cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4986194.v1
title: Supplementary Material for: Long-Term Neuropathological Changes Associated with Cerebral Palsy in a Nonhuman Primate Model of Hypoxic-Ischemic Encephalopathy

description: <b><i>Background:</i></b> Cerebral palsy (CP) is the most common motor disability in childhood, with a worldwide prevalence of 1.5-4/1,000 live births. Hypoxic-ischemic encephalopathy (HIE) contributes to the burden of CP, but the long-term neuropathological findings of this association remain limited. <b><i>Methodology:</i></b> Thirty-four term <i>Macaca nemestrina</i> macaques were included in this long-term neuropathological study: 9 control animals delivered by cesarean section and 25 animals with perinatal asphyxia delivered by cesarean section after 15-18 min of umbilical cord occlusion (UCO). UCO animals were randomized to saline (<i>n</i> = 11), therapeutic hypothermia (TH; <i>n</i> = 6), or TH + erythropoietin (Epo; <i>n</i> = 8). Epo was given on days 1, 2, 3, and 7. Animals had serial developmental assessments and underwent magnetic resonance imaging with diffusion tensor imaging at 9 months of age followed by necropsy. Histology and immunohistochemical (IHC) staining of brain and brainstem sections were performed. <b><i>Results:</i></b> All UCO animals demonstrated and met the standard diagnostic criteria for human neonates with moderate-to-severe HIE. Four animals developed moderate-to-severe CP (3 UCO and 1 UCO + TH), 9 had mild CP (2 UCO, 3 UCO + TH, 3 UCO + TH + Epo, and 1 control), and 2 UCO animals died. None of the animals treated with TH + Epo died, had moderate-to-severe CP, or demonstrated signs of long-term neuropathological toxicity. Compared to animals grouped together as having no CP (no-CP; controls and mild CP only), animals with CP (moderate and severe) demonstrated decreased fractional anisotropy of multiple white-matter tracts including the corpus callosum and internal capsule, when using Tract-Based Spatial Statistics (TBSS). Animals with CP had decreased staining for cortical neurons and increased brainstem glial scarring compared to animals without CP. The cerebellar cell density of the internal granular layer and white matter was decreased in CP animals compared to that in control animals without CP. <b><i>Conclusions/Significance:</i></b> In this nonhuman primate HIE model, animals treated with TH + Epo had less brain pathology noted on TBSS and IHC staining, which supports the long-term safety of TH + Epo in the setting of HIE. Animals that developed CP showed white-matter changes noted on TBSS, subtle histopathological changes in both the white and gray matter, and brainstem injury that correlated with CP severity. This HIE model may lend itself to further study of the relationship between brainstem injury and CP.
DOI: 10.6084/m9.figshare.9768020.v1
title: Kopec_Rothberg_deGroot_MthK_Gating_Source_Data.zip

description: Raw data from MD simulations of MthK gating.<br>
DOI: 10.6084/m9.figshare.13040540.v1
title: JULES-JRA55 soil moisture 1979-2017

description: JULES-JRA55 July-August monthly soil moisture over inner East Asia, 1979-2017
DOI: 10.6084/m9.figshare.18318584.v1
title: Genome-Wide Assessment of a Korean Composite Pig Breed, Woori-Heukdon

description: SNP genotype dataset for Korean Duroc pigs
DOI: 10.6084/m9.figshare.1008334.v1
title: A first attempt at modelling red deer (Cervus elaphus) distributions over Europe

description: The presence of red deer may be a contributing factor within the ecological and epidemiological systems contributing to the risk and spread of a range of vector-borne diseases. Deer are importan hosts for many vectors, and may therefore serve as a focal point or attractant for vectors or may themselves become a reservoir for vector-borne disease. Three spatial modelling techniques were used to generate an ensemble model describing the proportion of suitable red deer habitat within recorded distributions for Europe as identified from diverse sources. The resulting model is therefore an index of presence, which may be useful in supporting the modelling of vector-borne disease across Europe.
DOI: 10.6084/m9.figshare.7039481.v2
title: Traffic ants

description: Density and flow of ants on several bridges during foraging.<br>
DOI: 10.6084/m9.figshare.21632354.v2
title: Video Data Analysis and Police Body-Worn Camera Footage: Table 7 and supplemental analyses

