally; 28–37, equally-spaced semilandmarks marking the curve of the ventral aspect of the tail fin when viewed laterally; 38–45, equally-spaced semilandmarks marking the curve of the ventral aspect of the head/body when viewed laterally; 46–55, equally-spaced semilandmarks marking the curve of the notochord. Landmark configuration has been straightened from the eye to the tip of the tail along the notochord in order to standardise all specimens’ configurations (see Methods for details). <br>
DOI: 10.25909/5beb4c8ee9af3
title: Fire influences needle decomposition: tipping point in Pinus radiata carbon chemistry and soil nitrogen transformations

description: Fileset associated with a paper under review
DOI: 10.25909/5beb70de0ed07
title: The effect of fire affected Pinus radiata litter and char addition on soil nitrogen cycling

description: This fileset is associated with Stirling et al. 2019 'The effect of fire affected <i>Pinus radiata</i> litter and char addition on soil nitrogen cycling', Science of the Total Environment p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; color: #000000} p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; color: #000000}
DOI: 10.25909/5c5bb6777f249
title: Supplmentary data: Ultrastructural evidence of a mechanosensory function of scale ‘sensilla’ in sea snakes (Hydrophiinae)

description: Supplementary data: interactive digital scans of histology slides from two species of sea snake: <i>Aipysurus laevis</i> and <i>Hydrophis stokesii.</i><br>File codes:LPAA22R= A. laevis caudal (tail) scales dorsally located<br>LPAB2RT= <i>A. laevis</i> caudal (tail) scales ventrally locatedLPSL_6 =<i> A. laevis </i>6th supralabial scale (head)<br>NasalScale = H. stokesii nasal scale (head)
DOI: 10.5281/zenodo.17947190
title: ai plan de masse
DOI: 10.5281/zenodo.17947191
title: ai plan de masse
DOI: 10.17605/osf.io/tmc2d
title: Synthesizing Perspectives: Crafting a Interdisciplinary View of Social Media's Impact on Young People's Mental Health

description: Qualitative and Demographic Datasets for the Paper "Synthesizing Perspectives: Crafting a Interdisciplinary View of Social Media's Impact on Young People's Mental Health"

John Maltby, Thooba Rayes, Antara Nage, Sulaimaan Sharif, Maryama Omar (University of Leicester) and Nichani Sanjiv
(University Hospitals Leicester).
DOI: 10.17605/osf.io/rkds9
title: Jaguar (Panthera onca) distribution records for Colombia

description: Jaguar (Panthera onca) distribution records for Colombia

This dataset corresponds to a compilation of jaguar (Panthera onca) records for Colombia. The dataset consists in available jaguar records for Colombia from secondary sources including biodiversity data sets (i.e., GBif,, Species Link), literature, and our own data consistent of direct observations, camera-trap data, predation, among others.
DOI: 10.5517/ccdc.csd.cc2mqnxy
title: CCDC 2434861: Experimental Crystal Structure Determination

description: Related Article: Linfeng Chen, Erika Samolova, Mingjie Xu, Hang Yin, Hengchuan Zhang, Milan Gembicky, Alina M. Schimpf|2025|J.Am.Chem.Soc.|||doi:10.1021/jacs.5c15442
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2mqnz0
title: CCDC 2434863: Experimental Crystal Structure Determination

description: Related Article: Linfeng Chen, Erika Samolova, Mingjie Xu, Hang Yin, Hengchuan Zhang, Milan Gembicky, Alina M. Schimpf|2025|J.Am.Chem.Soc.|||doi:10.1021/jacs.5c15442
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.gt3kq4
title: Occurrence Download

description: A dataset containing 3830870 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is India",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is May",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 3830870 records from 76 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054249-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r9vcg9
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aechmea winkleri",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 19 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054255-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17937432
title: Novel insights into immune cell diversity and maturation in the pteropodid bat Eonycteris spelaea via single-cell transcriptome analysis

description: This Zenodo record provides the Eonycteris spelaea genome reference used for scRNA-seq analyses in this study: (i) the genome assembly (FASTA) and (ii) a Peaks2UTR-refined gene annotation (GTF) with improved 3′ UTR boundaries. Raw sequencing data supporting the assembly/annotation are available at NCBI under BioSample SAMN4835912 (and associated accessions therein).

