cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4004946
title: Supplementary Material for: Effects of Sulfate-Rich Mineral Water on Functional Constipation: A Double-Blind, Randomized, Placebo-Controlled Study

description: Background: Magnesium sulfate has a long tradition as a laxative. It osmotically prevents water absorption in the large bowel and thus leads to an acceleration of the intestinal transit and better stool consistency. We wanted to investigate the efficacy of a carbonated calcium/magnesium sulfate-rich natural mineral water in subjects with functional constipation (FC). Patients and Methods: In this double-blind, randomized, placebo-controlled study, subjects with FC (Rome III criteria) received 1 l/day (4 × 250 ml) of mineral water (Ensinger Schiller Quelle) or carbonated tap water (placebo) for 6 weeks. The primary endpoint was the change in the frequency of bowel movements per week between baseline and visit 4 (after 6 weeks). The prespecified main secondary endpoint was the change in the frequency of bowel movements per week between baseline and visit 3 (after 3 weeks). Results: Efficacy was analyzed in 100 subjects (intention-to-treat). After 6 weeks of treatment there was no statistical difference between the groups (p = 0.163). However, statistical significance was reached after 3 weeks, with an increase in the frequency of bowel movements per week of 2.02 ± 2.22 for the mineral water group compared to 0.88 ± 1.67 for the placebo group (p = 0.005). Conclusions: A 3-week treatment with 1 l/ day of the sulfate-rich mineral water improved the frequency of bowel movements in subjects with FC compared with tap water; however, the difference was no longer significant after 6 weeks. Further evaluation in rigorously designed clinical studies will be necessary to validate the impact of sulfate-rich natural mineral water on FC.
DOI: 10.7910/dvn/v1rjpf/69lhsx
title: ykc20160927_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004937
title: Supplementary Material for: In vivo Raman Microspectroscopy: Intra- and Intersubject Variability of Stratum Corneum Spectral Markers

description: <strong><em>Background:</em></strong> In vivo Raman spectroscopy is a powerful tool for real-time analysis and in situ evaluation of tissues such as the skin. The efficiency of this technique has been widely demonstrated as a label-free method for in vivo evaluation of the skin. The aim of this study is to gather information about inter- and intra-individual variations in the spectral descriptors of water content and structure, organization of the lipid barrier and structure of proteins in the stratum corneum (SC). <b><i>Methods:</i></b> In vivo SC measurements were performed on 17 female volunteers aged 20-30 years (phototypes I and II). For intra-individual variability, spectral collection was performed on 5 successive days per volunteer. Shapiro-Wilk and Cochran tests were applied to check the normality and the homoscedasticity of variances. ANOVA was then applied to evaluate intra- and intergroup variability. <b><i>Results:</i></b> ANOVA was performed on the spectral descriptors of water content and structure, organization of the lipid barrier and secondary structure of proteins in the SC. No significant intra- and interday variability was observed for all volunteers. Despite the low value of the total relative standard deviation, a highly significant variation was observed between volunteers. <b><i>Conclusion:</i></b> Interindividual variability for Raman measurements is significant for a set of volunteers with normal nondiseased SC and close phototypes. This variability should be taken into consideration as a threshold for significant variance when working in vivo.
DOI: 10.7910/dvn/v1rjpf/yyywyd
title: ykc20170711_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004925
title: NA

description: <br>
DOI: 10.7910/dvn/v1rjpf/ds60bw
title: ykc20160528_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004925.v2
title: Supplementary files

description: <b>Table S1. </b>List of analyzed isoforms along with their annotation expression and usage.<b>Table S2</b> List of isoform switches with predicted consequences.<b>Table S3</b>Overview of literature derived isoform switches as well as the extensions we make.<b>Table S4</b>Pan-cancer Isoform Switches with Predicted Consequences<b>Table S5</b> Pan-cancer predictors of patient survival.<b>File S1</b> Containing two SwitchAnalyzeRlists one with all genes containing an isoform switch in the TCGA data (‘tcgaSwitchAnalyzeRlistSignificant’) and one with information about all tested isoforms (‘tcgaSwitchAnalyzeRlistAll’). Both list are meant to work with IsoformSwitchAnalyzeR. Note that the biological sequences have been removed to conserve space but can easily be added with the extractSequence() function.
DOI: 10.7910/dvn/v1rjpf/mcdagb
title: ykc20170729_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004913
title: Supplementary Material for: Fluoxetine Treatment Rescues Energy Metabolism Pathway Alterations in a Posttraumatic Stress Disorder Mouse Model

