VESPA: Very large-scale Evolutionary and Selective Pressure Analyses

Background: Large-scale molecular evolutionary analyses of protein coding sequences requires a number of preparatory inter-related steps from finding gene families, to generating alignments and phylogenetic trees and assessing selective pressure variation. Each phase of these analyses can represent significant challenges, particularly when working with entire proteomes (all protein coding sequences in a genome) from a large number of species. Methods: We present VESPA, software capable of automating a selective pressure analysis using codeML in addition to the preparatory analyses and summary statistics. VESPA is written in python and Perl and is designed to run within a UNIX environment. Results: We have benchmarked VESPA and our results show that the method is consistent, performs well on both large scale and smaller scale datasets, and produces results in line with previously published datasets. Discussion: Large-scale gene family identification, sequence alignment, and phylogeny reconstruction are all important aspects of large-scale molecular evolutionary analyses. VESPA provides flexible software for simplifying these processes along with downstream selective pressure variation analyses. The software automatically interprets results from codeML and produces simplified summary files to assist the user in better understanding the results

Frequency of cannabis and illicit opioid use among people who use drugs and report chronic pain: A longitudinal analysis.

BACKGROUND:Ecological research suggests that increased access to cannabis may facilitate reductions in opioid use and harms, and medical cannabis patients describe the substitution of opioids with cannabis for pain management. However, there is a lack of research using individual-level data to explore this question. We aimed to investigate the longitudinal association between frequency of cannabis use and illicit opioid use among people who use drugs (PWUD) experiencing chronic pain. METHODS AND FINDINGS:This study included data from people in 2 prospective cohorts of PWUD in Vancouver, Canada, who reported major or persistent pain from June 1, 2014, to December 1, 2017 (n = 1,152). We used descriptive statistics to examine reasons for cannabis use and a multivariable generalized linear mixed-effects model to estimate the relationship between daily (once or more per day) cannabis use and daily illicit opioid use. There were 424 (36.8%) women in the study, and the median age at baseline was 49.3 years (IQR 42.3-54.9). In total, 455 (40%) reported daily illicit opioid use, and 410 (36%) reported daily cannabis use during at least one 6-month follow-up period. The most commonly reported therapeutic reasons for cannabis use were pain (36%), sleep (35%), stress (31%), and nausea (30%). After adjusting for demographic characteristics, substance use, and health-related factors, daily cannabis use was associated with significantly lower odds of daily illicit opioid use (adjusted odds ratio 0.50, 95% CI 0.34-0.74, p < 0.001). Limitations of the study included self-reported measures of substance use and chronic pain, and a lack of data for cannabis preparations, dosages, and modes of administration. CONCLUSIONS:We observed an independent negative association between frequent cannabis use and frequent illicit opioid use among PWUD with chronic pain. These findings provide longitudinal observational evidence that cannabis may serve as an adjunct to or substitute for illicit opioid use among PWUD with chronic pain

Post-exercise Hot Water Immersion Elicits Heat Acclimation Adaptations That Are Retained for at Least Two Weeks

Heat acclimation by post-exercise hot water immersion (HWI) on six consecutive days reduces thermal strain and improves exercise performance during heat stress. However, the retention of adaptations by this method remains unknown. Typically, adaptations to short-term, exercise-heat-acclimation ( 0.05). As such, the reduction in thermal strain during exercise-heat stress appears likely due to the reduction in resting T re evident at POST, WK 1, and WK 2. In summary, 6 days of post-exercise HWI is an effective, practical and accessible heat acclimation strategy that induces adaptations, which are retained for at least 2 weeks. Therefore, post-exercise HWI can be completed during an athlete's pre-taper phase and does not suffer from the same practical limitations as short-term, exercise-heat-acclimation

The Planetary Nebula NGC 3918

A detailed study of the planetary nebula NGC 3918, based on UV, optical, and radio observations, is presented. The central star has a predicted V magnitude of 14.6 and a luminosity of 6000 solar luminosities for a distance of 1.5 kpc. A contour map of the nebula in H-beta light is given. Velocity profiles of forbidden O II optical lines show that O(+) ions are mostly located at the front and rear of the nebula. A composite, biconical model is constructed which consists of optically thick cones at the front and rear with a low-density 'equatorial' region. The nebular expansion age of about 3000 yr is in reasonable agreement with the age of the nucleus found from evolutionary tracks. Silicon, magnesium, and iron are depleted by factors of 4, 3, and 100 respectively. It is shown that the Mg II 2800 A lines are affected by interstellar absorption in this and many other planetaries and thus often cannot be used for abundance determinations

