cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1397502.v3
title: Supplemental Materials to submitted paper

description: This file contains the supplemental materials to the paper: <em>Esteban O. et al., Surface-driven registration method for the structure-informed segmentation of diffusion MR images. NeuroImage (accepted), 2016. </em><em>doi: http://dx.doi.org/10.1016/j.neuroimage.2016.05.011</em><em><br></em> <strong>Abstract:</strong> Current methods for processing diffusion MRI (dMRI) to map the connectivity of the human brain require precise delineations of anatomical structures. This requirement has been approached either segmenting the data in native dMRI space or mapping the structural information from T1-weighted (T1w) images. The characteristic features of diffusion data in terms of signal-to-noise ratio, resolution, as well as the geometrical distortions caused by the inhomogeneity of magnetic susceptibility across tissues hinder both solutions. Unifying the two approaches, we propose regseg, a surface-to-volume nonlinear registration method that segments homogeneous regions within multivariate images by mapping a set of nested reference-surfaces. Accurate surfaces are extracted from a T1w image of the subject, using as target image the bivariate volume comprehending the fractional anisotropy (FA) and the apparent diffusion coefficient (ADC) maps derived from the dMRI dataset. We first verify the accuracy of regseg on a general context using digital phantoms. Then we establish an evaluation framework using undistorted dMRI data from the Human Connectome Project (HCP) and known deformations derived from real inhomogeneity fieldmaps. We analyze the performance of regseg computing the misregistration error of the surfaces estimated after being mapped with regseg onto 16 datasets from the HCP. The distribution of errors shows a 95% CI of 0.56–0.66 mm, that is below the dMRI resolution (1.25 mm, isotropic). Finally, we cross-compare the proposed tool against a nonlinear b0-to-T2w registration method, thereby obtaining a significantly lower misregistration error with<br>regseg. Therefore, we demonstrate that regseg allows the accurate mapping of structural information in dMRI space, enabling the application of new structure-informed techniques in the connectome extraction.
DOI: 10.6084/m9.figshare.13256174.v5
title: Sargassum Dataset

description: Neural Network training dataset for classification of Images with presence and absence of <i>sargassum</i>
DOI: 10.6084/m9.figshare.24124860.v1
title: Generative AI policies for academic publishers

description: This Microsoft Excel file contains data downloaded from a variety of academic publishers related to their policies on how authors can use Generative AI tools when submitting work for publication. The data was collected in July 2023 and the authors make no claims as to the present accuracy of the data.
DOI: 10.6084/m9.figshare.3518942.v1
title: Supplement 1. R and Matlab code for mortality estimators.

description: File List MortalityEstimators.zip (MD5: 09eaef6f667f615cc046e09947a96fa2)Description The associated file “MortalityEstimators.zip” contains Matlab (Mathworks 2012) and R (http://www.r-project.org/) files for the mortality extrapolations described in the manuscript Etterson, M. Hidden Markov models for estimating animal mortality from anthropogenic hazards. Matlab files have suffix “.m” and R files have suffix “.r”. Some of the Matlab functions require the Matlab Statistics Toolbox. Some of the R functions require the R package expm. Table S1 gives a basic description of each function, and each file contains a header giving function syntax. The Matlab and R functions may differ slightly due to differences in programming environment. Table S1. Algorithms provided for estimating animal mortality. -- TABLE: Please see in attached file. --
DOI: 10.6084/m9.figshare.28639523.v1
title: Neutrophil Extracellular Trap-borne C3-Driven Endothelial Dysfunction in <i>Klebsiella pneumoniae</i> Liver Abscess

