cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12143901.v1
title: Additional file 2 of Simultaneous quantification of natural and inducible regulatory T-cell subsets during interferon-β therapy of multiple sclerosis patients

description: Additional file 2: Table S2. Number of samples received at T12 and T24 for MxA quantification and patient subdivision according to MxA induction. The MxA quantification was performed before IFN-β therapy initiation (T0) and then after 12 (T12) and 24 (T24) months of therapy.
DOI: 10.6084/m9.figshare.12143892
title: Additional file 1 of Simultaneous quantification of natural and inducible regulatory T-cell subsets during interferon-β therapy of multiple sclerosis patients

description: Additional file 1: Table S1. Number of patients included in the study and dropouts occurring at each time points. The therapy time points were: T0, before therapy initiation; T6, T12, T18 and T24, after 6, 12, 18, and 24 months of IFN-β, respectively.
DOI: 10.6084/m9.figshare.12143892.v1
title: Additional file 1 of Simultaneous quantification of natural and inducible regulatory T-cell subsets during interferon-β therapy of multiple sclerosis patients

description: Additional file 1: Table S1. Number of patients included in the study and dropouts occurring at each time points. The therapy time points were: T0, before therapy initiation; T6, T12, T18 and T24, after 6, 12, 18, and 24 months of IFN-β, respectively.
DOI: 10.6084/m9.figshare.12143865
title: GO annotion analysis result.zip

description: The GO annotion analysis of DEGs during low temperature conditioning of postharvest <i>Phyllostachys violascens</i> shoot<br>
DOI: 10.6084/m9.figshare.12143859
title: DEG result for LTC.zip

description: The expression profile of DEGs under low temperature conditioning of lei bamboo shoots
DOI: 10.6084/m9.figshare.12143862
title: Transcriptome analysis provides insights into the regulation of Lei bamboo (Phyllostachys violascens) shoots during postharvest cold storage

description: The distribution of KEGG pathways annotations of DEGs during low temperature conditioning of postharvest <i>Phyllostachys violascens</i> shoot <br><br><br>
DOI: 10.6084/m9.figshare.12143865.v1
title: GO annotion analysis result.zip

description: The GO annotion analysis of DEGs during low temperature conditioning of postharvest <i>Phyllostachys violascens</i> shoot<br>
DOI: 10.6084/m9.figshare.12143808
title: Supplementary Material for: Utility of the Absolute Lymphocyte Count and Neutrophil/Lymphocyte Ratio for Predicting Survival in Patients with Metastatic Breast Cancer on Eribulin: A Real-World Observational Study

description: <b><i>Introduction:</i></b> Previous studies have suggested that the efficacy of eribulin is influenced by the activity of antitumor immunity of patients. Absolute lymphocyte count (ALC) and the neutrophil/lymphocyte ratio (NLR) are easily available parameters associated with the immunological status of patients. <b><i>Objective:</i></b> Here we tried to classify patients’ immunological status by using the scatter plot of ALC and NLR, and investigated its utility for predicting survival among patients with metastatic breast cancer receiving eribulin. <b><i>Methods:</i></b> The medical records of 125 patients who received eribulin for metastatic breast cancer at our hospital between July 2011 and April 2019 were retrospectively reviewed. Uni- and multivariate analyses were performed to determine the association between baseline ALC/NLR and progression-free survival (PFS)/overall survival (OS). The cutoff values for ALC and NLR were determined using scatter plot analysis. <b><i>Results:</i></b> The entire cohort was classified into immunologically favorable (ALC ≥1,500/µL, 30 patients), intermediate (ALC &lt;1,500/µL, NLR &lt;5.0, 76 patients), and unfavorable (NLR ≥5.0, 19 patients) groups. Univariate analysis showed significant differences in PFS and OS between the groups, whereas multivariate analysis revealed that ALC ≥1,500/µL and NLR ≥5.0 were independent predictors of PFS, with adjusted hazard ratios (95% CI) of 0.57 (0.33–0.99) and 1.78 (1.00–3.15), respectively. NLR ≥5.0 was also associated with worse OS (adjusted hazard ratio: 0.55; 95% CI 0.35–0.88; <i>p</i> = 0.013). <b><i>Conclusions:</i></b> Among patients with metastatic breast cancer receiving eribulin, survival outcomes were well stratified according to baseline peripheral blood ALC and NLR. Accordingly, high ALC and NLR can be used as predictive markers for longer disease control and worse survival, respectively.
DOI: 10.6084/m9.figshare.12143859.v1
title: DEG result for LTC.zip

