cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5242000.v1
title: Erratum: Endoplasmic Reticulum Stress Predicts Clinical Response to Cyclosporine Treatment in Primary Membranous Nephropathy

description: <b><i>Background:</i></b> Little is known about the endoplasmic reticulum stress (ERS) marker glucose regulated protein 78 (GRP78) and calcineurin in the kidney in primary membranous nephropathy (PMN) and if they could predict post-cyclosporine treatment outcome. <b><i>Methods:</i></b> This is a retrospective study using a dataset of biopsy-confirmed PMN from Peking Union Medical College Hospital from 1996 to 2014. Seventy-six adult patients treated with cyclosporine as primary immunosuppression for at least 6 months were studied. Immunohistochemistry was used to detect GRP78 and calcineurin in the kidney. Serum calcineurin was assayed by ELISA. Patients were grouped into no-remission (NR, n = 17), partial remission (PR, n = 39), or complete remission (CR, n = 20) at the end of 6 months of treatment. <b><i>Results:</i></b> There was no difference of initial dose of cyclosporine among NR, PR, and CR groups. Kidney calcineurin expression in PMN was significantly increased compared to that in controls (p &lt; 0.0083). The glomerular GRP78 in NR PMN was higher than that in control, CR and PR patients (p &lt; 0.0083). Kidney calcineurin expression and GRP78 expression was positively correlated. However, there were no differences in either serum calcineurin levels or kidney calcineurin expressions among NR, PR or CR groups. There was a negative correlation between serum calcineurin activity and whole kidney calcineurin expression (p = 0.034) or glomerular calcineurin expression (p = 0.007). Neither kidney calcineurin nor GRP78 expression was correlated with proteinuria. <b><i>Conclusions:</i></b> ERS marker GRP78 in the glomeruli but not serum or kidney calcineurin expression could be a useful marker in PMN to negatively predict the response to cyclosporine treatment at the sixth month.
DOI: 10.6084/m9.figshare.7295492.v1
title: Morphometrical analysis of <i>Ceiba</i> Mill. (Bombacoideae, Malvaceae) pollen: a sacred plant of the Mayan (Mesoamerican) civilisation

description: <i>Ceiba</i>, is a large tree used for ornamental landscaping in tropical regions of the world. It is found in tropical areas, including Mexico, Central America, South America, the Caribbean, West Africa, and Southeast Asia. The present work communicates the detailed pollen morphology of four <i>Ceiba</i> species growing in India including one hybrid, <i>C. speciosa</i> (A.St.-Hil.) Ravenna, <i>C. insignis</i> (Kunth) P. E. Gibbs & Semir, <i>C</i>. x <i>insignis</i> (cross between <i>C. insignis</i> and <i>C. speciosa</i>) and <i>C. pentandra</i> (L.) Gaertn., using Field Emission Scanning Electron Microscope (FESEM), Confocal Laser Scanning Microscope (CLSM) and Light Microscope (LM) to highlight the taxonomic characterization of these species and document finer morphological details to correlate them with other <i>Ceiba</i> spp., growing around the world. Pollen grain is 4-5-colporate, brevicolpate; sub-oblate to prolate-spheroidal to sub-prolate; sexine reticulate (muri provided with scattered spinuloid excrescences, lumina reticolumellate) and mostly thicker than nexine. The multivariate principal component analysis (PCA) was applied on <i>Ceiba</i> and <i>Bombax ceiba</i> to numerical data obtained from pollen morphometry which clearly revealed a significant variation between different genus and species. A pollen key, based on these micromorphological data (especially pollen aperture and size of muri), is also presented for the <i>Ceiba</i> and <i>B. ceiba</i>. The study provides an analogue for precise identification of <i>Ceiba</i> pollen grains recovered in Quaternary and pre-Quaternary sedimentary deposits in India and other tropical and subtropical regions of the world. Besides, pollen preservation, evolutionary trend and palaeoecology are the other important implications of this study.
DOI: 10.6084/m9.figshare.25254565.v3
title: Analysis output for figures in "Punctuated virus-driven succession generates dynamical alternations in CRISPR-mediated microbe-virus co-evolution"

description: Analysis output processed from simulated model output, and used for paper figures.
DOI: 10.6084/m9.figshare.28309295.v2
title: Data for arcane-icmes

description: This data belongs to https://github.com/hruedisser/arcane-icmes
DOI: 10.17632/xy8ggx9hn6
title: Turbulent flow past cylinders

