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Find video protocols related to scientific articles indexed in Pubmed.
Structural insights into magnetic clusters grown inside virus capsids.
ACS Appl Mater Interfaces
PUBLISHED: 11-19-2014
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Magnetic nanoparticles have multiple applications in materials science. In particular, virus capsids have been suggested as promising templates for building up nanometric-sized magnetic clusters by taking advantage of their inner cavity as a nanoreactor. In this study we investigate the magnetization of individual cobalt-filled Cowpea mosaic virus empty virus-like particles using Atomic Force Microscopy. We also combine the analysis of the effects of dehydration on the structure of virus particles with a comparison of their magnetic signal to that provided by commercially available magnetic nanoparticles of similar size. These two approaches allow evaluation of the structure of the metallic cluster grown inside the virus capsid. We conclude that, rather than forming solid clusters, cobalt inside viruses forms a discontinuous structure which does not completely fill the viral cavity and reaches about 10% of its volume.
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A Nonradioactive Approach to Investigate the Metabolism of Therapeutic Peptides by Tagging with 127I and Using Inductively-Coupled Plasma Mass Spectrometry Analysis.
Drug Metab. Dispos.
PUBLISHED: 10-14-2014
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The metabolic fate of adrenocorticotropic hormone (ACTH) fragment 4-10 (4-10) was evaluated following incorporation of a nonradioactive (127)I-tag and with selective detection of I(+) at m/z 127 by inductively coupled plasma mass spectrometry (ICP-MS). (127)I has all the advantages of radioactive (125)I as a metabolite tracer and, together with its detection in the femtogram range, has led to a successful metabolite profiling of (127)I-ACTH (4-10) in vitro. The observed metabolic stability of this peptide in tissue preparations from human was plasma > kidney S9 > liver microsomes > liver cytosol, liver S9. Metabolic turnover of (127)I-ACTH (4-10) was not NADPH-dependent and, together with inhibition by protease inhibitor cocktail and EDTA, is consistent with metabolism exclusively by proteases. Our preliminary studies using chemical inhibitors suggested the involvement of metalloprotease, serine peptidase, and aminopeptidase in (127)I-ACTH (4-10) metabolism. The liver is the primary site of metabolic clearance of (127)I-ACTH (4-10), with kidney S9 taking four times longer to produce a metabolite profile comparable to that produced by liver S9. A total of six metabolites retaining the (127)I-tag was detected by ICP-MS, and their structures were elucidated using a LTQ/Orbitrap. (127)I-ACTH (4-10) underwent both N- and C-terminal proteolysis to produce (127)I-Phe as the major metabolite. The (127)I-tag had minimal effect on the metabolic turnover and site of proteolysis of ACTH (4-10), which, together with ICP-MS providing essentially equimolar responses, suggests that the use of a (127)I-tag may have general utility as an alternative to radioiodination to investigate the metabolism of peptide therapeutics.
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A novel common variant in DCST2 is associated with length in early life and height in adulthood.
Ralf J P van der Valk, Eskil Kreiner-Møller, Marjolein N Kooijman, Mònica Guxens, Evangelia Stergiakouli, Annika Sääf, Jonathan P Bradfield, Frank Geller, M Geoffrey Hayes, Diana L Cousminer, Antje Körner, Elisabeth Thiering, John A Curtin, Ronny Myhre, Ville Huikari, Raimo Joro, Marjan Kerkhof, Nicole M Warrington, Niina Pitkänen, Ioanna Ntalla, Momoko Horikoshi, Riitta Veijola, Rachel M Freathy, Yik-Ying Teo, Sheila J Barton, David M Evans, John P Kemp, Beate St Pourcain, Susan M Ring, George Davey Smith, Anna Bergström, Inger Kull, Hakon Hakonarson, Frank D Mentch, Hans Bisgaard, Bo Chawes, Jakob Stokholm, Johannes Waage, Patrick Eriksen, Astrid Sevelsted, Mads Melbye, , Cornelia M van Duijn, Carolina Medina-Gomez, Albert Hofman, Johan C de Jongste, H Rob Taal, André G Uitterlinden, Loren L Armstrong, Johan Eriksson, Aarno Palotie, Mariona Bustamante, Xavier Estivill, Juan R Gonzalez, Sabrina Llop, Wieland Kiess, Anubha Mahajan, Claudia Flexeder, Carla M T Tiesler, Clare S Murray, Angela Simpson, Per Magnus, Verena Sengpiel, Anna-Liisa Hartikainen, Sirkka Keinänen-Kiukaanniemi, Alexandra Lewin, Alexessander Da Silva Couto Alves, Alexandra I Blakemore, Jessica L Buxton, Marika Kaakinen, Alina Rodriguez, Sylvain Sebert, Marja Vaarasmaki, Timo Lakka, Virpi Lindi, Ulrike Gehring, Dirkje S Postma, Wei Ang, John P Newnham, Leo-Pekka Lyytikäinen, Katja Pahkala, Olli T Raitakari, Kalliope Panoutsopoulou, Eleftheria Zeggini, Dorret I Boomsma, Maria Groen-Blokhuis, Jorma Ilonen, Lude Franke, Joel N Hirschhorn, Tune H Pers, Liming Liang, Jinyan Huang, Berthold Hocher, Mikael Knip, Seang-Mei Saw, John W Holloway, Erik Melén, Struan F A Grant, Bjarke Feenstra, William L Lowe, Elisabeth Widén, Elena Sergeyev, Harald Grallert, Adnan Custovic, Bo Jacobsson, Marjo-Riitta Järvelin, Mustafa Atalay, Gerard H Koppelman, Craig E Pennell, Harri Niinikoski, George V Dedoussis, Mark I McCarthy, Timothy M Frayling, Jordi Sunyer, Nicholas J Timpson, Fernando Rivadeneira, Klaus Bønnelykke, Vincent W V Jaddoe.
Hum. Mol. Genet.
PUBLISHED: 10-03-2014
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Common genetic variants have been identified for adult height, but not much is known about the genetics of skeletal growth in early life. To identify common genetic variants that influence fetal skeletal growth, we meta-analyzed 22 genome-wide association studies (Stage 1; N = 28 459). We identified seven independent top single nucleotide polymorphisms (SNPs) (P < 1 × 10(-6)) for birth length, of which three were novel and four were in or near loci known to be associated with adult height (LCORL, PTCH1, GPR126 and HMGA2). The three novel SNPs were followed-up in nine replication studies (Stage 2; N = 11 995), with rs905938 in DC-STAMP domain containing 2 (DCST2) genome-wide significantly associated with birth length in a joint analysis (Stages 1 + 2; ? = 0.046, SE = 0.008, P = 2.46 × 10(-8), explained variance = 0.05%). Rs905938 was also associated with infant length (N = 28 228; P = 5.54 × 10(-4)) and adult height (N = 127 513; P = 1.45 × 10(-5)). DCST2 is a DC-STAMP-like protein family member and DC-STAMP is an osteoclast cell-fusion regulator. Polygenic scores based on 180 SNPs previously associated with human adult stature explained 0.13% of variance in birth length. The same SNPs explained 2.95% of the variance of infant length. Of the 180 known adult height loci, 11 were genome-wide significantly associated with infant length (SF3B4, LCORL, SPAG17, C6orf173, PTCH1, GDF5, ZNFX1, HHIP, ACAN, HLA locus and HMGA2). This study highlights that common variation in DCST2 influences variation in early growth and adult height.
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Impact of drug shortages on patients receiving parenteral nutrition after laparotomy.
JPEN J Parenter Enteral Nutr
PUBLISHED: 09-19-2014
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Drug shortages, including parenteral nutrition (PN) product shortages, continue to increase and have a significant impact on healthcare. The extent to which product shortages affect bowel recovery and outcomes in patients receiving PN is unknown. The objective of this study is to examine the impact of extensive PN product shortages on patients receiving PN after laparotomy for bowel obstruction.
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Tips and tricks for deep jejunal enteral access: modifying techniques to maximize success.
Curr Gastroenterol Rep
PUBLISHED: 09-04-2014
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Endoscopic insertion of enteral feeding tubes is a major advance in the delivery of nutrition therapy. Since the first report of percutaneous endoscopic gastrostomy (PEG) in 1980 (Gauderer et al. J Pediatr Surg. 15:872-5, 1980), insertion techniques and equipment have been refined and improved. Despite this progress, deep jejunal enteral access remains a difficult procedure, and many endoscopists do not have experience with the techniques of nasojejunal (NJ) placement, percutaneous endoscopic gastrojejunostomy (PEGJ), or direct percutaneous endoscopic jejunostomy (DPEJ) (Shike and Latkany, Gastrointest Endosc Clin N Am. 8:569-80, 1998). The difference between an exasperating experience and a rewarding procedure lies in mastering the "tips and tricks" that make insertion easy. While the basic techniques are described elsewhere (McClave and Chang 2011), we review several universal basic principles to enhance deep jejunal access, which should promote a more efficient and successful procedure.
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MosaicSolver: a tool for determining recombinants of viral genomes from pileup data.
Nucleic Acids Res.
PUBLISHED: 08-12-2014
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Viral recombination is a key evolutionary mechanism, aiding escape from host immunity, contributing to changes in tropism and possibly assisting transmission across species barriers. The ability to determine whether recombination has occurred and to locate associated specific recombination junctions is thus of major importance in understanding emerging diseases and pathogenesis. This paper describes a method for determining recombinant mosaics (and their proportions) originating from two parent genomes, using high-throughput sequence data. The method involves setting the problem geometrically and the use of appropriately constrained quadratic programming. Recombinants of the honeybee deformed wing virus and the Varroa destructor virus-1 are inferred to illustrate the method from both siRNAs and reads sampling the viral genome population (cDNA library); our results are confirmed experimentally. Matlab software (MosaicSolver) is available.
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Targeted Physician Education Positively Affects Delivery of Nutrition Therapy and Patient Outcomes: Results of a Prospective Clinical Trial.
JPEN J Parenter Enteral Nutr
PUBLISHED: 07-04-2014
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Background: Malnutrition is a continuing epidemic among hospitalized patients. We hypothesize that targeted physician education should help reduce caloric deficits and improve patient outcomes. Materials and Methods: We performed a prospective trial of patients (n = 121) assigned to 1 of 2 trauma groups. The experimental group (EG) received targeted education consisting of strategies to increase delivery of early enteral nutrition. Strategies included early enteral access, avoidance of nil per os (NPO) and clear liquid diets (CLD), volume-based feeding, early resumption of feeds postprocedure, and charting caloric deficits. The control group (CG) did not receive targeted education but was allowed to practice in a standard ad hoc fashion. Both groups were provided with dietitian recommendations on a multidisciplinary nutrition team per standard practice. Results: The EG received a higher percentage of measured goal calories (30.1 ± 18.5%, 22.1 ± 23.7%, P = .024) compared with the CG. Mean caloric deficit was not significantly different between groups (-6796 ± 4164 kcal vs -8817 ± 7087 kcal, P = .305). CLD days per patient (0.1 ± 0.5 vs 0.6 ± 0.9), length of stay in the intensive care unit (3.5 ± 5.5 vs 5.2 ± 6.8 days), and duration of mechanical ventilation (1.6 ± 3.7 vs 2.8 ± 5.0 days) were all reduced in the EG compared with the CG (P < .05). EG patients had fewer nosocomial infections (10.6% vs 23.6%) and less organ failure (10.6% vs 18.2%) than did the CG, but these differences did not reach statistical significance. Conclusion: Implementation of specific educational strategies succeeded in greater delivery of nutrition therapy, which favorably affected patient care and outcomes.