description: The expression profile of DEGs under low temperature conditioning of lei bamboo shoots
DOI: 10.6084/m9.figshare.12143727
title: Data for Floodplain preconditioning of leaf litter modulates the subsidy of terrestrial C and nutrients in fluvial ecosystems

description: Complete dataset from the paper "Floodplain preconditioning of leaf litter modulates the subsidy of terrestrial C and nutrients in fluvial ecosystems" published in Ecosytems.<br>See readme.txt for files metadata.<br>General description:<br>The dataset compiled here combines data of leaf litter (Phragmites australis) decomposition under terrestrial and aquatic conditions, as well as the environmental data of the study systems where the decomposition experiments were carried out. <br>In short, leaf litter was incubated first for 105 day in two habitats (open- and closed-canopy) in three floodplain sites with different climatic conditions (floodplain experiment). Then, leaf litter exposed in all habitats and floodplain sites were incubated, together with a control (fresh leaf litter), in a single river for 89 days (river decomposition experiment). Leaf litter mass loss, cellobiohydrolase extracellular activity, fungal biomass (ergosterol) and changes in the chemical composition were measured during the floodplain and river incubation periods.Furthermore, aqueous leachates were extracted from control and floodplain-exposed leaf litter to measure the spectroscopic features of the leached dissolved organic matter and the biodegradability of leachates.<br><br>All the information about the experimental design, study sites and methods are available at the original <br>publication:<br>del Campo R., Marti E., Bastias E., Barberá G., Sánchez-Montoya M. M., Gómez, R. 2020. <br>Floodplain preconditioning of leaf litter modulates the subsidy of terrestrial C and nutrients in fluvial ecosystems.<br>Ecosystems<br><br>Contact main author for a copy of the original paper if needed:ruben.del-campo@uibk.ac.at or <br>ruben.dlcampo@gmail.com<br>
DOI: 10.6084/m9.figshare.12143808.v1
title: Supplementary Material for: Utility of the Absolute Lymphocyte Count and Neutrophil/Lymphocyte Ratio for Predicting Survival in Patients with Metastatic Breast Cancer on Eribulin: A Real-World Observational Study

description: <b><i>Introduction:</i></b> Previous studies have suggested that the efficacy of eribulin is influenced by the activity of antitumor immunity of patients. Absolute lymphocyte count (ALC) and the neutrophil/lymphocyte ratio (NLR) are easily available parameters associated with the immunological status of patients. <b><i>Objective:</i></b> Here we tried to classify patients’ immunological status by using the scatter plot of ALC and NLR, and investigated its utility for predicting survival among patients with metastatic breast cancer receiving eribulin. <b><i>Methods:</i></b> The medical records of 125 patients who received eribulin for metastatic breast cancer at our hospital between July 2011 and April 2019 were retrospectively reviewed. Uni- and multivariate analyses were performed to determine the association between baseline ALC/NLR and progression-free survival (PFS)/overall survival (OS). The cutoff values for ALC and NLR were determined using scatter plot analysis. <b><i>Results:</i></b> The entire cohort was classified into immunologically favorable (ALC ≥1,500/µL, 30 patients), intermediate (ALC &lt;1,500/µL, NLR &lt;5.0, 76 patients), and unfavorable (NLR ≥5.0, 19 patients) groups. Univariate analysis showed significant differences in PFS and OS between the groups, whereas multivariate analysis revealed that ALC ≥1,500/µL and NLR ≥5.0 were independent predictors of PFS, with adjusted hazard ratios (95% CI) of 0.57 (0.33–0.99) and 1.78 (1.00–3.15), respectively. NLR ≥5.0 was also associated with worse OS (adjusted hazard ratio: 0.55; 95% CI 0.35–0.88; <i>p</i> = 0.013). <b><i>Conclusions:</i></b> Among patients with metastatic breast cancer receiving eribulin, survival outcomes were well stratified according to baseline peripheral blood ALC and NLR. Accordingly, high ALC and NLR can be used as predictive markers for longer disease control and worse survival, respectively.
DOI: 10.6084/m9.figshare.12143862.v2
title: Transcriptome analysis provides insights into the regulation of Lei bamboo (Phyllostachys violascens) shoots during postharvest cold storage

