Estimation of starvation and diet variation of the RNA/DNA ratios in field-caught Sardina pilchardus larvae off the north of Spain

The aim of this study was to analyse the general larval condition, to determine the lncidence of starvation and to investigate the effect of time of day on RNA/DNA ratios among field-caught Sardina pilchardus (L.) larvae. The larvae were collected during 4 research cruises off northern Spain, during March, April, May and June 1992. A highly sensitive fluorometric method for nucleic acid quantification was applied to larvae of S. pilchardus. The means of the RNA/DNA ratio were relat~vely high, so the larvae collected off northern Spain were generally in good condition. Low percentages of starving larvae (RNA/DNA ratio less than 1.3), ranging from 0 to 3.23%, were found over the 4 mo. The RNA/DNA ratios were significantly correlated with zooplankton biomass. Larvae collected at night revealed higher RNA/DNA ratios compared to larvae caught during the day. This seems to indicate that there is some endogenous rhythm in the production of RNA. It would then follow that, if there are die1 changes in RNA concentrations, average RNA Indices can be unrepresentative if there IS any day/night bias in sampling

Correction: Emotional impact of screening: A systematic review and meta-analysis

<p>Abstract</p> <p>Background</p> <p>There is a widely held expectation that screening for disease has adverse emotional impacts. The aim of the current review is to estimate the short (< 4 weeks) and longer term (> 4 weeks) emotional impact of such screening.</p> <p>Methods</p> <p>Studies selected for inclusion were (a) randomised controlled trials in which (b) participants in one arm underwent screening and received test results, and those in a control arm did not, and (c) emotional outcomes were assessed in both arms. MEDLINE via PubMed (1950 to present), EMBASE (1980 to present), PsycINFO (1985 to present) using OVID SP, and CINAHL (1982 to present) via EBSCO were searched, using strategies developed with keywords and medical subject headings. Data were extracted on emotional outcomes, type of screening test and test results.</p> <p>Results</p> <p>Of the 12 studies that met the inclusion criteria, six involved screening for cancer, two for diabetes, and one each for abdominal aortic aneurysms, peptic ulcer, coronary heart disease and osteoporosis. Five studies reported data on anxiety, four on depression, two on general distress and eight on quality of life assessed between one week and 13 years after screening (median = 1.3 years).</p> <p>Meta-analyses revealed no significant impact of screening on longer term anxiety (pooled SMD 0.01, 95% CI -0.10, 0.11), depression (pooled SMD -0.04, 95% CI -.12, 0.20), or quality of life subscales (mental and self-assessed health pooled SMDs, respectively: 0.03; -0.01, (95% CI -.02, 0.04; 0.00, 95% CI -.04, 0.03).</p> <p>Conclusion</p> <p>Screening does not appear to have adverse emotional impacts in the longer term (> 4 weeks). Too few studies assessed outcomes before four weeks to comment on the shorter term emotional impact of screening.</p

Hybrid Algorithms Based on Integer Programming for the Search of Prioritized Test Data in Software Product Lines

In Software Product Lines (SPLs) it is not possible, in general, to test all products of the family. The number of products denoted by a SPL is very high due to the combinatorial explosion of features. For this reason, some coverage criteria have been proposed which try to test at least all feature interactions without the necessity to test all products, e.g., all pairs of features (pairwise coverage). In addition, it is desirable to first test products composed by a set of priority features. This problem is known as the Prioritized Pairwise Test Data Generation Problem. In this work we propose two hybrid algorithms using Integer Programming (IP) to generate a prioritized test suite. The first one is based on an integer linear formulation and the second one is based on a integer quadratic (nonlinear) formulation. We compare these techniques with two state-of-the-art algorithms, the Parallel Prioritized Genetic Solver (PPGS) and a greedy algorithm called prioritized-ICPL. Our study reveals that our hybrid nonlinear approach is clearly the best in both, solution quality and computation time. Moreover, the nonlinear variant (the fastest one) is 27 and 42 times faster than PPGS in the two groups of instances analyzed in this work.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. Partially funded by the Spanish Ministry of Economy and Competitiveness and FEDER under contract TIN2014-57341-R, the University of Málaga, Andalucía Tech and the Spanish Network TIN2015-71841-REDT (SEBASENet)

Host genetic factors associated with hepatocellular carcinoma in patients with hepatitis C virus infection: a systematic review

Hepatitis C virus (HCV)-infected patients are at risk of developing hepatocellular carcinoma (HCC). Individuals at heightened riskcould be targeted by intensive follow-up surveillance. We have conducted a systematic review of the literature to identify host genetic predisposition to HCC in HCV-infected patients. A comprehensive search of Medline and Embase databases was performed and the strength of evidence of associations for each gene on development of HCC was evaluated. We identified 166 relevant studies, relating to 137 different genes, or combinations thereof. 17 genes were classified as having “good” evidence of an association, a significant association was observed for 37 genes but this finding had not yet been replicated, 56 genes had mixed or limited evidence of an association, and 27 genes showed no association. IFNL3/4, TNF-α and PNPLA3 genes had the most evidence of an association. There was, however, considerable heterogeneity in study design and data quality. In conclusion, we identified a number of genes with evidence of association with HCC, but also a need for more standardised approaches to address this clinically critical question. It is important to consider the underlying mechanism of these relationships and which are confounded by the presence of other HCC risk factors and response to therapy. We also identified many genes where the evidence of association is contradictory or requires replication, as well as a number where associations have been studied but no evidence found. These findings should help to direct future studies on host genetic predisposition to HCC in patients with HCV infection

Current research into brain barriers and the delivery of therapeutics for neurological diseases: a report on CNS barrier congress London, UK, 2017.