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Novel approach identifies SNPs in SLC2A10 and KCNK9 with evidence for parent-of-origin effect on body mass index.
PLoS Genet.
PUBLISHED: 07-01-2014
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The phenotypic effect of some single nucleotide polymorphisms (SNPs) depends on their parental origin. We present a novel approach to detect parent-of-origin effects (POEs) in genome-wide genotype data of unrelated individuals. The method exploits increased phenotypic variance in the heterozygous genotype group relative to the homozygous groups. We applied the method to >56,000 unrelated individuals to search for POEs influencing body mass index (BMI). Six lead SNPs were carried forward for replication in five family-based studies (of ?4,000 trios). Two SNPs replicated: the paternal rs2471083-C allele (located near the imprinted KCNK9 gene) and the paternal rs3091869-T allele (located near the SLC2A10 gene) increased BMI equally (beta?=?0.11 (SD), P<0.0027) compared to the respective maternal alleles. Real-time PCR experiments of lymphoblastoid cell lines from the CEPH families showed that expression of both genes was dependent on parental origin of the SNPs alleles (P<0.01). Our scheme opens new opportunities to exploit GWAS data of unrelated individuals to identify POEs and demonstrates that they play an important role in adult obesity.
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Cis and trans effects of human genomic variants on gene expression.
PLoS Genet.
PUBLISHED: 07-01-2014
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Gene expression is a heritable cellular phenotype that defines the function of a cell and can lead to diseases in case of misregulation. In order to detect genetic variations affecting gene expression, we performed association analysis of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) with gene expression measured in 869 lymphoblastoid cell lines of the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort in cis and in trans. We discovered that 3,534 genes (false discovery rate (FDR)?=?5%) are affected by an expression quantitative trait locus (eQTL) in cis and 48 genes are affected in trans. We observed that CNVs are more likely to be eQTLs than SNPs. In addition, we found that variants associated to complex traits and diseases are enriched for trans-eQTLs and that trans-eQTLs are enriched for cis-eQTLs. As a variant affecting both a gene in cis and in trans suggests that the cis gene is functionally linked to the trans gene expression, we looked specifically for trans effects of cis-eQTLs. We discovered that 26 cis-eQTLs are associated to 92 genes in trans with the cis-eQTLs of the transcriptions factors BATF3 and HMX2 affecting the most genes. We then explored if the variation of the level of expression of the cis genes were causally affecting the level of expression of the trans genes and discovered several causal relationships between variation in the level of expression of the cis gene and variation of the level of expression of the trans gene. This analysis shows that a large sample size allows the discovery of secondary effects of human variations on gene expression that can be used to construct short directed gene regulatory networks.
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Genome wide association identifies common variants at the SERPINA6/SERPINA1 locus influencing plasma cortisol and corticosteroid binding globulin.
PLoS Genet.
PUBLISHED: 07-01-2014
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Variation in plasma levels of cortisol, an essential hormone in the stress response, is associated in population-based studies with cardio-metabolic, inflammatory and neuro-cognitive traits and diseases. Heritability of plasma cortisol is estimated at 30-60% but no common genetic contribution has been identified. The CORtisol NETwork (CORNET) consortium undertook genome wide association meta-analysis for plasma cortisol in 12,597 Caucasian participants, replicated in 2,795 participants. The results indicate that <1% of variance in plasma cortisol is accounted for by genetic variation in a single region of chromosome 14. This locus spans SERPINA6, encoding corticosteroid binding globulin (CBG, the major cortisol-binding protein in plasma), and SERPINA1, encoding ?1-antitrypsin (which inhibits cleavage of the reactive centre loop that releases cortisol from CBG). Three partially independent signals were identified within the region, represented by common SNPs; detailed biochemical investigation in a nested sub-cohort showed all these SNPs were associated with variation in total cortisol binding activity in plasma, but some variants influenced total CBG concentrations while the top hit (rs12589136) influenced the immunoreactivity of the reactive centre loop of CBG. Exome chip and 1000 Genomes imputation analysis of this locus in the CROATIA-Korcula cohort identified missense mutations in SERPINA6 and SERPINA1 that did not account for the effects of common variants. These findings reveal a novel common genetic source of variation in binding of cortisol by CBG, and reinforce the key role of CBG in determining plasma cortisol levels. In turn this genetic variation may contribute to cortisol-associated degenerative diseases.
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Effects of BMI, fat mass, and lean mass on asthma in childhood: a Mendelian randomization study.
PLoS Med.
PUBLISHED: 07-01-2014
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Observational studies have reported associations between body mass index (BMI) and asthma, but confounding and reverse causality remain plausible explanations. We aim to investigate evidence for a causal effect of BMI on asthma using a Mendelian randomization approach.
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Genetic engineering and characterization of Cowpea mosaic virus empty virus-like particles.
Methods Mol. Biol.
PUBLISHED: 06-21-2014
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The development of methods for the production of empty Cowpea mosaic virus (CPMV) virus-like particles (VLPs) that are devoid of RNA, eVLPs, has renewed promise in CPMV capsid technologies. The recombinant nature of CPMV eVLP production means that the extent and variety of genetic modifications that may be incorporated into the particles is theoretically much greater than those that can be made to infectious CPMV virions due to restrictions on viral propagation of the latter. Free of the infectious agent, the genomic RNA, these particles are now finding potential uses in vaccine development, in vivo imaging, drug delivery, and other nanotechnology applications that make use of internal loading of the empty particles. Here we describe methods for the genetic modification and production of CPMV eVLPs and describe techniques useful for their characterization.
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Polyelectrolyte-modified cowpea mosaic virus for the synthesis of gold nanoparticles.
Methods Mol. Biol.
PUBLISHED: 06-21-2014
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Polyelectrolyte surface-modified cowpea mosaic virus (CPMV) can be used for the templated synthesis of narrowly dispersed gold nanoparticles. Cationic polyelectrolyte, poly(allylamine) hydrochloride, is electrostatically bound to the external surface of the virus capsid. The polyelectrolyte-coated CPMV promotes adsorption of aqueous gold hydroxide anionic species, prepared from gold(III) chloride and potassium carbonate, that are easily reduced to form CPMV-templated gold nanoparticles. The process is simple and environmentally benign using only water as solvent at ambient temperature.
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Templated mineralization by charge-modified cowpea mosaic virus.
Methods Mol. Biol.
PUBLISHED: 06-21-2014
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Templated mineralization of virus particles provides routes to narrowly dispersed nanoparticles that are not readily prepared by other means. The templated mineralization of metal or metal oxide on the external surface of wild-type cowpea mosaic virus (CPMV), a plant virus, is facilitated by increasing the external surface negative charge. This is achieved by the chemical modification of surface lysine groups by succinic anhydride. Hence, for example, treatment of charge-modified CPMV succinamate with a 1:2 mixture of iron(II) and iron(III) salts, followed by raising the pH to 10.2, led to the formation of narrowly dispersed, CPMV-templated, magnetite (Fe3O4) nanoparticles.
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Resolving the effects of maternal and offspring genotype on dyadic outcomes in genome wide complex trait analysis ("M-GCTA").
Behav. Genet.
PUBLISHED: 06-10-2014
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Genome wide complex trait analysis (GCTA) is extended to include environmental effects of the maternal genotype on offspring phenotype ("maternal effects", M-GCTA). The model includes parameters for the direct effects of the offspring genotype, maternal effects and the covariance between direct and maternal effects. Analysis of simulated data, conducted in OpenMx, confirmed that model parameters could be recovered by full information maximum likelihood (FIML) and evaluated the biases that arise in conventional GCTA when indirect genetic effects are ignored. Estimates derived from FIML in OpenMx showed very close agreement to those obtained by restricted maximum likelihood using the published algorithm for GCTA. The method was also applied to illustrative perinatal phenotypes from ~4,000 mother-offspring pairs from the Avon Longitudinal Study of Parents and Children. The relative merits of extended GCTA in contrast to quantitative genetic approaches based on analyzing the phenotypic covariance structure of kinships are considered.
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The extinction of the dinosaurs.
Biol Rev Camb Philos Soc
PUBLISHED: 06-07-2014
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Non-avian dinosaurs went extinct 66?million years ago, geologically coincident with the impact of a large bolide (comet or asteroid) during an interval of massive volcanic eruptions and changes in temperature and sea level. There has long been fervent debate about how these events affected dinosaurs. We review a wealth of new data accumulated over the past two decades, provide updated and novel analyses of long-term dinosaur diversity trends during the latest Cretaceous, and discuss an emerging consensus on the extinction's tempo and causes. Little support exists for a global, long-term decline across non-avian dinosaur diversity prior to their extinction at the end of the Cretaceous. However, restructuring of latest Cretaceous dinosaur faunas in North America led to reduced diversity of large-bodied herbivores, perhaps making communities more susceptible to cascading extinctions. The abruptness of the dinosaur extinction suggests a key role for the bolide impact, although the coarseness of the fossil record makes testing the effects of Deccan volcanism difficult.
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A virulent strain of deformed wing virus (DWV) of honeybees (Apis mellifera) prevails after Varroa destructor-mediated, or in vitro, transmission.
PLoS Pathog.
PUBLISHED: 06-01-2014
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The globally distributed ectoparasite Varroa destructor is a vector for viral pathogens of the Western honeybee (Apis mellifera), in particular the Iflavirus Deformed Wing Virus (DWV). In the absence of Varroa low levels DWV occur, generally causing asymptomatic infections. Conversely, Varroa-infested colonies show markedly elevated virus levels, increased overwintering colony losses, with impairment of pupal development and symptomatic workers. To determine whether changes in the virus population were due Varroa amplifying and introducing virulent virus strains and/or suppressing the host immune responses, we exposed Varroa-naïve larvae to oral and Varroa-transmitted DWV. We monitored virus levels and diversity in developing pupae and associated Varroa, the resulting RNAi response and transcriptome changes in the host. Exposed pupae were stratified by Varroa association (presence/absence) and virus levels (low/high) into three groups. Varroa-free pupae all exhibited low levels of a highly diverse DWV population, with those exposed per os (group NV) exhibiting changes in the population composition. Varroa-associated pupae exhibited either low levels of a diverse DWV population (group VL) or high levels of a near-clonal virulent variant of DWV (group VH). These groups and unexposed controls (C) could be also discriminated by principal component analysis of the transcriptome changes observed, which included several genes involved in development and the immune response. All Varroa tested contained a diverse replicating DWV population implying the virulent variant present in group VH, and predominating in RNA-seq analysis of temporally and geographically separate Varroa-infested colonies, was selected upon transmission from Varroa, a conclusion supported by direct injection of pupae in vitro with mixed virus populations. Identification of a virulent variant of DWV, the role of Varroa in its transmission and the resulting host transcriptome changes furthers our understanding of this important viral pathogen of honeybees.
