cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1300979.v5
title: Heat can erase epigenetic marks of vernalization in <i>Arabidopsis</i>

description: Vernalization establishes a memory of winter that must be maintained for weeks or months in order to promote flowering the following spring. The stability of the vernalized state varies among plant species and depends on the duration of cold exposure. In <i>Arabidopsis thaliana</i>, winter leads to epigenetic silencing of the floral repressor gene <i>FLOWERING LOCUS C</i> (<i>FLC</i>) and the duration of cold is measured through the dynamics of chromatin modifications during and after cold. The growing conditions encountered post-vernalization are thus critical for the maintenance of the vernalized state. We reported that high temperature leads to devernalization and, consistently, to <i>FLC</i> reactivation in <i>Arabidopsis</i> seedlings. Here we show that the repressive epigenetic mark H3K27me3 decreases at the <i>FLC</i> locus when vernalized seedlings are grown at 30°C, unless they were first exposed to a stabilizing period at 20°C. Ambient temperature thus controls the epigenetic memory of winter.
DOI: 10.6084/m9.figshare.1300181
title: Symmetry is less than meets the eye: Supplemental Information

description: This represents additional material to support the publication in Current Biology, "Symmetry is less than meets the eye" - additional figures, tables and individual data to support the main paper are presented.
DOI: 10.6084/m9.figshare.1300168
title: S3_Dataset.pdf

description: Report of S/G ratio in thirteen Cactaceae species studied by HPLC.
DOI: 10.6084/m9.figshare.1300170
title: LINE1 methylation levels in pre-diagnostic leukocyte DNA and future renal cell carcinoma risk

description: Higher levels of LINE1 methylation in blood DNA have been associated with increased kidney cancer risk using post-diagnostically collected samples; however, this association has never been examined using pre-diagnostic samples. We examined the association between LINE1 %5mC and renal cell carcinoma (RCC) risk using pre-diagnostic blood DNA from the United States-based, Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) (215 cases/436 controls), and the Alpha-tocopherol, Beta-carotene Cancer Prevention Study (ATBC) of Finnish male smokers (191 cases/575 controls). Logistic regression adjusted for age at blood draw, study center, pack-years of smoking, body mass index, hypertension, dietary alcohol intake, family history of cancer, and sex was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) using cohort and sex-specific methylation categories. In PLCO, higher, although non-significant, RCC risk was observed for participants at or above median methylation level (M2) compared to those below the median (M1) (OR: 1.37, 95% CI: 0.96–1.95). The association was stronger in males (M2 vs. M1, OR: 1.54, 95% CI: 1.00–2.39) and statistically significant among male smokers (M2 vs. M1, OR: 2.60, 95% CI: 1.46–4.63). A significant interaction for smoking was also detected (<i>P</i>-interaction: 0.01). No association was found among females or female smokers. Findings for male smokers were replicated in ATBC (M2 vs. M1, OR: 1.31, 95% CI: 1.07–1.60). In a pooled analysis of PLCO and ATBC male smokers (281cases/755controls), the OR among subjects at or above median methylation level (M2) compared to those below the median (M1) was 1.89 (95% CI: 1.34–2.67, <i>P</i>-value: 3 x 10<sup>–4</sup>); a trend was also observed by methylation quartile (<i>P</i>-trend: 0.002). These findings suggest that higher LINE1 methylation levels measured prior to cancer diagnosis may be a biomarker of future RCC risk among male smokers.
DOI: 10.6084/m9.figshare.1300167
title: S2_Dataset.xls

description: Matrix for FTIR spectra. (data)
DOI: 10.6084/m9.figshare.1300168.v1
title: S3_Dataset.pdf

description: Report of S/G ratio in thirteen Cactaceae species studied by HPLC.
DOI: 10.6084/m9.figshare.1300165
title: S1_Table.xls

description: Supporting information of the S/G ratio in thirteen Cactaceae species studied by HPLC. (data, calculations)
DOI: 10.6084/m9.figshare.1300166
title: S2_Table.xls

description: Supporting information of the percentage of syringyl -size plant graphic.
DOI: 10.6084/m9.figshare.1300170.v1
title: LINE-1 methylation levels in pre-diagnostic leukocyte DNA and future renal cell carcinoma risk