A solar powered handheld plasma source for microbial decontamination applications

A fully portable atmospheric pressure air plasma system is reported to be suitable for the microbial decontamination of both surfaces and liquids. The device operates in quiescent air, and includes an integrated battery which is charged from a solar cell and weighs less than 750 g, making it highly amenable for a wide variety of applications beyond the laboratory. Using particle imaging velocimetry to visualise air flows around the device, the geometric configuration of the plasma generating electrodes was enhanced to induce a gas flow on the order of 0.5 m s-1 directed towards a sample placed downstream, thus improving the transport of plasma generated reactive species to the sample. The microbial decontamination efficiency of the system was assessed using potable water samples inoculated with common waterborne organisms Escherichia coli and Pseudomonas fluorescens. The reduction in the number of microorganisms was found to be in the range of 2-8 log and was strongly dependent on the plasma generation conditions

Some solutions to the multivariate Behrens-Fisher problem for dissimilarity-based analyses

The essence of the generalised multivariate Behrens–Fisher problem (BFP) is how to test the null hypothesis of equality of mean vectors for two or more populations when their dispersion matrices differ. Solutions to the BFP usually assume variables are multivariate normal and do not handle high‐dimensional data. In ecology, species' count data are often high‐dimensional, non‐normal and heterogeneous. Also, interest lies in analysing compositional dissimilarities among whole communities in non‐Euclidean (semi‐metric or non‐metric) multivariate space. Hence, dissimilarity‐based tests by permutation (e.g., PERMANOVA, ANOSIM) are used to detect differences among groups of multivariate samples. Such tests are not robust, however, to heterogeneity of dispersions in the space of the chosen dissimilarity measure, most conspicuously for unbalanced designs. Here, we propose a modification to the PERMANOVA test statistic, coupled with either permutation or bootstrap resampling methods, as a solution to the BFP for dissimilarity‐based tests. Empirical simulations demonstrate that the type I error remains close to nominal significance levels under classical scenarios known to cause problems for the un‐modified test. Furthermore, the permutation approach is found to be more powerful than the (more conservative) bootstrap for detecting changes in community structure for real ecological datasets. The utility of the approach is shown through analysis of 809 species of benthic soft‐sediment invertebrates from 101 sites in five areas spanning 1960 km along the Norwegian continental shelf, based on the Jaccard dissimilarity measure

Adaptive Evolution as a Predictor of Species-Specific Innate Immune Response

It has been proposed that positive selection may be associated with protein functional change. For example, human and macaque have different outcomes to HIV infection and it has been shown that residues under positive selection in the macaque TRIM5α receptor locate to the region known to influence species-specific response to HIV. In general, however, the relationship between sequence and function has proven difficult to fully elucidate, and it is the role of large-scale studies to help bridge this gap in our understanding by revealing major patterns in the data that correlate genotype with function or phenotype. In this study, we investigate the level of species-specific positive selection in innate immune genes from human and mouse. In total, we analyzed 456 innate immune genes using codon-based models of evolution, comparing human, mouse, and 19 other vertebrate species to identify putative species-specific positive selection. Then we used population genomic data from the recently completed Neanderthal genome project, the 1000 human genomes project, and the 17 laboratory mouse genomes project to determine whether the residues that were putatively positively selected are fixed or variable in these populations. We find evidence of species-specific positive selection on both the human and the mouse branches and we show that the classes of genes under positive selection cluster by function and by interaction. Data from this study provide us with targets to test the relationship between positive selection and protein function and ultimately to test the relationship between positive selection and discordant phenotypes

Preliminary estimation of fat depth in the lamb short loin using a hyperspectral camera

