cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7040342
title: Gene abundance files, meta files, and a mRNA file for the article RNA-seq transcriptomic profiling of crassulacean acid metabolism pathway in Dendrobium catenatum by Zou et al.

description: Gene abundance files, meta files, and a mRNA file for the article RNA-seq transcriptomic profiling of crassulacean acid metabolism pathway in Dendrobium catenatum by Zou et al. This file set contains the two datasets' associated files.
DOI: 10.6084/m9.figshare.7040342.v1
title: Gene abundance files, meta files, and a mRNA file for the article RNA-seq transcriptomic profiling of crassulacean acid metabolism pathway in Dendrobium catenatum by Zou et al.

description: Gene abundance files, meta files, and a mRNA file for the article RNA-seq transcriptomic profiling of crassulacean acid metabolism pathway in Dendrobium catenatum by Zou et al. This file set contains the two datasets' associated files.
DOI: 10.6084/m9.figshare.7040315
title: File S1. E. coli strains and plasmids, plasmid construction details, nucleotide sequences of select genetic parts, and primers.

description: File S1. <i>E. coli</i> strains and plasmids, plasmid construction details, nucleotide sequences of select genetic parts, and primers.
DOI: 10.6084/m9.figshare.7040333.v1
title: A Rscript for article RNA-seq transcriptomic profiling of crassulacean acid metabolism pathway in Dendrobium catenatum in Scientific data by Zou et al.

description: A Rscript for article RNA-seq transcriptomic profiling of crassulacean acid metabolism pathway in Dendrobium catenatum in Scientific data by Zou et al.
DOI: 10.6084/m9.figshare.7040312
title: Data S1. Excel spreadsheet containing data values plotted in main and supplemental figures.

description: Data S1. Excel spreadsheet containing data values plotted in main and supplemental figures.
DOI: 10.6084/m9.figshare.7040333.v2
title: A Rscript for article RNA-seq transcriptomic profiling of crassulacean acid metabolism pathway in Dendrobium catenatum by Zou et al.

description: A Rscript for article RNA-seq transcriptomic profiling of crassulacean acid metabolism pathway in Dendrobium catenatum in Scientific data by Zou et al.
DOI: 10.6084/m9.figshare.7040261
title: File S2. attTn7 and 16S rRNA Nucleotide Sequences.

description: File S2. <i>attTn7</i> and 16S rRNA Nucleotide Sequences.
DOI: 10.6084/m9.figshare.7040249
title: Table S1. Wild and Recombinant Bacteria.

description: Table S1. Wild and Recombinant Bacteria.
DOI: 10.6084/m9.figshare.7040255
title: Table S2. Summary of traits exhibited by bacterial symbionts within the larval zebrafish intestine.

description: Table S2. Summary of traits exhibited by bacterial symbionts within the larval zebrafish intestine.<br>
DOI: 10.6084/m9.figshare.7040201
title: 2014_Woo_DPSP_Pain_Rejection_contrast_images

description: This dataset contains sample fMRI data from pain and rejection. The primary publication is referenced below. <br>Woo, C. W., Koban, L., Kross, E., Lindquist, M. A., Banich, M. T., Ruzic, L., . . . Wager, T. D. (2014). Separate neural representations for physical pain and social rejection. <i>Nature communications, 5</i>, 5380. doi:10.1038/ncomms6380<br>Using CANlab toolboxes, one should be able to recreate the results and scripts included with this file set, and the sample HTML reports. These were created with the canlab_help_examples second-level batch scripts. See canlab.github.io for more information ('batch' section).<br>
DOI: 10.6084/m9.figshare.7040198
title: EMRBots: a 100,000-patient database

description: A 100,000-patient database that contains in total 100,000 virtual patients, 361,760 admissions, and 107,535,387 lab observations.
DOI: 10.6084/m9.figshare.7040201.v1
title: 2014_Woo_DPSP_Pain_Rejection_contrast_images

