cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5121427.v1
title: Supplementary Material for: A Role for All-Trans-Retinoic Acid in the Early Steps of Lymphatic Vasculature Development

description: The molecular mechanisms that regulate the earliest steps of lymphatic vascular system development are unknown. To identify regulators of lymphatic competence and commitment, we used an in vitro vascular assay with mouse embryonic stem cell-derived embryoid bodies (EBs). We found that incubation with retinoic acid (RA) and, more potently, with RA in combination with cAMP, induced the expression of the lymphatic competence marker LYVE-1 in the vascular structures of the EBs. This effect was dependent on RA receptor (RAR)-α and protein kinase A signaling. RA-cAMP incubation also promoted the development of CD31+/LYVE-1+/Prox1+ cell clusters. In situ studies revealed that RAR-α is expressed by endothelial cells of the cardinal vein in ED 9.5–11.5 mouse embryos. Timed exposure of mouse and <i>Xenopus</i> embryos to excess of RA upregulated LYVE-1 and VEGFR-3 on embryonic veins and increased formation of Prox1-positive lymphatic progenitors. These findings indicate that RA signaling mediates the earliest steps of lymphatic vasculature development.
DOI: 10.6084/m9.figshare.5121415
title: Supplementary Material for: Systematic Removal of Outliers to Reduce Heterogeneity in Case-Control Association Studies

description: <i>Background/Aims:</i> In human case-control association studies, population heterogeneity is often present and can lead to increased false-positive results. Various methods have been proposed and are in current use to remedy this situation. <i>Methods:</i> We assume that heterogeneity is due to a relatively small number of individuals whose allele frequencies differ from those of the remainder of the sample. For this situation, we propose a new method of handling heterogeneity by removing outliers in a controlled manner. In a coordinate system of the <i>c</i> largest principal components in multidimensional scaling (MDS), we systematically remove one after another of the most extreme outlying individuals and each time recompute the largest association test statistic. The smallest p value obtained within <i>M</i> removals serves as our test statistic whose significance level is assessed in randomization samples. <i>Results:</i> In power simulations of our method and three methods in current use, averaged over several different scenarios, the best method turned out to be logistic regression analysis (based on all individuals) with MDS components as covariates. <i>Conclusion:</i> Our proposed method ranked closely behind logistic regression analysis with MDS components but ahead of other commonly used approaches. In analyses of real datasets our method performed best.
DOI: 10.6084/m9.figshare.5121424.v1
title: Supplementary Material for: EIF2C Is Overexpressed and Amplified in Head and Neck Squamous Cell Carcinoma

description: <i>Aim:</i> To discover putative oncogenes in head and neck squamous cell carcinoma (HNSCC) by integrating data from whole-genome comparison of array-based comparative genomic hybridization (CGH) and expression microarray analysis of HNSCC. <i>Methods:</i> We integrated published data defining regions of loss/gain identified from the profiling of 21 HNSCC using high-resolution (&lt;1 Mb) CGH arrays and data from an mRNA expression microarray (approx. 12,000 genes) comparing 6 normal tissues and 8 HNSCC tumor tissues. Eukaryotic translation initiation factor 2C subunit 2<i> (EIF2C2)</i> was found to be the most significantly overexpressed gene by mRNA expression array, and corresponded to the most common region of amplification found by the CGH array described by Sparano et al. We validated <i>EIF2C2</i> overexpression in primary tissue, overexpression and amplification in HNSCC lines (JHU-011, JHU-012, FADU) relative to a minimally transformed oral keratinocyte cell line (OKF6) and performed knockdown experiments. <i>Results:</i> The tumor tissues had an average mRNA expression level of 123 (SD = 49) compared to the normal tissues (18.6, SD = 10) (p = 0.0005) by expression array. Quantitative RT-PCR validation of our expression arrays found that normal tissues had an average expression of 0.76 (SE = 0.08) and tumor tissues of 2.1 (SE = 0.35) (p = 0.0008). <i>EIF2C2</i> was found to be amplified and overexpressed in 3 HNSCC cell lines. Knockdown of <i>EIF2C2</i> in cell lines (JHU-012 and JHU-011) inhibited proliferation. <i>Conclusion:</i><i>EIF2C2</i> is amplified and overexpressed in HNSCC cell lines and primary tumors and functionally significant in cell lines.
DOI: 10.6084/m9.figshare.5121433.v1
title: Supplementary Material for: Characterization and Genomic Organization of <i>PERI</i>, a Repetitive DNA in the <i>Drosophila buzzatii</i> Cluster Related to <i>DINE-1</i> Transposable Elements and Highly Abundant in the Sex Chromosomes