description: : (N=281)Higher levels of LINE1 methylation in blood DNA have been associated with increased kidney cancer risk using post-diagnostically collected samples; however, this association has never been examined using pre-diagnostic samples. We examined the association between LINE1 %5mC and renal cell carcinoma (RCC) risk using pre-diagnostic blood DNA from the United States-based, prostate, lung, colorectal, and ovarian cancer screening trial (PLCO) (215 cases/436 controls), and the α-tocopherol, β-carotene cancer prevention study (ATBC) of Finnish male smokers (191 cases/575 controls). Logistic regression adjusted for age at blood draw, study center, pack-years of smoking, body mass index, hypertension, dietary alcohol intake, family history of cancer, and sex was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) using cohort and sex-specific methylation categories. In PLCO, higher, although non-significant, RCC risk was observed for participants at or above median methylation level (M2) compared to those below the median (M1) (OR: 1.37, 95% CI: 0.96-1.95). The association was stronger in males (M2 vs. M1, OR: 1.54, 95% CI: 1.00-2.39) and statistically significant among male smokers (M2 vs. M1, OR: 2.60, 95% CI: 1.46-4.63). A significant interaction for smoking was also detected (<i>P</i>-interaction: 0.01). No association was found among females or female smokers. Findings for male smokers were replicated in ATBC (M2 vs. M1, OR: 1.31, 95% CI: 1.07-1.60). In a pooled analysis of PLCO and ATBC male smokers (281cases/755controls), the OR among subjects at or above median methylation level (M2) compared to those below the median (M1) was 1.89 (95% CI: 1.34-2.67, <i>P</i>-value: 3 x 10<sup>−4</sup>); a trend was also observed by methylation quartile (<i>P</i>-trend: 0.002). These findings suggest that higher LINE1 methylation levels measured prior to cancer diagnosis may be a biomarker of future RCC risk among male smokers.
DOI: 10.6084/m9.figshare.1300164
title: S1_Dataset.xls

description: Complete dataset of chemical composition in Cactaceae wood. (data, calculations)
DOI: 10.6084/m9.figshare.1300165.v1
title: S1_Table.xls

description: Supporting information of the S/G ratio in thirteen Cactaceae species studied by HPLC. (data, calculations)
DOI: 10.6084/m9.figshare.1300166.v1
title: S2_Table.xls

description: Supporting information of the percentage of syringyl -size plant graphic.
DOI: 10.6084/m9.figshare.1300164.v1
title: S1_Dataset.xls

description: Complete dataset of chemical composition in Cactaceae wood. (data, calculations)
DOI: 10.6084/m9.figshare.1300155
title: IR

description: This a pdf wireframe
DOI: 10.6084/m9.figshare.1300170.v2
title: LINE1 methylation levels in pre-diagnostic leukocyte DNA and future renal cell carcinoma risk

description: Higher levels of LINE1 methylation in blood DNA have been associated with increased kidney cancer risk using post-diagnostically collected samples; however, this association has never been examined using pre-diagnostic samples. We examined the association between LINE1 %5mC and renal cell carcinoma (RCC) risk using pre-diagnostic blood DNA from the United States-based, Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) (215 cases/436 controls), and the Alpha-tocopherol, Beta-carotene Cancer Prevention Study (ATBC) of Finnish male smokers (191 cases/575 controls). Logistic regression adjusted for age at blood draw, study center, pack-years of smoking, body mass index, hypertension, dietary alcohol intake, family history of cancer, and sex was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) using cohort and sex-specific methylation categories. In PLCO, higher, although non-significant, RCC risk was observed for participants at or above median methylation level (M2) compared to those below the median (M1) (OR: 1.37, 95% CI: 0.96–1.95). The association was stronger in males (M2 vs. M1, OR: 1.54, 95% CI: 1.00–2.39) and statistically significant among male smokers (M2 vs. M1, OR: 2.60, 95% CI: 1.46–4.63). A significant interaction for smoking was also detected (<i>P</i>-interaction: 0.01). No association was found among females or female smokers. Findings for male smokers were replicated in ATBC (M2 vs. M1, OR: 1.31, 95% CI: 1.07–1.60). In a pooled analysis of PLCO and ATBC male smokers (281cases/755controls), the OR among subjects at or above median methylation level (M2) compared to those below the median (M1) was 1.89 (95% CI: 1.34–2.67, <i>P</i>-value: 3 x 10<sup>–4</sup>); a trend was also observed by methylation quartile (<i>P</i>-trend: 0.002). These findings suggest that higher LINE1 methylation levels measured prior to cancer diagnosis may be a biomarker of future RCC risk among male smokers.
DOI: 10.6084/m9.figshare.1300170.v3
title: LINE1 methylation levels in pre-diagnostic leukocyte DNA and future renal cell carcinoma risk