description: <i>Klebsiella pneumoniae</i> (<i>K</i><i>.</i><i> pneumoniae</i>) liver abscess (KPLA) is a severe bacterial infection that is frequently complicated by intrahepatic thrombophlebitis and extrahepatic metastatic infections leading to high mortality rates. This study investigates the role of neutrophil extracellular traps (NETs) in endothelial injury and disease progression in KPLA. Our findings reveal that KPLA patients with intrahepatic thrombophlebitis are more prone to developing sepsis and extrahepatic migratory infections. <i>K. pneumoniae</i> induces NET formation via the TLR4-PI3Kα-AKT signaling pathway, and C3 deposition on NETs significantly contributes to endothelial injury. In a KPLA mouse model, increased C3 levels were observed in the liver, with NETs carrying substantial amounts of C3, disrupting the endothelial barrier and exacerbating liver injury. Treatment with the C3 inhibitor AMY-101 reduced C3 deposition on NETs, alleviated endothelial damage, significantly improved survival, and reduced extrahepatic dissemination, inflammatory infiltration, and lung injury while also suppressing systemic inflammation. Our findings underscore the pivotal role of C3 in NET-mediated endothelial damage and the pathogenesis of KPLA. Thus, targeting C3 deposition on NETs may be a promising therapeutic strategy to reduce endothelial injury, thrombosis, and extrahepatic infections in KPLA without compromising neutrophil antimicrobial function.
DOI: 10.6084/m9.figshare.9896189.v1
title: HLPa1_1.fq.gz

description: The sequence of bacteria in 0-10 cm plantation soil in Hulunbuir Sandy Land
DOI: 10.6084/m9.figshare.29109167.v1
title: SA2_prol_2

description: NU1 cells Chipseq data
DOI: 10.6084/m9.figshare.20409360.v2
title: Distribution of soil carbon age and carbon input transit times

description: we constructed the soil carbon age and transit times of carbon input across global soil profiles.
DOI: 10.6084/m9.figshare.22285528.v1
title: Data from: Litter accumulation, not light limitation, drives early plant recruitment

description: Data were collected in a full-factorial litter removal-light addition-fertilization-herbivore exclusion experiment located in Central Germany, in Bad Lauchstädt (51°22060 N, 11°50060 E ) (for details on the basic experiment see Eskelinen et al. 2022, Nature) during May 2019. <br> The file contains data of seedling species number and richness (sheet 1), environmental variables: litter biomass weight, litter depth, light intensity at ground, red to far red ratio, soil C_N, soil moisture, soil temperature, soil pH and soil NH4 content (sheet 2) and temperature and precipitation data collected by the Germany Meteorological Service in Bad Lauchstädt from 2009 to 2019 (sheet 3).
DOI: 10.6084/m9.figshare.5435866.v7
title: MCA DGE Data

description: MCA single cell DGE data (Cells with &gt;500UMI ) for the following manuscript:Mapping the Mouse Cell Atlas by Microwell-seq<br>MCA_500more_dge.rar: The raw digital expression matrix (dge) of more than 400,000 single cells sorted by tissues. All cells have more than 500 transcripts. The batch genes were not removed.<br>MCA_BatchRemove_dge.zip: The batch gene removed dge of more than 200,000 primary single cells sorted by tissues. Some tissues are not included due to relatively strong batch effects. This dataset can be used to make global tissue tSNE plot and do cross-tissue analysis.<br>MCA_CellAssignments.csv: The annotation of cells, which includes the cell names, cluster ID, belonged tissues, experimental batches and cell barcodes.<br>MCA_Figure2-batch-removed.txt.tar.gz: The batch removed dge of approximately 60,000 cells of high quality. 1500 cells were sampled from 43 tissues respectively. This sampled data is used for Figure 2.<br>MCA_Figure2_Cell.info.xlsx: The annotations of cells used in Figure2. <br>Sheet1: The annotations of each cell used in Figure2, including cell names, cluster ID, belonged tissues. <br>Sheet2: The annotations of 98 clusters in Figure2. <br>Sheet3: The composition of cell numbers in 98 clusters and 43 tissues. <br>MCA_Batch Information.xlsx: The batch information, which includes the age and gender of the mouse, and experiment batches for MCA data.<br><br>Batch effect removalFor cross tissue comparison, we removed the batch gene background to improve presentation. We assume that for each batch of experiment, the cell barcodes with less than 500UMI correspond to the empty beads exposed free RNA during the cell lysis, RNA capture and washing steps. The batch gene background value is defined as the average gene detection for all cellular barcodes with less than 500 UMI, multiplied by a coefficient of 2, and then rounded to the nearest integer. Genes detected in less 25% of all cells are removed from the batch gene background list. We subtract the batch gene background for each cell from the digital expression matrix before making the cross tissue comparison figures.
DOI: 10.6084/m9.figshare.13073189.v1
title: Plantas medicinais e ritualísticas dos Kaiowá do Tekoha Taquara como contribuição para a demarcação da terra ancestral, Mato Grosso do Sul, Brasil –– Medicinal and ritualistic plants of the Kaiowá of Tekoha Taquara as a contribution to the demarcation of ancestral land, Mato Grosso do Sul, Brazil –– Material Suplementar / Supplementary Material

