cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5126356.v1
title: Supplementary Material for: Accuracy of the Spot Sign on Computed Tomography Angiography as a Predictor of Haematoma Enlargement after Acute Spontaneous Intracerebral Haemorrhage: A Systematic Review

description: <b><i>Background:</i></b> A common early complication of intracerebral haemorrhage (ICH) is haematoma enlargement (HE), a strong independent predictor of a poor outcome. Therapeutic options to limit haematoma progression are currently scarce. Haemostatic therapy may be effective in patients with ICH, but it carries the risk of thromboembolic events in unselected patients. Accurate patient selection would, therefore, be of key importance for delivering potentially successful therapeutic strategies. Currently, there is no gold standard to accurately predict HE. The presence of contrast extravasation within the haematoma on computed tomography angiography (CTA), the ‘spot sign', has been reported in several studies and seems a particularly promising marker but lacks a standardised evaluation so far. <b><i>Summary:</i></b> We conducted a systematic review of published data to address the research question: In adults with acute spontaneous ICH, how accurately does the spot sign predict HE on follow-up imaging and thus poor functional outcome or mortality? We searched PubMed and Embase databases (from 1980 to May 2012), using a highly sensitive search strategy and including all studies involving adult patients with spontaneous ICH evaluated with CTA and follow-up CT scans, reporting any measure of clinical outcome, and reporting or allowing calculation of accuracy measures of the spot sign in predicting HE and clinical outcome. Baseline characteristics, accuracy measures and effect measures, as well as bias assessment, were reported according to PRISMA recommendations. The quality of the studies was appraised using an adapted version of the REMARK reporting recommendations. From 259 potentially relevant studies, we finally selected 6 studies (1 of them was a multicentre cohort study) covering a total of 709 patients. Studies varied substantially in terms of size, methodological quality, definitions of terms, outcomes selected and results. In particular, definition of the spot sign was not consistent in all studies. Furthermore, the only outcome measure consistently available was HE, while definitions and analyses of clinical outcomes seemed not adequate. Lastly, the choice of candidate variables for univariate and multivariate analyses did not include all determinants of HE and poor functional outcome. High heterogeneity was demonstrated (I<sup>2</sup>: 94% for HE) with substantial potential of bias. <b><i>Key Messages:</i></b> Studies of the spot sign are diverse and therefore complex to interpret. Our research question could not be answered due to heterogeneity and potential of bias in the selected studies. Further appropriately powered studies using standardised definitions and taking all predictors of HE and poor clinical outcome into account are required for a proper clinical implementation.
DOI: 10.6084/m9.figshare.5126338
title: Supplementary Material for: Epigenetic Analyses and the Distribution of Repetitive DNA and Resistance Genes Reveal the Complexity of Common Bean (<b><i>Phaseolus vulgaris</i></b> L., Fabaceae) Heterochromatin

description: The common bean (<i>Phaseolus vulgaris</i> L.) is the main representative of its genus and one of most important sources of proteins in African and Latin American countries. Although it is a species with a small genome, its pericentromeric and subtelomeric heterochromatin fractions are interspersed with single-copy sequences and active genes, suggesting a less compartmentalized genome organization. The present study characterized its chromatin fractions, associating the distribution of repetitive sequences and resistance genes with histone and DNA epigenetic modifications with and without biotic stress. Immunostaining with H3K4me3 and H4K5ac were generally associated with euchromatic regions, whereas H3K9me2, H3K27me1, and 5mC preferentially labeled the pericentromeric heterochromatin. The 45S rDNA and centromeric DNA sequences were hypomethylated as were most of the terminal heterochromatic blocks. The largest of them, which is associated with resistance genes, was also hypomethylated after the plants were infected with virulent and avirulent strains of the fungus <i>Colletotrichum lindemuthianum</i>, suggesting no correlation with control of resistance gene expression. The results highlighted the differences between subtelomeric and pericentromeric heterochromatin as well as variation within the pericentromeric heterochromatin.
DOI: 10.6084/m9.figshare.5126341
title: Supplementary Material for: Glial Network Responses to Polymicrobial Invasion of Dentin