description: Higher levels of LINE1 methylation in blood DNA have been associated with increased kidney cancer risk using post-diagnostically collected samples; however, this association has never been examined using pre-diagnostic samples. We examined the association between LINE1 %5mC and renal cell carcinoma (RCC) risk using pre-diagnostic blood DNA from the United States-based, Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) (215 cases/436 controls), and the Alpha-tocopherol, Beta-carotene Cancer Prevention Study (ATBC) of Finnish male smokers (191 cases/575 controls). Logistic regression adjusted for age at blood draw, study center, pack-years of smoking, body mass index, hypertension, dietary alcohol intake, family history of cancer, and sex was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) using cohort and sex-specific methylation categories. In PLCO, higher, although non-significant, RCC risk was observed for participants at or above median methylation level (M2) compared to those below the median (M1) (OR: 1.37, 95% CI: 0.96–1.95). The association was stronger in males (M2 vs. M1, OR: 1.54, 95% CI: 1.00–2.39) and statistically significant among male smokers (M2 vs. M1, OR: 2.60, 95% CI: 1.46–4.63). A significant interaction for smoking was also detected (<i>P</i>-interaction: 0.01). No association was found among females or female smokers. Findings for male smokers were replicated in ATBC (M2 vs. M1, OR: 1.31, 95% CI: 1.07–1.60). In a pooled analysis of PLCO and ATBC male smokers (281cases/755controls), the OR among subjects at or above median methylation level (M2) compared to those below the median (M1) was 1.89 (95% CI: 1.34–2.67, <i>P</i>-value: 3 x 10<sup>–4</sup>); a trend was also observed by methylation quartile (<i>P</i>-trend: 0.002). These findings suggest that higher LINE1 methylation levels measured prior to cancer diagnosis may be a biomarker of future RCC risk among male smokers.
DOI: 10.6084/m9.figshare.1300104
title: Tuxedo bug report: H. saltator simulated data

description: I randomly selected a 150kb region from <em>Harpegnathos saltator </em>to create a demo data set for instruction. I extracted sequences for the transcripts encoded in the region and used wgsim to simulate Illumina reads for these transcripts. The idea was to use the Tuxedo workflow (Bowtie + Tophat + Cufflinks) to map the reads back to the genome, reconstruct transcripts, and do differential expression analysis. Unfortunately the latest version of Cufflinks (as of Feb 3 2015) fails for this data set, crashing with a segfault and without any helpful error message.
DOI: 10.6084/m9.figshare.1300170.v4
title: LINE1 methylation levels in pre-diagnostic leukocyte DNA and future renal cell carcinoma risk

description: Higher levels of LINE1 methylation in blood DNA have been associated with increased kidney cancer risk using post-diagnostically collected samples; however, this association has never been examined using pre-diagnostic samples. We examined the association between LINE1 %5mC and renal cell carcinoma (RCC) risk using pre-diagnostic blood DNA from the United States-based, Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) (215 cases/436 controls), and the Alpha-tocopherol, Beta-carotene Cancer Prevention Study (ATBC) of Finnish male smokers (191 cases/575 controls). Logistic regression adjusted for age at blood draw, study center, pack-years of smoking, body mass index, hypertension, dietary alcohol intake, family history of cancer, and sex was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) using cohort and sex-specific methylation categories. In PLCO, higher, although non-significant, RCC risk was observed for participants at or above median methylation level (M2) compared to those below the median (M1) (OR: 1.37, 95% CI: 0.96–1.95). The association was stronger in males (M2 vs. M1, OR: 1.54, 95% CI: 1.00–2.39) and statistically significant among male smokers (M2 vs. M1, OR: 2.60, 95% CI: 1.46–4.63). A significant interaction for smoking was also detected (<i>P</i>-interaction: 0.01). No association was found among females or female smokers. Findings for male smokers were replicated in ATBC (M2 vs. M1, OR: 1.31, 95% CI: 1.07–1.60). In a pooled analysis of PLCO and ATBC male smokers (281cases/755controls), the OR among subjects at or above median methylation level (M2) compared to those below the median (M1) was 1.89 (95% CI: 1.34–2.67, <i>P</i>-value: 3 x 10<sup>–4</sup>); a trend was also observed by methylation quartile (<i>P</i>-trend: 0.002). These findings suggest that higher LINE1 methylation levels measured prior to cancer diagnosis may be a biomarker of future RCC risk among male smokers.
DOI: 10.6084/m9.figshare.1300104.v1
title: Tuxedo bug report: H. saltator simulated data

