cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20155597.v1
title: Additional file 1 of Characterization of antibiotic resistance genes in drinking water sources of the Douhe Reservoir, Tangshan, northern China: the correlation with bacterial communities and environmental factors

description: Additional file 1: Table S1. GPS location of sampling locations. Table S2. Water quality of the selected samples. Table S3. Sediment quality of the selected samples. Table S4. Primer sets used in this study. MLSB (Macrolide–Lincosamide–Streptogramin B), MGEs (mobile genetic elements) and FCA (fluoroquinolone, quinolone, florfenicol, chloramphenicol, and amphenicol). Table S5. Relative mean abundance of each ARG and MGE subtypes in sample (copies/16S rRNA gene). Table S6. Average number of detected ARGs and MGEs of the each sample. Table S7. Diversity indices of bacterial communities in each sample. Table S8. Bacterial phyla percent in each water samples. Bacterial genus percent in each water samples. Bacterial phyla percent in each sediment samples. Bacterial genus percent in each sediment samples. Figure S1. Relative abundance of different bacterial phyla in water and sediment samples.
DOI: 10.6084/m9.figshare.20155597
title: Additional file 1 of Characterization of antibiotic resistance genes in drinking water sources of the Douhe Reservoir, Tangshan, northern China: the correlation with bacterial communities and environmental factors

description: Additional file 1: Table S1. GPS location of sampling locations. Table S2. Water quality of the selected samples. Table S3. Sediment quality of the selected samples. Table S4. Primer sets used in this study. MLSB (Macrolide–Lincosamide–Streptogramin B), MGEs (mobile genetic elements) and FCA (fluoroquinolone, quinolone, florfenicol, chloramphenicol, and amphenicol). Table S5. Relative mean abundance of each ARG and MGE subtypes in sample (copies/16S rRNA gene). Table S6. Average number of detected ARGs and MGEs of the each sample. Table S7. Diversity indices of bacterial communities in each sample. Table S8. Bacterial phyla percent in each water samples. Bacterial genus percent in each water samples. Bacterial phyla percent in each sediment samples. Bacterial genus percent in each sediment samples. Figure S1. Relative abundance of different bacterial phyla in water and sediment samples.
DOI: 10.34740/kaggle/ds/4442626
title: Colombo Cafes 🍵: Ratings & Insights Dataset
DOI: 10.6084/m9.figshare.12291407.v1
title: Additional file 2 of Evolution of Fusarium tricinctum and Fusarium avenaceum mitochondrial genomes is driven by mobility of introns and of a new type of palindromic microsatellite repeats

description: Additional file 2: GenBank formatted annotated sequence of the F. avenaceum strain FaLH27 MtDNA.
DOI: 10.6084/m9.figshare.20166897
title: Additional file 6 of Development and usability testing of tools to facilitate incorporating intersectionality in knowledge translation

description: Additional file 6: Supplementary Table 1. Summary of intersectionality and knowledge translation toolkit.
DOI: 10.6084/m9.figshare.20166897.v1
title: Additional file 6 of Development and usability testing of tools to facilitate incorporating intersectionality in knowledge translation

description: Additional file 6: Supplementary Table 1. Summary of intersectionality and knowledge translation toolkit.
DOI: 10.7924/r4js9v06m
title: Data from: Calcium image analysis in the moving gut (CIAMG)

description: The neural control of gastrointestinal muscle relies on circuit activity whose underlying motifs remain limited by small-sample calcium imaging recordings confounded by motion artifact, paralytics, and muscle dissections. We present a sequence of resources to register images from moving preparations and identify out-of-focus events in widefield fluorescent microscopy. Our algorithm uses piecewise rigid registration with pathfinding to correct movements associated with smooth muscle contractions. We developed methods to identify loss-of-focus events and to simulate calcium activity to evaluate registration. In proof-of-concept principal component analysis, we found populations of neurons exhibit distinct activity patterns in response to distinct stimuli, insight that was not possible without the image analysis pipeline. We provide access to the source code for our algorithms and make experimental and technical recommendations to increase data quality in calcium imaging experiments. This work makes feasible large-population, robust calcium imaging recordings and permits more sophisticated network analyses and insights into neural activity patterns in the gut.
DOI: 10.3886/e194188
title: Code for The Comparative Statics of Sorting

