cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4748083
title: Supplementary Material for: Vitamin D and Pre-Eclampsia: Original Data, Systematic Review and Meta-Analysis

description: <strong><em>Background/Aims:</em></strong> Vitamin D may protect from pre-eclampsia through influences on immune modulation and vascular function. To evaluate the role of vitamin D in the development of pre-eclampsia, we conducted a systematic review and meta-analysis including novel data from 2 large-scale epidemiological studies. <b><i>Methods:</i></b> PubMed, EMBASE and the Cochrane Central Register of Controlled Trials were searched for prospective observational studies of association between vitamin D supplementation or status (measured by maternal 25-hydroxyvitamin D, 25(OH)D) with a subsequent risk of pre-eclampsia, or randomised controlled trials using vitamin D supplementation to prevent pre-eclampsia. The Hungarian Case-Control Surveillance of Congenital Abnormalities (HCCSCA) and the Avon Longitudinal Study of Parents and Children (ALSPAC) were included in meta-analyses with published studies. <b><i>Results:</i></b> Mothers receiving vitamin D supplementation earlier in pregnancy had lower odds of pre-eclampsia [pooled odds ratios (OR) 0.81 and 95% confidence interval (CI) 0.75-0.87, p = 2.4 × 10<sup>-8</sup>, 2 studies] in the meta-analysis of published studies with HCCSCA. The meta-analysis of published studies with ALSPAC suggested an association between higher serum 25(OH)D levels and a reduced risk of pre-eclampsia (pooled OR 0.52 and 95% CI 0.30-0.89, p = 0.02, 6 studies). Randomised trials of supplementation were suggestive of protective association (pooled OR 0.66 and 95% CI 0.52-0.83, p = 0.001, 4 studies). <b><i>Conclusions:</i></b> This study suggests that low maternal serum 25(OH)D concentrations increase pre-eclampsia risk and that vitamin D supplementation lowers this risk. The quality of evidence is insufficient to determine a causal association, which highlights the need for adequately powered clinical trials.
DOI: 10.6084/m9.figshare.4748062
title: Mapping differential cellular protein response of mouse alveolar epithelial cells to multi-walled carbon nanotubes as a function of atomic layer deposition coating

description: Carbon nanotubes (CNTs), a prototypical engineered nanomaterial, have been increasingly manufactured for a variety of novel applications over the past two decades. However, since CNTs possess fiber-like shape and cause pulmonary fibrosis in rodents, there is concern that mass production of CNTs will lead to occupational exposure and associated pulmonary diseases. The aim of this study was to use contemporary proteomics to investigate the mechanisms of cellular response in E10 mouse alveolar epithelial cells <i>in vitro</i> after exposure to multi-walled CNTs (MWCNTs) that were functionalized by atomic layer deposition (ALD). ALD is a method used to generate highly uniform and conformal nanoscale thin-film coatings of metals to enhance novel conductive properties of CNTs. We hypothesized that specific types of metal oxide coatings applied to the surface of MWCNTs by ALD would determine distinct proteomic profiles in mouse alveolar epithelial cells <i>in vitro</i> that could be used to predict oxidative stress and pulmonary inflammation. Uncoated (U)-MWCNTs were functionalized by ALD with zinc oxide (ZnO) to yield Z-MWCNTs or aluminum oxide (Al<sub>2</sub>O<sub>3</sub>) to yield A-MWCNTs. Significant differential protein expression was found in the following critical pathways: mTOR/eIF4/p70S6K signaling and Nrf-2 mediated oxidative stress response increased following exposure to Z-MWCNTs, interleukin-1 signaling increased following U-MWCNT exposure, and inhibition of angiogenesis by thrombospondin-1, oxidative phosphorylation, and mitochondrial dysfunction increased following A-MWCNT exposure. This study demonstrates that specific types of metal oxide thin film coatings applied by ALD produce distinct cellular and biochemical responses related to lung inflammation and fibrosis compared to uncoated MWCNT exposure <i>in vitro</i>.
DOI: 10.6084/m9.figshare.4748035
title: Supplementary Material for: The Global Epidemiology of Hereditary Ataxia and Spastic Paraplegia: A Systematic Review of Prevalence Studies

