cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24615102.v1
title: Reconstructed surfaces and measured valve velocities

description: The reconstructed surfaces and measured valve velocities of the healthy volunteer belonging to the following publication:<br><br>L. Obermeier, J. Korte, K. Vellguth, F. Barbieri, F. Hellmeier, P. Berg, and L. Goubergrits, <i>Inter-model and inter-modality analysis of left ventricular hemodynamics: Comparative study of two CFD approaches</i> <i>based on echocardiography </i><i>and magnetic resonance imaging</i>, GAMM-Mitteilungen. (2023), e202370004. https://doi.org/10.1002/gamm.202370004<br><br>The dataset contains the geometries (as STL) of:the left ventricle, left atrium, aorta and both valves in end-diastolic statethe left ventricle as watertight surface mesh over the cardiac cycleFurthermore, the measured valve velocities are included.Data for both imaging modalities (transthoracic echocardiography, magnetic resonance imaging) are included.For further questions contact lukas.obermeier@charite.de
DOI: 10.6084/m9.figshare.895628.v1
title: GTF and GFF for maize

description: GFF and GTF files for maize versions 2 and 3
DOI: 10.17632/4hsr7gykzd
title: JDS19258_Supplementary_Material

description: Randomized controlled field trial comparing quarter and cow level selective dry cow treatment using the California Mastitis Test Supplementary Material - Table S1
DOI: 10.17632/8dnbrx3s6h
title: Thermoblocks for Loop-Mediated Isothermal Amplification

description: Files required to reproduce the LAMP device
DOI: 10.17632/f3s8h6dzzf
title: Job advertisement and salary monitoring dataset for Latvia in 2020

description: In 2018, 28 of November, in Latvia the amendments to Section 32 (3) of the Labor Law entered into force, according with it employers are obliged to indicate in the advertisement wage. This database continue wages monitoring started in 2019 and show data observation for 2020. 2019 year was first year in Latvia, when based on job advertisement analysis it is possible to conclude about salary by occupations, salary grow. Advertisement analysis is operational pointer in comparison with official statistic data. In addition, official statistic do not publish salaries by occupations on free of charge basis. This dataset represent job advertisement collection from biggest Latvian job advertisement web cv.lv . Data was collected every week in 2020, near 1700 advertisements per week. After collecting dataset was cleared from advertisements, in which it was not possible to identify occupations. After data cleaning dataset consist of 77 119 advertisements.
DOI: 10.6084/m9.figshare.25201631.v1
title: Fuhrländer FL2500 2.5MW wind turbine dataset.

description: The datasetThis is a Fuhrländer FL2500 2.5MW wind turbine dataset.FormatThe dataset is stored in JSON format inside the "dataset" folder. It contains five wind turbines (80,81,82,83,84), each one with three years of data with a time interval from 2012 to 2014. The data frequency is 5 minutes reporting four indicators of each 78 sensors (a total of 312 variables). The reported values for each sensor are minimum, maximum, mean, and standard deviation for each 5-minute interval. The dataset also contains the alarms events, indicating the system and subsystem and a small description.FunctionsI have included several functions for {R,MATLAB,...} languages to providing an interface that pre-processes and manipulates the RAW data into a table-like format. The table-like format is composed of the variables at the columns and each five-minute data entry in rows.AlgorithmsIn the case of matlab code, I have included a ELM (extreme learning machines) classificator model to make some predictions as an example. The ELM model is provided by ‪Pere Marti-PuigFAQERRORSJava exception occurred: java.lang.OutOfMemoryError: Java heap spacePlease increase the matlab java heap memory to more than 4GB following the next instructions: https://es.mathworks.com/help/matlab/matlab_external/java-heap-memory-preferences.html
DOI: 10.6084/m9.figshare.13082207.v1
title: Holz Human Trafficking Compliance DataRule of Law:State Compliance and Human Trafficking Protocols

description: Data set used in "The Rule of Law and State Compliance with Human Trafficking and Slavery Protocols". This is the original data set and is available for replication purposes.<br>
DOI: 10.6084/m9.figshare.24971781.v1
title: Supplementary Material for: The prenatal hypoxic pathology associated with maternal stress predisposes to dysregulated expression of the chrna7 gene and the subsequent development of nicotine addiction in adult offspring