description: Mathematica files used to solve for the support of the optimal matching in the numeric examples presented in The Comparative Statics of Sorting in Figures 4 and 8-12. This paper does not involve analysis of external data.
DOI: 10.3886/e194188v1
title: Code for The Comparative Statics of Sorting

description: Mathematica files used to solve for the support of the optimal matching in the numeric examples presented in The Comparative Statics of Sorting in Figures 4 and 8-12. This paper does not involve analysis of external data.
DOI: 10.6084/m9.figshare.20166993.v1
title: Additional file 1 of VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features

description: Additional file 1: Supplementary Table 1. The 82 genomes built in to VisProDom.
DOI: 10.6084/m9.figshare.20166993
title: Additional file 1 of VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features

description: Additional file 1: Supplementary Table 1. The 82 genomes built in to VisProDom.
DOI: 10.6073/pasta/ffaaee4fd4c8c7cfc93dda2fd06211bf
title: Soil moisture and snowdepth measurements in the Black Sand experiment for East Knoll, Audubon, Lefty, Soddie and Trough, 2018 - 2023.

description: The purpose of the Black Sand experiment is to measure treatment
 effects on date of snowmelt on Niwot Ridge. Five sites with paired
 plots (treatment and control) were implemented across Niwot as part
 of the extended summer research program in order to understand the
 effects of earlier snowmelt. This dataset contains measurements of
 snowdepth throughout the melt season, manual measurements of
 volumetric water content and temperature data as an indication of
 snowmelt timing.
DOI: 10.6084/m9.figshare.20166951.v1
title: Additional file 5 of Multiple epigenetic factors co-localize with HMGN proteins in A-compartment chromatin

description: Additional file 5: Table S3. Proteins—HMGN1 and HMGN2 partners in top GO categories.
DOI: 10.6084/m9.figshare.7584152
title: Supplementary Material-Genotype data of the indel loci from Goat <i>PDGFRB</i>: unique mRNA expression profile in gonad and significant association between genetic variation and litter size.

description: It includes all the genotype data of the indel loci
DOI: 10.6084/m9.figshare.7584152.v2
title: Supplementary Material-Genotype data of the indel loci from Goat <i>PDGFRB</i>: unique mRNA expression profile in gonad and significant association between genetic variation and litter size.

description: It includes all the genotype data of the indel loci
DOI: 10.6084/m9.figshare.7584152.v1
title: Supplementary Material-Genotype data of the indel loci from Goat <i>PDGFRB</i>: unique mRNA expression profile in gonad and significant association between genetic variation and litter size

description: It includes all the genotype data of the indel loci
DOI: 10.6084/m9.figshare.12291347.v1
title: Additional file 1 of Provenance of terrigenous sediments in the central Bay of Bengal and its relationship to climate changes since 25 ka

description: Additional file 1..
DOI: 10.6084/m9.figshare.19642735
title: Additional file 3 of SARS-COV-2 as potential microRNA sponge in COVID-19 patients

description: Additional file 3. 885 genes significantly enriched by targeting VTMs.
DOI: 10.6084/m9.figshare.19642729
title: Additional file 1 of SARS-COV-2 as potential microRNA sponge in COVID-19 patients

description: Additional file 1. 26 miRNA families enriched in VTMs.
DOI: 10.6084/m9.figshare.19642735.v1
title: Additional file 3 of SARS-COV-2 as potential microRNA sponge in COVID-19 patients

description: Additional file 3. 885 genes significantly enriched by targeting VTMs.
DOI: 10.6084/m9.figshare.19642738
title: Additional file 4 of SARS-COV-2 as potential microRNA sponge in COVID-19 patients

description: Additional file 4: miRWalk pathways identified using candidate VTMs.
DOI: 10.6084/m9.figshare.19642732.v1
title: Additional file 2 of SARS-COV-2 as potential microRNA sponge in COVID-19 patients

description: Additional file 2. 218 candidate VTM-gene pairs.
DOI: 10.6084/m9.figshare.19642741.v1
title: Additional file 5 of SARS-COV-2 as potential microRNA sponge in COVID-19 patients