description: The distribution of KEGG pathways annotations of DEGs during low temperature conditioning of postharvest <i>Phyllostachys violascens</i> shoot <br><br><br>
DOI: 10.6084/m9.figshare.12143727.v1
title: Data for Floodplain preconditioning of leaf litter modulates the subsidy of terrestrial C and nutrients in fluvial ecosystems

description: Complete dataset from the paper "Floodplain preconditioning of leaf litter modulates the subsidy of terrestrial C and nutrients in fluvial ecosystems" published in Ecosytems.<br>See readme.txt for files metadata.<br>General description:<br>The dataset compiled here combines data of leaf litter (Phragmites australis) decomposition under terrestrial and aquatic conditions, as well as the environmental data of the study systems where the decomposition experiments were carried out. <br>In short, leaf litter was incubated first for 105 day in two habitats (open- and closed-canopy) in three floodplain sites with different climatic conditions (floodplain experiment). Then, leaf litter exposed in all habitats and floodplain sites were incubated, together with a control (fresh leaf litter), in a single river for 89 days (river decomposition experiment). Leaf litter mass loss, cellobiohydrolase extracellular activity, fungal biomass (ergosterol) and changes in the chemical composition were measured during the floodplain and river incubation periods.Furthermore, aqueous leachates were extracted from control and floodplain-exposed leaf litter to measure the spectroscopic features of the leached dissolved organic matter and the biodegradability of leachates.<br><br>All the information about the experimental design, study sites and methods are available at the original <br>publication:<br>del Campo R., Marti E., Bastias E., Barberá G., Sánchez-Montoya M. M., Gómez, R. 2020. <br>Floodplain preconditioning of leaf litter modulates the subsidy of terrestrial C and nutrients in fluvial ecosystems.<br>Ecosystems<br><br>Contact main author for a copy of the original paper if needed:ruben.del-campo@uibk.ac.at or <br>ruben.dlcampo@gmail.com<br>
DOI: 10.6084/m9.figshare.12143862.v1
title: KEGG pathways analysis result.zip

description: The distribution of KEGG pathways annotations of DEGs during low temperature conditioning of postharvest <i>Phyllostachys violascens</i> shoot <br><br><br>
DOI: 10.6084/m9.figshare.12143598
title: Supplementary Material for: Congenital Hypogonadotropic Hypogonadism with Anosmia and Gorlin Features Caused by a <b><i>PTCH1</i></b> Mutation Reveals a New Candidate Gene for Kallmann Syndrome

