cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5103856.v1
title: Supplementary Material for: Prediction of Time to Castration-Resistant Prostate Cancer Using Bone Scan Index in Men with Metastatic Hormone-Sensitive Prostate Cancer

description: <b><i>Introduction:</i></b> We evaluated bone scan index (BSI) as a predictive biomarker for time to castration-resistant prostate cancer (CRPC) in patients with metastatic hormone-sensitive prostate cancer (mHSPC). <b><i>Materials and Methods:</i></b> We identified 85 consecutive mHSPC patients treated with first-line androgen deprivation therapy. We analyzed the correlations between time to CRPC and clinicopathological characteristics, including age, prostate-specific antigen (PSA) level, Gleason score, clinical TNM stage, hemoglobin, lactate dehydrogenase, C-reactive protein, and BSI. <b><i>Results:</i></b> The median BSI was 2.7%. Progression to CRPC occurred in 55 (64.7%) patients and the median time to CRPC was 12.9 months. In multivariate analysis, 3 significant risk factors for time to CRPC were identified: age (&gt;73 vs. ≤73 years; hazard ratio [HR] 0.53), <i>p</i> = 0.038, PSA level (&gt;270 vs. ≤270 ng/mL; HR 0.53, <i>p</i> = 0.038), and BSI (&gt;2.7 vs. ≤2.7%; HR 2.97, <i>p</i> &lt; 0.001). <b><i>Conclusion:</i></b> Age, PSA level, and BSI were found to be significant predictive factors for time to CRPC in patients with mHSPC.
DOI: 10.6084/m9.figshare.5103796
title: Groundwater recharge in Africa data and code

description: Data and code to support the paper:<br>Cuthbert et al. (2019). Observed controls on resilience of groundwater to climate variability in sub-Saharan Africa.Nature 572, 230-234.<br>https://www.nature.com/articles/s41586-019-1441-7<br>https://doi.org/10.1038/s41586-019-1441-7<br>
DOI: 10.6084/m9.figshare.5103838
title: Sugarcane Illumina RNA-Seq de novo assembled transcriptome

description: <b>Sugarcane transcriptome assembled from Illumina RNA-Seq data. Predicted by Portrait and Evidential Gene.</b>
DOI: 10.6084/m9.figshare.5103838.v1
title: Sugarcane Illumina RNA-Seq de novo assembled transcriptome

description: <b>Sugarcane transcriptome assembled from Illumina RNA-Seq data. Predicted by Portrait and Evidential Gene.</b>
DOI: 10.6084/m9.figshare.5103793
title: File 5 Gene family annotation of 3K RG

description: This file includes gene family annotations of 3k RG pan-genome genes. Each line in the file represents one gene family with the gene family id followed by a ":" and then followed by all gene members of this gene family seperated by space. <br>
DOI: 10.6084/m9.figshare.5103796.v1
title: Groundwater recharge in Africa data and code

description: Data and code to support the paper:<br>Cuthbert et al. (2019). Observed controls on resilience of groundwater to climate variability in sub-Saharan Africa. Nature.
DOI: 10.6084/m9.figshare.5103793.v1
title: Gene family annotation of 3K RG

description: This file includes gene family annotations of 3k RG pan-genome genes. Each line in the file represents one gene family with the gene family id followed by a ":" and then followed by all gene members of this gene family seperated by space. <br>
DOI: 10.6084/m9.figshare.5103778
title: File 2 The an-genome sequences of O.sativa

description: This file includes the pan-genome sequences of rice as a key output of 3k RG. The pan-genome is built by combining IRGSP-1.0 genome and non-redundant novel sequences from de novo assemblies of 3,010 rice genomes. The novel sequences were combined to artifitial chromosomes by connecting sequences with 100 consecutive Ns. This file is also available in the rice pan-genome database (RPAN, http://cgm.sjtu.edu.cn/3kricedb/).<br>
DOI: 10.6084/m9.figshare.5103787
title: File 3 Protein-coding gene annotation of the pan-genome sequences

