cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4055622
title: Concatenated alignment of 9,080 putative orthologs of 16 Diptera: Orthorrhapha species for phylogeny reconstruction

description: Concatenated alignment of 9,080 putative orthologs of 16 Diptera: Orthorrhapha species obtained from de novo transcriptome sequencing for phylogeny reconstruction, fast format
DOI: 10.7910/dvn/v1rjpf/uruevh
title: blc20151010_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055622.v1
title: Concatenated alignment of 9,080 putative orthologs of 16 Diptera: Orthorrhapha species for phylogeny reconstruction

description: Concatenated alignment of 9,080 putative orthologs of 16 Diptera: Orthorrhapha species obtained from de novo transcriptome sequencing for phylogeny reconstruction, fast format
DOI: 10.6084/m9.figshare.4055661.v3
title: How I learned to stop worrying and love ISO 16363

description: Presentation at PASIG in NYC on ISO16363.
DOI: 10.7910/dvn/v1rjpf/44usmj
title: blc20151019_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055556
title: Aguirre_2016_PLOSOne_MPRAGE_Data.tgz

description: These are MPRAGE images of the brain obtained from sighted and blind subjects. The data are the basis of this preprint:<br>http://biorxiv.org/content/early/2016/08/31/065441<br>And this in press paper:<br>Aguirre GK, Datta R, Benson N, Prasad S, Jacobson SG, Cideciyan AV, et al. (In Press) Patterns of individual variation in visual pathway structure and function in the sighted and blind. PLoS One
DOI: 10.7910/dvn/v1rjpf/atglnn
title: blc20150128_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055544
title: Supplemental data 1.xls

description: Table of the results given by HPLC analysis of the samples. Key: Rt, retention time; +, presence of peak; -, absence of peak.
DOI: 10.7910/dvn/v1rjpf/pmktvj
title: blc20150727_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/rjril2
title: blc20151203_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/joz0av
title: blc20150706_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/5xwimy
title: blc20151130_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/srfid3
title: blc20150626_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055469
title: Multiplex PCR results.xls

description: 276 APEC were investigated for R type, phylogroup and virulence factors using multiplex pcr as described in Comparative genomics of European Avian Pathogenic E. coli (APEC) (in press)
DOI: 10.6084/m9.figshare.4055472
title: Supplementary Material for: Epilepsy in Punjab (India): A Population-Based Epidemiologic Study

description: <br><strong><em>Aims:</em></strong> To assess the prevalence of epilepsy in a rural area adjoining a city. <b><i>Methods:</i></b> A door-to-door, cross-sectional epidemiological survey was carried out covering an entire rural population of 103,693 people. <b><i>Results:</i></b> Crude period and point prevalence rates for active epilepsy were 7.67 and 7.44 per 1,000 respectively. Crude incidence rate was 60.76 per 100,000 during the year 2007. Mean, SD, median and variance were 17.2, 16, 13 and 257.6 years respectively for age at onset of active epilepsy patients. The overall prevalence patterns among males and females were not significantly different. Active epilepsy cases (n = 795) included electro-clinical syndromes and constellations (n = 117, 14.7%), symptomatic epilepsy (n = 153, 19.2%), epilepsy due to unknown cause (n = 513, 64.5%) and dual diagnosis (n = 12, 1.5%). <b><i>Conclusions:</i></b> The present study showed that the prevalence rate, in the rural area adjoining a city, was comparable to that of the urban area and significantly less than that of the remote rural area as described by another study. Age- and sex-specific prevalence and incidence rates were similar to the rates reported by other studies. The reason for a lower number of symptomatic cases to be reported, per this study, may be due to lack of neuroimaging.
DOI: 10.6084/m9.figshare.4055472.v1
title: Supplementary Material for: Epilepsy in Punjab (India): A Population-Based Epidemiologic Study

