cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5120473
title: Supplementary Material for: Single Nucleotide Polymorphisms Associated with Coronary Heart Disease Predict Incident Ischemic Stroke in the Atherosclerosis Risk in Communities Study

description: Ischemic stroke and coronary heart disease (CHD) may share genetic factors contributing to a common etiology. This study investigates whether 51 single nucleotide polymorphisms (SNPs) associated with CHD in multiple antecedent studies are associated with incident ischemic stroke in the Atherosclerosis Risk in Communities (ARIC) study. From the multiethnic ARIC cohort of 14,215 individuals, 495 validated ischemic strokes were identified. Cox proportional hazards models, adjusted for age and gender, identified three SNPs in Whites and two SNPs in Blacks associated with incident stroke (p ≤ 0.05). The rs11628722 polymorphism in <i>SERPINA9</i> was associated with incident stroke in Whites and Blacks, even after taking into account traditional risk factors. The idea that ischemic stroke and CHD may share some common genetic factors, such as variation in <i>SERPINA9,</i> should be investigated in other studies.
DOI: 10.6084/m9.figshare.5120476
title: Supplementary Material for: Economic Evaluation alongside a Phase II, Multi-Centre, Randomised Controlled Trial of Very Early Rehabilitation after Stroke (AVERT)

description: <i>Background/Purpose:</i> The effectiveness and costs of very early rehabilitation after stroke are unknown. This study assessed the cost effectiveness of very early mobilisation in addition to standard care (VEM) compared with standard care alone (SC). <i>Methods:</i> Cost-effectiveness analysis alongside a phase II, multi-centre, randomised controlled trial (RCT) with blinded outcome assessments. Less than 24 h after stroke, patients were recruited from two stroke units and randomised to receive VEM or SC. The intervention continued until discharge or 14 days, whichever was sooner. The efficacy measure was a dichotomised modified Rankin Scale (mRS) at 3 months with mRS ≤2 representing good outcome. Costs were determined from medical records and patient interviews at 3, 6 and 12 months. National average (where available) or local costs were applied for the reference year 2004. Differences in mean total costs at 3 and 12 months were tested using t test assuming unequal variances. An incremental cost-effectiveness ratio was calculated and probabilistic uncertainty analysis was undertaken. <i>Results:</i> The sample consisted of 38 VEM and 33 SC patients. A trend for good outcome with VEM compared to SC was found (adjusted OR 4.10, 95% CI 0.99–16.88, p = 0.051). Patients receiving VEM incurred significantly less costs at 3 months (AUD 13,559) compared with SC (AUD 21,860; p = 0.02). This difference in mean per patient total cost persisted at the 12-month assessment (VEM: AUD 17,564; SC: AUD 29,750; p = 0.03). VEM was found to be a ‘dominant’ (more effective, less cost) intervention when compared to SC at 3 months. <i>Conclusion:</i> These findings provide preliminary evidence that VEM is likely to be cost-effective. A large RCT is currently underway to confirm the cost effectiveness of VEM.
DOI: 10.6084/m9.figshare.5120482.v1
title: Supplementary Material for: Hippocampal Estrogen Receptor-Alpha Splice Variant TADDI in the Human Brain in Aging and Alzheimer’s Disease

description: <i>Background/Aims:</i> Estrogen receptor-α (ERα) splice variants are important for understanding estrogen effects on the brain and estrogen therapy pitfalls. We addressed the question whether a novel ERα splice variant TADDI is expressed at the protein level in the human brain and whether it changes in relation to aging and Alzheimer’s disease (AD). <i>Methods:</i> Immunoreactivity (-ir) for TADDI was assessed on postmortem human brain material from a total of 116 cases. <i>Results:</i> The highest levels of this splice form were found in the hypothalamic supraoptic nucleus (SON), pontine nuclei, medulla oblongata, gray matter of the spinal cord, the hippocampus, glomeruli of the cerebellum, the nucleus basalis of Meynert (NBM), and the tuberomamillary nucleus (TMN). TADDI-ir was mainly confined to the cytoplasm but was also determined in the nuclei of hippocampal neurons from young patients. In the hippocampus, the NBM, and the TMN, TADDI-ir was higher in postmenopausal women than in women ≤50 years old. In these brain areas and in the SON, it was diminished in AD women. In the NBM of AD men, TADDI-ir was enhanced. <i>Conclusion:</i> Aging- and AD-related changes in TADDI-ir show that it should be considered for the sensitivity of the neural tissue to estrogen therapy.
DOI: 10.6084/m9.figshare.5120467
title: Supplementary Material for: Striated Myogenesis and Peristalsis in the Fetal Murine Esophagus Occur without Cell Migration or Interstitial Cells of Cajal