description: Lista das espécies vegetais citadas por informantes da Comunidade Kaiowá do <i>Tekoha</i> <i>Taquara</i>, Juti, MS, organizadas por família, espécie, voucher de herbário, nome em Guarani, tradução do nome Guarani para português, nome popular, parte da planta usada, uso relatado, categoria de uso conforme a Classificação Internacional de Doenças (ICD 2016) da Organização Mundial da Saúde, e o bioma em qual a planta foi coletada. List of botanical species cited by informants of the Kaiowá community of <i>Tekoha Taquara, </i>Juti, MS, organized by family, species, herbarium voucher, Guarani name, translation of Guarani name to Portuguese, popular name, part of the plant used, related use, use category given by the International Classification of Diseases (ICD 2016) of the World Health Organization, the biome in which the plant was collected.
DOI: 10.6084/m9.figshare.22812227.v1
title: asthma during pregnancy.xlsx

description: Asthma exacerbation (AE) is a significant clinical problem during pregnancy. This study aimed to identify factors and perinatal and offspring outcomes associated with AE during pregnancy. We conducted a retrospective cohort study using the Peking University Third Hospital database from January 1, 2013 to December 31, 2020.This study established a retrospective cohort study to investigate the clinical characteristics and perinatal outcomes of AE to provide reference for the management of patients with asthma during pregnancy and insights for reducing the occurrence of AE and the associated adverse outcomes.
DOI: 10.6084/m9.figshare.19136909.v1
title: Additional file 18

description: <b>Genomic regions for RNA-FISH probes and their lengths.</b>
DOI: 10.6084/m9.figshare.24750117.v2
title: Untamed atlas (Graph Learning for Cortical Parcellation from Tensor Decomposition of Resting-State fMRI)

description: Atlases generated from resting-state fMRI of the 1400 subjects in Brain Genomics Superstruct Project (GSP) dataset. Available in fsaverage6 and fsLR 32K surface space.
DOI: 10.17632/6p7345t8xr
title: XPS Survey spectra of Graphene oxide

description: XPS spectra were obtained in a Kratos Axis Ultra DLD irradiating the samples with an Al monochromatic Kα radiation of energy (1486.6 eV) at a power of 150 W. Survey spectra of all samples were performed with pass energy of 160 eV. Graphite XPS spectra presents its main peak related to the energy layer C1s (at 285 eV) of the carbon element, while the GOs spectra are composed by two main peaks, related to the photoelectrons emitted in the energy layers C1s (at 285 eV) and O1s (at 531 eV) of carbon and oxygen elements.
DOI: 10.6084/m9.figshare.24535135.v1
title: Characterisation of volatile and particulate emissions from home 3D printers

description: This dataset was obtained by characterising volatile and particulate emissions from home 3D printers. <br>
DOI: 10.6084/m9.figshare.28560071.v1
title: 2 photon imaging and target-directed behavior data in larval zebrafish

