cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12199781.v1
title: Metadata associated with the published article: Pleomorphic adenomas and mucoepidermoid carcinomas of the breast are underpinned by fusion genes

description: <b>Summary</b>This metadata record describes the data generated and analysed in the published article “Pleomorphic adenomas and mucoepidermoid carcinomas of the breast are underpinned by fusion genes”. The data include histologic images, RNA sequencing, Archer FusionPlex sequencing, Sanger sequencing and Fluorescence in situ hybridization data.The study which generated the data described here investigated whether primary pleomorphic adenomas (PAs) and mucoepidermoid carcinomas (MECs) of the breast would be underpinned by the fusion genes reported to occur in their salivary gland counterparts. <br><b>Data description and access</b>Histologic images: These support figures 1, 2 and 3. They are in <b>.jpg</b> format and can be requested from Dr. Fresia Pareja.RNA sequencing data (PAs, n=2; MEC, n=1): These support figures 1, 2 and 3, and supplementary tables 1 and 2. They are in <b>BAM </b>format, and are openly available from NCBI Sequence Read Archive under the project accession number SRP257886. The project contains three experiments, with accession numbers: SRX8155358, SRX8155357 and SRX8155356. The identifiers.org link to the project is https://identifiers.org/ncbi/insdc.sra:SRP257886Archer FusionPlex sequencing data (PA, n=1): These support figures 1 and 2, and supplementary tables 1 and 2. They are in Archer FusionPlex sequencing <b>BAM </b>format and can be requested from Dr. Da Cruz Paula.Fluorescence in situ hybridization data: These support figures 1, 2 and 3. They are in <b>.jpg</b> format and can be requested from Dr. Fresia Pareja.Sanger sequencing data: These support figures 2 and 3. They are in <b>SnapGene </b>format and can be requested from Dr. Fresia Pareja. The corresponding authors for this study are: :Dr. Jorge S. Reis-Filho, MD PhD FRCPath, Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA. Phone: +1-212-639-8054. reisfilj@mskcc.orgDr. Fresia Pareja, MD PhD, Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA. Phone: +1-212-639-3707/+1-212-639-6070. parejaf@mskcc.org<br><b>Ethics </b>Following approval by the Memorial Sloan Kettering Cancer Center Institutional Review Board (IRB) the authors’ institutions, formalin fixed paraffin embedded (FFPE) tissue blocks of three breast PAs and one breast MEC were retrieved from the pathology archives of the authors’ institutions. All samples were anonymized before analysis.
DOI: 10.6084/m9.figshare.20069969
title: Identification of upregulated proteins from 6 pairs of gastric cancer tissues with iTRAQ quantitative proteomic analysis.

description: Identification of upregulated proteins from 6 pairs of gastric cancer tissues with  iTRAQ quantitative proteomic analysis. The description of the material and method is attached as "supplemental materials". The supplemental table 1 contains the 415 upregulated proteins from this proteomic analysis. The supplemental table 2 contains the list of protein accession numbers, protein ID, protein probability, protein length and T/N ratio of 3344 proteins in six pairs of GC and their adjacent non-tumorous mucosa.
DOI: 10.6084/m9.figshare.19545709
title: AFR-BERT-main.zip

description: Engineering Research.
DOI: 10.15129/4266be87-5f01-4e92-a5ab-29333e58935b
title: Data For "Numerical studies of colinear laser-assisted injection from a foil as an alternate injection method"

description: Simulation input scripts
DOI: 10.6084/m9.figshare.14821139
title: Additional file 7 of Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

description: Additional file 7: Tandom duplicated genes analyzed for gene conversion.
DOI: 10.6084/m9.figshare.14821139.v1
title: Additional file 7 of Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

description: Additional file 7: Tandom duplicated genes analyzed for gene conversion.
DOI: 10.6084/m9.figshare.14821136
title: Additional file 6 of Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

description: Additional file 6: Devergence time among AhRLKs tandem duplication pairs and segmental duplication pairs.
DOI: 10.6084/m9.figshare.14821127.v1
title: Additional file 4 of Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