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Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment.
PLoS Genet.
PUBLISHED: 06-01-2014
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Heritability of bone mineral density (BMD) varies across skeletal sites, reflecting different relative contributions of genetic and environmental influences. To quantify the degree to which common genetic variants tag and environmental factors influence BMD, at different sites, we estimated the genetic (rg) and residual (re) correlations between BMD measured at the upper limbs (UL-BMD), lower limbs (LL-BMD) and skull (SK-BMD), using total-body DXA scans of ? 4,890 participants recruited by the Avon Longitudinal Study of Parents and their Children (ALSPAC). Point estimates of rg indicated that appendicular sites have a greater proportion of shared genetic architecture (LL-/UL-BMD rg = 0.78) between them, than with the skull (UL-/SK-BMD rg = 0.58 and LL-/SK-BMD rg = 0.43). Likewise, the residual correlation between BMD at appendicular sites (r(e) = 0.55) was higher than the residual correlation between SK-BMD and BMD at appendicular sites (r(e) = 0.20-0.24). To explore the basis for the observed differences in rg and re, genome-wide association meta-analyses were performed (n ? 9,395), combining data from ALSPAC and the Generation R Study identifying 15 independent signals from 13 loci associated at genome-wide significant level across different skeletal regions. Results suggested that previously identified BMD-associated variants may exert site-specific effects (i.e. differ in the strength of their association and magnitude of effect across different skeletal sites). In particular, variants at CPED1 exerted a larger influence on SK-BMD and UL-BMD when compared to LL-BMD (P = 2.01 × 10(-37)), whilst variants at WNT16 influenced UL-BMD to a greater degree when compared to SK- and LL-BMD (P = 2.31 × 10(-14)). In addition, we report a novel association between RIN3 (previously associated with Paget's disease) and LL-BMD (rs754388: ? = 0.13, SE = 0.02, P = 1.4 × 10(-10)). Our results suggest that BMD at different skeletal sites is under a mixture of shared and specific genetic and environmental influences. Allowing for these differences by performing genome-wide association at different skeletal sites may help uncover new genetic influences on BMD.
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Recombination in enteroviruses is a biphasic replicative process involving the generation of greater-than genome length 'imprecise' intermediates.
PLoS Pathog.
PUBLISHED: 06-01-2014
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Recombination in enteroviruses provides an evolutionary mechanism for acquiring extensive regions of novel sequence, is suggested to have a role in genotype diversity and is known to have been key to the emergence of novel neuropathogenic variants of poliovirus. Despite the importance of this evolutionary mechanism, the recombination process remains relatively poorly understood. We investigated heterologous recombination using a novel reverse genetic approach that resulted in the isolation of intermediate chimeric intertypic polioviruses bearing genomes with extensive duplicated sequences at the recombination junction. Serial passage of viruses exhibiting such imprecise junctions yielded progeny with increased fitness which had lost the duplicated sequences. Mutations or inhibitors that changed polymerase fidelity or the coalescence of replication complexes markedly altered the yield of recombinants (but did not influence non-replicative recombination) indicating both that the process is replicative and that it may be possible to enhance or reduce recombination-mediated viral evolution if required. We propose that extant recombinants result from a biphasic process in which an initial recombination event is followed by a process of resolution, deleting extraneous sequences and optimizing viral fitness. This process has implications for our wider understanding of 'evolution by duplication' in the positive-strand RNA viruses.
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Genetic dissection of acute anterior uveitis reveals similarities and differences in associations observed with ankylosing spondylitis.
PUBLISHED: 05-02-2014
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To use high density genotyping to investigate the genetic associations of acute anterior uveitis (AAU) in patients both with and without ankylosing spondylitis (AS). Method We genotyped 1,711 patients with AAU (either primary or with AAU and AS), 2,339 AS patients without AAU, and 10,000 controls on the Illumina Immunochip Infinium microarray. We also used data on AS patients from previous genomewide association studies to investigate the AS risk locus ANTXR2 for its putative effect in AAU. ANTXR2 expression in mouse eyes was investigated by RT-PCR. Results Comparing all AAU cases with HC, strong association was seen over HLA-B corresponding to the HLA-B27 tag SNP rs116488202. Three non-MHC loci IL23R, the intergenic region 2p15 and ERAP1 were associated at genome-wide significance (P < 5x10(-8) ). Five loci harboring the immune-related genes IL10-IL19, IL18R1-IL1R1, IL6R, the chromosome 1q32 locus harboring KIF21B, as well as the eye related gene EYS, were also associated at a suggestive level of significance (P < 5x10(-6) ). A number of previously confirmed AS associations demonstrated significant differences in effect size between AS patients with AAU and AS patients without AAU. ANTXR2 expression was found to vary across eye compartments. Conclusion These findings, with both novel AAU specific associations, and associations shared with AS demonstrate overlapping but also distinct genetic susceptibility loci for AAU and AS. The associations in IL10 and IL18R1 are shared with inflammatory bowel disease, suggesting common etiologic pathways. © 2014 American College of Rheumatology.
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Rates of dinosaur body mass evolution indicate 170 million years of sustained ecological innovation on the avian stem lineage.
PLoS Biol.
PUBLISHED: 05-01-2014
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Large-scale adaptive radiations might explain the runaway success of a minority of extant vertebrate clades. This hypothesis predicts, among other things, rapid rates of morphological evolution during the early history of major groups, as lineages invade disparate ecological niches. However, few studies of adaptive radiation have included deep time data, so the links between extant diversity and major extinct radiations are unclear. The intensively studied Mesozoic dinosaur record provides a model system for such investigation, representing an ecologically diverse group that dominated terrestrial ecosystems for 170 million years. Furthermore, with 10,000 species, extant dinosaurs (birds) are the most speciose living tetrapod clade. We assembled composite trees of 614-622 Mesozoic dinosaurs/birds, and a comprehensive body mass dataset using the scaling relationship of limb bone robustness. Maximum-likelihood modelling and the node height test reveal rapid evolutionary rates and a predominance of rapid shifts among size classes in early (Triassic) dinosaurs. This indicates an early burst niche-filling pattern and contrasts with previous studies that favoured gradualistic rates. Subsequently, rates declined in most lineages, which rarely exploited new ecological niches. However, feathered maniraptoran dinosaurs (including Mesozoic birds) sustained rapid evolution from at least the Middle Jurassic, suggesting that these taxa evaded the effects of niche saturation. This indicates that a long evolutionary history of continuing ecological innovation paved the way for a second great radiation of dinosaurs, in birds. We therefore demonstrate links between the predominantly extinct deep time adaptive radiation of non-avian dinosaurs and the phenomenal diversification of birds, via continuing rapid rates of evolution along the phylogenetic stem lineage. This raises the possibility that the uneven distribution of biodiversity results not just from large-scale extrapolation of the process of adaptive radiation in a few extant clades, but also from the maintenance of evolvability on vast time scales across the history of life, in key lineages.
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Two Methods of Hemodynamic and Volume Status Assessment in Critically Ill Patients: A Study of Disagreement.
J Intensive Care Med
PUBLISHED: 04-24-2014
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The invasive nature and potential complications associated with pulmonary artery (PA) catheters (PACs) have prompted the pursuit of less invasive monitoring options. Before implementing new hemodynamic monitoring technologies, it is important to determine the interchangeability of these modalities. This study examines monitoring concordance between the PAC and the arterial waveform analysis (AWA) hemodynamic monitoring system.
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Genetic variation in prostate-specific antigen-detected prostate cancer and the effect of control selection on genetic association studies.
Cancer Epidemiol. Biomarkers Prev.
PUBLISHED: 04-21-2014
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Only a minority of the genetic components of prostate cancer risk have been explained. Some observed associations of SNPs with prostate cancer might arise from associations of these SNPs with circulating prostate-specific antigen (PSA) because PSA values are used to select controls.
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Genome-wide association study for refractive astigmatism reveals genetic co-determination with spherical equivalent refractive error: the CREAM consortium.
Hum. Genet.
PUBLISHED: 04-14-2014
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To identify genetic variants associated with refractive astigmatism in the general population, meta-analyses of genome-wide association studies were performed for: White Europeans aged at least 25 years (20 cohorts, N = 31,968); Asian subjects aged at least 25 years (7 cohorts, N = 9,295); White Europeans aged <25 years (4 cohorts, N = 5,640); and all independent individuals from the above three samples combined with a sample of Chinese subjects aged <25 years (N = 45,931). Participants were classified as cases with refractive astigmatism if the average cylinder power in their two eyes was at least 1.00 diopter and as controls otherwise. Genome-wide association analysis was carried out for each cohort separately using logistic regression. Meta-analysis was conducted using a fixed effects model. In the older European group the most strongly associated marker was downstream of the neurexin-1 (NRXN1) gene (rs1401327, P = 3.92E-8). No other region reached genome-wide significance, and association signals were lower for the younger European group and Asian group. In the meta-analysis of all cohorts, no marker reached genome-wide significance: The most strongly associated regions were, NRXN1 (rs1401327, P = 2.93E-07), TOX (rs7823467, P = 3.47E-07) and LINC00340 (rs12212674, P = 1.49E-06). For 34 markers identified in prior GWAS for spherical equivalent refractive error, the beta coefficients for genotype versus spherical equivalent, and genotype versus refractive astigmatism, were highly correlated (r = -0.59, P = 2.10E-04). This work revealed no consistent or strong genetic signals for refractive astigmatism; however, the TOX gene region previously identified in GWAS for spherical equivalent refractive error was the second most strongly associated region. Analysis of additional markers provided evidence supporting widespread genetic co-susceptibility for spherical and astigmatic refractive errors.
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Cytotoxic clinical isolates of Pseudomonas aeruginosa identified during the Steroids for Corneal Ulcers Trial show elevated resistance to fluoroquinolones.
BMC Ophthalmol
PUBLISHED: 04-11-2014
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To determine the relationship between type three secretion genotype and fluoroquinolone resistance for P. aeruginosa strains isolated from microbial keratitis during the Steroids for Corneal Ulcers Trial (SCUT) and for two laboratory strains, PA103 and PAO1.
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Genome-wide association study of height-adjusted BMI in childhood identifies functional variant in ADCY3.
Obesity (Silver Spring)
PUBLISHED: 04-04-2014
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Genome-wide association studies (GWAS) of BMI are mostly undertaken under the assumption that "kg/m(2) " is an index of weight fully adjusted for height, but in general this is not true. The aim here was to assess the contribution of common genetic variation to a adjusted version of that phenotype which appropriately accounts for covariation in height in children.