description: Additional file 5: VTM-gene pairs by cell type identified from single-cell RNA-seq based analyses.
DOI: 10.6084/m9.figshare.19642738.v1
title: Additional file 4 of SARS-COV-2 as potential microRNA sponge in COVID-19 patients

description: Additional file 4: miRWalk pathways identified using candidate VTMs.
DOI: 10.6084/m9.figshare.19642741
title: Additional file 5 of SARS-COV-2 as potential microRNA sponge in COVID-19 patients

description: Additional file 5: VTM-gene pairs by cell type identified from single-cell RNA-seq based analyses.
DOI: 10.6084/m9.figshare.19642732
title: Additional file 2 of SARS-COV-2 as potential microRNA sponge in COVID-19 patients

description: Additional file 2. 218 candidate VTM-gene pairs.
DOI: 10.6084/m9.figshare.7584347
title: Differential alternative splicing events in Mecp2-null mice.

description: DAS events identified in Mecp2-null mice for RTT mouse model. Column descriptions are added in the second sheet.
DOI: 10.6084/m9.figshare.7584353.v1
title: Identification of the candidate splicing factors for regulating gene expression changes in Mecp2-null mice.

description: Identified key SFs for regulating gene expression changes in Mecp2-null mice. The column description has been added in the second sheet.
DOI: 10.6084/m9.figshare.7584347.v1
title: Differential alternative splicing events in Mecp2-null mice.

description: DAS events identified in Mecp2-null mice for RTT mouse model. Column descriptions are added in the second sheet.
DOI: 10.6084/m9.figshare.7584353
title: Identification of the candidate splicing factors for regulating gene expression changes in Mecp2-null mice.

description: Identified key SFs for regulating gene expression changes in Mecp2-null mice. The column description has been added in the second sheet.
DOI: 10.6084/m9.figshare.7584356
title: Identification of the candidate splicing factors for regulating splicing changes in CIT.

description: Identified key SFs for regulating splicing changes in CIT. The column description is same as Table S2.
DOI: 10.6084/m9.figshare.7584350.v1
title: Identification of the candidate splicing factors for regulating splicing changes in Mecp2-null mice.

description: Identified key SFs for regulating splicing changes in Mecp2-null mice. The column description has been added in the second sheet.
DOI: 10.6084/m9.figshare.7584362
title: Differentially expressed genes in Mecp2-null mice.

description: DEGs identified in Mecp2-null mice for RTT mouse model.
DOI: 10.6084/m9.figshare.7584356.v1
title: Identification of the candidate splicing factors for regulating splicing changes in CIT.

description: Identified key SFs for regulating splicing changes in CIT. The column description is same as Table S2.
DOI: 10.6084/m9.figshare.7584359
title: Identification of the candidate splicing factors for regulating gene expression changes in CIT.

description: Identified key SFs for regulating gene expression changes in CIT. The column description is same as Table S4.
DOI: 10.17894/ucph.67df682d-9688-4b3e-8ec7-6b64bc6854f5
title: Identification of antibiotic induced persister cells in Streptococcus agalactiae
DOI: 10.6084/m9.figshare.7584371
title: GEO datasets for MSFs identified in signature comparison analyses of CIT and RTT.

description: GEO datasets for MSFs identified in signature comparison analyses of CIT and RTT.
DOI: 10.6084/m9.figshare.7584368.v1
title: Differentially expressed genes in CIT.

description: DEGs identified in CIT.
DOI: 10.6084/m9.figshare.12291347
title: Additional file 1 of Provenance of terrigenous sediments in the central Bay of Bengal and its relationship to climate changes since 25 ka

description: Additional file 1..
DOI: 10.6084/m9.figshare.7584350
title: Identification of the candidate splicing factors for regulating splicing changes in Mecp2-null mice.

description: Identified key SFs for regulating splicing changes in Mecp2-null mice. The column description has been added in the second sheet.
DOI: 10.6084/m9.figshare.7584362.v1
title: Differentially expressed genes in Mecp2-null mice.

description: DEGs identified in Mecp2-null mice for RTT mouse model.
DOI: 10.6084/m9.figshare.7584368
title: Differentially expressed genes in CIT.

