cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19947294
title: Additional file 1 of Genetic modifications of critical regulators provide new insights into regulation modes of raw-starch-digesting enzyme expression in Penicillium

description: Additional file 1: Fig. S1. Southern blot analysis of the genomic DNA of OamyR, OhepA, ΔCreA, and Mpga3 mutants. The location of the probes and restriction enzyme sites for Southern blot analysis are shown. The primers are listed in Table S2. (A) The overexpression strains OamyR and OhepA generated 5.6 and 4.7 kb DNA bands, respectively, while the parental strain 114–2 did not produce a detectable band, indicating that the overexpression cassettes were integrated into the genome. (B) Southern blot analysis of the genomic DNA of 114-2 and Mpga3. The 114-2 strain generated a 1.3 kb DNA band, while a 3.1 kb band was obtained in Mpga3 indicating that the targeted gene was correctly replaced. Sequencing of the mutated pga3 (Mpga3) gene in strain Mpga3. The mutated codon is indicated. (C) Southern blot analysis of the genomic DNA of 114-2 and ΔCreA. The 114-2 strain generated a 3.3 kb DNA band, while a 6.3 kb band was obtained in ΔCreA indicating that the targeted gene was correctly replaced. Fig. S2. RSDE activity assay of WT and various mutants. The strains were cultivated in liquid VMM supplemented with 1% starch and cultivated at 30 °C for 5 days. Soluble starch was used as a reaction substrate for RSDE activity assays. Fig. S3. RSDE activity assay of WT, ΔHepA and ΔPGA3 strain. The strains were cultivated in liquid VMM supplemented with 1% starch and cultivated at 30 °C for 5 days. Raw rice starch was used as a reaction substrate for RSDE activity assays. Fig. S4. Extracellular proteins of 114-2 on starch analysed by SDS-PAGE. 32 μL culture supernatant of 114-2 strain was loaded after cultivating in 1% starch medium for 72 h, respectively. Lane M was the molecular weight marker, lanes 1 and 2 represent two independent cultivations for 114-2 strain. Fig. S5. SDS-PAGE analysis of the purified raw starch digesting enzyme Amy15A. Lane M indicates protein molecular weight marker; lane 1 indicates the purified Amy15A. Fig. S6. Effects of pH and temperature on enzymatic activity and the stability of the RSDE Amy15A. (A) The effect of pH on enzyme activity. The enzyme activity was assayed in a citrate–phosphate buffer (pH 3.0–7.0) at 37 °C. (B) The pH stability of Amy15A was measured by pre-incubating the enzyme in various buffers for 24 h at 4 °C, and the residual enzyme activity was determined using the standard method. (C) The influence of temperature on enzyme activity. The enzyme activity was determined between 35 °C and 80 °C under optimum pH condition. (D) The influence of temperature on enzyme stability. Temperature stability was determined by the standard method after pre-incubating the enzyme at pH 4.5 between 30 °C and 75 °C for 1 h. Data given are mean ± standard deviation from three replicates. The results are from a representative experiment, and similar results were obtained in two other independent experiments. Table S1. Quality control statistics. Table S2. Primers used in this study.
DOI: 10.6084/m9.figshare.19947294.v1
title: Additional file 1 of Genetic modifications of critical regulators provide new insights into regulation modes of raw-starch-digesting enzyme expression in Penicillium