description: This dataset contains sample fMRI data from pain and rejection. The primary publication is referenced below. <br>Woo, C. W., Koban, L., Kross, E., Lindquist, M. A., Banich, M. T., Ruzic, L., . . . Wager, T. D. (2014). Separate neural representations for physical pain and social rejection. <i>Nature communications, 5</i>, 5380. doi:10.1038/ncomms6380<br>Using CANlab toolboxes, one should be able to recreate the results and scripts included with this file set, and the sample HTML reports. These were created with the canlab_help_examples second-level batch scripts. See canlab.github.io for more information ('batch' section).<br>
DOI: 10.6084/m9.figshare.7040171
title: 2014_Woo_DPSP_Pain_Rejection

description: Finished product with complete results and scripts folders pertaining to previously published dataset. This folder acts to supplement 2014_Woo_DPSP_Pain_Rejection_contrast_images by providing an example of a complete analysis pipeline and by demonstrating what contents should be present in the results directory following analysis.<br>The primary paper on this dataset is:<br>Woo, C. W., Koban, L., Kross, E., Lindquist, M. A., Banich, M. T., Ruzic, L., . . . Wager, T. D. (2014). Separate neural representations for physical pain and social rejection. <i>Nature communications, 5</i>, 5380. doi:10.1038/ncomms6380<br>All output were generated with the CANlab help examples second-level batch scripts. See canlab.github.io for more information.<br>
DOI: 10.6084/m9.figshare.7040174
title: Parallel damage in mitochondria and lysosomes is an efficient way to photoinduce cell death

description: Cells challenged by photosensitized oxidations face strong redox stresses and rely on autophagy to either survive or die. However, the use of macroautophagy/autophagy to improve the efficiency of photosensitizers, in terms of inducing cell death, remains unexplored. Here, we addressed the concept that a parallel damage in the membranes of mitochondria and lysosomes leads to a scenario of autophagy malfunction that can greatly improve the efficiency of the photosensitizer to cause cell death. Specific damage to these organelles was induced by irradiation of cells pretreated with 2 phenothiazinium salts, methylene blue (MB) and 1,9-dimethyl methylene blue (DMMB). At a low concentration level (10 nM), only DMMB could induce mitochondrial damage, leading to mitophagy activation, which did not progress to completion because of the parallel damage in lysosome, triggering cell death. MB-induced photodamage was perceived almost instantaneously after irradiation, in response to a massive and nonspecific oxidative stress at a higher concentration range (2 µM). We showed that the parallel damage in mitochondria and lysosomes activates and inhibits mitophagy, leading to a late and more efficient cell death, offering significant advantage (2 orders of magnitude) over photosensitizers that cause unspecific oxidative stress. We are confident that this concept can be used to develop better light-activated drugs. <b>Abbreviations:</b> ΔΨm: mitochondrial transmembrane inner potential; AAU: autophagy arbitrary units; ATG5, autophagy related 5; ATG7: autophagy related 7; BAF: bafilomycin A<sub>1</sub>; BSA: bovine serum albumin; CASP3: caspase 3; CF: carboxyfluorescein; CTSB: cathepsin B; CVS: crystal violet staining; DCF: dichlorofluorescein; DCFH<sub>2</sub>: 2ʹ,7ʹ-dichlorodihydrofluorescein; DMMB: 1,9-dimethyl methylene blue; ER: endoplasmic reticulum; HaCaT: non-malignant immortal keratinocyte cell line from adult human skin; HP: hydrogen peroxide; LC3B-II: microtubule associated protein 1 light chain 3 beta-II; LMP: lysosomal membrane permeabilization; LTG: LysoTracker™ Green DND-26; LTR: LysoTracker™ Red DND-99; 3-MA: 3-methyladenine; MB: methylene blue; mtDNA: mitochondrial DNA; MitoSOX™: red mitochondrial superoxide probe; MTDR: MitoTracker™ Deep Red FM; MTO: MitoTracker™ Orange CMTMRos; MT-ND1: mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1; MTT: methylthiazolyldiphenyl-tetrazolium bromide; <sup>1</sup>O<sub>2</sub>: singlet oxygen; OH<sup>.</sup> hydroxil radical; PRKN/parkin: parkin RBR E3 ubiquitin protein ligase; PBS: phosphate-buffered saline; PI: propidium iodide; PDT: photodynamic therapy; PS: photosensitizer; QPCR: gene-specific quantitative PCR-based; Rh123: rhodamine 123; ROS: reactive oxygen species RTN: rotenone; SQSTM1/p62: sequestosome 1; SUVs: small unilamellar vesicles; TBS: Tris-buffered saline
DOI: 10.6084/m9.figshare.7040174.v1
title: Parallel damage in mitochondria and lysosomes is an efficient way to photoinduce cell death

