cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4476323
title: Dataset for the article "Genome-wide analysis of differential RNA editing in epilepsy"

description: The study design used for the genome-wide differential RNA-Edited (RE) association analysis (GWRAS) of epilepsy was a case control analysis using a mouse model of acquired symptomatic TLE. High-throughput sequencing of mRNA (RNA-seq) was carried out in whole hippocampus samples from 100 epileptic (files starting with Epileptic_mice_) and 100 control (Control_mice_) littermate mice (same age) as previously described (Johnson et al. 2015). All mice underwent continuous video monitoring for 14 consecutive days beginning 28 days following pilocarpine induced status epilepticus (SE) to document the occurrence and frequency of spontaneous behavioural epileptic seizures, as previously described (Mazzuferi et al. 2012). All RNA-seq profiles generated in epileptic and control mice (n=200) were initially used for the prediction of RNA editing events and the identified RE events were then further analysed in epileptic and control mice to identify differential RE (DRE) between cases and controls.<br><br>The data provided here are raw sequence reads in bam file format. Files contains reads for the identified RNA-edited sites. Files with names: <b><br><br>Epileptic_mice_</b>* : are files containing reads for the set of pilocarpine treated Epileptic mice (N=100)<br><br><b>Control_mice_</b>* : are files containing reads for set of mice that were NOT treated and used as controls in this study (N=100)<br><br><b>Table_expression.xlsx</b>: is an excel file containing information regarding differential expression and expression levels in Epileptic cases and controls<br><br>Here, * is a number between 1 and 100<br>
DOI: 10.6084/m9.figshare.4476323.v1
title: Dataset for the article "Genome-wide analysis of differential RNA editing in epilepsy"

description: The study design used for the genome-wide differential RNA-Edited (RE) association analysis (GWRAS) of epilepsy was a case control analysis using a mouse model of acquired symptomatic TLE. High-throughput sequencing of mRNA (RNA-seq) was carried out in whole hippocampus samples from 100 epileptic (files starting with Epileptic_mice_) and 100 control (Control_mice_) littermate mice (same age) as previously described (Johnson et al. 2015). All mice underwent continuous video monitoring for 14 consecutive days beginning 28 days following pilocarpine induced status epilepticus (SE) to document the occurrence and frequency of spontaneous behavioural epileptic seizures, as previously described (Mazzuferi et al. 2012). All RNA-seq profiles generated in epileptic and control mice (n=200) were initially used for the prediction of RNA editing events and the identified RE events were then further analysed in epileptic and control mice to identify differential RE (DRE) between cases and controls.<br><br>The data provided here are raw sequence reads in bam file format. Files contains reads for the identified RNA-edited sites. Files with names: <b><br><br>Epileptic_mice_</b>* : are files containing reads for the set of pilocarpine treated Epileptic mice (N=100)<br><br><b>Control_mice_</b>* : are files containing reads for set of mice that were NOT treated and used as controls in this study (N=100)<br><br>Here, * is a number between 1 and 100<br>
DOI: 10.6084/m9.figshare.4476260
title: Supplementary Material for: Expression of Kisspeptin in Gonadotrope Precursors in the Mouse Pituitary during Embryonic and Postnatal Development and in Adulthood

description: <b><i>Background:</i></b> Kisspeptins are important regulators of the development and function of the hypothalamic-pituitary-gonadal axis. However, the importance of kisspeptin at the pituitary level is unclear. <b><i>Methods:</i></b> We examined the expression profile of kisspeptin in the mouse pituitary during development and in adulthood using RT-PCR, quantitative PCR and immunohistochemistry.<b><i> Results:</i></b> Kiss1 mRNA was detected in both embryonic and postnatal pituitaries. Kisspeptin-immunoreactive (<sup>+</sup>) cells were detected from embryonic day (E) 13.5 throughout adulthood, being localized to the rostroventral portion in the anterior pituitary (AP) in embryos, and also to the dorsocaudal AP postnatally. A large proportion of kisspeptin<sup>+</sup> cells were double-labeled with gonadotrope markers including Foxl2, SF-1, and LHβ, and the percentage of LHβ<sup>+</sup> cells in kisspeptin<sup>+</sup> cells increased during development. No kisspeptin<sup>+</sup> cells were positive for the proliferating cell marker MCM7 (minichromosome maintenance protein 7), but a few kisspeptin<sup>+</sup> cells co-expressed the stem/progenitor cell marker Sox2. Kisspeptin expression was similar between sexes and between agonadal SF-1 knockout embryos and wild-type littermates. Kiss1 mRNA levels were not significantly different between sexes or during early postnatal development, but levels in females increased when puberty began and were significantly higher than in males at postpubertal ages. <b><i>Conclusions:</i></b> These results suggest that kisspeptin is expressed in gonadotrope precursors during gonadotrope differentiation, and that kisspeptin expression begins soon after the initiation of αGSU production and is extinguished soon after the initiation of LH production. Furthermore, pituitary kisspeptin expression may be regulated in a gonad-independent manner during development, but may be associated with gonadotrope function in adulthood.
DOI: 10.6084/m9.figshare.4476245
title: Zoon - Supporting reproducible and shareable Species Distribution Modelling