description: Esophageal striated myogenesis progresses differently from appendicular myogenesis, but the mechanism underlying this process is incompletely understood. Early theories of transdifferentiation of smooth muscle into striated muscle are not supported by transgenic fate-mapping experiments; however, the origin of esophageal striated muscle remains unknown. To better define the process of striated myogenesis, we examined myogenesis in murine fetal cultured esophageal whole-organ explants. Embryonic day 14.5 (E14.5) esophagi maintained a functional contractile phenotype for up to 7 days in culture. Striated myogenesis, as evidenced by myogenin expression, proceeded in a craniocaudal direction along the length of the esophagus. Esophageal length did not change during this process. Complete, but not partial, mechanical disruption of the rostral esophagus inhibited myogenesis distally. Addition of fibroblast growth factor-2 (FGF-2) to the culture media failed to inhibit striated myogenesis, but attenuated smooth muscle actin expression and reduced peristaltic activity. Inhibition of c-kit failed to inhibit peristalsis. These results suggest that striated myogenic precursors are resident along the entire length of the esophagus by day 14.5 and do not migrate along the esophagus after E14.5. Induction of myogenesis craniocaudally appears to require physical continuity of the esophagus and is not inhibited by FGF-2. Finally, peristalsis in E14.5 esophagi appears not to be regulated by interstitial cells of Cajal.
DOI: 10.6084/m9.figshare.5120473.v1
title: Supplementary Material for: Single Nucleotide Polymorphisms Associated with Coronary Heart Disease Predict Incident Ischemic Stroke in the Atherosclerosis Risk in Communities Study

description: Ischemic stroke and coronary heart disease (CHD) may share genetic factors contributing to a common etiology. This study investigates whether 51 single nucleotide polymorphisms (SNPs) associated with CHD in multiple antecedent studies are associated with incident ischemic stroke in the Atherosclerosis Risk in Communities (ARIC) study. From the multiethnic ARIC cohort of 14,215 individuals, 495 validated ischemic strokes were identified. Cox proportional hazards models, adjusted for age and gender, identified three SNPs in Whites and two SNPs in Blacks associated with incident stroke (p ≤ 0.05). The rs11628722 polymorphism in <i>SERPINA9</i> was associated with incident stroke in Whites and Blacks, even after taking into account traditional risk factors. The idea that ischemic stroke and CHD may share some common genetic factors, such as variation in <i>SERPINA9,</i> should be investigated in other studies.
DOI: 10.6084/m9.figshare.5120461
title: Supplementary Material for: Molecular Profiling of Isolated Histological Components of Wilms Tumor Implicates a Common Role for the Wnt Signaling Pathway in Kidney and Tumor Development

description: Wilms tumor (WT), a tumor composed of three histological components – blastema (BL), epithelia and stroma – is considered an appropriate model system to study the biological relationship between differentiation and tumorigenesis. To investigate molecular associations between nephrogenesis and WT, the gene expression pattern of individual cellular components was analyzed, using a customized platform containing 4,608 genes. WT gene expression patterns were compared to genes regulated during kidney differentiation. BL had a closer gene expression pattern to the earliest stage of normal renal development. The BL gene expression pattern was compared to that of fetal kidney (FK) and also between FK and mature kidney, identifying 25 common deregulated genes supposedly involved in the earliest events of WT onset. Quantitative RT-PCR was performed, confirming the difference in expression levels for 13 of 16 genes (81.2%) in the initial set and 8 of 13 (61.5%) in an independent set of samples. An overrepresentation of genes belonging to the Wnt signaling pathway was identified, namely PLCG2, ROCK2 and adenomatous polyposis coli <i>(</i>APC<i>)</i>. Activation of the Wnt pathway was confirmed in WT, using APC at protein level and PLCG2 at mRNA and protein level. APC showed positive nuclear immunostaining for an independent set of WT samples, similarly to the FK in week 11. Lack of PLCG2 expression was confirmed in WT and in FK until week 18. Taken together, these results provided molecular evidence of the recapitulation of the embryonic kidney by WT as well as involvement of the Wnt pathway in the earliest events of WT onset.
DOI: 10.6084/m9.figshare.5120464
title: Supplementary Material for: Differential Gene Expression Profiles of Metastases in Paired Primary and Metastatic Colorectal Carcinomas

