cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4747810
title: Supplementary Material for: The Value of Regenotyping Older Linkage Data Sets with Denser Marker Panels

description: <strong><em>Objectives:</em></strong> Linkage analysis can help determine regions of interest in whole-genome sequence studies. However, many linkage studies rely on older microsatellite (MSAT) panels. We set out to determine whether results would change if we regenotyped families using a dense map of SNPs. <b><i>Methods:</i></b> We selected 47 Hispanic-American families from the NIMH Repository and Genomics Resource (NRGR) schizophrenia data repository. We regenotyped all individuals with DNA available from the NRGR on the Affymetrix Lat Array. After optimizing SNP selection for inclusion on the linkage map, we compared information content (IC) and linkage results using MSAT, SNP and MSAT+SNP maps. <b><i>Results:</i></b> As expected, SNP provided a higher average IC (0.78, SD 0.03) than MSAT (0.51, SD 0.10) in a direct ‘apples-to-apples' comparison using only individuals genotyped on both platforms; while MSAT+SNP provided only a slightly higher IC (0.82, SD 0.03). However, when utilizing all available individuals, including those who had genotypes available on only one platform, the IC was substantially increased using MSAT+SNP (0.76, SD 0.05) compared to SNP (0.61, SD 0.02). Linkage results changed appreciably between MSAT and MSAT+SNP in terms of magnitude, rank ordering and localization of peaks. <b><i>Conclusions:</i></b> Regenotyping older family data can substantially alter the conclusions of linkage analyses.
DOI: 10.6084/m9.figshare.4747909.v1
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.
DOI: 10.6084/m9.figshare.4747792
title: Supplementary Material for: Cytosine Methylation of an Ancient Satellite Family in the Wild Beet Beta procumbens

description: DNA methylation is an essential epigenetic feature for the regulation and maintenance of heterochromatin. Satellite DNA is a repetitive sequence component that often occurs in large arrays in heterochromatin of subtelomeric, intercalary and centromeric regions. Knowledge about the methylation status of satellite DNA is important for understanding the role of repetitive DNA in heterochromatization. In this study, we investigated the cytosine methylation of the ancient satellite family pEV in the wild beet <i>Beta procumbens</i>. The pEV satellite is widespread in species-specific pEV subfamilies in the genus <i>Beta</i> and most likely originated before the radiation of the Betoideae and Chenopodioideae. In <i>B. procumbens</i>, the pEV subfamily occurs abundantly and spans intercalary and centromeric regions. To uncover its cytosine methylation, we performed chromosome-wide immunostaining and bisulfite sequencing of pEV satellite repeats. We found that CG and CHG sites are highly methylated while CHH sites show only low levels of methylation. As a consequence of the low frequency of CG and CHG sites and the preferential occurrence of most cytosines in the CHH motif in pEV monomers, this satellite family displays only low levels of total cytosine methylation.
DOI: 10.6084/m9.figshare.4747786
title: Supplementary Material for: Prognostic Relevance of Aberrant DNA Methylation in G1 and G2 Pancreatic Neuroendocrine Tumors