description: Additional file 4: Subfamily and chromosome distribution of AhLecRLKs in peanut.
DOI: 10.6084/m9.figshare.14821118
title: Additional file 1 of Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

description: Additional file 1: Complete list and classification of 1311 AhRLKs in peanut.
DOI: 10.6084/m9.figshare.14821265
title: Additional file 7 of Systems pharmacogenomics identifies novel targets and clinically actionable therapeutics for medulloblastoma

description: Additional file 7: Supplementary Table S4. Summary of mutational status in human Medulloblastoma of key CIS genes identified in the mutagenesis screen,
DOI: 10.6084/m9.figshare.14821121
title: Additional file 2 of Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

description: Additional file 2: Complete list and classification of Al response AhRLKs in peanut.
DOI: 10.6084/m9.figshare.14821145
title: Additional file 9 of Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

description: Additional file 9: Expression Profiles of Al-responsive AhRLKs under Al stress.
DOI: 10.6084/m9.figshare.20063877
title: Additional file 2 of Mettl14-mediated m6A modification is essential for visual function and retinal photoreceptor survival

description: Additional file 2. Enriched GO terms in terms of biological processes.
DOI: 10.6084/m9.figshare.12199781
title: Metadata associated with the published article: Pleomorphic adenomas and mucoepidermoid carcinomas of the breast are underpinned by fusion genes

description: <b>Summary</b>This metadata record describes the data generated and analysed in the published article “Pleomorphic adenomas and mucoepidermoid carcinomas of the breast are underpinned by fusion genes”. The data include histologic images, RNA sequencing, Archer FusionPlex sequencing, Sanger sequencing and Fluorescence in situ hybridization data.The study which generated the data described here investigated whether primary pleomorphic adenomas (PAs) and mucoepidermoid carcinomas (MECs) of the breast would be underpinned by the fusion genes reported to occur in their salivary gland counterparts. <br><b>Data description and access</b>Histologic images: These support figures 1, 2 and 3. They are in <b>.jpg</b> format and can be requested from Dr. Fresia Pareja.RNA sequencing data (PAs, n=2; MEC, n=1): These support figures 1, 2 and 3, and supplementary tables 1 and 2. They are in <b>BAM </b>format, and are openly available from NCBI Sequence Read Archive under the project accession number SRP257886. The project contains three experiments, with accession numbers: SRX8155358, SRX8155357 and SRX8155356. The identifiers.org link to the project is https://identifiers.org/ncbi/insdc.sra:SRP257886Archer FusionPlex sequencing data (PA, n=1): These support figures 1 and 2, and supplementary tables 1 and 2. They are in Archer FusionPlex sequencing <b>BAM </b>format and can be requested from Dr. Da Cruz Paula.Fluorescence in situ hybridization data: These support figures 1, 2 and 3. They are in <b>.jpg</b> format and can be requested from Dr. Fresia Pareja.Sanger sequencing data: These support figures 2 and 3. They are in <b>SnapGene </b>format and can be requested from Dr. Fresia Pareja. The corresponding authors for this study are: :Dr. Jorge S. Reis-Filho, MD PhD FRCPath, Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA. Phone: +1-212-639-8054. reisfilj@mskcc.orgDr. Fresia Pareja, MD PhD, Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA. Phone: +1-212-639-3707/+1-212-639-6070. parejaf@mskcc.org<br><b>Ethics </b>Following approval by the Memorial Sloan Kettering Cancer Center Institutional Review Board (IRB) the authors’ institutions, formalin fixed paraffin embedded (FFPE) tissue blocks of three breast PAs and one breast MEC were retrieved from the pathology archives of the authors’ institutions. All samples were anonymized before analysis.
DOI: 10.6084/m9.figshare.20063880.v1
title: Additional file 3 of Mettl14-mediated m6A modification is essential for visual function and retinal photoreceptor survival

description: Additional file 3. Enriched GO terms in terms of cellular component.
DOI: 10.6084/m9.figshare.20063877.v1
title: Additional file 2 of Mettl14-mediated m6A modification is essential for visual function and retinal photoreceptor survival