To improve 3′ transcript end annotation, we refined the baseline GTF using Peaks2UTR which leverages aggregated read coverage to infer and extend 3′ UTR boundaries. Briefly, all scRNA-seq libraries (bone marrow, blood, liver) were first aligned to the in-house reference (FASTA + baseline GTF) using Cell Ranger to produce coordinate-sorted BAM files. BAM files were then merged across libraries to increase coverage at transcript termini and provided as input to Peaks2UTR to identify 3′ end peaks and update transcript models accordingly. Peaks2UTR output annotations (GFF) were converted to GTF format and used, together with the unchanged genome FASTA, to build the final reference for remapping all scRNA-seq datasets in this study with Cell Ranger prior to downstream analyses.
DOI: 10.5281/zenodo.17937433
title: Novel insights into immune cell diversity and maturation in the pteropodid bat Eonycteris spelaea via single-cell transcriptome analysis

description: This Zenodo record provides the Eonycteris spelaea genome reference used for scRNA-seq analyses in this study: (i) the genome assembly (FASTA) and (ii) a Peaks2UTR-refined gene annotation (GTF) with improved 3′ UTR boundaries. Raw sequencing data supporting the assembly/annotation are available at NCBI under BioSample SAMN4835912 (and associated accessions therein).

To improve 3′ transcript end annotation, we refined the baseline GTF using Peaks2UTR which leverages aggregated read coverage to infer and extend 3′ UTR boundaries. Briefly, all scRNA-seq libraries (bone marrow, blood, liver) were first aligned to the in-house reference (FASTA + baseline GTF) using Cell Ranger to produce coordinate-sorted BAM files. BAM files were then merged across libraries to increase coverage at transcript termini and provided as input to Peaks2UTR to identify 3′ end peaks and update transcript models accordingly. Peaks2UTR output annotations (GFF) were converted to GTF format and used, together with the unchanged genome FASTA, to build the final reference for remapping all scRNA-seq datasets in this study with Cell Ranger prior to downstream analyses.
DOI: 10.6084/m9.figshare.30891154
title: Prefrontal cortex responses to different footwear comfort conditions: a feasibility study using functional near-infrared spectroscopy

description: Existing evaluation for footwear comfort relies on subjective self-reported measures like questionnaires, while objective neurophysiological real-time indicators have not been established yet. Even though functional near-infrared spectroscopy (fNIRS) signals on the prefrontal cortex have been investigated during locomotion tasks, there is limited research on the effects of footwear comfort levels on brain response using fNIRS. This study aims to investigate the effect of two varying footwear comfort conditions (manipulated by shoe size) on prefrontal cortex activation while walking, and to determine whether it is possible to distinguish between more comfortable and less comfortable footwear through prefrontal cortex fNIRS measurements. Twenty-seven participants walked at a set speed of 5 km/h while wearing less and more comfortable footwear to elicit differences in their perceived comfort level. Their prefrontal cortex real-time activation was recorded by a 15-channel fNIRS device. Signals from 23 participants were analyzed, because four participants failed to distinguish the comfort differences between the two shoes. Statistical analyses were performed on averaged oxy-Hb and deoxy-Hb concentration changes of subdivided walking task phases to compare the two footwear comfort conditions. For the more comfortable condition, data showed significantly enhanced hemodynamic responses, reflected by increased oxy-Hb levels and/or decreased deoxy-Hb levels in channels 2, 3, 11, 12 and 14, which are located in the left and right dorsal prefrontal cortex (dlPFC) and the left frontopolar prefrontal cortex (FPC). In conclusion, comfort level of footwear may influence prefrontal cortex activation, as observed through fNIRS measurements. The present study implies the possibility to distinguish more (or less) comfortable footwear through prefrontal cortex hemodynamic analysis, which may provide a novel method for footwear comfort evaluation.
DOI: 10.6084/m9.figshare.30891154.v1
title: Prefrontal cortex responses to different footwear comfort conditions: a feasibility study using functional near-infrared spectroscopy