description: The data is archived in STATA (ver 15) format, which takes advantage of Bonferroni correction and box-whiskers results plots. The syntax (.do file) runs against the archived data to produce: Table 7, Supplemental Tables 1 and 2 (in the appendix), and the Box-Whisker plot featured in Figure 1. <br> in the forthcoming article by McCluskey and Uchida in Sociological Methods and Research - Video Data Analysis and Police Body-Worn Camera Footage
DOI: 10.6084/m9.figshare.25403515.v1
title: nonharvest mortality rates.csv

description: State- and cell-specific mortality rates from nonharvest mortality for juvenile cougars.
DOI: 10.6084/m9.figshare.4635310.v1
title: Data: Age- and environment-dependent changes in chemical defences of larval and post-metamorphic toads

description: We used high-performance liquid chromatography with diode-array detection and mass spectrometry (HPLC-DAD-MS) to identify and quantify bufadienolide compounds. We homogenized specimens of the common toad <i>(Bufo bufo)</i> using a VWR VDI 12 homogenizer with an IKA S12N-7S dispersing tool. After drying samples <i>in vacuo</i> at 45 °C using a Büchi Rotavapor R-134 rotary evaporator, we measured dry weight of samples using an Ohaus Pioneer PA-114 analytical balance to the nearest 0.1 mg and subsequently re-dissolved samples in 1 ml HPLC-grade absolute methanol, which was further aided by exposing the samples briefly to ultrasound in a Tesla UC005AJ1 bath sonicator. We filtered the samples using FilterBio nylon syringe filters (pore size = 0.22 μm). We identified compounds as bufadienolides by inspecting the UV spectrum of peaks (Hagman et al. 2009, Hayes et al. 2009, Bókony et al. 2016) and by using commercially acquired bufalin, bufotalin, resibufogenin, gamabufotalin, areno- and telocinobufagin (Biopurify Phytochemicals, Chengdu, China), cinobufagin (Chembest, Shanghai, China), cinobufotalin (Quality Phytochemicals, New Jersey, USA) and digitoxigenin (Santa Cruz Biotechnology, Dallas, TX, USA) as standards. Identification of compounds present in low quantities was further aided by the analysis of a sample obtained from an adult male common toad by gently massaging the parotoid glands. <br>A single-quadrupole HPLC-MS system (Model: LC-MS-2020, Shimadzu, Kyoto, Japan) equipped with a binary gradient solvent pump, a vacuum degasser, a thermostated autosampler, a column oven, a diode array detector and a mass analyser with electrospray ionization (ESI-MS) was used. Chromatographic separations were carried out at 35 °C on a Kinetex C18 2.6 µm column (100 mm x 3 mm i.d.) in series with a C18 guard column (4 mm × 3 mm i.d.) using 10 µL injections. The mobile phase consisted of water containing 0.05% formic acid (solvent A) and acetonitrile containing 0.05% formic acid (solvent B). The flow rate was 0.8 mL/min and the gradient was as follows: 0-2 min, 15-25% B; 2-15 min, 25-35% B; 15-24 min, 30-50% B; 24-25 min, 50-90% B; 25-30 min 90% B; 30-35 min 15% B. ESI worked under the following conditions: desolvation line (DL) temperature, 250 °C; heat block temperature, 400 °C; drying N2 gas flow, 15 L/min; nebulizer N2 gas flow, 1.5 L/min; positive ionization mode. Data was acquired and processed using the programme LabSolutions 5.42v (Shimadzu, Kyoto, Japan).
DOI: 10.6084/m9.figshare.28045388.v1
title: Monitoring data of particulate matter emission stations in 2020

description: Monitoring data of particulate matter emission stations in China in 2020
DOI: 10.6084/m9.figshare.8132285.v3
title: VGG-360 Face

description: <b>--------------------------------</b><b>VGG-360 Face Dataset</b><b>--------------------------------</b><b><br></b><b><br></b>Description:<br><b><br></b>This dataset uses images from the <b>VGG Face Dataset</b> of Oxford University (http://www.robots.ox.ac.uk/~vgg/data/vgg_face) to simulate, for each face image, 10 different projections on a 360º camera. This is done by using camera angle information from <b>MOT-360 Face Dataset</b> (which can be downloaded at https://figshare.com/s/5f8a69937014e4720625) and the pixel coordinates of the eyes of each face image. As these coordinates are not provided by the original authors, the Dlib Face Detector (http://dlib.net/) was used in this process. However, the detector could not be able to detect all faces from the VGG Face Dataset. Therefore, approximately 750K from this dataset images were used to simulate the projections, yielding a total of 7.5M images in this dataset.<br>Citation:<br><br>When referencing the dataset, please use the following BibTex citation:<br>@inproceedings{Cirne2019,author = "M. Cirne and F. Andalo and R. Dias and T. Resek and G. Bertocco and R. Torres and A. Rocha",title = "Deep Face Verification for Spherical Images",booktitle = "{IEEE} International Conference on Image Processing",year = "2019"}<br>
DOI: 10.6084/m9.figshare.15112182.v1
title: Picozoa: BUSCO results