description: Additional file 2. Enriched GO terms in terms of biological processes.
DOI: 10.6084/m9.figshare.14821124
title: Additional file 3 of Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

description: Additional file 3: Subfamily and chromosome distribution of AhLRR-RLKs in peanut.
DOI: 10.6084/m9.figshare.14821124.v1
title: Additional file 3 of Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

description: Additional file 3: Subfamily and chromosome distribution of AhLRR-RLKs in peanut.
DOI: 10.6084/m9.figshare.14821127
title: Additional file 4 of Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

description: Additional file 4: Subfamily and chromosome distribution of AhLecRLKs in peanut.
DOI: 10.6084/m9.figshare.14821256.v1
title: Additional file 4 of Systems pharmacogenomics identifies novel targets and clinically actionable therapeutics for medulloblastoma

description: Additional file 4: Supplementary Table S3. Expression Data associated with Figure 1.
DOI: 10.6084/m9.figshare.14821118.v1
title: Additional file 1 of Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

description: Additional file 1: Complete list and classification of 1311 AhRLKs in peanut.
DOI: 10.6084/m9.figshare.14821130
title: Additional file 5 of Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

description: Additional file 5: Tandem duplication clusters of AhRLKs.
DOI: 10.6084/m9.figshare.14821250.v1
title: Additional file 2 of Systems pharmacogenomics identifies novel targets and clinically actionable therapeutics for medulloblastoma

description: Additional file 2: Supplementary Table S1. Network parameters for subgroup-specific network analysis.
DOI: 10.6084/m9.figshare.19924224
title: Geochemistry of acid mine drainage from a coal mining area and processes controlling metal attenuation in stream waters, southern Brazil

description: Acid drainage influence on the water and sediment quality was investigated in a coal mining area (southern Brazil). Mine drainage showed pH between 3.2 and 4.6 and elevated concentrations of sulfate, As and metals, of which, Fe, Mn and Zn exceeded the limits for the emission of effluents stated in the Brazilian legislation. Arsenic also exceeded the limit, but only slightly. Groundwater monitoring wells from active mines and tailings piles showed pH interval and chemical concentrations similar to those of mine drainage. However, the river and ground water samples of municipal public water supplies revealed a pH range from 7.2 to 7.5 and low chemical concentrations, although Cd concentration slightly exceeded the limit adopted by Brazilian legislation for groundwater. In general, surface waters showed large pH range (6 to 10.8), and changes caused by acid drainage in the chemical composition of these waters were not very significant. Locally, acid drainage seemed to have dissolved carbonate rocks present in the local stratigraphic sequence, attenuating the dispersion of metals and As. Stream sediments presented anomalies of these elements, which were strongly dependent on the proximity of tailings piles and abandoned mines. We found that precipitation processes in sediments and the dilution of dissolved phases were responsible for the attenuation of the concentrations of the metals and As in the acid drainage and river water mixing zone. In general, a larger influence of mining activities on the chemical composition of the surface waters and sediments was observed when enrichment factors in relation to regional background levels were used.
DOI: 10.6084/m9.figshare.19924224.v1
title: Geochemistry of acid mine drainage from a coal mining area and processes controlling metal attenuation in stream waters, southern Brazil

description: Acid drainage influence on the water and sediment quality was investigated in a coal mining area (southern Brazil). Mine drainage showed pH between 3.2 and 4.6 and elevated concentrations of sulfate, As and metals, of which, Fe, Mn and Zn exceeded the limits for the emission of effluents stated in the Brazilian legislation. Arsenic also exceeded the limit, but only slightly. Groundwater monitoring wells from active mines and tailings piles showed pH interval and chemical concentrations similar to those of mine drainage. However, the river and ground water samples of municipal public water supplies revealed a pH range from 7.2 to 7.5 and low chemical concentrations, although Cd concentration slightly exceeded the limit adopted by Brazilian legislation for groundwater. In general, surface waters showed large pH range (6 to 10.8), and changes caused by acid drainage in the chemical composition of these waters were not very significant. Locally, acid drainage seemed to have dissolved carbonate rocks present in the local stratigraphic sequence, attenuating the dispersion of metals and As. Stream sediments presented anomalies of these elements, which were strongly dependent on the proximity of tailings piles and abandoned mines. We found that precipitation processes in sediments and the dilution of dissolved phases were responsible for the attenuation of the concentrations of the metals and As in the acid drainage and river water mixing zone. In general, a larger influence of mining activities on the chemical composition of the surface waters and sediments was observed when enrichment factors in relation to regional background levels were used.
DOI: 10.6084/m9.figshare.19924230
title: Tools used to estimate soil quality in coal combustion waste areas