description: <br><strong><em>Aims:</em></strong> To assess the prevalence of epilepsy in a rural area adjoining a city. <b><i>Methods:</i></b> A door-to-door, cross-sectional epidemiological survey was carried out covering an entire rural population of 103,693 people. <b><i>Results:</i></b> Crude period and point prevalence rates for active epilepsy were 7.67 and 7.44 per 1,000 respectively. Crude incidence rate was 60.76 per 100,000 during the year 2007. Mean, SD, median and variance were 17.2, 16, 13 and 257.6 years respectively for age at onset of active epilepsy patients. The overall prevalence patterns among males and females were not significantly different. Active epilepsy cases (n = 795) included electro-clinical syndromes and constellations (n = 117, 14.7%), symptomatic epilepsy (n = 153, 19.2%), epilepsy due to unknown cause (n = 513, 64.5%) and dual diagnosis (n = 12, 1.5%). <b><i>Conclusions:</i></b> The present study showed that the prevalence rate, in the rural area adjoining a city, was comparable to that of the urban area and significantly less than that of the remote rural area as described by another study. Age- and sex-specific prevalence and incidence rates were similar to the rates reported by other studies. The reason for a lower number of symptomatic cases to be reported, per this study, may be due to lack of neuroimaging.
DOI: 10.7910/dvn/v1rjpf/gitnwn
title: blc20150728_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/hczzw2
title: blc20150404_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/3odrnk
title: blc20150622_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/thd6zz
title: blc20150422_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055403.v1
title: Small sample methods for cluster-robust variance estimation and hypothesis testing in fixed effects models

description: In panel data models and other regressions with unobserved effects, fixed effects estimation is often paired with cluster-robust variance estimation (CRVE) in order to account for heteroskedasticity and un-modeled dependence among the errors. Although asymptotically consistent, CRVE can be biased downward when the number of clusters is small, leading to hypothesis tests with rejection rates that are too high. More accurate tests can be constructed using bias-reduced linearization (BRL), which corrects the CRVE based on a working model, in conjunction with a Satterthwaite approximation for t-tests. We propose a generalization of BRL that can be applied in models with arbitrary sets of fixed effects, where the original BRL method is undefined, and describe how to apply the method when the regression is estimated after absorbing the fixed effects. We also propose a small-sample test for multiple-parameter hypotheses, which generalizes the Satterthwaite approximation for t-tests. In simulations covering a wide range of scenarios, we find that the conventional cluster-robust Wald test can severely over-reject while the proposed small-sample test maintains Type I error close to nominal levels. The proposed methods are implemented in an R package called clubSandwich. This article has online supplementary materials.
DOI: 10.7910/dvn/v1rjpf/kujjqc
title: blc20150724_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/mosyrb
title: blc20151207_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/sa555z
title: blc20151212_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/wn1spf
title: blc20150126_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055322
title: Electronic supplementary material S2: summary of diet, prey type, body size and macrohabitat data for snake species included in the comparative survey from Postnatal ontogeny and the evolution of macrostomy in snakes

description: Macrostomy is the anatomical feature present in macrostomatan snakes that permit the ingestion of entire prey with high cross-sectional area. It depends on several anatomical traits in the skeleton and soft tissues, which the elongation of gnathic complex and backward rotation of the quadrate represent crucial skeletal requirements. Here, the relevance of postnatal development of these skull structures and their relationship with macrohabitat and diet are explored. Contrary to the condition present in lizards and basal snakes that occupy underground macrohabitats, elements of the gnathic complex of most macrostomatan snakes that exploit surface macrohabitats display conspicuous elongation during postnatal growth, relative to the rest of the skull, as well as further backward rotation of the quadrate bone. Remarkably, several clades of small cryptozoic macrostomatans reverse these postnatal transformations and return to a diet based on prey with low cross-sectional area such as annelids, insects or elongated vertebrates, thus resembling the condition present in underground basal snakes. Dietary ontogenetic shift observed in most macrostomatan snakes is directly linked with this ontogenetic trajectory, indicating that this shift is acquired progressively as the gnathic complex elongates and the quadrate rotates backward during postnatal ontogeny. The numerous independent events of reversion in the gnathic complex and prey type choice observed in underground macrostomatans and the presence of skeletal requirements for macrostomy in extinct non-macrostomatan species reinforce the possibility that basal snakes represent underground survivors of clades that had the skeletal requirements for macrostomy. Taken together, the data presented here suggest that macrostomy have been shaped during multiple episodes of occupation of underground and surface macrohabitats throughout the evolution of snakes.
DOI: 10.7910/dvn/v1rjpf/f0fbha
title: blc20150502_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055316
title: Table S8 from Why many Batesian mimics are inaccurate: evidence from hoverfly colour patterns