description: <br>Posttraumatic stress disorder (PTSD) is a prevalent psychiatric disorder. Several studies have attempted to characterize molecular alterations associated with PTSD, but most findings were limited to the investigation of specific cellular markers in the periphery or defined brain regions. In the current study, we aimed to unravel affected molecular pathways/mechanisms in the fear circuitry associated with PTSD. We interrogated a foot shock-induced PTSD mouse model by integrating proteomics and metabolomics profiling data. Alterations at the proteome level were analyzed using in vivo <sup>15</sup>N metabolic labeling combined with mass spectrometry in the prelimbic cortex (PrL), anterior cingulate cortex (ACC), basolateral amygdala, central nucleus of the amygdala and CA1 of the hippocampus between shocked and nonshocked (control) mice, with and without fluoxetine treatment. In silico pathway analyses revealed an upregulation of the citric acid cycle pathway in PrL, and downregulation in ACC and nucleus accumbens (NAc). Chronic fluoxetine treatment prevented decreased citric acid cycle activity in NAc and ACC and ameliorated conditioned fear response in shocked mice. Our results shed light on the role of energy metabolism in PTSD pathogenesis and suggest potential therapy through mitochondrial targeting.
DOI: 10.6084/m9.figshare.4004925.v1
title: Supplementary tables

description: <b>Table S1. </b>List of analyzed isoforms along with their annotation expression and usage.<b>Table S2</b> List of isoform switches with predicted consequences.<b>Table S3</b>Overview of literature derived isoform switches as well as the extensions we make.<b>Table S4</b>Pan-cancer Isoform Switches with Predicted Consequences<b>Table S5</b> Pan-cancer predictors of patient survival.
DOI: 10.7910/dvn/v1rjpf/pkd3nd
title: ykc20161208_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/zm2xh9
title: ykc20170602_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004880
title: Supplementary Material for: A Cost-Effective Mutation Screening Strategy for Inherited Retinal Dystrophies

description: <br><strong><em>Objective:</em></strong> We developed a simple, time- and cost-effective Excel-based genetic screening strategy for the diagnosis of inherited retinal dystrophies (IRD). <b><i>Design:</i></b> 76 patients diagnosed with IRD and 112 nonaffected family members, from 55 unrelated families, were included. DNA samples were analyzed using Axiom Exome Genotyping Array Plates (Affymetrix) that contain over 300,000 genetic variants, including more than 5,000 variants present in 181 genes involved in IRD. We used a simple Excel-based data mining strategy in order to screen IRD variants likely involved in the development of IRD. <b><i>Results:</i></b> A total of 5 relevant genetic variants were found in 5 IRD genes. Four variants were reported either as pathogenic or with a prediction of probably damaging, and 1 variant was reported to affect a regulatory region. These variants were present in 14 patients and in 11 carriers, in 10 unrelated families. <b><i>Conclusion:</i></b> Using our Excel-based data screening strategy, we were able to assign likely genetic diagnoses in a fast and cost-effective manner to over 18% of patients analyzed, with a comparable ratio of genetic findings to that reported with retina-specific arrays for about 1/5 of the cost. Our approach proved efficient in reducing costs and time for IRD diagnosis as a first tier genetic screening method.
DOI: 10.6084/m9.figshare.4004880.v1
title: Supplementary Material for: A Cost-Effective Mutation Screening Strategy for Inherited Retinal Dystrophies

description: <br><strong><em>Objective:</em></strong> We developed a simple, time- and cost-effective Excel-based genetic screening strategy for the diagnosis of inherited retinal dystrophies (IRD). <b><i>Design:</i></b> 76 patients diagnosed with IRD and 112 nonaffected family members, from 55 unrelated families, were included. DNA samples were analyzed using Axiom Exome Genotyping Array Plates (Affymetrix) that contain over 300,000 genetic variants, including more than 5,000 variants present in 181 genes involved in IRD. We used a simple Excel-based data mining strategy in order to screen IRD variants likely involved in the development of IRD. <b><i>Results:</i></b> A total of 5 relevant genetic variants were found in 5 IRD genes. Four variants were reported either as pathogenic or with a prediction of probably damaging, and 1 variant was reported to affect a regulatory region. These variants were present in 14 patients and in 11 carriers, in 10 unrelated families. <b><i>Conclusion:</i></b> Using our Excel-based data screening strategy, we were able to assign likely genetic diagnoses in a fast and cost-effective manner to over 18% of patients analyzed, with a comparable ratio of genetic findings to that reported with retina-specific arrays for about 1/5 of the cost. Our approach proved efficient in reducing costs and time for IRD diagnosis as a first tier genetic screening method.
DOI: 10.6084/m9.figshare.4004874
title: Table 4. Zircon and monazite geochronology of deformation in the Pielavesi Shear Zone, Finland: multistage evolution of the Archaean–Proterozoic boundary in the Fennoscandian Shield