description: This is the protein-coding gene annotation of the 3k RG pan-genome sequences.
DOI: 10.6084/m9.figshare.5103790.v2
title: Presence/Absence matrix of structural variation matrix

description: Presence/Absence (1/0) matrix of SVs (deletion, duplication, inversion and translocation) in 453 rice accessions. In the matrix, '1' represents that SV is present in the accession, while '0' means absent. Before creating the matrix, SV were detected in 3,010 rice accession using NovoBreak. SVs passed the filter cretia were remained to make the presence/absence (1/0) matrix for 453 high depth sequenced rice accessions.
DOI: 10.6084/m9.figshare.5103790.v1
title: Presence/Absence matrix of structural variation matrix

description: Presence/Absence (1/0) matrix of SVs (deletion, duplication, inversion and translocation) in 453 rice accessions. In the matrix, '1' represents that SV is present in the accession, while '0' means absent. Before creating the matrix, SV were detected in 3,010 rice accession using NovoBreak. SVs passed the filter cretia were remained to make the presence/absence (1/0) matrix for 453 high depth sequenced rice accessions.
DOI: 10.6084/m9.figshare.5103769
title: File 4 Gene presence/absence variations of 453 rice accessions

description: This file includes gene presence/absence variations of 453 rice accessions as a key output of 3k RG. The first column represents the gene ids and the next 453 columns represent the 453 rice accessions. The file contains a binary (0/1) matrix, where 1 means presence of a gene while 0 means absence of a gene. <br>
DOI: 10.6084/m9.figshare.5103787.v1
title: Protein-coding gene annotation

description: This is the protein-coding gene annotation of the 3k RG pan-genome sequences.
DOI: 10.6084/m9.figshare.5103751
title: File 6 Gene family presence/absence variations of 453 rice accessions

description: This file includes gene family presence/absence variations of 453 rice accessions as a key output of 3k RG. The first column represents the gene family ids and the next 453 columns represent the 453 rice accessions. The file contains a binary (0/1) matrix, where 1 means presence of a gene family while 0 means absence of a gene family. <br>
DOI: 10.6084/m9.figshare.5103778.v1
title: Pan-genome sequences of 3k RG

description: This file includes the pan-genome sequences of rice as a key output of 3k RG. The pan-genome is built by combining IRGSP-1.0 genome and non-redundant novel sequences from de novo assemblies of 3,010 rice genomes. The novel sequences were combined to artifitial chromosomes by connecting sequences with 100 consecutive Ns. This file is also available in the rice pan-genome database (RPAN, http://cgm.sjtu.edu.cn/3kricedb/).<br>
DOI: 10.6084/m9.figshare.5103787.v2
title: Protein-coding gene annotation

description: This is the protein-coding gene annotation of the 3k RG pan-genome sequences.
DOI: 10.6084/m9.figshare.5103769.v1
title: Gene presence/absence variations of 453 rice accessions

description: This file includes gene presence/absence variations of 453 rice accessions as a key output of 3k RG. The first column represents the gene ids and the next 453 columns represent the 453 rice accessions. The file contains a binary (0/1) matrix, where 1 means presence of a gene while 0 means absence of a gene. <br>
DOI: 10.6084/m9.figshare.5103751.v1
title: Gene family presence/absence variations of 453 rice accessions

description: This file includes gene family presence/absence variations of 453 rice accessions as a key output of 3k RG. The first column represents the gene family ids and the next 453 columns represent the 453 rice accessions. The file contains a binary (0/1) matrix, where 1 means presence of a gene family while 0 means absence of a gene family. <br>
DOI: 10.6084/m9.figshare.5103778.v2
title: Pan-genome sequences of 3k RG

description: This file includes the pan-genome sequences of rice as a key output of 3k RG. The pan-genome is built by combining IRGSP-1.0 genome and non-redundant novel sequences from de novo assemblies of 3,010 rice genomes. The novel sequences were combined to artifitial chromosomes by connecting sequences with 100 consecutive Ns. This file is also available in the rice pan-genome database (RPAN, http://cgm.sjtu.edu.cn/3kricedb/).<br>
DOI: 10.6084/m9.figshare.5103751.v2
title: Gene family presence/absence variations of 453 rice accessions

