Genomic analysis reveals neutral and adaptive patterns that challenge the current management regime for East Atlantic cod Gadus morhua L

Challenging long‐held perceptions of fish management units can help to protect vulnerable stocks. When a fishery consisting of multiple genetic stocks is managed as a single unit, overexploitation and depletion of minor genetic units can occur. Atlantic cod (Gadus morhua) is an economically and ecologically important marine species across the North Atlantic. The application of new genomic resources, including SNP arrays, allows us to detect and explore novel structure within specific cod management units. In Norwegian waters, coastal cod (i.e. those not undertaking extensive migrations) are divided into two arbitrary management units defined by ICES: one between 62° and 70°N (Norwegian coastal cod; NCC) and one between 58° and 62°N (Norwegian coastal south; NCS). Together, these capture a fishery area of >25,000 km2 containing many spawning grounds. To assess whether these geographic units correctly represent genetic stocks, we analysed spawning cod of NCC and NCS for more than 8,000 SNPs along with samples of Russian White Sea cod, north‐east Arctic cod (NEAC: the largest Atlantic stock), and outgroup samples representing the Irish and Faroe Sea's. Our analyses revealed large differences in spatial patterns of genetic differentiation across the genome and revealed a complex biological structure within NCC and NCS. Haplotype maps from four chromosome sets show regional specific SNP indicating a complex genetic structure. The current management plan dividing the coastal cod into only two management units does not accurately reflect the genetic units and needs to be revised. Coastal cod in Norway, while highly heterogenous, is also genetically distinct from neighbouring stocks in the north (NEAC), west (Faroe Island) and the south. The White Sea cod are highly divergent from other cod, possibly yielding support to the earlier notion of subspecies rank.publishedVersio

Tyrosinase expression in the peripheral blood of stage III melanoma patients is associated with a poor prognosis: a clinical follow-up study of 110 patients

The aim of this study is to define the relationship between the tyrosinase expression in the peripheral blood and the clinical course of the disease in stage III disease-free melanoma patients after radical lymph node dissection. RT-PCR techniques were used to identify tyrosinase mRNA in 110 patients; a total of 542 blood samples were investigated. In all, 54 patients (49%) showed at least one positive result; 13 patients (11.8%) showed baseline positive results: six became negative thereafter, whereas seven showed follow-up positive results until disease progression occurred. One or more positive determinations were found during follow-up in 41 patients with negative baseline tyrosinase. No correlation was found between baseline results and the relapse rate or disease-free survival (DFS), whereas a significant correlation was found between positive tyrosinase results and disease recurrence during follow-up. In fact, 72.9% of positive patients relapsed, but only 19.3% of negative cases did so. The median interval between the positive results and the clinical demonstration of the relapse was 1.9 months (range 1-6.6). Disease-free survival multivariate analysis selected, as independent variables, Breslow thickness (P=0.05), lymph node involvement according to the AJCC classification (P=0.05) and tyrosinase expression (P=0.0001). In conclusion, RT-PCR tyrosinase mRNA expression is a reliable and reproducible marker associated with a high risk of melanoma progression and we encourage its clinical use in routine follow-up

RXJ0806.3+1527: a double degenerate binary with the shortest known orbital period (321s)

We carried out optical observations of the field of the X-ray pulsator RXJ0806.3+1527. A blue V=21.1 star was found to be the only object consistent with the X-ray position. VLT FORS spectra revealed a blue continuum with no intrinsic absorption lines. Broad (v~1500 km/s), low equivalent width (about -1/-6A) emission lines from the HeII Pickering series were clearly detected. B, V and R time-resolved photometry revealed the presence of about 15% pulsations at the 321s X-ray period, confirming the identification. These findings, together with the period stability and absence of any additional modulation in the 1min-5hr period range, argue in favour of the orbital interpretation of the 321s pulsations. The most likely scenario is thus that RXJ0806.3+1527 is a double degenerate system of the AM CVn class. This would make RXJ0806.3+1527 the shortest orbital period binary currently known and one of the best candidates for gravitational wave detection.Comment: Accepted for publication on A&A Letter

Reducing corruption in a Mexican medical school: impact assessment across two cross-sectional surveys

<p>Abstract</p> <p>Background</p> <p>Corruption pervades educational and other institutions worldwide and medical schools are not exempt. Empirical evidence about levels and types of corruption in medical schools is sparse. We conducted surveys in 2000 and 2007 in the medical school of the Autonomous University of Guerrero in Mexico to document student perceptions and experience of corruption and to support the medical school to take actions to tackle corruption.</p> <p>Methods</p> <p>In both 2000 and 2007 medical students completed a self-administered questionnaire in the classroom without the teacher present. The questionnaire asked about unofficial payments for admission to medical school, for passing an examination and for administrative procedures. We examined factors related to the experience of corruption in multivariate analysis. Focus groups of students discussed the quantitative findings.</p> <p>Results</p> <p>In 2000, 6% of 725 responding students had paid unofficially to obtain entry into the medical school; this proportion fell to 1.6% of the 436 respondents in 2007. In 2000, 15% of students reported having paid a bribe to pass an examination, not significantly different from the 18% who reported this in 2007. In 2007, students were significantly more likely to have bribed a teacher to pass an examination if they were in the fourth year, if they had been subjected to sexual harassment or political pressure, and if they had been in the university for five years or more. Students resented the need to make unofficial payments and suggested tackling the problem by disciplining corrupt teachers. The university administration made several changes to the system of admissions and examinations in the medical school, based on the findings of the 2000 survey.</p> <p>Conclusion</p> <p>The fall in the rate of bribery to enter the medical school was probably the result of the new admissions system instituted after the first survey. Further actions will be necessary to tackle the continuing presence of bribery to pass examinations and for administrative procedures. The social audit helped to draw attention to corruption and to stimulate actions to tackle it.</p

