cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5793657
title: Genetic and landscape characterization of ancient autochthonous olive trees in northern Italy

description: Several ancient olive plants with different genetic, agronomic and morphological characteristics are widespread in the Emilia-Romagna region. In this study, details of 206 trees located in four provinces were collected and their phytometric traits were recorded. Easily recognizable varieties were identified, while plants of uncertain genetic identity were submitted for molecular analysis with SSR markers and compared with cultivars widespread in central Italy and Emilia-Romagna. The genetic analyses showed that most of the ancient olive trees belonged to 10 cultivars that are already characterized, with different cases of intra-varietal clones. The remaining accessions belonged to 19 different genotypes of unknown origin. The highest percentage of policormic trees was found in the Bologna and Rimini provinces. A high percentage of plants located under unfavourable aspects (west to east) was found only in the Rimini territory, which presents peculiar and milder climatic conditions compared to the other provinces. Slope appeared not to be a limiting factor for tree survival. The information obtained could help the rational reintroduction of olive growing in suitable areas of Emilia-Romagna, with the subsequent economic advantages, erosion preservation and germplasm enrichment.
DOI: 10.6084/m9.figshare.5793657.v1
title: Genetic and landscape characterization of ancient autochthonous olive trees in northern Italy

description: Several ancient olive plants with different genetic, agronomic and morphological characteristics are widespread in the Emilia-Romagna region. In this study, details of 206 trees located in four provinces were collected and their phytometric traits were recorded. Easily recognizable varieties were identified, while plants of uncertain genetic identity were submitted for molecular analysis with SSR markers and compared with cultivars widespread in central Italy and Emilia-Romagna. The genetic analyses showed that most of the ancient olive trees belonged to 10 cultivars that are already characterized, with different cases of intra-varietal clones. The remaining accessions belonged to 19 different genotypes of unknown origin. The highest percentage of policormic trees was found in the Bologna and Rimini provinces. A high percentage of plants located under unfavourable aspects (west to east) was found only in the Rimini territory, which presents peculiar and milder climatic conditions compared to the other provinces. Slope appeared not to be a limiting factor for tree survival. The information obtained could help the rational reintroduction of olive growing in suitable areas of Emilia-Romagna, with the subsequent economic advantages, erosion preservation and germplasm enrichment.
DOI: 10.6084/m9.figshare.5793636
title: Ginsenoside Rh1: A Systematic Review of Its Pharmacological Properties

description: Ginsenoside Rh1 is one of major bioactive compounds extracted from red ginseng, which has been increasingly used for enhancing cognition and physical health worldwide. The objective of this study was to review the pharmacological effects of ginsenoside Rh1 in a systematic manner. We performed searches on eight electronic databases including MEDLINE (Pubmed), Scopus, Google Scholar, POPLINE, Global Health Library, Virtual Health Library, the System for Information on Grey Literature in Europe, and the New York Academy of Medicine Grey Literature Report to select the original research publications reporting the biological and pharmacological effects of ginsenoside Rh1 from in vitro and in vivostudies regardless of publication language and study design. Upon applying the inclusion and exclusion criteria, we included a total of 57 studies for our systemic review. Ginsenoside Rh1 exhibited the potent characteristics of anti-inflammatory, antioxidant, immunomodulatory effects, and positive effects on the nervous system. The cytotoxic effects of ginsenoside Rh1 were dependent on different types of cell lines. Other pharmacological effects including estrogenic, enzymatic, anti-microorganism activities, and cardiovascular effects have been mentioned, but the results were considerably diverged. A higher quality of evidence on clinical trial studies is highly recommended to confirm the consistent efficacy of ginsenoside Rh1.
DOI: 10.6084/m9.figshare.5793636.v2
title: Ginsenoside Rh1: A Systematic Review of Its Pharmacological Properties