description: Introduction: Previous studies have shown that fetal hypoxia predisposes individuals to develop addictive disorders in adulthood. However, the specific impact of maternal stress, mediated through glucocorticoids and often coexisting with fetal hypoxia, is not yet fully comprehended. Methods: To delineate the potential effects of these pathological factors, we designed models of prenatal severe hypoxia (PSH) in conjunction with maternal stress and prenatal intrauterine ischemia (PII). We assessed the suitability of these models for our research objectives by measuring HIF1α levels and evaluating the glucocorticoid neuroendocrine system. To ascertain nicotine dependence, we employed the conditioned place aversion test and the startle response test. To identify the key factor implicated in nicotine addiction associated with PSH, we employed techniques such as western blot, immunohistochemistry, and correlational analysis between chrna7 and nr3c1 genes across different brain structures. Results: In adult rats exposed to PSH and PII, we observed increased levels of HIF1α in the hippocampus (HPC). However, the PSH group alone exhibited reduced glucocorticoid receptor (GR) levels and disturbed circadian glucocorticoid rhythms. Additionally, they displayed signs of nicotine addiction in the conditioned place aversion and startle response tests. We also observed elevated levels of phosphorylated DARPP-32 protein in the nucleus accumbens (NAc) indicated compromised glutamatergic efferent signaling. Furthermore, there was reduced expression of α7 nAChR, which modulates glutamate release, in the medial prefrontal cortex (PFC) and HPC. Correlation analysis revealed strong associations between chrna7 and nr3c1 expression in both brain structures.
Conclusion: Perturbations in the glucocorticoid neuroendocrine system and glucocorticoid-dependent gene expression of chrna7 associated with maternal stress response to hypoxia in prenatal period favor the development of nicotine addiction in adulthood.
DOI: 10.6084/m9.figshare.28246451.v1
title: Improving carbon budgets by accounting for inorganic carbon in seagrass ecosystems

description: Inorganic Carbon's Role in Seagrass Carbon Budgets
DOI: 10.17632/gcrdw33hsd
title: Automated medicinal plant identification from leaf images

description: Here is the code for assessing the performance of the deep learning algorithm for the identification of medicinal plants.
DOI: 10.17632/fbvymg3jbn
title: Data from a meta-analysis of the effects of biochar on hydrological properties of soils with different textures

description: The database was built by searching literature published on the Web of Science and Google Scholar. The search keywords included biochar and soil hydraulic property and/or soil physical property, and/or water retention, and/or field capacity, and/or wilting point, and/or plant-available water, and/or saturated hydraulic conductivity. A total of 104 articles were selected to form the database, categorize and assign appropriate levels to the collected data, considering both categorical and continuous variables。The data were used to assess the effects of biochar on the hydrological properties of soils with different textures by meta-analysis.
DOI: 10.6084/m9.figshare.13264121.v1
title: Processed gene counts matrices from scRNA-seq datasets

description: Gene counts matrices extracted from scRNA-seq datasets processed with different pipelines.
DOI: 10.6084/m9.figshare.24220987.v3
title: CDC Youth Risk Behavior Survey (includes LGBTQ info)

description: The CDC's Youth Risk Behavior Surveillance Survey data is from https://www.cdc.gov/healthyyouth/data/. We were interested in this data as this is one of the few surveys that did collect information on LGBTQ+ status of students in grades 9-12. The curated datasets are included here. See the codebook for full details.
DOI: 10.6084/m9.figshare.27852174.v1
title: Single-cell profiling highlight pathogenic myeloid features in house dust mite-induced murine model of airway inflammation

description: Myeloid cells, particularly dendritic cells (DCs) and macrophages, play pivotal roles during asthma exacerbation by producing various cytokines and chemokines. However, the heterogeneity and function of these cells remains inadequately explored. In this study, we performed an established HDM-induced allergic asthma mouse model and generated a single-cell landscape on immune counterpart in lungPlease find the attached Seurat object stored in rds files. You can load them with R readRDS() function. <code>IC.rds</code> stores the immune cells' scRNA-seq profiles. `nonIC.rds` stores the non-immune cells' scRNA-seq profiles. You may refer to the <code>ann210320</code> column in the metadata for cell type annotation reference.<br><br>Please consider citing our work if this dataset is helpful to you:<br>Liu, J., Lv, J., Chen, S., Ma, J., Yao, J., Yuan, Z., Yang, C., Li, X., Zhang, X., Zhu, Y., Zhang, J. and Wu, L. (2024), Single-cell profiling highlight pathogenic myeloid features in house dust mite-induced murine model of airway inflammation. Allergy. https://doi.org/10.1111/all.16156
DOI: 10.6084/m9.figshare.97571.v1
title: Test scores for each cognitive trait and haemoglobin levels of study participants