description: <strong><em>Background:</em></strong> Hereditary cerebellar ataxias (HCA) and hereditary spastic paraplegias (HSP) are two groups of neurodegenerative disorders that usually present with progressive gait impairment, often leading to permanent disability. Advances in genetic research in the last decades have improved their diagnosis and brought new possibilities for prevention and future treatments. Still, there is great uncertainty regarding their global epidemiology. <b><i>Summary:</i></b> Our objective was to assess the global distribution and prevalence of HCA and HSP by a systematic review and meta-analysis of prevalence studies. The MEDLINE, ISI Web of Science and Scopus databases were searched (1983-2013) for studies performed in well-defined populations and geographical regions. Two independent reviewers assessed the studies and extracted data and predefined methodological parameters. Overall, 22 studies were included, reporting on 14,539 patients from 16 countries. Multisource population-based studies yielded higher prevalence values than studies based primarily on hospitals or genetic centres. The prevalence range of dominant HCA was 0.0-5.6/10<sup>5</sup>, with an average of 2.7/10<sup>5</sup> (1.5-4.0/10<sup>5</sup>). Spinocerebellar ataxia type 3 (SCA3)/Machado-Joseph disease was the most common dominant ataxia, followed by SCA2 and SCA6. The autosomal recessive (AR) HCA (AR-HCA) prevalence range was 0.0-7.2/10<sup>5</sup>, the average being 3.3/10<sup>5</sup> (1.8-4.9/10<sup>5</sup>). Friedreich ataxia was the most frequent AR-HCA, followed by ataxia with oculomotor apraxia or ataxia-telangiectasia. The prevalence of autosomal dominant (AD) HSP (AD-HSP) ranged from 0.5 to 5.5/10<sup>5</sup> and that of AR-HSP from 0.0 to 5.3/10<sup>5</sup>, with pooled averages of 1.8/10<sup>5</sup> (95% CI: 1.0-2.7/10<sup>5</sup>) and 1.8/10<sup>5</sup> (95% CI: 1.0-2.6/10<sup>5</sup>), respectively. The most common AD-HSP form in every population was spastic paraplegia, autosomal dominant, type 4 (SPG4), followed by SPG3A, while SPG11 was the most frequent AR-HSP, followed by SPG15. In population-based studies, the number of families without genetic diagnosis after systematic testing ranged from 33 to 92% in the AD-HCA group, and was 40-46% in the AR-HCA, 45-67% in the AD-HSP and 71-82% in the AR-HSP groups. <b><i>Key Messages:</i></b> Highly variable prevalence values for HCA and HSP are reported across the world. This variation reflects the different genetic make-up of the populations, but also methodological heterogeneity. Large areas of the world remain without prevalence studies. From the available data, we estimated that around 1:10,000 people are affected by HCA or HSP. In spite of advances in genetic research, most families in population-based series remain without identified genetic mutation after extensive testing.
DOI: 10.6084/m9.figshare.4748026
title: Supplementary Material for: Anti-Phosphorylated Histone H2AThr120: A Universal Microscopic Marker for Centromeric Chromatin of Mono- and Holocentric Plant Species

description: Based on the analysis of 20 different monocot and eudicot species, we propose that the centromeric distribution of the phosphorylated histone H2AThr120 is evolutionary highly conserved across species with mono- and holocentric chromosomes. Therefore, antibodies recognizing the phosphorylated threonine 120 of the histone H2A can serve as a universal marker for the cytological detection of centromeres of mono- and holokinetic plant species. In addition, super resolution microscopy of signals specific to the centromere-specific histone H3 variant CENH3 and to H2AThr120ph revealed that these histone variants are incorporated into different nucleosomes, which form distinct, partly intermingled chromatin domains. This specific arrangement of both histone variants suggests different centromeric functions during the cell cycle.
DOI: 10.6084/m9.figshare.4748026.v1
title: Supplementary Material for: Anti-Phosphorylated Histone H2AThr120: A Universal Microscopic Marker for Centromeric Chromatin of Mono- and Holocentric Plant Species

description: Based on the analysis of 20 different monocot and eudicot species, we propose that the centromeric distribution of the phosphorylated histone H2AThr120 is evolutionary highly conserved across species with mono- and holocentric chromosomes. Therefore, antibodies recognizing the phosphorylated threonine 120 of the histone H2A can serve as a universal marker for the cytological detection of centromeres of mono- and holokinetic plant species. In addition, super resolution microscopy of signals specific to the centromere-specific histone H3 variant CENH3 and to H2AThr120ph revealed that these histone variants are incorporated into different nucleosomes, which form distinct, partly intermingled chromatin domains. This specific arrangement of both histone variants suggests different centromeric functions during the cell cycle.
DOI: 10.6084/m9.figshare.4748008
title: Supplementary Material for: An Epigenetic Screen Unmasks Metallothioneins as Putative Contributors to Renal Cell Carcinogenesis