description: Talk given at BES 2016 by Tom August
DOI: 10.6084/m9.figshare.4476260.v1
title: Supplementary Material for: Expression of Kisspeptin in Gonadotrope Precursors in the Mouse Pituitary during Embryonic and Postnatal Development and in Adulthood

description: <b><i>Background:</i></b> Kisspeptins are important regulators of the development and function of the hypothalamic-pituitary-gonadal axis. However, the importance of kisspeptin at the pituitary level is unclear. <b><i>Methods:</i></b> We examined the expression profile of kisspeptin in the mouse pituitary during development and in adulthood using RT-PCR, quantitative PCR and immunohistochemistry.<b><i> Results:</i></b> Kiss1 mRNA was detected in both embryonic and postnatal pituitaries. Kisspeptin-immunoreactive (<sup>+</sup>) cells were detected from embryonic day (E) 13.5 throughout adulthood, being localized to the rostroventral portion in the anterior pituitary (AP) in embryos, and also to the dorsocaudal AP postnatally. A large proportion of kisspeptin<sup>+</sup> cells were double-labeled with gonadotrope markers including Foxl2, SF-1, and LHβ, and the percentage of LHβ<sup>+</sup> cells in kisspeptin<sup>+</sup> cells increased during development. No kisspeptin<sup>+</sup> cells were positive for the proliferating cell marker MCM7 (minichromosome maintenance protein 7), but a few kisspeptin<sup>+</sup> cells co-expressed the stem/progenitor cell marker Sox2. Kisspeptin expression was similar between sexes and between agonadal SF-1 knockout embryos and wild-type littermates. Kiss1 mRNA levels were not significantly different between sexes or during early postnatal development, but levels in females increased when puberty began and were significantly higher than in males at postpubertal ages. <b><i>Conclusions:</i></b> These results suggest that kisspeptin is expressed in gonadotrope precursors during gonadotrope differentiation, and that kisspeptin expression begins soon after the initiation of αGSU production and is extinguished soon after the initiation of LH production. Furthermore, pituitary kisspeptin expression may be regulated in a gonad-independent manner during development, but may be associated with gonadotrope function in adulthood.
DOI: 10.6084/m9.figshare.4476227
title: Supplementary Material for: MicroRNAs for the Prediction of Early Response to Sorafenib Treatment in Human Hepatocellular Carcinoma

description: <b><i>Background:</i></b> Several studies suggest the role of circulating microRNAs (miRNAs) as biomarkers of hepatocellular carcinoma (HCC). However, the serum miRNA profile associated with the response to sorafenib remains to be elucidated. The aim of this study was to clarify the specific miRNAs in serum that could predict the early response of HCC to sorafenib treatment. <b><i>Summary:</i></b> Analyzing the sera from 16 HCC patients, we selected five miRNAs that showed differences in serum levels between patients with and without tumor responses among 179 known secretory miRNAs by using locked nucleic acid probe-based quantitative PCR. Through further analysis using a validation cohort that included 53 HCC patients who underwent sorafenib treatment and 8 healthy control subjects, we found that miR-181a-5p and miR-339-5p showed significant differences in serum levels among patients with partial response (PR), stable disease (SD), and progressive disease (PD), where PR patients showed the highest and PD the lowest levels. We also analyzed the factors associated with disease control (DC; PR or SD) 3 months after the initiation of sorafenib treatment; patients with DC showed a significantly higher level of serum miR-181a-5p than non-DC patients or healthy control subjects (p = 0.0349 and 0.0180 for DC vs. non-DC and control vs. non-DC by Tukey-Kramer test, respectively). We further conducted multivariate analysis among HCC patients with Barcelona Clinic Liver Cancer stage C using extrahepatic metastasis, serum decarboxyprothrombin, and miR-181a-5p levels as covariables; serum miR-181a-5p was the only independent factor for achieving DC (p = 0.0092, odds ratio 0.139, and 95% confidence interval 0.011-0.658). In addition, miR-181a-5p level was also the only independent factor affecting overall survival (p = 0.0194, hazard ratio 0.267, and 95% confidence interval 0.070-0.818). <b><i>Key Messages:</i></b> A high serum level of miR-181a-5p before treatment is associated with DC after the initiation of sorafenib.
DOI: 10.6084/m9.figshare.4476245.v2
title: Zoon - Supporting reproducible and shareable Species Distribution Modelling

description: Talk given at BES 2016 by Tom August
DOI: 10.6084/m9.figshare.4476227.v1
title: Supplementary Material for: MicroRNAs for the Prediction of Early Response to Sorafenib Treatment in Human Hepatocellular Carcinoma

description: <b><i>Background:</i></b> Several studies suggest the role of circulating microRNAs (miRNAs) as biomarkers of hepatocellular carcinoma (HCC). However, the serum miRNA profile associated with the response to sorafenib remains to be elucidated. The aim of this study was to clarify the specific miRNAs in serum that could predict the early response of HCC to sorafenib treatment. <b><i>Summary:</i></b> Analyzing the sera from 16 HCC patients, we selected five miRNAs that showed differences in serum levels between patients with and without tumor responses among 179 known secretory miRNAs by using locked nucleic acid probe-based quantitative PCR. Through further analysis using a validation cohort that included 53 HCC patients who underwent sorafenib treatment and 8 healthy control subjects, we found that miR-181a-5p and miR-339-5p showed significant differences in serum levels among patients with partial response (PR), stable disease (SD), and progressive disease (PD), where PR patients showed the highest and PD the lowest levels. We also analyzed the factors associated with disease control (DC; PR or SD) 3 months after the initiation of sorafenib treatment; patients with DC showed a significantly higher level of serum miR-181a-5p than non-DC patients or healthy control subjects (p = 0.0349 and 0.0180 for DC vs. non-DC and control vs. non-DC by Tukey-Kramer test, respectively). We further conducted multivariate analysis among HCC patients with Barcelona Clinic Liver Cancer stage C using extrahepatic metastasis, serum decarboxyprothrombin, and miR-181a-5p levels as covariables; serum miR-181a-5p was the only independent factor for achieving DC (p = 0.0092, odds ratio 0.139, and 95% confidence interval 0.011-0.658). In addition, miR-181a-5p level was also the only independent factor affecting overall survival (p = 0.0194, hazard ratio 0.267, and 95% confidence interval 0.070-0.818). <b><i>Key Messages:</i></b> A high serum level of miR-181a-5p before treatment is associated with DC after the initiation of sorafenib.
DOI: 10.6084/m9.figshare.4476221
title: Supplementary Material for: Factors Influencing Surveillance for Hepatocellular Carcinoma in Patients with Liver Cirrhosis

description: <b><i>Objective:</i></b> Hepatocellular carcinoma (HCC) is the second most common cause of cancer-related mortality worldwide, and a rising cause of cancer mortality in the U.S. Liver cirrhosis is the major risk factor for HCC. Surveillance of persons with cirrhosis facilitates early detection and improves outcomes. We assessed the surveillance rate for HCC within a major academic health system and identified factors influencing surveillance. <b><i>Patients and Methods:</i></b> We examined the surveillance rate for HCC using liver ultrasound, CT, or MRI, and factors influencing surveillance in a cohort of 369 Minnesota residents with cirrhosis seen at the Mayo Clinic between 2007 and 2009. <b><i>Results:</i></b> Ninety-three percent of cirrhosis patients received at least one surveillance study, but only 14% received the recommended uninterrupted semiannual surveillance. Thirty percent received ≥75% of recommended surveillance, and 59% received ≥50% of recommended surveillance. Factors increasing surveillance included gastroenterology or hepatology specialist visits (p &lt; 0.0001), advanced liver disease as assessed by hepatic encephalopathy (p = 0.0008), and comorbid illness as assessed by diabetes mellitus (p = 0.02). Age, sex, race, residence, cirrhosis etiology, or number of primary care visits did not significantly affect the rate of surveillance. <b><i>Conclusions:</i></b> While the rate of surveillance in a major academic health system was higher than reported in other studies, surveillance was heavily dependent on visits to a subspecialist. This suggests a major and urgent national need to improve identification of individuals at risk for HCC in the primary care setting and the initiation and maintenance of surveillance by primary care practitioners.
DOI: 10.6084/m9.figshare.4476218
title: RNA-seq - Enrichment Results