description: Supplementary Data Table 4. Whole-rock Sm–Nd TIMS data
DOI: 10.7910/dvn/v1rjpf/34sq7j
title: ykc20170709_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004874.v1
title: Table 4. Zircon and monazite geochronology of deformation in the Pielavesi Shear Zone, Finland: multistage evolution of the Archaean–Proterozoic boundary in the Fennoscandian Shield

description: Supplementary Data Table 4. Whole-rock Sm–Nd TIMS data
DOI: 10.7910/dvn/v1rjpf/pkk2vl
title: ykc20161031_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004868
title: Table 2. Zircon and monazite geochronology of deformation in the Pielavesi Shear Zone, Finland: multistage evolution of the Archaean–Proterozoic boundary in the Fennoscandian Shield

description: Supplementary Data Table 2. U–Pb zircon TIMS data
DOI: 10.6084/m9.figshare.4004871
title: Table 3. Zircon and monazite geochronology of deformation in the Pielavesi Shear Zone, Finland: multistage evolution of the Archaean–Proterozoic boundary in the Fennoscandian Shield

description: Supplementary Data Table 3. Lu–Hf zircon LA–ICP–MS data
DOI: 10.7910/dvn/v1rjpf/invige
title: ykc20160311_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004865
title: Table 1. Zircon and monazite geochronology of deformation in the Pielavesi Shear Zone, Finland: multistage evolution of the Archaean–Proterozoic boundary in the Fennoscandian Shield

description: Supplementary Data Table 1. U–(Th)–Pb SIMS data for zircon and monazite
DOI: 10.6084/m9.figshare.4004868.v1
title: Table 2. Zircon and monazite geochronology of deformation in the Pielavesi Shear Zone, Finland: multistage evolution of the Archaean–Proterozoic boundary in the Fennoscandian Shield

description: Supplementary Data Table 2. U–Pb zircon TIMS data
DOI: 10.6084/m9.figshare.4004862
title: Supplementary Material for: Microdeletion 15q26.2qter and Microduplication 18q23 in a Patient with Prader-Willi-Like Syndrome: Clinical Findings

description: <br>The small interstitial deletion in the long arm of chromosome 15 causing Prader-Willi/Angelman syndrome is well known, whereas cases that report terminal deletions in 15q in association with the Prader-Willi-like phenotype are very rare. By using GTG-banding analysis, metaphase FISH, MLPA analysis, and genome-wide array CGH, we detected an unbalanced translocation involving a microdeletion of the distal part of 15q and a microduplication of the distal part of 18q. The unbalanced translocation was found in a boy that was referred with clinical suspicion of Prader-Willi syndrome. In the 15q-deleted region, 23 genes have been identified, and 13 of them are included in the OMIM database. Among these, the deleted <i>IGFR1</i>,<i> MEF2A</i>,<i> CHSY1</i>, and <i>TM2D3 </i>genes could contribute to the patient's phenotype. Seven genes are included in the duplicated chromosome segment 18q, but only one <i>(CTDP1)</i> is present in the OMIM database. We suggest that the deleted chromosome segment 15q26.2qter may be responsible for the phenotype of our case and may also be a candidate locus of Prader-Willi-like syndrome.
DOI: 10.7910/dvn/v1rjpf/u3hllr
title: ykc20160719_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004865.v1
title: Table 1. Zircon and monazite geochronology of deformation in the Pielavesi Shear Zone, Finland: multistage evolution of the Archaean–Proterozoic boundary in the Fennoscandian Shield

description: Supplementary Data Table 1. U–(Th)–Pb SIMS data for zircon and monazite
DOI: 10.7910/dvn/v1rjpf/x9hvew
title: ykc20160123_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/bhhrgy
title: ykc20171021_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004832
title: Dataset for: A pathogenic role for the integrin CD103 in experimental allergic airways disease