description: <i>Background/Aims: </i>Transposable elements (TEs) are dynamic components of eukaryotic genomes. We aimed to characterize TEs to help elucidate their impact on the genomic architecture, diversity and evolution of chromosomes in the <i>D. buzzatii</i> cluster of species (<i>repleta</i> group). <i>Methods: </i>A full TE element of <i>D. buzzatii</i>, named <i>PERI</i>, was identified in a BAC clone available in GenBank. <i>PERI</i> was further analysed using bioinformatics tools, PCR and in-situ hybridization to metaphase chromosomes and DNA fibers. <i>Results: </i><i>PERI</i> shares several structures in common with <i>DINE-1</i>, an abundant TE found widespread along the <i>Drosophila</i> genus. The central region of <i>PERI</i> is very dynamic but revealed a disrupted pattern of nucleotide variability among its internal tandem repeats. The minimal sequence variation in <i>D. serido</i> suggests recent amplification. <i>PERI</i> accumulates near or at heterochromatic regions of all 6 pairs of chromosomes, especially on the sex chromosomes, with some clustering. <i>Conclusions: </i><i>PERI</i> is an abundant type of <i>DINE-1</i> transposon but with characteristic sequence signatures and probably restricted to the <i>buzzatii </i>complex. The conservation of different central domains and association with genes suggests selective constraints. Although at or near heterochromatin, the distribution of <i>PERI</i> does not overlap with satDNAs, probably a consequence of functional or molecular constraints.
DOI: 10.6084/m9.figshare.5121415.v1
title: Supplementary Material for: Systematic Removal of Outliers to Reduce Heterogeneity in Case-Control Association Studies

description: <i>Background/Aims:</i> In human case-control association studies, population heterogeneity is often present and can lead to increased false-positive results. Various methods have been proposed and are in current use to remedy this situation. <i>Methods:</i> We assume that heterogeneity is due to a relatively small number of individuals whose allele frequencies differ from those of the remainder of the sample. For this situation, we propose a new method of handling heterogeneity by removing outliers in a controlled manner. In a coordinate system of the <i>c</i> largest principal components in multidimensional scaling (MDS), we systematically remove one after another of the most extreme outlying individuals and each time recompute the largest association test statistic. The smallest p value obtained within <i>M</i> removals serves as our test statistic whose significance level is assessed in randomization samples. <i>Results:</i> In power simulations of our method and three methods in current use, averaged over several different scenarios, the best method turned out to be logistic regression analysis (based on all individuals) with MDS components as covariates. <i>Conclusion:</i> Our proposed method ranked closely behind logistic regression analysis with MDS components but ahead of other commonly used approaches. In analyses of real datasets our method performed best.
DOI: 10.6084/m9.figshare.5121418
title: Supplementary Material for: Association of Genetic Polymorphisms in <i>STAT1</i> Gene with Increased Risk of Hepatocellular Carcinoma

description: <i>Objective:</i> Although signal transducer and activator of transcription 1 (STAT1), a transcription factor, plays a critical role in carcinogenesis and has been implicated as a tumor suppressor, few studies have investigated the associations between polymorphisms of this gene and the risk of cancer development. The aim of this study was to examine whether <i>STAT1</i> gene polymorphisms are associated with the risk of hepatocellular carcinoma (HCC). <i>Methods:</i> Ten single nucleotide polymorphisms in the <i>STAT1</i> gene were genotyped by TaqMan assays in 469 HCC cases and 558 age-, sex- and HBsAg-matched controls in a Chinese population. <i>Results:</i> Minor allele homozygous genotypes at rs867637 (9,046 bp 3′ of STP A&gt;G), rs3771300 (IVS24–153T&gt;G), and rs2280235 (IVS20–103G&gt;A), compared with their homozygote genotypes of common alleles, were associated with 1.6- (95% CI 1.1–2.3), 1.6- (95% CI 1.1–2.4), and 1.4-fold (95% CI 0.95–1.9) increased risk of HCC, respectively. The GGA haplotype, comprised of risk alleles at rs867637, rs3771300 and rs2280235, conferred a 1.2-fold (95% CI 1.0–1.5) increased risk of HCC, as compared to the most common haplotype of ATG. Diplotype GGA/GGA conferred a 1.6-fold (95% CI 1.0–2.5) increased risk of HCC compared with diplotype ATG/ATG. <i>Conclusion:</i> Our results demonstrate for the first time that polymorphisms in the <i>STAT1</i> gene are associated with HCC susceptibility.
DOI: 10.6084/m9.figshare.5121406
title: Supplementary Material for: Common Carotid Artery Intima-Media Thickness: The Cardiovascular Risk Factor Multiple Evaluation in Latin America (CARMELA) Study Results