description: <strong><em>Background/Aims:</em></strong> The occurrence and clinical relevance of DNA hypermethylation and global hypomethylation in pancreatic neuroendocrine tumours (PanNETs) are still unknown. We evaluated the frequency of both epigenetic alterations in PanNETs to assess the relationship between methylation profiles and chromosomal instability, tumour phenotypes and prognosis. <b><i>Methods:</i></b> In a well-characterized series of 56 sporadic G1 and G2 PanNETs, methylation-sensitive multiple ligation-dependent probe amplification was performed to assess hypermethylayion of 33 genes and copy number alterations (CNAs) of 53 chromosomal regions. Long interspersed nucleotide element-1 (LINE-1) hypomethylation was quantified by pyrosequencing. <b><i>Results:</i></b> Unsupervised hierarchical clustering allowed to identify a subset of 22 PanNETs (39%) exhibiting high frequency of gene-specific methylation and low CNA percentages. This tumour cluster was significantly associated with stage IV (p = 0.04) and with poor prognosis in univariable analysis (p = 0.004). LINE-1 methylation levels in PanNETs were significantly lower than in normal samples (p &lt; 0.01) and were approximately normally distributed. 12 tumours (21%) were highly hypomethylated, showing variable levels of CNA. Interestingly, only 5 PanNETs (9%) were observed to show simultaneously LINE-1 hypomethylation and high frequency of gene-specific methylation. LINE-1 hypomethylation was strongly correlated with advanced stage (p = 0.002) and with poor prognosis (p &lt; 0.0001). In the multivariable analysis, low LINE-1 methylation status and methylation clusters were the only independent significant predictors of outcome (p = 0.034 and p = 0.029, respectively). <b><i>Conclusion:</i></b> The combination of global DNA hypomethylation and gene hypermethylation analyses may be useful to define distinct subsets of PanNETs. Both alterations are common in PanNETs and could be directly correlated with tumour progression.
DOI: 10.6084/m9.figshare.4747810.v1
title: Supplementary Material for: The Value of Regenotyping Older Linkage Data Sets with Denser Marker Panels

description: <strong><em>Objectives:</em></strong> Linkage analysis can help determine regions of interest in whole-genome sequence studies. However, many linkage studies rely on older microsatellite (MSAT) panels. We set out to determine whether results would change if we regenotyped families using a dense map of SNPs. <b><i>Methods:</i></b> We selected 47 Hispanic-American families from the NIMH Repository and Genomics Resource (NRGR) schizophrenia data repository. We regenotyped all individuals with DNA available from the NRGR on the Affymetrix Lat Array. After optimizing SNP selection for inclusion on the linkage map, we compared information content (IC) and linkage results using MSAT, SNP and MSAT+SNP maps. <b><i>Results:</i></b> As expected, SNP provided a higher average IC (0.78, SD 0.03) than MSAT (0.51, SD 0.10) in a direct ‘apples-to-apples' comparison using only individuals genotyped on both platforms; while MSAT+SNP provided only a slightly higher IC (0.82, SD 0.03). However, when utilizing all available individuals, including those who had genotypes available on only one platform, the IC was substantially increased using MSAT+SNP (0.76, SD 0.05) compared to SNP (0.61, SD 0.02). Linkage results changed appreciably between MSAT and MSAT+SNP in terms of magnitude, rank ordering and localization of peaks. <b><i>Conclusions:</i></b> Regenotyping older family data can substantially alter the conclusions of linkage analyses.
DOI: 10.6084/m9.figshare.4747747
title: Dark side personality, perceived organisational support, and turnover intentions

description: dataset from the plosone submitted manuscript
DOI: 10.6084/m9.figshare.4747747.v1
title: Dark side personality, perceived organisational support, and turnover intentions

description: dataset from the plosone submitted manuscript
DOI: 10.6084/m9.figshare.4747750
title: Datasets

description: This folder contains 12 large scale technician and task scheduling problems that I generated under the framework of the ROADEF 2007 challenge.
DOI: 10.6084/m9.figshare.4747750.v2
title: Datasets

description: This folder contains 12 large scale technician and task scheduling problems that I generated under the framework of the ROADEF 2007 challenge.
DOI: 10.6084/m9.figshare.4747729
title: Supplementary online 3D model S3 from Form function relationships in dragonfly mandibles under an evolutionary perspective

description: 3D models of mandible joint-tip triangles. Please use the program Blender to open the file with full functionality
DOI: 10.6084/m9.figshare.4747750.v1
title: Datasets

description: This folder contains 12 large scale technician and task scheduling problems that I generated under the framework of the ROADEF 2007 challenge.
DOI: 10.6084/m9.figshare.4747720
title: Supplementary Table I: List of articles from search in PubMed from Does deforestation promote or inhibit malaria transmission in the Amazon? A systematic literature review and critical appraisal of current evidence