description: BUSCO runs for each final SAG/COSAG<br>
DOI: 10.6084/m9.figshare.8003318.v1
title: Mid-upper arm circumference predicts death in adult patients admitted to a TB ward in the Philippines: a prospective cohort study

description: Dataset and data dictionary for the published paper.<br>
DOI: 10.6084/m9.figshare.26345338.v1
title: ­­­­­­Genome assembly of the <i>Bos gaurus</i> in Vietnam using nanopore sequencing­­­Genome assembly of the <i>Bos gaurus</i> in Vietnam using nanopore sequencing

description: The gaur (<i>Bos gaurus</i>) is one of the largest wild cattle species in the Bovidae family and is among the most threatened mammals in Vietnam. Listed as vulnerable on the IUCN Red List since 1986, gaurs are found in various provinces across Vietnam, including Lai Chau, Son La, Thanh Hoa, Nghe An, and several others. Their population has drastically declined, with current estimates showing about 30-50 individuals in the Northwest and fewer than 300 in the Central Highlands. Conservation efforts are crucial, and genome assembly is vital, providing valuable information for effective conservation strategies.Using Oxford Nanopore sequencing technologies, this study generated over 49 Giga-bases of trimmed whole genome sequencing reads from the muscle tissue of a deceased gaur collected in 2014 in Quang Nam, Vietnam. These reads were assembled into a 2.61 Gb draft genome, comprising 32,004 contigs, 54 scaffolds, with an N50 of 324.5 kilobases and a GC content of 41.86%. The BUSCO completeness value, using the mammalia_odb10 dataset, was 83.4%. This Vietnamese gaur genome assembly will serve as a valuable resource for conservation genetic research in this species.
DOI: 10.6084/m9.figshare.3486998.v1
title: Supplementary Material for: Association Study and Meta-Analysis of Polymorphisms, Methylation Profiles, and Peripheral mRNA Expression of the Serotonin Transporter Gene in Patients with Alzheimer's Disease

description: <i>Background/Aim:</i> The aim of this study was to elucidate the relationship between Alzheimer's disease (AD) and the serotonin transporter gene <i>(SLC6A4)</i>. <i>Methods:</i> AD subjects (n = 43) and controls (n = 47) were recruited and evaluated. In leukocytes, we evaluated two polymorphisms in <i>SLC6A4,</i> the serotonin transporter length polymorphic region (5-HTT-LPR) and rs25531, as well as methylation rates of the<i>SLC6A4</i> promoter region and the<i> SLC6A4</i> mRNA expression level. We also performed a meta-analysis to examine the relationship between the frequency of the L allele and the risk of AD. <i>Results:</i> The distributions of 5-HTT-LPR and rs25531 polymorphisms in AD subjects were not different from those of controls. Although the methylation rates in AD subjects were not significantly different from those of controls, the expression level in AD subjects was significantly higher than in controls. Additionally, the expression level in AD subjects was significantly correlated with apathy. Meta-analysis revealed that the L/L genotype significantly reduced the risk of AD, but only in the Caucasian population. <i>Conclusion:</i> Higher <i>SLC6A4</i> mRNA expression in leukocytes in AD was associated with apathy regardless of <i>SLC6A4</i> genotypes and methylation rates of the promoter region. The L/L genotype may reduce the risk of AD in the Caucasian population.
DOI: 10.6084/m9.figshare.5125411.v1
title: Supplementary Material for: From Structure to Function: Mitochondrial Morphology, Motion and Shaping in Vascular Smooth Muscle