This is a report on the CNS barrier congress held in London, UK, March 22-23rd 2017 and sponsored by Kisaco Research Ltd. The two 1-day sessions were chaired by John Greenwood and Margareta Hammarlund-Udenaes, respectively, and each session ended with a discussion led by the chair. Speakers consisted of invited academic researchers studying the brain barriers in relation to neurological diseases and industry researchers studying new methods to deliver therapeutics to treat neurological diseases. We include here brief reports from the speakers

Two-Loop Renormalization Group Equations for Soft Supersymmetry-Breaking Couplings

We compute the two-loop renormalization group equations for all soft supersymmetry-breaking couplings in a general softly broken N=1 supersymmetric model. We also specialize these results to the Minimal Supersymmetric Standard Model.Comment: 26 pages. [v4: Signs of equations (4.2) and (4.3) are fixed.

Exploration of the Eucalyptus globulus gene pool

The first Europeans to discover Eucalyptus globulus were French explorers in 1792. Its seed was rapidly spread throughout the world in the 19th century and this was the species by which much of the world first knew the genus. However, it was in the industrial forests of the 20th century that this species, once considered the ‘Prince of Eucalypts’, achieved greatest prominence due to its fast growth and superior pulp qualities. Formal breeding first commenced in 1966 in Portugal and in the late 1980’s large base population trials from open-pollinated seed collections from native stands were established in many countries. These trials have provided unprecedented insights into the quantitative genetic control of numerous traits of economic and ecological importance and how this variation is spatially distributed in the native range of the species. However with large, fully pedigreed breeding populations becoming available for quantitative analysis and the rapidly expanding knowledge of DNA sequence variation, we are now at the threshold of a new understanding of this important eucalypt gene pool. Indications of the significance of non-additive genetic effects are becoming available. The E. globulus chloroplast genome has now been sequenced and several genome maps have been published. Studies of the variation in nuclear microsatellites and the lignin biosynthesis gene CCR confirm the complex, spatially structured nature of the native gene pool. Strong spatial structuring of the chloroplast genome has provided a tool for tracking seed migration and the geographic origin of exotic landraces. Highly divergent lineages of chloroplast DNA have been discovered and studies of the hypervariable JLA+ region argue that some components of the E. globulus gene pool have been assimilated from other species following hybridisation

Deep generative modeling for single-cell transcriptomics.

Single-cell transcriptome measurements can reveal unexplored biological diversity, but they suffer from technical noise and bias that must be modeled to account for the resulting uncertainty in downstream analyses. Here we introduce single-cell variational inference (scVI), a ready-to-use scalable framework for the probabilistic representation and analysis of gene expression in single cells ( https://github.com/YosefLab/scVI ). scVI uses stochastic optimization and deep neural networks to aggregate information across similar cells and genes and to approximate the distributions that underlie observed expression values, while accounting for batch effects and limited sensitivity. We used scVI for a range of fundamental analysis tasks including batch correction, visualization, clustering, and differential expression, and achieved high accuracy for each task

Heritability Estimation of Reliable Connectomic Features*

Brain imaging genetics is an emerging research field to explore the underlying genetic architecture of brain structure and function measured by different imaging modalities. However, not all the changes in the brain are a consequential result of genetic effect and it is usually unknown which imaging phenotypes are promising for genetic analyses. In this paper, we focus on identifying highly heritable measures of structural brain networks derived from diffusion weighted imaging data. Using the twin data from the Human Connectome Project (HCP), we evaluated the reliability of fractional anisotropy measure, fiber length and fiber number of each edge in the structural connectome and seven network level measures using intraclass correlation coefficients. We then estimated the heritability of those reliable network measures using SOLAR-Eclipse software. Across all 64,620 network edges between 360 brain regions in the Glasser parcellation, we observed ~5% of them with significantly high heritability in fractional anisotropy, fiber length or fiber number. All the tested network level measures, capturing the network integrality, segregation or resilience, are highly heritable, with variance explained by the additive genetic effect ranging from 59% to 77%