description: This study investigated the distribution patterns of glial networks disclosed by reactivity for glial fibrillary acidic protein (GFAP) and S100B in healthy and carious human teeth. The objective was to determine the assembly and collapse of glial networks in response to encroaching infection. 15 healthy and 37 carious posterior teeth from adults were studied. Immediately after extraction, teeth were cleaned and vertically split and the half with pulp fixed and prepared for resin or frozen sections. Sections were stained with toluidine blue and for immunofluorescence, with observation by confocal laser microscopy and analysis by ImageJ software. Carious teeth were subdivided into three groups according to degree of carious involvement: microbial penetration through enamel (stage A), extension into dentin (stage B) and advanced penetration into dentin but without invasion of underlying pulp tissue (stage C). In stage A lesions there was marked increase in glial networks in dental pulp tissue that extended beyond the zone of microbial invasion. This response was maintained in stage B lesions. In advanced stage C lesions these networks were degraded in the zone of invasion in association with failure to contain infection. Cells expressing the glial markers GFAP and S100B showed a response to initial microbial invasion of dentin by increase in number and altered anatomical arrangement. The late stage of dentinal caries was marked by collapse of these networks in the region adjacent to advancing bacteria. This behaviour is important for understanding and explaining the defensive response of the neurosensory peripheral dental pulp apparatus to infection.
DOI: 10.6084/m9.figshare.5126344.v1
title: Supplementary Material for: SNP-Based Linkage Analysis in Extended Pedigrees: Comparison between Two Alternative Approaches

description: <b><i>Background:</i></b> Linkage analysis on extended pedigrees is often challenged by the high computational demand of exact identity-by-descent (IBD) matrix reconstruction. When such an analysis becomes not feasible, two alternative solutions are contrasted: a full pedigree analysis based on approximate IBD estimation versus a pedigree splitting followed by exact IBD estimation. A multiple splitting (MS) approach, which combines linkage results across different splitting configurations, has been proposed to increase the power of single-split solutions. <b><i>Methods:</i></b> To assess whether MS can achieve a comparable power to a full pedigree analysis, we compared the power of linkage on a very large pedigree in both simulated and real-case scenarios, using variance components linkage analysis of a dense SNP array. <b><i>Results:</i></b> Our results confirm that the power to detect linkage is affected by the pedigree size. The MS approach showed higher power than the single-split analysis, but it was substantially less powerful than the full pedigree approach in both scenarios, at any level of significance and variance explained by a quantitative trait locus. <b><i>Conclusion:</i></b> The MS approach should always be preferred to analyses based on a single split but, when adequate computational resources are available, a full pedigree analysis is better than the MS analysis. Rather than focusing on how to best split a pedigree, it might be more valuable to identify computational solutions that can make the IBD estimation of dense-marker maps practically feasible, thus allowing a full pedigree analysis.
DOI: 10.6084/m9.figshare.5126332
title: Supplementary Material for: Pharmacological Characteristics of the Inhibitory Effects of Docosahexaenoic Acid on Vascular Contractions Studied in Rat Mesenteric Artery

description: <b><i>Background/Aims:</i></b> Effects of docosahexaenoic acid (DHA) on blood vessel contractions to various constrictors were investigated in rat mesenteric artery and compared with those of eicosapentaenoic acid (EPA) and linoleic acid (LA). <b><i>Methods:</i></b> Tension changes in mesenteric ring segments were isometrically recorded. <b><i>Results:</i></b> On sustained contractions induced by a thromboxane A<sub>2</sub> mimetic (U46619), DHA exerted a strong inhibitory effect. This inhibitory effect of DHA on U46619 appeared both in endothelium-intact and endothelium-denuded preparations. Although the inhibitory effect of DHA on prostaglandin F<sub>2α</sub> (PGF<sub>2α</sub>)-induced contractions was also significant, contractions to phenylephrine (PE) and high-KCI were not affected by DHA. As well as DHA, EPA strongly diminished U46619- and PGF<sub>2α</sub>-induced contractions without showing a substantial inhibition of PE- and high-KCl-induced contractions. By contrast, LA did not show any significant inhibitory effects on any contractions. The DHA-induced inhibitory actions exerted on U46619 and PGF<sub>2α</sub> also emerged if ring preparations were pretreated with this ω-3 polyunsaturated fatty acid (PUFA). <b><i>Conclusion:</i></b> DHA and EPA are found to more pronouncedly inhibit prostanoid receptor-mediated contractions than other constrictor responses of the mesenteric artery via endothelium-independent mechanisms. These inhibitory effects of ω-3 PUFAs on prostanoid receptor-mediated contractions may partly underlie the mechanisms by which these ω-3 PUFAs elicit protective actions against circulatory disorders.
DOI: 10.6084/m9.figshare.5126335
title: Supplementary Material for: Sudden Death in Incident Dialysis Patients