description: Complete list of articles returned from initial search in the PubMed database (n=182) with reasons for exclusion, where applicable.
DOI: 10.6084/m9.figshare.4747729.v1
title: Supplementary online 3D model S3 from Form function relationships in dragonfly mandibles under an evolutionary perspective

description: 3D models of mandible joint-tip triangles. Please use the program Blender to open the file with full functionality
DOI: 10.6084/m9.figshare.4747711
title: Supplementary Material II. Entomological data from Peru from Does deforestation promote or inhibit malaria transmission in the Amazon? A systematic literature review and critical appraisal of current evidence

description: Human-biting rate by mosquito species and land-use land-cover class from the Iquitos-Nauta road (Peruvian Amazon).
DOI: 10.6084/m9.figshare.4747720.v1
title: Supplementary Table I: List of articles from search in PubMed from Does deforestation promote or inhibit malaria transmission in the Amazon? A systematic literature review and critical appraisal of current evidence

description: Complete list of articles returned from initial search in the PubMed database (n=182) with reasons for exclusion, where applicable.
DOI: 10.6084/m9.figshare.4747711.v1
title: Supplementary Material II. Entomological data from Peru from Does deforestation promote or inhibit malaria transmission in the Amazon? A systematic literature review and critical appraisal of current evidence

description: Human-biting rate by mosquito species and land-use land-cover class from the Iquitos-Nauta road (Peruvian Amazon).
DOI: 10.6084/m9.figshare.4747687
title: Supplementary material - Raw data from experiments from The dynamic association between ovariole loss and sterility in adult honeybee workers

description: In the social insects, ovary state (the presence or absence of mature oocytes) and ovary size (the number of ovarioles) are often used as proxies for the reproductive capacity of an individual worker. Ovary size is assumed to be fixed post-eclosion whereas ovary state is demonstrably plastic post-eclosion. Here, we show that in fact ovary size declines as honeybee workers age. This finding is robust across two honeybee species: <i>Apis mellifera</i> and <i>A. cerana</i>. The ovariole loss is likely to be due to the regression of particular ovarioles via programmed cell death. We also provide further support for the observation that honeybee workers with activated ovaries (mature oocytes present) most commonly have five ovarioles rather than a greater or smaller number. This result suggests that workers with more than five ovarioles are unable to physiologically support more than five activated ovarioles and that workers with fewer than five ovarioles are below a threshold necessary for ovary activation. As a worker's ovariole number declines with age, studies on worker ovariole number need to take this plasticity into account.
DOI: 10.6084/m9.figshare.4747660
title: Supplementar Material for: Population-Genetic Influences on Genomic Estimates of the Inbreeding Coefficient: A Global Perspective

description: <strong><em>Background/Aims:</em></strong> Culturally driven marital practices provide a key instance of an interaction between social and genetic processes in shaping patterns of human genetic variation, producing, for example, increased identity by descent through consanguineous marriage. A commonly used measure to quantify identity by descent in an individual is the inbreeding coefficient, a quantity that reflects not only consanguinity, but also other aspects of kinship in the population to which the individual belongs. Here, in populations worldwide, we examine the relationship between genomic estimates of the inbreeding coefficient and population patterns in genetic variation. <b><i>Methods:</i></b> Using genotypes at 645 microsatellites, we compare inbreeding coefficients from 5,043 individuals representing 237 populations worldwide to demographic consanguinity frequency estimates available for 26 populations as well as to other quantities that can illuminate population-genetic influences on inbreeding coefficients. <b><i>Results:</i></b> We observe higher inbreeding coefficient estimates in populations and geographic regions with known high levels of consanguinity or genetic isolation and in populations with an increased effect of genetic drift and decreased genetic diversity with increasing distance from Africa. For the small number of populations with specific consanguinity estimates, we find a correlation between inbreeding coefficients and consanguinity frequency (<i>r</i> = 0.349, p = 0.040). <b><i>Conclusions:</i></b> The results emphasize the importance of both consanguinity and population-genetic factors in influencing variation in inbreeding coefficients, and they provide insight into factors useful for assessing the effect of consanguinity on genomic patterns in different populations.
DOI: 10.6084/m9.figshare.4747657
title: Supplementary Material for: A MAVS/TICAM-1-Independent Interferon-Inducing Pathway Contributes to Regulation of Hepatitis B Virus Replication in the Mouse Hydrodynamic Injection Model

