cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/2dghmb62fg
title: Complications of Post-Abdominal Surgeries in Diabetic Patients vs. Non-Diabetics in Saudi Arabia between 2016-2021 (2020-2022)

description: Background: Diabetic patients are a subset of emergency and general surgery patients and have a higher risk of postoperative complications including pulmonary and urinary infections, acute cardiac infarction, kidney failure, and death compared to non-diabetic patients. Objectives: The study assessed the prevalence of postoperative complications in diabetic patients and nondiabetics in Saudi Arabia from 2016 to 2021. Methodology: This was a community-based observational descriptive cross-sectional study. Sample is 205 diabetic and non-diabetic participants over 18 years underwent abdominal surgery between 2016 and 2021 in Saudi Arabia. A self-administered questionnaire was used to collect data. Results: Regarding SSI, diabetic patients reported 27% wound erythema, 25% wound pain, and 24% wound pus. It was discovered that 34.1% of patients with poor wound healing,50% of individuals identified with DVT as a postoperative consequence,32.35% with UTI, 54.6% confirmed cases of post-operative incisional hernias, and 42.85% of patients with metabolic acidosis all of them were having diabetes millets. Regarding thrombophlebitis, 28.6% of patients with limb erythema and 21.1 percent of patients with hot and painful limbs were diabetics. Regarding bowel obstruction, only 23.68 percent of patients with acute stomach pain, 28 percent of patients with sudden vomiting, and 22.58 percent of patients with chronic constipation with gas retention had diabetes. Conclusion: DVT, UTI, and incisional hernia have all been found to be more common post-operative problems among diabetics. There was a modest difference in wound healing, wound infection, intestinal obstruction, thrombophlebitis, and metabolic acidosis between diabetics and non-diabetics.
DOI: 10.17632/b57ytpv4ws
title: Banco de Dados - Análise de erros de imunização nas cadernetas de vacinação de crianças menores de cinco anos

description: Banco de dados do projeto de pesquisa de Mestrado intitulado "ANÁLISE DE ERROS DE IMUNIZAÇÃO NAS CADERNETAS DE VACINAÇÃO DE CRIANÇAS MENORES DE CINCO ANOS" vinculado ao Programa de Pós-Graduação em Enfermagem da Universidade Federal de São João del-Rei - Campus Centro-Oeste orientado pela Profa. Dra. Valéria Conceição de Oliveira.
DOI: 10.6084/m9.figshare.10310771.v1
title: predicted protein sequences of Folsomia cadida

description: predicted protein sequences of Folsomia cadida
DOI: 10.6084/m9.figshare.13060634.v1
title: Assembled Genome and Transcriptome of heterotardigrade Echiniscus testudo

description: We conducted a multi-omics study of a heterotardigrade <i>Echiniscus testudo</i>, one of the most desiccation tolerant species caught from the wild. Using ultra-low input library sequencing protocol from a single individual, we sequenced and assembled genome, and was annotated using RNA-Seq data. The genomic DNA was extracted and the sequencing library was sequenced on the MiSeq platform. The MiSeq reads were assembled with MaSuRCA. For RNA-Seq, the total RNA was extracted, and the sequencing library was sequenced on the NextSeq 500 platform. The RNA-Seq was assembled with Trinity.<br>
DOI: 10.6084/m9.figshare.16620421.v1
title: Raw ACL Data.xlsx

description: Raw study dataset
DOI: 10.6084/m9.figshare.23764572.v1
title: ProjecTILs murine reference atlas of virus-specific CD8 T cells, version 2