description: I randomly selected a 150kb region from <em>Harpegnathos saltator </em>to create a demo data set for instruction. I extracted sequences for the transcripts encoded in the region and used wgsim to simulate Illumina reads for these transcripts. The idea was to use the Tuxedo workflow (Bowtie + Tophat + Cufflinks) to map the reads back to the genome, reconstruct transcripts, and do differential expression analysis. Unfortunately the latest version of Cufflinks (as of Feb 3 2015) fails for this data set, crashing with a segfault and without any helpful error message.
DOI: 10.6084/m9.figshare.1300170.v6
title: LINE1 methylation levels in pre-diagnostic leukocyte DNA and future renal cell carcinoma risk

description: Higher levels of LINE1 methylation in blood DNA have been associated with increased kidney cancer risk using post-diagnostically collected samples; however, this association has never been examined using pre-diagnostic samples. We examined the association between LINE1 %5mC and renal cell carcinoma (RCC) risk using pre-diagnostic blood DNA from the United States-based, Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) (215 cases/436 controls), and the Alpha-tocopherol, Beta-carotene Cancer Prevention Study (ATBC) of Finnish male smokers (191 cases/575 controls). Logistic regression adjusted for age at blood draw, study center, pack-years of smoking, body mass index, hypertension, dietary alcohol intake, family history of cancer, and sex was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) using cohort and sex-specific methylation categories. In PLCO, higher, although non-significant, RCC risk was observed for participants at or above median methylation level (M2) compared to those below the median (M1) (OR: 1.37, 95% CI: 0.96–1.95). The association was stronger in males (M2 vs. M1, OR: 1.54, 95% CI: 1.00–2.39) and statistically significant among male smokers (M2 vs. M1, OR: 2.60, 95% CI: 1.46–4.63). A significant interaction for smoking was also detected (<i>P</i>-interaction: 0.01). No association was found among females or female smokers. Findings for male smokers were replicated in ATBC (M2 vs. M1, OR: 1.31, 95% CI: 1.07–1.60). In a pooled analysis of PLCO and ATBC male smokers (281cases/755controls), the OR among subjects at or above median methylation level (M2) compared to those below the median (M1) was 1.89 (95% CI: 1.34–2.67, <i>P</i>-value: 3 x 10<sup>–4</sup>); a trend was also observed by methylation quartile (<i>P</i>-trend: 0.002). These findings suggest that higher LINE1 methylation levels measured prior to cancer diagnosis may be a biomarker of future RCC risk among male smokers.
DOI: 10.6084/m9.figshare.1300084
title: Amygdala development

description: The DWI connectivity of 166 individuals ranging from ages 5-30 is provided in this mat file, along with other demographic information (e.g. sex, age, group). The mean connectivity of each amygdala voxel to each brain region is provided, along with overall connectivity, and connectivity of each individual nucleus group. Please email the corresponding author for further information as needed.
DOI: 10.6084/m9.figshare.1300170.v5
title: LINE1 methylation levels in pre-diagnostic leukocyte DNA and future renal cell carcinoma risk

description: Higher levels of LINE1 methylation in blood DNA have been associated with increased kidney cancer risk using post-diagnostically collected samples; however, this association has never been examined using pre-diagnostic samples. We examined the association between LINE1 %5mC and renal cell carcinoma (RCC) risk using pre-diagnostic blood DNA from the United States-based, Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) (215 cases/436 controls), and the Alpha-tocopherol, Beta-carotene Cancer Prevention Study (ATBC) of Finnish male smokers (191 cases/575 controls). Logistic regression adjusted for age at blood draw, study center, pack-years of smoking, body mass index, hypertension, dietary alcohol intake, family history of cancer, and sex was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) using cohort and sex-specific methylation categories. In PLCO, higher, although non-significant, RCC risk was observed for participants at or above median methylation level (M2) compared to those below the median (M1) (OR: 1.37, 95% CI: 0.96–1.95). The association was stronger in males (M2 vs. M1, OR: 1.54, 95% CI: 1.00–2.39) and statistically significant among male smokers (M2 vs. M1, OR: 2.60, 95% CI: 1.46–4.63). A significant interaction for smoking was also detected (<i>P</i>-interaction: 0.01). No association was found among females or female smokers. Findings for male smokers were replicated in ATBC (M2 vs. M1, OR: 1.31, 95% CI: 1.07–1.60). In a pooled analysis of PLCO and ATBC male smokers (281cases/755controls), the OR among subjects at or above median methylation level (M2) compared to those below the median (M1) was 1.89 (95% CI: 1.34–2.67, <i>P</i>-value: 3 x 10<sup>–4</sup>); a trend was also observed by methylation quartile (<i>P</i>-trend: 0.002). These findings suggest that higher LINE1 methylation levels measured prior to cancer diagnosis may be a biomarker of future RCC risk among male smokers.
DOI: 10.6084/m9.figshare.1300071
title: SASA-based hotspot prediction dataset S2