description: This file includes gene family presence/absence variations of 453 rice accessions as a key output of 3k RG. The first column represents the gene family ids and the next 453 columns represent the 453 rice accessions. The file contains a binary (0/1) matrix, where 1 means presence of a gene family while 0 means absence of a gene family. <br>
DOI: 10.6084/m9.figshare.5103769.v2
title: Gene presence/absence variations of 453 rice accessions

description: This file includes gene presence/absence variations of 453 rice accessions as a key output of 3k RG. The first column represents the gene ids and the next 453 columns represent the 453 rice accessions. The file contains a binary (0/1) matrix, where 1 means presence of a gene while 0 means absence of a gene. <br>
DOI: 10.6084/m9.figshare.5103696
title: Supplementary Material for: Associations of Polyethylenimine-Coated AN69ST Membrane in Continuous Renal Replacement Therapy with the Intensive Care Outcomes: Observations from a Claims Database from Japan

description: <i>Background/Aims:</i> Polyethylenimine-coated polyacrylonitrile (AN69ST) membrane is expected to improve the outcomes of critically ill patients treated by continuous renal replacement therapy (CRRT). <i>Methods:</i> Using a Japanese health insurance claim database, we identified adult patients receiving CRRT in intensive care units (ICUs) from April 2014 to October 2015. We used a multivariable logistic regression model to assess in-hospital mortality and Fine and Gray's proportional subhazards model to assess the ICU length of stay (ICU-LOS) accounting for the competing risks. <i>Results:</i> Of 2,469 ICU patients, 156 were treated by AN69ST membrane. Crude in-hospital mortality was 50.0% in the AN69ST group and 54.0% in the non-AN69ST group. Adjusted odds ratio (OR) of AN69ST membrane use for in-hospital mortality was 0.65 (95% CI 0.45-0.93). The use of AN69ST membrane was also independently associated with shorter ICU-LOS. <i>Conclusion:</i> This retrospective observational study suggested that CRRT with AN69ST membrane might be associated with better in-hospital outcomes.
DOI: 10.6084/m9.figshare.5103696.v1
title: Supplementary Material for: Associations of Polyethylenimine-Coated AN69ST Membrane in Continuous Renal Replacement Therapy with the Intensive Care Outcomes: Observations from a Claims Database from Japan

description: <i>Background/Aims:</i> Polyethylenimine-coated polyacrylonitrile (AN69ST) membrane is expected to improve the outcomes of critically ill patients treated by continuous renal replacement therapy (CRRT). <i>Methods:</i> Using a Japanese health insurance claim database, we identified adult patients receiving CRRT in intensive care units (ICUs) from April 2014 to October 2015. We used a multivariable logistic regression model to assess in-hospital mortality and Fine and Gray's proportional subhazards model to assess the ICU length of stay (ICU-LOS) accounting for the competing risks. <i>Results:</i> Of 2,469 ICU patients, 156 were treated by AN69ST membrane. Crude in-hospital mortality was 50.0% in the AN69ST group and 54.0% in the non-AN69ST group. Adjusted odds ratio (OR) of AN69ST membrane use for in-hospital mortality was 0.65 (95% CI 0.45-0.93). The use of AN69ST membrane was also independently associated with shorter ICU-LOS. <i>Conclusion:</i> This retrospective observational study suggested that CRRT with AN69ST membrane might be associated with better in-hospital outcomes.
DOI: 10.6084/m9.figshare.5103280
title: Fig5d_6f_05162016

description: Metabolomic analysis of Lactate on HFSCs isolated from UK-5099 and RCGD423 treated skin for 48 hours
DOI: 10.6084/m9.figshare.5103277
title: Fig5d_6f_07082016

description: Metabolomic analysis of Lactate on HFSCs isolated from UK-5099 and RCGD423 treated skin for 48 hours.
DOI: 10.6084/m9.figshare.5103280.v1
title: Fig5d_6f_05162016