description: We have developed ProjecTILs, a computational approach to project new data sets into a reference map of T cells, enabling their direct comparison in a stable, annotated system of coordinates. Because new cells are embedded in the same space of the reference, ProjecTILs enables the classification of query cells into annotated, discrete states, but also over a continuous space of intermediate states. By comparing multiple samples over the same map, and across alternative embeddings, the method allows exploring the effect of cellular perturbations (e.g. as the result of therapy or genetic engineering) and identifying genetic programs significantly altered in the query compared to a control set or to the reference map. We illustrate the projection of several data sets from recent publications over two cross-study murine T cell reference atlases: the first describing tumor-infiltrating T lymphocytes (TILs), the second characterizing acute and chronic viral infection. Single-cell data to build the virus-specific CD8 T cell reference map were downloaded from GEO under the following entries: GSE131535, GSE134139 and GSE119943, selecting only samples in wild type conditions. Data for the Ptpn2-KO, Tox-KO and CD4-depletion projections were obtained from entries GSE134139, GSE119943, and GSE137007 and were not included in the construction of the reference map. To construct the LCMV reference map, we split the dataset into five batches that displayed strong batch effects, and applied STACAS (https://github.com/carmonalab/STACAS) to mitigate its confounding effects. We computed 800 variable genes per batch, excluding cell cycling genes, ribosomal and mitochondrial genes, and computed pairwise anchors using 200 integration genes, and otherwise default STACAS parameters. Anchors were filtered at the default threshold 0.8 percentile, and integration was performed with the IntegrateData Seurat3 function with the guide tree suggested by STACAS. Next, we performed unsupervised clustering of the integrated cell embeddings using the Shared Nearest Neighbor (SNN) clustering method implemented in Seurat 3 with parameters {resolution=0.4, reduction=”pca”, k.param=20}. We then manually annotated individual clusters (merging clusters when necessary) based on several criteria: i) average expression of key marker genes in individual clusters; ii) gradients of gene expression over the UMAP representation of the reference map; iii) gene-set enrichment analysis to determine over- and under- expressed genes per cluster using MAST. In order to have access to predictive methods for UMAP, we recomputed PCA and UMAP embeddings independently of Seurat3 using respectively the prcomp function from basic R package “stats”, and the “umap” R package (https://github.com/tkonopka/umap).
DOI: 10.6084/m9.figshare.26771680.v1
title: <b>Magnetoelectric Nanodiscs Enable Wireless Transgene-Free Neuromodulation</b>

description: <b>Datasets for figures in paper titled 'Magnetoelectric Nanodiscs Enable Wireless Transgene-Free Neuromodulation'</b>
DOI: 10.6084/m9.figshare.28933973.v3
title: Leaky pollination barrier in edaphic vicarious alpine plants - Supplementary material

description: Abstract:Adaptation to siliceous versus carbonate substrates is thought to be an important driver of speciation in the alpine flora. The role of the pollination system in the formation and maintenance of such species is presently unclear. Here, we chose three species pairs in the genera <i>Gentiana</i>, <i>Primula</i>, and <i>Rhododendron</i> which often occur in geographic proximity or even sympatry to study the existence of pollination barriers in these lineages. Using remote camera and direct observation approaches, scent and color analyses, we tested the hypothesis whether divergent pollinator communities exist that could help to maintain genetic separation of plant populations adapted to different soil types. We found differences in frequency, diurnal activity and to some extent also community composition of flower visitors in edaphic vicarious species pairs. Floral traits like color and scent as well as flower-visitor co-distributions indicate that our study species have divergent but overlapping pollination systems. Our results do not suggest a strong reproductive barrier function of the pollination system. Whilst adaptation to different soils still seems to be the main force keeping edaphic vicarious alpine plants genetically separated, pollinators might mediate hybridization in contact areas.
DOI: 10.6084/m9.figshare.7172417.v1
title: Crassi_NMSG1984.15.3 L isch, R tib(pathology), R fib, presac. rib 0.0651

description: [XTekCT]Name=Crassigyrinusscoticus1984.15.1associatedfragmentsInputSeparator=_OutputSeparator=_InputFolderName=OutputFolderName=Crassigyrinusscoticus1984.15.1associatedfragmentsVoxelsX=1068VoxelsY=1294VoxelsZ=1999VoxelSizeX=0.0651400875080678VoxelSizeY=0.0651400875080678VoxelSizeZ=0.0651400875080678OffsetX=2.08448280025817OffsetY=3.71298498795986OffsetZ=0.0325700437540339SrcToObject=382.401927947998SrcToDetector=1174.091MaskRadius=65.1400875080678DetectorPixelsX=2000DetectorPixelsY=2000DetectorPixelSizeX=0.2DetectorPixelSizeY=0.2DetectorOffsetX=0.0DetectorOffsetY=0CentreOfRotationTop=0.0CentreOfRotationBottom=0.0WhiteLevel=60000.0Scattering=0.0CoefX4=0CoefX3=0CoefX2=0CoefX1=1CoefX0=0Scale=1RegionStartX=0RegionStartY=0RegionPixelsX=2000RegionPixelsY=2000Projections=1080InitialAngle=183.019744873047AngularStep=0.333313199275746FilterType=0CutOffFrequency=2.4999999627471Exponent=1.0Normalisation=1.0InterpolationType=0MedianFilterKernelSize=1Scaling=1000.0OutputUnits=/mUnits=mmAutomaticCentreOfRotation=1AutomaticCentreOfRotationOffsetZ1=0AutomaticCentreOfRotationOffsetZ2=0
DOI: 10.6084/m9.figshare.7629263.v2
title: Supplementary Tables: Differentially expressed genes in Six2TGC ;miR-17~92 fl/fl nephron progenitors.

