A statistical model for genotype determination at a major locus in a progeny test design

Considering a normally distributed quantitative trait whose genetic variation is controlled by both an autosomal major locus and a polygenic component, and whose expression is influenced by environmental factors, a mixed model was developed to classify sires and daughters for their genotypes at the major locus in a progeny test design. Repeatability and genetic parameters reflecting the polygenic variation were assumed to be known. Posterior distribution of the sire genotypes and that of the daughters given the sire genotypes were derived. A method was proposed to estimate these posterior probabilities as well as the unknown parameters, and a method using the likelihood ratios to test specific genetic hypotheses was suggested. An iterative two-step procedure similar to the EM (expectation-maximization) algorithm was used to estimate the posterior probabilities and the unknown parameters. The operational value of this approach was tested with simulated data.S’appliquant à un caractère quantitatif à distribution normale, dont la variabilité génétique est contrôlée à la fois par un locus majeur autosomal et par une composante polygénique et dont l’expression est influencée par des facteurs de milieu, un modèle mixte est développé afin de déterminer le génotype (au locus majeur) des pères et de leurs filles dans un test sur descendance. La répétabilité et les paramètres génétiques relatifs à la composante polygénique sont supposés connus. La loi a posteriori des génotypes des pères et celles des génotypes de leurs filles, conditionnellement aux génotypes des pères, sont établies. Une méthode est proposée pour estimer ces probabilités a posteriori, ainsi que les paramètres inconnus, et une méthode utilisant les rapports de vraisemblance est suggérée afin de tester des hypothèses génétiques spécifiques. Une procédure itérative en deux étapes, similaire à l’algorithme EM (expectation-maximization), est présentée afin d’estimer les probabilités a posteriori et les paramètres inconnus. L’intérêt opérationnel de cette approche est éprouvé sur des données simulées

CT scanning for diagnosing blunt ureteral and ureteropelvic junction injuries

<p>Abstract</p> <p>Background</p> <p>Blunt ureteral and ureteropelvic (UPJ) injuries are extremely rare and very difficult to diagnose. Many of these injuries are missed by the initial trauma evaluation.</p> <p>Methods</p> <p>Trauma registry data was used to identify all blunt trauma patients with ureteral or UPJ injuries, from 1 April 2001 to 30 November 2006. Demographics, injury information and outcomes were determined. Chart review was then performed to record initial clinical and all CT findings.</p> <p>Results</p> <p>Eight patients had ureteral or UPJ injuries. Subtle findings such as perinephric stranding and hematomas, and low density retroperitoneal fluid were evident on all initial scans, and prompted delayed excretory scans in 7/8 cases. As a result, ureteral and UPJ injuries were diagnosed immediately for these seven patients. These findings were initially missed in the eighth patient because significant associated visceral findings mandated emergency laparotomy. All ureteral and UPJ injuries have completely healed except for the case with the delay in diagnosis.</p> <p>Conclusion</p> <p>Most blunt ureteral and UPJ injuries can be identified if delayed excretory CT scans are performed based on initial CT findings of perinephric stranding and hematomas, or the finding of low density retroperitoneal fluid.</p

New Physics Models of Direct CP Violation in Charm Decays

In view of the recent LHCb measurement of Delta A_CP, the difference between the time-integrated CP asymmetries in D --> K+K- and D --> pi+pi- decays, we perform a comparative study of the possible impact of New Physics degrees of freedom on the direct CP asymmetries in singly Cabibbo suppressed D meson decays. We systematically discuss scenarios with a minimal set of new degrees of freedom that have renormalizable couplings to the SM particles and that are heavy enough such that their effects on the D meson decays can be described by local operators. We take into account both constraints from low energy flavor observables, in particular D0-D0bar mixing, and from direct searches. While models that explain the large measured value for Delta A_CP with chirally enhanced chromomagnetic penguins are least constrained, we identify a few viable models that contribute to the D meson decays at tree level or through loop induced QCD penguins. We emphasize that such models motivate direct searches at the LHC.Comment: 24 pages, 13 figures. v2: typos corrected, reference added, published versio

Systematic review and meta-analysis of hepatitis C virus infection and HIV viral load: New insights into epidemiologic synergy

INTRODUCTION: Hepatitis C virus (HCV) and HIV infection frequently co-occur due to shared transmission routes. Co-infection is associated with higher HCV viral load (VL), but less is known about the effect of HCV infection on HIV VL and risk of onward transmission. METHODS: We undertook a systematic review comparing 1) HIV VL among ART-naïve, HCV co-infected individuals versus HIV mono-infected individuals and 2) HIV VL among treated versus untreated HCV co-infected individuals. We performed a random-effects meta-analysis and quantified heterogeneity using the I2 statistic. We followed Cochrane Collaboration guidelines in conducting our review and PRISMA guidelines in reporting results. RESULTS AND DISCUSSION: We screened 3925 articles and identified 17 relevant publications. A meta-analysis found no evidence of increased HIV VL associated with HCV co-infection or between HIV VL and HCV treatment with pegylated interferon-alpha-2a/b and ribavirin. CONCLUSIONS: This finding is in contrast to the substantial increases in HIV VL observed with several other systemic infections. It presents opportunities to elucidate the biological pathways that underpin epidemiological synergy in HIV co-infections and may enable prediction of which co-infections are most important to epidemic control

Clinical array-based karyotyping of breast cancer with equivocal HER2 status resolves gene copy number and reveals chromosome 17 complexity