description: Cells challenged by photosensitized oxidations face strong redox stresses and rely on autophagy to either survive or die. However, the use of macroautophagy/autophagy to improve the efficiency of photosensitizers, in terms of inducing cell death, remains unexplored. Here, we addressed the concept that a parallel damage in the membranes of mitochondria and lysosomes leads to a scenario of autophagy malfunction that can greatly improve the efficiency of the photosensitizer to cause cell death. Specific damage to these organelles was induced by irradiation of cells pretreated with 2 phenothiazinium salts, methylene blue (MB) and 1,9-dimethyl methylene blue (DMMB). At a low concentration level (10 nM), only DMMB could induce mitochondrial damage, leading to mitophagy activation, which did not progress to completion because of the parallel damage in lysosome, triggering cell death. MB-induced photodamage was perceived almost instantaneously after irradiation, in response to a massive and nonspecific oxidative stress at a higher concentration range (2 µM). We showed that the parallel damage in mitochondria and lysosomes activates and inhibits mitophagy, leading to a late and more efficient cell death, offering significant advantage (2 orders of magnitude) over photosensitizers that cause unspecific oxidative stress. We are confident that this concept can be used to develop better light-activated drugs. <b>Abbreviations:</b> ΔΨm: mitochondrial transmembrane inner potential; AAU: autophagy arbitrary units; ATG5, autophagy related 5; ATG7: autophagy related 7; BAF: bafilomycin A<sub>1</sub>; BSA: bovine serum albumin; CASP3: caspase 3; CF: carboxyfluorescein; CTSB: cathepsin B; CVS: crystal violet staining; DCF: dichlorofluorescein; DCFH<sub>2</sub>: 2ʹ,7ʹ-dichlorodihydrofluorescein; DMMB: 1,9-dimethyl methylene blue; ER: endoplasmic reticulum; HaCaT: non-malignant immortal keratinocyte cell line from adult human skin; HP: hydrogen peroxide; LC3B-II: microtubule associated protein 1 light chain 3 beta-II; LMP: lysosomal membrane permeabilization; LTG: LysoTracker™ Green DND-26; LTR: LysoTracker™ Red DND-99; 3-MA: 3-methyladenine; MB: methylene blue; mtDNA: mitochondrial DNA; MitoSOX™: red mitochondrial superoxide probe; MTDR: MitoTracker™ Deep Red FM; MTO: MitoTracker™ Orange CMTMRos; MT-ND1: mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1; MTT: methylthiazolyldiphenyl-tetrazolium bromide; <sup>1</sup>O<sub>2</sub>: singlet oxygen; OH<sup>.</sup> hydroxil radical; PRKN/parkin: parkin RBR E3 ubiquitin protein ligase; PBS: phosphate-buffered saline; PI: propidium iodide; PDT: photodynamic therapy; PS: photosensitizer; QPCR: gene-specific quantitative PCR-based; Rh123: rhodamine 123; ROS: reactive oxygen species RTN: rotenone; SQSTM1/p62: sequestosome 1; SUVs: small unilamellar vesicles; TBS: Tris-buffered saline
DOI: 10.6084/m9.figshare.7040150
title: Digester sample analysis

description: mothur output files and R code for analysis of digester samplessamples were subsampled for analysis<br>
DOI: 10.6084/m9.figshare.7040153
title: Liquid effluent sample analysis

description: mothur output files and R code for analysis of liquid effluent samples were subsampled for analysis<br><br>
DOI: 10.6084/m9.figshare.7040150.v1
title: Digester sample analysis

description: mothur output files and R code for analysis of digester samplessamples were subsampled for analysis<br>
DOI: 10.6084/m9.figshare.7040129
title: Negative control analysis

description: mothur output files and R code for analysis of negative controls (not subsampled, includes digester and liquid effluent samples, does not include mock community)<br>LW56 = negative kit controlLW57 = no-template control<br>
DOI: 10.6084/m9.figshare.7040111
title: Mock community analysis