© 2018 CSIRO. The objectives of the present study were to describe the approach used for classifying surface tissue, and for estimating fat depth in lamb short loins and validating the approach. Fat versus non-fat pixels were classified and then used to estimate the fat depth for each pixel in the hyperspectral image. Estimated reflectance, instead of image intensity or radiance, was used as the input feature for classification. The relationship between reflectance and the fat/non-fat classification label was learnt using support vector machines. Gaussian processes were used to learn regression for fat depth as a function of reflectance. Data to train and test the machine learning algorithms was collected by scanning 16 short loins. The near-infrared hyperspectral camera captured lines of data of the side of the short loin (i.e. with the subcutaneous fat facing the camera). Advanced single-lens reflex camera took photos of the same cuts from above, such that a ground truth of fat depth could be semi-automatically extracted and associated with the hyperspectral data. A subset of the data was used to train the machine learning model, and to test it. The results of classifying pixels as either fat or non-fat achieved a 96% accuracy. Fat depths of up to 12 mm were estimated, with an R 2 of 0.59, a mean absolute bias of 1.72 mm and root mean square error of 2.34 mm. The techniques developed and validated in the present study will be used to estimate fat coverage to predict total fat, and, subsequently, lean meat yield in the carcass

Impact and cost-effectiveness of hepatitis B virus prophylaxis in pregnancy: a dynamic simulation modelling study

BACKGROUND: In 2020, WHO recommended the addition of peripartum antiviral prophylaxis (PAP) to hepatitis B birth dose vaccination (HepB-BD) and hepatitis B infant vaccination (HepB3) to reduce mother-to-child transmission of hepatitis B virus (HBV) infection in pregnant women who have a marker of high infectivity (ie, HBV DNA ≥200 000 international units per mL or HBeAg-positive). We aimed to evaluate the impact and cost-effectiveness of this recommendation and of a theoretical simplified strategy whereby PAP is given to all pregnant women who are HBsAg-positive without risk stratification. METHODS: This modelling study used a dynamic simulation model of the HBV epidemic in 110 countries in all WHO regions, structured by age, sex, and country. We assessed three strategies of scaling up PAP for pregnant women: PAP for those with high viral load (PAP-VL); PAP for those who are HBeAg-positive (PAP-HBeAg); and PAP for all pregnant women who are HBsAg-positive (PAP-universal), in comparison with neonatal vaccination alone (HepB-BD). We investigated how different diagnostic and antiviral drug costs affected the cost-effectiveness of the strategies evaluated. Using a health-care provider perspective, we calculated incremental cost-effectiveness ratios in cost (US$) per disability-adjusted life-year (DALY) averted in each country's population and compared these with country-specific cost-effectiveness thresholds. We also calculated new neonatal infections averted for each of the strategies. FINDINGS: Adding PAP-VL to HepB-BD could avert around 1·1 million (95% uncertainty interval 1·0 million-1·2 million) new neonatal infections by 2030 and around 3·2 million (95% uncertainty interval 3·0 million-3·4 million) new neonatal infections and approximately 8·8 million (7·8 million-9·7 million) DALYs by 2100 across all the countries modelled. This strategy would probably be cost-effective up to 2100 in 28 (26%) of 106 countries analysed (which included some of the countries that have the greatest HBV burden) if costs are as currently expected to be, and in 74 (70%) countries if diagnostic and monitoring costs were lowered (by about 60-75%). The relative cost-effectiveness of PAP-VL and PAP-HBeAg was finely balanced and depended on the respective diagnostic and monitoring costs. The PAP-universal strategy could be more cost-effective than either of these strategies in most countries, but the use of antiviral treatment could be five times as high than with PAP-VL. INTERPRETATION: PAP can provide substantial health benefits, and, although the current approach might already be cost-effective in some high-burden settings, decreased diagnostic costs would probably be needed for PAP to be cost-effective in most countries. Therefore, careful consideration needs to be given about how such a strategy is implemented, and securing reduced costs for diagnostics should be a priority. The theoretical strategy of offering PAP to all women who are HBsAg-positive (eg, if diagnostic tests to identify mothers at risk of transmission are not available) could be a cost-effective alternative, depending on prevailing costs of diagnostics and antiviral therapy. FUNDING: UK Medical Research Council, UK National Institute for Health and Care Research, and the Vaccine Impact Modelling Consortium