description: <b><i>Background:</i></b> Two loci (CHD7 and SOX10) underlying Kallmann syndrome (KS) were discovered through clinical and genetic analysis of CHARGE and Waardenburg syndromes, conditions that include congenital anosmia caused by olfactory bulb (CA/OBs) defects and congenital hypogonadotropic hypogonadism (CHH). We hypothesized that other candidate genes for KS could be discovered by analyzing rare syndromes presenting with these signs. <b><i>Study Design, Size, Duration:</i></b> We first investigated a family with Gorlin-Goltz syndrome (GGS) in which affected members exhibited clinical signs suggesting KS. <b><i>Participants/Materials, Methods:</i></b> Proband and family members underwent detailed clinical assessment. The proband received detailed neuroendocrine evaluation. Genetic analyses included sequencing the PTCH1 gene at diagnosis, followed by exome analyses of causative or candidate KS/CHH genes, in order to exclude contribution to the phenotypes of additional mutations. Exome analyses in additional 124 patients with KS/CHH probands with no additional GGS signs. <b><i>Results:</i></b> The proband exhibited CA, absent OBs on magnetic resonance imaging, and had CHH with unilateral cryptorchidism, consistent with KS. Pulsatile Gonadotropin-releasing hormone (GnRH) therapy normalized serum gonadotropins and increased testosterone levels, supporting GnRH deficiency. Genetic studies revealed 3 affected family members harbor a novel mutation of PTCH1 (c.838G&gt; T; p.Glu280*). This unreported nonsense deleterious mutation results in either a putative truncated Ptch1 protein or in an absence of translated Ptch1 protein related to nonsense mediated messenger RNA decay. This heterozygous mutation cosegregates in the pedigree with GGS and CA with OBs aplasia/hypoplasia and with CHH in the proband suggesting a genetic linkage and an autosomal dominant mode of inheritance. No pathogenic rare variants in other KS/CHH genes cosegregated with these phenotypes. In additional 124 KS/CHH patients, 3 additional heterozygous, rare missense variants were found and predicted in silico to be damaging: p.Ser1203Arg, p.Arg1192Ser, and p.Ile108Met. <b><i>Conclusion:</i></b> This family suggests that the 2 main signs of KS can be included in GGS associated with PTCH1 mutations. Our data combined with mice models suggest that PTCH1 could be a novel candidate gene for KS/CHH and reinforce the role of the Hedgehog signaling pathway in pathophysiology of KS and GnRH neuron migration.
DOI: 10.6084/m9.figshare.12143568
title: Rock physics model of complex electrical conductivity to reproduce pore-fluid dependent characteristics of sulfide ores in seafloor hydrothermal areas

description: Electrical conductivity data set for several frequencies and several pore fluid electrical conductivity
DOI: 10.6084/m9.figshare.12143598.v1
title: Supplementary Material for: Congenital Hypogonadotropic Hypogonadism with Anosmia and Gorlin Features Caused by a <b><i>PTCH1</i></b> Mutation Reveals a New Candidate Gene for Kallmann Syndrome

description: <b><i>Background:</i></b> Two loci (CHD7 and SOX10) underlying Kallmann syndrome (KS) were discovered through clinical and genetic analysis of CHARGE and Waardenburg syndromes, conditions that include congenital anosmia caused by olfactory bulb (CA/OBs) defects and congenital hypogonadotropic hypogonadism (CHH). We hypothesized that other candidate genes for KS could be discovered by analyzing rare syndromes presenting with these signs. <b><i>Study Design, Size, Duration:</i></b> We first investigated a family with Gorlin-Goltz syndrome (GGS) in which affected members exhibited clinical signs suggesting KS. <b><i>Participants/Materials, Methods:</i></b> Proband and family members underwent detailed clinical assessment. The proband received detailed neuroendocrine evaluation. Genetic analyses included sequencing the PTCH1 gene at diagnosis, followed by exome analyses of causative or candidate KS/CHH genes, in order to exclude contribution to the phenotypes of additional mutations. Exome analyses in additional 124 patients with KS/CHH probands with no additional GGS signs. <b><i>Results:</i></b> The proband exhibited CA, absent OBs on magnetic resonance imaging, and had CHH with unilateral cryptorchidism, consistent with KS. Pulsatile Gonadotropin-releasing hormone (GnRH) therapy normalized serum gonadotropins and increased testosterone levels, supporting GnRH deficiency. Genetic studies revealed 3 affected family members harbor a novel mutation of PTCH1 (c.838G&gt; T; p.Glu280*). This unreported nonsense deleterious mutation results in either a putative truncated Ptch1 protein or in an absence of translated Ptch1 protein related to nonsense mediated messenger RNA decay. This heterozygous mutation cosegregates in the pedigree with GGS and CA with OBs aplasia/hypoplasia and with CHH in the proband suggesting a genetic linkage and an autosomal dominant mode of inheritance. No pathogenic rare variants in other KS/CHH genes cosegregated with these phenotypes. In additional 124 KS/CHH patients, 3 additional heterozygous, rare missense variants were found and predicted in silico to be damaging: p.Ser1203Arg, p.Arg1192Ser, and p.Ile108Met. <b><i>Conclusion:</i></b> This family suggests that the 2 main signs of KS can be included in GGS associated with PTCH1 mutations. Our data combined with mice models suggest that PTCH1 could be a novel candidate gene for KS/CHH and reinforce the role of the Hedgehog signaling pathway in pathophysiology of KS and GnRH neuron migration.
DOI: 10.6084/m9.figshare.12143568.v1
title: Rock physics model of complex electrical conductivity to reproduce pore-fluid dependent characteristics of sulfide ores in seafloor hydrothermal areas

