cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28303301
title: <b>How STARA Technology Application Shapes Employees’ Innovative Behavior</b>

description: With the application of intelligent technology, artificial intelligence, robotics, and algorithms (STARA) in workplace settings, creative work has become increasingly important for humans. While STARA has the potential to enhance employees’ innovative behavior, there is also evidence suggesting that it may have negative impacts on employees’ mental health, thereby weakening their innovative behavior.
DOI: 10.15468/dl.7pnq9u
title: Occurrence Download

description: A dataset containing 985 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepiota brunneoincarnata Chodat & C.Martín"
 ]
}

 The dataset includes 985 records from 105 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003843-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8hpr4t
title: Occurrence Download

description: A dataset containing 47063492 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Anas Linnaeus, 1758"
 ]
}

 The dataset includes 47063492 records from 5462 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003814-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fcntvx
title: Occurrence Download

description: A dataset containing 103 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Limonium supinum (Girard) Pignatti",
 "HasCoordinate is true",
 "Continent is Europe",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 103 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022898-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yyuswg
title: Occurrence Download

description: A dataset containing 618901 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((1.8796086666666671 32.097476, 35.924964333333335 32.097476, 35.924964333333335 49.184106666666665, 1.8796086666666671 49.184106666666665, 1.8796086666666671 32.097476))",
 "EventDate is 2017-04-01,2017-04-30"
 ]
}

 The dataset includes 618901 records from 905 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022889-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kxryyd
title: Occurrence Download

description: A dataset containing 745 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 2) Benthic foraminifers at DSDP Hole 72-518"
 ]
}

 The dataset includes 745 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006229-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bwecqx
title: Occurrence Download

description: A dataset containing 29893 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hypericum gramineum G.Forst."
 ]
}

 The dataset includes 29893 records from 107 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026786-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wee4fc
title: Occurrence Download

description: A dataset listing the 5311 species recorded in GBIF matching the query:
{
 "and" : [
 "MediaType is Image",
 "TaxonKey is Cypriniformes"
 ]
}

 The dataset's 5311 records were derived from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022907-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2m1ihu
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Suaeda moschata Scott"
 ]
}

 The dataset includes 19 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006229-171002173027117/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12786372
title: Source data from Weiner et al 2024

description: This repository provides the processed data necessay to produce the figures from the Weiner, et al., Nature Communications paper entitled "Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data".

The data is organized into directories based on figure numbers of the paper. For instance, the directory source_data/fig2_S3/ contains all data pertaining to main figure 2 and supplementary figure 3. Within each directory, subdirectories are organized by figure panel, meaning that the file source_data/fig2_S3/2fg_S3g/cell_metrics.tsv only pertains to data which appears in Fig 2f, Fig 2g, and Fig S3g. 

Certain figure panels incorporate data from multiple samples. Sample ID subdirectories are used for these panels. For example, Fig S8a-c use data at the following paths source_data/fig5_S8/S8abc/{sample_id}/s_phase_bafs.csv.gz

All source code for upstream data preprocessing and downstream plotting can be found at the corresponding github repository for this manuscript: https://github.com/shahcompbio/scdna_replication_paper.In addition to source data, we are also including two additional files which contain series of sample-specific heatmaps. Below are the descriptions of each file.

Additional File 1: HMMcopy and SIGNALS heatmaps of high-quality G1/2-phase cells across all samples. Matrices of somatic copy number state called by HMMcopy (Ha, et al, 2012) (left) and allelic imbalance state called by SIGNALS (Funnell, et al, 2022) (right) for all cells in a sample. Only high-quality G1/2-phase cells are included in this analysis. The rows are sorted the same in both heatmaps to preserve mapping of cell IDs. Clone IDs for all cells are shown using the colorbar to the left of both heatmaps. Each page represents a unique sample in the metacohort of breast and ovarian cell lines and PDXs (Fig 4a). The sample ID and number of high quality G1/2-phase cells (i.e. SIGNALS cells) are shown at the top of each page. 