description: <i>Background and Methods:</i> Despite the overwhelming clinical significance of metastases, the cellular and molecular mechanisms involved are largely unknown. In order to define significant differences between primary colon carcinomas and their metastases, we analyzed gene expression profiles of 12 sets of triple-paired tissues using 19 K human oligonucleotide microarrays. A total of 36 microarray experiments were analyzed by unsupervised two-way hierarchical clustering and multi-dimensional scaling (MDS). <i>Results:</i> Both methods completely distinguished normal mucosa from carcinoma, but failed to demonstrate a complete classification of primary and metastatic carcinomas. We found a separable tendency to be classified into the primary and metastatic colon carcinomas by MDS. In supervised hierarchical clustering, we identified 80 genes that were differentially expressed between paired primary and metastatic colon carcinomas. The 80 identified genes also successfully distinguished three validation sets of primary and lung-metastatic colon carcinomas. A specific set of genes was identified that distinguished the metastasis from the corresponding primary tumor in nearly half of the metastases analyzed. <i>Conclusions:</i> We suggest that a more accurate model of the metastatic potential is based on a global tumor expression pattern along with the appearance of distinct metastatic variants. This molecular profiling may be useful for the future study of colon cancer metastasis.
DOI: 10.6084/m9.figshare.5120470.v1
title: Supplementary Material for: Effect of Influenza Vaccination on Risk of Stroke: A Systematic Review and Meta-Analysis

description: <i>Background:</i> Despite the presence of a strong association between influenza infection and stroke, whether influenza vaccination reduces the risk of stroke is yet a matter of controversy. We conducted a meta-analysis to determine whether influenza vaccination protects against stroke. <i>Methods:</i> We searched PubMed, EMBASE, and the Cochrane Library from database inception date to November 18, 2016, without language restrictions, to identify studies investigating the effect of influenza vaccination on subsequent risk of stroke. We conducted a meta-analysis to quantify the risk of stroke in overall and subgroup analyses and calculated a pooled OR for developing stroke with a 95% CI. Publication bias was assessed by Begg's rank correlation test. <i>Results:</i> Eleven studies fulfilled our inclusion criteria. In a random-effects model, vaccinated individuals had a decreased risk of stroke compared with unvaccinated individuals (OR 0.82; 95% CI 0.75-0.91; <i>p</i> &lt; 0.001). The relationship between influenza vaccination and stroke risk remained robust in subgroup analyses. The significant effect of influenza vaccination was associated with ascertainment of vaccination status and stage of prevention. <i>Conclusion:</i> Vaccination against influenza is associated with a lower risk of stroke. Well-designed prospective studies are needed to provide stronger evidence of the protective effect of influenza vaccination against stroke.
DOI: 10.6084/m9.figshare.5120452
title: Supplementary Material for: A 4,103 marker integrated physical and comparative map of the horse genome