description: The diversity of mitochondrial arrangements, which arise from the organelle being static or moving, or fusing and dividing in a dynamically reshaping network, is only beginning to be appreciated. While significant progress has been made in understanding the proteins that reorganise mitochondria, the physiological significance of the various arrangements is poorly understood. The lack of understanding may occur partly because mitochondrial morphology is studied most often in cultured cells. The simple anatomy of cultured cells presents an attractive model for visualizing mitochondrial behaviour but contrasts with the complexity of native cells in which elaborate mitochondrial movements and morphologies may not occur. Mitochondrial changes may take place in native cells (in response to stress and proliferation), but over a slow time-course and the cellular function contributed is unclear. To determine the role mitochondrial arrangements play in cell function, a crucial first step is characterisation of the interactions among mitochondrial components. Three aspects of mitochondrial behaviour are described in this review: (1) morphology, (2) motion and (3) rapid shape changes. The proposed physiological roles to which various mitochondrial arrangements contribute and difficulties in interpreting some of the physiological conclusions are also outlined.
DOI: 10.6084/m9.figshare.19641429.v1
title: Food Matching Task v1.0

description: Food Matching test v1.0 as used in Gauthier & Fiestan's "Food neophobia predicts visual ability in the recognition of prepared food" (submitted in April 2022). <br> The test consists of 1 practice trial and 60 test trials. The trials are made available as a series of 126 image file, numbered arbitrarily starting at 002. The name of the image file indicates whether the subjects should click to advance the trial (clickable) or, alternatively, if the image is to be displayed for a fixed amount (limit-xxxx). <br> Also in the name of each image file is the correct-answer and whether feedback (correct/incorrect) was provided (first 10 trials). Trial-029 is included as an attention check and should not be used to compute test score. Chance performance on the task is 1/3. <br> These test materials are available free of charge. We do not provide support for adapting them in the software of your choice. Please contact isabel.gauthier@vanderbilt.edu for the updated citation for the test.
DOI: 10.6084/m9.figshare.27044263.v1
title: Supplementary Material for: Identification of Novel Genetic Risk Variants Associated with Hidradenitis Suppurativa in an Exome Sequencing Cohort of 92,455 Individuals

description: Introduction. Hidradenitis suppurativa (HS) is a prevalent and persistent inflammatory skin disorder, lacking a known cure or effective biomarkers for early diagnosis at present. 
The genetic determinants of HS have not been fully documented, but it is believed to result from a combination of genetic and environmental factors. 
Methods. To identify relevant HS gene variants in sporadic HS patients, this study utilized longitudinal electronic health records (EHRs) and whole-exome sequencing (WES). DNA exome sequencing data from 92,455 participant samples in the MyCode biobank, linked to Geisinger's EHR, were analyzed. This cohort included 1,092 HS cases and 91,363 healthy controls. The MyCode EHR has a median longitudinal follow-up of 15 years per participant, with an average of 87 clinical encounters, 687 laboratory tests, and 7 procedures.
Results: There were 1092 (901 females (F) & 191 males (M) participants aged 14 to 89 years (median 47 years) with HS (L73.2), indicating 1.18% prevalence and accounting for a 4.7:1 female to male ratio among the individuals presenting for clinical care. γ-secretase complex, syndromic, and autoinflammatory gene variants were assessed. Potential pathogenic variants were identified among 66 individuals in the HS genes studied. Molecularly, the estimated HS variant prevalence was 1:1400 in the cohort, 12.3% of variant carriers had HS diagnosis in EHR.
Conclusions: Using longitudinal EHR data, genomic screening identified HS-associated gene variants in a defined group of sporadic HS patients to augment the clinical diagnosis, particularly in cases of ambiguity. Based on this study, the field of skin disorders can benefit from a personalized approach to HS diagnosis using large-scale sequencing.
DOI: 10.6084/m9.figshare.25879375.v1
title: MS# 2024GL110373 Model outputs

description: Arabian Gulf regional hydrodynamic simulation outputs
DOI: 10.6084/m9.figshare.27905793.v2
title: Manipulated diet experiment data and metadata associated with The role of wetlands in pelagic food webs: Metagenomics reveals how wetland plant detritus may promote zooplankton growth and survival

description: These data are part of a project titled: The role of wetlands in pelagic food webs: Metagenomics reveals how wetland plant detritus may promote zooplankton growth and survivalThe project was funded by the California Department of Fish and Wildlife Delta Water Quality And Ecosystem Restoration Grant Program (agreement Q1996021 awarded to Peter Hernes at University of California - Davis)These data are specifically for the manipulated diet experiments which involved assessing growth and survival of laboratory cultured copepods under diets spanning a gradient of phytoplankton availability, with and without tule detritussee description in metadata_manipulated_diet_exp.xlsx
DOI: 10.6084/m9.figshare.12890768.v1
title: Whole genome sequencing data from maize landraces