description: This dataset presents a collection of time-velocity series from hot wire measurements in an aerodynamic channel. Measurements were performed in the wake of single cylinders, with diameters of 25.1, 32 and 50 mm, and a Reynolds number varying from 8.25×10³ to 5.17×10^4 with a sampling frequency of 1000 Hz and a low pass filter at 300 Hz. Each data series has 2^17 elements, corresponding to a time of 131.072 s.
DOI: 10.6084/m9.figshare.21499071.v7
title: Example datasets for singleCellHaystack GitHub vignettes (2022)

description: Example single-cell and spatial transcriptomics/genomics datasets for use in the vignettes of SinglCellHaystack on GitHub. These are for the updated, continuous version of singleCellHaystack, made publis in 2022.
DOI: 10.6084/m9.figshare.22779080.v1
title: Student Health Survey - Form Responses 1 (2).csv

description: Student health data was collected from all over the university via survey, there are 18 features in the dataset.
DOI: 10.6084/m9.figshare.24452677.v1
title: Rodent Sleep Spindle Detector Supplementary Datasets and Video

description: Supplementary Datasets and Video for Rodent Sleep Spindle Detector (RSSD).
DOI: 10.6084/m9.figshare.26241992.v4
title: S-wave traveltimes & Vs anomaly model of SET

description: teleseismic S-wave relative traveltimes & Vs anomaly model of SET from the joint inversion of surface wave phase velocity and body wave traveltime
DOI: 10.6084/m9.figshare.5127169.v1
title: Supplementary Material for: <b><i>SH2B1</i></b> CpG-SNP Is Associated with Body Weight Reduction in Obese Subjects Following a Dietary Restriction Program

description: The objective of this study was to examine whether 7 SNPs previously associated with obesity-related traits that add or remove potential sites of DNA methylation are accompanied by differential DNA methylation and subsequently affect adiposity variables or body weight reduction in WBC from obese subjects under an energy-restricted program. <b><i>Material and Methods:</i></b> Anthropometric measurements were assessed in 47 volunteers recruited within the RESMENA study (Spain). At baseline, DNA from white blood cells was isolated and 7 obesity-related trait CpG-SNPs were genotyped by TaqMan-PCR. Then, methylation levels of CpG-SNP sites were quantified by MassArray® EpiTyper™ or MS-HRM approaches. <b><i>Results:</i></b> Differential DNA methylation levels were observed by genotypes in all of the CpG-SNPs analyzed. The <i>FTO</i> and <i>BDNF </i>methylation levels were further correlated with baseline body weight and, <i>BDNF</i> mRNA levels and body weight change, respectively. Moreover, the rs7359397 <i>(SH2B1) </i>was associated with the body weight, body mass index, and truncal fat mass reduction. <b><i>Conclusions:</i></b> Our results reveal the interaction of epigenetic and genetic variations in CpG-SNPs, especially in <i>BDNF</i> and <i>SH2B1</i> genes, and how allele-specific methylation may contribute to elucidate the possible molecular mechanisms as these SNPs are affecting the decrease of mRNA levels and contributing to a lower body weight reduction. © 2014 S. Karger AG, Basel
DOI: 10.17632/7tk2c47vkf
title: CAM assay data for chorioallantoic membrane treated with Insulin-Like Growth Factor-1 (IGF-1), with Platelet-Derived Growth Factor-BB (PDGF-BB), or with both growth factors

description: We present data assessed in the chorioallantoic membrane assay (CAM assay), where either the growth factor IGF-1 was dropped on the surface of the CAM, PDGF-BB, or IGF-1 and PDGF-BB (mixed group) in different concentrations. We present survival data for the chicken embryos, data on number of junctions in the CAM, vessel density, vessel length, number of sprouts, and vessel hierarchy (four levels) at days 2, 4, and 7 after dripping the growth factors for the first time on the CAM surface. Data are presented as fold change towards control (medium without growth factor). In addition, data for an angiogenic activity index are provided.
DOI: 10.17632/ncxsxhyg56
title: Apendi, et al_ refugee data

description: The data include measures of trauma exposure, PTSD, Resilience and PTG among adult refugees. These were collected from a refugee camp in western Uganda. We sought to measure the relationship between trauma exposure, PTSD, resilience and PTG and the mediating role of Resilience/PTSD in the relationship between Trauma exposure and PTG. The data show that there is a significant relationship between Trauma exposure, Post traumatic stress disorder, Resilience and Post traumatic growth.
DOI: 10.6084/m9.figshare.13238453.v1
title: Target enrichment gene set, alignments and partition files for the study:" Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota)"