description: mothur output files from analysis of all samples (not subsampled)<br>used to assess mock community (LW43) as a positive control<br>
DOI: 10.6084/m9.figshare.7040111.v1
title: Mock community analysis

description: mothur output files from analysis of all samples (not subsampled)<br>used to assess mock community (LW43) as a positive control<br>
DOI: 10.6084/m9.figshare.7040129.v1
title: Negative control analysis

description: mothur output files and R code for analysis of negative controls (not subsampled, includes digester and liquid effluent samples, does not include mock community)<br>LW56 = negative kit controlLW57 = no-template control<br>
DOI: 10.6084/m9.figshare.7040075
title: DeFilippo et al 2018 Evolutionary Applications Data

description: This database contains ADF&G's historical numbers at age data for the Frazer Lake sockeye salmon population and values of all covariates examined that are not publicly available elsewhere.<br><br>Disclaimer: ADF&G retains intellectual property rights to data collected by or for ADF&G. Any dissemination of the data must credit ADF&G as the source, with a disclaimer that exonerates the department for errors or deficiencies in reproduction, subsequent analysis, or interpretation.
DOI: 10.6084/m9.figshare.7040075.v1
title: DeFilippo et al 2018 Evolutionary Applications Data

description: This database contains ADF&G's historical numbers at age data for the Frazer Lake sockeye salmon population and values of all covariates examined that are not publicly available elsewhere.<br><br>Disclaimer: ADF&G retains intellectual property rights to data collected by or for ADF&G. Any dissemination of the data must credit ADF&G as the source, with a disclaimer that exonerates the department for errors or deficiencies in reproduction, subsequent analysis, or interpretation.
DOI: 10.6084/m9.figshare.7040060
title: EMRBots: a 10,000-patient database

description: A 10,000-patient database that contains in total 10,000 virtual patients, 36,143 admissions, and 10,726,505 lab observations.
DOI: 10.6084/m9.figshare.7040069
title: Data

description: Data for the numerical values written in the tables. <br>
DOI: 10.6084/m9.figshare.7040051
title: ptr_tave.0000631152.surf.nc

description: Model output from MITgcm-Michigan-Phosphorus. Daily averages of surface phosphorus for year 2009.
DOI: 10.6084/m9.figshare.7040051.v1
title: ptr_tave.0000631152.surf.nc

description: Model output from MITgcm-Michigan-Phosphorus. Daily averages of surface phosphorus for year 2009.
DOI: 10.6084/m9.figshare.12706595.v1
title: Polyandry Blocks Gene Drive in a Wild House Mouse Population

description: Containing the 5 data files used in the manuscript: <i><br></i><b><i>Polyandry blocks gene drive in a wild house mouse population</i></b><b>Andri Manser, Barbara König, Anna Lindholm</b><br>Here a brief description of the data columns and their meaning:<br><b>1. Measuring polyandry (file: litters.txt) | Figure 1, Supplementary Figure 3</b>LitterID [character]: Unique ID of the litterMotherID [character]: Unique ID of the motherPolyandry [numeric]: 0 if monandrous, 1 if polyandrouslitterSize [numeric]: Number of offspring in the littergenotype [factor]: t genotype of the mother, t if +/t, w if +/+populationSize [numeric]: Population size at the time of birthtemperature [numeric]: Temperature at the time of birth<br><b>2. Impact of polyandry on male fitness (file: males.txt) | Figure 2</b>MaleID [character]: Unique ID of the malegenotype [factor]: t genotype of the male, t if +/t, w if +/+offspring [numeric]: overall number of offspring producedlitterNr [numeric]: number of littersspermCompetitors [numeric]: level of sperm competition<br><b>3. The impact of polyandry on drive frequency dynamics (file: tFrequency.txt) | Figure 3</b>date [character]: Date when the litter was borntOffspring [numeric]: The number of +/t genotypes among offspringlitterSize [numeric]: The total number of offspring (littersize)<br><b>4. Impact of polyandry on female fitness (file: females.txt) | Supplementary Figure 2</b>FemaleID [character]: Unique ID of the femalegenotype [factor]: t genotype of the female, t if +/t, w if +/+offspring [numeric]: overall number of offspring producedlitterNr [numeric]: number of littersmultipleMating [numeric]: propensity of polyandry as predicted by analysis 1 (BLUP)<b><br></b><b>5. Demography | Supplementary Figure 3</b>date [character]: Date of population censusfemales [numeric]: Number of adult femalesmales [numeric]: Number of adult males<br>
DOI: 10.6084/m9.figshare.7040048
title: ptr_tave.0000473040.surf.nc