description: Toll-like receptors (TLRs) and cytoplasmic RNA sensors have been reported to be involved in the regulation of hepatitis B virus (HBV) replication, but remain controversial due to the lack of a natural infectious model. Our current study sets out to characterize aspects of the role of the innate immune system in eliminating HBV using hydrodynamic-based injection of HBV replicative plasmid and knockout mice deficient in specific pathways of the innate system. The evidence indicated that viral replication was not affected by MAVS or TICAM-1 knockout, but absence of interferon regulatory factor 3 (IRF-3) and IRF-7 transcription factors, as well as the interferon (IFN) receptor, had an adverse effect on the inhibition of HBV replication, demonstrating the dispensability of MAVS and TICAM-1 pathways in the early innate response against HBV. <i>Myd88</i><sup><i>-/-</i></sup> mice did not have a significant increase in the initial viremia, but substantial viral antigen persisted in the mice sera, a response similar to <i>Rag2</i><sup><i>-/-</i></sup> mice, suggesting that the MyD88-dependent pathway participated in evoking an adaptive immune response against the clearance of intrahepatic HBV. Taken together, we show that the RNA-sensing pathways do not participate in the regulation of HBV replication in a mouse model; meanwhile MyD88 is implicated in the HBV clearance.
DOI: 10.6084/m9.figshare.4747663
title: Supplementary Material for: Inbreeding Coefficient Estimation with Dense SNP Data: Comparison of Strategies and Application to HapMap III

description: <strong><em>Background/Aims:</em></strong> If the parents of an individual are related, it is possible for the individual to have received at 1 locus 2 identical-by-descent alleles that are copies of a single allele carried by the parents' common ancestor. The inbreeding coefficient measures the probability of this event and increases with increasing relatedness between the parents. It is traditionally computed from the observed inbreeding loops in the genealogies and its accuracy thus depends on the depth and reliability of the genealogies. With the availability of genome-wide genetic data, it has become possible to compute a genome-based inbreeding coefficient <i>f</i>, and different methods have been developed to estimate <i>f</i> and identify inbred individuals in a sample from the observed patterns of homozygosity at markers. <b><i>Methods:</i></b> For this paper, we performed simulations with known genealogies using different SNP panels with different levels of linkage disequilibrium (LD) to compare several estimators of <i>f</i>, including single-point estimates, methods based on the length of runs of homozygosity (ROHs) and different methods that use hidden Markov models (HMMs). We also compared the performances of some of these estimators to identify inbred individuals in a sample using either HMM likelihood ratio tests or an adapted version of the ERSA software. <b><i>Results:</i></b> Single-point methods were found to have higher standard deviations than other methods. ROHs gave the best estimates provided the correct length threshold is known. HMMs on sparse data gave equivalent or better results than HMMs modeling LD. Provided LD is correctly accounted for, the inbreeding estimates were very similar using the different SNP panels. The HMM likelihood ratio tests were found to perform better at detecting inbred individuals in a sample than the adapted ERSA. All methods accurately detected inbreeding up to second-cousin offspring. We applied the best method on release 3 of the HapMap phase III project, found up to 4% of inbred individuals, and created HAP1067, an unrelated and outbred dataset of this release. <b><i>Conclusions:</i></b> We recommend using HMMs on multiple sparse maps to estimate and detect inbreeding in large samples. If the sample of individuals is too small to estimate allele frequencies, we advise to estimate them on reference panels or to use 1,500-kb ROHs. Finally, we suggest to investigators using HapMap to be careful with inbred individuals, especially in the GIH (Gujarati Indians from Houston in Texas) population.
DOI: 10.6084/m9.figshare.4747651
title: Supplementary Material for: Proteomic Investigation of the Hippocampus in Prenatally Stressed Mice Implicates Changes in Membrane Trafficking, Cytoskeletal, and Metabolic Function