description: <strong><em>Objective:</em></strong> Functional epigenetic studies aimed to re-express transcriptionally silenced genes in renal cell carcinoma (RCC) may facilitate the ongoing search for appropriate markers supporting clinical decision-making. <b><i>Methods:</i></b> The RCC cell line A-498 was treated with the DNA methyltransferase inhibitor zebularine under low-cytotoxicity conditions. RNA chip analyses revealed several upregulated transcripts that were further validated by qPCR on 49 matched pairs of human kidney tissues to identify suitable marker candidates. <b><i>Results:</i></b> Members of the metallothionein (MT) group were remarkably downregulated in tumor tissues. MT1G and MT1H expression was decreased in 98% of cases, whereas MT2A expression was downregulated in 73% of all cases. Comparison of 308 reactivated transcripts upregulated more than 1.5-fold to published data revealed a high number of shared candidates, which supports the consistency of this experimental approach. <b><i>Conclusion:</i></b> MTs were found to be transcriptionally inactivated in human RCC. Our observations support the hypothesis of a possible involvement of these metalloproteins in renal cell carcinogenesis. Additional functional studies of these genes may provide clues for understanding renal cancers as essentially metabolic diseases.
DOI: 10.6084/m9.figshare.4748002
title: Optimization of A-TIG process parameters using response surface methodology

description: In the present work, the influence of process parameters such as welding current (I), welding speed (S), and flux coating density (F) on different aspects of weld bead geometry for example depth of penetration (DOP), bead width (BW), depth to width ratio (D/W), and weld fusion zone area (WA) were investigated by using the central composite design (CCD). 9–12% Cr ferritic stainless steel (FSS) plates were welded using A-TIG welding. It was observed that all input variables have a direct influence on the DOP, BW, and D/W. However, flux coating density has no significant effect on WA. Mathematical models were generated from the obtained responses to predict the weld bead geometry. An optimized DOP, BW, D/W, and WA of 6.95 mm, 8.76 mm, 0.80, and 41.99 mm<sup>2</sup>, respectively, were predicted at the welding current of 213.78 A, the welding speed of 96.22 mm/min, and the flux coating density of 1.99 mg/cm<sup>2</sup>. Conformity test was done to check the practicability of the developed models. The conformity test results were in good agreement with the predicted values. Arc constriction and reversal in Marangoni convection were considered as major mechanisms for the deep and narrow weld bead during A-TIG welding.
DOI: 10.6084/m9.figshare.4747984
title: Supplementary Material for: Synaptosomal Lactate Dehydrogenase Isoenzyme Composition Is Shifted toward Aerobic Forms in Primate Brain Evolution

description: With the evolution of a relatively large brain size in haplorhine primates (i.e. tarsiers, monkeys, apes, and humans), there have been associated changes in the molecular machinery that delivers energy to the neocortex. Here we investigated variation in lactate dehydrogenase (LDH) expression and isoenzyme composition of the neocortex and striatum in primates using quantitative Western blotting and isoenzyme analysis of total homogenates and synaptosomal fractions. Analysis of isoform expression revealed that LDH in synaptosomal fractions from both forebrain regions shifted towards a predominance of the heart-type, aerobic isoform LDH-B among haplorhines as compared to strepsirrhines (i.e. lorises and lemurs), while in the total homogenate of the neocortex and striatum there was no significant difference in LDH isoenzyme composition between the primate suborders. The largest increase occurred in synapse-associated LDH-B expression in the neocortex, with an especially remarkable elevation in the ratio of LDH-B/LDH-A in humans. The phylogenetic variation in the ratio of LDH-B/LDH-A was correlated with species-typical brain mass but not the encephalization quotient. A significant LDH-B increase in the subneuronal fraction from haplorhine neocortex and striatum suggests a relatively higher rate of aerobic glycolysis that is linked to synaptosomal mitochondrial metabolism. Our results indicate that there is a differential composition of LDH isoenzymes and metabolism in synaptic terminals that evolved in primates to meet increased energy requirements in association with brain enlargement.
DOI: 10.6084/m9.figshare.4748002.v2
title: Optimization of A-TIG process parameters using response surface methodology