<p>Abstract</p> <p>Background</p> <p><it>HER2 </it>gene copy status, and concomitant administration of trastuzumab (Herceptin), remains one of the best examples of targeted cancer therapy based on understanding the genomic etiology of disease. However, newly diagnosed breast cancer cases with equivocal HER2 results present a challenge for the oncologist who must make treatment decisions despite the patient's unresolved HER2 status. In some cases both immunohistochemistry (IHC) and fluorescence <it>in situ </it>hybridization (FISH) are reported as equivocal, whereas in other cases IHC results and FISH are discordant for positive versus negative results. The recent validation of array-based, molecular karyotyping for clinical oncology testing provides an alternative method for determination of HER2 gene copy number status in cases remaining unresolved by traditional methods.</p> <p>Methods</p> <p>In the current study, DNA extracted from 20 formalin fixed paraffin embedded (FFPE) tissue samples from newly diagnosed cases of invasive ductal carcinoma referred to our laboratory with unresolved HER2 status, were analyzed using a clinically validated genomic array containing 127 probes covering the HER2 amplicon, the pericentromeric regions, and both chromosome 17 arms.</p> <p>Results</p> <p>Array-based comparative genomic hybridization (array CGH) analysis of chromosome 17 resolved HER2 gene status in [20/20] (100%) of cases and revealed additional chromosome 17 copy number changes in [18/20] (90%) of cases. Array CGH analysis also revealed two false positives and one false negative by FISH due to "ratio skewing" caused by chromosomal gains and losses in the centromeric region. All cases with complex rearrangements of chromosome 17 showed genome-wide chromosomal instability.</p> <p>Conclusions</p> <p>These results illustrate the analytical power of array-based genomic analysis as a clinical laboratory technique for resolution of HER2 status in breast cancer cases with equivocal results. The frequency of complex chromosome 17 abnormalities in these cases suggests that the two probe FISH interphase analysis is inadequate and results interpreted using the HER2/CEP17 ratio should be reported "with caution" when the presence of centromeric amplification or monosomy is suspected by FISH signal gains or losses. The presence of these pericentromeric copy number changes may result in artificial skewing of the HER2/CEP17 ratio towards false negative or false positive results in breast cancer with chromosome 17 complexity. Full genomic analysis should be considered in all cases with complex chromosome 17 aneusomy as these cases are likely to have genome-wide instability, amplifications, and a poor prognosis.</p

Academic and social integration and study progress in problem based learning

The present study explores the effects of problem-based learning (PBL) on social and academic integration and study progress. Three hundred and five first-year students from three different psychology curricula completed a questionnaire on social and academic integration. Effects of a full-fledged PBL environment were compared to (1) effects of a conventional lecture-based learning environment, and (2) effects of a learning environment that combined lectures and other methods aimed at activating students. Lisrel analyses show direct positive effects of the learning environment on study progress: students in PBL obtained more credits compared to students in more conventional curricula. Moreover, the levels of social and academic integration were also higher among students in the PBL curriculum. The links between integration and study progress were less straightforward. Formal social integration positively affected study progress, but informal academic integration was negatively related to study progress

Multi-level evidence of an allelic hierarchy of USH2A variants in hearing, auditory processing and speech/language outcomes.

Language development builds upon a complex network of interacting subservient systems. It therefore follows that variations in, and subclinical disruptions of, these systems may have secondary effects on emergent language. In this paper, we consider the relationship between genetic variants, hearing, auditory processing and language development. We employ whole genome sequencing in a discovery family to target association and gene x environment interaction analyses in two large population cohorts; the Avon Longitudinal Study of Parents and Children (ALSPAC) and UK10K. These investigations indicate that USH2A variants are associated with altered low-frequency sound perception which, in turn, increases the risk of developmental language disorder. We further show that Ush2a heterozygote mice have low-level hearing impairments, persistent higher-order acoustic processing deficits and altered vocalizations. These findings provide new insights into the complexity of genetic mechanisms serving language development and disorders and the relationships between developmental auditory and neural systems

A simplified method to measure choroidal thickness using adaptive compensation in enhanced depth imaging optical coherence tomography

10.1371/journal.pone.0096661PLoS ONE95-POLN

Aqueductal developmental venous anomaly as an unusual cause of congenital hydrocephalus: a case report and review of the literature

<p>Abstract</p> <p>Introduction</p> <p>Aqueductal stenosis may be caused by a number of etiologies including congenital stenosis, tumor, inflammation, and, very rarely, vascular malformation. However, aqueductal stenosis caused by a developmental venous anomaly presenting as congenital hydrocephalus is even more rare, and, to the best of our knowledge, has not yet been reported in the literature. In this study, we review the literature and report the first case of congenital hydrocephalus associated with aqueductal stenosis from a developmental venous anomaly.</p> <p>Case presentation</p> <p>The patient is a three-day-old, African-American baby girl with a prenatal diagnosis of hydrocephalus. She presented with a full fontanelle, splayed sutures, and macrocephaly. Postnatal magnetic resonance imaging showed triventricular hydrocephalus, suggesting aqueductal stenosis. Examination of the T1-weighted sagittal magnetic resonance imaging enhanced with gadolinium revealed a developmental venous anomaly passing through the orifice of the aqueduct. We treated the patient with a ventriculoperitoneal shunt.</p> <p>Conclusions</p> <p>Ten cases of aqueductal stenosis due to venous lesions have been reported and, although these venous angiomas and developmental venous anomalies are usually considered congenital lesions, all 10 cases became symptomatic as older children and adults. Our case is the first in which aqueductal stenosis caused by a developmental venous anomaly presents as congenital hydrocephalus. We hope adding to the literature will improve understanding of this very uncommon cause of hydrocephalus and, therefore, will aid in treatment.</p