description: Model output from MITgcm-Michigan-Phosphorus. Daily averages of surface phosphorus for year 2008.
DOI: 10.6084/m9.figshare.12706595
title: Polyandry Blocks Gene Drive in a Wild House Mouse Population

description: Containing the 5 data files used in the manuscript: <i><br></i><b><i>Polyandry blocks gene drive in a wild house mouse population</i></b><b>Andri Manser, Barbara König, Anna Lindholm</b><br>Here a brief description of the data columns and their meaning:<br><b>1. Measuring polyandry (file: litters.txt) | Figure 1, Supplementary Figure 3</b>LitterID [character]: Unique ID of the litterMotherID [character]: Unique ID of the motherPolyandry [numeric]: 0 if monandrous, 1 if polyandrouslitterSize [numeric]: Number of offspring in the littergenotype [factor]: t genotype of the mother, t if +/t, w if +/+populationSize [numeric]: Population size at the time of birthtemperature [numeric]: Temperature at the time of birth<br><b>2. Impact of polyandry on male fitness (file: males.txt) | Figure 2</b>MaleID [character]: Unique ID of the malegenotype [factor]: t genotype of the male, t if +/t, w if +/+offspring [numeric]: overall number of offspring producedlitterNr [numeric]: number of littersspermCompetitors [numeric]: level of sperm competition<br><b>3. The impact of polyandry on drive frequency dynamics (file: tFrequency.txt) | Figure 3</b>date [character]: Date when the litter was borntOffspring [numeric]: The number of +/t genotypes among offspringlitterSize [numeric]: The total number of offspring (littersize)<br><b>4. Impact of polyandry on female fitness (file: females.txt) | Supplementary Figure 2</b>FemaleID [character]: Unique ID of the femalegenotype [factor]: t genotype of the female, t if +/t, w if +/+offspring [numeric]: overall number of offspring producedlitterNr [numeric]: number of littersmultipleMating [numeric]: propensity of polyandry as predicted by analysis 1 (BLUP)<b><br></b><b>5. Demography | Supplementary Figure 3</b>date [character]: Date of population censusfemales [numeric]: Number of adult femalesmales [numeric]: Number of adult males<br>
DOI: 10.6084/m9.figshare.7040048.v1
title: ptr_tave.0000473040.surf.nc

description: Model output from MITgcm-Michigan-Phosphorus. Daily averages of surface phosphorus for year 2008.
DOI: 10.6084/m9.figshare.7040039
title: EMRBots: a 100-patient database

description: A 100-patient database that contains in total 100 virtual patients, 372 admissions, and 111,483 lab observations.
DOI: 10.6084/m9.figshare.7040042
title: ptr_tave.0000315360.surf.nc

description: Model output from MITgcm-Michigan-Phosphorus. Daily averages of surface phosphorus for year 2007.
DOI: 10.6084/m9.figshare.7040042.v1
title: ptr_tave.0000315360.surf.nc

description: Model output from MITgcm-Michigan-Phosphorus. Daily averages of surface phosphorus for year 2007.
DOI: 10.6084/m9.figshare.7040009
title: MiSeq data and sample guide

description: 16S amplicon MiSeq data used as input for mothurSample guide for MiSeq files<br>
DOI: 10.6084/m9.figshare.7040009.v1
title: MiSeq data and sample guide

description: 16S amplicon MiSeq data used as input for mothurSample guide for MiSeq files<br>
DOI: 10.6084/m9.figshare.7040039.v2
title: EMRBots: 100-patient database

description: A 100-patient database that contains in total 100 virtual patients, 372 admissions, and 111,483 lab observations.
DOI: 10.6084/m9.figshare.7040000
title: Dataset analysed in Pfister et al. (2018) "Dominance of cropland reduces the pollen deposition from bumble bees"

