Phytosterols: From Preclinical Evidence to Potential Clinical Applications

Phytosterols (PSs) are plant-originated steroids. Over 250 PSs have been isolated, and each plant species contains a characteristic phytosterol composition. A wide number of studies have reported remarkable pharmacological effects of PSs, acting as chemopreventive, anti-inflammatory, antioxidant, antidiabetic, and antiatherosclerotic agents. However, PS bioavailability is a key issue, as it can be influenced by several factors (type, source, processing, preparation, delivery method, food matrix, dose, time of administration into the body, and genetic factors), and the existence of a close relationship between their chemical structures (e.g., saturation degree and side-chain length) and low absorption rates has been stated. In this sense, the present review intends to provide in-depth data on PS therapeutic potential for human health, also emphasizing their preclinical effects and bioavailability-related issues.NCM acknowledges the Portuguese Foundation for Science and Technology under the Horizon 2020 Program (PTDC/PSI-GER/ 28076/2017)

Ten Simple Rules for Taking Advantage of Git and GitHub.

Bioinformatics is a broad discipline in which one common denominator is the need to produce and/or use software that can be applied to biological data in different contexts. To enable and ensure the replicability and traceability of scientific claims, it is essential that the scientific publication, the corresponding datasets, and the data analysis are made publicly available [1,2]. All software used for the analysis should be either carefully documented (e.g., for commercial software) or, better yet, openly shared and directly accessible to others [3,4]. The rise of openly available software and source code alongside concomitant collaborative development is facilitated by the existence of several code repository services such as SourceForge, Bitbucket, GitLab, and GitHub, among others. These resources are also essential for collaborative software projects because they enable the organization and sharing of programming tasks between different remote contributors. Here, we introduce the main features of GitHub, a popular web-based platform that offers a free and integrated environment for hosting the source code, documentation, and project-related web content for open-source projects. GitHub also offers paid plans for private repositories (see Box 1) for individuals and businesses as well as free plans including private repositories for research and educational use.Biotechnology and Biological Sciences Research CouncilThis is the final version of the article. It first appeared from Public Library of Science via https://doi.org/10.1371/journal.pcbi.1004947

PCA-based population structure inference with generic clustering algorithms

<p>Abstract</p> <p>Background</p> <p>Handling genotype data typed at hundreds of thousands of loci is very time-consuming and it is no exception for population structure inference. Therefore, we propose to apply PCA to the genotype data of a population, select the significant principal components using the Tracy-Widom distribution, and assign the individuals to one or more subpopulations using generic clustering algorithms.</p> <p>Results</p> <p>We investigated K-means, soft K-means and spectral clustering and made comparison to STRUCTURE, a model-based algorithm specifically designed for population structure inference. Moreover, we investigated methods for predicting the number of subpopulations in a population. The results on four simulated datasets and two real datasets indicate that our approach performs comparably well to STRUCTURE. For the simulated datasets, STRUCTURE and soft K-means with BIC produced identical predictions on the number of subpopulations. We also showed that, for real dataset, BIC is a better index than likelihood in predicting the number of subpopulations.</p> <p>Conclusion</p> <p>Our approach has the advantage of being fast and scalable, while STRUCTURE is very time-consuming because of the nature of MCMC in parameter estimation. Therefore, we suggest choosing the proper algorithm based on the application of population structure inference.</p

Genetic diversity and population structure of Glossina pallidipes in Uganda and western Kenya

<p>Abstract</p> <p>Background</p> <p><it>Glossina pallidipes </it>has been implicated in the spread of sleeping sickness from southeastern Uganda into Kenya. Recent studies indicated resurgence of <it>G. pallidipes </it>in Lambwe Valley and southeastern Uganda after what were deemed to be effective control efforts. It is unknown whether the <it>G. pallidipes </it>belt in southeastern Uganda extends into western Kenya. We investigated the genetic diversity and population structure of <it>G. pallidipes </it>in Uganda and western Kenya.</p> <p>Results</p> <p>AMOVA indicated that differences among sampling sites explained a significant proportion of the genetic variation. Principal component analysis and Bayesian assignment of microsatellite genotypes identified three distinct clusters: western Uganda, southeastern Uganda/Lambwe Valley, and Nguruman in central-southern Kenya. Analyses of mtDNA confirmed the results of microsatellite analysis, except in western Uganda, where Kabunkanga and Murchison Falls populations exhibited haplotypes that differed despite homogeneous microsatellite signatures. To better understand possible causes of the contrast between mitochondrial and nuclear markers we tested for sex-biased dispersal. Mean pairwise relatedness was significantly higher in females than in males within populations, while mean genetic distance was lower and relatedness higher in males than females in between-population comparisons. Two populations sampled on the Kenya/Uganda border, exhibited the lowest levels of genetic diversity. Microsatellite alleles and mtDNA haplotypes in these two populations were a subset of those found in neighboring Lambwe Valley, suggesting that Lambwe was the source population for flies in southeastern Uganda. The relatively high genetic diversity of <it>G. pallidipes </it>in Lambwe Valley suggest large relict populations remained even after repeated control efforts.</p> <p>Conclusion</p> <p>Our research demonstrated that <it>G. pallidipes </it>populations in Kenya and Uganda do not form a contiguous tsetse belt. While Lambwe Valley appears to be a source population for flies colonizing southeastern Uganda, this dispersal does not extend to western Uganda. The complicated phylogeography of <it>G. pallidipes </it>warrants further efforts to distinguish the role of historical and modern gene flow and possible sex-biased dispersal in structuring populations.</p