description: file .fas: alignmentsfile .txt: RAxML style partition files <br>file Pseude_target_CDS_translation.fasta: Target enrichment gene set (amino acid)<br>
DOI: 10.6084/m9.figshare.5661919.v1
title: apple_leaf

description: Contains genetic data and binary images associated with the manuscript "Morphometrics reveals complex and heritable apple leaf shapes" ####Folder: genetic_dataContains the genetic data (ped and map files) used in this study.File 1: ApeKI_PstI-EcoT22I_Malv1.0p_bwa_maf0.01_min2alleles_noIndels_dp5_miss70_imputed_plink_leaf_miss0_maf05_hetero90.pedDescription: Genotype table in PLINK .ped format. Genotypes were obtained using GBS (ApeKI and PstI-EcoT221I). The PED file is a white-space (space or tab) delimited file. the first six columns are:Family ID / Individual ID / Paternal ID / Maternal ID / Sex (1=male; 2=female; other=unknown) / PhenotypeGenotypes (biallelic) are column 7 onwards. apple_ids (unique per cultivar) are used for Family ID and Individual ID, these can be linked with the binary images using leaf_binary_image_info.txt File 2: ApeKI_PstI-EcoT22I_Malv1.0p_bwa_maf0.01_min2alleles_noIndels_dp5_miss70_imputed_plink_leaf_miss0_maf05_hetero90.mapDescription:Each line of the .map file describes a single marker and contains 4 columns:chromosome (1-18, X, Y or 0 if unplaced) / rs# or snp identifier / Genetic distance (morgans) / Base-pair position (bp units)chromosome 18 indicates contigs that are unanchored to the reference genome ###Folder: apple_leaf_binary_imagesDescription:Contains all binary images of apple leaves used in this study. Files are named after the nursery ID, which is the value before “-“ and can be linked with the apple IDs used in this study through the leaf_binary_image_info.txt info file. ###Folder: leaf_genetic_image_infoDescription:Info file (leaf_binary_image_info.txt) which links the name of the images (image_name) with the nursery_id (unique per tree in the orchard) and apple_id (unique per cultivar) for the study. The image_name/nursery_id is used in the leaf images, but the apple IDs are used in the genotype files.
DOI: 10.6084/m9.figshare.24841239.v1
title: Supplementary_material_1.xlsx

description: Classification of individual changes in quadriceps cross-sectional area and maximum dynamic strength based on the typical error of measurement.
DOI: 10.17632/2jcpxc7v73
title: Data for: Alternatives to neonicotinoids
DOI: 10.17632/8ftcb2v4d8
title: Indian Ministry of Health and Family Welfare's annual yearbooks (1970-2000)

description: Digitalization of state-level information from the Indian Ministry of Health and Family Welfare's annual yearbooks, for the period 1970-71 to 2000-01. This work was financially supported by CEPREMAP.
DOI: 10.17632/tdr9jhyk62
title: Instances for the Two-Dimensional Cutting Stock Problem with Usable Leftovers and Uncertainty in Demand

description: Full description of instances for the Two-Dimensional Cutting Stock Problem with Usable Leftovers and Uncertainty in Demand (2D-CSPULUD). 

The 2D-CSPULUD was formulated as a two-stage stochastic problem. The first stage refers to the decisions made to meet a known deterministic demand, while the second stage determines the best cutting plan for a finite set of possible scenarios for the uncertain demand, adjusting the first stage decisions and optimizing the use of the generated usable leftovers. 

16 classes of instances were defined with 'S' = 2 types of standard plates and varying the number of types of leftovers in stock ('R' = 1 and 2). The number of types of items varied with 'I' = 3, 5, 8 and 10, and their dimensions were generated according to the dimensions of the plates and leftovers in stock. 

For each class, 10 instances were generated.
DOI: 10.6084/m9.figshare.12770201.v1
title: Metaheuristic parameter tuning dateset

description: All thee metaheuristic algorithms (Ant Colony Optimization, Evolutionary Strategy, Imperialist Competitive Algorithm) contain multiple numerical parameters, that can be tuned to increase the efficiency of the search. These parameters are summarised below. Candidate configurations are generated by dividing each parameter into discrete sets - Full Fractional Design (FDD) approach. This creates a total of 12,000 candidate configurations for ACO, 1000 for ES and 5760 for ICA, a total of 18,760 across all algorithms.<b>ACO: </b>Parallel instances; Number of ants; Relative pheromone strength; relative heuristic information strength; exploitation to exploration ratio; cunning rate<b>ES:</b> Population size; mutation rate; number of local iterations; swap ratio<b>ICA:</b> Number of countries, imperialist ratio; number of local iterations; assimilation rate; average power of empire's colonies; independence rate<br><br>Dataset divided into three worksheets, one for each algorithm. For each configuration 10 run fitnesses are provided as well as average. With NaN representing values that did not finish within 60 seconds.
DOI: 10.6084/m9.figshare.20297118.v1
title: train_dataset_RAW