description: Dataset used in the Structural equation model (R-Code also uploaded in this figshare project). The results are published in Pfister et al. (2018) "Dominance of cropland reduces the pollen deposition from bumble bees". Scientific Reports.<b>DOI : </b>10.1038/s41598-018-31826-3
DOI: 10.6084/m9.figshare.7039997
title: Oxford RUG Talk September 2018

description: This deposit contains the presentation slides and code written during the live coding components of a talk delivered to the Meetup.com Oxford R User Group on 2018-09-03 by Martin John Hadley.<br>The "2018-09-03 Oxford R Meetup Talk.pdf" file contains the slides (written using Google Slides).<br>The README.md file provides further details about this deposit
DOI: 10.6084/m9.figshare.7040000.v1
title: Dataset analysed in Pfister et al. (2018) "Dominance of cropland reduces the pollen deposition from bumble bees"

description: Dataset used in the Structural equation model (R-Code also uploaded in this figshare project). The results are published in Pfister et al. (2018) "Dominance of cropland reduces the pollen deposition from bumble bees". Scientific Reports.<b>DOI : </b>10.1038/s41598-018-31826-3
DOI: 10.6084/m9.figshare.7039874
title: A comparative study of edetate calcium disodium and dimercaptosuccinic acid in the treatment of lead poisoning in adults

description: <b>Background:</b> We evaluated the efficacy of two antidotes, edetate calcium disodium (CaNa<sub>2</sub>EDTA) and dimercaptosuccinic acid (DMSA), for the treatment of lead poisoning in adults. <b>Methods:</b> Thirty-seven patients with blood lead concentrations &gt;40 μg/dL and positive CaNa<sub>2</sub>EDTA lead mobilization were randomized to receive 1050 mg/m<sup>2</sup>/day of oral DMSA (<i>n</i> = 21) or 500 mg/m<sup>2</sup>/day of intravenous CaNa<sub>2</sub>EDTA (<i>n</i> = 16) over two five-day courses separated by a 10-day rest period. Efficacy of treatment was evaluated by blood lead assays on the first day of the two courses and 14 days after the end of treatment and baseline CaNa<sub>2</sub>EDTA lead mobilization test and 14 days after the end of treatment. <b>Results and conclusion:</b> Both treatments significantly reduced the prevalence of clinical symptoms, blood lead levels and CaNa<sub>2</sub>EDTA lead mobilization and were well tolerated. DMSA had a greater impact on reducing blood lead concentrations (<i>p</i> = .005) and CaNa<sub>2</sub>EDTA on lead mobilization (<i>p</i> = .04). Comparison of equimolar doses showed that CaNa<sub>2</sub>EDTA was more effective than DMSA (<i>p</i>
DOI: 10.6084/m9.figshare.7039874.v1
title: A comparative study of edetate calcium disodium and dimercaptosuccinic acid in the treatment of lead poisoning in adults

description: <b>Background:</b> We evaluated the efficacy of two antidotes, edetate calcium disodium (CaNa<sub>2</sub>EDTA) and dimercaptosuccinic acid (DMSA), for the treatment of lead poisoning in adults. <b>Methods:</b> Thirty-seven patients with blood lead concentrations &gt;40 μg/dL and positive CaNa<sub>2</sub>EDTA lead mobilization were randomized to receive 1050 mg/m<sup>2</sup>/day of oral DMSA (<i>n</i> = 21) or 500 mg/m<sup>2</sup>/day of intravenous CaNa<sub>2</sub>EDTA (<i>n</i> = 16) over two five-day courses separated by a 10-day rest period. Efficacy of treatment was evaluated by blood lead assays on the first day of the two courses and 14 days after the end of treatment and baseline CaNa<sub>2</sub>EDTA lead mobilization test and 14 days after the end of treatment. <b>Results and conclusion:</b> Both treatments significantly reduced the prevalence of clinical symptoms, blood lead levels and CaNa<sub>2</sub>EDTA lead mobilization and were well tolerated. DMSA had a greater impact on reducing blood lead concentrations (<i>p</i> = .005) and CaNa<sub>2</sub>EDTA on lead mobilization (<i>p</i> = .04). Comparison of equimolar doses showed that CaNa<sub>2</sub>EDTA was more effective than DMSA (<i>p</i>