description: Enrichment results of differentially expressed genes identified with RNA-seq.
DOI: 10.6084/m9.figshare.4476221.v1
title: Supplementary Material for: Factors Influencing Surveillance for Hepatocellular Carcinoma in Patients with Liver Cirrhosis

description: <b><i>Objective:</i></b> Hepatocellular carcinoma (HCC) is the second most common cause of cancer-related mortality worldwide, and a rising cause of cancer mortality in the U.S. Liver cirrhosis is the major risk factor for HCC. Surveillance of persons with cirrhosis facilitates early detection and improves outcomes. We assessed the surveillance rate for HCC within a major academic health system and identified factors influencing surveillance. <b><i>Patients and Methods:</i></b> We examined the surveillance rate for HCC using liver ultrasound, CT, or MRI, and factors influencing surveillance in a cohort of 369 Minnesota residents with cirrhosis seen at the Mayo Clinic between 2007 and 2009. <b><i>Results:</i></b> Ninety-three percent of cirrhosis patients received at least one surveillance study, but only 14% received the recommended uninterrupted semiannual surveillance. Thirty percent received ≥75% of recommended surveillance, and 59% received ≥50% of recommended surveillance. Factors increasing surveillance included gastroenterology or hepatology specialist visits (p &lt; 0.0001), advanced liver disease as assessed by hepatic encephalopathy (p = 0.0008), and comorbid illness as assessed by diabetes mellitus (p = 0.02). Age, sex, race, residence, cirrhosis etiology, or number of primary care visits did not significantly affect the rate of surveillance. <b><i>Conclusions:</i></b> While the rate of surveillance in a major academic health system was higher than reported in other studies, surveillance was heavily dependent on visits to a subspecialist. This suggests a major and urgent national need to improve identification of individuals at risk for HCC in the primary care setting and the initiation and maintenance of surveillance by primary care practitioners.
DOI: 10.6084/m9.figshare.4476206
title: Healthcare resource utilization in patients receiving idarucizumab for reversal of dabigatran anticoagulation due to major bleeding, urgent surgery, or procedural interventions: interim results from the RE-VERSE AD™ study

description: <b>Aims:</b> Patients treated with anticoagulants may experience serious bleeding or require urgent surgery or intervention, and may benefit from rapid anticoagulant reversal. This exploratory analysis assessed healthcare resource utilization (HCRU) in patients treated with idarucizumab, a specific reversal agent for dabigatran etexilate. <b>Materials and methods:</b> RE-VERSE AD™ (NCT02104947), a prospective, multi-center open-label study, is evaluating idarucizumab for dabigatran reversal in patients with serious bleeding (Group A) or undergoing emergency surgery/procedures (Group B). HCRU outcome measures evaluated in the first 90 patients enrolled were use of blood products and pro-hemostatic agents, length of stay (LOS) in hospital, and LOS in intensive care unit (ICU). <b>Results:</b> Blood products or pro-hemostatic agents were given to 63% (32/51) of patients in Group A and 23% (9/39) of patients in Group B on the day of/day after surgery. An overnight hospital stay was reported for 82% (42/51) of patients in Group A with median LOS = 7 (range = 1–71) bed-days. For Group B, 92% (36/39) had an overnight hospital stay with a median LOS = 9 (range = 1–92) bed-days. In Group A, 17 patients were admitted to the ICU for at least 1 day with median LOS = 4 (range = 1–44) days; in Group B the number was 15 with median LOS = 2 (range = 1–92) days. <b>Limitations:</b> The lack of a control group and the small patient numbers limit the strength of the conclusions. <b>Conclusions:</b> The use of idarucizumab may simplify emergency management of dabigatran-treated patients with life-threatening bleeds and reduce perioperative complications in patients undergoing emergency surgery.
DOI: 10.6084/m9.figshare.4476218.v2
title: RNA-seq - Enrichment Results

