Bayesian Gaussian Copula Factor Models for Mixed Data.

Gaussian factor models have proven widely useful for parsimoniously characterizing dependence in multivariate data. There is a rich literature on their extension to mixed categorical and continuous variables, using latent Gaussian variables or through generalized latent trait models acommodating measurements in the exponential family. However, when generalizing to non-Gaussian measured variables the latent variables typically influence both the dependence structure and the form of the marginal distributions, complicating interpretation and introducing artifacts. To address this problem we propose a novel class of Bayesian Gaussian copula factor models which decouple the latent factors from the marginal distributions. A semiparametric specification for the marginals based on the extended rank likelihood yields straightforward implementation and substantial computational gains. We provide new theoretical and empirical justifications for using this likelihood in Bayesian inference. We propose new default priors for the factor loadings and develop efficient parameter-expanded Gibbs sampling for posterior computation. The methods are evaluated through simulations and applied to a dataset in political science. The models in this paper are implemented in the R package bfa

Low specificity of determine HIV1/2 RDT using whole blood in south west Tanzania

Objective: To evaluate the diagnostic performance of two rapid detection tests (RDTs) for HIV 1/2 in plasma and in whole blood samples. Methods: More than 15,000 study subjects above the age of two years participated in two rounds of a cohort study to determine the prevalence of HIV. HIV testing was performed using the Determine HIV 1/2 test (Abbott) in the first (2006/2007) and the HIV 1/2 STAT-PAK Dipstick Assay (Chembio) in the second round (2007/2008) of the survey. Positive results were classified into faint and strong bands depending on the visual appearance of the test strip and confirmed by ELISA and Western blot. Results: The sensitivity and specificity of the Determine RDT were 100% (95% confidence interval = 86.8 to 100%) and 96.8% (95.9 to 97.6%) in whole blood and 100% (99.7 to 100%) and 97.9% (97.6 to 98.1%) in plasma respectively. Specificity was highly dependent on the tested sample type: when using whole blood, 67.1% of positive results were false positive, as opposed to 17.4% in plasma. Test strips with only faint positive bands were more often false positive than strips showing strong bands and were more common in whole blood than in plasma. Evaluation of the STAT-PAK RDT in plasma during the second year resulted in a sensitivity of 99.7% (99.1 to 99.9%) and a specificity of 99.3% (99.1 to 99.4%) with 6.9% of the positive results being false. Conclusions: Our study shows that the Determine HIV 1/2 strip test with its high sensitivity is an excellent tool to screen for HIV infection, but that – at least in our setting – it can not be recommended as a confirmatory test in VCT campaigns where whole blood is used

Higher education and unemployment in Europe : an analysis of the academic subject and national effects

This paper examines the impact of an academic degree and field of study on short and long-term unemployment across Europe (EU15). Labour Force Survey (LFS) data on over half a million individuals are utilised for that purpose. The harmonized LFS classification of level of education and field of study overcomes past problems of comparability across Europe. The study analyses (i) the effect of an academic degree at a European level, (ii) the specific effect of 14 academic subjects and (iii) country specific effects. The results indicate that an academic degree is more effective on reducing the likelihood of short-term than long-term unemployment. This general pattern even though it is observed for most of the academic subjects its levels show significant variation across disciplines and countries

Unique and conserved MicroRNAs in wheat chromosome 5D revealed by next-generation sequencing

MicroRNAs are a class of short, non-coding, single-stranded RNAs that act as post-transcriptional regulators in gene expression. miRNA analysis of Triticum aestivum chromosome 5D was performed on 454 GS FLX Titanium sequences of flow sorted chromosome 5D with a total of 3,208,630 good quality reads representing 1.34x and 1.61x coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. In silico and structural analyses revealed a total of 55 miRNAs; 48 and 42 miRNAs were found to be present on 5DL and 5DS respectively, of which 35 were common to both chromosome arms, while 13 miRNAs were specific to 5DL and 7 miRNAs were specific to 5DS. In total, 14 of the predicted miRNAs were identified in wheat for the first time. Representation (the copy number of each miRNA) was also found to be higher in 5DL (1,949) compared to 5DS (1,191). Targets were predicted for each miRNA, while expression analysis gave evidence of expression for 6 out of 55 miRNAs. Occurrences of the same miRNAs were also found in Brachypodium distachyon and Oryza sativa genome sequences to identify syntenic miRNA coding sequences. Based on this analysis, two other miRNAs: miR1133 and miR167 were detected in B. distachyon syntenic region of wheat 5DS. Five of the predicted miRNA coding regions (miR6220, miR5070, miR169, miR5085, miR2118) were experimentally verified to be located to the 5D chromosome and three of them : miR2118, miR169 and miR5085, were shown to be 5D specific. Furthermore miR2118 was shown to be expressed in Chinese Spring adult leaves. miRNA genes identified in this study will expand our understanding of gene regulation in bread wheat