description: A comprehensive second-generation whole genome radiation hybrid (RH II), cytogenetic and comparative map of the horse genome (2n = 64) has been developed using the 5000rad horse × hamster radiation hybrid panel and fluorescence in situ hybridization (FISH). The map contains 4,103 markers (3,816 RH; 1,144 FISH) assigned to all 31 pairs of autosomes and the X chromosome. The RH maps of individual chromosomes are anchored and oriented using 857 cytogenetic markers. The overall resolution of the map is one marker per 775 kilobase pairs (kb), which represents a more than five-fold improvement over the first-generation map. The RH II incorporates 920 markers shared jointly with the two recently reported meiotic maps. Consequently the two maps were aligned with the RH II maps of individual autosomes and the X chromosome. Additionally, a comparative map of the horse genome was generated by connecting 1,904 loci on the horse map with genome sequences available for eight diverse vertebrates to highlight regions of evolutionarily conserved syntenies, linkages, and chromosomal breakpoints. The integrated map thus obtained presents the most comprehensive information on the physical and comparative organization of the equine genome and will assist future assemblies of whole genome BAC fingerprint maps and the genome sequence. It will also serve as a tool to identify genes governing health, disease and performance traits in horses and assist us in understanding the evolution of the equine genome in relation to other species.
DOI: 10.6084/m9.figshare.5120455
title: Supplementary Material for: Distribution patterns of phosphorylated Thr 3 and Thr 32 of histone H3 in plant mitosis and meiosis

description: Cell cycle dependent phosphorylation of conserved N-terminal tail residues of histone H3 has been described in both animal and plant cells. Through cytogenetic approaches using different plant species we show a detailed description of distribution patterns of phosphorylated histone H3 at either threonine 3 or threonine 32 in mitosis and meiosis. In meristematic cells of the large genome species <i>Secale cereale, Vicia faba </i>and <i>Hordeum vulgare </i>we have found that phosphorylation of both threonine residues begins in prophase, and dephosphorylation occurs in late anaphase. However, in the small genome species <i>Arabidopsis thaliana </i>dephosphorylation occurs at anaphase. In the first division of meiosis of species with large genomes phosphorylation of histone H3 at either threonine 3 or threonine 32 is seen first in diakinesis and extends to anaphase I, whereas in the second division these post-translational modifications are visible at metaphase II through anaphase II. While in <i>A. thaliana </i>dephosphorylation takes place at anaphase I and II. In all species analysed phosphorylated H3 at either threonine 3 or threonine 32 are distributed along the entire length of chromosomes during mitotic metaphase and metaphase I. In the second meiotic division threonine 3 phosphorylation is restricted to the pericentromeric domain, while phosphorylation of threonine 32 is widespread along chromosome arms of all species analysed.
DOI: 10.6084/m9.figshare.5120458
title: Supplementary Material for: Distinct Gene Expression Profiles: Nodal versus Extranodal Diffuse Large B-Cell Lymphoma

description: <i>Introduction:</i> Approximately one third of diffuse large B-cell lymphomas (DLBCL) arises from tissues different from the lymph node. Perceived differences in outcome between extranodal and nodal DLBCL raise the possibility that these subgroups may represent different biological and clinical entities. <i>Methods:</i> Microarray GeneChip technology was used for global gene expression profiles from nodal (n = 19) and extranodal (n = 8) DLBCL, to examine possible differences between these subgroups. Quantitative RT-PCR was employed for validation of microarray data. Differential expression levels of p16 (CDKN2A) were confirmed by means of immunohistochemistry on a tissue microarray comprising more than 200 lymphoma samples. <i>Results:</i> A total of 218, over (124)- and underexpressed (94) genes were found to be differentially expressed in extranodal DLBCL compared with nodal DLBCL, including cytokines/chemokines, chromosome-replication-related genes and DNA repair genes. Quantitative RT-PCR confirmed the microarray data. A higher rate of p16 positivity was found in extranodal lymphomas. However, prognostic importance of p16 was associated with nodal rather than extranodal lymphomas. <i>Conclusion:</i> Our data suggest that a better distinction of these subgroups based on molecular classifiers is feasible and may greatly facilitate the determination of specific relevant clinical features and therapeutic implications of DLBCL with primary extranodal or nodal location.
DOI: 10.6084/m9.figshare.5120461.v1
title: Supplementary Material for: Molecular Profiling of Isolated Histological Components of Wilms Tumor Implicates a Common Role for the Wnt Signaling Pathway in Kidney and Tumor Development