description: The integrin CD103 is the E chain of integrin αEβ7 that is important in the maintenance of intraepithelial lymphocytes and recruitment of T cells and dendritic cells (DC) to mucosal surfaces. The role of CD103 in intestinal immune homeostasis has been well described, however its role in allergic airway inflammation is less well understood. In this study, we used an ovalbumin (OVA)-induced, CD103-knockout (KO) BALB/c mouse model of experimental allergic airways disease (EAAD) to investigate the role of CD103 in disease expression, CD4+ T cell activation and DC activation and function in airways and lymph nodes. We found reduced airways hyper-responsiveness and eosinophil recruitment to airways after aerosol challenge of CD103 KO compared to wild type (WT) mice, although CD103 KO mice showed enhanced serum OVA-specific IgE levels. Following aerosol challenge, total numbers of effector and regulatory CD4+ T cell subsets were significantly increased in the airways of WT but not CD103 KO mice, as well as a lack of DC recruitment into the airways in the absence of CD103. While total airway DC numbers, and their in vivo allergen capture activity, were essentially normal in steady-state CD103 KO mice, migration of allergen-laden airway DC to draining lymph nodes was disrupted in the absence of CD103 at 24 hours after aerosol challenge. These data support a role for CD103 in the pathogenesis of EAAD in BALB/c mice through local control of CD4+ T cell and DC subset recruitment to, and migration from, the airway mucosa during induction of allergic inflammation.
DOI: 10.6084/m9.figshare.4004826
title: Supplementary Material for: Analysis of Shared Haplotypes amongst Palauans Maps Loci for Psychotic Disorders to 4q28 and 5q23-q31

description: To localize genetic variation affecting risk for psychotic disorders in the population of Palau, we genotyped DNA samples from 203 Palauan individuals diagnosed with psychotic disorders, broadly defined, and 125 control subjects using a genome-wide single nucleotide polymorphism array. Palau has unique features advantageous for this study: due to its population history, Palauans are substantially interrelated; affected individuals often, but not always, cluster in families; and we have essentially complete ascertainment of affected individuals. To localize risk variants to genomic regions, we evaluated long-shared haplotypes, ≥10 Mb, identifying clusters of affected individuals who share such haplotypes. This extensive sharing, typically identical by descent, was significantly greater in cases than population controls, even after controlling for relatedness. Several regions of the genome exhibited substantial excess of shared haplotypes for affected individuals, including 3p21, 3p12, 4q28, and 5q23-q31. Two of these regions, 4q28 and 5q23-q31, showed significant linkage by traditional LOD score analysis and could harbor variants of more sizeable risk for psychosis or a multiplicity of risk variants. The pattern of haplotype sharing in 4q28 highlights <i>PCDH10</i>, encoding a cadherin-related neuronal receptor, as possibly involved in risk.
DOI: 10.6084/m9.figshare.4004832.v1
title: Dataset for: A pathogenic role for the integrin CD103 in experimental allergic airways disease

description: The integrin CD103 is the E chain of integrin αEβ7 that is important in the maintenance of intraepithelial lymphocytes and recruitment of T cells and dendritic cells (DC) to mucosal surfaces. The role of CD103 in intestinal immune homeostasis has been well described, however its role in allergic airway inflammation is less well understood. In this study, we used an ovalbumin (OVA)-induced, CD103-knockout (KO) BALB/c mouse model of experimental allergic airways disease (EAAD) to investigate the role of CD103 in disease expression, CD4+ T cell activation and DC activation and function in airways and lymph nodes. We found reduced airways hyper-responsiveness and eosinophil recruitment to airways after aerosol challenge of CD103 KO compared to wild type (WT) mice, although CD103 KO mice showed enhanced serum OVA-specific IgE levels. Following aerosol challenge, total numbers of effector and regulatory CD4+ T cell subsets were significantly increased in the airways of WT but not CD103 KO mice, as well as a lack of DC recruitment into the airways in the absence of CD103. While total airway DC numbers, and their in vivo allergen capture activity, were essentially normal in steady-state CD103 KO mice, migration of allergen-laden airway DC to draining lymph nodes was disrupted in the absence of CD103 at 24 hours after aerosol challenge. These data support a role for CD103 in the pathogenesis of EAAD in BALB/c mice through local control of CD4+ T cell and DC subset recruitment to, and migration from, the airway mucosa during induction of allergic inflammation.
DOI: 10.7910/dvn/v1rjpf/5btsqg
title: ykc20170906_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004823
title: Supplementary Material for: Nucleolar Dominance and Repression of 45S Ribosomal RNA Genes in Hybrids between Xenopus borealis and X. muelleri (2n = 36)