description: Metabolomic analysis of Lactate on HFSCs isolated from UK-5099 and RCGD423 treated skin for 48 hours
DOI: 10.6084/m9.figshare.5103271
title: Fig3e_09252015

description: Relative levels of glycolytic and TCA cycle metabolites extracted from <i>Ldha<sup>+/+</sup> </i>HFSCs and<i> Ldha</i><i><sup>fl/fl</sup> </i>HFSCs and measured by LC-MS.
DOI: 10.6084/m9.figshare.5103274
title: Fig3i_02132017-Exp-2

description: LC-MS analysis of metabolites from <i>Lgr5CreER;Ldha<sup>fl/fl</sup></i><b> </b> mice. Data shown were generated from n=3 animals per condition pooled from 3 independent experiments.
DOI: 10.6084/m9.figshare.5103274.v1
title: Fig3i_02132017-Exp-2

description: LC-MS analysis of metabolites from <i>Lgr5CreER;Ldha<sup>fl/fl</sup></i><b> </b> mice. Data shown were generated from n=3 animals per condition pooled from 3 independent experiments.
DOI: 10.6084/m9.figshare.5103268
title: Fig2e_02132017-Exp1

description: Relative levels of glycolytic and TCA cycle metabolites extracted from quiescent (Telogen, day 50), activated (Telogen-Anagen, day 70) and HFSCs that have returned to the quiescent state (Anagen, day 90). Data shown were generated from n=3 animals per timepoint in 3 independent experiments.
DOI: 10.6084/m9.figshare.5103271.v1
title: Fig3e_09252015

description: Relative levels of glycolytic and TCA cycle metabolites extracted from <i>Ldha<sup>+/+</sup> </i>HFSCs and<i> Ldha</i><i><sup>fl/fl</sup> </i>HFSCs and measured by LC-MS.
DOI: 10.6084/m9.figshare.5103256
title: Fig1e_10122014

description: HFSCs and epidermal cells were isolated during telogen (day 50) by FACS, and metabolites were extracted and analyzed by LC-MS.
DOI: 10.6084/m9.figshare.5103259
title: Fig1e_12042014

description: HFSCs and epidermal cells were isolated during telogen (day 50) by FACS, and metabolites were extracted and analyzed by LC-MS.
DOI: 10.6084/m9.figshare.5103262
title: Fig1e_12292014

description: HFSCs and epidermal cells were isolated during telogen (day 50) by FACS, and metabolites were extracted and analyzed by LC-MS.
DOI: 10.6084/m9.figshare.5103268.v1
title: Fig2e_02132017-Exp1

description: Relative levels of glycolytic and TCA cycle metabolites extracted from quiescent (Telogen, day 50), activated (Telogen-Anagen, day 70) and HFSCs that have returned to the quiescent state (Anagen, day 90). Data shown were generated from n=3 animals per timepoint in 3 independent experiments.
DOI: 10.6084/m9.figshare.5103259.v1
title: Fig1e_12042014

description: HFSCs and epidermal cells were isolated during telogen (day 50) by FACS, and metabolites were extracted and analyzed by LC-MS.
DOI: 10.6084/m9.figshare.5103139
title: Patterns in invasiveness of the colonial ascidian <i>Didemnum vexillum</i> (Kott 2002)