description: <i>Background:</i> Measurement of far wall common carotid artery intima-media thickness (CCAIMT) has emerged as a predictor of incident cardiovascular events. The Cardiovascular Risk Factor Multiple Evaluation in Latin America (CARMELA) study was the first large-scale population-based assessment of both CCAIMT and cardiovascular risk factor prevalence in 7 Latin American cities; the relationship between CCAIMT and cardiovascular risk markers was assessed in these urban Latin American centers. <i>Methods:</i> CARMELA was across-sectional, population-based, observational study using stratified, multistage sampling. The participants completed a questionnaire, were evaluated in a clinical visit and underwent carotid ultrasonography. Clinical measurements were obtained by health personnel trained, certified and supervised by CARMELA investigators. Mannheim intima-media thickness consensus guidelines were followed for measurement of CCAIMT. <i>Results:</i> In all cities and for both sexes, CCAIMT increased with higher age. CCAIMT was greater in the presence of cardiovascular risk factors than in their absence. In all cities, there was a statistically significant linear trend between increasing CCAIMT and a growing number of cardiovascular risk factors (p &lt; 0.001). After adjustment for age and sex, metabolic syndrome was strongly associated with increased CCAIMT (p &lt; 0.001 in all cities), as were hypercholesterolemia, obesity and diabetes (p &lt; 0.001 in most cities). By multivariate analysis, hypertension was independently associated with an increase in CCAIMT in all cities (p &lt; 0.01). <i>Conclusions:</i> CARMELA was the first large-scale population study to provide normal CCAIMT values according to age and sex in urban Latin American populations and to show CCAIMT increases in the presence of cardiovascular risk factors and metabolic syndrome.
DOI: 10.6084/m9.figshare.5121409
title: Supplementary Material for: Increasing Genotype-Phenotype Model Determinism: Application to Bivariate Reading/Language Traits and Epistatic Interactions in Language-Impaired Families

description: While advances in network and pathway analysis have flourished in the era of genome-wide association analysis, understanding the genetic mechanism of individual loci on phenotypes is still readily accomplished using genetic modeling approaches. Here, we demonstrate two novel genotype-phenotype models implemented in a flexible genetic modeling platform. The examples come from analysis of families with specific language impairment (SLI), a failure to develop normal language without explanatory factors such as low IQ or inadequate environment. In previous genome-wide studies, we observed strong evidence for linkage to 13q21 with a reading phenotype in language-impaired families. First, we elucidate the genetic architecture of reading impairment and quantitative language variation in our samples using a bivariate analysis of reading impairment in affected individuals jointly with language quantitative phenotypes in unaffected individuals. This analysis largely recapitulates the baseline analysis using the categorical trait data (posterior probability of linkage (PPL) = 80%), indicating that our reading impairment phenotype captured poor readers who also have low language ability. Second, we performed epistasis analysis using a functional coding variant in the brain-derived neurotrophic factor <i>(BDNF)</i> gene previously associated with reduced performance on working memory tasks. Modeling epistasis doubled the evidence on 13q21 and raised the PPL to 99.9%, indicating that BDNF and 13q21 susceptibility alleles are jointly part of the genetic architecture of SLI. These analyses provide possible mechanistic insights for further cognitive neuroscience studies based on the models developed herein.
DOI: 10.6084/m9.figshare.5121412
title: Supplementary Material for: Real-Time Live Confocal Fluorescence Microscopy as a New Tool for Assessing Platelet Vitality