description: ## 1 FILE CONTENTS ############################################# <br> 2101 x 40010 values: <br> - 1 header row, which corresponds to the 40002 resolved wavelengths and 8 element names (C, Si, Mn, Cr, Mo, Ni, Cu, Fe). <br> - 2100 spectra (rows): 50 spectra of 42 distinct targets. <br> Note that the dataset occupies significantly less RAM when loaded than the file's disk sizes (cca. 50 %). <br> Note that the column names may be modified by the software/library used for processing the spectra. Hence, we advise increased caution when extracting the wavelengths. <br> Alternatively, you can use the wavelength values provided separately in the wavelengths.csv file. <br> ## 2 DATA ACQUISITION ############################################# <br> The dataset was collected from metallic targets. Each target's surface was homogenized using a 800 grid sandpaper and cleaned with isopropyl alcohol using paper towels. <br> The targets were sampled at distinct spots in single-shot mode, collecting a single spectrum from each individual spot. There are a total of 50 spectra available for each target. <br> A 1064 nm Nd:YAG laser was used for ablation with a pulse energy of 95 mJ, 10 ns pulse width. The laser pulse was focused into a spot with a diameter of 0.2 mm. <br> The collected emission was resolved with an echelle spectrograph in the 240--1000 nm spectral range (40002 resolved wavelength values), resolving power {\lambda} / {\Delta\lambda} = 6000. <br> The resolved emission was recorded using an EMCCD camera with a 1.5 us delay and 50 us gate width (exposition time). <br> The spectra were not intensity calibrated! This, in combination with the long gate width is part of the challenge.
DOI: 10.6084/m9.figshare.22289614.v8
title: Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the yeast noncanonical translatome

description: This is supplementary data files for the publication entitled ""Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the yeast noncanonical translatome"
DOI: 10.25452/figshare.plus.27209637.v1
title: <b>DDS3 - Dataset of mosaic sputum smear microscopy images for evaluation of bacillus detection algorithms</b>

description: <b>DDS3 - Dataset of mosaic sputum smear microscopy images for evaluation of bacillus detection algorithms</b>This data set corresponds to mosaic images that are composed of a 10x10 arrangement of patches (negatives and positives) from the DDS1 dataset, resulting in a 400x400 pixel image. For each mosaic image, there is a corresponding binary mask, where the bacilli are presented as white pixels and the background as black pixels. This dataset was generated to enable the training, validation and testing of bacillus detection algorithms. There are 8,000 mosaic images with corresponding binary masks. 6,000 for training set, 1,000 for validation set and 1,000 for testing set. The folders are stored individually as tar.gz files with a total size of 2.15 GB.
DOI: 10.6084/m9.figshare.24153618.v2
title: Childhood abuse- depression

description: The database recorded information on childhood abuse, self-esteem, coping styles and depression levels among 809 male prisoners.
DOI: 10.6084/m9.figshare.24780387.v1
title: <b>Dataset for: Putting space into trait ecology: t</b><b>rait, environment and biodiversity relationships at multiple spatial scales</b>

description: This dataset present species richness, community functional structure (inter and intraspecific trait variation, trait-trait covariation and functional diversity) and environmental data (soil Nitrogen, Carbon and moisture) from a subtropical forest. The dataset includes all the variables for 25 m<sup>2</sup>, 100 m<sup>2</sup>, 400 m<sup>2,</sup> and 1936 m<sup>2</sup> spatial grains, and further separation in adults and sapling categories for 400 m<sup>2,</sup> and 1936 m<sup>2</sup> spatial grains. Reference: Biswas, S.R, He, D., Li, J., Gong, L., Biswas, P.L., Zhuo, Z., Xu., M., Yang, X. and Yan, E. (2023) Putting space into trait ecology: trait, environment and biodiversity relationships at multiple spatial scales. Journal of Ecology
DOI: 10.6084/m9.figshare.26409373.v1
title: Complete CosMx dataset used by most analyses in "Single cell spatial transcriptomic profiling of childhood-onset lupus nephritis reveals complex interactions between kidney stroma and infiltrating immune cells." Dataset includes a failed slide removed midway through analysis.