Ancestral Informative Marker Selection and Population Structure Visualization Using Sparse Laplacian Eigenfunctions

Identification of a small panel of population structure informative markers can reduce genotyping cost and is useful in various applications, such as ancestry inference in association mapping, forensics and evolutionary theory in population genetics. Traditional methods to ascertain ancestral informative markers usually require the prior knowledge of individual ancestry and have difficulty for admixed populations. Recently Principal Components Analysis (PCA) has been employed with success to select SNPs which are highly correlated with top significant principal components (PCs) without use of individual ancestral information. The approach is also applicable to admixed populations. Here we propose a novel approach based on our recent result on summarizing population structure by graph Laplacian eigenfunctions, which differs from PCA in that it is geometric and robust to outliers. Our approach also takes advantage of the priori sparseness of informative markers in the genome. Through simulation of a ring population and the real global population sample HGDP of 650K SNPs genotyped in 940 unrelated individuals, we validate the proposed algorithm at selecting most informative markers, a small fraction of which can recover the similar underlying population structure efficiently. Employing a standard Support Vector Machine (SVM) to predict individuals' continental memberships on HGDP dataset of seven continents, we demonstrate that the selected SNPs by our method are more informative but less redundant than those selected by PCA. Our algorithm is a promising tool in genome-wide association studies and population genetics, facilitating the selection of structure informative markers, efficient detection of population substructure and ancestral inference

Prevalence and pattern of HIV-related malnutrition among women in sub-Saharan Africa: a meta-analysis of demographic health surveys

<p>Abstract</p> <p>Background</p> <p>The world's highest HIV infection rates are found in Sub-Saharan Africa (SSA), where adult prevalence in most countries exceeds 25%. Food shortages and malnutrition have combined with HIV/AIDS to bring some countries to the brink of crisis. The aim of this study was to describe prevalence of malnutrition among HIV-infected women and variations across socioeconomic status using data from 11 countries in SSA.</p> <p>Methods</p> <p>This study uses meta-analytic procedures to synthesize the results of most recent data sets available from Demographic and Health Surveys of 11 countries in SSA. Pooled prevalence estimates and 95% confidence intervals were calculated using random-and fixed-effects models. Subgroup and leave-one-country-out sensitivity analyses were also carried out.</p> <p>Results</p> <p>Pooling the prevalence estimates of HIV-related malnutrition yielded an overall prevalence of 10.3% (95% CI 7.4% to 14.1%) with no statistically significant heterogeneity (<it>I</it>²= 0.0%, p = .903). The prevalence estimates decreased with increasing wealth index and education attainment. The pooled prevalence of HIV-related malnutrition was higher among women residing in rural areas than among women residing in urban areas; and lower among women that were professionally employed than unemployed or women in agricultural or manual work.</p> <p>Conclusion</p> <p>Prevalence of HIV-related malnutrition among women varies by wealth status, education attainment, occupation, and type of residence (rural/urban). The observed socioeconomic disparities can help provide more information about population subgroups in particular need and high risk groups, which may in turn lead to the development and implementation of more effective intervention programs.</p

The Relationship between Oral Squamous Cell Carcinoma and Human Papillomavirus: A Meta-Analysis of a Chinese Population (1994–2011)

Background: Previous studies indicated that oral squamous cell carcinomas (OSCC) might be related to human papilloma virus (HPV) infection. However, up to now, there still lacks a large sample study to analyze the relationship between OSCC in a Chinese population and oral HPV infection. In the present study, we used a meta-analysis to evaluate the relationship of OSCC with HPV infection in a Chinese population. Methods: The reports on HPV and OSCC in a Chinese population published between January, 1994, and September, 2011 were retrieved via CNKI/WANFANG/OVID/MEDLINE databases. According to the inclusion criteria, we selected 18 eligible case-control studies. After testing the heterogeneity of the studies by the Cochran Q test, the meta-analyses for HPV and HPV16 were performed using the fixed effects model. Results: The overall positive rates of HPV and HPV16 in OSCC were 58.0 % (354/610; 95 % confidence interval [CI], 54.1–61.9) and 47.47 % (169/356; 95 % CI: 42.3–52.7), respectively; which were significantly higher than those in normal controls 10.44% (26/249; 95 % CI: 7.2–14.7) and 7.1 % (13/182; 95 % CI: 4.2–11.8). Quantitative meta-analysis revealed that, compared with normal controls, the combined odds ratios of OSCC with HPV or HPV16 infection were 12.7 (95 % CI: 8.0–20.0) and 9.0 (95% CI: 5.1–15.6), respectively. Both Begg’s test and funnel plots revealed that no publication bias was found in this present study (P.0.05)