description: Ginsenoside Rh1 is one of major bioactive compounds extracted from red ginseng, which has been increasingly used for enhancing cognition and physical health worldwide. The objective of this study was to review the pharmacological effects of ginsenoside Rh1 in a systematic manner. We performed searches on eight electronic databases including MEDLINE (Pubmed), Scopus, Google Scholar, POPLINE, Global Health Library, Virtual Health Library, the System for Information on Grey Literature in Europe, and the New York Academy of Medicine Grey Literature Report to select the original research publications reporting the biological and pharmacological effects of ginsenoside Rh1 from in vitro and in vivostudies regardless of publication language and study design. Upon applying the inclusion and exclusion criteria, we included a total of 57 studies for our systemic review. Ginsenoside Rh1 exhibited the potent characteristics of anti-inflammatory, antioxidant, immunomodulatory effects, and positive effects on the nervous system. The cytotoxic effects of ginsenoside Rh1 were dependent on different types of cell lines. Other pharmacological effects including estrogenic, enzymatic, anti-microorganism activities, and cardiovascular effects have been mentioned, but the results were considerably diverged. A higher quality of evidence on clinical trial studies is highly recommended to confirm the consistent efficacy of ginsenoside Rh1.
DOI: 10.6084/m9.figshare.5793549
title: Additional file 7: of A live cell assay of GPCR coupling allows identification of optogenetic tools for controlling Go and Gi signaling

description: Curve-fitting results for pooled dose–response data shown in Fig. 3c. For each opsin/G-protein combination, pooled irradiance–response data were analyzed with an F-test comparing a three-parameter sigmoid model (test hypothesis) to a flat-line model (null hypothesis), with significance threshold p
DOI: 10.6084/m9.figshare.5793549.v1
title: Additional file 7: of A live cell assay of GPCR coupling allows identification of optogenetic tools for controlling Go and Gi signaling

description: Curve-fitting results for pooled dose–response data shown in Fig. 3c. For each opsin/G-protein combination, pooled irradiance–response data were analyzed with an F-test comparing a three-parameter sigmoid model (test hypothesis) to a flat-line model (null hypothesis), with significance threshold p
DOI: 10.6084/m9.figshare.5793537
title: MOESM4 of Structural alteration of DNA induced by viral protein R of HIV-1 triggers the DNA damage response

description: Additional file 4: Table S1. Knockdown efficiency of siRNA target genes. Relative expression levels compared to cont-si (100%: shaded) are shown. Data were obtained from at least three independent experiments.
DOI: 10.6084/m9.figshare.5793537.v1
title: MOESM4 of Structural alteration of DNA induced by viral protein R of HIV-1 triggers the DNA damage response

description: Additional file 4: Table S1. Knockdown efficiency of siRNA target genes. Relative expression levels compared to cont-si (100%: shaded) are shown. Data were obtained from at least three independent experiments.
DOI: 10.6084/m9.figshare.5793516
title: MOESM21 of Structural alteration of DNA induced by viral protein R of HIV-1 triggers the DNA damage response

description: Additional file 21: Table S4. List of primers for qRT-PCR.
DOI: 10.6084/m9.figshare.5793516.v1
title: MOESM21 of Structural alteration of DNA induced by viral protein R of HIV-1 triggers the DNA damage response

description: Additional file 21: Table S4. List of primers for qRT-PCR.
DOI: 10.6084/m9.figshare.5793507
title: MOESM20 of Structural alteration of DNA induced by viral protein R of HIV-1 triggers the DNA damage response

description: Additional file 20: Table S3. List of oligonucleotides used in this study.
DOI: 10.6084/m9.figshare.5793507.v1
title: MOESM20 of Structural alteration of DNA induced by viral protein R of HIV-1 triggers the DNA damage response

description: Additional file 20: Table S3. List of oligonucleotides used in this study.
DOI: 10.6084/m9.figshare.5793495
title: Additional file 1: of A live cell assay of GPCR coupling allows identification of optogenetic tools for controlling Go and Gi signaling