description: Existing evaluation for footwear comfort relies on subjective self-reported measures like questionnaires, while objective neurophysiological real-time indicators have not been established yet. Even though functional near-infrared spectroscopy (fNIRS) signals on the prefrontal cortex have been investigated during locomotion tasks, there is limited research on the effects of footwear comfort levels on brain response using fNIRS. This study aims to investigate the effect of two varying footwear comfort conditions (manipulated by shoe size) on prefrontal cortex activation while walking, and to determine whether it is possible to distinguish between more comfortable and less comfortable footwear through prefrontal cortex fNIRS measurements. Twenty-seven participants walked at a set speed of 5 km/h while wearing less and more comfortable footwear to elicit differences in their perceived comfort level. Their prefrontal cortex real-time activation was recorded by a 15-channel fNIRS device. Signals from 23 participants were analyzed, because four participants failed to distinguish the comfort differences between the two shoes. Statistical analyses were performed on averaged oxy-Hb and deoxy-Hb concentration changes of subdivided walking task phases to compare the two footwear comfort conditions. For the more comfortable condition, data showed significantly enhanced hemodynamic responses, reflected by increased oxy-Hb levels and/or decreased deoxy-Hb levels in channels 2, 3, 11, 12 and 14, which are located in the left and right dorsal prefrontal cortex (dlPFC) and the left frontopolar prefrontal cortex (FPC). In conclusion, comfort level of footwear may influence prefrontal cortex activation, as observed through fNIRS measurements. The present study implies the possibility to distinguish more (or less) comfortable footwear through prefrontal cortex hemodynamic analysis, which may provide a novel method for footwear comfort evaluation.
DOI: 10.6084/m9.figshare.30891155
title: Platelet-to-high-density lipoprotein cholesterol ratio as a potential mediator in the obesity-chronic kidney disease association among hypertensive patients

description: This study investigated the relationship between the platelet-to-high-density lipoprotein cholesterol ratio (PHR) and chronic kidney disease (CKD) in a hypertensive population, exploring its mediating role in the obesity–CKD association. Using data from the National Health and Nutrition Examination Survey (NHANES) 2009–2018 on 10,467 hypertensive adults, we observed a complex association. Overall, PHR was positively correlated with CKD (odds ratio [OR] = 1.08, 95% CI: 1.05–1.14). However, the relationship was nonlinear and U-shaped, with an inflection point at a PHR Z-score of −0.32 (PHR = 166). Below this point, the association was negative (OR = 0.78, 95% CI: 0.65–0.91), whereas above it, the association was strongly positive (OR = 1.24, 95% CI: 1.15–1.36), particularly among individuals with obesity (BMI ≥ 30 kg/m<sup>2</sup>). Furthermore, PHR significantly mediated the relationship between obesity and CKD, accounting for 21.46% of the effect from BMI and 18.01% from waist circumference. In conclusion, PHR exhibits a U-shaped relationship with CKD in hypertensive individuals, most prominently in those with obesity, and may serve as an accessible biomarker of obesity-related inflammation for CKD risk stratification.
DOI: 10.6084/m9.figshare.30891155.v1
title: Platelet-to-high-density lipoprotein cholesterol ratio as a potential mediator in the obesity-chronic kidney disease association among hypertensive patients