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Plastic Surgery Undergraduate Training: How a Single Local Event Can Inspire and Educate Medical Students.
Ann Plast Surg
PUBLISHED: 04-03-2014
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Plastic surgery teaching has a limited role in the undergraduate curriculum. We held a 1-day national course in plastic surgery for undergraduates. Our aim was to introduce delegates to plastic surgery and teach basic plastic surgical skills. We assessed change in perceptions of plastic surgery and change in confidence in basic plastic surgical skills.
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Pre-injury beta blocker use does not affect the hyperdynamic response in older trauma patients.
J Emerg Trauma Shock
PUBLISHED: 04-02-2014
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Trauma dogma dictates that the physiologic response to injury is blunted by beta-blockers and other cardiac medications. We sought to determine how the pre-injury cardiac medication profile influences admission physiology and post-injury outcomes.
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Physician nutrition education.
Nutr Clin Pract
PUBLISHED: 04-01-2014
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Nutrition education for physicians in the United States is limited in scope, quality, and duration due to a variety of factors. As new data and quality improvement initiatives highlight the importance of nutrition and a generation of nutrition experts retire, there is a need for new physician educators and leaders in clinical nutrition. Traditional nutrition fellowships and increased didactic lecture time in school and postgraduate training are not feasible strategies to develop the next generation of physician nutrition specialists in the current environment. One strategy is the development of short immersion courses for advanced trainees and junior attendings. The most promising courses include a combination of close mentorship and adult learning techniques such as lectures, clinical experiences, literature review, curricular development, research and writing, multidisciplinary interactions, and extensive group discussion. These courses also allow the opportunity for advanced discourse, development of long-term collaborative relationships, and continued longitudinal career development for alumni after the course ends. Despite these curricular developments, ultimately the field of nutrition will not mature until the American Board of Medical Specialties recognizes nutrition medicine with specialty board certification.
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Shedding new light on viral photosynthesis.
Photosyn. Res.
PUBLISHED: 03-28-2014
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Viruses infecting the environmentally important marine cyanobacteria Prochlorococcus and Synechococcus encode 'auxiliary metabolic genes' (AMGs) involved in the light and dark reactions of photosynthesis. Here, we discuss progress on the inventory of such AMGs in the ever-increasing number of viral genome sequences as well as in metagenomic datasets. We contextualise these gene acquisitions with reference to a hypothesised fitness gain to the phage. We also report new evidence with regard to the sequence and predicted structural properties of viral petE genes encoding the soluble electron carrier plastocyanin. Viral copies of PetE exhibit extensive modifications to the N-terminal signal peptide and possess several novel residues in a region responsible for interaction with redox partners. We also highlight potential knowledge gaps in this field and discuss future opportunities to discover novel phage-host interactions involved in the photosynthetic process.
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Prospective evaluation of intravascular volume status in critically ill patients: does inferior vena cava collapsibility correlate with central venous pressure?
J Trauma Acute Care Surg
PUBLISHED: 03-26-2014
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In search of a standardized noninvasive assessment of intravascular volume status, we prospectively compared the sonographic inferior vena cava collapsibility index (IVC-CI) and central venous pressures (CVPs). Our goals included the determination of CVP behavior across clinically relevant IVC-CI ranges, examination of unitary behavior of IVC-CI with changes in CVP, and estimation of the effect of positive end-expiratory pressure (PEEP) on the IVC-CI/CVP relationship.
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Applying polygenic risk scores to postpartum depression.
Arch Womens Ment Health
PUBLISHED: 03-24-2014
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The etiology of major depressive disorder (MDD) is likely to be heterogeneous, but postpartum depression (PPD) is hypothesized to represent a more homogenous subset of MDD. We use genome-wide SNP data to explore this hypothesis. We assembled a total cohort of 1,420 self-report cases of PPD and 9,473 controls with genome-wide genotypes from Australia, The Netherlands, Sweden and the UK. We estimated the total variance attributable to genotyped variants. We used association results from the Psychiatric Genomics Consortia (PGC) of bipolar disorder (BPD) and MDD to create polygenic scores in PPD and related MDD data sets to estimate the genetic overlap between the disorders. We estimated that the percentage of variance on the liability scale explained by common genetic variants to be 0.22 with a standard error of 0.12, p?=?0.02. The proportion of variance (R (2)) from a logistic regression of PPD case/control status in all four cohorts on a SNP profile score weighted by PGC-BPD association results was small (0.1 %) but significant (p?=?0.004) indicating a genetic overlap between BPD and PPD. The results were highly significant in the Australian and Dutch cohorts (R (2)?>?1.1 %, p?
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Harmonization of Neuroticism and Extraversion phenotypes across inventories and cohorts in the Genetics of Personality Consortium: an application of Item Response Theory.
Behav. Genet.
PUBLISHED: 03-20-2014
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Mega- or meta-analytic studies (e.g. genome-wide association studies) are increasingly used in behavior genetics. An issue in such studies is that phenotypes are often measured by different instruments across study cohorts, requiring harmonization of measures so that more powerful fixed effect meta-analyses can be employed. Within the Genetics of Personality Consortium, we demonstrate for two clinically relevant personality traits, Neuroticism and Extraversion, how Item-Response Theory (IRT) can be applied to map item data from different inventories to the same underlying constructs. Personality item data were analyzed in >160,000 individuals from 23 cohorts across Europe, USA and Australia in which Neuroticism and Extraversion were assessed by nine different personality inventories. Results showed that harmonization was very successful for most personality inventories and moderately successful for some. Neuroticism and Extraversion inventories were largely measurement invariant across cohorts, in particular when comparing cohorts from countries where the same language is spoken. The IRT-based scores for Neuroticism and Extraversion were heritable (48 and 49 %, respectively, based on a meta-analysis of six twin cohorts, total N = 29,496 and 29,501 twin pairs, respectively) with a significant part of the heritability due to non-additive genetic factors. For Extraversion, these genetic factors qualitatively differ across sexes. We showed that our IRT method can lead to a large increase in sample size and therefore statistical power. The IRT approach may be applied to any mega- or meta-analytic study in which item-based behavioral measures need to be harmonized.
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Polygenic scores predict alcohol problems in an independent sample and show moderation by the environment.
Genes (Basel)
PUBLISHED: 03-20-2014
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Alcohol problems represent a classic example of a complex behavioral outcome that is likely influenced by many genes of small effect. A polygenic approach, which examines aggregate measured genetic effects, can have predictive power in cases where individual genes or genetic variants do not. In the current study, we first tested whether polygenic risk for alcohol problems-derived from genome-wide association estimates of an alcohol problems factor score from the age 18 assessment of the Avon Longitudinal Study of Parents and Children (ALSPAC; n = 4304 individuals of European descent; 57% female)-predicted alcohol problems earlier in development (age 14) in an independent sample (FinnTwin12; n = 1162; 53% female). We then tested whether environmental factors (parental knowledge and peer deviance) moderated polygenic risk to predict alcohol problems in the FinnTwin12 sample. We found evidence for both polygenic association and for additive polygene-environment interaction. Higher polygenic scores predicted a greater number of alcohol problems (range of Pearson partial correlations 0.07-0.08, all p-values ? 0.01). Moreover, genetic influences were significantly more pronounced under conditions of low parental knowledge or high peer deviance (unstandardized regression coefficients (b), p-values (p), and percent of variance (R2) accounted for by interaction terms: b = 1.54, p = 0.02, R2 = 0.33%; b = 0.94, p = 0.04, R2 = 0.30%, respectively). Supplementary set-based analyses indicated that the individual top single nucleotide polymorphisms (SNPs) contributing to the polygenic scores were not individually enriched for gene-environment interaction. Although the magnitude of the observed effects are small, this study illustrates the usefulness of polygenic approaches for understanding the pathways by which measured genetic predispositions come together with environmental factors to predict complex behavioral outcomes.
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Wall shear stress distributions in a model of normal and constricted small airways.
Proc Inst Mech Eng H
PUBLISHED: 03-11-2014
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Previous studies have highlighted flow shear stress as a possible damage mechanism for small airways, in particular those liable to constriction through disease or injury due to mechanical ventilation. Flow experiments in vitro have implicated shear stress as a relevant factor for mechanotransduction pathways with respect to airway epithelial cell function. Using computational fluid dynamics analysis, this study reports velocity profiles and calculations for wall shear stress distributions in a three-generation, asymmetric section of the small airways subjected to a steady, inspiratory flow. The results show distal variation of wall shear stress distributions due to velocity gradients on the carina side of each daughter airway branch. The maximum wall shear stresses in both normal and constricted small airways are shown to exceed those calculated using data from previous simpler one-dimensional experimental analyses. These findings have implications for lung cell flow experiments involving shear stress in the consideration of both normal airway function and pathology due to mechanotransduction mechanisms.
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Geriatric-Specific Triage Criteria Are More Sensitive Than Standard Adult Criteria in Identifying Need for Trauma Center Care in Injured Older Adults.
Ann Emerg Med
PUBLISHED: 02-25-2014
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We evaluate the sensitivity of Ohio's 2009 emergency medical services (EMS) geriatric trauma triage criteria compared with the previous adult triage criteria in identifying need for trauma center care among older adults.
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Metabolism and excretion of canagliflozin in mice, rats, dogs, and humans.
Drug Metab. Dispos.
PUBLISHED: 02-25-2014
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Canagliflozin is an oral antihyperglycemic agent used for the treatment of type 2 diabetes mellitus. It blocks the reabsorption of glucose in the proximal renal tubule by inhibiting the sodium-glucose cotransporter 2. This article describes the in vivo biotransformation and disposition of canagliflozin after a single oral dose of [(14)C]canagliflozin to intact and bile duct-cannulated (BDC) mice and rats and to intact dogs and humans. Fecal excretion was the primary route of elimination of drug-derived radioactivity in both animals and humans. In BDC mice and rats, most radioactivity was excreted in bile. The extent of radioactivity excreted in urine as a percentage of the administered [(14)C]canagliflozin dose was 1.2%-7.6% in animals and approximately 33% in humans. The primary pathways contributing to the metabolic clearance of canagliflozin were oxidation in animals and direct glucuronidation of canagliflozin in humans. Unchanged canagliflozin was the major component in systemic circulation in all species. In human plasma, two pharmacologically inactive O-glucuronide conjugates of canagliflozin, M5 and M7, represented 19% and 14% of total drug-related exposure and were considered major human metabolites. Plasma concentrations of M5 and M7 in mice and rats from repeated dose safety studies were lower than those in humans given canagliflozin at the maximum recommended dose of 300 mg. However, biliary metabolite profiling in rodents indicated that mouse and rat livers had significant exposure to M5 and M7. Pharmacologic inactivity and high water solubility of M5 and M7 support glucuronidation of canagliflozin as a safe detoxification pathway.
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Genome-wide association study for radiographic vertebral fractures: a potential role for the 16q24 BMD locus.