description: Analysis of RNA-seq data for differentially expressed genes in Six2-TGC; miR-17~92 fl/fl nephron progenitors (Supplementary Table 1) and unbiased pathway analysis with Toppfun (Supplementary Table 2).
DOI: 10.17632/2mvy9bgrxs
title: Benthic habitats using EUNIS classification for the Brazilian EEZ

description: The dataset cointains the shapefile of marine benthic broad habitats classified according to EUNIS classification for the Brazilian Exclusive Economic Zone region. It was developed using open access databases and GIS operations to develop two intermediate layers: (i) biological zones and (ii) substrate type. Both layers were combined to form the first continuous map of marine habitats for the entire region.
DOI: 10.17632/88y8dzpkjv
title: Data for "A thermal-mechanical coupling-inspired inelastic constitutive law for the growth and atrophy of soft tissues"

description: Data for "A thermal-mechanical coupling-inspired inelastic constitutive law for the growth and atrophy of soft tissues"
DOI: 10.17632/dvmz6pkzvb
title: BigMHC Training and Evaluation Data

description: All training and evaluation data used in the BigMHC study

(https://doi.org/10.1101/2022.08.29.505690).

All code is freely available at https://github.com/KarchinLab/bigmhc 

--------------------------------------------------------------------------------
CSV Columns

mhc - MHC-I allele
pep - peptide sequence if epitope data or mutated peptide sequence if neoepitope data
tgt - target value of 1 (presented/immunogenic) or 0 (non-presented/non-immunogenic)

manafest.csv columns also include wtp (wild-type peptide) and gene (the name of the mutated gene)

pseudoseqs.csv columns include the MHC-I allele along with the index and amino acid of the aligned positions.

All other columns are the outputs of MHC-I epitope presentation and immunogenicity predictors. -------------------------------------------------------------------------------- 

datasets.zip contains the curated training, validation, and testing datasets along with a summary of the number of negatives and positives for each allele in each dataset (summary.csv):
- el_test.csv - epitope presentation evaluation data and all evaluated model predictions
- el_train.csv - epitope presentation training data
- el_val.csv - epitope presentation validation data
- im_test.csv - immunogenicity transfer learning evaluation data and all model predictions
- im_train.csv - immunogenicity transfer learning training data
- im_val.csv - immunogenicity transfer learning validation data
- iedb.csv - infectious disease epitope evaluation data and all model predictions
- summary.csv - table of positives and negatives across each allele for each dataset

- manafest.csv - neoepitope immunogenicity data validated using MANAFEST assays

- pseudoseqs.csv - one-hot encoded MHC representations

el.csv.zip contains the predictions of the BigMHC production models and all other methods on all EL data (train, val, test). The pMHCs were filtered so that all other methods can score them (e.g. peptide lengths 8-11).

eltrainval_models.zip contains the the models used to evaluate BigMHC on el_test.csv (the production models can be found in the GitHub repository)
-------------------------------------------------------------------------------- 

sha256 sums are below:

datasets.zip - 0d152a452756cf2e0014ffced6afc25118e7c11cf1f626b26e49f50f79edffaa
el.csv.zip - cb94b42406b96a3b13d941cf87dd43f4f53e9ebfbc3d1619f0e43327f1fb6395
eltrainval_models.zip - e8500173cb2afbe5f8e8c0ebc60785c0de6d91aab622f8b83fff3b4e65b43223
manafest.csv - accf19b8bb797ec842c3ee1b1ce1966feb35035df746f7a56b2994403ba1ad99
pseudoseqs.csv - cd1fa24fb4c9fc0ee592a3d753458c4e3abed0d5cc4ca76e325aa274df8e900a
DOI: 10.17632/gh8dt278wy
title: Gen Z Turnover Intention

description: This dataset supports a study on how employer branding influences turnover intention among Generation Z employees in Indonesia’s FMCG industry
DOI: 10.6084/m9.figshare.19130429.v2
title: Genome assembly of the diploid oat Avena longiglumis reveals the landscape of repetitive sequences, genes and chromosome evolution in grasses