description: <b><i>Background:</i></b> Sudden death (SD) constitutes one of the principal causes of death and is an important problem in healthcare provision. Cardiovascular diseases have a high prevalence in dialysis patients and constitute the principal cause of death. We sought to analyze retrospectively the incidence of SD in patients commencing dialysis and the factors related to its presence. <b><i>Methods:</i></b> We evaluated all the patients who began dialysis in our center between 1/11/2003 and 15/9/2007, and who were followed up until death, transplant, or study completion on 31/12/2012. We determined the presence of SD according to the following criteria: SD at 24 h (SD 24H): unexpected death occurring in the 24 h following the start of symptoms, or when the patient was found dead and had been seen alive 24 h earlier; SD at 1 h (SD 1H): death witnessed as occurring in the first hour following the start of symptoms. <b><i>Results:</i></b> We evaluated 285 patients, mean age 65.67 ± 15.7 years. In a follow-up of 39.9 ± 34.2 months (947.6 patient-years of follow-up) 168 died (59%), 28 (10%) patients presented SD 24H (2.9/100 patient-years), and 16 (6%) patients presented SD 1H (1.7/100 patient-years). In the multivariate analysis, having had a myocardial infarction or having had electrocardiographic abnormalities (Q wave, negative T wave, subendocardial lesion or QRS &gt;120 ms) were the principal independent predictors of SD 24H (OR 7.83; 95% CI 2.20-27.86; p = 0.001) and of SD 1H (OR 13.43; 95% CI 1.56-115.42; p = 0.018). <b><i>Conclusions:</i></b> SD on dialysis is very frequent. Two groups can be identified easily, with risk profiles clearly differentiated.
DOI: 10.6084/m9.figshare.5126329
title: Supplementary Material for: Differential Placental Gene Expression in Term Pregnancies Affected by Fetal Growth Restriction and Macrosomia

description: <b><i>Introduction:</i></b> Extremes of fetal growth are associated with increased perinatal mortality and morbidity and a higher prevalence of cardiovascular disease, obesity and diabetes in later life. We aimed to identify changes in placental gene expression in pregnancies with evidence of growth dysfunction and candidate genes that may be used to identify abnormal patterns of growth prior to delivery. <b><i>Methods:</i></b> Growth-restricted (n = 4), macrosomic (n = 6) and normal term (n = 5) placentas were selected from a banked series (n = 200) collected immediately after caesarean section. RNA was extracted prior to microarray analysis using Affymetrix HG-U219 arrays to determine variation in gene expression. Genes of interest were confirmed using qRT-PCR. <b><i>Results:</i></b> 338 genes in the growth-restricted and 41 genes in the macrosomic group were identified to be significantly dysregulated (&gt;2-fold change; p &lt; 0.05). <i>CPXM2</i> and <i>CLDN1</i> were upregulated and <i>TXNDC5</i> and <i>LRP2</i> downregulated in fetal growth restriction. In macrosomia, <i>PHLDB2</i> and <i>CLDN1</i> were upregulated and <i>LEP</i> and <i>GCH1</i> were downregulated. <b><i>Discussion:</i></b> Dysfunctional growth is associated with differential placental gene expression and affects genes with a whole spectrum of developmental and cellular functions. Better elucidation of these pathways may allow the development of biomarkers to identify growth abnormalities and effective prenatal intervention.
DOI: 10.6084/m9.figshare.5126338.v1
title: Supplementary Material for: Epigenetic Analyses and the Distribution of Repetitive DNA and Resistance Genes Reveal the Complexity of Common Bean (<b><i>Phaseolus vulgaris</i></b> L., Fabaceae) Heterochromatin