description: Additional file 1: Fig. S1. Southern blot analysis of the genomic DNA of OamyR, OhepA, ΔCreA, and Mpga3 mutants. The location of the probes and restriction enzyme sites for Southern blot analysis are shown. The primers are listed in Table S2. (A) The overexpression strains OamyR and OhepA generated 5.6 and 4.7 kb DNA bands, respectively, while the parental strain 114–2 did not produce a detectable band, indicating that the overexpression cassettes were integrated into the genome. (B) Southern blot analysis of the genomic DNA of 114-2 and Mpga3. The 114-2 strain generated a 1.3 kb DNA band, while a 3.1 kb band was obtained in Mpga3 indicating that the targeted gene was correctly replaced. Sequencing of the mutated pga3 (Mpga3) gene in strain Mpga3. The mutated codon is indicated. (C) Southern blot analysis of the genomic DNA of 114-2 and ΔCreA. The 114-2 strain generated a 3.3 kb DNA band, while a 6.3 kb band was obtained in ΔCreA indicating that the targeted gene was correctly replaced. Fig. S2. RSDE activity assay of WT and various mutants. The strains were cultivated in liquid VMM supplemented with 1% starch and cultivated at 30 °C for 5 days. Soluble starch was used as a reaction substrate for RSDE activity assays. Fig. S3. RSDE activity assay of WT, ΔHepA and ΔPGA3 strain. The strains were cultivated in liquid VMM supplemented with 1% starch and cultivated at 30 °C for 5 days. Raw rice starch was used as a reaction substrate for RSDE activity assays. Fig. S4. Extracellular proteins of 114-2 on starch analysed by SDS-PAGE. 32 μL culture supernatant of 114-2 strain was loaded after cultivating in 1% starch medium for 72 h, respectively. Lane M was the molecular weight marker, lanes 1 and 2 represent two independent cultivations for 114-2 strain. Fig. S5. SDS-PAGE analysis of the purified raw starch digesting enzyme Amy15A. Lane M indicates protein molecular weight marker; lane 1 indicates the purified Amy15A. Fig. S6. Effects of pH and temperature on enzymatic activity and the stability of the RSDE Amy15A. (A) The effect of pH on enzyme activity. The enzyme activity was assayed in a citrate–phosphate buffer (pH 3.0–7.0) at 37 °C. (B) The pH stability of Amy15A was measured by pre-incubating the enzyme in various buffers for 24 h at 4 °C, and the residual enzyme activity was determined using the standard method. (C) The influence of temperature on enzyme activity. The enzyme activity was determined between 35 °C and 80 °C under optimum pH condition. (D) The influence of temperature on enzyme stability. Temperature stability was determined by the standard method after pre-incubating the enzyme at pH 4.5 between 30 °C and 75 °C for 1 h. Data given are mean ± standard deviation from three replicates. The results are from a representative experiment, and similar results were obtained in two other independent experiments. Table S1. Quality control statistics. Table S2. Primers used in this study.
DOI: 10.6084/m9.figshare.19947296
title: Additional file 1 of Hypoxia classifier for transcriptome datasets

description: Additional file 1: Table S1. Classification tree validation. Sheet 1: metadata for the experiments used for model generation. Sheet 2: metadata for each of the experiments used in the validation process. Sheet 3: summary of tree variables and validation accuracy. Sheets 4-7: performance measurements for each human validation dataset. Sheet 8: Proportion of TCGA tumor samples classified as hypoxic by primary site. Sheet 9: performance measurements for the mouse validation dataset.
DOI: 10.6084/m9.figshare.19947296.v1
title: Additional file 1 of Hypoxia classifier for transcriptome datasets

description: Additional file 1: Table S1. Classification tree validation. Sheet 1: metadata for the experiments used for model generation. Sheet 2: metadata for each of the experiments used in the validation process. Sheet 3: summary of tree variables and validation accuracy. Sheets 4-7: performance measurements for each human validation dataset. Sheet 8: Proportion of TCGA tumor samples classified as hypoxic by primary site. Sheet 9: performance measurements for the mouse validation dataset.
DOI: 10.6084/m9.figshare.19947299
title: Additional file 2 of Hypoxia classifier for transcriptome datasets

description: Additional file 2: Table S2. Differential expression in unsupervised clustering of spatial gene expression datasets: Differentially expressed genes between clusters containing a high proportion of spots classified as hypoxic and clusters with low or no hypoxic spots. Sheet 1: Prostate cancer, C7 vs C0. Sheet 2: Prostate cancer, C11 vs C2. Sheet 3: Mouse kidney, C3 vs C1. Sheet 4: Mouse kidney, C5 vs C6.Sheet 5: Glioblastoma, C12 vs C8.Sheet 6: Glioblastoma, C1 vs C5 . Sheet 7: Colorectal cancer, C14 vs C2. Sheet 8: Colorectal cancer, C7 vs C8. Sheet 9: Mann–Whitney test results for differences in p-values among genes up-regulated between clusters according to their up-regulation status in our hypoxia meta-analysis (random effect&gt;0.7, FDR&lt;0.01).
DOI: 10.6084/m9.figshare.19947302
title: Additional file 3 of Hypoxia classifier for transcriptome datasets