Paternity of Subordinates Raises Cooperative Effort in Cichlids

Background In cooperative breeders, subordinates generally help a dominant breeding pair to raise offspring. Parentage studies have shown that in several species subordinates can participate in reproduction. This suggests an important role of direct fitness benefits for cooperation, particularly where groups contain unrelated subordinates. In this situation parentage should influence levels of cooperation. Here we combine parentage analyses and detailed behavioural observations in the field to study whether in the highly social cichlid Neolamprologus pulcher subordinates participate in reproduction and if so, whether and how this affects their cooperative care, controlling for the effect of kinship. Methodology/Principal Findings We show that: (i) male subordinates gained paternity in 27.8% of all clutches and (ii) if they participated in reproduction, they sired on average 11.8% of young. Subordinate males sharing in reproduction showed more defence against experimentally presented egg predators compared to subordinates not participating in reproduction, and they tended to stay closer to the breeding shelter. No effects of relatedness between subordinates and dominants (to mid-parent, dominant female or dominant male) were detected on parentage and on helping behaviour. Conclusions/Significance This is the first evidence in a cooperatively breeding fish species that the helping effort of male subordinates may depend on obtained paternity, which stresses the need to consider direct fitness benefits in evolutionary studies of helping behaviour

Measurement of the polarisation of W bosons produced with large transverse momentum in pp collisions at sqrt(s) = 7 TeV with the ATLAS experiment

This paper describes an analysis of the angular distribution of W->enu and W->munu decays, using data from pp collisions at sqrt(s) = 7 TeV recorded with the ATLAS detector at the LHC in 2010, corresponding to an integrated luminosity of about 35 pb^-1. Using the decay lepton transverse momentum and the missing transverse energy, the W decay angular distribution projected onto the transverse plane is obtained and analysed in terms of helicity fractions f0, fL and fR over two ranges of W transverse momentum (ptw): 35 < ptw < 50 GeV and ptw > 50 GeV. Good agreement is found with theoretical predictions. For ptw > 50 GeV, the values of f0 and fL-fR, averaged over charge and lepton flavour, are measured to be : f0 = 0.127 +/- 0.030 +/- 0.108 and fL-fR = 0.252 +/- 0.017 +/- 0.030, where the first uncertainties are statistical, and the second include all systematic effects.Comment: 19 pages plus author list (34 pages total), 9 figures, 11 tables, revised author list, matches European Journal of Physics C versio

Observation of a new chi_b state in radiative transitions to Upsilon(1S) and Upsilon(2S) at ATLAS

The chi_b(nP) quarkonium states are produced in proton-proton collisions at the Large Hadron Collider (LHC) at sqrt(s) = 7 TeV and recorded by the ATLAS detector. Using a data sample corresponding to an integrated luminosity of 4.4 fb^-1, these states are reconstructed through their radiative decays to Upsilon(1S,2S) with Upsilon->mu+mu-. In addition to the mass peaks corresponding to the decay modes chi_b(1P,2P)->Upsilon(1S)gamma, a new structure centered at a mass of 10.530+/-0.005 (stat.)+/-0.009 (syst.) GeV is also observed, in both the Upsilon(1S)gamma and Upsilon(2S)gamma decay modes. This is interpreted as the chi_b(3P) system.Comment: 5 pages plus author list (18 pages total), 2 figures, 1 table, corrected author list, matches final version in Physical Review Letter

Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS

We present the results of a search for new, heavy particles that decay at a significant distance from their production point into a final state containing charged hadrons in association with a high-momentum muon. The search is conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS detector operating at the Large Hadron Collider. Production of such particles is expected in various scenarios of physics beyond the standard model. We observe no signal and place limits on the production cross-section of supersymmetric particles in an R-parity-violating scenario as a function of the neutralino lifetime. Limits are presented for different squark and neutralino masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final version to appear in Physics Letters

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011