Finding all maximal perfect haplotype blocks in linear time

Recent large-scale community sequencing efforts allow at an unprecedented level of detail the identification of genomic regions that show signatures of natural selection. Traditional methods for identifying such regions from individuals' haplotype data, however, require excessive computing times and therefore are not applicable to current datasets. In 2019, Cunha et al. (Advances in bioinformatics and computational biology: 11th Brazilian symposium on bioinformatics, BSB 2018, Niteroi, Brazil, October 30 - November 1, 2018, Proceedings, 2018. 10.1007/978-3-030-01722-4_3) suggested the maximal perfect haplotype block as a very simple combinatorial pattern, forming the basis of a new method to perform rapid genome-wide selection scans. The algorithm they presented for identifying these blocks, however, had a worst-case running time quadratic in the genome length. It was posed as an open problem whether an optimal, linear-time algorithm exists. In this paper we give two algorithms that achieve this time bound, one conceptually very simple one using suffix trees and a second one using the positional Burrows-Wheeler Transform, that is very efficient also in practice.Peer reviewe

Revealed Price Preference: Theory and Stochastic Testing

We develop a model of demand where consumers trade-off the utility of consumption against the disutility of expenditure. This model is appropriate whenever a consumer’s demand over a strict subset of all available goods is being analyzed. Data sets consistent with this model are characterized by the absence of revealed preference cycles over prices. The model is readily generalized to the random utility setting, for which we develop nonparametric statistical tests. Our application on national household consumption data provides support for the model

The xenotropic murine leukemia virus-related retrovirus debate continues at first international workshop

The 1st International Workshop on Xenotropic Murine Leukemia Virus-Related Retrovirus (XMRV), co-sponsored by the National Institutes of Health, The Department of Health and Human Services and Abbott Diagnostics, was convened on September 7/8, 2010 on the NIH campus, Bethesda, MD. Attracting an international audience of over 200 participants, the 2-day event combined a series of plenary talks with updates on different aspects of XMRV research, addressing basic gammaretrovirus biology, host response, association of XMRV with chronic fatigue syndrome and prostate cancer, assay development and epidemiology. The current status of XMRV research, concerns among the scientific community and suggestions for future actions are summarized in this meeting report

Cleaning of soft-solid soil layers on vertical and horizontal surfaces by stationary coherent impinging liquid jets

The cleaning action of stationary coherent liquid jets impinging (a) vertically downwards on horizontal plates, and (b) horizontally on vertical plates, was investigated using three soft-solid model soil layers: (i) PVA glue on glass and polymethylmethacrylate (Perspex) substrates; (ii) Xanthan gum on stainless steel; and (iii) petroleum jelly on glass. The liquid stream nozzle sizes, mass and volumetric flow rates and mean jet velocities investigated were: PVA, 2 mm, 17-50 g s^-1 (0.06-0.139 m^3 h^-1), 5.3-15.9 m s^-1; Xanthan gum, 0.39-3.3 mm, 2.1-148 g s^-1 (0.008-0.53 m^3 h^-1); 4.5-31.7 m s^-1; petroleum jelly, 2 mm, 7.8-50 g s^-1 (0.06-0.139 m^3 h^-1); 2.5-15.9 m s^-1. For all three soils, rapid initial removal of soil from the jet footprint was followed by the growth of a nearly circular, clean region centred at the point of jet impingement. The rate of removal of soil decreased sharply when the cleaning front reached the hydraulic or film jump. The data for the radial growth removal stage were compared with a mathematical model describing removal of the adhesive soil layer, where the force on the cleaning front was evaluated using the result reported by Wilson et al. (2011): their theory gave the momentum of the liquid film; this momentum was balanced against the soil strength, giving a simple relation between the cleaned radius and time. All three soils showed reasonable agreement with the model, across the range of flow rates and temperatures studied. The kinetic constant in the model was sensitive to soil layer thickness and the nature of the soil. Cleaning tests on the petroleum jelly soils at different temperatures, and separate rheological measurements, showed that the kinetic time constant for coating removal was proportional to the (critical shear stress)^-1.8. There was good agreement between results obtained with vertical and horizontal plates for the PVA and Xanthan gum soil layers. The petroleum jelly results differed, which is partly attributed to differences in preparing the layers of this rheologically complex material.This is the author's accepted manuscript and is under embargo until 3/2/16. The final published version can be found in Chemical Engineering Science here: http://www.sciencedirect.com/science/article/pii/S000925091400044X

