cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5051725.v4
title: Stern_et_al_2017_Applied_Env_Microbiology(1of2)

description: Raw (joined, paired-end Illumina MiSeq) 16S sequences and Mapping files for data in experiments CF1 and DCF from: <br>Stern, N., Ginder-Vogel, M., Stegen, J.C., Arntzen, B., Kennedy, W.K., Larget, B.R., Roden, E.R. (2017). Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor. Applied Environmental Microbiology. Accepted March 2017(Under Revision).<br>Unassembled reads are listed in un1 (forward) and un2 (reverse).<br>
DOI: 10.6084/m9.figshare.5051611.v1
title: CF1_MappingFile

description: Mapping file for CF1 experiment.
DOI: 10.6084/m9.figshare.5051725.v3
title: Stern_et_al_2017_Applied_Environmental_Microbiology(1of2)

description: Raw (joined, paired-end Illumina MiSeq) 16S sequences and Mapping files for data in experiments CF1 and DCF from: <br>Stern, N., Ginder-Vogel, M., Stegen, J.C., Arntzen, B., Kennedy, W.K., Larget, B.R., Roden, E.R. (2017). Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor. Applied Environmental Microbiology. Accepted March 2017(Under Revision).
DOI: 10.6084/m9.figshare.5051536
title: CF2_fastqjoin.un2.fastq

description: Raw paired-end Illumina MiSeq 16S sequences for experiments CF2. Associated mapping files found in main project folder at the following link:<br>https://figshare.com/projects/Stern_et_al_2017_Applied_Environmental_Microbiology/22213<br>Data from: Stern, N., Ginder-Vogel, M., Stegen, J.C., Arntzen, B., Kennedy, W.K., Larget, B.R., Roden, E.R. (2017). Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor. Applied Environmental Microbiology. Accepted March 2017(Under Revision).<br>
DOI: 10.6084/m9.figshare.5051536.v1
title: CF2_fastqjoin.un2.fastq

description: Raw paired-end Illumina MiSeq 16S sequences for experiments CF2. Associated mapping files found in main project folder at the following link:<br>https://figshare.com/projects/Stern_et_al_2017_Applied_Environmental_Microbiology/22213<br>Data from: Stern, N., Ginder-Vogel, M., Stegen, J.C., Arntzen, B., Kennedy, W.K., Larget, B.R., Roden, E.R. (2017). Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor. Applied Environmental Microbiology. Accepted March 2017(Under Revision).<br>
DOI: 10.6084/m9.figshare.5051596.v1
title: Short-term EEG dynamics and neural generators evoked by navigational images

description: Data from the paper entitled: "Short-term EEG dynamics and neural generators evoked by navigational images"<br>Files structure is as stated in: filestructure.txt<br>Data studies and analysis generated in eeglab for high density EEG recorded from navigational images.All recordings were unipolar against the left earlobe electrode Vertical eye movements (EOG) were recorded unipolarly against the common reference and horizontal EOG was recorded bipolarly. All electrode impedances were maintained below 5 kΩ. Scalp potentials were amplified by ANT DC-amplifiers (ANT, the Netherlands) and digitized with a rate of 2.048 Hz, a resolution of 16 bit (range 11 mV). A band pass from DC to 256 Hz and a notch filter (47.5-52.5 Hz) were also applied.
DOI: 10.6084/m9.figshare.5051593.v1
title: P3HT and PCBM atomistic force fields

description: GROMOS 53A6 based atomistic force field for the conjugated polymer P3HT, the fullerene derivative PCBM and chlorobenzene.<br>The provided files are in GROMACS format (see GROMACS manual and tutorial in case of need). A pre-equilibrated system containing a P3HT chain (24 repeat units) and a PCBM molecule solvated in chlorobenzene is provided. The associated top(ology) file (and files included therein) is provided, along with run parameter files for an energy minimization (em.mdp), NVT equilibration (shortNVT.mdp), NPT equilibration (shortNPT.mdp), and production run (prodNPT.mdp).<br>NOTE! The archive "p3ht_v_1_0_RA.ff.zip" needs to be unzipped first (command: unzip p3ht_v_1_0_RA.ff.zip). For details on the atomistic force fields, see the associated publication:<br><b>Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations</b>Riccardo Alessandri, Jaakko J. Uusitalo, Alex H. de Vries, Remco W. A. Havenith, and Siewert J. Marrink<i>J. Am. Chem. Soc.</i>, <b>2017</b>, 139 (10), pp 3697–3705<br>
DOI: 10.6084/m9.figshare.5051608.v1
title: CF2_fastqjoin.join.fastq