description: Beyond gene diversity, the high-continuity genome assembly shows chromosomal structure and copy number variation, providing a reference for the<i> Avena</i> pangenome, defining the full spectrum of diversity. The chromosomal rearrangements and genome expansion demonstrate features of evolution across the genus and grass BOP-clade, contributing to exploitation of gene and genome diversity through precision breeding.
DOI: 10.6084/m9.figshare.7588706.v1
title: Supplementary Material for: Adenosine Deaminase Two and Immunoglobulin M Accurately Differentiate Adult Sneddon’s Syndrome of Unknown Cause

description: <b><i>Background:</i></b> The association that exists between livedo reticularis (LR) and stroke is known as Sneddon’s syndrome (SnS). The disorder is classified as primary SnS (PSnS), if the cause remains unknown and secondary SnS. The condition is rare and it occurs mainly sporadically. In 2014, 2 independent teams described a new genetic disorder with childhood-onset, which was called deficiency of adenosine deaminase 2 (DADA2), characterized by recurrent fevers and vascular pathologic features that included LR and stroke. All the patients carried recessively inherited mutations in cat eye syndrome chromosome region candidate 1 gene (<i>CECR1</i>), encoding the adenosine deaminase 2 (ADA2) protein. Genetic testing is the standard for the diagnosis of DADA2. However, the diagnostic accuracy of more affordable laboratorial analysis in <i>CECR1</i>-mutated individuals remains to be established. We aim to determine whether plasma ADA2 activity and serum immunoglobulin M (IgM) levels can distinguish (1) DADA2 from other adult patients within the SnS spectrum, and (2) healthy <i>CECR1</i> heterozygous (HHZ) from healthy controls (HC). <b><i>Methods:</i></b> ADA2 activity in plasma and serum IgM concentrations was measured in adult patients within the SnS spectrum, healthy first-degree relatives and HC. Genetic results were used as the reference standard. The primary outcome measures were sensitivity and specificity derived from receiver operating curve analysis. <b><i>Results:</i></b> A total of 73 participants were included in the study: 26 patients with PSnS with no CECR1 mutation (PSnS), 6 bi-allelic (DADA2 patients) and 7 HHZ CECR1 mutations and 34 HC. Plasma ADA2 activity and serum IgM levels were significantly lower in DADA2 patients than in PSnS. With the use of the best indexes, plasma ADA2 activity differentiated PSnS from DADA2 with a sensitivity and specificity of 100.0% and HHZ from HC with a sensitivity of 97.1% and specificity of 85.7%. Serum IgM levels also differentiated PSnS from DADA2 with a sensitivity of 85.2% and specificity of 83.3%. <b><i>Conclusion:</i></b> Serum IgM levels might be used as a triage tool and plasma ADA2 activity performs perfectly as a diagnostic test for DADA2 in adult patients within the SnS spectrum. ADA2 activity in plasma also reliably distinguishes HHZ from HC.
DOI: 10.6084/m9.figshare.c.3711712_d2.v1
title: MOESM2 of ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics

description: Additional file 2: Table S1. The list of selected activity types in the PubChem.
DOI: 10.6084/m9.figshare.22773776.v1
title: FUCCI RPE1 cells

description: FUCCI RPE2 cells originally published here. Data can be downloaded and preprocessed into provided H5AD file from GEO here with accession number GSE128365.
DOI: 10.6084/m9.figshare.4547149.v1
title: Supplementary Material for: Framework for the Integration of Genomics, Epigenomics and Transcriptomics in Complex Diseases

description: <strong><em>Objectives:</em></strong> Different types of ‘-omics' data are becoming available in the post-genome era; still a single -omics assessment provides limited insights to understand the biological mechanism of complex diseases. Genomics, epigenomics and transcriptomics data provide insight into the molecular dysregulation of neoplastic diseases, among them urothelial bladder cancer (UBC). Here, we propose a detailed analytical framework necessary to achieve an adequate integration of the three sets of -omics data to ultimately identify previously hidden genetic mechanisms in UBC. <b><i>Methods:</i></b> We built a multi-staged framework to study possible pair-wise combinations and integrated the data in three-way relationships. SNP genotypes, CpG methylation levels and gene expression levels were determined for a total of 70 individuals with UBC and with fresh tumour tissue available. <b><i>Results:</i></b> We suggest two main hypothesis-based scenarios for gene regulation based on the -omics integration analysis, where DNA methylation affects gene expression and genetic variants co-regulate gene expression and DNA methylation. We identified several three-way trans-association ‘hotspots' that are found at the molecular level and that deserve further studies. <b><i>Conclusions:</i></b> The proposed integrative framework allowed us to identify relationships at the whole-genome level providing some new biological insights and highlighting the importance of integrating -omics data.
DOI: 10.6084/m9.figshare.5738439.v7
title: Tattooed Human Mummies, List Version 4.0