description: <i>Background:</i> Assessment of platelet vitality is important for patients presenting with inherited or acquired disorders of platelet function and for quality assessment of platelet concentrates. <i>Methods:</i> Herein we combined live stains with intra-vital confocal fluorescence microscopy in order to obtain an imaging method that allows fast and accurate assessment of platelet vitality. Three fluorescent dyes, FITC-coupled wheat germ agglutinin (WGA), tetramethylrhodamine methyl ester perchlorate (TMRM) and acetoxymethylester (Rhod-2), were used to assess platelet morphology, mitochondrial activity and intra-platelet calcium levels. Microscopy was performed with a microlens-enhanced Nipkow spinning disk-based system allowing live confocal imaging. <i>Results:</i> Comparison of ten samples of donor platelets collected before apheresis and platelets collected on days 5 and 7 of storage showed an increase in the percentage of Rhod-2positive platelets from 3.6 to 47 and finally to 71%. Mitochondrial potential was demonstrated in 95.4% of donor platelets and in 92.5% of platelets stored for 7 days. <i>Conclusion:</i> Such fast and accurate visualization of known key parameters of platelet function could be of relevance for studies addressing the quality of platelets after storage and additional manipulation, such as pathogen inactivation, as well as for the analysis of inherited platelet function disorders.
DOI: 10.6084/m9.figshare.5121418.v1
title: Supplementary Material for: Association of Genetic Polymorphisms in <i>STAT1</i> Gene with Increased Risk of Hepatocellular Carcinoma

description: <i>Objective:</i> Although signal transducer and activator of transcription 1 (STAT1), a transcription factor, plays a critical role in carcinogenesis and has been implicated as a tumor suppressor, few studies have investigated the associations between polymorphisms of this gene and the risk of cancer development. The aim of this study was to examine whether <i>STAT1</i> gene polymorphisms are associated with the risk of hepatocellular carcinoma (HCC). <i>Methods:</i> Ten single nucleotide polymorphisms in the <i>STAT1</i> gene were genotyped by TaqMan assays in 469 HCC cases and 558 age-, sex- and HBsAg-matched controls in a Chinese population. <i>Results:</i> Minor allele homozygous genotypes at rs867637 (9,046 bp 3′ of STP A&gt;G), rs3771300 (IVS24–153T&gt;G), and rs2280235 (IVS20–103G&gt;A), compared with their homozygote genotypes of common alleles, were associated with 1.6- (95% CI 1.1–2.3), 1.6- (95% CI 1.1–2.4), and 1.4-fold (95% CI 0.95–1.9) increased risk of HCC, respectively. The GGA haplotype, comprised of risk alleles at rs867637, rs3771300 and rs2280235, conferred a 1.2-fold (95% CI 1.0–1.5) increased risk of HCC, as compared to the most common haplotype of ATG. Diplotype GGA/GGA conferred a 1.6-fold (95% CI 1.0–2.5) increased risk of HCC compared with diplotype ATG/ATG. <i>Conclusion:</i> Our results demonstrate for the first time that polymorphisms in the <i>STAT1</i> gene are associated with HCC susceptibility.
DOI: 10.6084/m9.figshare.5121421.v1
title: Supplementary Material for: Portrayal of the Notch System in Embryonic Stem Cell-Derived Embryoid Bodies

description: We portrayed the Notch system in embryonic stem cell (ESC)-derived embryoid bodies (EBs) differentiating under the standard protocols used to assess yolk sac (YS) hematopoiesis in vitro. Notch receptors and Notch ligands were detected in virtually all cells throughout EB development. Notch1 and Notch 2, but not Notch4, were visualized in the nucleus of EB cells, and all these receptors were also observed as patent cytoplasmic foci. Notch ligands (Delta-like1 and 4, Jagged1 and 2) were immunodetected mostly as cytoplasmic foci. Widespread Notch1 activation was evident at days 2–4 of EB differentiation, the time window of hemangioblast generation in this in vitro system. EBs experienced major spatial remodeling beyond culture day 4, the time point coincident with the transition between primitive and multilineage waves of YS hematopoiesis in vitro. At day 6, where definitive YS hematopoiesis is established in EBs, these exhibit an immature densely packed cellular region (DCR) surrounded by a territory of mesodermal-like cells and an outer layer of endodermal cells. Immunolabeling of Notch receptors and ligands was usually higher in the DCR. Our results show that Notch system components are continuously and abundantly expressed in the multicellular environments arising in differentiating EBs. In such an active Notch system, receptors and ligands do not accumulate extensively at the cell surface but instead localize at cytoplasmic foci, an observation that fits current knowledge on endocytic modulation of Notch signaling. Our data thus suggest that Notch may function as a territorial modulator during early development, where it may eventually influence YS hematopoiesis.
DOI: 10.6084/m9.figshare.5121394
title: Supplementary Material for: Mutations of the SRY-Responsive Enhancer of <i>SOX9</i> Are Uncommon in XY Gonadal Dysgenesis