description: Supporting data for:The visuomotor transformations underlying target-directed behavior. Peixiong Zhao*, Yuxin Tong<i>*</i>, Ivan P. Lazarte, Biswadeep Khan, Guangnan Tian, Kenny K. Y. Chen, Thomas K. C. Lam, Yu Hu, Julie L. Semmelhack.<i> </i><i>Proc. Natl. Acad. Sci</i>.<i> USA</i>. 2025<br>* equal contribution<br><br>Data collected by Peixiong Zhao<br>Data preprocessed by Yuxin TongContact: Dr. Julie Semmelhack jsemmelhack@ust.hk <br>Simultaneous behavioral and neural recording data from 7 fish. Behavior videos contain both top and side view. The visual stimulus information of each trial is stored in "vsinfo" file. Neural data is recorded at 2Hz per volume, ~25k neurons are segemented per fish. The brain region masks and atlas (downloaded from mapZebrain) used in data analysis are also attached. Details of behavioral and neural analysis are described in the method section of paper.<br>
DOI: 10.6084/m9.figshare.8273102.v1
title: Processed files (to use with scanpy)

description: h5ad files to use with scanpy
DOI: 10.6084/m9.figshare.26112565.v1
title: The genome sequences of <i>Colletotrichum scovillei</i> KC05 and the related files.

description: The genome assembly of Colletotrichum scovillei KC05 and the related files, including the gene feature format (GFF), CDS, and translated CDS files. The NCBI GenBank accession for this genome is GCA_001593745.2, and the WGS accession is LUXP02000000.
DOI: 10.6084/m9.figshare.26978527.v1
title: Supplementary Material from Trade-off between photo-symbiosis and innate immunity influences cnidarian’s response to pathogenic bacteria

description: Emery_et_al_2024_ESM_file1.xlsx
DOI: 10.6084/m9.figshare.725715.v1
title: Error correction assemblies

description: These are the assemblies analyzed in the error correction paper
DOI: 10.17632/vtkbn2zhfj
title: ideal other congruence

description: This is a raw dataset for the project "game character congruence with ideal others predicts purchase intention"
DOI: 10.6084/m9.figshare.1082512.v1
title: Motion Capture of Bicycling on a Treadmill

description: This data set provides kinematic motion capture marker trajectories of a bicycle and rider performing various maneuvers while bicycling on a large treadmill. Also included are various computed variables for a prinicipal component analysis study of the data which is reported on in Moore, J. K., Kooijman, J. D. G., Schwab, A. L. & Hubbard, M., Rider motion identification during normal bicycling by means of principal component analysis. Multibody System Dynamics, Springer Netherlands, 2011, 25, 225-244. See the README.rst file for more detailed information about the data.
DOI: 10.6084/m9.figshare.11965725.v1
title: Quality pattern evaluation of frozen soursop pulps: an assessment based on chemical composition and chemometric analysis

description: Abstract In the present study, the physicochemical properties and mineral composition of commercially-frozen soursop pulps from the southern region of the state of Bahia, Brazil, were evaluated. The physicochemical parameters such as soluble solids (°Brix), acidity and pH were determined according to reference methodologies. For mineral composition evaluation, samples were digested in a closed microwave system and the elements K, P, S, Ca, Mg, Fe, Cu, Zn, and Mn were quantified through inductively coupled plasma optical emission spectrometry (ICP OES). Soluble solids content ranged from 4.77 to 15.37 °Brix among the different brands of analyzed frozen pulps. Titratable acidity (equivalent to citric acid) and pH ranged from 0.49 to 1.00 and 3.61 to 4.57, respectively. Some samples presented irregularities in regard to quality pattern established in the Brazilian legislation. The following range of concentration, in μg g-1, were found for essential elements: K (544-1761), P (44.3-139), S (71.8-174), Ca (24.3-77.0), Mg (47.2-132), Fe (1.40-4.05), Mn (0.32-1.22), Cu (0.30-0.88) and Zn (0.36-0.84). The use of principal component analysis (PCA) enabled a more in-depth data analysis, performing correlations between different variables and frozen pulp brands.
DOI: 10.6084/m9.figshare.24867165.v1
title: Drug response data