description: Raw joined Illumina MiSeq 16S sequences for experiment CF2. File is compressed due to large size, must be unzipped for data analysis. Associated mapping files found in main project folder at the following link:<br>https://figshare.com/projects/Stern_et_al_2017_Applied_Environmental_Microbiology/22213<br>Data from: Stern, N., Ginder-Vogel, M., Stegen, J.C., Arntzen, B., Kennedy, W.K., Larget, B.R., Roden, E.R. (2017). Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor. Applied Environmental Microbiology. Accepted March 2017(Under Revision).<br>
DOI: 10.6084/m9.figshare.5051596.v2
title: Short-term EEG dynamics and neural generators evoked by navigational images

description: Data from the paper entitled: "Short-term EEG dynamics and neural generators evoked by navigational images"<br>Files structure is as stated in: filestructure.txt<br>Raw data from subjects.All recordings were unipolar against the left earlobe electrode Vertical eye movements (EOG) were recorded unipolarly against the common reference and horizontal EOG was recorded bipolarly. All electrode impedances were maintained below 5 kΩ. Scalp potentials were amplified by ANT DC-amplifiers (ANT, the Netherlands) and digitized with a rate of 2.048 Hz, a resolution of 16 bit (range 11 mV). A band pass from DC to 256 Hz and a notch filter (47.5-52.5 Hz) were also applied.
DOI: 10.6084/m9.figshare.5051386
title: Environmental data flooding experiment

description: Data from soil flooded after 0, 1, 3, 5, 7, 10, 14, 17, 21, 24 and 31 days. Data from flux experiment from same experiment.<br>
DOI: 10.6084/m9.figshare.5051593.v2
title: P3HT and PCBM atomistic force fields

description: GROMOS 53A6 based atomistic force field for the conjugated polymer P3HT, the fullerene derivative PCBM and chlorobenzene.<br>The provided files are in GROMACS format (see GROMACS manual and tutorial in case of need). A pre-equilibrated system containing a P3HT chain (24 repeat units) and a PCBM molecule solvated in chlorobenzene is provided. The associated top(ology) file (and files included therein) is provided, along with run parameter files for an energy minimization (em.mdp), NVT equilibration (shortNVT.mdp), NPT equilibration (shortNPT.mdp), and production run (prodNPT.mdp).<br>NOTE! The archive "p3ht_v_1_0_RA.ff.zip" needs to be unzipped first (command: unzip p3ht_v_1_0_RA.ff.zip).<br> For details on the atomistic force fields, see the associated publication (and please cite it if you find the files useful for your work):<br><b>Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations</b>Riccardo Alessandri, Jaakko J. Uusitalo, Alex H. de Vries, Remco W. A. Havenith, and Siewert J. Marrink<i>J. Am. Chem. Soc.</i>, <b>2017</b>, 139 (10), pp 3697–3705<br>
DOI: 10.6084/m9.figshare.5051608.v2
title: CF2_fastqjoin.join.fastq

description: Raw joined Illumina MiSeq 16S sequences for experiment CF2. File is compressed due to large size, must be unzipped for data analysis. Associated mapping files found in main project folder at the following link:<br>https://figshare.com/projects/Stern_et_al_2017_Applied_Environmental_Microbiology/22213<br>Data from: Stern, N., Ginder-Vogel, M., Stegen, J.C., Arntzen, B., Kennedy, W.K., Larget, B.R., Roden, E.R. (2017). Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor. Applied Environmental Microbiology. Accepted March 2017(Under Revision).<br>
DOI: 10.6084/m9.figshare.5051386.v1
title: Environmental data flooding experimant

description: Data from soil flooded after 0, 1, 3, 5, 7, 10, 14, 17, 21, 24 and 31 days. Data from flux experiment from same experiment.<br>
DOI: 10.6084/m9.figshare.5051608.v4
title: Stern_et_al_2017_Applied_Env_Microbiology(2of2)