description: Soil is a highly complex environmental compartment that has suffered with the contamination of substances of various origins. Among the main activities that affect soil quality are power generation activities that use fossil fuels, such as mineral coal. Environmental protection agencies encourage scientific investigations using tools described in legal devices or standard protocols to evaluate the potential of coal as a pollutant, especially in places that have large reserves of this mineral like the state of Rio Grande do Sul. The aim of this study was to characterize the leached extracts of different soils from an area influenced by coal waste, to classify them according to the guideline values for groundwater described in CONAMA's n. 420/2009, and to estimate the effects of the leachates ingestion in DNA mutation rates. The volume of soil needed to induce a 100% increase in the spontaneous mutation rate varied between 129.3 and 1544.1 mg of soil among the soils studied. Metals such as Mn, Pb, Cd and Ni surpassed the investigation limits for groundwater at least in one soil sample. The results showed that there can be transfer of soil contaminants to groundwater and soil intake in the area could contribute to the increased mutagenic risk.
DOI: 10.6084/m9.figshare.19924230.v1
title: Tools used to estimate soil quality in coal combustion waste areas

description: Soil is a highly complex environmental compartment that has suffered with the contamination of substances of various origins. Among the main activities that affect soil quality are power generation activities that use fossil fuels, such as mineral coal. Environmental protection agencies encourage scientific investigations using tools described in legal devices or standard protocols to evaluate the potential of coal as a pollutant, especially in places that have large reserves of this mineral like the state of Rio Grande do Sul. The aim of this study was to characterize the leached extracts of different soils from an area influenced by coal waste, to classify them according to the guideline values for groundwater described in CONAMA's n. 420/2009, and to estimate the effects of the leachates ingestion in DNA mutation rates. The volume of soil needed to induce a 100% increase in the spontaneous mutation rate varied between 129.3 and 1544.1 mg of soil among the soils studied. Metals such as Mn, Pb, Cd and Ni surpassed the investigation limits for groundwater at least in one soil sample. The results showed that there can be transfer of soil contaminants to groundwater and soil intake in the area could contribute to the increased mutagenic risk.
DOI: 10.6084/m9.figshare.19924228
title: Hydrodynamic Aspects at Vitória Bay Mouth, ES

description: Understading the hydrodynamic behavior and suspended particulated matter (SPM) transport are of great importance in port regions such as Vitória Harbor, which is located at Vitória Bay, Vitória – ES, Brazil. Vitória Bay is an estuary that has not been systematically assessed through a temporal analysis in order to identify its hydrodynamics characteristics and SPM exchange. This study aims to investigate salt and suspended particulate matter flux at the estuarine mouth of Vitória Bay by understanding the temporal variation of salinity, temperature and tidal currents within the water column and at the channel crosssection. Results showed that the estuarine mouth tended to present partial stratification periods during neap tides and little stratification in spring tides. The circulation pattern was mainly influenced by the tide, with little influence from river discharge. With regard to the SPM, the mouth of the estuary tended to show low concentrations, with the highest values occurring during the dry season. A close relationship between momentary discharge, SPM and salt fluxes was observed. Despite all the data was collected at the mouth of the estuary, the system showed an importation trend of salt in all cycles and SPM importation for three of the four studied tidal cycles. Thus, Vitoria Bay is not exporting SPM to the adjacent inner shelf.
DOI: 10.6084/m9.figshare.19924228.v1
title: Hydrodynamic Aspects at Vitória Bay Mouth, ES