description: preprocessed GDSC drug response data Raw data source: https://www.cancerrxgene.org/downloads/bulk_download Subset to the record with a higher AUC value If multiple entries are found for a given cell line and drug in the metadata.<br>
DOI: 10.6084/m9.figshare.25690689.v1
title: <b>Genome-wide association studies</b><b>reveal novel </b><b>QTLs</b><b>for </b><b>agronomic traits</b><b>in soybean</b>

description: Soybean, as a globally significant crop, has garnered substantial attention due to its agricultural importance. The utilization of molecular approaches to enhance grain yield in soybean has gained popularity. In this study, we conducted a genome-wide association study (GWAS) using 156 Chinese soybean accessions over a two-year period. We employed the general linear model (GLM) and the mixed linear model (MLM) to analyze three agronomic traits: pod number, grain number, and grain weight. Our findings revealed significant associations between qgPNpP-98, qgGNpP-89 and qgHGW-85QTLs and pod number, grain number, and grain weight, respectively. These QTLs were identified on chromosome 16, a region spanning 413171bp exhibited associations with all three traits. These QTL markers identified in this study hold potential for improving yield and agronomic traits through marker-assisted selection and genomic selection in breeding programs.
DOI: 10.6084/m9.figshare.25927369.v2
title: Dataset and Supplementary Material - Andersen, Robertson, MacMillan - Thermal sensitivity of spreading depolarization in the CNS of <i>Drosophila melanogaster</i>

description: This file contains all data used for production of the figures presented in the paper and supplementary materials, which are also in this file."Thermal sensitivity of spreading depolarization in the CNS of <i>Drosophila melanogaster</i>"<br><br>by Mads Kuhlmann Andersen<sup>1,3</sup>*, R. Meldrum Robertson<sup>2</sup> and Heath A. MacMillan<sup>1</sup><br><sup><em>1</em></sup><i>Department of Biology, Carleton University, Ottawa, ON, Canada</i><br><sup><em>2</em></sup><i>Department of Biology, Queen’s University, Kingston, ON, Canada</i><sup><em>3</em></sup><i>Current address: Department of Biology, Aarhus University, Aarhus, Denmark</i>
DOI: 10.6084/m9.figshare.13397651.v3
title: REFERENCE DATASET: Expression of 97 surface markers and 462 mRNAs in 49057 cells from healthy young and healthy old bone marrow

description: Seurat v3 object<b><br></b><b>ASSAYS</b>:AB: Antibody expression dataRNA: mRNA expression dataBOTH: mRNA and Antibody expression data, concatenatedintegrated: Antibody and mRNA expression matrices were concatenated and data was integrated across patients using scanorama<br><b>DIMENSIONALITY REDUCTION</b><b>MOFAUMAP</b>: UMAP performed on MOFA dimensions. Display used in the manuscript. Set reduction="MOFAUMAP"in most cases!<br>ProjectedMOFA: Multi-OMICS factor analysis to integrate AB and RNA data. MOFA was run on scanorama-integrated data and served as input for clustering and further dimensionality reduction.MOFATSNE: UMAP performed on MOFA dimensions.<br><br><b>METADATA</b>Batch: Source individual (BM1-3, Aged1-3).class: Type of individual (healthy young, healthy old).<br><b>Change log: </b>Compared to the previous version of this file, the 3 AML patients were removed. A new object with 15 AML patients has been created: https://doi.org/10.6084/m9.figshare.14780127.v1<br>
DOI: 10.6084/m9.figshare.20505723.v1
title: RdRp profile HMMs

description: profile HMMs used for viral discovery. all_rdrps.hmm is combined HMM for all other HMMs and was used in paper
DOI: 10.17632/g7824s3x5c
title: Raw Impedance Experimental Data for Platinum wire & Graphite rod & Nichrome wire

description: 1. Here are the following Raw Experimental Data:
1.1. Impedance measurements for Platinum wire.
1.2. Impedance measurements for Graphite rod.
1.3. Impedance measurements for Nichrome wire.