description: Additional file 3: Table S3. Comparison between tree classifiers and previously published hypoxia gene signatures. Application of the method described in [56] of 8 hypoxic gene signatures to the validation datasets. Each table includes, for every sample, the hypoxic score derived from each signature, as well as the probability of being hypoxic assigned by our ensemble of the 20 trees with higher F1-score. Sheet 1: PRJNA561635 time series. Sheet 2: specific RNA fractions other than total mRNA. Sheet 3: ccRCC tumor and healthy adjacent tissue samples. Sheet 4: murine datasets.
DOI: 10.6084/m9.figshare.19947299.v1
title: Additional file 2 of Hypoxia classifier for transcriptome datasets

description: Additional file 2: Table S2. Differential expression in unsupervised clustering of spatial gene expression datasets: Differentially expressed genes between clusters containing a high proportion of spots classified as hypoxic and clusters with low or no hypoxic spots. Sheet 1: Prostate cancer, C7 vs C0. Sheet 2: Prostate cancer, C11 vs C2. Sheet 3: Mouse kidney, C3 vs C1. Sheet 4: Mouse kidney, C5 vs C6.Sheet 5: Glioblastoma, C12 vs C8.Sheet 6: Glioblastoma, C1 vs C5 . Sheet 7: Colorectal cancer, C14 vs C2. Sheet 8: Colorectal cancer, C7 vs C8. Sheet 9: Mann–Whitney test results for differences in p-values among genes up-regulated between clusters according to their up-regulation status in our hypoxia meta-analysis (random effect&gt;0.7, FDR&lt;0.01).
DOI: 10.6084/m9.figshare.19947302.v1
title: Additional file 3 of Hypoxia classifier for transcriptome datasets

description: Additional file 3: Table S3. Comparison between tree classifiers and previously published hypoxia gene signatures. Application of the method described in [56] of 8 hypoxic gene signatures to the validation datasets. Each table includes, for every sample, the hypoxic score derived from each signature, as well as the probability of being hypoxic assigned by our ensemble of the 20 trees with higher F1-score. Sheet 1: PRJNA561635 time series. Sheet 2: specific RNA fractions other than total mRNA. Sheet 3: ccRCC tumor and healthy adjacent tissue samples. Sheet 4: murine datasets.
DOI: 10.6084/m9.figshare.19947314
title: Additional file 1 of Alternative splicing diversifies the skeletal muscle transcriptome during prolonged spaceflight

description: Additional file 1. Complete list of DGE genes in the gastrocnemius. 120 genes were significantly differentially expressed across spaceflight in the gastrocnemius. Reported here are the gene symbol, log2 fold change (log2 FC), and FDR-adjusted p-value as reported by DeSeq2. Genes are ordered by significance of DGE as measured by FDR.
DOI: 10.6084/m9.figshare.19947314.v1
title: Additional file 1 of Alternative splicing diversifies the skeletal muscle transcriptome during prolonged spaceflight

description: Additional file 1. Complete list of DGE genes in the gastrocnemius. 120 genes were significantly differentially expressed across spaceflight in the gastrocnemius. Reported here are the gene symbol, log2 fold change (log2 FC), and FDR-adjusted p-value as reported by DeSeq2. Genes are ordered by significance of DGE as measured by FDR.
DOI: 10.6084/m9.figshare.19947317.v1
title: Additional file 2 of Alternative splicing diversifies the skeletal muscle transcriptome during prolonged spaceflight

description: Additional file 2. Complete list of DGE genes in the quadriceps. 70 genes were significantly differentially expressed across spaceflight in the quadriceps. Reported here are the gene symbol, log2 fold change (log2 FC), and FDR-adjusted p-value as reported by DeSeq2. Genes are ordered by significance of DGE as measured by FDR.
DOI: 10.6084/m9.figshare.19947317
title: Additional file 2 of Alternative splicing diversifies the skeletal muscle transcriptome during prolonged spaceflight

description: Additional file 2. Complete list of DGE genes in the quadriceps. 70 genes were significantly differentially expressed across spaceflight in the quadriceps. Reported here are the gene symbol, log2 fold change (log2 FC), and FDR-adjusted p-value as reported by DeSeq2. Genes are ordered by significance of DGE as measured by FDR.
DOI: 10.6084/m9.figshare.19947326
title: Additional file 5 of Alternative splicing diversifies the skeletal muscle transcriptome during prolonged spaceflight