description: Cleaned dataset used in analyses from the manuscript "Single cell spatial transcriptomic profiling of childhood-onset lupus nephritis reveals complex interactions between kidney stroma and infiltrating immune cells". Called by code hosted at https://github.com/Nanostring-Biostats/childhood-onset-lupus-nephritis-analyses.
DOI: 10.6084/m9.figshare.28105127.v2
title: Age-Related Renal Changes and Biomarkers: Glomerular and Tubular Evaluation in Rats<b> </b>

description: This study investigates the structural changes in the kidneys of young adult, and aged rats and their relationship with biomarkers.<br>Renal tissues from different age groups were analyzed histologically. Key metrics such as glomerular diameter, Bowman's capsule diameter, and their ratios were measured. Histological parameters, including the percentage of sclerotic glomeruli, apoptotic cells, tubular dilatation, and epithelial desquamation, were evaluated. Additionally, inflammatory biomarkers (IL-6, TNF-α), cellular stress indicators (GRP78, MAPK), and other proteins were assessed.<br>The research aims to understand the effects of aging on kidney structures and identify the relationships between these changes and biomarkers, contributing to early detection and prevention strategies for renal dysfunction.<br>This study provides insights into age-related renal changes and their associations with key biomarkers, offering valuable data for biomedical and clinical research.
DOI: 10.6084/m9.figshare.28596953.v1
title: Nano-CT data and histological sections of <i>Pediculus humanus capitis</i> and <i>Echinophthirius horridus</i>

description: These datasets are part of the manuscript: <b>Tracheal system, spiracle closing apparatus, and buoyancy in the ectoparasitic seal louse </b><b><i>Echinophthirius horridus</i></b> by Preuss et al. 2025<br>10x maginificationImage Pixel size: 1.22 µmA combination of 1 and 2 is always necessary for receiving the whole dataset
DOI: 10.17632/pyywj9hd3f
title: Body image, weight stigma, health behaviors among adolescents

description: Measures include:
Perceived weight status. Very underweight, somewhat underweight, about the right weight, somewhat overweight, or very overweight.
Experiences of weight-based victimization. 3-item measure that assessed how frequently they had been teased or bullied because of their weight at school, home, or somewhere else on a scale from 1 (never) to 5 (very often). Based on a longer measure of weight-based victimization (Puhl et al., 2011; Puhl, Peterson, & Luedicke, 2013a; Puhl et al., 2013b).
Weight-stigmatizing attitudes. Fat Phobia Scale (F-scale; Bacon, Scheltema, & Robinson, 2001). 
Internalization of body ideals. The Ideal-Body Stereotype Scale-Revised (IBSS-R; Stice et al., 1996) was used to assess thin ideal internalization among females. The 6-item Drive For Leanness Scale (DFLS; Smolak & Murnen, 2008) was included to assess internalized body image ideals among males. 
Body image concerns. Weight and Shape Concerns Scale (WCS; Killen et al., 1993, 1994) was used with female participants.
Body image concerns among males was assessed with the Male Body Image Concerns Scale (MBICS; Weisman et al., 2014b). 
Both the WCS and the MBICS produce standardized scores that range from 0 to 100.
Eating psychopathology. Youth Eating Disorder Examination Questionnaire (YEDE-Q; Goldschmidt, Doyle, & Wilfley, 2007) global composite score. 
Physical activity. PACE+ Adolescent Physical Activity Measure (Prochaska, Sallis, & Long, 2001).
Nutrition. The PACE+ Fruit and Vegetable Measure (Prochaska & Sallis, 2004).
Acculturation:
Practices. Bicultural Involvement Questionnaire – Short Version (BIQ-S; Guo et al., 2009). 
Values. Sixteen items developed by Triandis and Gelfand (1998) were used to determine individualism and collectivism subscale scores. Some items were adapted to be more appropriate for an adolescent population.
Identifications. The Multigroup Ethnic Identity Measure – Revised (MEIM-R; Phinney & Ong, 2007) was used to assess identification with the heritage culture. The American Identity Measure (AIM; Schwartz et al., 2012) was used to assess American identification. The measure was adapted for this study to only include the six items on the MEIM-R; hence, it is referred to as the American Identity Measure – Revised (AIM-R).
Mischievous or dishonest responding. Students were asked in the demographics section (a) if they were deaf or had a hearing impairment, (b) if they were blind or had a severe vision impairment, and (c) when their last visit to the dentist occurred (within the past 6 months, about a year ago, or about 2 years ago). It is not plausible that an honest participant would endorse all these low incidence items. Two questions were included on the last page of the survey: How many questions in this survey did you answer honestly? And, how many other students at your school do you think answered the questions in this survey honestly? (All of them, most of them, only some of them, hardly any of them).