description: Curve-fitting results for pooled dose–response data shown in Fig. 1d. For each GPCR/G protein combination, pooled dose–response data were analyzed by F-test comparing a three-parameter sigmoid model (test hypothesis) to a flat-line model (null hypothesis), with significance threshold p
DOI: 10.6084/m9.figshare.5793495.v1
title: Additional file 1: of A live cell assay of GPCR coupling allows identification of optogenetic tools for controlling Go and Gi signaling

description: Curve-fitting results for pooled dose–response data shown in Fig. 1d. For each GPCR/G protein combination, pooled dose–response data were analyzed by F-test comparing a three-parameter sigmoid model (test hypothesis) to a flat-line model (null hypothesis), with significance threshold p
DOI: 10.6084/m9.figshare.5793489
title: MOESM19 of Structural alteration of DNA induced by viral protein R of HIV-1 triggers the DNA damage response

description: Additional file 19: Table S2. List of resources used in this study.
DOI: 10.6084/m9.figshare.5793489.v1
title: MOESM19 of Structural alteration of DNA induced by viral protein R of HIV-1 triggers the DNA damage response

description: Additional file 19: Table S2. List of resources used in this study.
DOI: 10.6084/m9.figshare.5793486
title: Additional file 11: of A live cell assay of GPCR coupling allows identification of optogenetic tools for controlling Go and Gi signaling

description: Raw and analyzed data for all multi-well luminescent recordings used to generate Figs.Â 1, 2, 3, 4, and 5 and Additional file 2: Figure S1, Additional file 3: Figure S2, Additional file 4: Figure S3, Additional file 5: Figure S4, Additional file 6: Figure S5, and Additional file 8: Figure S6. (XLSX 1795 kb)
DOI: 10.6084/m9.figshare.5793486.v1
title: Additional file 11: of A live cell assay of GPCR coupling allows identification of optogenetic tools for controlling Go and Gi signaling

description: Raw and analyzed data for all multi-well luminescent recordings used to generate Figs.Â 1, 2, 3, 4, and 5 and Additional file 2: Figure S1, Additional file 3: Figure S2, Additional file 4: Figure S3, Additional file 5: Figure S4, Additional file 6: Figure S5, and Additional file 8: Figure S6. (XLSX 1795 kb)
DOI: 10.6084/m9.figshare.5793474
title: Additional file 10: of A live cell assay of GPCR coupling allows identification of optogenetic tools for controlling Go and Gi signaling

description: Curve-fitting results for individual dose–response data in Fig. 3 and results of ANOVAs shown in Fig. 3 and Additional file 8: Figure S6. For RHO, LWS cone opsin, SWS cone opsin, RL3Sc, RL3Am, and RL3m6L2, the irradiance–response data from each individual trial was analyzed with an F-test comparing a three-parameter sigmoid model (test hypothesis) to a flat-line model (null hypothesis), with significance threshold p
DOI: 10.6084/m9.figshare.5793474.v1
title: Additional file 10: of A live cell assay of GPCR coupling allows identification of optogenetic tools for controlling Go and Gi signaling

description: Curve-fitting results for individual dose–response data in Fig. 3 and results of ANOVAs shown in Fig. 3 and Additional file 8: Figure S6. For RHO, LWS cone opsin, SWS cone opsin, RL3Sc, RL3Am, and RL3m6L2, the irradiance–response data from each individual trial was analyzed with an F-test comparing a three-parameter sigmoid model (test hypothesis) to a flat-line model (null hypothesis), with significance threshold p
DOI: 10.6084/m9.figshare.5793363
title: Additional file 1 of Donor age affects proteome composition of tenocyte-derived engineered tendon

description: All proteins identified by PEAKS in young and old tendon-derived TEC with correpsonding cellular sublocations defined by IPA and Matrisome Project. (XLSX 57Â kb)
DOI: 10.6084/m9.figshare.5793363.v1
title: Additional file 1 of Donor age affects proteome composition of tenocyte-derived engineered tendon