description: SASA-based hotspot prediction dataset S2
DOI: 10.6084/m9.figshare.1300072
title: SASA-based hotspot prediction dataset Pronit

description: SASA-based hotspot prediction dataset Pronit
DOI: 10.6084/m9.figshare.1300084.v2
title: Amygdala development

description: The DWI connectivity of 166 individuals ranging from ages 5-30 is provided in this mat file, along with other demographic information (e.g. sex, age, group). The mean connectivity of each amygdala voxel to each brain region is provided, along with overall connectivity, and connectivity of each individual nucleus group. Please email the corresponding author for further information as needed.
DOI: 10.6084/m9.figshare.1300071.v1
title: SASA-based hotspot prediction dataset S2

description: SASA-based hotspot prediction dataset S2
DOI: 10.6084/m9.figshare.1300084.v1
title: Amygdala development

description: The DWI connectivity of 166 individuals ranging from ages 5-30 is provided in this mat file, along with other demographic information (e.g. sex, age, group). The mean connectivity of each amygdala voxel to each brain region is provided, along with overall connectivity, and connectivity of each individual nucleus group. Please email the corresponding author for further information as needed.
DOI: 10.6084/m9.figshare.1300069
title: SASA-based hotspot prediction dataset S1

description: SASA-based hotspot prediction dataset S1
DOI: 10.6084/m9.figshare.1300072.v1
title: SASA-based hotspot prediction dataset Pronit

description: SASA-based hotspot prediction dataset Pronit
DOI: 10.6084/m9.figshare.1300072.v3
title: SASA-based hotspot prediction dataset Pronit

description: SASA-based hotspot prediction dataset Pronit
DOI: 10.6084/m9.figshare.1300072.v2
title: SASA-based hotspot prediction dataset Pronit

description: SASA-based hotspot prediction dataset Pronit
DOI: 10.6084/m9.figshare.1300069.v1
title: SASA-based hotspot prediction dataset S1

description: SASA-based hotspot prediction dataset S1
DOI: 10.6084/m9.figshare.1300069.v3
title: SASA-based hotspot prediction dataset S1

description: SASA-based hotspot prediction dataset S1
DOI: 10.6084/m9.figshare.1300046
title: Data Inter-training interval

description: These data show the results of four tests, one pretest and three posttest. It consist of three variables. Each task is performed three times (three trials). The movement times, the time it took to perform three different functional tasks. The duration of the maximal handopening during one of these tasks. And the deviation of the grip force control, in a task where a handle needed to be grasped with the correct amount of force.
DOI: 10.6084/m9.figshare.1300069.v2
title: SASA-based hotspot prediction dataset S1

description: SASA-based hotspot prediction dataset S1
DOI: 10.6084/m9.figshare.1300046.v1
title: Data Inter-training interval

description: These data show the results of four tests, one pretest and three posttest. It consist of three variables. Each task is performed three times (three trials). The movement times, the time it took to perform three different functional tasks. The duration of the maximal handopening during one of these tasks. And the deviation of the grip force control, in a task where a handle needed to be grasped with the correct amount of force.
DOI: 10.6084/m9.figshare.1300000
title: A complete mandible of a new amphisbaenian reptile (Squamata, Amphisbaenia) from the late middle eocene (Bartonian, Mp 16) of France

description: ABSTRACTA new genus of amphisbaenian reptile, <i>Cuvieribaena carlgansi</i>, is decribed from the late middle Eocene of France. This material from the locality of Le Bretou (Phosphorites du Quercy) is an almost completely preserved mandible. The dentary bears six teeth, with the anterior-most one the largest. The anterior teeth are blunt and enlarged (‘amblyodont’), and their size and amblyodonty decrease posteriorly. The presence of well-developed amblyodont teeth indicates a durophagous diet. Durophagy has already been recognized in some amphisbaenids, and their high skull, short jaws, and robust tooth morphology predispose them to this durophagous lifestyle. Several other amphisbaenid specimens have also been recovered from Le Bretou, mainly trunk vertebrae and two incomplete dentaries. This material and the complete mandible show unambiguous morphological features tying them to Blanidae. <i>Cuvieribaena</i> is the earliest secure record of blanid lizards in the fossil record, confirmed by phylogenetic analysis.http://zoobank.org/urn:lsid:zoobank.org:pub:17454922-A121-447F-9D01-E4992ADB7D60SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP