cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3996216.v1
title: Supplementary Material for: Another Piece of the Puzzle of Podocyte B7-1 Expression: Lupus Nephritis

description: <b><i>Background/Aims:</i></b> Lupus nephritis (LN) is a frequent complication and a major predictor of poor prognosis of systemic lupus erythematosus. Immune complex deposition and T cell infiltration are crucial events in LN pathogenesis. B7-1 (CD80), normally expressed by antigen-presenting cells, is one of the major co-stimulators of T-cell activation through the binding with its counter-receptors CD28 and cytotoxic T-lymphocyte antigen-4. Unexpectedly, B7-1 induction was described at the podocyte level in patients affected by different renal diseases, including LN. These observations suggested a novel exciting function for B7-1 as a biomarker of podocyte injury, and hence that B7-1 inhibitory drugs could serve as podocyte-targeted treatment of intractable renal diseases. However, subsequent studies hardly questioned the reliability of B7-1 detection assays and the therapeutic efficacy of B7-1 blockade in proteinuric patients, casting doubts on B7-1 expression by podocytes. Here, we thoroughly investigated whether B7-1 was indeed expressed by podocytes in LN, before even considering employing B7-1 blockade in patients with severe manifestations of LN and unfavourable prognosis. <b><i>Methods:</i></b> Applying different immunohistochemical assays with 4 primary antibodies, we analysed kidney biopsies from 42 LN patients at different stages of the disease, and from NZB/NZW mice, an LN model. <b><i>Results:</i></b> B7-1 was not induced in podocytes in human and murine LN; instead its expression was confined to infiltrating inflammatory cells. <b><i>Conclusion:</i></b> B7-1 is not expressed by podocytes in LN. A renoprotective effect of B7-1 blockade in LN patients cannot be ruled out but, if confirmed, cannot be the result of an effect on podocyte B7-1.
DOI: 10.7910/dvn/v1rjpf/26pxg9
title: snk20150507_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3996204
title: isolatedSchools.csv

description: A copy of the dataset used in the paper 'Lonely schools: The relationship between geographic isolation and academic attainment.' The paper is currently under review at the journal Educational Research.<br>
DOI: 10.7910/dvn/v1rjpf/0vwty5
title: snk20160206_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3996204.v1
title: isolatedSchools.csv

description: A copy of the dataset used in the paper 'Lonely schools: The relationship between geographic isolation and academic attainment.' The paper is currently under review at the journal Educational Research.<br>
DOI: 10.6084/m9.figshare.3996213.v2
title: Expression and methylation of <i>BDNF</i> in the human brain in schizophrenia

description: <b>Objectives:</b> To examine the combined effect of the <i>BDNF</i> Val66Met (rs6265) polymorphism and <i>BDNF</i> DNA methylation on transcriptional regulation of the <i>BDNF</i> gene. <b>Methods:</b> DNA methylation profiles were generated for CpG sites proximal to Val66Met, within <i>BDNF</i> promoter I and exon V for prefrontal cortex samples from 25 schizophrenia and 25 control subjects. Val66Met genotypes and <i>BDNF</i> mRNA expression data were generated by transcriptome sequencing. Expression, methylation and genotype data were correlated and examined for association with schizophrenia. <b>Results:</b> There was 43% more of the <i>BDNF</i> V-VIII-IX transcript in schizophrenia samples. <i>BDNF</i> mRNA expression and DNA methylation of seven CpG sites were not associated with schizophrenia after accounting for age and PMI effects. <i>BDNF</i> mRNA expression and DNA methylation were not altered by Val66Met after accounting for age and PMI effects. DNA methylation of one CpG site had a marginally significant positive correlation with mRNA expression in schizophrenia subjects. <b>Conclusions:</b> Schizophrenia risk was not associated with differential <i>BDNF</i> mRNA expression and DNA methylation. A larger age-matched cohort with comprehensive clinical history is required to accurately identify the effects of genotype, mRNA expression and DNA methylation on schizophrenia risk.
DOI: 10.7910/dvn/v1rjpf/muot0a
title: snk20150216_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3996201
title: Supplementary Material for: Group- and Home-Based Cognitive Intervention for Patients with Mild Cognitive Impairment: A Randomized Controlled Trial

description: <b><i>Background:</i></b> We examined the efficacy of group-based cognitive intervention (GCI) and home-based cognitive intervention (HCI) in amnestic mild cognitive impairment (aMCI) and intervention effects on serum brain-derived neurotrophic factor (BDNF). <b><i>Methods:</i></b> In this randomized and rater-blinded trial, 293 patients with aMCI from 18 nationwide hospitals were randomized: 96 to the GCI group, 98 to the HCI group and 99 to the control group. For 12 weeks, subjects receiving GCI participated twice per week in group sessions led by trained instructors, and those receiving HCI completed homework materials 5 days per week. They were assessed at baseline, postintervention (PI) and at the 6-month follow-up after the intervention. The primary endpoint was the change from baseline to PI in the modified Alzheimer's Disease Assessment Scale-cognitive subscale (ADAS-Cog). <b><i>Results:</i></b> In comparison to the controls (a 0.8-point decrease), the subjects receiving GCI (a 2.3-point decrease, p = 0.01) or HCI (a 2.5-point decrease, p = 0.02) showed significant improvements in the modified ADAS-Cog at PI, respectively. By the 6-month follow-up, those receiving GCI or HCI had better scores in the modified ADAS-Cog than the controls. The changes in BDNF levels significantly correlated with the changes in the modified ADAS-Cog in the GCI (r<i> = </i>-0.29, p = 0.02 at PI) and HCI (r<i> = </i>-0.27, p = 0.03 at 6-month follow-up) groups, respectively. <b><i>Conclusions:</i></b> The GCI and HCI resulted in cognitive improvements in aMCI. An enhanced brain plasticity may be a component of the mechanism underpinning the cognitive improvements associated with the cognitive interventions.
DOI: 10.6084/m9.figshare.3996213.v1
title: Expression and Methylation of <i>BDNF</i> in Human Schizophrenia Brain

description: Objective: To examine the combined effect of the <i>BDNF</i> Val66Met (rs6265) polymorphism and <i>BDNF</i> DNA methylation on transcriptional regulation of the <i>BDNF</i> gene. Methods: DNA methylation profiles were generated for CpG sites proximal to Val66Met, within <i>BDNF</i> promoter I and exon V for prefrontal cortex samples from 25 schizophrenia and 25 control subjects. Val66Met genotypes and <i>BDNF</i> mRNA expression data were generated by transcriptome sequencing. Expression, methylation and genotype data were correlated and examined for association with schizophrenia. Results: There was 43% more of the <i>BDNF</i> V-VIII-IX transcript in schizophrenia samples. <i>BDNF</i> mRNA expression and DNA methylation of seven CpG sites were not associated with schizophrenia after accounting for age and PMI effects. <i>BDNF</i> mRNA expression and DNA methylation were not altered by Val66Met after accounting for age and PMI effects. DNA methylation of one CpG site had a marginally-significant positive correlation with mRNA expression in schizophrenia subjects. Conclusion: Schizophrenia risk was not associated with differential <i>BDNF</i> mRNA expression and DNA methylation. A larger age-matched cohort with comprehensive clinical history is required to accurately identify the effects of genotype, mRNA expression and DNA methylation on schizophrenia risk.
DOI: 10.6084/m9.figshare.3996201.v1
title: Supplementary Material for: Group- and Home-Based Cognitive Intervention for Patients with Mild Cognitive Impairment: A Randomized Controlled Trial

description: <b><i>Background:</i></b> We examined the efficacy of group-based cognitive intervention (GCI) and home-based cognitive intervention (HCI) in amnestic mild cognitive impairment (aMCI) and intervention effects on serum brain-derived neurotrophic factor (BDNF). <b><i>Methods:</i></b> In this randomized and rater-blinded trial, 293 patients with aMCI from 18 nationwide hospitals were randomized: 96 to the GCI group, 98 to the HCI group and 99 to the control group. For 12 weeks, subjects receiving GCI participated twice per week in group sessions led by trained instructors, and those receiving HCI completed homework materials 5 days per week. They were assessed at baseline, postintervention (PI) and at the 6-month follow-up after the intervention. The primary endpoint was the change from baseline to PI in the modified Alzheimer's Disease Assessment Scale-cognitive subscale (ADAS-Cog). <b><i>Results:</i></b> In comparison to the controls (a 0.8-point decrease), the subjects receiving GCI (a 2.3-point decrease, p = 0.01) or HCI (a 2.5-point decrease, p = 0.02) showed significant improvements in the modified ADAS-Cog at PI, respectively. By the 6-month follow-up, those receiving GCI or HCI had better scores in the modified ADAS-Cog than the controls. The changes in BDNF levels significantly correlated with the changes in the modified ADAS-Cog in the GCI (r<i> = </i>-0.29, p = 0.02 at PI) and HCI (r<i> = </i>-0.27, p = 0.03 at 6-month follow-up) groups, respectively. <b><i>Conclusions:</i></b> The GCI and HCI resulted in cognitive improvements in aMCI. An enhanced brain plasticity may be a component of the mechanism underpinning the cognitive improvements associated with the cognitive interventions.
DOI: 10.6084/m9.figshare.3996192
title: Aortic valve leaflet wall shear stress characterization revisited: impact of coronary flow

description: Computational characterizations of aortic valve hemodynamics have typically discarded the effects of coronary flow. The objective of this study was to complement our previous fluid–structure interaction aortic valve model with a physiologic coronary circulation model to quantify the impact of coronary flow on aortic sinus hemodynamics and leaflet wall shear stress (WSS). Coronary flow suppressed vortex development in the two coronary sinuses and altered WSS magnitude and directionality on the three leaflets, with the most substantial differences occurring in the belly and tip regions.
DOI: 10.7910/dvn/v1rjpf/x4ay2w
title: snk20150301_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3996195
title: Supplementary Material for: Effects of a Psychological Internet Intervention in the Treatment of Mild to Moderate Depressive Symptoms: Results of the EVIDENT Study, a Randomized Controlled Trial

description: <b><i>Background:</i></b> Mild to moderate depressive symptoms are common but often remain unrecognized and treated inadequately. We hypothesized that an Internet intervention in addition to usual care is superior to care as usual alone (CAU) in the treatment of mild to moderate depressive symptoms in adults. <b><i>Methods:</i></b> This trial was controlled, randomized and assessor-blinded. Participants with mild to moderate depressive symptoms (Patient Health Questionnaire, PHQ-9, score 5-14) were recruited from clinical and non-clinical settings and randomized to either CAU or a 12-week Internet intervention (Deprexis) adjunctive to usual care. Outcomes were assessed at baseline, 3 months (post-assessment) and 6 months (follow-up). The primary outcome measure was self-rated depression severity (PHQ-9). The main analysis was based on the intention-to-treat principle and used linear mixed models. <b><i>Results:</i></b> A total of 1,013 participants were randomized. Changes in PHQ-9 from baseline differed signiﬁcantly between groups (t<sub>825</sub> = 6.12, p &lt; 0.001 for the main effect of group). The post-assessment between-group effect size in favour of the intervention was <i>d</i> = 0.39 (95% CI: 0.13-0.64). It was stable at follow-up, with <i>d</i> = 0.32 (95% CI: 0.06-0.69). The rate of participants experiencing at least minimally clinically important PHQ-9 change at the post-assessment was higher in the intervention group (35.6 vs. 20.2%) with a number needed to treat of 7 (95% CI: 5-10). <b><i>Conclusions:</i></b> The Internet intervention examined in this trial was superior to CAU alone in reducing mild to moderate depressive symptoms. The magnitude of the effect is clinically important and has public health implications.<br>
DOI: 10.7910/dvn/v1rjpf/loo8oh
title: snk20161126_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3996192.v2
title: Aortic valve leaflet wall shear stress characterization revisited: impact of coronary flow

description: Computational characterizations of aortic valve hemodynamics have typically discarded the effects of coronary flow. The objective of this study was to complement our previous fluid–structure interaction aortic valve model with a physiologic coronary circulation model to quantify the impact of coronary flow on aortic sinus hemodynamics and leaflet wall shear stress (WSS). Coronary flow suppressed vortex development in the two coronary sinuses and altered WSS magnitude and directionality on the three leaflets, with the most substantial differences occurring in the belly and tip regions.
DOI: 10.6084/m9.figshare.3996195.v1
title: Supplementary Material for: Effects of a Psychological Internet Intervention in the Treatment of Mild to Moderate Depressive Symptoms: Results of the EVIDENT Study, a Randomized Controlled Trial

description: <b><i>Background:</i></b> Mild to moderate depressive symptoms are common but often remain unrecognized and treated inadequately. We hypothesized that an Internet intervention in addition to usual care is superior to care as usual alone (CAU) in the treatment of mild to moderate depressive symptoms in adults. <b><i>Methods:</i></b> This trial was controlled, randomized and assessor-blinded. Participants with mild to moderate depressive symptoms (Patient Health Questionnaire, PHQ-9, score 5-14) were recruited from clinical and non-clinical settings and randomized to either CAU or a 12-week Internet intervention (Deprexis) adjunctive to usual care. Outcomes were assessed at baseline, 3 months (post-assessment) and 6 months (follow-up). The primary outcome measure was self-rated depression severity (PHQ-9). The main analysis was based on the intention-to-treat principle and used linear mixed models. <b><i>Results:</i></b> A total of 1,013 participants were randomized. Changes in PHQ-9 from baseline differed signiﬁcantly between groups (t<sub>825</sub> = 6.12, p &lt; 0.001 for the main effect of group). The post-assessment between-group effect size in favour of the intervention was <i>d</i> = 0.39 (95% CI: 0.13-0.64). It was stable at follow-up, with <i>d</i> = 0.32 (95% CI: 0.06-0.69). The rate of participants experiencing at least minimally clinically important PHQ-9 change at the post-assessment was higher in the intervention group (35.6 vs. 20.2%) with a number needed to treat of 7 (95% CI: 5-10). <b><i>Conclusions:</i></b> The Internet intervention examined in this trial was superior to CAU alone in reducing mild to moderate depressive symptoms. The magnitude of the effect is clinically important and has public health implications.<br>
DOI: 10.7910/dvn/v1rjpf/61n7xi
title: snk20161206_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3996105
title: Supplementary Material for: Genetic Variants of Thymic Stromal Lymphopoietin in Nonsteroidal Anti-Inflammatory Drug-Induced Urticaria/Angioedema

description: <b><i>Background:</i></b> Nonsteroidal anti-inflammatory drugs (NSAIDs) are the most frequent agents involved in hypersensitivity drug reactions, with NSAID-induced urticaria and/or angioedema (NIUA) being the most common entity. Mast cells are key players in NIUA and are activated by thymic stromal lymphopoietin (TSLP). This cytokine functions through recognition by its receptor, composed of IL7Rα (interleukin-7 receptor alpha) and TSLPR (TSLP receptor). These genes have been previously associated with other inflammatory diseases. <b><i>Methods:</i></b> We assessed the genetic association between single nucleotide polymorphisms (SNPs) in<i> TSLP</i>, <i>IL7R</i> and <i>TSLPR </i>and NIUA in Spanish individuals, using genotyped and imputed data. A total of 369 unrelated NIUA patients and 580 NSAID-tolerant control subjects were included, and 6 SNPs in<i> TSLP</i>, 6 in <i>IL7R</i> and 3 in <i>TSLPR </i>were genotyped. Further variants were imputed using Mach and the 1,000 Genomes Project (Phase 3) data. Association testing and statistical analyses were performed with Mach2dat and R. <b><i>Results:</i></b> A total of 139 SNPs were tested for association following quality control. Two SNPs in <i>TSLP</i> (rs1816678 and rs764917) showed a nominal association (p = 0.033 and 0.024, respectively) with NIUA, although these results were not statistically significant after correcting for multiple comparisons. <b><i>Conclusions:</i></b> Although <i>TSLP, IL7R </i>and<i> TSLPR</i> are important genes involved in the development of the inflammatory response, we found no significant genetic association with NIUA in our population for common SNPs in these genes.
DOI: 10.6084/m9.figshare.3996111
title: Geochemistry, geochronology, and petrogenesis of mid-Cretaceous Talabuco volcanic rocks, central Tibet: implications for the evolution of the Bangong Meso-Tethys

description: The widespread mid-Cretaceous igneous rocks in the northern margin of the Lhasa Block play an important role in understanding deep geologic processes, matter exchange at depth, and tectonic evolution of the Tibetan Plateau. In this paper, we report new zircon U-Pb ages, whole-rock major and trace element data, and Sr-Nd-Pb-Hf isotope data from the Talabuco andesites and basalts, which were dated at ~111 Ma. These rocks belong to the high-K calc-alkaline and shoshonite series, and show enrichment in terms of large-ion-lithophile elements (LILEs, e.g. Rb, U, and Th) and light rare earth elements (LREEs), but depletion of high-field-strength elements (HFSEs, e.g. Nb and Ti). The (<sup>87</sup>Sr/<sup>86</sup>Sr)<i><sub>i</sub></i> ratios of the Talabuco andesites range from 0.7043 to 0.7048, and the <i>ε</i><sub>Nd</sub>(<i>t</i>) contents range from 0.68 to 4.33. The ratios of <sup>206</sup>Pb/<sup>204</sup>Pb, <sup>207</sup>Pb/<sup>204</sup>Pb, and <sup>208</sup>Pb/<sup>204</sup>Pb are 18.6064–18.8993, 15.6233–15.6707, and 38.8634–39.1720, respectively. The <sup>176</sup>Lu/<sup>177</sup>Hf and <sup>176</sup>Hf/<sup>177</sup>Hf ratios of one sample range from 0.00081 to 0.00206 and 0.28280 to 0.28296, respectively. The <i>ε</i><sub>Hf</sub>(<i>t</i>) values for this sample range from 3.4 to 9.1, and the two-stage model Hf age (<i>T</i><sub>DM2</sub>) is 0.59–0.95 Ga. Combined with previous studies, the geochemical and isotopic data reveal that the parental magma of the Talabuco andesites was probably derived by partial melting of EM II-type sub-continental lithospheric mantle (SCLM). The Talabuco andesites are most likely generated by fractionation of mafic magma contaminated by subducted oceanic sediment and represent product of arc magmatism due to northward subduction of the Yarlung Zangbo Neo-Tethyan slab or southward subduction of the Bangong Meso-Tethyan slab.
DOI: 10.7910/dvn/v1rjpf/lquwcg
title: snk20150618_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3996111.v1
title: Geochemistry, geochronology, and petrogenesis of mid-Cretaceous Talabuco volcanic rocks, central Tibet: implications for the evolution of the Bangong Meso-Tethys

description: The widespread mid-Cretaceous igneous rocks in the northern margin of the Lhasa Block play an important role in understanding deep geologic processes, matter exchange at depth, and tectonic evolution of the Tibetan Plateau. In this paper, we report new zircon U-Pb ages, whole-rock major and trace element data, and Sr-Nd-Pb-Hf isotope data from the Talabuco andesites and basalts, which were dated at ~111 Ma. These rocks belong to the high-K calc-alkaline and shoshonite series, and show enrichment in terms of large-ion-lithophile elements (LILEs, e.g. Rb, U, and Th) and light rare earth elements (LREEs), but depletion of high-field-strength elements (HFSEs, e.g. Nb and Ti). The (<sup>87</sup>Sr/<sup>86</sup>Sr)<i><sub>i</sub></i> ratios of the Talabuco andesites range from 0.7043 to 0.7048, and the <i>ε</i><sub>Nd</sub>(<i>t</i>) contents range from 0.68 to 4.33. The ratios of <sup>206</sup>Pb/<sup>204</sup>Pb, <sup>207</sup>Pb/<sup>204</sup>Pb, and <sup>208</sup>Pb/<sup>204</sup>Pb are 18.6064–18.8993, 15.6233–15.6707, and 38.8634–39.1720, respectively. The <sup>176</sup>Lu/<sup>177</sup>Hf and <sup>176</sup>Hf/<sup>177</sup>Hf ratios of one sample range from 0.00081 to 0.00206 and 0.28280 to 0.28296, respectively. The <i>ε</i><sub>Hf</sub>(<i>t</i>) values for this sample range from 3.4 to 9.1, and the two-stage model Hf age (<i>T</i><sub>DM2</sub>) is 0.59–0.95 Ga. Combined with previous studies, the geochemical and isotopic data reveal that the parental magma of the Talabuco andesites was probably derived by partial melting of EM II-type sub-continental lithospheric mantle (SCLM). The Talabuco andesites are most likely generated by fractionation of mafic magma contaminated by subducted oceanic sediment and represent product of arc magmatism due to northward subduction of the Yarlung Zangbo Neo-Tethyan slab or southward subduction of the Bangong Meso-Tethyan slab.
DOI: 10.6084/m9.figshare.3996102
title: Supplementary Material for: A DNA Hypermethylation Profile Independently Predicts Biochemical Recurrence Following Radical Prostatectomy

description: <b><i>Purpose:</i></b> Detection of DNA hypermethylation is emerging as a novel molecular biomarker for different malignancies. We intend to define whether a hypermethylation profile of patients with prostate cancer (PCa) predicts biochemical recurrence (BCR) after radical prostatectomy (RP). <b><i>Material and Methods:</i></b> Genome-wide methylation analysis was performed using the GoldenGate Methylation Cancer Panel-I (Illumina, Inc.) on 10 normal prostate tissues and 58 tumor samples from patients treated by RP followed for prostate-specific antigen (PSA) failure (&gt;0.4 ng/ml) and disease progression. Patients were classified on the basis of D'Amico criteria according to clinical staging, PSA at diagnosis and Gleason score after pathologist review. Hypermethylation status of 1505 CpGs present in the promoter region of 807 genes was studied. Hierarchical clustering analysis was performed and relationships with outcome were investigated using log-rank analysis and Cox regression model. <b><i>Results:</i></b> We found 28 genes significantly hypermethylated in &gt;20% of the tumors analyzed. Four clusters of patients were characterized by their DNA methylation profile, one at higher risk to develop BCR (p = 0.005). Multivariate analysis revealed patients in this cluster (HR 2.56), and high-risk patients (HR 4.34) according to D'Amico classification were independent predictors of BCR after prostatectomy. From the selected genes <i>MT1A</i>, <i>ALOX12</i>, <i>GSTM2</i>, <i>APC</i>, <i>MYCL2</i> and <i>RARB</i> hypermethylation predicted BCR and <i>GSTM2 </i>(HR 3.78) and <i>MYCL2 </i>hypermethylation (HR 2.71) did so independently. <b><i>Conclusion:</i></b> Epigenetic silencing of <i>GSTM2</i> and <i>MYCL2</i> comprise novel molecular markers to predict BCR after surgery for medium- and high-risk localized PCa undergoing surgical treatment and hypermethylation of these genes could be incorporated to the clinical and pathological factors defining the patient at higher risk of PSA failure after prostatectomy. The limitation of the study is that no independent validation cohort is analysed.
DOI: 10.7910/dvn/v1rjpf/kzyxwu
title: snk20160327_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3996099
title: Habitat_suitability_models.zip

description: Habitat suitability models for the 20 species used in the connectivity modelling. The models are at a resolution of 10km and projected in Mollweide. The cell values are expressed as percentage of 300m suitable cells (original resolution of the habitat suitability models in Rondinini et al. 2011).