2. The data is opened using the EC-Lab program (BioLogic - Science Instrument) with the SP-240 virtual firmware, version V11.42 and higher (available at: https://www.biologic.net/biologic-ec-lab-software-demo/).

3. If necessary, the EC-Lab program allows for data division into separate measurement cycles and conversion into various formats.
DOI: 10.6084/m9.figshare.5665699.v1
title: Additional file 1: of Functional SNP allele discovery (fSNPd): an approach to find highly penetrant, environmental-triggered genotypes underlying complex human phenotypes

description: Use of fSNPd and the Supplementary Figure. This firstly documents the instructions for the installation of fSNPd, and its use. Secondly, it contains the Supplemental Figure entitled: Average read depth per base of genes in a test cohort of 40 individualsâ exomes - data derived from Supplemental Table S1. This shows a graph of calculate the average read coverage by all genes, and the legend details the methodology used. References used are given after the legend. Read number statistics of average depth of sequence reads for each exon of each gene included in the exomes of forty individuals. This is a large spreadsheet giving the detailed analysis of read depth achieved. Results and statistics are given for each gene and exon of each gene. Thus, the coverage of an exome of any desired exon can be determined. Simulations of the performance of fSNPd compared to an Association study approach in a variety of scenarios. Simulations were performed assuming that a rare SNP allele was fully penetrant when present (unless otherwise stated). For each Simulation SNP-1 is a common SNP (such as are used in Association studies) with allele A frequency = allele B frequency = 0.5 and SNP-2 (analysed in fSNPd) has the rare allele A frequency = .01 and the common allele B frequency = .99. The SNP-2 allele A is disease associated and always on a SNP-1 allele A background. Simulation are of: the number of SNPs causing a phenotype; different SNP-2 rare allele frequencies; if half of cases are non-genetic or rare SNPs allele penetrance 50%; and of using a cohort size of 3000, rather than 100 as used for all other simulations. (ZIP 8041 kb)
DOI: 10.17632/c696dvvynf
title: Genetic determinants of host tropism in Klebsiella phages

description: Bacteriophages play key roles in bacterial ecology and evolution and are potential antimicrobials. However, the determinants of phage-host specificity remain elusive. Here, we isolate 46 phages to challenge 138 representative clinical isolates of Klebsiella pneumoniae, a widespread opportunistic pathogen. Spot tests show a narrow host range for most phages, with <2% of 6,319 phage-host combinations tested yielding detectable interactions. Bacterial capsule diversity is the main factor restricting phage host range. Consequently, phage-encoded depolymerases are key determinants of host tropism, and depolymerase sequence types are associated with the ability to infect specific capsular types across phage families. However, all phages with a broader host range found do not encode canonical depolymerases, suggesting alternative modes of entry. These findings expand our knowledge of the complex interactions between bacteria and their viruses and point out the feasibility of predicting the first steps of phage infection using bacterial and phage genome sequences.

List of contents:

1. Tables: 
   1.1 Depolymerase_DB (used to detect Dpos in phages)
   1.2 Klebsiella_phages_review (Phages from the literature with known capsular tropism)
   1.3 Phage_killing_curves (raw data of bactericidal assays performed)
   1.4. Phage_receptors (list of candidate bacterial receptors) 

2. Scripts: 
To obtain the True Positive Rate (TPR) of bacterial and phage traits to predict strain spotting and phage capsular tropism, respectively. 

3. PDB files of predicted receptor binding proteins (RBPs) of phages