description: DEGs identified in CIT.
DOI: 10.6084/m9.figshare.7584371.v1
title: GEO datasets for MSFs identified in signature comparison analyses of CIT and RTT.

description: GEO datasets for MSFs identified in signature comparison analyses of CIT and RTT.
DOI: 10.6084/m9.figshare.7584359.v1
title: Identification of the candidate splicing factors for regulating gene expression changes in CIT.

description: Identified key SFs for regulating gene expression changes in CIT. The column description is same as Table S4.
DOI: 10.6084/m9.figshare.7584365
title: Differential alternative splicing events in cold exposed BAT and sWAT.

description: DAS events identified in cold exposed BAT and sWAT. The column description is same as the Table S1.
DOI: 10.6084/m9.figshare.7584365.v1
title: Differential alternative splicing events in cold exposed BAT and sWAT.

description: DAS events identified in cold exposed BAT and sWAT. The column description is same as the Table S1.
DOI: 10.6084/m9.figshare.21215884.v2
title: A Mass-Shifting Phenomenon of Truncated Multivariate Normal Priors

description: We show that lower-dimensional marginal densities of dependent zero-mean normal distributions truncated to the positive orthant exhibit a <i>mass-shifting</i> phenomenon. Despite the truncated multivariate normal density having a mode at the origin, the marginal density assigns increasingly small mass near the origin as the dimension increases. The phenomenon accentuates with stronger correlation between the random variables. This surprising behavior has serious implications toward Bayesian constrained estimation and inference, where the prior, in addition to having a full support, is required to assign a substantial probability near the origin to capture flat parts of the true function of interest. A precise quantification of the mass-shifting phenomenon for both the prior and the posterior, characterizing the role of the dimension as well as the dependence, is provided under a variety of correlation structures. Without further modification, we show that truncated normal priors are not suitable for modeling flat regions and propose a novel alternative strategy based on shrinking the coordinates using a multiplicative scale parameter. The proposed shrinkage prior is shown to achieve optimal posterior contraction around true functions with potentially flat regions. Synthetic and real data studies demonstrate how the modification guards against the mass shifting phenomenon while retaining computational efficiency. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12827453.v2
title: Supplementary Tables 1-8 from Multi-omic detection of <i>Mycobacterium leprae</i> in archaeological human dental calculus

description: Mineralized dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. Here, we present a <i>Mycobacterium leprae</i> genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing of sixteenth-century human dental calculus from an individual from Trondheim, Norway. When phylogenetically placed, this genome falls in branch 3I among the diversity of other contemporary ancient strains from Northern Europe. Moreover, ancient mycobacterial peptides were retrieved via mass spectrometry-based proteomics, further validating the presence of the pathogen. <i>Mycobacterium leprae</i> can readily be detected in the oral cavity and associated mucosal membranes, which likely contributed to it being incorporated into this individual's dental calculus. This individual showed some possible, but not definitive, evidence of skeletal lesions associated with early-stage leprosy. This study is the first known example of successful multi-omics retrieval of <i>M. leprae</i> from archaeological dental calculus. Furthermore, we offer new insights into dental calculus as an alternative sample source to bones or teeth for detecting and molecularly characterizing <i>M. leprae</i> in individuals from the archaeological record.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
DOI: 10.6084/m9.figshare.25215956
title: Knoxville TN Georeferenced 1917 Sanborn Maps

description: This is a dataset of georeferenced 1917 Sanborn Fire Insurance maps of Knoxville TN, including individual sheets, a sheet index, a seamless mosaic, and a map key. Digital images of the data sheets were downloaded from the University of Tennessee Library https://digital.lib.utk.edu/collections/sanbornmapcollection. Multi-part sheets were clipped into pieces for georeferencing. Chris DeRolph georeferenced each sheet and piece, where possible. There were a few outlying images that were unable to be georeferenced due to lack of recognizable common features between the sheets and reference maps/imagery in the sheet vicinity. The sheet index shapefile includes a field with a hyperlink to the UTK library download page for the sheet. The seamless mosaic was created using the Mosaic to New Raster tool in ArcGIS Pro with all georeferenced sheets/pieces as inputs and the Minimum Mosaic Operator. No attempt was made prior to the mosaicking process to remove sheet numbers, scale bars, north arrows, overlapping labels/annotation, etc. Viewing individual sheets will provide the cleanest look at an area, while the seamless mosaic provides the most comprehensive view of the city at the time the maps were created.
DOI: 10.6084/m9.figshare.25215956.v1
title: Knoxville TN Georeferenced 1917 Sanborn Maps