description: Enrichment results of differentially expressed genes identified with RNA-seq.
DOI: 10.6084/m9.figshare.4476218.v1
title: RNA-seq - Enrichment Results

description: Enrichment results of differentially expressed genes identified with RNA-seq.
DOI: 10.6084/m9.figshare.4476197
title: Simon Delso et al 2016 - Supplementary 2_Raw_data_and_analyses.zip

description: Raw data and analyses of article: <b>The challenges of predicting pesticide exposure of honey bees at landscape level</b><br> To evaluate the risks of pesticides for pollinators, we must not only evaluate their toxicity but also understand how pollinators are exposed to these xenobiotics in the field. We focused on this last point and modeled honey bee exposure to pesticides at the landscape level. Pollen pellet samples (n = 60) from 40 Belgian apiaries were collected from late July to October 2011 and underwent palynological and pesticide residue analyses. Areas of various crops around each apiary were measured at 4 spatial scales. The most frequently detected pesticides were the fungicides boscalid (n = 19, 31.7%) and pyrimethanil (n = 10, 16.7%) and the insecticide dimethoate (n = 10, 16.7%). We were able to predict exposure probability for boscalid and dimethoate by using broad indicators of cropping intensity, but it remained difficult to identify the precise source of contamination (e.g. specific crops in which the use of the pesticide is authorized). For pyrimethanil, we were not able to build any convincing landscape model that could explain the contamination. Our results, combined with the late sampling period, strongly suggest that pesticides applied to crops unattractive to pollinators, and therefore considered of no risk for them, may be sources of exposure through weeds, drift to neighboring plants, or succeeding crops.<br><br>DOI - 10.1038/s41598-017-03467-5
DOI: 10.6084/m9.figshare.4476206.v2
title: Healthcare resource utilization in patients receiving idarucizumab for reversal of dabigatran anticoagulation due to major bleeding, urgent surgery, or procedural interventions: interim results from the RE-VERSE AD™ study

description: <b>Aims:</b> Patients treated with anticoagulants may experience serious bleeding or require urgent surgery or intervention, and may benefit from rapid anticoagulant reversal. This exploratory analysis assessed healthcare resource utilization (HCRU) in patients treated with idarucizumab, a specific reversal agent for dabigatran etexilate. <b>Materials and methods:</b> RE-VERSE AD™ (NCT02104947), a prospective, multi-center open-label study, is evaluating idarucizumab for dabigatran reversal in patients with serious bleeding (Group A) or undergoing emergency surgery/procedures (Group B). HCRU outcome measures evaluated in the first 90 patients enrolled were use of blood products and pro-hemostatic agents, length of stay (LOS) in hospital, and LOS in intensive care unit (ICU). <b>Results:</b> Blood products or pro-hemostatic agents were given to 63% (32/51) of patients in Group A and 23% (9/39) of patients in Group B on the day of/day after surgery. An overnight hospital stay was reported for 82% (42/51) of patients in Group A with median LOS = 7 (range = 1–71) bed-days. For Group B, 92% (36/39) had an overnight hospital stay with a median LOS = 9 (range = 1–92) bed-days. In Group A, 17 patients were admitted to the ICU for at least 1 day with median LOS = 4 (range = 1–44) days; in Group B the number was 15 with median LOS = 2 (range = 1–92) days. <b>Limitations:</b> The lack of a control group and the small patient numbers limit the strength of the conclusions. <b>Conclusions:</b> The use of idarucizumab may simplify emergency management of dabigatran-treated patients with life-threatening bleeds and reduce perioperative complications in patients undergoing emergency surgery.
DOI: 10.6084/m9.figshare.4476188
title: Supplemental data for "Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses"

description: Supplementary data, including gene trees from both the site-only and gene-only resampling pseudoreplicates, the phylogenetic trees inferred for each resampling pseudoreplicate, trees with reference clades, and a Microsoft Excel file containing the raw and summarized data.
DOI: 10.6084/m9.figshare.4476191
title: Appendix S1 for "Phylogeography of the wild and cultivated stimulant plant qat (Catha edulis, Celastraceae) in areas of historic cultivation"

description: Appendix S1 Matrix of SSR lengths, clone grouping numbers and geo-reference data for each of the sampled specimens<br>