description: Confidence level, work pattern and physical distraction test scores of dental students (higher grades signfy greater confidence, non-restricted work patter and low levels of distraction) together with their haemoglobin levels
DOI: 10.17632/rdwd9rkf2p
title: Experimental lunar magma ocean crystallization

description: The accretion of the Moon was followed by a lunar magma ocean stage. The fractional crystallization of this magma ocean was experimentally simulated.  The results yield the primordial stratification of the Moon from the cumulative mantle to the primordial crust. In detail, the mineral composition, the thickness of each layer and the evolving melt composition are determined. The results show that reworking (likely through overturn induced by Rayleigh-Taylor instabilities)  of this primordial cumulate layers is required to explain some of the lunar magmatic suites and also to explain a very much reduced modern crustal thickness with respect to the primordial one. The data file contains the analyses of minerals and melts across the entire fractional crystallization interval as well as mineral modes and layer thicknesses of each fractionation step.
DOI: 10.6084/m9.figshare.28942967.v1
title: Metabolomic data of root system and root nodules of soybean W82

description: Metabolomic data of root system and root nodules of soybean W82 planted in the soil with pH9.03.
DOI: 10.6084/m9.figshare.29128250.v1
title: Supplementary data for Arxan volcanic group.

description: These data are the ones we used when studying the seismic activity of the Arxan volcanic group.
DOI: 10.17632/wstfmr4z57
title: Datasets exploring putative lncRNA-miRNA-mRNA axes in breast cancer cell lines

description: Data accompanied with the paper "Datasets exploring putative lncRNA-miRNA-mRNA axes in breast cancer cell lines" by Wasson et al. in Data in Brief. Please refer to this article for full project details. The data consists of : * .txt files containing predicted lncRNA/miRNA/mRNA axis for four long non-coding RNAs (LincIN, SPRY4-IT1, AC009283.1, LincK) * .R script we used to generate predicted lncRNA/miRNA/mRNA microarray data obtained from GEO datasets (GSE79214, GSE62507, GSE134254, GSE109007)
DOI: 10.6084/m9.figshare.12901013.v1
title: Light_field_endoscope.zmx

description: The Zemax lens design file of the main lens of a light field endoscope
DOI: 10.6084/m9.figshare.14267219.v1
title: Tabula Sapiens release 1.0

description: Our goal is to make sequence data rapidly and broadly available to the scientific community as a community resource. It is our intention to publish the work of this project in a timely fashion, and we welcome collaborative interaction on the project and analyses. However, considerable investment was made in generating these data and we ask that you respect rights of first publication and acknowledgment as outlined in the Toronto agreement (Toronto International Data Release Workshop Authors. Prepublication data sharing. Nature. 2009 Sep 10;461(7261):168-70). By accessing these data, you agree not to publish any articles containing analyses of genes, cell types or transcriptomic data on a whole atlas or tissue scale prior to initial publication by the Tabula Sapiens Consortium and its collaborating scientists. If you wish to make use of restricted data for publication or are interested in collaborating on the analyses of these data, please use email or contact form available from the portal (https://tabula-sapiens-portal.ds.czbiohub.org/). Redistribution of these data should include the full text of the data use policy.<br>
DOI: 10.6084/m9.figshare.22691044.v2
title: Untitled Item

description: The MIDOG++ dataset represents an extension of the data set used in the MIDOG 2021 and 2022 challenges. We provide region of interest images from 503 histological specimens of seven different tumor types with variable morphology: breast carcinoma, lung carcinoma, lymphosarcoma, neuroendocrine tumor, cutaneous mast cell tumor, cutaneous melanoma, and (sub)cutaneous soft tissue sarcoma. The human and canine samples were processed and stained at different human and veterinary pathology laboratories with standard H&E dye and digitized with different digital whole slide image scanners. We provide labels for 11,937 mitotic figures that have been differentiated against 14,351 imposter cells in a blinded consensus by two pathologists and a final decision by a third pathologist for disagreed labels.
DOI: 10.6084/m9.figshare.25061324.v2
title: Dataset for the paper "Climate Correlates of Bluetongue Incidence in Southern Portugal"

description: Species distributions for the four BTV vector species studied:i) <i>Culicoides imicola</i>; ii) <i>C. obsoletus</i> complex; iii) <i>C. pulicaris</i>, and iv) <i>C. dewulfi</i>.
DOI: 10.17632/8pkk8y3xht
title: Comparative Transcriptome Analysis of Wild-Type and Metabolically Engineered Pichia pastoris (Komagataella phaffii) for β-Lactam Precursor δ-(L-α-aminoadipyl)-L-cysteinyl-D-valine (ACV) Production

description: This dataset "Comparative Transcriptome Analysis of Wild-Type and Metabolically Engineered Pichia pastoris (Komagataella phaffii) for β-Lactam Precursor ACV Production" supports the manuscript titled “Metabolic Engineering of Pichia pastoris for Production of the β-Lactam Precursor δ-(L-α-aminoadipyl)-L-cysteinyl-D-valine (ACV)”. It includes raw transcriptomic data (RNA-Seq FASTQ files) and the results of Differential Gene Expression (DEG) analysis comparing a wild-type strain of Pichia pastoris (also known as Komagataella phaffii) with a genome engineered strain designed to produce the β-Lactam precursor δ-(L-α-aminoadipyl)-L-cysteinyl-D-valine (ACV). Two biological replicates were analyzed via RNA-Seq for each condition (wild-type and engineered).


The dataset contains:
1. Raw sequencing reads (FASTQ]).
2. Processed DEG analysis results (tables in CSV format) including gene identifiers, log2 fold changes, p-values, and adjusted p-values (FDR).

Pichia pastoris is a widely used host for heterologous protein and metabolite production. This transcriptomic data provides insights into the global gene expression changes resulting from the metabolic engineering strategies employed for ACV synthesis.
DOI: 10.6084/m9.figshare.12951257.v1
title: League Table + Gini Dataset

description: Supporting data for Hubbard et al., 'Levelling the Playing Field: The effect of including widening participation in university league tables', in press at International Review of Education.<br>For analysis script see 10.6084/m9.figshare.12951278<br> <br><br>
DOI: 10.6084/m9.figshare.24456370.v1
title: Dissolved oragnic matter reactome extracted from biotreatment processes of 12 full-scale wastewater treatment plants

description: The Cytoscape (.cys) network file of the core reactome of wastewater DOM<br>
DOI: 10.6084/m9.figshare.28938458.v1
title: Flevoland Planetscope-LULC Dataset

description: Planetscope imagery of Flevoland in 2021 with training and validation LULC samples.
DOI: 10.6084/m9.figshare.7663010.v4
title: Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma

description: This repository contains raw data and all scripts for the in situ sequencing processing pipeline (Mats Nilsson Lab, Stockholm University) and downstream analysis applied in the manuscript “<b>Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma”. </b><b><br></b><b>Raw images:</b>All 16bit tiff images are for 12 weeks_section1Format is baseX_cY_ORGX indicates the hybridization round (1-4)Y indicates the channel: 1: DAPI2: FITC (T)3: Cy3 (G)4: TexR (C)5: Cy5 (A)6: AF750 (Anchor primer)<br> <b><i></i><i></i>Raw data in folders:</b> Lung csv files Bacteria csv files DAPI for plotting HE folder<br> <b>Scripts folder:</b> Matlab scripts Cellprofiler pipelines<br> <b>Identification and plotting of transcripts:</b> For all matlab scripts: Download the “Matlab scripts” folder, add lib to MATLAB path. Except MATLAB, no additional Mathworks product is required. Tested on R2017b. <br> <b>InSituSequencing.m</b> is the top-level script processing sequencing images to positional visualization of decoded transcripts. Use raw images for 12weeks_section1 as input images (others are available on request) . After Tiling in "InsituSequencing.m", process tiled images in the cell profiler pipeline “Blob identification”. Run decode and threshold in "InSituSequencing.m" to generate csv files containing position and intensity of each identified signal.<br>csv files for all lung scans (3 per time point) are in “lung csv files” folder and can be plotted on DAPI images (10% of original size) found in “DAPI for plotting” folder using Plotting global in "InSituSequencing.m". High resolution H&E scans of in situ-sequenced lungs for lung section per time point are in the “HE folder” at 50% of original size. For all images 1 pixel corresponds to 0.325 mm.<br> <b>Identification and plotting of transcripts in given proximity to bacteria:</b> Use the cellprofiler pipeline “Bacteria identification” instead of “Blob identification” to identify signal in indicated distances from identified bacteria. The folder “bacteria csv files” contains identified signals in the indicated distances to identified bacteria. Input images are available on request.<br> <b>Downstream analysis (Matlab Scripts folder)</b> <b>DensityEstimation.m</b> was used to display not absolute reads but a kernel density estimation of a certain gene in a 2log scale. <b>ROI_draw_onImage.m</b> was applied to extract reads from annotated regions. Pictures of annotations can be found in the manuscript supplementary figure S1. <b>HexbinClustering.m </b>performed an unsupervised clustering (kmeans) of spatial data with a given number of distinct clusters in a given radius.<br><b>Table 1-3 </b>contain sequences of used specific primers, padlock probes and detection oligos. <br>
DOI: 10.17632/g5cf3z4fbv
title: Linking Microbial Communities and Molecular Transformations of Dissolved Organic Matter to the Fate of Nitrogen in Karst Aquifers