description: Raw data: specimen information and dissimilarity measures for each individual
DOI: 10.6084/m9.figshare.4055316.v1
title: Table S8 from Why many Batesian mimics are inaccurate: evidence from hoverfly colour patterns

description: Raw data: specimen information and dissimilarity measures for each individual
DOI: 10.7910/dvn/v1rjpf/2sl1iq
title: blc20151004_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055310
title: Table of microsatellite genotypes from Adaptive capabilities and fitness consequences associated with pollution exposure in fish

description: Genotypes of a microsatellite within the Cyp1A1 locus from guppies from four Trinidad rivers
DOI: 10.7910/dvn/v1rjpf/hgprlo
title: blc20150615_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055310.v1
title: Table of microsatellite genotypes from Adaptive capabilities and fitness consequences associated with pollution exposure in fish

description: Genotypes of a microsatellite within the Cyp1A1 locus from guppies from four Trinidad rivers
DOI: 10.7910/dvn/v1rjpf/klkvsv
title: blc20150304_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055259
title: Supplementary Material for: Evidence of Mitochondrial Dysfunction within the Complex Genetic Etiology of Schizophrenia

description: <br>Genetic evidence has supported the hypothesis that schizophrenia (SZ) is a polygenic disorder caused by the disruption in function of several or many genes. The most common and reproducible cellular phenotype associated with SZ is a reduction in dendritic spines within the neocortex, suggesting alterations in dendritic architecture may cause aberrant cortical circuitry and SZ symptoms. Here, we review evidence supporting a multifactorial model of mitochondrial dysfunction in SZ etiology and discuss how these multiple paths to mitochondrial dysfunction may contribute to dendritic spine loss and/or underdevelopment in some SZ subjects. The pathophysiological role of mitochondrial dysfunction in SZ is based upon genomic analyses of both the mitochondrial genome and nuclear genes involved in mitochondrial function. Previous studies and preliminary data suggest SZ is associated with specific alleles and haplogroups of the mitochondrial genome, and also correlates with a reduction in mitochondrial copy number and an increase in synonymous and nonsynonymous substitutions of mitochondrial DNA. Mitochondrial dysfunction has also been widely implicated in SZ by genome-wide association, exome sequencing, altered gene expression, proteomics, microscopy analyses, and induced pluripotent stem cell studies. Together, these data support the hypothesis that SZ is a polygenic disorder with an enrichment of mitochondrial targets.
DOI: 10.7910/dvn/v1rjpf/2wp1ip
title: blc20151022_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055259.v1
title: Supplementary Material for: Evidence of Mitochondrial Dysfunction within the Complex Genetic Etiology of Schizophrenia

description: <br>Genetic evidence has supported the hypothesis that schizophrenia (SZ) is a polygenic disorder caused by the disruption in function of several or many genes. The most common and reproducible cellular phenotype associated with SZ is a reduction in dendritic spines within the neocortex, suggesting alterations in dendritic architecture may cause aberrant cortical circuitry and SZ symptoms. Here, we review evidence supporting a multifactorial model of mitochondrial dysfunction in SZ etiology and discuss how these multiple paths to mitochondrial dysfunction may contribute to dendritic spine loss and/or underdevelopment in some SZ subjects. The pathophysiological role of mitochondrial dysfunction in SZ is based upon genomic analyses of both the mitochondrial genome and nuclear genes involved in mitochondrial function. Previous studies and preliminary data suggest SZ is associated with specific alleles and haplogroups of the mitochondrial genome, and also correlates with a reduction in mitochondrial copy number and an increase in synonymous and nonsynonymous substitutions of mitochondrial DNA. Mitochondrial dysfunction has also been widely implicated in SZ by genome-wide association, exome sequencing, altered gene expression, proteomics, microscopy analyses, and induced pluripotent stem cell studies. Together, these data support the hypothesis that SZ is a polygenic disorder with an enrichment of mitochondrial targets.
DOI: 10.7910/dvn/v1rjpf/zlhghz
title: blc20151125_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055229
title: Supplementary Material for: Clinicopathological Correlations and Concomitant Pathologies in Rapidly Progressive Dementia: A Brain Bank Series