Bone
PUBLISHED: 02-12-2014
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Vertebral fracture risk is a heritable complex trait. The aim of this study was to identify genetic susceptibility factors for osteoporotic vertebral fractures applying a genome-wide association study (GWAS) approach. The GWAS discovery was based on the Rotterdam Study, a population-based study of elderly Dutch individuals aged > 55 years; and comprising 329 cases and 2666 controls with radiographic scoring (McCloskey–Kanis) and genetic data. Replication of one top-associated SNP was pursued by de-novo genotyping of 15 independent studies across Europe, the United States, and Australia and one Asian study. Radiographic vertebral fracture assessment was performed using McCloskey–Kanis or Genant semi-quantitative definitions. SNPs were analyzed in relation to vertebral fracture using logistic regression models corrected for age and sex. Fixed effects inverse variance and Han–Eskin alternative random effects meta-analyses were applied. Genome-wide significance was set at p < 5 × 10? 8. In the discovery, a SNP (rs11645938) on chromosome 16q24 was associated with the risk for vertebral fractures at p = 4.6 × 10? 8. However, the association was not significant across 5720 cases and 21,791 controls from 14 studies. Fixed-effects meta-analysis summary estimate was 1.06 (95% CI: 0.98–1.14; p = 0.17), displaying high degree of heterogeneity (I2 = 57%; Qhet p = 0.0006). Under Han–Eskin alternative random effects model the summary effect was significant (p = 0.0005). The SNP maps to a region previously found associated with lumbar spine bone mineral density (LS-BMD) in two large meta-analyses from the GEFOS consortium. A false positive association in the GWAS discovery cannot be excluded, yet, the low-powered setting of the discovery and replication settings (appropriate to identify risk effect size > 1.25) may still be consistent with an effect size < 1.10, more of the type expected in complex traits. Larger effort in studies with standardized phenotype definitions is needed to confirm or reject the involvement of this locus on the risk for vertebral fractures.
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A new chasmosaurine from northern Laramidia expands frill disparity in ceratopsid dinosaurs.
Naturwissenschaften
PUBLISHED: 02-04-2014
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A new taxon of chasmosaurine ceratopsid demonstrates unexpected disparity in parietosquamosal frill shape among ceratopsid dinosaurs early in their evolutionary radiation. The new taxon is described based on two apomorphic squamosals collected from approximately time equivalent (approximately 77 million years old) sections of the upper Judith River Formation, Montana, and the lower Dinosaur Park Formation of Dinosaur Provincial Park, Alberta. It is referred to Chasmosaurinae based on the inferred elongate morphology. The typical chasmosaurine squamosal forms an obtuse triangle in dorsal view that tapers towards the posterolateral corner of the frill. In the dorsal view of the new taxon, the lateral margin of the squamosal is hatchet-shaped with the posterior portion modified into a constricted narrow bar that would have supported the lateral margin of a robust parietal. The new taxon represents the oldest chasmosaurine from Canada, and the first pre-Maastrichtian ceratopsid to have been collected on both sides of the Canada-US border, with a minimum north-south range of 380 km. This squamosal morphology would have given the frill of the new taxon a unique dorsal profile that represents evolutionary experimentation in frill signalling near the origin of chasmosaurine ceratopsids and reinforces biogeographic differences between northern and southern faunal provinces in the Campanian of North America.
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Variability in the common genetic architecture of social-communication spectrum phenotypes during childhood and adolescence.
Mol Autism
PUBLISHED: 02-04-2014
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Social-communication abilities are heritable traits, and their impairments overlap with the autism continuum. To characterise the genetic architecture of social-communication difficulties developmentally and identify genetic links with the autistic dimension, we conducted a genome-wide screen of social-communication problems at multiple time-points during childhood and adolescence.
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The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication.
Nucleic Acids Res.
PUBLISHED: 01-26-2014
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Most RNA viruses infecting mammals and other vertebrates show profound suppression of CpG and UpA dinucleotide frequencies. To investigate this functionally, mutants of the picornavirus, echovirus 7 (E7), were constructed with altered CpG and UpA compositions in two 1.1-1.3 Kbase regions. Those with increased frequencies of CpG and UpA showed impaired replication kinetics and higher RNA/infectivity ratios compared with wild-type virus. Remarkably, mutants with CpGs and UpAs removed showed enhanced replication, larger plaques and rapidly outcompeted wild-type virus on co-infections. Luciferase-expressing E7 sub-genomic replicons with CpGs and UpAs removed from the reporter gene showed 100-fold greater luminescence. E7 and mutants were equivalently sensitive to exogenously added interferon-?, showed no evidence for differential recognition by ADAR1 or pattern recognition receptors RIG-I, MDA5 or PKR. However, kinase inhibitors roscovitine and C16 partially or entirely reversed the attenuated phenotype of high CpG and UpA mutants, potentially through inhibition of currently uncharacterized pattern recognition receptors that respond to RNA composition. Generating viruses with enhanced replication kinetics has applications in vaccine production and reporter gene construction. More fundamentally, the findings introduce a new evolutionary paradigm where dinucleotide composition of viral genomes is subjected to selection pressures independently of coding capacity and profoundly influences host-pathogen interactions.
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Natural history of retained surgical items supports the need for team training, early recognition, and prompt retrieval.
Am. J. Surg.
PUBLISHED: 01-16-2014
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Unintentionally retained items feature prominently among surgical "never events." Our knowledge of these rare occurrences, including natural history and intraoperative safety omission or variance (SOV) profile, is limited. We sought to bridge existing knowledge gaps by presenting a secondary analysis of a multicenter study focused on these important aspects of retained surgical items (RSIs).
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Common variation near ROBO2 is associated with expressive vocabulary in infancy.
Nat Commun
PUBLISHED: 01-15-2014
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Twin studies suggest that expressive vocabulary at ~24 months is modestly heritable. However, the genes influencing this early linguistic phenotype are unknown. Here we conduct a genome-wide screen and follow-up study of expressive vocabulary in toddlers of European descent from up to four studies of the EArly Genetics and Lifecourse Epidemiology consortium, analysing an early (15-18 months, 'one-word stage', N(Total) = 8,889) and a later (24-30 months, 'two-word stage', N(Total)=10,819) phase of language acquisition. For the early phase, one single-nucleotide polymorphism (rs7642482) at 3p12.3 near ROBO2, encoding a conserved axon-binding receptor, reaches the genome-wide significance level (P=1.3 × 10(-8)) in the combined sample. This association links language-related common genetic variation in the general population to a potential autism susceptibility locus and a linkage region for dyslexia, speech-sound disorder and reading. The contribution of common genetic influences is, although modest, supported by genome-wide complex trait analysis (meta-GCTA h(2)(15-18-months) = 0.13, meta-GCTA h(2)(24-30-months) = 0.14) and in concordance with additional twin analysis (5,733 pairs of European descent, h(2)(24-months) = 0.20).
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A systematic review of the need for MRI for the clearance of cervical spine injury in obtunded blunt trauma patients after normal cervical spine CT.
J Emerg Trauma Shock
PUBLISHED: 01-14-2014
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Clearance of cervical spine injury (CSI) in the obtunded or comatose blunt trauma patient remains controversial. In patients with unreliable physical examination and no evidence of CSI on computed tomography (CT), magnetic resonance imaging of the cervical spine (CS-MRI) is the typical follow-up study. There is a growing body of evidence suggesting that CS-MRI is unnecessary with negative findings on a multi-detector CT (MDCT) scan. This review article systematically analyzes current literature to address the controversies surrounding clearance of CSI in obtunded blunt trauma patients. A literature search through MEDLINE database was conducted using all databases on the National Center for Biotechnology Information (NCBI) website (www.ncbi.nlm.nih.gov) for keywords: "cervical spine injury," "obtunded," and "MRI." The search was limited to studies published within the last 10 years and with populations of patients older than 18 years old. Eleven studies were included in the analysis yielding data on 1535 patients. CS-MRI detected abnormalities in 256 patients (16.6%). The abnormalities reported on CS-MRI resulted in prolonged rigid c-collar immobilization in 74 patients (4.9%). Eleven patients (0.7%) had unstable injury detected on CS-MRI alone that required surgical intervention. In the obtunded blunt trauma patient with unreliable clinical examination and a normal CT scan, there is still a role for CS-MRI in detecting clinically significant injuries when MRI resources are available. However, when a reliable clinical exam reveals intact gross motor function, CS-MRI may be unnecessary.
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Genome-wide association analysis identifies 11 risk variants associated with the asthma with hay fever phenotype.
J. Allergy Clin. Immunol.
PUBLISHED: 01-07-2014
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To date, no genome-wide association study (GWAS) has considered the combined phenotype of asthma with hay fever. Previous analyses of family data from the Tasmanian Longitudinal Health Study provide evidence that this phenotype has a stronger genetic cause than asthma without hay fever.
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Results of a prospective, randomized, controlled study of the use of carboxymethylcellulose sodium hyaluronate adhesion barrier in trauma open abdomens.
Surgery
PUBLISHED: 01-02-2014
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The open abdominal (OA) approach is a management strategy used in the most severely injured trauma patients. In addition to the morbidity and mortality, a major challenge is the gradual development of dense adhesions that make reoperations progressively more difficult. This randomized, prospective, proof-of-concept study was conducted to determine the effect of carboxymethylcellulose sodium hyaluronate adhesion barrier (CMHAB; Seprafilm, Genzyme Biosurgery, Bridgewater, NJ) on abdominal adhesions and wound characteristics in trauma open abdomens.
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Error correction and diversity analysis of population mixtures determined by NGS.
PeerJ
PUBLISHED: 01-01-2014
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The impetus for this work was the need to analyse nucleotide diversity in a viral mix taken from honeybees. The paper has two findings. First, a method for correction of next generation sequencing error in the distribution of nucleotides at a site is developed. Second, a package of methods for assessment of nucleotide diversity is assembled. The error correction method is statistically based and works at the level of the nucleotide distribution rather than the level of individual nucleotides. The method relies on an error model and a sample of known viral genotypes that is used for model calibration. A compendium of existing and new diversity analysis tools is also presented, allowing hypotheses about diversity and mean diversity to be tested and associated confidence intervals to be calculated. The methods are illustrated using honeybee viral samples. Software in both Excel and Matlab and a guide are available at http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/, the Warwick University Systems Biology Centre software download site.
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Genetic variation associated with differential educational attainment in adults has anticipated associations with school performance in children.