Additional File 2: PERT input and output matrices for gastric cancer cell lines at 500kb and 20kb resolution. Matrices of PERT input (left: reads per million and HMMcopy states) and PERT output (right: PERT somatic copy number and replication states) for the three gastric cancer cell lines sequenced with 10X Chromium single-cell DNA (Andor, et al, 2020). The top heatmaps on each page contains the cells predicted to be in S-phase by PERT and the bottom heatmaps contains the cells predicted to be in G1/2-phase by PERT. The rows are sorted the same in all four columns going from right to left to preserve mapping of cell IDs. Clone IDs for all cells are shown using the colorbar to the left of all four heatmaps. The first three pages represent PERT runs on each cell line at 500kb resolution. The final two pages represent PERT runs for two of the three cell lines at 20kb resolution. We did not run PERT at 20kb resolution for the SNU-668 cell line as there were too few S-phase cells to infer the RT profile at 20kb higher resolution.For further information please reach out to Adam Weiner (weinera2@mskcc.org)
DOI: 10.5281/zenodo.12786373
title: Source data from Weiner et al 2024

description: This repository provides the processed data necessay to produce the figures from the Weiner, et al., Nature Communications paper entitled "Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data".

The data is organized into directories based on figure numbers of the paper. For instance, the directory source_data/fig2_S3/ contains all data pertaining to main figure 2 and supplementary figure 3. Within each directory, subdirectories are organized by figure panel, meaning that the file source_data/fig2_S3/2fg_S3g/cell_metrics.tsv only pertains to data which appears in Fig 2f, Fig 2g, and Fig S3g. 

Certain figure panels incorporate data from multiple samples. Sample ID subdirectories are used for these panels. For example, Fig S8a-c use data at the following paths source_data/fig5_S8/S8abc/{sample_id}/s_phase_bafs.csv.gz

All source code for upstream data preprocessing and downstream plotting can be found at the corresponding github repository for this manuscript: https://github.com/shahcompbio/scdna_replication_paper.In addition to source data, we are also including two additional files which contain series of sample-specific heatmaps. Below are the descriptions of each file.

Additional File 1: HMMcopy and SIGNALS heatmaps of high-quality G1/2-phase cells across all samples. Matrices of somatic copy number state called by HMMcopy (Ha, et al, 2012) (left) and allelic imbalance state called by SIGNALS (Funnell, et al, 2022) (right) for all cells in a sample. Only high-quality G1/2-phase cells are included in this analysis. The rows are sorted the same in both heatmaps to preserve mapping of cell IDs. Clone IDs for all cells are shown using the colorbar to the left of both heatmaps. Each page represents a unique sample in the metacohort of breast and ovarian cell lines and PDXs (Fig 4a). The sample ID and number of high quality G1/2-phase cells (i.e. SIGNALS cells) are shown at the top of each page. 

Additional File 2: PERT input and output matrices for gastric cancer cell lines at 500kb and 20kb resolution. Matrices of PERT input (left: reads per million and HMMcopy states) and PERT output (right: PERT somatic copy number and replication states) for the three gastric cancer cell lines sequenced with 10X Chromium single-cell DNA (Andor, et al, 2020). The top heatmaps on each page contains the cells predicted to be in S-phase by PERT and the bottom heatmaps contains the cells predicted to be in G1/2-phase by PERT. The rows are sorted the same in all four columns going from right to left to preserve mapping of cell IDs. Clone IDs for all cells are shown using the colorbar to the left of all four heatmaps. The first three pages represent PERT runs on each cell line at 500kb resolution. The final two pages represent PERT runs for two of the three cell lines at 20kb resolution. We did not run PERT at 20kb resolution for the SNU-668 cell line as there were too few S-phase cells to infer the RT profile at 20kb higher resolution.For further information please reach out to Adam Weiner (weinera2@mskcc.org)
DOI: 10.6084/m9.figshare.26371779
title: Development and evaluation of a single-tube nested PCR with colorimetric assay for <i>Mycobacterium tuberculosis</i> detection