description: Low-coverage (~1x) whole genome sequence data of 108 maize landraces from Mexico or South America. Landraces were sampled according to a latitudinally stratification strategy with pairs of highland and lowland landraces selected from the same 0.5 degree latitudinal band. Paired-end 150bp reads were generated on the Illumina HiSeq X 10. Raw reads are available here: /iplant/home/deruncie/HiLo/WGS
DOI: 10.6084/m9.figshare.c.3615806_d4.v1
title: Additional file 8: Table S5. of Single-cell analysis of long non-coding RNAs in the developing human neocortex

description: Related to Fig.Â 2c. Expression table of all bulk tissue samples showing genes enriched in either total RNA-seq or polyA RNA-seq. Both polyA and total RNA-seq data are represented for each tissue sample. Expression values are in TPM (Transcripts per Million). (XLS 58 kb)
DOI: 10.6084/m9.figshare.20528154.v4
title: Implementing blended learning for clinician teachers: a qualitative study identifying their needs and the impact on faculty development initiatives

description: Learning Technologies has been a fast-growing field in Health Professions Education (HPE). Approaches to teaching, learning and assessment has been increasingly influenced by learning technologies which requires HPE teachers to adapt their teaching practices and with that identify areas for professional development. The implementation of blended learning in HPE, has shown improvements in student performance. However, it seems as if there are challenges with the implementation of a blended learning approach and that there might be some needs that clinical teachers have that are not being addressed in order to implement blended learning successfully. We used a qualitative exploratory design to identify clinician teachers’ needs. Semi-structured, individual interviews were conducted with a total of eight (n=8) module coordinators in the third year of the MBChB programme, Stellenbosch University, Faculty of Medicine and Health Sciences. Results indicated the need for continuous technical and pedagogical support which refers to a longitudinal faculty development approach. Additionally, faculty development should include the support in structuring and rethinking the blended curriculum, as well as assisting in the clinicians’ development in their role and identity as a clinical teacher. These results reveal the importance of faculty development as a targeted longitudinal approach
DOI: 10.6084/m9.figshare.3523937.v1
title: Appendix B. Figures showing type I error in simulations involving n=144 (Fig. B1) and n=36 experimental units (Fig. B2).

description: Figures showing type I error in simulations involving n=144 (Fig. B1) and n=36 experimental units (Fig. B2).
DOI: 10.6084/m9.figshare.14459124.v1
title: Greenhouse gas emissions

description: Bioeconomy-based greenhouse gas emissions. The data is used to calculate the Climate Footprint of consumption of Germany.
DOI: 10.6084/m9.figshare.3568590.v1
title: Appendix D. Examples of other formation-level classifications.

description: Examples of other formation-level classifications.
DOI: 10.4121/14865225.v1
title: Photogrammetry Images from DJI P4, point clouds scripts and supporting data

description: These images were taken at the Luangwa Bridge in Zambia as part of research study under the ZAMSECUR program by PhD candidate, Hubert Samboko. The respective clouds which were processed in WEBODM are provided. It is recommended to view these in a free and open source software called Cloud Compare.
DOI: 10.6084/m9.figshare.1431873.v1
title: The Functional Connectome of Speech Control

description: Connectivity matrices used to construct the functional connenctome and community structure of the resting state, sequential finger tapping, auditory pure tone discrimination, syllable production, and speech production.
DOI: 10.6084/m9.figshare.21729116.v2
title: Visual Inspection test data and procedures

description: All inspections involved photographic evidence collection and conversations with Delaware DOT managers or engineers.
DOI: 10.4121/uuid:0c60edf1-6f83-4e75-9367-4c63b3e9d5bb
title: Dataset belonging to the help desk log of an Italian Company

description: Event log concerning the ticketing management process of the Help desk of an Italian software company
DOI: 10.6084/m9.figshare.24658662.v1
title: Supplementary Data Tables - S-type Zircon

description: Supplementary Data for "Revisiting the discrimination and distribution of S-type granites from zircon trace element compositions" by Nick Roberts et al.
DOI: 10.6084/m9.figshare.24902367.v2
title: Replication Package -&gt; "On the Executability of R Markdown Files"

description: This is a replication package for "On the Executability of R Markdown Files"
DOI: 10.6084/m9.figshare.19137785.v1
title: CODCLAB_Level0

description: Basic geographic information data contains lake basin boundary, lake max extent, lake sub-basin boundary, and national lake zones.