description: In the present work, the influence of process parameters such as welding current (I), welding speed (S), and flux coating density (F) on different aspects of weld bead geometry for example depth of penetration (DOP), bead width (BW), depth to width ratio (D/W), and weld fusion zone area (WA) were investigated by using the central composite design (CCD). 9–12% Cr ferritic stainless steel (FSS) plates were welded using A-TIG welding. It was observed that all input variables have a direct influence on the DOP, BW, and D/W. However, flux coating density has no significant effect on WA. Mathematical models were generated from the obtained responses to predict the weld bead geometry. An optimized DOP, BW, D/W, and WA of 6.95 mm, 8.76 mm, 0.80, and 41.99 mm<sup>2</sup>, respectively, were predicted at the welding current of 213.78 A, the welding speed of 96.22 mm/min, and the flux coating density of 1.99 mg/cm<sup>2</sup>. Conformity test was done to check the practicability of the developed models. The conformity test results were in good agreement with the predicted values. Arc constriction and reversal in Marangoni convection were considered as major mechanisms for the deep and narrow weld bead during A-TIG welding.
DOI: 10.6084/m9.figshare.4747984.v1
title: Supplementary Material for: Synaptosomal Lactate Dehydrogenase Isoenzyme Composition Is Shifted toward Aerobic Forms in Primate Brain Evolution

description: With the evolution of a relatively large brain size in haplorhine primates (i.e. tarsiers, monkeys, apes, and humans), there have been associated changes in the molecular machinery that delivers energy to the neocortex. Here we investigated variation in lactate dehydrogenase (LDH) expression and isoenzyme composition of the neocortex and striatum in primates using quantitative Western blotting and isoenzyme analysis of total homogenates and synaptosomal fractions. Analysis of isoform expression revealed that LDH in synaptosomal fractions from both forebrain regions shifted towards a predominance of the heart-type, aerobic isoform LDH-B among haplorhines as compared to strepsirrhines (i.e. lorises and lemurs), while in the total homogenate of the neocortex and striatum there was no significant difference in LDH isoenzyme composition between the primate suborders. The largest increase occurred in synapse-associated LDH-B expression in the neocortex, with an especially remarkable elevation in the ratio of LDH-B/LDH-A in humans. The phylogenetic variation in the ratio of LDH-B/LDH-A was correlated with species-typical brain mass but not the encephalization quotient. A significant LDH-B increase in the subneuronal fraction from haplorhine neocortex and striatum suggests a relatively higher rate of aerobic glycolysis that is linked to synaptosomal mitochondrial metabolism. Our results indicate that there is a differential composition of LDH isoenzymes and metabolism in synaptic terminals that evolved in primates to meet increased energy requirements in association with brain enlargement.
DOI: 10.6084/m9.figshare.4747930
title: Supplementary Material for: Ciliary Beating Plane and Wave Propagation in the Bovine Oviduct

description: The uterine tube is an essential conduit for the gametes and zygote during reproduction. The necessary bidirectional conveyance occurs through peristalsis and ciliary activity, but unlike in respiratory tract, little is known about mucociliary transport in the uterine tube, and the direction of transport and the alignment of oviductal cilia have not been conclusively characterized. This study aimed to determine the uniformity in the axonemal orientation of motile cilia in the bovine uterine tube, to identify the direction of mucociliary transport and to relate the presumptive beating plane and the mucociliary transport direction to the long axis of the uterine tube. The angular spread of oviductal motile cilia was determined by electron microscopy, and by maintaining the accurate alignment of the samples throughout the processing steps, axonemal orientation was determined relative to the long axis of the oviduct. The direction of the effective mucociliary transport was determined by the analysis of video microscopic data recorded on explants. Vector-based analysis of electron micrographs yielded the mean angle of deviation between the ‘effective ciliary stroke', as derived from axonemal orientation, and the tubal longitudinal axis pointing towards the uterus to be 0.8°, with a standard deviation of 35.2°. The corresponding angular deviation of the short-wave propagation was -6.8° (SD 34.6°). These results show that oviductal motile cilia are rigorously aligned, that the beating plane of the cilia is parallel to the long axis of the uterine tube and that the ‘effective stroke' and mucociliary transport are directed towards the uterus.
DOI: 10.6084/m9.figshare.4747927
title: COR1 Clustering Plots