description: Understading the hydrodynamic behavior and suspended particulated matter (SPM) transport are of great importance in port regions such as Vitória Harbor, which is located at Vitória Bay, Vitória – ES, Brazil. Vitória Bay is an estuary that has not been systematically assessed through a temporal analysis in order to identify its hydrodynamics characteristics and SPM exchange. This study aims to investigate salt and suspended particulate matter flux at the estuarine mouth of Vitória Bay by understanding the temporal variation of salinity, temperature and tidal currents within the water column and at the channel crosssection. Results showed that the estuarine mouth tended to present partial stratification periods during neap tides and little stratification in spring tides. The circulation pattern was mainly influenced by the tide, with little influence from river discharge. With regard to the SPM, the mouth of the estuary tended to show low concentrations, with the highest values occurring during the dry season. A close relationship between momentary discharge, SPM and salt fluxes was observed. Despite all the data was collected at the mouth of the estuary, the system showed an importation trend of salt in all cycles and SPM importation for three of the four studied tidal cycles. Thus, Vitoria Bay is not exporting SPM to the adjacent inner shelf.
DOI: 10.6084/m9.figshare.19924233
title: Polymorphisms in CYP2E1, GSTM1 and GSTT1 and anti-tuberculosis drug-induced hepatotoxicity

description: Anti-tuberculosis drug-induced hepatitis (ATD- induced hepatitis) has been linked to polymorphisms in genes encoding drug metabolizing enzymes. N-acetyltransferase 2 (NAT2), cytochrome P450 2E1 (CYP2E1) and glutathione S-transferase (loci GSTM1 and GSTT1) are involved in the metabolism of isoniazid, the most toxic drug for the treatment of tuberculosis (TB). This study was designed to determine the frequency and to evaluate whether polymorphisms at CYP2E1, GSTM1 and GSTT1 genes are associated with drug response, as well as to identify clinical risk factors for ATD-induced hepatitis. A total of 245 Brazilian patients undergoing treatment for TB were genotyped using polymerase chain reaction and restriction fragment length polymorphism and sequencing methods. The frequencies of the CYP2E1 polymorphic alleles RsaI, PstI and DraI are 8%, 8.5% and 12%, respectively. GSTM1 and GSTT1 genes are deleted in 42.9% and 12.4% of the population, respectively. Fifteen patients (6.1%) developed hepatotoxicity. Clinical (HIV, female sex and extrapulmonary TB) and genetic characteristics (CYP2E1 without any mutations, having NAT2 slow acetylator profile) are at higher risk of developing ATD-induced hepatitis in this population. Genotyping for GSTM1 and GSTT1 showed no influence on drug response.
DOI: 10.6084/m9.figshare.19924233.v1
title: Polymorphisms in CYP2E1, GSTM1 and GSTT1 and anti-tuberculosis drug-induced hepatotoxicity

description: Anti-tuberculosis drug-induced hepatitis (ATD- induced hepatitis) has been linked to polymorphisms in genes encoding drug metabolizing enzymes. N-acetyltransferase 2 (NAT2), cytochrome P450 2E1 (CYP2E1) and glutathione S-transferase (loci GSTM1 and GSTT1) are involved in the metabolism of isoniazid, the most toxic drug for the treatment of tuberculosis (TB). This study was designed to determine the frequency and to evaluate whether polymorphisms at CYP2E1, GSTM1 and GSTT1 genes are associated with drug response, as well as to identify clinical risk factors for ATD-induced hepatitis. A total of 245 Brazilian patients undergoing treatment for TB were genotyped using polymerase chain reaction and restriction fragment length polymorphism and sequencing methods. The frequencies of the CYP2E1 polymorphic alleles RsaI, PstI and DraI are 8%, 8.5% and 12%, respectively. GSTM1 and GSTT1 genes are deleted in 42.9% and 12.4% of the population, respectively. Fifteen patients (6.1%) developed hepatotoxicity. Clinical (HIV, female sex and extrapulmonary TB) and genetic characteristics (CYP2E1 without any mutations, having NAT2 slow acetylator profile) are at higher risk of developing ATD-induced hepatitis in this population. Genotyping for GSTM1 and GSTT1 showed no influence on drug response.