description: <br><strong><em>Background:</em></strong> Rapidly progressive dementia (RPD) is caused by a heterogeneous group of both neurodegenerative and non-neurodegenerative disorders. The presence of concomitant pathologies, mainly Alzheimer's disease (AD), may act as a confounding variable in the diagnostic process of this group of diseases. <b><i>Objectives:</i></b> We aimed to describe clinicopathological features, including Alzheimer's co-pathology, and diagnostic accuracy in a postmortem series of RPD. <b><i>Methods:</i></b> Retrospective analysis of 160 brain donors with RPD (defined as 2 years of disease duration from the first symptom to death) registered at the Neurological Tissue Bank of the Biobanc-Hospital Clínic-IDIBAPS, from 2001 to 2011. <b><i>Results:</i></b> Prion diseases were the most frequent neuropathological diagnosis (67%), followed by non-prion neurodegenerative pathologies (17%), mostly AD and dementia with Lewy bodies, and non-neurodegenerative diseases (16%). We observed clinicopathological diagnostic agreement in 94% of the patients with prion RPD but only in 21% of those with non-prion RPD. Four patients with potentially treatable disorders were diagnosed, while still alive, as having Creutzfeldt-Jakob disease. Concomitant pathologies were detected in 117 (73%). Among all RPD cases, 51 presented moderate or frequent mature β-amyloid plaques (neuritic plaques), which are considered to be associated with positive amyloid biomarkers in vivo. <b><i>Conclusions:</i></b> Prion diseases were accurately identified in our series. In contrast, non-prion RPD diagnosis was poor while the patients were still alive, supporting the need for better diagnostic tools and confirmatory neuropathological studies. The presence of concomitant AD pathology in RPD should be taken into account in the interpretation of amyloid biomarkers.
DOI: 10.7910/dvn/v1rjpf/1rdcll
title: blc20150413_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/5npnrc
title: blc20150520_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055172
title: Data_repository.xlsx

description: This study identifies individual spatiotemporal structure of widespread musculoskeletal pain and links exertive pain with fibromyalgia (FM) syndrome. Three individual and consistent dynamic patterns of discomfort and pain emerged during cycling and running: <i>adder</i> (e.g., adding pain locations throughout effort), <i>jumper</i> (switching among pain locations throughout effort), and <i>adder-jumper</i> (e.g., adding and switching among pain locations throughout effort).
DOI: 10.7910/dvn/v1rjpf/mzooxe
title: blc20150119_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055172.v1
title: Data_repository.xlsx

description: This study identifies individual spatiotemporal structure of widespread musculoskeletal pain and links exertive pain with fibromyalgia (FM) syndrome. Three individual and consistent dynamic patterns of discomfort and pain emerged during cycling and running: <i>adder</i> (e.g., adding pain locations throughout effort), <i>jumper</i> (switching among pain locations throughout effort), and <i>adder-jumper</i> (e.g., adding and switching among pain locations throughout effort).
DOI: 10.7910/dvn/v1rjpf/wncpaq
title: blc20150708_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055136
title: Antioxidant activity of commercial food grade tannins exemplified in a wine model

description: Although commercial tannins are widely used in foods and beverages, an improved understanding of the structure and composition of vegetable tannins is needed to promote the exploitation of agri-food by-products and waste and their valorisation in more sustainable industrial applications. This study aims to characterise the phytochemical composition and antioxidant activity of 13 food grade tannins using multiple analytical approaches, including spectrophotometry and HPLC-ECD to determine the amount of targeted polyphenolic compounds. Moreover, the antioxidant activity of tannins was assessed in terms of radical scavenging activity (DPPH• assay), reducing power (FRAP assay), and redox properties (cyclic voltammetry, CV). A statistical univariate and multivariate correlation analysis was performed on 17 parameters including tannin content (range: 0.71–1.62 mM), gallic acid, (+)-catechin, syringic acid and (‒)-epicatechin. The compositional profile of tannins was related to their chemical moiety, antioxidant activity and the botanical origin of the extracts. In particular, the CV signal at 500 mV was highly correlated with DPPH• value due to the catechol ring of flavonoids and trigalloyl moieties of gallic acid–based compounds. Practical examples of tannins application in winemaking are discussed.
DOI: 10.6084/m9.figshare.4055136.v1
title: Antioxidant activity of commercial food grade tannins exemplified in a wine model