Industry in Motion: Using Smart Phones to Explore the Spatial Network of the Garment Industry in New York City

Industrial agglomerations have long been thought to offer economic and social benefits to firms and people that are only captured by location within their specified geographies. Using the case study of New York City’s garment industry along with data acquired from cell phones and social media, this study set out to understand the discrete activities underpinning the economic dynamics of an industrial agglomeration. Over a two week period, data was collected by employing the geo-locative capabilities of Foursquare, a social media application, to record every movement of fashion workers employed at fashion design firms located both inside and outside the geographical boundaries of New York City’s Garment District. This unique method of studying worker activity exposed the day-to-day dynamics of an industrial district with a precision thus far undocumented in literature. Our work suggests that having access to the cluster provides almost the same agglomeration economies as residing within its borders.Rockefeller Foundatio

Growth and energy and protein intake of preterm newborns in the first year of gestation-corrected age

CONTEXT: There are few longitudinal studies that analyze the growth and nutritional status parameters of children born prematurely. OBJECTIVE: To evaluate the growth and dietary intake of preterm newborns in the first year of gestation-corrected age. DESIGN: Prospective clinical study. SETTING: Tertiary care hospital. PATIENTS: 19 children (7 male) who were born prematurely, with birth weight between 1000g and 2000g, which was adequate for the gestational age. PROCEDURES: At 3, 6, 9 and 12 months of gestation-corrected age, children were evaluated in relation to weight, height and cephalic perimeter, using the National Center for Health Statistics as the standard reference, and the Rozalez-Lopez and Frisancho standards for brachial perimeter and triceps and subscapular skinfolds. The calculated dietary intake was compared to the Recommended Dietary Allowances. MAIN MEASUREMENTS: The Z score was calculated for the weight/age, height/age and weight/height relationships, and the percentiles of the perimeters and skinfolds were considered. Dietary intake records were made using the 24-hour Dietary Recall and the Food Frequency Intake Questionnaire methods. The Virtual Nutri software was used to calculate energy and protein intake. RESULTS: The weight/age, height/age and weight/height relationships and the brachial perimeter and triceps skinfold were statistically greater in the first semester in relation to the second. The cephalic perimeter remained above the 50th percentile for the ages studied and there was no difference in the subscapular skinfold between the first and second semesters, remaining below the 50th percentile. The calorie and protein intake, although statistically lower in the first than in the second semester, always remained above the recommended. CONCLUSIONS: The pace of growth is greater in the first semester than in the second, not reaching the standard expected for full-term newborns, with the exception of the cephalic perimeter, which remains adequate. Calorie/protein intake shows an inverse relationship with growth speed, remaining above the recommended for full-term newborns, although with difficulty in depositing subcutaneous fat, in spite of the high caloric intake.CONTEXTO: Atualmente há estudos longitudinais limitados que definem parâmetros de crescimento e estado nutricional de crianças nascidas prematuras. OBJETIVO: Avaliar o crescimento e a ingestão dietética em recém-nascidos pré-termo no primeiro ano de idade corrigida. TIPO DE ESTUDO: Estudo clínico prospectivo. LOCAL: Hospital de cuidados terciários. PACIENTES: 19 crianças (sete do sexo masculino) nascidas prematuras, adequadas para a idade gestacional, com peso de nascimento entre 1.000 g e 2.000 g, acompanhadas aos 3, 6, 9 e 12 meses de idade corrigida. PROCEDIMENTOS: Aos 3, 6, 9 e 12 meses de idade corrigida, as crianças foram avaliadas quanto ao peso, estatura e perímetros utilizando-se, como padrão de referência, o National Center of Health Statistics e quanto à circunferência braquial e às dobras cutâneas triciptal e subescapular, utilizando-se o padrão de Ronalez-Lopez e de Frisancho. A ingestão dietética calculada foi comparada às Recommended Dietary Allowances. RESULTADOS: As relações peso/idade, estatura/idade, peso/estatura, circunferência braquial e dobra cutânea do tríceps foram estatisticamente maiores no primeiro semestre em relação ao segundo. O perímetro cefálico manteve-se acima do percentil 50 nas idades estudadas e a dobra cutânea subescapular não mostrou diferença entre o primeiro e o segundo semestres, mantendo-se abaixo do percentil 50. A ingestão de calorias e proteínas, apesar de estatisticamente menor no primeiro do que no segundo semestre, permaneceu sempre maior do que o recomendado. CONCLUSÕES: O ritmo de crescimento mostra maior velocidade no primeiro semestre do que no segundo, não atingindo o padrão esperado para os recém-nascidos a termo, com exceção do perímetro cefálico, que se mantém adequado. A ingestão de calorias/proteínas mostra relação inversa com o ritmo de crescimento, permanecendo acima do recomendado para nascidos a termo, havendo, porém, dificuldade de deposição de gordura subcutânea, apesar da alta ingestão calórica.Universidade PaulistaUniversidade Federal de São Paulo (UNIFESP) Escola Paulista de MedicinaUNIFESP, EPMSciEL