description: Electrical conductivity data set for several frequencies and several pore fluid electrical conductivity
DOI: 10.6084/m9.figshare.12143562.v1
title: A mass and energy conservation analysis of drift in the CMIP6 ensemble: supplementary metadata

description: This repository contains the details of the computational aspects of the following study: <br>Irving D, Hobbs W, Church J & Zika J (submitted)<i>.</i> A mass and energy conservation analysis of drift in the CMIP6 ensemble. <i>Journal of Climate. </i> <br>The figures in the paper were generated by running a series of Python scripts at the command line. Those commands (denoted by the $ prompt) are outlined below with additional notes where necessary.<br>Any scripts in this repository that aren't referred to by name below are modules that are used by some/all of the scripts.<br><br>The software environment that the scripts were executed in is described by <i>environment.yml</i>. That environment can be installed using conda:$ conda env create -f environment.yml<br><br>(See https://docs.conda.io/en/latest/ for details.)<br><br><b>Figure 1</b><br>$ python plot_global_budget_variables.py ACCESS-CM2 r1i1p1f1 cmip6 --compfile figure1.png<br><br>In addition to creating a plot for one particular model, the <i>plot_global_budget_variables.py</i> script writes a text file containing the various trends/drifts and regression coefficients presented in the paper. The trends and coefficients for every model were stored in <i>drifts.csv</i> and <i>regression_coefficients.csv</i> respectively, which were then used to create most of the figures below.<br><br><b>Figure 2 </b><br><br>$ python plot_ohc_masso.py figure2.png --models ACCESS-CM2 ACCESS-ESM1-5 BCC-CSM2-MR BCC-ESM1 CNRM-CM6-1 CNRM-ESM2-1 E3SM-1-0 E3SM-1-1 EC-Earth3 EC-Earth3-Veg GFDL-CM4 GISS-E2-1-G GISS-E2-1-G-CC HadGEM3-GC31-LL IPSL-CM6A-LR MPI-ESM-1-2-HAM MPI-ESM1-2-HR MPI-ESM1-2-LR UKESM1-0-LL --runs r1i1p1f1 r1i1p1f1 r1i1p1f1 r1i1p1f1 r1i1p1f2 r1i1p1f2 r1i1p1f1 r1i1p1f1 r1i1p1f1 r1i1p1f1 r1i1p1f1 r1i1p1f1 r1i1p1f1 r1i1p1f1 r1i1p1f1 r1i1p1f1 r1i1p1f1 r1i1p1f1 r1i1p1f2 --colors tab:blue tab:blue tab:orange tab:orange tab:green tab:green tab:red tab:red tab:purple tab:purple tab:brown tab:brown tab:pink tab:pink tab:olive tab:olive tab:cyan tab:cyan tab:gray --linestyles solid dotted solid dotted solid dotted solid dotted solid dotted solid dotted solid dotted solid dotted solid dotted solid --ohc_outlier 1e24 --runmean_window 10<br><br><b>Figure 3</b><br><br>$ python plot_ohc_drift.py drifts.csv figure3.png<br><br><b>Figure 4 (and Table 4)</b><br><br>$ python plot_conservation_scatter.py drifts.csv figure4.png <br><br>In addition to creating a plot, the <i>plot_conservation_scatter.py</i> script outputs the ensemble median and interquartile range values shown in Table 4.<br><br><b>Figure 5</b><br><br>$ python plot_leakage.py drifts.csv figure5.png<br><br><b>Figure 6</b><br><br>$ python plot_regression_boxplot.py regression_coefficients.csv figure6.png<br><br><b>Figure S1</b><br><br>$ python plot_regression_coefs.py drifts.csv energy figureS1.png --cmip_line 21.5<br><br><b>Figure S2</b><br><br>$ python plot_regression_coefs.py drifts.csv mass figureS2.png --cmip_line 21.5<br>
DOI: 10.6084/m9.figshare.12143457
title: Supplemental Table 2 from Asymmetrical gene flow in five co-distributed syngnathids explained by ocean currents and rafting propensity