description: The common bean (<i>Phaseolus vulgaris</i> L.) is the main representative of its genus and one of most important sources of proteins in African and Latin American countries. Although it is a species with a small genome, its pericentromeric and subtelomeric heterochromatin fractions are interspersed with single-copy sequences and active genes, suggesting a less compartmentalized genome organization. The present study characterized its chromatin fractions, associating the distribution of repetitive sequences and resistance genes with histone and DNA epigenetic modifications with and without biotic stress. Immunostaining with H3K4me3 and H4K5ac were generally associated with euchromatic regions, whereas H3K9me2, H3K27me1, and 5mC preferentially labeled the pericentromeric heterochromatin. The 45S rDNA and centromeric DNA sequences were hypomethylated as were most of the terminal heterochromatic blocks. The largest of them, which is associated with resistance genes, was also hypomethylated after the plants were infected with virulent and avirulent strains of the fungus <i>Colletotrichum lindemuthianum</i>, suggesting no correlation with control of resistance gene expression. The results highlighted the differences between subtelomeric and pericentromeric heterochromatin as well as variation within the pericentromeric heterochromatin.
DOI: 10.6084/m9.figshare.5126341.v1
title: Supplementary Material for: Glial Network Responses to Polymicrobial Invasion of Dentin

description: This study investigated the distribution patterns of glial networks disclosed by reactivity for glial fibrillary acidic protein (GFAP) and S100B in healthy and carious human teeth. The objective was to determine the assembly and collapse of glial networks in response to encroaching infection. 15 healthy and 37 carious posterior teeth from adults were studied. Immediately after extraction, teeth were cleaned and vertically split and the half with pulp fixed and prepared for resin or frozen sections. Sections were stained with toluidine blue and for immunofluorescence, with observation by confocal laser microscopy and analysis by ImageJ software. Carious teeth were subdivided into three groups according to degree of carious involvement: microbial penetration through enamel (stage A), extension into dentin (stage B) and advanced penetration into dentin but without invasion of underlying pulp tissue (stage C). In stage A lesions there was marked increase in glial networks in dental pulp tissue that extended beyond the zone of microbial invasion. This response was maintained in stage B lesions. In advanced stage C lesions these networks were degraded in the zone of invasion in association with failure to contain infection. Cells expressing the glial markers GFAP and S100B showed a response to initial microbial invasion of dentin by increase in number and altered anatomical arrangement. The late stage of dentinal caries was marked by collapse of these networks in the region adjacent to advancing bacteria. This behaviour is important for understanding and explaining the defensive response of the neurosensory peripheral dental pulp apparatus to infection.
DOI: 10.6084/m9.figshare.5126326
title: High-level prediction signals in a low-level area of the macaque face-processing hierarchy

description: Data for Schwiedrzik & Freiwald, 2017<br><br>Electrophysiology:<br>electrophys.mat and electrophys.xlsx<br><br>Contains average spike density functions per neuron (80) and per condition (4) in the time range 50:450 ms (the time range analyzed in the paper) for successor stimuli. Sampling rate is 1000 Hz. The order of conditions is: identity violation, view violation, identity+view violation, trained. Data are available as Matlab (.mat) and Excel (.xlsx) files. <br><br>Psychophysics:<br>psychophys.mat and psychophys.xlsx<br><br>Contains d-prime and average reaction times per subject (13) and per condition (4). The order of conditions is: trained, view violation, identity violation, identity+view violation. Data are available as Matlab (.mat) and Excel (.xlsx) files. <br><br><br>For questions, please contact<br>Caspar M. Schwiedrzik, c.schwiedrzik@eni-g.de<br><br>
DOI: 10.6084/m9.figshare.5126332.v1
title: Supplementary Material for: Pharmacological Characteristics of the Inhibitory Effects of Docosahexaenoic Acid on Vascular Contractions Studied in Rat Mesenteric Artery

description: <b><i>Background/Aims:</i></b> Effects of docosahexaenoic acid (DHA) on blood vessel contractions to various constrictors were investigated in rat mesenteric artery and compared with those of eicosapentaenoic acid (EPA) and linoleic acid (LA). <b><i>Methods:</i></b> Tension changes in mesenteric ring segments were isometrically recorded. <b><i>Results:</i></b> On sustained contractions induced by a thromboxane A<sub>2</sub> mimetic (U46619), DHA exerted a strong inhibitory effect. This inhibitory effect of DHA on U46619 appeared both in endothelium-intact and endothelium-denuded preparations. Although the inhibitory effect of DHA on prostaglandin F<sub>2α</sub> (PGF<sub>2α</sub>)-induced contractions was also significant, contractions to phenylephrine (PE) and high-KCI were not affected by DHA. As well as DHA, EPA strongly diminished U46619- and PGF<sub>2α</sub>-induced contractions without showing a substantial inhibition of PE- and high-KCl-induced contractions. By contrast, LA did not show any significant inhibitory effects on any contractions. The DHA-induced inhibitory actions exerted on U46619 and PGF<sub>2α</sub> also emerged if ring preparations were pretreated with this ω-3 polyunsaturated fatty acid (PUFA). <b><i>Conclusion:</i></b> DHA and EPA are found to more pronouncedly inhibit prostanoid receptor-mediated contractions than other constrictor responses of the mesenteric artery via endothelium-independent mechanisms. These inhibitory effects of ω-3 PUFAs on prostanoid receptor-mediated contractions may partly underlie the mechanisms by which these ω-3 PUFAs elicit protective actions against circulatory disorders.
DOI: 10.6084/m9.figshare.5126317
title: Supplementary Material for: Israeli Society of Medical Genetics NIPT Committee Opinion 072013: Non-Invasive Prenatal Testing of Cell-Free DNA in Maternal Plasma for Detection of Fetal Aneuploidy