description: Temporal patterns of biofouling establishment and persistence were investigated at two field sites (Nelson, hereafter NN; Ruakaka Bay, hereafter RK) over a 19-month period between 19 December 2007 and 29 July 2009 (Fletcher et al. data.csv). The RK study site was situated within a fish farm located in New Zealand’s Marlborough Sounds region (41°12'40.2"S, 174°08'26.1"E), whereas the NN site was situated approximately 60 km west (41°15'23.7"S 173°16'33.7"E) within a commercial port at Nelson. The RK site was in relatively deep water (c. 30 m depth), while the NN site was shallower (c. 5 m depth) with a large (c. 4 m) tidal exchange.<br>Arrays of roughened black Perspex settlement plates (20 x 20 cm; n = 3 plates per array) were deployed from floating structures at each site (steel fish farm pontoons at RK and plastic marina pontoons at NN), with arrays spaced approximately 5 m apart. The settlement plates were positioned horizontally within each array, and configured to ensure they remained at a constant depth (0.5 - 1.5 m) with respect to the water surface. Sampling involved taking photographs of the downward-facing surface of each plate, reflecting the orientation where maximum D. vexillum recruitment occurs [32]. Plate photos were analysed using the random dot method in Coral Point Count software (CPCe v4.1), with 50 stratified random points overlaid on each image. Based on the frequency of occurrence of D. vexillum, other major taxa, bare space, or sediment at each point, percent cover was calculated. A margin of 1 cm around each experimental plate was excluded from analyses to avoid edge effects.<br>In a second concurrent study (Fletcher et al. data2.csv), we investigated the establishment and persistence of D. vexillum following exposure of settlement plates to ambient larval recruitment, compared with plates also exposed to larval recruitment, but to which a fragment of colony tissue was also attached. The treatments consisted of 10 blank settlement plates (‘Recruitment’ treatment) and 10 blank plates to which a D. vexillum fragment was attached to the downward-facing side (‘Fragment’ treatment). Hence, whereas all plates were exposed to ambient larval recruitment, half of them were additionally subjected to a single fragment inoculation event. Each fragment was c. 10 cm² in area (c. 20 g) and was secured within the central portion of each plate using two rubber bands. All Fragment plates were photographed and initial fragment size determined using the image analysis software ImageJ.
DOI: 10.6084/m9.figshare.5103136
title: gcmsmethod

description: gcms method
DOI: 10.6084/m9.figshare.5103118
title: GCMSdatafiles

description: gcms data collected from fecal headspace via SPME extraction. samples were collected from cattle that were non-vaccinated or vaccinated with BCG prior to and after challenge with virulent M. bovis.
DOI: 10.6084/m9.figshare.5103094
title: CATTLE044.ELU

description: GCMS DATA COLLECTED FROM HEADSPACE OVER FECES.
DOI: 10.6084/m9.figshare.5103139.v2
title: Patterns in invasiveness of the colonial ascidian <i>Didemnum vexillum</i> (Kott 2002)

description: Temporal patterns of biofouling establishment and persistence were investigated at two field sites (Nelson, hereafter NN; Ruakaka Bay, hereafter RK) over a 19-month period between 19 December 2007 and 29 July 2009 (Fletcher et al. data.csv). The RK study site was situated within a fish farm located in New Zealand’s Marlborough Sounds region (41°12'40.2"S, 174°08'26.1"E), whereas the NN site was situated approximately 60 km west (41°15'23.7"S 173°16'33.7"E) within a commercial port at Nelson. The RK site was in relatively deep water (c. 30 m depth), while the NN site was shallower (c. 5 m depth) with a large (c. 4 m) tidal exchange.<br>Arrays of roughened black Perspex settlement plates (20 x 20 cm; n = 3 plates per array) were deployed from floating structures at each site (steel fish farm pontoons at RK and plastic marina pontoons at NN), with arrays spaced approximately 5 m apart. The settlement plates were positioned horizontally within each array, and configured to ensure they remained at a constant depth (0.5 - 1.5 m) with respect to the water surface. Sampling involved taking photographs of the downward-facing surface of each plate, reflecting the orientation where maximum D. vexillum recruitment occurs [32]. Plate photos were analysed using the random dot method in Coral Point Count software (CPCe v4.1), with 50 stratified random points overlaid on each image. Based on the frequency of occurrence of D. vexillum, other major taxa, bare space, or sediment at each point, percent cover was calculated. A margin of 1 cm around each experimental plate was excluded from analyses to avoid edge effects.<br>In a second concurrent study (Fletcher et al. data2.csv), we investigated the establishment and persistence of D. vexillum following exposure of settlement plates to ambient larval recruitment, compared with plates also exposed to larval recruitment, but to which a fragment of colony tissue was also attached. The treatments consisted of 10 blank settlement plates (‘Recruitment’ treatment) and 10 blank plates to which a D. vexillum fragment was attached to the downward-facing side (‘Fragment’ treatment). Hence, whereas all plates were exposed to ambient larval recruitment, half of them were additionally subjected to a single fragment inoculation event. Each fragment was c. 10 cm² in area (c. 20 g) and was secured within the central portion of each plate using two rubber bands. All Fragment plates were photographed and initial fragment size determined using the image analysis software ImageJ.
DOI: 10.6084/m9.figshare.5103094.v1
title: CATTLE044.ELU