Functional impact and evolution of a novel human polymorphic inversion that disrupts a gene and creates a fusion transcript

Since the discovery of chromosomal inversions almost 100 years ago, how they are maintained in natural populations has been a highly debated issue. One of the hypotheses is that inversion breakpoints could affect genes and modify gene expression levels, although evidence of this came only from laboratory mutants. In humans, a few inversions have been shown to associate with expression differences, but in all cases the molecular causes have remained elusive. Here, we have carried out a complete characterization of a new human polymorphic inversion and determined that it is specific to East Asian populations. In addition, we demonstrate that it disrupts the ZNF257 gene and, through the translocation of the first exon and regulatory sequences, creates a previously nonexistent fusion transcript, which together are associated to expression changes in several other genes. Finally, we investigate the potential evolutionary and phenotypic consequences of the inversion, and suggest that it is probably deleterious. This is therefore the first example of a natural polymorphic inversion that has position effects and creates a new chimeric gene, contributing to answer an old question in evolutionary biology

Missense mutation of Brain Derived Neurotrophic Factor (BDNF) alters neurocognitive performance in patients with mild traumatic brain injury: a longitudinal study

The predictability of neurocognitive outcomes in patients with traumatic brain injury is not straightforward. The extent and nature of recovery in patients with mild traumatic brain injury (mTBI) are usually heterogeneous and not substantially explained by the commonly known demographic and injury-related prognostic factors despite having sustained similar injuries or injury severity. Hence, this study evaluated the effects and association of the Brain Derived Neurotrophic Factor (BDNF) missense mutations in relation to neurocognitive performance among patients with mTBI. 48 patients with mTBI were prospectively recruited and MRI scans of the brain were performed within an average 10.1 (SD 4.2) hours post trauma with assessment of their neuropsychological performance post full Glasgow Coma Scale (GCS) recovery. Neurocognitive assessments were repeated again at 6 months follow-up. The paired t-test, Cohen’s d effect size and repeated measure ANOVA were performed to delineate statistically significant differences between the groups [wildtype G allele (Val homozygotes) vs. minor A allele (Met carriers)] and their neuropsychological performance across the time point (T1 = baseline/ admission vs. T2 = 6th month follow-up). Minor A allele carriers in this study generally performed more poorly on neuropsychological testing in comparison wildtype G allele group at both time points. Significant mean differences were observed among the wildtype group in the domains of memory (M = -11.44, SD = 10.0, p = .01, d = 1.22), executive function (M = -11.56, SD = 11.7, p = .02, d = 1.05) and overall performance (M = -6.89 SD = 5.3, p = .00, d = 1.39), while the minor A allele carriers showed significant mean differences in the domains of attention (M = -11.0, SD = 13.1, p = .00, d = .86) and overall cognitive performance (M = -5.25, SD = 8.1, p = .01, d = .66).The minor A allele carriers in comparison to the wildtype G allele group, showed considerably lower scores at admission and remained impaired in most domains across the timepoints, although delayed signs of recovery were noted to be significant in the domains attention and overall cognition. In conclusion, the current study has demonstrated the role of the BDNF rs6265 Val66Met polymorphism in influencing specific neurocognitive outcomes in patients with mTBI. Findings were more detrimentally profound among Met allele carriers

Recommendations for the diagnosis of pediatric tuberculosis

Tuberculosis (TB) is still the world's second most frequent cause of death due to infectious diseases after HIV infection, and this has aroused greater interest in identifying and managing exposed subjects, whether they are simply infected or have developed one of the clinical variants of the disease. Unfortunately, not even the latest laboratory techniques are always successful in identifying affected children because they are more likely to have negative cultures and tuberculin skin test results, equivocal chest X-ray findings, and atypical clinical manifestations than adults. Furthermore, they are at greater risk of progressing from infection to active disease, particularly if they are very young. Consequently, pediatricians have to use different diagnostic strategies that specifically address the needs of children. This document describes the recommendations of a group of scientific societies concerning the signs and symptoms suggesting pediatric TB, and the diagnostic approach towards children with suspected disease