description: Non-invasive prenatal testing (NIPT) of cell-free fetal DNA in maternal plasma is a novel approach, designed for detecting common aneuploidies in the fetus. The Israeli Society of Medical Geneticists (ISMG) supports its use according to the guidelines stated herein. The clinical data collected thus far indicate that NIPT is highly sensitive in detecting trisomies 21 and 18, and fairly sensitive in detecting trisomy 13 and sex chromosome aneuploidies. Because false-positive results may occur, an abnormal result must be validated by invasive prenatal testing. At this juncture, NIPT does not replace existing prenatal screening tests for Down syndrome, as these are relatively inexpensive and cost-effective. Nonetheless, NIPT may be offered to women considered to be at high risk for fetal chromosomal abnormalities as early as 10 weeks of gestation. The ISMG states that NIPT should be an informed patient choice, and that pretest counseling regarding the limitations of NIPT is warranted. Women at high risk for genetic disorders not detected by NIPT should be referred for genetic counseling. A normal test result may be conveyed by a relevant healthcare provider, while an abnormal result should be discussed during a formal genetic consultation session.
DOI: 10.6084/m9.figshare.5126320
title: Supplementary Material for: High Penetrance of a Pan-<b><i>Canina</i></b> Type rDNA Family in Intersection <b><i>Rosa</i></b> Hybrids Suggests Strong Selection of Bivalent Chromosomes in the Section <b><i>Caninae</i></b>

description: All dogroses <i>(Rosa</i> sect. <i>Caninae)</i> are characterized by the peculiar <i>canina</i> meiosis in which genetic material is unevenly distributed between female and male gametes. The pan-<i>canina</i> rDNA family (termed beta) appears to be conserved in all dogroses analyzed so far. Here, we have studied rDNAs in experimental hybrids obtained from open pollination of F1 plants derived from 2 independent intersectional crosses between the pentaploid dogrose species (2n = 5x = 35) <i>Rosa rubiginosa</i> as female parent (producing 4x egg cells due to the unique asymmetrical <i>canina</i> meiosis) and the tetraploid (2n = 4x = 28) garden rose <i>R. hybrida</i> ‘André Brichet' as male parent (producing 2x pollen after normal meiosis). We analyzed the structure of rDNA units by molecular methods [CAPS and extensive sequencing of internal transcribed spacers (ITS)] and determined the number of loci on chromosomes by FISH. FISH showed that <i>R. rubiginosa</i> and ‘André Brichet' harbored 5 and 4 highly heteromorphic rDNA loci, respectively. In the second generation of hybrid lines, we observed a reduced number of loci (4 and 5 instead of the expected 6). In <i>R. rubiginosa</i> and ‘André Brichet', 2-3 major ITS types were found which is consistent with a weak homogenization pressure maintaining high diversity of ITS types in this genus. In contrast to expectation (the null hypothesis of Mendelian inheritance of ITS families), we observed reduced ITS diversity in some individuals of the second generation which might derive from self-fertilization or from a backcross to <i>R. rubiginosa</i>. In these individuals, the pan-<i>canina</i> beta family appeared to be markedly enriched, while the paternal families were lost or diminished in copies. Although the mechanism of biased meiotic transmission of certain rDNA types is currently unknown, we speculate that the bivalent-forming chromosomes carrying the beta rDNA family exhibit extraordinary pairing efficiency and/or are subjected to strong selection in <i>Caninae</i> polyploids.