description: All proteins identified by PEAKS in young and old tendon-derived TEC with correpsonding cellular sublocations defined by IPA and Matrisome Project. (XLSX 57Â kb)
DOI: 10.6084/m9.figshare.5793360
title: Additional file 9: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains fold-change data for sigma factor genes and corresponding regulon genes for each during mercurial exposure based on RegulonDB annotation. (XLSX 237 kb)
DOI: 10.6084/m9.figshare.5793360.v1
title: Additional file 9: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains fold-change data for sigma factor genes and corresponding regulon genes for each during mercurial exposure based on RegulonDB annotation. (XLSX 237 kb)
DOI: 10.6084/m9.figshare.5793357
title: Additional file 5: of Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

description: A zip archive with the R script and necessary input files needed to reproduce all statistical analyses and graphics. (R 159 kb)
DOI: 10.6084/m9.figshare.5793357.v1
title: Additional file 5: of Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

description: A zip archive with the R script and necessary input files needed to reproduce all statistical analyses and graphics. (R 159 kb)
DOI: 10.6084/m9.figshare.5793348
title: Additional file 8: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains fold-change data for genes involved transcription and RNA turnover. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.5793348.v1
title: Additional file 8: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains fold-change data for genes involved transcription and RNA turnover. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.5793345
title: Additional file 4: of Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

description: A zip archive comprising the command line code and necessary input files needed to replicate bioinformatic analysis. (ZIP 628 kb)
DOI: 10.6084/m9.figshare.5793345.v1
title: Additional file 4: of Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

description: A zip archive comprising the command line code and necessary input files needed to replicate bioinformatic analysis. (ZIP 628 kb)
DOI: 10.6084/m9.figshare.5793333
title: Additional file 7: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains fold-change data for genes involved in DNA replication, recombination, degradation, and repair. (XLSX â 41 kb)
DOI: 10.6084/m9.figshare.5793333.v1
title: Additional file 7: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains fold-change data for genes involved in DNA replication, recombination, degradation, and repair. (XLSX â 41 kb)
DOI: 10.6084/m9.figshare.5793330
title: Additional file 3: of Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

description: An XLSX table reporting the indicator species and edgeR results and the assignments to cropping sensitive OTUs and network modules. This information is provided in separate sheets for the bacteria and fungi in soil and roots. (XLSX 278 kb)
DOI: 10.6084/m9.figshare.5793330.v1
title: Additional file 3: of Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

description: An XLSX table reporting the indicator species and edgeR results and the assignments to cropping sensitive OTUs and network modules. This information is provided in separate sheets for the bacteria and fungi in soil and roots. (XLSX 278 kb)
DOI: 10.6084/m9.figshare.5793324
title: Additional file 6: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains fold-change, log2 fold-change, and false discovery rate values for significantly differentially expressed genes (≤ 1% FDR and ≥ 2 fold-change) for unexposed condition at each time point compared to time 0 or for sub-intervals. “n.s.” indicates that expression was not significantly different from that of the indicated prior time comparison. (XLSX – 1566 kb)
DOI: 10.6084/m9.figshare.5793324.v1
title: Additional file 6: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains fold-change, log2 fold-change, and false discovery rate values for significantly differentially expressed genes (≤ 1% FDR and ≥ 2 fold-change) for unexposed condition at each time point compared to time 0 or for sub-intervals. “n.s.” indicates that expression was not significantly different from that of the indicated prior time comparison. (XLSX – 1566 kb)
DOI: 10.6084/m9.figshare.5793321
title: Additional file 2: of Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

description: An XLSX table contains the experimental design (Sample ID, sample type and cropping system), chemical soil data and sequencing information (barcodes and sequence counts). (XLSX 46 kb)
DOI: 10.6084/m9.figshare.5793321.v1
title: Additional file 2: of Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