description: During mouse sex determination, SRY upregulates the core testis-specific enhancer of <i>Sox9</i>, TESCO. Mutations in human <i>SRY</i> are found in one third of cases with XY pure gonadal dysgenesis (XY GD; Swyer syndrome), while two thirds remain unexplained. Heterozygous <i>SOX9</i> mutations can cause XY GD in association with the skeletal malformation syndrome campomelic dysplasia. We hypothesized that human TESCO mutations could cause isolated XY GD. Sixty-six XY GD cases with an intact <i>SRY</i> were analyzed for TESCO point mutations or deletions. No mutations were identified. We conclude that TESCO mutations are not a common cause of XY GD.
DOI: 10.6084/m9.figshare.5121397
title: Supplementary Material for: Spatiotemporal Localization of Periostin and Its Potential Role in Epithelial-Mesenchymal Transition during Palatal Fusion

description: The medial epithelial seam (MES) between the palatal shelves degrades during palatal fusion to achieve the confluence of palatal mesenchyme. Cellular mechanisms underlying the degradation of MES have been proposed, such as apoptosis, epithelial-mesenchymal transition (EMT) and migration of medial edge epithelia (MEE). Extracellular matrix components have been shown to play an important role in EMT in many model systems. Periostin (also known as osteoblast-specific factor-2) is a secreted mesenchymal extracellular matrix component that affects the ability of cells to migrate and/or facilitates EMT during both embryonic development and pathologic conditions. In this study, we evaluated the spatiotemporal expression patterns of periostin during mouse palatal fusion by in situ hybridization and immunofluorescence. Periostin mRNA and protein were present in the palatal mesenchyme, the protein being distributed in a fine fibrillar network and in the basement membrane, but absent from the epithelium. During MES degradation, the protein was strongly expressed in the basement membrane underlying the MES and in some select MEE. Confocal microscopic analysis using an EMT marker, twist1, and an epithelial marker, cytokeratin 14, provided evidence that select MEE were undergoing EMT in association with periostin. Moreover, the major extracellular matrix molecules in basement membrane, laminin and collagen type IV were degraded earlier than periostin. The result is that select MEE establish interactions with periostin in the mesenchymal extracellular matrix, and these new cell-matrix interactions may regulate MEE transdifferentiation during palatal fusion.
DOI: 10.6084/m9.figshare.5121400
title: Supplementary Material for: Cooperative Signaling between Oncostatin M, Hepatocyte Growth Factor and Transforming Growth Factor-β Enhances Epithelial to Mesenchymal Transition in Lung and Pancreatic Tumor Models

description: Epithelial to mesenchymal transition (EMT) plays a dual role in tumor progression. It enhances metastasis of tumor cells by increasing invasive capacity and promoting survival, and it decreases tumor cell sensitivity to epithelial cell-targeting agents such as epithelial growth factor receptor kinase inhibitors. In order to study EMT in tumor cells, we have characterized 3 new models of ligand-driven EMT: the CFPAC1 pancreatic tumor model and the H358 and H1650 lung tumor models. We identified a diverse set of ligands that drives EMT in these models. Hepatocyte growth factor and oncostatin M induced EMT in all models, while transforming growth factor-β induced EMT in both lung models. We observed morphologic, marker and phenotypic changes in response to chronic ligand treatment. Interestingly, stimulation with 2 ligands resulted in more pronounced EMT compared with single-ligand treatment, demonstrating a spectrum of EMT states induced by parallel signaling, such as the JAK and PI3K pathways. The EMT changes observed in response to the ligand were reversed upon ligand withdrawal, demonstrating the ‘metastable’ nature of these models. To study the impact of EMT on cell morphology and invasion in a 3D setting, we cultured cells in a semisolid basement membrane extract. Upon stimulation with EMT ligands, the colonies exhibited changes to EMT markers and showed phenotypes ranging from modest differences in colony architecture (CFPAC1) to complex branching structures (H358, H1650). Collectively, these 3 models offer robust cell systems with which to study the roles that EMT plays in cancer progression.