description: Oceanographic connectivity from 6 sampling sites to the corresponding coastal regions based on an empirical data set of drifter tracks spanning 30-years.
DOI: 10.6084/m9.figshare.12143454
title: Supplemental Table 4 from Asymmetrical gene flow in five co-distributed syngnathids explained by ocean currents and rafting propensity

description: Summary of the results from the G-PhoCS analyses. Figure 3 depicts scaled values for theta (population size) and tau (divergence time), and migrants/generation (converted from scaled m parameter). Lower and upper bounds indicate the 95% confidence interval.
DOI: 10.6084/m9.figshare.12143457.v1
title: Supplemental Table 2 from Asymmetrical gene flow in five co-distributed syngnathids explained by ocean currents and rafting propensity

description: Oceanographic connectivity from 6 sampling sites to the corresponding coastal regions based on an empirical data set of drifter tracks spanning 30-years.
DOI: 10.6084/m9.figshare.12143451
title: Supplemental Table 3 from Asymmetrical gene flow in five co-distributed syngnathids explained by ocean currents and rafting propensity

description: Number of samples, RADseq reads, resulting loci and SNPs for each of the species of Hippocampus and Syngnathus. No. of unlinked SNPs entails that no more than one SNP per locus was included.
DOI: 10.6084/m9.figshare.12143445
title: Supplemental Table 1 from Asymmetrical gene flow in five co-distributed syngnathids explained by ocean currents and rafting propensity

description: List of locations which were sampled for Hippocampus spp. and Syngnathus spp., including population designation, labels used in analyses and GPS coördinates. Last six columns contain the numbers of samples per species which were included from each locality.
DOI: 10.6084/m9.figshare.12143454.v1
title: Supplemental Table 4 from Asymmetrical gene flow in five co-distributed syngnathids explained by ocean currents and rafting propensity

description: Summary of the results from the G-PhoCS analyses. Figure 3 depicts scaled values for theta (population size) and tau (divergence time), and migrants/generation (converted from scaled m parameter). Lower and upper bounds indicate the 95% confidence interval.
DOI: 10.6084/m9.figshare.12143445.v1
title: Supplemental Table 1 from Asymmetrical gene flow in five co-distributed syngnathids explained by ocean currents and rafting propensity

description: List of locations which were sampled for Hippocampus spp. and Syngnathus spp., including population designation, labels used in analyses and GPS coördinates. Last six columns contain the numbers of samples per species which were included from each locality.
DOI: 10.6084/m9.figshare.12143451.v1
title: Supplemental Table 3 from Asymmetrical gene flow in five co-distributed syngnathids explained by ocean currents and rafting propensity

description: Number of samples, RADseq reads, resulting loci and SNPs for each of the species of Hippocampus and Syngnathus. No. of unlinked SNPs entails that no more than one SNP per locus was included.
DOI: 10.6084/m9.figshare.12143109.v1
title: offlaping well.xlsx

description: Representative offlapping wells in the Qaidam basin