description: Although commercial tannins are widely used in foods and beverages, an improved understanding of the structure and composition of vegetable tannins is needed to promote the exploitation of agri-food by-products and waste and their valorisation in more sustainable industrial applications. This study aims to characterise the phytochemical composition and antioxidant activity of 13 food grade tannins using multiple analytical approaches, including spectrophotometry and HPLC-ECD to determine the amount of targeted polyphenolic compounds. Moreover, the antioxidant activity of tannins was assessed in terms of radical scavenging activity (DPPH• assay), reducing power (FRAP assay), and redox properties (cyclic voltammetry, CV). A statistical univariate and multivariate correlation analysis was performed on 17 parameters including tannin content (range: 0.71–1.62 mM), gallic acid, (+)-catechin, syringic acid and (‒)-epicatechin. The compositional profile of tannins was related to their chemical moiety, antioxidant activity and the botanical origin of the extracts. In particular, the CV signal at 500 mV was highly correlated with DPPH• value due to the catechol ring of flavonoids and trigalloyl moieties of gallic acid–based compounds. Practical examples of tannins application in winemaking are discussed.
DOI: 10.7910/dvn/v1rjpf/64jizf
title: blc20150710_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055130
title: Young adult composite faces

description: This image set comprises 5 male and 5 female composite images (4 individuals per composite) of adult individuals of African, East Asian, West Asian and White ethnic backgrounds, plus a composite image of all 4 ethnic groupings. Images are 1350x1350 pixels in full colour.<br><br>Ages:<br>f_african (21,24,25,30)<br>f_easian (24,24,28,31)<br>f_wasian (22,25,31,NA-appears early 20s)<br>f_white (23,26,26,28)<br>m_african (20,20,21,27)<br>m_easian (21,28,29,47)<br>m_wasian (25,26,31,37)<br>m_white (19,24,24,26)<br><br>Template files mark out 189 coordinates delineating face shape, for use with Psychomorph or WebMorph.org.<br><br>All individuals gave signed consent for their images to be "<i>used in lab-based and web-based studies in their original or altered forms and to illustrate research (e.g., in scientific journals, news media or presentations).</i>" Images were taken in London, UK, in April 2012.<br><br>
DOI: 10.6084/m9.figshare.4055133
title: Rawdata for "Difficulties when using video playback to investigate social cognition in California scrub-jays (Aphelocoma californica)"

description: Raw data for the manuscript "Difficulties when using video playback to investigate social cognition in California scrub-jays (<i>Aphelocoma californica</i>)"<b><i> <br></i></b>
DOI: 10.7910/dvn/v1rjpf/joe8xi
title: blc20151029_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/mf5pmu
title: blc20150225_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055133.v1
title: Rawdata for "Difficulties when using video playback to investigate social cognition in California scrub-jays (Aphelocoma californica)"

description: Raw data for the manuscript "Difficulties when using video playback to investigate social cognition in California scrub-jays (<i>Aphelocoma californica</i>)"<b><i> <br></i></b>
DOI: 10.7910/dvn/v1rjpf/89z2pz
title: blc20150813_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/73h9nd
title: blc20150527_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055100
title: Optimized case: C2t30

description: Windpower, turbine controls, and 3D time-averaged flow field quantities for optimized case with maximum thrust coefficient 2 and slow turbine response (tau = 30 s).<br><br>3D time-averaged flow fields can be loaded using Python script load_BLfieldstat.py<br><br>Data accompanying research paper<br>W. Munters, J. Meyers, "An optimal control framework for dynamic induction control of wind farms and their interaction with the atmospheric boundary layer", Phil Trans R Soc A (under review)
DOI: 10.7910/dvn/v1rjpf/mborv1
title: blc20150528_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/7c52ui
title: blc20150223_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/tselyx
title: blc20150825_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4055094
title: Optimized case: C2t5

description: Windpower, turbine controls, and 3D time-averaged flow field quantities for optimized case with maximum thrust coefficient 2 and fast turbine response (tau = 5 s).<br><br>3D time-averaged flow fields can be loaded using Python script load_BLfieldstat.py<br><br>Data accompanying research paper<br>W. Munters, J. Meyers, "An optimal control framework for dynamic induction control of wind farms and their interaction with the atmospheric boundary layer", Phil Trans R Soc A (under review)