description: This is a dataset of georeferenced 1917 Sanborn Fire Insurance maps of Knoxville TN, including individual sheets, a sheet index, and a seamless mosaic. Digital images of the data sheets were downloaded from the University of Tennessee Library https://digital.lib.utk.edu/collections/sanbornmapcollection. Multi-part sheets were clipped into pieces for georeferencing. Chris DeRolph georeferenced each sheet and piece, where possible. There were a few outlying images that were unable to be georeferenced due to lack of recognizable common features between the sheets and reference maps/imagery in the sheet vicinity. The sheet index shapefile includes a field with a hyperlink to the UTK library download page for the sheet. The seamless mosaic was created using the Mosaic to New Raster tool in ArcGIS Pro with all georeferenced sheets/pieces as inputs and the Minimum Mosaic Operator. No attempt was made prior to the mosaicking process to remove sheet numbers, scale bars, north arrows, overlapping labels/annotation, etc. Viewing individual sheets will provide the cleanest look at an area, while the seamless mosaic provides the most comprehensive view of the city at the time the maps were created.
DOI: 10.5281/zenodo.10656919
title: Close-Space Sublimation as a Scalable Method for Perovskite Solar Cells
DOI: 10.5281/zenodo.10656920
title: Close-Space Sublimation as a Scalable Method for Perovskite Solar Cells
DOI: 10.6084/m9.figshare.21215884
title: A Mass-Shifting Phenomenon of Truncated Multivariate Normal Priors

description: We show that lower-dimensional marginal densities of dependent zero-mean normal distributions truncated to the positive orthant exhibit a <i>mass-shifting</i> phenomenon. Despite the truncated multivariate normal density having a mode at the origin, the marginal density assigns increasingly small mass near the origin as the dimension increases. The phenomenon accentuates with stronger correlation between the random variables. This surprising behavior has serious implications toward Bayesian constrained estimation and inference, where the prior, in addition to having a full support, is required to assign a substantial probability near the origin to capture flat parts of the true function of interest. A precise quantification of the mass-shifting phenomenon for both the prior and the posterior, characterizing the role of the dimension as well as the dependence, is provided under a variety of correlation structures. Without further modification, we show that truncated normal priors are not suitable for modeling flat regions and propose a novel alternative strategy based on shrinking the coordinates using a multiplicative scale parameter. The proposed shrinkage prior is shown to achieve optimal posterior contraction around true functions with potentially flat regions. Synthetic and real data studies demonstrate how the modification guards against the mass shifting phenomenon while retaining computational efficiency. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.21215884.v1
title: A mass-shifting phenomenon of truncated multivariate normal priors

description: We show that lower-dimensional marginal densities of dependent zero-mean normal distributions truncated to the positive orthant exhibit a <i>mass-shifting</i> phenomenon. Despite the truncated multivariate normal density having a mode at the origin, the marginal density assigns increasingly small mass near the origin as the dimension increases. The phenomenon accentuates with stronger correlation between the random variables. This surprising behavior has serious implications towards Bayesian constrained estimation and inference, where the prior, in addition to having a full support, is required to assign a substantial probability near the origin to capture flat parts of the true function of interest. A precise quantification of the mass-shifting phenomenon for both the prior and the posterior, characterizing the role of the dimension as well as the dependence, is provided under a variety of correlation structures. Without further modification, we show that truncated normal priors are not suitable for modeling flat regions and propose a novel alternative strategy based on shrinking the coordinates using a multiplicative scale parameter. The proposed shrinkage prior is shown to achieve optimal posterior contraction around true functions with potentially flat regions. Synthetic and real data studies demonstrate how the modification guards against the mass shifting phenomenon while retaining computational efficiency.
DOI: 10.6084/m9.figshare.22788794
title: Clone of: TF-C Pretrain ECG

description: Original data: https://figshare.com/articles/dataset/TF-C_Pretrain_ECG/19930253