description: Plots showing the time and position angle grids created to identify clusters from the Solar Stormwatch 'Track-it-back' observations. These observations were created when participants tracked CMEs through SECCHI COR1 images taken from the STEREO spacecraft. The above plot shows the density of observations. The below plot shows the individual submissions in red and the regions associated with a CME candidate in black.<br>
DOI: 10.6084/m9.figshare.4747927.v1
title: COR1 Clustering Plots

description: Plots showing the time and position angle grids created to identify clusters from the Solar Stormwatch 'Track-it-back' observations. These observations were created when participants tracked CMEs through SECCHI COR1 images taken from the STEREO spacecraft. The above plot shows the density of observations. The below plot shows the individual submissions in red and the regions associated with a CME candidate in black.<br>
DOI: 10.6084/m9.figshare.4747918
title: Supplementary Material for: Implications of Population History of European Romani on Genetic Susceptibility to Disease

description: <strong><em>Objectives:</em></strong> The population history of European Romani is characterized by extensive bottleneck and admixture events, but the impact of this unique demographic history on the genetic risk for disease remains unresolved. <b><i>Methods:</i></b> Genome-wide SNP data on Romani, non-Romani Europeans and Indians were analyzed. The excess of homozygous variants in Romani genomes was assessed according to their potential functional effect. We also explored the frequencies of risk variants associated with five common diseases which are present at an increased prevalence in Romani compared to other Europeans. <b><i>Results:</i></b> Slightly deleterious variants are present at increased frequencies in European Romani, likely a result of relaxed purifying selection due to bottlenecks in their population history. The frequencies of SNPs associated with common metabolic and cardiovascular diseases are also increased compared to their European hosts. <b><i>Conclusions: </i></b>As observed in other founder populations, we confirm the impact of bottlenecks on the abundance of slightly deleterious variants in Romani groups, probably including metabolic and cardiovascular risk variants.
DOI: 10.6084/m9.figshare.4747912
title: Computational study of one-step polar Diels–Alder reactions using the NEB method for the minimum energy paths search

description: The Nudged Elastic Band (NEB) method is an algorithm to search the minimum energy path (MEP), which has been successfully applied for studying several processes that involve solid-state models; however, it has not been widely tested in discrete molecular systems. Performing density functional theory calculations, this method was employed in NWChem to find the MEP of reactions between cyclopentadiene and cyano-substituted ethylenes. Results suggest that the reaction mechanism is concerted in all systems. Also, kinetics and thermodynamics analysis were done: With respect to experimental data, energetic parameters are computed better at the M06-2X/6-31++G** level; entropy and frequency factors were poorly predicted. This is a simple methodology, where the NEB method is evaluated to find the MEP in some prototypical Diels–Alder reactions.
DOI: 10.6084/m9.figshare.4747909
title: Supplementary Material for: A New HLA Map of Europe: Regional Genetic Variation and Its Implication for Peopling History, Disease-Association Studies and Tissue Transplantation

description: <strong><em>Objectives:</em></strong> HLA genes are highly polymorphic in human populations as a result of diversifying selection related to their immune function. However, HLA geographic variation worldwide suggests that demographic factors also shaped their evolution. We here analyzed in detail HLA genetic variation in Europe in order to identify signatures of migration history and/or natural selection. <b><i>Methods:</i></b> Relationships between HLA diversity and geography were analyzed at 7 loci through several approaches including linear regression on gene diversity and haplotype frequencies. Regional variation was also assessed on HLA multi-locus phenotypes through <i>structure</i> analysis. Deviation from neutrality was tested by resampling. <b><i>Results:</i></b> Geographic distance was a strong predictor of HLA variation at 5 loci (A, B, C, DRB1 and DPB1) in Europe, and latitude significantly shaped HLA gene diversity and haplotype frequencies. Whereas the main level of genetic diversity was found within populations, both HLA gene frequencies and phenotypic profiles revealed regional variation, Southeast Europe, Great Britain and Finland being the most distinctive. Effects of natural selection were suggested at the DQ loci. <b><i>Conclusions:</i></b> HLA regional variation was observed in Europe and can be related to population history, locus HLA-A providing by far the strongest signals. This new HLA map of Europe represents an invaluable reference for disease-association studies and tissue transplantation.