description: Prenatal stress influences the development of the fetal brain and so contributes to the risk of the development of psychiatric disorders in later life. The hippocampus is particularly sensitive to prenatal stress, and robust abnormalities have been described in the hippocampus in schizophrenia and depression. The aim of this study was to determine whether prenatal stress is associated with distinct patterns of differential protein expression in the hippocampus using a validated mouse model. We therefore performed a comparative proteomic study assessing female hippocampal samples from 8 prenatally stressed mice and 8 control mice. Differential protein expression was assessed using 2-dimensional difference in gel electrophoresis and subsequent mass spectrometry. The observed changes in a selected group of differentially expressed proteins were confirmed by Western blotting. In comparison to controls, 47 protein spots (38 individual proteins) were found to be differentially expressed in the hippocampus of prenatally stressed mice. Functional grouping of these proteins revealed that prenatal stress influenced the expression of proteins involved in brain development, cytoskeletal composition, stress response, and energy metabolism. Western blotting was utilized to validate the changes in calretinin, hippocalcin, profilin-1 and the signal-transducing adaptor molecule STAM1. Septin-5 could not be validated via Western blotting due to methodological issues. Closer investigation of the validated proteins also pointed to an interesting role for membrane trafficking deficits mediated by prenatal stress. Our findings demonstrate that prenatal stress leads to altered hippocampal protein expression, implicating numerous molecular pathways that may provide new targets for psychotropic drug development.
DOI: 10.6084/m9.figshare.4747657.v1
title: Supplementary Material for: A MAVS/TICAM-1-Independent Interferon-Inducing Pathway Contributes to Regulation of Hepatitis B Virus Replication in the Mouse Hydrodynamic Injection Model

description: Toll-like receptors (TLRs) and cytoplasmic RNA sensors have been reported to be involved in the regulation of hepatitis B virus (HBV) replication, but remain controversial due to the lack of a natural infectious model. Our current study sets out to characterize aspects of the role of the innate immune system in eliminating HBV using hydrodynamic-based injection of HBV replicative plasmid and knockout mice deficient in specific pathways of the innate system. The evidence indicated that viral replication was not affected by MAVS or TICAM-1 knockout, but absence of interferon regulatory factor 3 (IRF-3) and IRF-7 transcription factors, as well as the interferon (IFN) receptor, had an adverse effect on the inhibition of HBV replication, demonstrating the dispensability of MAVS and TICAM-1 pathways in the early innate response against HBV. <i>Myd88</i><sup><i>-/-</i></sup> mice did not have a significant increase in the initial viremia, but substantial viral antigen persisted in the mice sera, a response similar to <i>Rag2</i><sup><i>-/-</i></sup> mice, suggesting that the MyD88-dependent pathway participated in evoking an adaptive immune response against the clearance of intrahepatic HBV. Taken together, we show that the RNA-sensing pathways do not participate in the regulation of HBV replication in a mouse model; meanwhile MyD88 is implicated in the HBV clearance.
DOI: 10.17633/rd.brunel.4747573
title: Masque of Augurs - Full Performance

description: Film of workshop performance of The Masque of Augurs at the Banqueting House Whitehall, performed on 10th May 2016 as part of the collaborative research project, 'Exploring the potential of combining performance and digital research in a heritage context'. The project was funded by the AHRC and was a partnership between Brunel University London, Historic Royal Palaces and Edinburgh University.