description: GCMS DATA COLLECTED FROM HEADSPACE OVER FECES.
DOI: 10.6084/m9.figshare.5103118.v1
title: GCMSdatafiles

description: gcms data collected from fecal headspace via SPME extraction. samples were collected from cattle that were non-vaccinated or vaccinated with BCG prior to and after challenge with virulent M. bovis.
DOI: 10.6084/m9.figshare.5103088
title: VOC table from lit review

description: spreadsheet containing all VOCs that could be found in relevant literature
DOI: 10.6084/m9.figshare.5103139.v1
title: Patterns in invasiveness of the colonial ascidian Didemnum vexillum (Kott 2002)

description: Temporal patterns of biofouling establishment and persistence were investigated at two field sites (Nelson, hereafter NN; Ruakaka Bay, hereafter RK) over a 19-month period between 19 December 2007 and 29 July 2009 (Fletcher et al. data.csv). The RK study site was situated within a fish farm located in New Zealand’s Marlborough Sounds region (41°12'40.2"S, 174°08'26.1"E), whereas the NN site was situated approximately 60 km west (41°15'23.7"S 173°16'33.7"E) within a commercial port at Nelson. The RK site was in relatively deep water (c. 30 m depth), while the NN site was shallower (c. 5 m depth) with a large (c. 4 m) tidal exchange.<br>Arrays of roughened black Perspex settlement plates (20 x 20 cm; n = 3 plates per array) were deployed from floating structures at each site (steel fish farm pontoons at RK and plastic marina pontoons at NN), with arrays spaced approximately 5 m apart. The settlement plates were positioned horizontally within each array, and configured to ensure they remained at a constant depth (0.5 - 1.5 m) with respect to the water surface. Sampling involved taking photographs of the downward-facing surface of each plate, reflecting the orientation where maximum D. vexillum recruitment occurs [32]. Plate photos were analysed using the random dot method in Coral Point Count software (CPCe v4.1), with 50 stratified random points overlaid on each image. Based on the frequency of occurrence of D. vexillum, other major taxa, bare space, or sediment at each point, percent cover was calculated. A margin of 1 cm around each experimental plate was excluded from analyses to avoid edge effects.<br>In a second concurrent study (Fletcher et al. data2.csv), we investigated the establishment and persistence of D. vexillum following exposure of settlement plates to ambient larval recruitment, compared with plates also exposed to larval recruitment, but to which a fragment of colony tissue was also attached. The treatments consisted of 10 blank settlement plates (‘Recruitment’ treatment) and 10 blank plates to which a D. vexillum fragment was attached to the downward-facing side (‘Fragment’ treatment). Hence, whereas all plates were exposed to ambient larval recruitment, half of them were additionally subjected to a single fragment inoculation event. Each fragment was c. 10 cm² in area (c. 20 g) and was secured within the central portion of each plate using two rubber bands. All Fragment plates were photographed and initial fragment size determined using the image analysis software ImageJ.
DOI: 10.6084/m9.figshare.5103052
title: Morales-Williams_etal_2017_CyanoCCM_BG_dataset

description: This dataset is associated with the manuscript: <br>Morales-Williams, A.M., A.D. Wanamaker, and J.A. Downing (2017) Cyanobacterial carbon concentrating mechanisms facilitate sustained CO<sub>2</sub> depletion in eutrophic lakes. <i>Biogeosciences</i> <b>14</b>, 1-11.