description: This study investigated the relationship between the platelet-to-high-density lipoprotein cholesterol ratio (PHR) and chronic kidney disease (CKD) in a hypertensive population, exploring its mediating role in the obesity–CKD association. Using data from the National Health and Nutrition Examination Survey (NHANES) 2009–2018 on 10,467 hypertensive adults, we observed a complex association. Overall, PHR was positively correlated with CKD (odds ratio [OR] = 1.08, 95% CI: 1.05–1.14). However, the relationship was nonlinear and U-shaped, with an inflection point at a PHR Z-score of −0.32 (PHR = 166). Below this point, the association was negative (OR = 0.78, 95% CI: 0.65–0.91), whereas above it, the association was strongly positive (OR = 1.24, 95% CI: 1.15–1.36), particularly among individuals with obesity (BMI ≥ 30 kg/m<sup>2</sup>). Furthermore, PHR significantly mediated the relationship between obesity and CKD, accounting for 21.46% of the effect from BMI and 18.01% from waist circumference. In conclusion, PHR exhibits a U-shaped relationship with CKD in hypertensive individuals, most prominently in those with obesity, and may serve as an accessible biomarker of obesity-related inflammation for CKD risk stratification.
DOI: 10.6084/m9.figshare.30891158
title: Adaptation and implementation of the Cultural Formulation Interview and training module for pediatric neuropsychology providers

description: Conceptual frameworks for cultural competence are essential in psychological care. The assessment of implementation efforts in pediatric neuropsychological contexts is particularly lacking. This study investigated an adapted training program for the Cultural Formulation Interview (CFI), including impact on provider cultural competence and perspectives on adaptation and implementation. Neuropsychological care providers (<i>N</i> = 16) participated in an adapted, group-based CFI training. The training included review of an online module, supplemented with reflective discussion. Participants completed pre- and post-training measures of perceived cultural competence, as well as a post-training survey assessing acceptability and utility of the CFI and training, facilitators and barriers to implementation, and potential adaptations to the CFI. The CFI and adapted training were rated highly on acceptability and utility. Self-reported confidence and competence in delivering culturally responsive care increased from pre- to post-training (<i>z</i> = −3.4; <i>p</i> = .0007). Key barriers and facilitators to implementation included resource needs, continuing education, and systemic change. Participants identified a theoretical, abbreviated 5-item CFI including alternative wording to fit their clinical needs. Overall, the adapted CFI training enhanced perceived cultural competence among pediatric neuropsychological providers, with strong acceptability and relevance to clinical practice. Recommendations will guide future training and systemic implementation.
DOI: 10.6084/m9.figshare.30891158.v1
title: Adaptation and implementation of the Cultural Formulation Interview and training module for pediatric neuropsychology providers

description: Conceptual frameworks for cultural competence are essential in psychological care. The assessment of implementation efforts in pediatric neuropsychological contexts is particularly lacking. This study investigated an adapted training program for the Cultural Formulation Interview (CFI), including impact on provider cultural competence and perspectives on adaptation and implementation. Neuropsychological care providers (<i>N</i> = 16) participated in an adapted, group-based CFI training. The training included review of an online module, supplemented with reflective discussion. Participants completed pre- and post-training measures of perceived cultural competence, as well as a post-training survey assessing acceptability and utility of the CFI and training, facilitators and barriers to implementation, and potential adaptations to the CFI. The CFI and adapted training were rated highly on acceptability and utility. Self-reported confidence and competence in delivering culturally responsive care increased from pre- to post-training (<i>z</i> = −3.4; <i>p</i> = .0007). Key barriers and facilitators to implementation included resource needs, continuing education, and systemic change. Participants identified a theoretical, abbreviated 5-item CFI including alternative wording to fit their clinical needs. Overall, the adapted CFI training enhanced perceived cultural competence among pediatric neuropsychological providers, with strong acceptability and relevance to clinical practice. Recommendations will guide future training and systemic implementation.
DOI: 10.17605/osf.io/2qs5w
title: Two-Stage MLE for SR-SEM

description: Online supplementary materials to support reproducing analyses in our paper (see Wiki)