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Abstract:&nbsp; Although the nasopharyngeal swab (NPS) is considered the optimal sample for the diagnosis of SARS-CoV-2 infection, the nasal swab (NS) is usually used since it is less invasive and of greater adherence. Our aim was to evaluate the performance of the nasal antigen detection test as a massive testing strategy in outpatients in Córdoba. Two hundred and forty-eight samples from persons (symptomatic n=126, asymptomatic n=122) who voluntarily agreed to the simultaneous collection of samples of NPS, NS and oropharyngeal swab (OPS) for the detection of the rapid antigen PanbioTM COVID-19 Ag Rapid Test (Ag-NS), PanbioTM COVID-19 Ag Rapid Test (Ag-NPS) and real time RT-PCR for RNA detection in OPS (DisCoVery SARS-CoV-2 Nucleic Acid Detection Kit) were included. Fifty samples resulted positive for RNA-SARS-CoV-2 molecular detection, from which 45 and 40 were positive for Ag-NPS and Ag-NS, respectively. Five samples were positive only for Ag-NPS and negative for Ag-NS [symptomatic n=4 and asymptomatic n=1, mean Ct=30.7 (28.3-32.6)]. One sample was false positive for Ag-NPS. Five samples were false negative by both rapid Ag tests [symptomatic n=3, asymptomatic n=2, mean Cts=33.3 (30.8-36.2)]. The Ag-NPS rapid test yielded a sensitivity of 90.0% (95% CI: 80.7-99.3) and the Ag-NS rapid test a sensitivity of 80.0% (95% CI: 67.9 -92.1), kappa index = 0.89. In symptomatic patients, the Ag-NPS test presented a sensitivity of 91.9% (95% CI: 81.8-100.0), while the Ag-NS test had a sensitivity of 81.1% (95% CI: 67.1-95.1), kappa index=0.90. In asymptomatic patients, the sensitivity for the Ag-NPS test was 86.6% (95% CI: 61.2-100.0) and 76.9% (95% CI: 50.2-100.0) for Ag-NS, kappa index=0.82. The results obtained show an adequate sensitivity of the Ag-NPS (90%) and Ag-NS (80%) tests for the detection of SARS-CoV-2 infection. Although the use of NS has lower sensitivity, in accordance with previous studies, the results found indicate that its use would be acceptable, due to its operative capacity as it is less invasive, increasing adherence and the evaluation of a greater number of patients, improving efficient contact management and early isolation.Resumen:&nbsp; Si bien el hisopado nasofaríngeo (HNF) es considerado la muestra óptima para el diagnóstico de la infección por SARS-CoV-2, el hisopado nasal (HN) es usualmente utilizado ya que resulta menos invasivo y de mayor adherencia. El objetivo fue evaluar el rendimiento de la prueba de detección de antígeno nasal como estrategia de testeos masivos en pacientes ambulatorios de Córdoba. Se incluyeron 248 muestras de personas (sintomáticas n=126, asintomáticas n=122) que accedieron voluntariamente a la toma simultánea de muestras de HNF, HN e hisopado orofaríngeo (HOF) para la detección de antígeno rápido PanbioTM COVID-19 Ag Rapid Test (Ag-HN), PanbioTM COVID-19 Ag Rapid Test (Ag-HNF) y qPCR para la detección de RNA en HOF (DisCoVery SARS-CoV-2 Nucleic Acid Detection Kit). Cincuenta muestras resultaron RNA-SARS-CoV-2 positivas, de las cuales 45 y 40 fueron positivas para las pruebas de Ag-HNF y Ag-HN, respectivamente. Cinco muestras resultaron positivas sólo para Ag-HNF y negativas para Ag-HN [sintomáticas n=4 y asintomáticas n=1, Cts promedio=30,7 (28,3-32.6)]. Una muestra resultó falsa positiva para Ag-HNF. Cinco muestras resultaron falsas negativas por ambos test rápidos de Ag [sintomáticas n=3, asintomáticas n=2, Cts promedio=33,3 (30,8-36,2)]. El test rápido de Ag-HNF arrojó una sensibilidad del 90,0% (IC 95%: 80,7-99,3) y el test rápido Ag-HN una sensibilidad del 80,0% (IC 95%: 67,9-92,1), índice kappa=0,89. En pacientes sintomáticos, el test de Ag-HNF presentó una sensibilidad del 91,9% (IC 95%: 81,8-100,0), mientras que el de Ag-HN una sensibilidad del 81,1% (IC 95%: 67,1-95,1), índice kappa=0,90. En pacientes asintomáticos, la sensibilidad para el test de Ag-HNF fue 86,6% (IC 95%: 61,2-100,0) y 76,9% (IC 95%: 50,2-100,0) para Ag-HN, índice kappa=0,82. Los resultados obtenidos muestran una adecuada sensibilidad de los tests Ag-HNF (90%) y Ag-HN (80%) para la detección de la infección por SARS-CoV-2. Si bien el uso de HN posee menor sensibilidad, en concordancia con estudios previos, los resultados hallados indican que su uso sería aceptable, debido a su capacidad operativa por ser menos invasivo, aumentando la adherencia y la evaluación de una mayor cantidad de pacientes, mejorando la eficiencia en el manejo de los contactos y el aislamiento precoz.