Louse (Insecta : Phthiraptera) mitochondrial 12S rRNA secondary structure is highly variable

Lice are ectoparasitic insects hosted by birds and mammals. Mitochondrial 12S rRNA sequences obtained from lice show considerable length variation and are very difficult to align. We show that the louse 12S rRNA domain III secondary structure displays considerable variation compared to other insects, in both the shape and number of stems and loops. Phylogenetic trees constructed from tree edit distances between louse 12S rRNA structures do not closely resemble trees constructed from sequence data, suggesting that at least some of this structural variation has arisen independently in different louse lineages. Taken together with previous work on mitochondrial gene order and elevated rates of substitution in louse mitochondrial sequences, the structural variation in louse 12S rRNA confirms the highly distinctive nature of molecular evolution in these insects

GUIDANCE: a web server for assessing alignment confidence scores

Evaluating the accuracy of multiple sequence alignment (MSA) is critical for virtually every comparative sequence analysis that uses an MSA as input. Here we present the GUIDANCE web-server, a user-friendly, open access tool for the identification of unreliable alignment regions. The web-server accepts as input a set of unaligned sequences. The server aligns the sequences and provides a simple graphic visualization of the confidence score of each column, residue and sequence of an alignment, using a color-coding scheme. The method is generic and the user is allowed to choose the alignment algorithm (ClustalW, MAFFT and PRANK are supported) as well as any type of molecular sequences (nucleotide, protein or codon sequences). The server implements two different algorithms for evaluating confidence scores: (i) the heads-or-tails (HoT) method, which measures alignment uncertainty due to co-optimal solutions; (ii) the GUIDANCE method, which measures the robustness of the alignment to guide-tree uncertainty. The server projects the confidence scores onto the MSA and points to columns and sequences that are unreliably aligned. These can be automatically removed in preparation for downstream analyses. GUIDANCE is freely available for use at http://guidance.tau.ac.il

The extraordinary evolutionary history of the reticuloendotheliosis viruses

The reticuloendotheliosis viruses (REVs) comprise several closely related amphotropic retroviruses isolated from birds. These viruses exhibit several highly unusual characteristics that have not so far been adequately explained, including their extremely close relationship to mammalian retroviruses, and their presence as endogenous sequences within the genomes of certain large DNA viruses. We present evidence for an iatrogenic origin of REVs that accounts for these phenomena. Firstly, we identify endogenous retroviral fossils in mammalian genomes that share a unique recombinant structure with REVs—unequivocally demonstrating that REVs derive directly from mammalian retroviruses. Secondly, through sequencing of archived REV isolates, we confirm that contaminated Plasmodium lophurae stocks have been the source of multiple REV outbreaks in experimentally infected birds. Finally, we show that both phylogenetic and historical evidence support a scenario wherein REVs originated as mammalian retroviruses that were accidentally introduced into avian hosts in the late 1930s, during experimental studies of P. lophurae, and subsequently integrated into the fowlpox virus (FWPV) and gallid herpesvirus type 2 (GHV-2) genomes, generating recombinant DNA viruses that now circulate in wild birds and poultry. Our findings provide a novel perspective on the origin and evolution of REV, and indicate that horizontal gene transfer between virus families can expand the impact of iatrogenic transmission events

Search for the standard model Higgs boson in the H to ZZ to 2l 2nu channel in pp collisions at sqrt(s) = 7 TeV

A search for the standard model Higgs boson in the H to ZZ to 2l 2nu decay channel, where l = e or mu, in pp collisions at a center-of-mass energy of 7 TeV is presented. The data were collected at the LHC, with the CMS detector, and correspond to an integrated luminosity of 4.6 inverse femtobarns. No significant excess is observed above the background expectation, and upper limits are set on the Higgs boson production cross section. The presence of the standard model Higgs boson with a mass in the 270-440 GeV range is excluded at 95% confidence level.Comment: Submitted to JHE