description: Additional file 5. Gene ontology analyses. Enrichment by gene ontology of upregulated (first), downregulated (second), and alternatively spliced (third) genes in the gastrocnemius (left column) and quadriceps (right column). Reported here are the GO term [top five for each category (biological process, molecular function and cellular component)] and adjusted p-value. Asterisks represent significance as reported by EnrichR.
DOI: 10.6084/m9.figshare.19947323.v1
title: Additional file 4 of Alternative splicing diversifies the skeletal muscle transcriptome during prolonged spaceflight

description: Additional file 4. Complete list of DAS events in the quadriceps. 285 DAS events in 180 genes were identified across spaceflight in the quadriceps. Reported here are the gene symbol, event type (SE, skipped exon; MXE, mutually exclusive exons), △PSI (change in percent spliced in of a specific exon), FDR-adjusted p-value as reported by rMATS-turbo, and genome coordinates. Events are ordered first by gene symbol in alphabetical order and then by significance of DAS as measured by FDR.
DOI: 10.6084/m9.figshare.19947320
title: Additional file 3 of Alternative splicing diversifies the skeletal muscle transcriptome during prolonged spaceflight

description: Additional file 3. Complete list of DAS events in the gastrocnemius. 159 DAS events in 72 genes were identified across spaceflight in the gastrocnemius. Reported here are the gene symbol, event type (SE, skipped exon; MXE, mutually exclusive exons), △PSI (change in percent spliced in of a specific exon), FDR-adjusted p-value as reported by rMATS-turbo, and genome coordinates. Events are ordered first by gene symbol in alphabetical order and then by significance of DAS as measured by FDR.
DOI: 10.6084/m9.figshare.19947326.v1
title: Additional file 5 of Alternative splicing diversifies the skeletal muscle transcriptome during prolonged spaceflight

description: Additional file 5. Gene ontology analyses. Enrichment by gene ontology of upregulated (first), downregulated (second), and alternatively spliced (third) genes in the gastrocnemius (left column) and quadriceps (right column). Reported here are the GO term [top five for each category (biological process, molecular function and cellular component)] and adjusted p-value. Asterisks represent significance as reported by EnrichR.
DOI: 10.6084/m9.figshare.19947320.v1
title: Additional file 3 of Alternative splicing diversifies the skeletal muscle transcriptome during prolonged spaceflight

description: Additional file 3. Complete list of DAS events in the gastrocnemius. 159 DAS events in 72 genes were identified across spaceflight in the gastrocnemius. Reported here are the gene symbol, event type (SE, skipped exon; MXE, mutually exclusive exons), △PSI (change in percent spliced in of a specific exon), FDR-adjusted p-value as reported by rMATS-turbo, and genome coordinates. Events are ordered first by gene symbol in alphabetical order and then by significance of DAS as measured by FDR.
DOI: 10.6084/m9.figshare.19947323
title: Additional file 4 of Alternative splicing diversifies the skeletal muscle transcriptome during prolonged spaceflight

description: Additional file 4. Complete list of DAS events in the quadriceps. 285 DAS events in 180 genes were identified across spaceflight in the quadriceps. Reported here are the gene symbol, event type (SE, skipped exon; MXE, mutually exclusive exons), △PSI (change in percent spliced in of a specific exon), FDR-adjusted p-value as reported by rMATS-turbo, and genome coordinates. Events are ordered first by gene symbol in alphabetical order and then by significance of DAS as measured by FDR.
DOI: 10.6084/m9.figshare.19947336
title: Additional file 1 of Mosaic loss of chromosome Y in peripheral blood cells is associated with age-related macular degeneration in men

description: Additional file 1: Table S1. Y-chromosome euchomatic genes associate to cell cycle meiosis/proliferation and apoptotic signaling.
DOI: 10.6084/m9.figshare.19947339
title: Additional file 2 of Mosaic loss of chromosome Y in peripheral blood cells is associated with age-related macular degeneration in men

description: Additional file 2: Table S2. AMD genes and Y-chromosome function categorized as the proliferation and apoptotic signaling.
DOI: 10.6084/m9.figshare.19947339.v1
title: Additional file 2 of Mosaic loss of chromosome Y in peripheral blood cells is associated with age-related macular degeneration in men

description: Additional file 2: Table S2. AMD genes and Y-chromosome function categorized as the proliferation and apoptotic signaling.
DOI: 10.6084/m9.figshare.19947336.v1
title: Additional file 1 of Mosaic loss of chromosome Y in peripheral blood cells is associated with age-related macular degeneration in men