description: The following presents a global data set identifying naturally- and deliberately preserved tattooed human remains from the archaeological record. The initial version of this list (Version 1.0) was compiled in 2016 for inclusion as Table 1 in the journal article “The World’s Oldest Tattoos” (Deter-Wolf et al. 2016). Benoît Robitaille, Lars Krutak, and Sébastien Galliot all contributed to that initial effort. Changes between versions are detailed below.<b><br></b>Entries in the data table are organized broadly by date, and rely on direct dating wherever possible. Where radiocarbon data is available, dates represent calibrated ranges. Each entry also includes documentation as to the associated archaeological culture, site, and significant source material. At the present time, unpublished and/or unprovenienced specimens from museums and private collections are not generally included in the data set.<b><br><br></b>Changes from Version 3.0 to 4.0 (2021):-Citations added and updated source hyperlinks-New entries for Andean and Hawai’ian examples-Reorganized Andean entries to account for unprovenienced examples-Collapsed single site entries except where dates differ<b><br></b>Changes from Version 2.0 to 3.0 (2019):-Citations added-New entries for additional Andean and Egyptian examples-Added hyperlinks for source material<b><br></b>Changes from Version 1.0 to 2.0 (2017):-Deleted “Loulan Beauty” from Gumugou, Qäwrighul, China, who is not tattooed-Updated Egyptian data-Improved citations and corrected date ranges as necessary-New entries for Timbac Rockshelter and Andean examples
DOI: 10.17632/8fbdhh72gs
title: Database of influencers' tweets in cryptocurrency (2021-2023).

description: Authors, through Twitter API, collected this database over eight months. These data are tweets of over 50 experts regarding market analysis of 40 cryptocurrencies. These experts are known as influencers on social networks such as Twitter. The theory of Behavioral economics shows that the opinions of people, especially experts, can impact the stock market trend (here, cryptocurrencies). Existing databases often cover tweets related to one or more cryptocurrencies. Also, in these databases, no attention is paid to the user's expertise, and most of the data is extracted using hashtags. Failure to pay attention to the user's expertise causes the irrelevant volume to increase and the neutral polarity to increase considerably. This database has a main table named "Tweets1" with 11 columns and 40 tables to separate comments related to each cryptocurrency. The columns of the main table and the cryptocurrency tables are explained in the attached document. Researchers can use this dataset in various machine learning tasks, such as sentiment analysis and deep transfer learning with sentiment analysis. Also, this data can be used to check the impact of influencers' opinions on the cryptocurrency market trend. The use of this database is allowed by mentioning the source.
Also, in this version, we have added the excel version of the database and Python code to extract the names of influencers and tweets.
in Version(3): In the new version, three datasets related to historical prices and sentiments related to Bitcoin, Ethereum, and Binance have been added as Excel files from January 1, 2023, to June 12, 2023. Also, two datasets of 52 influential tweets in cryptocurrencies have been published, along with the score and polarity of sentiments regarding more than 300 cryptocurrencies from February 2021 to June 2023. Also, two Python codes related to the sentiment analysis algorithm of tweets with Python have been published. This algorithm combines RoBERTa pre-trained deep neural network and BiGRU deep neural network with an attention layer (see code Preprocessing_and_sentiment_analysis with python).
DOI: 10.17632/dzszp4pbc7
title: Distinct Immunological Features Compared to Lichen Planus and Oral Lichen Planus

description: Single Cell 3' libraries were prepared using standard Illumina paired-end constructs, which include the P5 and P7 adaptors. The libraries incorporated a 16 bp 10x Barcode and a 12 bp Unique Molecular Identifier (UMI) within Read 1. The cDNA fragments in the 3' Gene Expression libraries were sequenced using Read 2, while the DNA from Cell Multiplexing Oligo Feature Barcodes in the Cell Multiplexing libraries was sequenced using Read 2N. The libraries were subjected to paired-end sequencing on an Illumina platform. Sample indexing was achieved using i7 and i5 index sequences. The following standard Illumina sequencing primer sites were utilized: for the 3' Gene Expression libraries, TruSeq Read 1 and TruSeq Read 2 primers were employed; for the Cell Multiplexing libraries, Nextera Read 1 and Nextera Read 2 primers were used. This method ensured accurate and efficient sequencing of both gene expression and multiplexing features, facilitating comprehensive single-cell analysis.