description: Molecular techniques have revolutionized tuberculosis (TB) diagnosis by offering a faster and more sensitive approach, detecting <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) DNA directly from samples. Single-tube nested PCR (STNPCR) combines two PCR reactions with separate oligonucleotide sets in a single tube. Moreover, colorimetric methods in PCR products have been studied for pathogen detection. Thus, this study aimed to establish a novel system based on colorimetric STNPCR for <i>Mtb</i> detection using microtiter plates with <i>IS6110</i>-amplified fragments. The results showed a general colorimetric STNPCR detection limit of 1 pg/μl. Its general sensitivity and specificity were 76.62 and 60.53%, respectively, with kappa index agreement of 0.166. A total of 318 biological samples (urine, plasma, peripheral blood mononuclear cells, pleural fluid and sputum) from pulmonary/extrapulmonary TB and non-TB patients were used in this study. The colorimetric STNPCR assay using <i>IS6110</i> as the target gene was developed and optimized for <i>Mtb</i> detection based on similar validated systems. Cut-off values based on receiver operator characteristic curve analysis were defined to determine the sensitivity and specificity for each sample type. The technique's performance was assessed according to kappa index calculations and interpretation. To improve rapid molecular tuberculosis (TB) diagnosis, a novel molecular test was developed and evaluated in different biological samples. This test is based on single-tube nested PCR (STNPCR) with colorimetric assay using <i>IS6110</i> as the target gene for <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) detection. A total of 318 biological samples from pulmonary/extrapulmonary TB and non-TB patients were used in this study. The colorimetric STNPCR assay used <i>IS6110</i> as the molecular target optimized for <i>Mtb</i> detection based on validated similar systems. The results showed a detection limit of 1 pg/μl according to the absorbance analysis. The colorimetric STNPCR assay general sensitivity and specificity were 76.62% and 60.53%, respectively, with kappa index agreement of 0.166. Its sensitivity and specificity for the biological samples were: plasma (55.5% and 80%), PBMC (72.3% and 54.3%), urine (61.3% and 51.5%), pleural fluid (75% and 100%) and sputum (64.7% and 66.7%). The study demonstrated a quick and straightforward test with promising results, suggesting the automated colorimetric STNPCR assay as a potential addition to laboratory routines for both pulmonary and extrapulmonary TB diagnosis.
DOI: 10.6084/m9.figshare.26371779.v1
title: Development and evaluation of a single-tube nested PCR with colorimetric assay for <i>Mycobacterium tuberculosis</i> detection

description: Molecular techniques have revolutionized tuberculosis (TB) diagnosis by offering a faster and more sensitive approach, detecting <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) DNA directly from samples. Single-tube nested PCR (STNPCR) combines two PCR reactions with separate oligonucleotide sets in a single tube. Moreover, colorimetric methods in PCR products have been studied for pathogen detection. Thus, this study aimed to establish a novel system based on colorimetric STNPCR for <i>Mtb</i> detection using microtiter plates with <i>IS6110</i>-amplified fragments. The results showed a general colorimetric STNPCR detection limit of 1 pg/μl. Its general sensitivity and specificity were 76.62 and 60.53%, respectively, with kappa index agreement of 0.166. A total of 318 biological samples (urine, plasma, peripheral blood mononuclear cells, pleural fluid and sputum) from pulmonary/extrapulmonary TB and non-TB patients were used in this study. The colorimetric STNPCR assay using <i>IS6110</i> as the target gene was developed and optimized for <i>Mtb</i> detection based on similar validated systems. Cut-off values based on receiver operator characteristic curve analysis were defined to determine the sensitivity and specificity for each sample type. The technique's performance was assessed according to kappa index calculations and interpretation. To improve rapid molecular tuberculosis (TB) diagnosis, a novel molecular test was developed and evaluated in different biological samples. This test is based on single-tube nested PCR (STNPCR) with colorimetric assay using <i>IS6110</i> as the target gene for <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) detection. A total of 318 biological samples from pulmonary/extrapulmonary TB and non-TB patients were used in this study. The colorimetric STNPCR assay used <i>IS6110</i> as the molecular target optimized for <i>Mtb</i> detection based on validated similar systems. The results showed a detection limit of 1 pg/μl according to the absorbance analysis. The colorimetric STNPCR assay general sensitivity and specificity were 76.62% and 60.53%, respectively, with kappa index agreement of 0.166. Its sensitivity and specificity for the biological samples were: plasma (55.5% and 80%), PBMC (72.3% and 54.3%), urine (61.3% and 51.5%), pleural fluid (75% and 100%) and sputum (64.7% and 66.7%). The study demonstrated a quick and straightforward test with promising results, suggesting the automated colorimetric STNPCR assay as a potential addition to laboratory routines for both pulmonary and extrapulmonary TB diagnosis.
DOI: 10.6084/m9.figshare.26371782
title: ‘Gel-Stacks’ gently confine or reversibly immobilize arrays of single DNA molecules for manipulation and study