PLoS ONE
PUBLISHED: 01-01-2014
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Genome-wide association study results have yielded evidence for the association of common genetic variants with crude measures of completed educational attainment in adults. Whilst informative, these results do not inform as to the mechanism of these effects or their presence at earlier ages and where educational performance is more routinely and more precisely assessed. Single nucleotide polymorphisms exhibiting genome-wide significant associations with adult educational attainment were combined to derive an unweighted allele score in 5,979 and 6,145 young participants from the Avon Longitudinal Study of Parents and Children with key stage 3 national curriculum test results (SATS results) available at age 13 to 14 years in English and mathematics respectively. Standardised (z-scored) results for English and mathematics showed an expected relationship with sex, with girls exhibiting an advantage over boys in English (0.433 SD (95%CI 0.395, 0.470), p<10(-10)) with more similar results (though in the opposite direction) in mathematics (0.042 SD (95%CI 0.004, 0.080), p?=?0.030). Each additional adult educational attainment increasing allele was associated with 0.041 SD (95%CI 0.020, 0.063), p?=?1.79×10(-04) and 0.028 SD (95%CI 0.007, 0.050), p?=?0.01 increases in standardised SATS score for English and mathematics respectively. Educational attainment is a complex multifactorial behavioural trait which has not had heritable contributions to it fully characterised. We were able to apply the results from a large study of adult educational attainment to a study of child exam performance marking events in the process of learning rather than realised adult end product. Our results support evidence for common, small genetic contributions to educational attainment, but also emphasise the likely lifecourse nature of this genetic effect. Results here also, by an alternative route, suggest that existing methods for child examination are able to recognise early life variation likely to be related to ultimate educational attainment.
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The association between primary tooth emergence and anthropometric measures in young adults: findings from a large prospective cohort study.
PLoS ONE
PUBLISHED: 01-01-2014
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Cross sectional studies suggest a link may exist between tooth emergence and obesity. To explore this relationship, we aimed to evaluate the prospective associations between primary tooth emergence and anthropometric measures in young adults. Multivariable linear regression was used to analyse relationships between primary tooth emergence, and anthropometric measures measured at 17.8 years, in 2977 participants (1362 males and 1615 females) from the Avon Longitudinal Study of Parents and Children (ALSPAC). In minimally adjusted models, 'quintiles of number of paired teeth' (assessed by questionnaire at 15 months) was positively associated with height [change in height (cm) per quintile increase in 'number of paired teeth' (?)?= 0.35 (95%CI: 0.18, 0.52) P = 0.0001] and weight [ratio of geometric mean weight per quintile increase in 'number of paired teeth' (RGM)?= 1.015 (95%CI: 1.010, 1.019) P<0.0001]. The relationship with weight was largely driven by fat mass, which showed an equivalent relationship with 'quintiles of number of paired teeth' to that seen for weight [RGM?= 1.036 (95%CI: 1.022, 1.051) P<0.0001] (adjusted for height)]. Conversely, no association was seen between 'quintiles of number of paired teeth' and lean mass. An increase in 'quintiles of number of paired teeth' at age 15 months was associated with a higher Tanner stage at age 13 in girls but not boys, but further adjustment of associations between 'quintiles of number of paired teeth' and anthropometric traits for Tanner stage was without effect. Primary tooth emergence is associated with subsequent fat mass, suggesting these could share common constitutive factors, and that early primary tooth emergence may represent a hitherto unrecognised risk factor for the development of obesity in later life.
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Nutrition Optimization Prior to Surgery.
Nutr Clin Pract
PUBLISHED: 12-17-2013
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Optimization of metabolic state prior to major surgery leads to improved surgical outcomes. Nutrition screening protocols should be implemented in the preoperative evaluation, possibly as part of a bundle. Strategies to minimize hyperglycemia and insulin resistance by aggressive preoperative nutrition and carbohydrate loading may promote maintenance of a perioperative anabolic state, improving healing, reducing complications, and shortening the time to recovery of bowel function and hospital discharge. Short courses of preoperative immune-modulating formulas, using combinations of arginine, ?-3 fatty acids, and other nutrients, have been associated with improved surgical outcomes. These immune-modulating nutrients are key elements of metabolic pathways that promote attenuation of the metabolic response to stress and improve both wound healing and immune function. Patients with severe malnutrition and gastrointestinal dysfunction may benefit from preoperative parenteral nutrition. Continuation of feeding through the intraoperative period for severely stressed hypermetabolic patients undergoing nongastrointestinal surgery is another strategy to optimize metabolic state and reduce prolonged nutrition deficits. In this paper, we review the importance of preoperative nutrition and strategies for effective preoperative nutrition optimization.
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The influence of viral RNA secondary structure on interactions with innate host cell defences.
Nucleic Acids Res.
PUBLISHED: 12-13-2013
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RNA viruses infecting vertebrates differ fundamentally in their ability to establish persistent infections with markedly different patterns of transmission, disease mechanisms and evolutionary relationships with their hosts. Although interactions with host innate and adaptive responses are complex and persistence mechanisms likely multi-factorial, we previously observed associations between bioinformatically predicted RNA secondary formation in genomes of positive-stranded RNA viruses with their in vivo fitness and persistence. To analyse this interactions functionally, we transfected fibroblasts with non-replicating, non-translated RNA transcripts from RNA viral genomes with differing degrees of genome-scale ordered RNA structure (GORS). Single-stranded RNA transcripts induced interferon-? mediated though RIG-I and PKR activation, the latter associated with rapid induction of antiviral stress granules. A striking inverse correlation was observed between induction of both cellular responses with transcript RNA structure formation that was independent of both nucleotide composition and sequence length. The consistent inability of cells to recognize RNA transcripts possessing GORS extended to downstream differences from unstructured transcripts in expression of TNF-?, other interferon-stimulated genes and induction of apoptosis. This functional association provides novel insights into interactions between virus and host early after infection and provides evidence for a novel mechanism for evading intrinsic and innate immune responses.
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Genetic influences on trajectories of systolic blood pressure across childhood and adolescence.
Circ Cardiovasc Genet
PUBLISHED: 11-07-2013
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Background- Blood pressure (BP) tends to increase across childhood and adolescence, but the genetic influences on rates of BP change are not known. Potentially important genetic influences could include genetic variants identified in genome-wide association studies of adults as being associated with BP, height, and body mass index. Understanding the contribution of these genetic variants to changes in BP across childhood and adolescence could yield understanding into the life course development of cardiovascular risk. Methods and Results- Pooling data from 2 cohorts (the Avon Longitudinal Study of Parents and Children [n=7013] and the Western Australian Pregnancy Cohort [n=1459]), we examined the associations of allelic scores of 29 single-nucleotide polymorphisms (SNPs) for adult BP, 180 height SNPs, and 32 body mass index SNPs, with trajectories of systolic BP (SBP) from 6 to 17 years of age, using linear spline multilevel models. The allelic scores of BP and body mass index SNPs were associated with SBP at 6 years of age (per-allele effect sizes, 0.097 mm Hg [SE, 0.039 mm Hg] and 0.107 mm Hg [SE, 0.037 mm Hg]); associations with age-related changes in SBP between 6 and 17 years of age were of small magnitude and imprecisely estimated. The allelic score of height SNPs was only weakly associated with SBP changes. No sex or cohort differences in genetic effects were observed. Conclusions- Allelic scores of BP and body mass index SNPs demonstrated associations with SBP at 6 years of age with a similar magnitude but were not strongly associated with changes in SBP with age between 6 and 17 years. Further work is required to identify variants associated with changes with age in BP.
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A Population-Based Study of Genetic Variation and Psychotic Experiences in Adolescents.
Schizophr Bull
PUBLISHED: 10-30-2013
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Psychotic experiences are not uncommon in general population samples, but no studies have examined to what extent confirmed risk variants for schizophrenia are associated with such experiences. A total of 3483 children in a birth cohort study participated in semistructured interviews for psychotic experiences at ages 12 and 18. We examined whether (1) a composite measure of risk for schizophrenia conferred by common alleles (polygenic score) was associated with psychotic experiences, (2) variants with genome-wide evidence for association with schizophrenia were associated with psychotic experiences, and (3) we could identify genetic variants for psychotic experiences using a genome-wide association (GWA) approach. We found no evidence that a schizophrenia polygenic score, or variants showing genome-wide evidence of association with schizophrenia, were associated with adolescent psychotic experiences within the general population. In fact, individuals who had a higher number of risk alleles for genome-wide hits for schizophrenia showed a decreased risk of psychotic experiences. In the GWA study, no variants showed GWA for psychotic experiences, and there was no evidence that the strongest hits (P < 5 × 10(-5)) were enriched for variants associated with schizophrenia in large consortia. Although polygenic scores are weak tools for prediction of schizophrenia, they show strong evidence of association with this disorder. Our findings, however, lend little support to the hypothesis that psychotic experiences in population-based samples of adolescents share a comparable genetic architecture to schizophrenia, or that utilizing a broader and more common phenotype of psychotic experiences will be an efficient approach to increase understanding of the genetic etiology of schizophrenia.
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Anion gap as a predictor of trauma outcomes in the older trauma population: correlations with injury severity and mortality.
Am Surg
PUBLISHED: 10-30-2013
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The relationship among traumatic injury, the associated metabolic/physiologic responses, and mortality is well established. Tissue hypoperfusion and metabolic derangement may not universally correlate with initial clinical presentation. We hypothesized that anion gap (AG) could be a useful gauge of trauma-related physiologic response and mortality in older patients with relatively lower injury acuity. We retrospectively analyzed data from 711 trauma patients older than 45 years. Parameters examined included demographics, injury characteristics, laboratories, morbidity, and mortality. Univariate and survival analyses were performed using PASW 18. A stepwise correlation exists between increasing Injury Severity Score and AG. Although AG less than 8 to 15 was not associated with a significant increase in mortality, greater mortality was seen for AG greater than 16 with further stepwise increases for AGs greater than 22. Anion gap correlated moderately with serum lactate and poorly with base excess. Increasing AG also correlated with morbidity and greater incidence of intensive care admissions. The presence of any complication increased from 28.6 per cent for patients with AG 12 or less to 45.5 per cent for patients with AG 22 or greater (P < 0.04). These findings support the contention that "low acuity" trauma patients with high AGs may not appear acutely ill but may harbor significant underlying metabolic and physiologic disturbances that could contribute to morbidity and mortality. Higher AG values (i.e., greater than 16) may be associated with worse clinical outcomes.
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Mining the human phenome using allelic scores that index biological intermediates.
PLoS Genet.
PUBLISHED: 10-01-2013
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It is common practice in genome-wide association studies (GWAS) to focus on the relationship between disease risk and genetic variants one marker at a time. When relevant genes are identified it is often possible to implicate biological intermediates and pathways likely to be involved in disease aetiology. However, single genetic variants typically explain small amounts of disease risk. Our idea is to construct allelic scores that explain greater proportions of the variance in biological intermediates, and subsequently use these scores to data mine GWAS. To investigate the approachs properties, we indexed three biological intermediates where the results of large GWAS meta-analyses were available: body mass index, C-reactive protein and low density lipoprotein levels. We generated allelic scores in the Avon Longitudinal Study of Parents and Children, and in publicly available data from the first Wellcome Trust Case Control Consortium. We compared the explanatory ability of allelic scores in terms of their capacity to proxy for the intermediate of interest, and the extent to which they associated with disease. We found that allelic scores derived from known variants and allelic scores derived from hundreds of thousands of genetic markers explained significant portions of the variance in biological intermediates of interest, and many of these scores showed expected correlations with disease. Genome-wide allelic scores however tended to lack specificity suggesting that they should be used with caution and perhaps only to proxy biological intermediates for which there are no known individual variants. Power calculations confirm the feasibility of extending our strategy to the analysis of tens of thousands of molecular phenotypes in large genome-wide meta-analyses. We conclude that our method represents a simple way in which potentially tens of thousands of molecular phenotypes could be screened for causal relationships with disease without having to expensively measure these variables in individual disease collections.