description: Nucleolar dominance is a dramatic disruption in the formation of nucleoli and the expression of ribosomal RNA (rRNA) genes, characteristic of some plant and animal hybrids. Here, we report that F<sub>1</sub> hybrids produced from reciprocal crosses between 2 sister species of <i>Xenopus</i> clawed frogs, <i>X. muelleri</i> and <i>X. borealis</i>, undergo nucleolar dominance somewhat distinct from a pattern previously reported in hybrids between phylogenetically more distant <i>Xenopus</i> species. Patterns of nucleolar development, 45S rRNA expression, and gene copy inheritance were investigated using a combination of immunostaining, pyrosequencing, droplet digital PCR, flow cytometry, and epigenetic inhibition. In <i>X. muelleri</i> × <i>X. borealis</i> hybrids, typically only 1 nucleolus is formed, and 45S rRNA genes are predominantly expressed from 1 progenitor's alleles, <i>X. muelleri</i>, regardless of the cross-direction. These changes are accompanied by an extensive (∼80%) loss of rRNA gene copies in the hybrids relative to their parents, with the transcriptionally underdominant variant <i>(X. borealis)</i> being preferentially lost. Chemical treatment of hybrid larvae with a histone deacetylase inhibitor resulted in a partial derepression of the underdominant variant. Together, these observations shed light on the genetic and epigenetic basis of nucleolar dominance as an underappreciated manifestation of genetic conflicts within a hybrid genome.
DOI: 10.6084/m9.figshare.4004826.v1
title: Supplementary Material for: Analysis of Shared Haplotypes amongst Palauans Maps Loci for Psychotic Disorders to 4q28 and 5q23-q31

description: To localize genetic variation affecting risk for psychotic disorders in the population of Palau, we genotyped DNA samples from 203 Palauan individuals diagnosed with psychotic disorders, broadly defined, and 125 control subjects using a genome-wide single nucleotide polymorphism array. Palau has unique features advantageous for this study: due to its population history, Palauans are substantially interrelated; affected individuals often, but not always, cluster in families; and we have essentially complete ascertainment of affected individuals. To localize risk variants to genomic regions, we evaluated long-shared haplotypes, ≥10 Mb, identifying clusters of affected individuals who share such haplotypes. This extensive sharing, typically identical by descent, was significantly greater in cases than population controls, even after controlling for relatedness. Several regions of the genome exhibited substantial excess of shared haplotypes for affected individuals, including 3p21, 3p12, 4q28, and 5q23-q31. Two of these regions, 4q28 and 5q23-q31, showed significant linkage by traditional LOD score analysis and could harbor variants of more sizeable risk for psychosis or a multiplicity of risk variants. The pattern of haplotype sharing in 4q28 highlights <i>PCDH10</i>, encoding a cadherin-related neuronal receptor, as possibly involved in risk.
DOI: 10.7910/dvn/v1rjpf/vmrnle
title: ykc20170308_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4004823.v1
title: Supplementary Material for: Nucleolar Dominance and Repression of 45S Ribosomal RNA Genes in Hybrids between Xenopus borealis and X. muelleri (2n = 36)

description: Nucleolar dominance is a dramatic disruption in the formation of nucleoli and the expression of ribosomal RNA (rRNA) genes, characteristic of some plant and animal hybrids. Here, we report that F<sub>1</sub> hybrids produced from reciprocal crosses between 2 sister species of <i>Xenopus</i> clawed frogs, <i>X. muelleri</i> and <i>X. borealis</i>, undergo nucleolar dominance somewhat distinct from a pattern previously reported in hybrids between phylogenetically more distant <i>Xenopus</i> species. Patterns of nucleolar development, 45S rRNA expression, and gene copy inheritance were investigated using a combination of immunostaining, pyrosequencing, droplet digital PCR, flow cytometry, and epigenetic inhibition. In <i>X. muelleri</i> × <i>X. borealis</i> hybrids, typically only 1 nucleolus is formed, and 45S rRNA genes are predominantly expressed from 1 progenitor's alleles, <i>X. muelleri</i>, regardless of the cross-direction. These changes are accompanied by an extensive (∼80%) loss of rRNA gene copies in the hybrids relative to their parents, with the transcriptionally underdominant variant <i>(X. borealis)</i> being preferentially lost. Chemical treatment of hybrid larvae with a histone deacetylase inhibitor resulted in a partial derepression of the underdominant variant. Together, these observations shed light on the genetic and epigenetic basis of nucleolar dominance as an underappreciated manifestation of genetic conflicts within a hybrid genome.
DOI: 10.7910/dvn/v1rjpf/v2uvdv
title: ykc20170813_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/hvhz7b
title: ykc20170406_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/fnp2vb
title: ykc20160119_03.txt.gz

description: :unav