description: Additional file 1: Table S1. Y-chromosome euchomatic genes associate to cell cycle meiosis/proliferation and apoptotic signaling.
DOI: 10.6084/m9.figshare.19947351
title: Additional file 1 of Malaria time series in the extra-Amazon region of Brazil: epidemiological scenario and a two-year prediction model

description: Additional file 1. A script for software R containing programming used to develop the analysis.
DOI: 10.6084/m9.figshare.19947351.v1
title: Additional file 1 of Malaria time series in the extra-Amazon region of Brazil: epidemiological scenario and a two-year prediction model

description: Additional file 1. A script for software R containing programming used to develop the analysis.
DOI: 10.6084/m9.figshare.19947354
title: Additional file 2 of Malaria time series in the extra-Amazon region of Brazil: epidemiological scenario and a two-year prediction model

description: Additional file 2. The study database containing malaria cases in brazil’s extra-amazon region for the analyzed period.
DOI: 10.6084/m9.figshare.19947354.v1
title: Additional file 2 of Malaria time series in the extra-Amazon region of Brazil: epidemiological scenario and a two-year prediction model

description: Additional file 2. The study database containing malaria cases in brazil’s extra-amazon region for the analyzed period.
DOI: 10.6084/m9.figshare.19947357
title: Additional file 3 of Malaria time series in the extra-Amazon region of Brazil: epidemiological scenario and a two-year prediction model

description: Additional file 3. The study database containing malaria deaths in brazil’s extra-amazon region for the analyzed period.
DOI: 10.6084/m9.figshare.19947357.v1
title: Additional file 3 of Malaria time series in the extra-Amazon region of Brazil: epidemiological scenario and a two-year prediction model

description: Additional file 3. The study database containing malaria deaths in brazil’s extra-amazon region for the analyzed period.
DOI: 10.6084/m9.figshare.19947363.v1
title: Additional file 2 of Perioperative use of antibiotics in full-thickness rectal biopsies for Hirschsprung’s disease

description: Additional file 2.
DOI: 10.6084/m9.figshare.19947363
title: Additional file 2 of Perioperative use of antibiotics in full-thickness rectal biopsies for Hirschsprung’s disease

description: Additional file 2.
DOI: 10.3886/e123042v1-119640
title: National Neighborhood Data Archive (NaNDA): Grocery Stores by ZIP Code Tabulation Area, United States, 2003-2017

description: This dataset contains measures of the number and density of grocery stores – including supermarkets, specialty food stores, and warehouse clubs – per ZIP code tabulation area (ZCTA) in the United States from 2003 through 2017. These types of businesses represent places where neighborhood residents can obtain fresh and healthy foods.
description: Grocery stores in all ZIP code tabulation areas in the United States, including Puerto Rico and the US Virgin Islands. Smallest Geographic Unit: ZIP code tabulation area
description: A ZIP code to ZCTA crosswalk must be used to combine this dataset with ZIP code geocoded data. Such a crosswalk is available on the UDS Mapper website at https://udsmapper.org/zip-code-to-zcta-crosswalk/. Sample code for merging the UDS Mapper crosswalk with NaNDA datasets is available on the NaNDA repository at https://www.openicpsr.org/openicpsr/project/120088/.
DOI: 10.5281/zenodo.6323551
title: Cloud Properties and Changes in RCEMIP

description: Derived data and scripts used in Stauffer and Wing (2022)
DOI: 10.34681/j5kf-eh33
title: The Flint MDT Study (March 2014- January 2016)

description: The Flint MDT Study is one of the projects of the the National Quality Improvement Center on the Representation of Children in Child Welfare (QIC-ChildRep). The Study partnered with a group of five lawyers-guardian ad litem to observe and evaluate a multidisciplinary approach to representing children in child protection proceedings. The study provided the LGALs two social workers and randomly assigned cases to be either represented by the attorney/social worker team or by the attorney alone. This study provides both a description of the functioning of these teams collaborating to represent children and a rigorous evaluation of outcomes compared to a control group. Only quantitative data have been deposited with NDACAN.
DOI: 10.6084/m9.figshare.19694782.v1
title: Amide CNLs

description: Amide CNLs dataset <br>
DOI: 10.6084/m9.figshare.19694782
title: Amide CNLs

description: Amide CNLs dataset <br>
DOI: 10.6084/m9.figshare.19694773
title: Norman CNLs

description: Norman CNLs dataset