description: Physiochemical parameters, optical parameters, molecular characteristics and molecules degradation processes number of DOM in different karst aquifer media (karst fissure media, karst conduit media, karst window groundwater) derived from EEM, PARAFAC, and FT-ICR MS analysis. The average values of indices based on FT-ICR MS data here are all calculated as intensity-weighted average (e.g., H/Cwa, O/Cwa, DBEwa, NOSCwa, and (AImod)wa).
DOI: 10.17632/hxd382z2fg
title: A Real-Time Dataset of Pond Water for Fish Farming using IoT devices

description: This is the real-time dataset. This dataset is created for monitoring the real-time aquatic environment using an IoT framework. Three sensors named pH, Temperature, and turbidity along with an Arduino controller are used for monitoring the water quality of 5 ponds. It has 4 columns and 40280 rows. They are- pH, Temperature, Turbidity, and Fish. Here fish is the target variable and others are the independent variable. There are 11 fish categories, having distinct values of tilapia 8830 rui 6336 pangas 5314 silverCup 3906 katla 3786 sing 3776 shrimp 3204 karpio 2112 prawn 1348 koi 964 magur 704.
DOI: 10.6084/m9.figshare.24657762.v1
title: Supplementary Material for: Molecular Profile of Subungual Melanoma: a MelaNostrum Consortium Study of 68 Cases Reporting BRAF, NRAS, KIT, and TERT promoter status.

description: Background: Subungual melanoma (SM) is an unusual type of melanocytic tumor affecting the nail apparatus. The mutational prevalence of the most prominently mutated genes in melanoma has been reported in small cohorts of SM, with unclear conclusions on whether SM is different from the rest of melanomas arising in acral locations or not. Hence, the molecular profile of a large series of SM is yet to be described. Objectives: The aim of this study was to describe the molecular characteristics of a large series of SM and their association with demographic and histopathological features. Methods: Patients diagnosed with SM between 2001 and 2021 were identified from six Spanish and Italian healthcare centers. The mutational status for BRAF, NRAS, KIT, and the promoter region of TERT (TERTp) were determined either by Sanger sequencing or Next-Generation Sequencing. Clinical data were retrieved from the hospital databases to elucidate potential associations. Results: A total of 68 SM cases were included. Mutations were most common in BRAF (10.3%) and KIT (10%), followed by NRAS (7.6%), and TERTp (3.8%). Their prevalence was similar to that of non-subungual acral melanoma, but higher in SM located on the hand than on the foot. Conclusions: To date, this study represents the largest cohort of SM patients with data on the known driver gene mutations. The low mutation rate supports a different etiopathogenic mechanism for SM in comparison of non-acral cutaneous melanoma, particularly for SM of the foot.
DOI: 10.6084/m9.figshare.22691419.v2
title: Untitled Item

description: The MIDOG++ dataset represents an extension of the data set used in the MIDOG 2021 and 2022 challenges. We provide region of interest images from 503 histological specimens of seven different tumor types with variable morphology: breast carcinoma, lung carcinoma, lymphosarcoma, neuroendocrine tumor, cutaneous mast cell tumor, cutaneous melanoma, and (sub)cutaneous soft tissue sarcoma. The human and canine samples were processed and stained at different human and veterinary pathology laboratories with standard H&E dye and digitized with different digital whole slide image scanners. We provide labels for 11,937 mitotic figures that have been differentiated against 14,351 imposter cells in a blinded consensus by two pathologists and a final decision by a third pathologist for disagreed labels.