description: An XLSX table contains the experimental design (Sample ID, sample type and cropping system), chemical soil data and sequencing information (barcodes and sequence counts). (XLSX 46 kb)
DOI: 10.6084/m9.figshare.5793291
title: Additional file 5: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains data from STRING v10.0 network analysis of up- regulated genes with â Ľ 5 foldchange for mercury exposure conditions and all up- regulated genes for unexposed conditions. Network maps for mercury exposures are in Figure S8 and unexposed conditions in Figure S10. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.5793291.v1
title: Additional file 5: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains data from STRING v10.0 network analysis of up- regulated genes with â Ľ 5 foldchange for mercury exposure conditions and all up- regulated genes for unexposed conditions. Network maps for mercury exposures are in Figure S8 and unexposed conditions in Figure S10. (XLSX 54 kb)
DOI: 10.6084/m9.figshare.5793276
title: Additional file 4: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains data from Table S5 grouped by COGâ s 2014 functional category annotation. Gene IDâ s and names highlighted in red indicate duplicate entries that are annotated in more than one category. (XLSX 583 kb)
DOI: 10.6084/m9.figshare.5793276.v1
title: Additional file 4: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains data from Table S5 grouped by COGâ s 2014 functional category annotation. Gene IDâ s and names highlighted in red indicate duplicate entries that are annotated in more than one category. (XLSX 583 kb)
DOI: 10.6084/m9.figshare.5793258
title: Additional file 3: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains fold-change, log2 fold-change, and false discovery rate values for significantly differentially expressed genes (≤ 1% FDR and ≥ 2 fold-change) for mercury exposed conditions as determined by baySeq analysis and “n.s.” designates expression that was not significantly different from unexposed culture at the same time point. (XLSX 1966 kb)
DOI: 10.6084/m9.figshare.5793258.v1
title: Additional file 3: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains fold-change, log2 fold-change, and false discovery rate values for significantly differentially expressed genes (≤ 1% FDR and ≥ 2 fold-change) for mercury exposed conditions as determined by baySeq analysis and “n.s.” designates expression that was not significantly different from unexposed culture at the same time point. (XLSX 1966 kb)
DOI: 10.6084/m9.figshare.5793234
title: Additional file 2: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains raw read counts for each gene across all conditions as determined by counting mapped paired-end reads using HTseq-count. (XLSX 1157 kb)
DOI: 10.6084/m9.figshare.5793234.v1
title: Additional file 2: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains raw read counts for each gene across all conditions as determined by counting mapped paired-end reads using HTseq-count. (XLSX 1157 kb)
DOI: 10.6084/m9.figshare.5793192
title: Additional file 15: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains data for genes that were not significantly differentially expressed at 10 min, but were at 30 and 60 min or just 60 min after mercurial exposure. Data is organized by just upregulated, just down-regulated, or combined. â n.s.â designates expression that was not significantly different from unexposed culture at the same time point. (XLSX 103 kb)
DOI: 10.6084/m9.figshare.5793192.v1
title: Additional file 15: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains data for genes that were not significantly differentially expressed at 10 min, but were at 30 and 60 min or just 60 min after mercurial exposure. Data is organized by just upregulated, just down-regulated, or combined. â n.s.â designates expression that was not significantly different from unexposed culture at the same time point. (XLSX 103 kb)
DOI: 10.6084/m9.figshare.5793174
title: Additional file 14: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains fold-change data for genes regulated by OxyRS or SoxRS regulons based on annotations. (XLSX 58 kb)
DOI: 10.6084/m9.figshare.5793174.v1
title: Additional file 14: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains fold-change data for genes regulated by OxyRS or SoxRS regulons based on annotations. (XLSX 58 kb)
DOI: 10.6084/m9.figshare.5793159
title: Additional file 13: of Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure

description: Contains fold-change data for genes grouped by metal bound by each protein based on gene ontology (GO) annotation in UniProtKB database. (XLSX 143 kb)