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Creating a gold medal Olympic and Paralympics health care team: a satisfaction survey of the mobile medical unit/polyclinic team training for the Vancouver 2010 winter games.
BMC Res Notes
PUBLISHED: 09-03-2013
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The mobile medical unit/polyclinic (MMU/PC) was an essential part of the medical services to support ill or injured Olympic or Paralympics family during the 2010 Olympic and Paralympics winter games. The objective of this study was to survey the satisfaction of the clinical staff that completed the training programs prior to deployment to the MMU.
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Common variants in left/right asymmetry genes and pathways are associated with relative hand skill.
PLoS Genet.
PUBLISHED: 09-01-2013
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Humans display structural and functional asymmetries in brain organization, strikingly with respect to language and handedness. The molecular basis of these asymmetries is unknown. We report a genome-wide association study meta-analysis for a quantitative measure of relative hand skill in individuals with dyslexia [reading disability (RD)] (n = 728). The most strongly associated variant, rs7182874 (P = 8.68 × 10(-9)), is located in PCSK6, further supporting an association we previously reported. We also confirmed the specificity of this association in individuals with RD; the same locus was not associated with relative hand skill in a general population cohort (n = 2,666). As PCSK6 is known to regulate NODAL in the development of left/right (LR) asymmetry in mice, we developed a novel approach to GWAS pathway analysis, using gene-set enrichment to test for an over-representation of highly associated variants within the orthologs of genes whose disruption in mice yields LR asymmetry phenotypes. Four out of 15 LR asymmetry phenotypes showed an over-representation (FDR ? 5%). We replicated three of these phenotypes; situs inversus, heterotaxia, and double outlet right ventricle, in the general population cohort (FDR ? 5%). Our findings lead us to propose that handedness is a polygenic trait controlled in part by the molecular mechanisms that establish LR body asymmetry early in development.
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Normal-to-abnormal rearrangement and NHC activation in three-coordinate iron(II) carbene complexes.
J. Am. Chem. Soc.
PUBLISHED: 08-30-2013
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The normal three-coordinate iron-NHC complex [(IPr)Fe(N)2] (N? = N(SiMe3)2) rearranges to its abnormal NHC analogue [(aIPr)Fe(N?)2] (6) on heating, providing a rare abnormal iron-aNHC complex, and the first such three-coordinate complex. The tert-butyl-substituted complex [(I(t)Bu)Fe(N?)2] (4) undergoes a thermal decomposition that has not previously been observed in iron-NHC chemistry, resulting in the bis(imidazole) complex [((t)BuIm)2Fe(N?)2] (7). A mechanism that involves consecutive C-H and C-N activation is proposed to account for the formation of 7.
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Wind disasters: A comprehensive review of current management strategies.
Int J Crit Illn Inj Sci
PUBLISHED: 08-21-2013
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Wind disasters are responsible for tremendous physical destruction, injury, loss of life and economic damage. In this review, we discuss disaster preparedness and effective medical response to wind disasters. The epidemiology of disease and injury patterns observed in the early and late phases of wind disasters are reviewed. The authors highlight the importance of advance planning and adequate preparation as well as prompt and well-organized response to potential damage involving healthcare infrastructure and the associated consequences to the medical response system. Ways to minimize both the extent of infrastructure damage and its effects on the healthcare system are discussed, focusing on lessons learned from recent major wind disasters around the globe. Finally, aspects of healthcare delivery in disaster zones are reviewed.
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A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci.
Nat. Genet.
PUBLISHED: 06-05-2013
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Allergic disease is very common and carries substantial public-health burdens. We conducted a meta-analysis of genome-wide associations with self-reported cat, dust-mite and pollen allergies in 53,862 individuals. We used generalized estimating equations to model shared and allergy-specific genetic effects. We identified 16 shared susceptibility loci with association P<5×10(-8), including 8 loci previously associated with asthma, as well as 4p14 near TLR1, TLR6 and TLR10 (rs2101521, P=5.3×10(-21)); 6p21.33 near HLA-C and MICA (rs9266772, P=3.2×10(-12)); 5p13.1 near PTGER4 (rs7720838, P=8.2×10(-11)); 2q33.1 in PLCL1 (rs10497813, P=6.1×10(-10)), 3q28 in LPP (rs9860547, P=1.2×10(-9)); 20q13.2 in NFATC2 (rs6021270, P=6.9×10(-9)), 4q27 in ADAD1 (rs17388568, P=3.9×10(-8)); and 14q21.1 near FOXA1 and TTC6 (rs1998359, P=4.8×10(-8)). We identified one locus with substantial evidence of differences in effects across allergies at 6p21.32 in the class II human leukocyte antigen (HLA) region (rs17533090, P=1.7×10(-12)), which was strongly associated with cat allergy. Our study sheds new light on the shared etiology of immune and autoimmune disease.
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Septic embolism in the intensive care unit.
Int J Crit Illn Inj Sci
PUBLISHED: 06-01-2013
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Septic embolism encompasses a wide range of presentations and clinical considerations. From asymptomatic, incidental finding on advanced imaging to devastating cardiovascular or cerebral events, this important clinico-pathologic entity continues to affect critically ill patients. Septic emboli are challenging because they represent two insults-the early embolic/ischemic insult due to vascular occlusion and the infectious insult from a deep-seated nidus of infection frequently not amenable to adequate source control. Mycotic aneurysms and intravascular or end-organ abscesses can occur. The diagnosis of septic embolism should be considered in any patient with certain risk factors including bacterial endocarditis or infected intravascular devices. Treatment consists of long-term antibiotics and source control when possible. This manuscript provides a much-needed synopsis of the different forms and clinical presentations of septic embolism, basic diagnostic considerations, general clinical approaches, and an overview of potential complications.
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Genome-wide meta-analysis identifies new susceptibility loci for migraine.
Verneri Anttila, Bendik S Winsvold, Padhraig Gormley, Tobias Kurth, Francesco Bettella, George McMahon, Mikko Kallela, Rainer Malik, Boukje de Vries, Gisela Terwindt, Sarah E Medland, Unda Todt, Wendy L McArdle, Lydia Quaye, Markku Koiranen, M Arfan Ikram, Terho Lehtimäki, Anine H Stam, Lannie Ligthart, Juho Wedenoja, Ian Dunham, Benjamin M Neale, Priit Palta, Eija Hämäläinen, Markus Schürks, Lynda M Rose, Julie E Buring, Paul M Ridker, Stacy Steinberg, Hreinn Stefansson, Finnbogi Jakobsson, Debbie A Lawlor, David M Evans, Susan M Ring, Markus Färkkilä, Ville Artto, Mari A Kaunisto, Tobias Freilinger, Jean Schoenen, Rune R Frants, Nadine Pelzer, Claudia M Weller, Ronald Zielman, Andrew C Heath, Pamela A F Madden, Grant W Montgomery, Nicholas G Martin, Guntram Borck, Hartmut Göbel, Axel Heinze, Katja Heinze-Kuhn, Frances M K Williams, Anna-Liisa Hartikainen, Anneli Pouta, Joyce van den Ende, André G Uitterlinden, Albert Hofman, Najaf Amin, Jouke-Jan Hottenga, Jacqueline M Vink, Kauko Heikkilä, Michael Alexander, Bertram Müller-Myhsok, Stefan Schreiber, Thomas Meitinger, Heinz Erich Wichmann, Arpo Aromaa, Johan G Eriksson, Bryan J Traynor, Daniah Trabzuni, Elizabeth Rossin, Kasper Lage, Suzanne B R Jacobs, J Raphael Gibbs, Ewan Birney, Jaakko Kaprio, Brenda W Penninx, Dorret I Boomsma, Cornelia van Duijn, Olli Raitakari, Marjo-Riitta Järvelin, John-Anker Zwart, Lynn Cherkas, David P Strachan, Christian Kubisch, Michel D Ferrari, Arn M J M van den Maagdenberg, Martin Dichgans, Maija Wessman, George Davey Smith, Kari Stefansson, Mark J Daly, Dale R Nyholt, Daniel I Chasman, Aarno Palotie, .
Nat. Genet.
PUBLISHED: 05-30-2013
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Migraine is the most common brain disorder, affecting approximately 14% of the adult population, but its molecular mechanisms are poorly understood. We report the results of a meta-analysis across 29 genome-wide association studies, including a total of 23,285 individuals with migraine (cases) and 95,425 population-matched controls. We identified 12 loci associated with migraine susceptibility (P<5×10(-8)). Five loci are new: near AJAP1 at 1p36, near TSPAN2 at 1p13, within FHL5 at 6q16, within C7orf10 at 7p14 and near MMP16 at 8q21. Three of these loci were identified in disease subgroup analyses. Brain tissue expression quantitative trait locus analysis suggests potential functional candidate genes at four loci: APOA1BP, TBC1D7, FUT9, STAT6 and ATP5B.
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GWAS of 126,559 individuals identifies genetic variants associated with educational attainment.