description: Raw (joined, paired-end Illumina MiSeq) 16S sequences and Mapping file for data in experiment CF2 from: <br>Stern, N., Ginder-Vogel, M., Stegen, J.C., Arntzen, B., Kennedy, W.K., Larget, B.R., Roden, E.R. (2017). Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor. Applied Environmental Microbiology. Accepted March 2017(Under Revision).<br>Unassembled reads are listed in un1 (forward) and un2 (reverse).<br>
DOI: 10.6084/m9.figshare.5050855.v1
title: Tracking SBRT for liver tumors with a gimbaled linac system: a single institution experience

description: Tracking SBRT for liver tumors with a gimbaled linac system: a single institution experience
DOI: 10.6084/m9.figshare.5050840
title: Soil data

description: Soil from soil flooded after 0, 1, 3, 5, 7, 10, 14, 17, 21, 24 and 31 days.<br>
DOI: 10.6084/m9.figshare.5051608.v3
title: Stern_et_al_2017_Applied_Environmental_Microbiology(2of2)

description: Raw (joined, paired-end Illumina MiSeq) 16S sequences and Mapping file for data in experiment CF2 from: <br>Stern, N., Ginder-Vogel, M., Stegen, J.C., Arntzen, B., Kennedy, W.K., Larget, B.R., Roden, E.R. (2017). Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor. Applied Environmental Microbiology. Accepted March 2017(Under Revision).
DOI: 10.6084/m9.figshare.5050687
title: Comparative analysis of 12 different kits for bisulfite conversion of circulating cell-free DNA

description: Blood circulating cell-free DNA (cfDNA) is becoming popular in the search of promising predictive and prognostic biomarkers. Among these biomarkers, cfDNA methylation markers have especially gained considerable attention. A significant challenge in the utilization of cfDNA methylation markers is the limited amount of cfDNA available for analyses; reportedly, bisulfite conversion (BSC) reduce cfDNA amounts even further. Nevertheless, few efforts have focused on ensuring high cfDNA conversion efficiency and recovery after BSC. To compare cfDNA recovery of different BSC methods, we compared 12 different commercially available BSC kits. We tested whether DNA recovery was affected by the molecular weight and/or quantity of input DNA. We also tested BSC efficiency for each kit. We found that recovery varied for DNA fragments of different lengths: certain kits recovered short fragments better than others, and only 3 kits recovered DNA fragments of &lt;100 bp well. In contrast, DNA input amount did not seem to affect DNA recovery: for quantities spanning between 820 and ∼25,000 genome equivalents per BSC, a linear relation was found between input and recovery amount. Overall, mean recovery ranged between 9 and 32%, with BSC efficiency of 97–99.9%. When plasma cfDNA was used as input for BSC, recovery varied from 22% for the poorest and 66% for the best performing kits, while conversion efficiency ranged from 96 to 100% among different kits. In conclusion, clear performance differences exist between commercially available BSC kits, both in terms of DNA recovery and conversion efficiency. The choice of BSC kit can substantially impact the amount of converted cfDNA available for downstream analysis, which is critical in a cfDNA methylation marker setting.
DOI: 10.6084/m9.figshare.5050582
title: Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis

description: Aberrant DNA methylation patterns have been reported in inflamed tissues and may play a role in disease. We studied DNA methylation and gene expression profiles of purified intestinal epithelial cells from ulcerative colitis patients, comparing inflamed and non-inflamed areas of the colon. We identified 577 differentially methylated sites (false discovery rate &lt;0.2) mapping to 210 genes. From gene expression data from the same epithelial cells, we identified 62 differentially expressed genes with increased expression in the presence of inflammation at prostate cancer susceptibility genes <i>PRAC1</i> and <i>PRAC2</i>. Four genes showed inverse correlation between methylation and gene expression; <i>ROR1, GXYLT2, FOXA2,</i> and, notably, <i>RARB</i>, a gene previously identified as a tumor suppressor in colorectal adenocarcinoma as well as breast, lung and prostate cancer. We highlight targeted and specific patterns of DNA methylation and gene expression in epithelial cells from inflamed colon, while challenging the importance of epithelial cells in the pathogenesis of chronic inflammation.
DOI: 10.6084/m9.figshare.5050687.v1
title: Comparative analysis of 12 different kits for bisulfite conversion of circulating cell-free DNA