description: Large DNA molecules (&gt;20 kb) are difficult analytes prone to breakage during serial manipulations and cannot be ‘rescued’ as full-length amplicons. Accordingly, to present, modify and analyze arrays of large, single DNA molecules, we created an easily realizable approach offering gentle confinement conditions or immobilization via spermidine condensation for controlled delivery of reagents that support live imaging by epifluorescence microscopy termed ‘Gel-Stacks.’ Molecules are locally confined between two hydrogel surfaces without covalent tethering to support time-lapse imaging and multistep workflows that accommodate large DNA molecules. With a thin polyacrylamide gel layer covalently bound to a glass surface as the base and swappable, reagent-infused, agarose slabs on top, DNA molecules are stably presented for imaging during reagent delivery by passive diffusion. Gel-Stacks technology provides multiple non-covalent molecular presentation modes, coupled with an unusually facile reagent delivery system designed for large-scale analytes, enhancing live imaging and manipulation. Enhanced further by modeling and software, Gel-Stacks technology becomes adaptable to a broad range of experimental applications.
DOI: 10.6084/m9.figshare.26371782.v1
title: ‘Gel-Stacks’ gently confine or reversibly immobilize arrays of single DNA molecules for manipulation and study

description: Large DNA molecules (&gt;20 kb) are difficult analytes prone to breakage during serial manipulations and cannot be ‘rescued’ as full-length amplicons. Accordingly, to present, modify and analyze arrays of large, single DNA molecules, we created an easily realizable approach offering gentle confinement conditions or immobilization via spermidine condensation for controlled delivery of reagents that support live imaging by epifluorescence microscopy termed ‘Gel-Stacks.’ Molecules are locally confined between two hydrogel surfaces without covalent tethering to support time-lapse imaging and multistep workflows that accommodate large DNA molecules. With a thin polyacrylamide gel layer covalently bound to a glass surface as the base and swappable, reagent-infused, agarose slabs on top, DNA molecules are stably presented for imaging during reagent delivery by passive diffusion. Gel-Stacks technology provides multiple non-covalent molecular presentation modes, coupled with an unusually facile reagent delivery system designed for large-scale analytes, enhancing live imaging and manipulation. Enhanced further by modeling and software, Gel-Stacks technology becomes adaptable to a broad range of experimental applications.
DOI: 10.6084/m9.figshare.26068318
title: Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples

description: Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results. We studied a set of methods used to generate ancient genome data from archaeological human samples from different sites and periods, and with varying levels of preservation. In these experiments we compared two sample preparation techniques, two silica-based DNA extraction protocols, and two aDNA library preparation protocols. Finally, we explored the efficiency of whole-genome capture (WGC) on aDNA libraries with different characteristics by comparing a set of protocol modifications.
DOI: 10.6084/m9.figshare.26068318.v1
title: Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples

description: Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results. We studied a set of methods used to generate ancient genome data from archaeological human samples from different sites and periods, and with varying levels of preservation. In these experiments we compared two sample preparation techniques, two silica-based DNA extraction protocols, and two aDNA library preparation protocols. Finally, we explored the efficiency of whole-genome capture (WGC) on aDNA libraries with different characteristics by comparing a set of protocol modifications.