Cornelius A Rietveld, Sarah E Medland, Jaime Derringer, Jian Yang, Tonu Esko, Nicolas W Martin, Harm-Jan Westra, Konstantin Shakhbazov, Abdel Abdellaoui, Arpana Agrawal, Eva Albrecht, Behrooz Z Alizadeh, Najaf Amin, John Barnard, Sebastian E Baumeister, Kelly S Benke, Lawrence F Bielak, Jeffrey A Boatman, Patricia A Boyle, Gail Davies, Christiaan de Leeuw, Niina Eklund, Daniel S Evans, Rudolf Ferhmann, Krista Fischer, Christian Gieger, Håkon K Gjessing, Sara Hägg, Jennifer R Harris, Caroline Hayward, Christina Holzapfel, Carla A Ibrahim-Verbaas, Erik Ingelsson, Bo Jacobsson, Peter K Joshi, Astanand Jugessur, Marika Kaakinen, Stavroula Kanoni, Juha Karjalainen, Ivana Kolčić, Kati Kristiansson, Zoltan Kutalik, Jari Lahti, Sang H Lee, Peng Lin, Penelope A Lind, Yongmei Liu, Kurt Lohman, Marisa Loitfelder, George McMahon, Pedro Marques Vidal, Osorio Meirelles, Lili Milani, Ronny Myhre, Marja-Liisa Nuotio, Christopher J Oldmeadow, Katja E Petrovic, Wouter J Peyrot, Ozren Polašek, Lydia Quaye, Eva Reinmaa, John P Rice, Thais S Rizzi, Helena Schmidt, Reinhold Schmidt, Albert V Smith, Jennifer A Smith, Toshiko Tanaka, Antonio Terracciano, Matthijs J H M van der Loos, Veronique Vitart, Henry Völzke, Jürgen Wellmann, Lei Yu, Wei Zhao, Jüri Allik, John R Attia, Stefania Bandinelli, François Bastardot, Jonathan Beauchamp, David A Bennett, Klaus Berger, Laura J Bierut, Dorret I Boomsma, Ute Bültmann, Harry Campbell, Christopher F Chabris, Lynn Cherkas, Mina K Chung, Francesco Cucca, Mariza de Andrade, Philip L De Jager, Jan-Emmanuel De Neve, Ian J Deary, George V Dedoussis, Panos Deloukas, Maria Dimitriou, Guðný Eiríksdóttir, Martin F Elderson, Johan G Eriksson, David M Evans, Jessica D Faul, Luigi Ferrucci, Melissa E Garcia, Henrik Grönberg, Vilmundur Guðnason, Per Hall, Juliette M Harris, Tamara B Harris, Nicholas D Hastie, Andrew C Heath, Dena G Hernandez, Wolfgang Hoffmann, Adriaan Hofman, Rolf Holle, Elizabeth G Holliday, Jouke-Jan Hottenga, William G Iacono, Thomas Illig, Marjo-Riitta Järvelin, Mika Kähönen, Jaakko Kaprio, Robert M Kirkpatrick, Matthew Kowgier, Antti Latvala, Lenore J Launer, Debbie A Lawlor, Terho Lehtimäki, Jingmei Li, Paul Lichtenstein, Peter Lichtner, David C Liewald, Pamela A Madden, Patrik K E Magnusson, Tomi E Mäkinen, Marco Masala, Matt McGue, Andres Metspalu, Andreas Mielck, Michael B Miller, Grant W Montgomery, Sutapa Mukherjee, Dale R Nyholt, Ben A Oostra, Lyle J Palmer, Aarno Palotie, Brenda W J H Penninx, Markus Perola, Patricia A Peyser, Martin Preisig, Katri Räikkönen, Olli T Raitakari, Anu Realo, Susan M Ring, Samuli Ripatti, Fernando Rivadeneira, Igor Rudan, Aldo Rustichini, Veikko Salomaa, Antti-Pekka Sarin, David Schlessinger, Rodney J Scott, Harold Snieder, Beate St Pourcain, John M Starr, Jae Hoon Sul, Ida Surakka, Rauli Svento, Alexander Teumer, , Henning Tiemeier, Frank J A van Rooij, David R Van Wagoner, Erkki Vartiainen, Jorma Viikari, Peter Vollenweider, Judith M Vonk, Gérard Waeber, David R Weir, H-Erich Wichmann, Elisabeth Widén, Gonneke Willemsen, James F Wilson, Alan F Wright, Dalton Conley, George Davey-Smith, Lude Franke, Patrick J F Groenen, Albert Hofman, Magnus Johannesson, Sharon L R Kardia, Robert F Krueger, David Laibson, Nicholas G Martin, Michelle N Meyer, Danielle Posthuma, A Roy Thurik, Nicholas J Timpson, André G Uitterlinden, Cornelia M van Duijn, Peter M Visscher, Daniel J Benjamin, David Cesarini, Philipp D Koellinger.
Science
PUBLISHED: 05-30-2013
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A genome-wide association study (GWAS) of educational attainment was conducted in a discovery sample of 101,069 individuals and a replication sample of 25,490. Three independent single-nucleotide polymorphisms (SNPs) are genome-wide significant (rs9320913, rs11584700, rs4851266), and all three replicate. Estimated effects sizes are small (coefficient of determination R(2) ? 0.02%), approximately 1 month of schooling per allele. A linear polygenic score from all measured SNPs accounts for ?2% of the variance in both educational attainment and cognitive function. Genes in the region of the loci have previously been associated with health, cognitive, and central nervous system phenotypes, and bioinformatics analyses suggest the involvement of the anterior caudate nucleus. These findings provide promising candidate SNPs for follow-up work, and our effect size estimates can anchor power analyses in social-science genetics.
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Genome-wide association study identifies loci affecting blood copper, selenium and zinc.
Hum. Mol. Genet.
PUBLISHED: 05-29-2013
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Genetic variation affecting absorption, distribution or excretion of essential trace elements may lead to health effects related to sub-clinical deficiency. We have tested for allelic effects of single-nucleotide polymorphisms (SNPs) on blood copper, selenium and zinc in a genome-wide association study using two adult cohorts from Australia and the UK. Participants were recruited in Australia from twins and their families and in the UK from pregnant women. We measured erythrocyte Cu, Se and Zn (Australian samples) or whole blood Se (UK samples) using inductively coupled plasma mass spectrometry. Genotyping was performed with Illumina chips and > 2.5 m SNPs were imputed from HapMap data. Genome-wide significant associations were found for each element. For Cu, there were two loci on chromosome 1 (most significant SNPs rs1175550, P = 5.03 × 10(-10), and rs2769264, P = 2.63 × 10(-20)); for Se, a locus on chromosome 5 was significant in both cohorts (combined P = 9.40 × 10(-28) at rs921943); and for Zn three loci on chromosomes 8, 15 and X showed significant results (rs1532423, P = 6.40 × 10(-12); rs2120019, P = 1.55 × 10(-18); and rs4826508, P = 1.40 × 10(-12), respectively). The Se locus covers three genes involved in metabolism of sulphur-containing amino acids and potentially of the analogous Se compounds; the chromosome 8 locus for Zn contains multiple genes for the Zn-containing enzyme carbonic anhydrase. Where potentially relevant genes were identified, they relate to metabolism of the element (Se) or to the presence at high concentration of a metal-containing protein (Cu).
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Genome-wide association study of primary tooth eruption identifies pleiotropic loci associated with height and craniofacial distances.
Hum. Mol. Genet.
PUBLISHED: 05-23-2013
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Twin and family studies indicate that the timing of primary tooth eruption is highly heritable, with estimates typically exceeding 80%. To identify variants involved in primary tooth eruption, we performed a population-based genome-wide association study of age at first tooth and number of teeth using 5998 and 6609 individuals, respectively, from the Avon Longitudinal Study of Parents and Children (ALSPAC) and 5403 individuals from the 1966 Northern Finland Birth Cohort (NFBC1966). We tested 2 446 724 SNPs imputed in both studies. Analyses were controlled for the effect of gestational age, sex and age of measurement. Results from the two studies were combined using fixed effects inverse variance meta-analysis. We identified a total of 15 independent loci, with 10 loci reaching genome-wide significance (P < 5 × 10(-8)) for age at first tooth and 11 loci for number of teeth. Together, these associations explain 6.06% of the variation in age of first tooth and 4.76% of the variation in number of teeth. The identified loci included eight previously unidentified loci, some containing genes known to play a role in tooth and other developmental pathways, including an SNP in the protein-coding region of BMP4 (rs17563, P = 9.080 × 10(-17)). Three of these loci, containing the genes HMGA2, AJUBA and ADK, also showed evidence of association with craniofacial distances, particularly those indexing facial width. Our results suggest that the genome-wide association approach is a powerful strategy for detecting variants involved in tooth eruption, and potentially craniofacial growth and more generally organ development.
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Identification of multiple risk variants for ankylosing spondylitis through high-density genotyping of immune-related loci.
Nat. Genet.
PUBLISHED: 05-15-2013
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Ankylosing spondylitis is a common, highly heritable inflammatory arthritis affecting primarily the spine and pelvis. In addition to HLA-B*27 alleles, 12 loci have previously been identified that are associated with ankylosing spondylitis in populations of European ancestry, and 2 associated loci have been identified in Asians. In this study, we used the Illumina Immunochip microarray to perform a case-control association study involving 10,619 individuals with ankylosing spondylitis (cases) and 15,145 controls. We identified 13 new risk loci and 12 additional ankylosing spondylitis-associated haplotypes at 11 loci. Two ankylosing spondylitis-associated regions have now been identified encoding four aminopeptidases that are involved in peptide processing before major histocompatibility complex (MHC) class I presentation. Protective variants at two of these loci are associated both with reduced aminopeptidase function and with MHC class I cell surface expression.
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Microbial keratitis: could contact lens material affect disease pathogenesis?
Eye Contact Lens
PUBLISHED: 05-15-2013
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Microbial keratitis is a sight-threatening complication associated with contact lenses. The introduction of silicone hydrogel lens materials with increased oxygen transmission to the ocular surface has not significantly altered the incidence of microbial keratitis. These data suggest that alternate, or additional, predisposing factors involving lens wear must be addressed to reduce or eliminate these infections. The contact lens can provide a surface for microbial growth in situ and can also influence ocular surface homeostasis through effects on the tear fluid and corneal epithelium. Thus, it is intuitive that future contact lens materials could make a significant contribution to preventing microbial keratitis. Design of the "right" material to prevent microbial keratitis requires understanding the effects of current materials on bacterial virulence in the cornea and on ocular surface innate defenses. Current knowledge in each of these areas will be presented with a discussion of future directions needed to understand the influence of lens material on the pathogenesis of microbial keratitis.
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Influence of genome-scale RNA structure disruption on the replication of murine norovirus--similar replication kinetics in cell culture but attenuation of viral fitness in vivo.
Nucleic Acids Res.
PUBLISHED: 04-29-2013
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Mechanisms by which certain RNA viruses, such as hepatitis C virus, establish persistent infections and cause chronic disease are of fundamental importance in viral pathogenesis. Mammalian positive-stranded RNA viruses establishing persistence typically possess genome-scale ordered RNA secondary structure (GORS) in their genomes. Murine norovirus (MNV) persists in immunocompetent mice and provides an experimental model to functionally characterize GORS. Substitution mutants were constructed with coding sequences in NS3/4- and NS6/7-coding regions replaced with sequences with identical coding and (di-)nucleotide composition but disrupted RNA secondary structure (F1, F2, F1/F2 mutants). Mutants replicated with similar kinetics to wild-type (WT) MNV3 in RAW264.7 cells and primary macrophages, exhibited similar (highly restricted) induction and susceptibility to interferon-coupled cellular responses and equal replication fitness by serial passaging of co-cultures. In vivo, both WT and F1/F2 mutant viruses persistently infected mice, although F1, F2 and F1/F2 mutant viruses were rapidly eliminated 1-7 days post-inoculation in competition experiments with WT. F1/F2 mutants recovered from tissues at 9 months showed higher synonymous substitution rates than WT and nucleotide substitutions that potentially restored of RNA secondary structure. GORS plays no role in basic replication of MNV but potentially contributes to viral fitness and persistence in vivo.
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Common variation contributes to the genetic architecture of social communication traits.
Mol Autism
PUBLISHED: 04-16-2013
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Social communication difficulties represent an autistic trait that is highly heritable and persistent during the course of development. However, little is known about the underlying genetic architecture of this phenotype.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.