description: Blood circulating cell-free DNA (cfDNA) is becoming popular in the search of promising predictive and prognostic biomarkers. Among these biomarkers, cfDNA methylation markers have especially gained considerable attention. A significant challenge in the utilization of cfDNA methylation markers is the limited amount of cfDNA available for analyses; reportedly, bisulfite conversion (BSC) reduce cfDNA amounts even further. Nevertheless, few efforts have focused on ensuring high cfDNA conversion efficiency and recovery after BSC. To compare cfDNA recovery of different BSC methods, we compared 12 different commercially available BSC kits. We tested whether DNA recovery was affected by the molecular weight and/or quantity of input DNA. We also tested BSC efficiency for each kit. We found that recovery varied for DNA fragments of different lengths: certain kits recovered short fragments better than others, and only 3 kits recovered DNA fragments of &lt;100 bp well. In contrast, DNA input amount did not seem to affect DNA recovery: for quantities spanning between 820 and ∼25,000 genome equivalents per BSC, a linear relation was found between input and recovery amount. Overall, mean recovery ranged between 9 and 32%, with BSC efficiency of 97–99.9%. When plasma cfDNA was used as input for BSC, recovery varied from 22% for the poorest and 66% for the best performing kits, while conversion efficiency ranged from 96 to 100% among different kits. In conclusion, clear performance differences exist between commercially available BSC kits, both in terms of DNA recovery and conversion efficiency. The choice of BSC kit can substantially impact the amount of converted cfDNA available for downstream analysis, which is critical in a cfDNA methylation marker setting.
DOI: 10.6084/m9.figshare.5050582.v1
title: Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis

description: Aberrant DNA methylation patterns have been reported in inflamed tissues and may play a role in disease. We studied DNA methylation and gene expression profiles of purified intestinal epithelial cells from ulcerative colitis patients, comparing inflamed and non-inflamed areas of the colon. We identified 577 differentially methylated sites (false discovery rate &lt;0.2) mapping to 210 genes. From gene expression data from the same epithelial cells, we identified 62 differentially expressed genes with increased expression in the presence of inflammation at prostate cancer susceptibility genes <i>PRAC1</i> and <i>PRAC2</i>. Four genes showed inverse correlation between methylation and gene expression; <i>ROR1, GXYLT2, FOXA2,</i> and, notably, <i>RARB</i>, a gene previously identified as a tumor suppressor in colorectal adenocarcinoma as well as breast, lung and prostate cancer. We highlight targeted and specific patterns of DNA methylation and gene expression in epithelial cells from inflamed colon, while challenging the importance of epithelial cells in the pathogenesis of chronic inflammation.
DOI: 10.6084/m9.figshare.5050765
title: Genome-wide Methyl-Seq analysis of blood-brain targets of glucocorticoid exposure

description: Chronic exposure to glucocorticoids (GCs) can lead to psychiatric complications through epigenetic mechanisms such as DNA methylation (DNAm). We sought to determine whether epigenetic changes in a peripheral tissue can serve as a surrogate for those in a relatively inaccessible tissue such as the brain. DNA extracted from the hippocampus and blood of mice treated with GCs or vehicle solution was assayed using a genome-wide DNAm platform (Methyl-Seq) to identify differentially methylated regions (DMRs) induced by GC treatment. We observed that ∼70% of the DMRs in both tissues lost methylation following GC treatment. Of the 3,095 DMRs that mapped to the same genes in both tissues, 1,853 DMRs underwent DNAm changes in the same direction. Interestingly, only 209 DMRs (&lt;7%) overlapped in genomic coordinates between the 2 tissues, suggesting tissue-specific differences in GC-targeted loci. Pathway analysis showed that the DMR-associated genes were members of pathways involved in metabolism, immune function, and neurodevelopment. Also, changes in cell type composition of blood and brain were examined by fluorescence-activated cell sorting. Separation of the cortex into neuronal and non-neuronal fractions and the leukocytes into T-cells, B-cells, and neutrophils showed that GC-induced methylation changes primarily occurred in neurons and T-cells, with the blood tissue also undergoing a shift in the proportion of constituent cell types while the proportion of neurons and glia in the brain remained stable. From the current pilot study, we found that despite tissue-specific epigenetic changes and cellular heterogeneity, blood can serve as a surrogate for GC-induced changes in the brain.
DOI: 10.6084/m9.figshare.5050288
title: Prediction of long-term survival in patients with metastatic gastrointestinal stromal tumor: analysis of a large, single-institution cohort