description: Wilms tumor (WT), a tumor composed of three histological components – blastema (BL), epithelia and stroma – is considered an appropriate model system to study the biological relationship between differentiation and tumorigenesis. To investigate molecular associations between nephrogenesis and WT, the gene expression pattern of individual cellular components was analyzed, using a customized platform containing 4,608 genes. WT gene expression patterns were compared to genes regulated during kidney differentiation. BL had a closer gene expression pattern to the earliest stage of normal renal development. The BL gene expression pattern was compared to that of fetal kidney (FK) and also between FK and mature kidney, identifying 25 common deregulated genes supposedly involved in the earliest events of WT onset. Quantitative RT-PCR was performed, confirming the difference in expression levels for 13 of 16 genes (81.2%) in the initial set and 8 of 13 (61.5%) in an independent set of samples. An overrepresentation of genes belonging to the Wnt signaling pathway was identified, namely PLCG2, ROCK2 and adenomatous polyposis coli <i>(</i>APC<i>)</i>. Activation of the Wnt pathway was confirmed in WT, using APC at protein level and PLCG2 at mRNA and protein level. APC showed positive nuclear immunostaining for an independent set of WT samples, similarly to the FK in week 11. Lack of PLCG2 expression was confirmed in WT and in FK until week 18. Taken together, these results provided molecular evidence of the recapitulation of the embryonic kidney by WT as well as involvement of the Wnt pathway in the earliest events of WT onset.
DOI: 10.6084/m9.figshare.5120449
title: Supplementary Material for: Effect of Dietary Calcium and Dairy Proteins on the Adipose Tissue Gene Expression Profile in Diet-Induced Obesity

description: <i>Background/Aims:</i> Calcium and dairy proteins have been postulated to explain why the intake of dairy products correlates inversely with body mass index in several populations. We have shown that a high-calcium diet with whey protein attenuates weight gain and now we describe the effects of this diet on adipose tissue gene expression. <i>Methods:</i> Nine-week-old C57Bl/6J mice were divided into two groups (n = 10/group). The control diet was a standard high-fat diet (60% of energy) low in calcium (0.4%). The whey protein diet was a high-calcium (1.8%), high-fat diet with whey protein. After the 21-week treatment, adipose tissue transcript profiling (2 mice/group) was performed using Affymetrix Mouse Genome 430 2.0. <i>Results:</i> The high-calcium diet with whey protein altered the expression of 129 genes (± 1.2 fold). Quantitative RT-PCR analysis confirmed the significant up-regulation of Adrb3 (p = 0.002) and leptin (p = 0.0019) in the high-calcium whey group. Insulin and adipocytokine signaling pathways were enriched among the up-regulated genes and the fatty acid metabolism pathway among the down-regulated genes. <i>Conclusions:</i> High-calcium diet with whey protein significantly modifies adipose tissue gene expression. These preliminary findings reveal that targets of a high-calcium diet with whey protein include genes for Adrb3 and leptin, and help to explain how the intake of dairy products might attenuate obesity.
DOI: 10.6084/m9.figshare.5120455.v1
title: Supplementary Material for: Distribution patterns of phosphorylated Thr 3 and Thr 32 of histone H3 in plant mitosis and meiosis

description: Cell cycle dependent phosphorylation of conserved N-terminal tail residues of histone H3 has been described in both animal and plant cells. Through cytogenetic approaches using different plant species we show a detailed description of distribution patterns of phosphorylated histone H3 at either threonine 3 or threonine 32 in mitosis and meiosis. In meristematic cells of the large genome species <i>Secale cereale, Vicia faba </i>and <i>Hordeum vulgare </i>we have found that phosphorylation of both threonine residues begins in prophase, and dephosphorylation occurs in late anaphase. However, in the small genome species <i>Arabidopsis thaliana </i>dephosphorylation occurs at anaphase. In the first division of meiosis of species with large genomes phosphorylation of histone H3 at either threonine 3 or threonine 32 is seen first in diakinesis and extends to anaphase I, whereas in the second division these post-translational modifications are visible at metaphase II through anaphase II. While in <i>A. thaliana </i>dephosphorylation takes place at anaphase I and II. In all species analysed phosphorylated H3 at either threonine 3 or threonine 32 are distributed along the entire length of chromosomes during mitotic metaphase and metaphase I. In the second meiotic division threonine 3 phosphorylation is restricted to the pericentromeric domain, while phosphorylation of threonine 32 is widespread along chromosome arms of all species analysed.