description: <b>Background:</b> A subset of patients with metastatic GIST become long-term survivors, and a more precise prediction of outcome could improve clinical decision-making. <b>Material and methods:</b> One-hundred and thirty-three patients diagnosed with metastatic GIST from 1995 to 2013 were identified from the sarcoma database at Oslo University Hospital. Clinical data prospectively registered in the database were supplemented with retrospective review of medical records. Factors associated with survival were analyzed using Kaplan–Meier curves, log-rank test, univariate and multivariate Cox regression analyses. <b>Results:</b> One-hundred and fifteen patients with metastatic GIST were included in the final study cohort. Median overall survival (OS) was 6.9 years (95% CI 5.6–8.3). Factors associated with long-term survival in univariate analysis were good baseline performance status (ECOG ≤1; <i>p</i> p = .022), oligometastatic disease (OMD) (≤3 metastases; <i>p</i> p p = .005), surgery of the primary tumor (<i>p</i> p = .05), normal baseline albumin level (<i>p</i> = .001) and normal baseline neutrophil count (<i>p</i> = .03). On multivariate analysis, good performance status, small tumor diameter and, OMD were the factors associated with long-term survival. Five and 10-year OS for patients with OMD were 89% and 71%, respectively, compared to 38% and 20% for patients with polymetastatic disease (<i>p</i> <b>Conclusions:</b> In this single-institution cohort of patients, OMD was as a strong prognostic factor in patients with metastatic GIST. Patients with OMD had an outcome similar to patients with high-risk localized disease, and should be regarded as a separate category among patients with metastatic GIST.
DOI: 10.6084/m9.figshare.5050765.v1
title: Genome-wide Methyl-Seq analysis of blood-brain targets of glucocorticoid exposure

description: Chronic exposure to glucocorticoids (GCs) can lead to psychiatric complications through epigenetic mechanisms such as DNA methylation (DNAm). We sought to determine whether epigenetic changes in a peripheral tissue can serve as a surrogate for those in a relatively inaccessible tissue such as the brain. DNA extracted from the hippocampus and blood of mice treated with GCs or vehicle solution was assayed using a genome-wide DNAm platform (Methyl-Seq) to identify differentially methylated regions (DMRs) induced by GC treatment. We observed that ∼70% of the DMRs in both tissues lost methylation following GC treatment. Of the 3,095 DMRs that mapped to the same genes in both tissues, 1,853 DMRs underwent DNAm changes in the same direction. Interestingly, only 209 DMRs (&lt;7%) overlapped in genomic coordinates between the 2 tissues, suggesting tissue-specific differences in GC-targeted loci. Pathway analysis showed that the DMR-associated genes were members of pathways involved in metabolism, immune function, and neurodevelopment. Also, changes in cell type composition of blood and brain were examined by fluorescence-activated cell sorting. Separation of the cortex into neuronal and non-neuronal fractions and the leukocytes into T-cells, B-cells, and neutrophils showed that GC-induced methylation changes primarily occurred in neurons and T-cells, with the blood tissue also undergoing a shift in the proportion of constituent cell types while the proportion of neurons and glia in the brain remained stable. From the current pilot study, we found that despite tissue-specific epigenetic changes and cellular heterogeneity, blood can serve as a surrogate for GC-induced changes in the brain.
DOI: 10.6084/m9.figshare.5049166
title: CF2_fastqjoin.un1.fastq

description: Raw paired-end Illumina MiSeq 16S sequences for experiment CF2. Associated mapping files found in main project folder at the following link:<br>https://figshare.com/projects/Stern_et_al_2017_Applied_Environmental_Microbiology/22213<br>Data from: Stern, N., Ginder-Vogel, M., Stegen, J.C., Arntzen, B., Kennedy, W.K., Larget, B.R., Roden, E.R. (2017). Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor. Applied Environmental Microbiology. Accepted March 2017(Under Revision).<br><br>