1,966 research outputs found

    PHFinder: Assisted detection of point heteroplasmy in Sanger sequencing chromatograms

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    Heteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide position. Visual inspection of chromatograms is both consuming and highly subjective, as heteroplasmy is difficult to differentiate from background noise. Few software solutions are available to automate the detection of point heteroplasmies, and those that are available are typically proprietary, lack customization or are unsuitable for automated heteroplasmy assessment in large datasets. Here, we present PHFinder, a Python-based, open source tool to assist in the detection of point heteroplasmies in large numbers of Sanger chromatograms. PHFinder automatically identifies point heteroplasmies directly from the chromatogram trace data. The program was tested with Sanger sequencing data from 100 humpback whale (Megaptera novaeangliae) tissue samples with known heteroplasmies. PHFinder detected most (90%) of the known heteroplasmies thereby greatly reducing the amount of visual inspection required. PHFinder is flexible, enabling explicit specification of key parameters to infer double peaks (i.e., heteroplasmies)

    Non-native species in the north Gulf of Aqaba (Red Sea) revealed from environmental DNA

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    The movement of organisms facilitated by anthropogenic activities is a serious threat to marine diversity, especially for endemic species that may be outcompeted from non-indigenous species (NIS). In this study, we have analyzed communities inhabiting the north of the Gulf of Aqaba, Red Sea, employing environmental DNA (eDNA) metabarcoding. That gulf is especially rich in species and population endemism. We have detected NIS representing 36% of the total number of species found from eDNA. Primary producers were more abundant in the NIS than in the native fraction of species, suggesting that functional diversity could be altered if NIS thrive there. We discuss maritime traffic as a factor that may enhance the introduction of non-natives in this region and emphasize the importance of the control of these species that may threaten the rich endemic biota of the Red Sea

    The relationship of the atlantic diet with cardiovascular risk factors and markers of arterial stiffness in adults without cardiovascular disease

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    Background: Studying the adherence of the population to the Atlantic Diet (AD) could be simplified by an easy and quickly applied dietary index. The aim of this study is to analyse the relationship of an index measuring compliance with recommendations regarding the Atlantic diet and physical activity with cardiovascular disease risk factors, cardiovascular risk factors, obesity indexes and arterial stiffness markers. Methods: We included 791 individuals from the EVIDENT study (lifestyles and arterial ageing), (52.3 ± 12 years, 61.7% women) without cardiovascular disease. Compliance with recommendations on AD was collected through the responses to a food frequency questionnaire, while physical activity was measured by accelerometer. The number of recommendations being met was estimated using a global scale between 0 and 14 points (a higher score representing greater adherence). Blood pressure, plasma lipid and glucose values and obesity rates were measured. Cardiovascular risk was estimated with the Framingham equation. Results: In the overall sample, 184 individuals (23.3%) scored between 0–3 on the 14-point index we created, 308 (38.9%) between 4 and 5 points, and 299 (37.8%) 6 or more points. The results of multivariate analysis yield a common tendency in which the group with an adherence score of at least 6 points shows lower figures for total cholesterol (p = 0.007) and triglycerides (p = 0.002). Similarly, overall cardiovascular risk in this group is the lowest (p < 0.001), as is pulse wave velocity (p = 0.050) and the mean values of the obesity indexes studied (p < 0.05 in all cases). Conclusion: The rate of compliance with the Atlantic diet and physical activity shows that greater adherence to these recommendations is linked to lower cardiovascular risk, lower total cholesterol and triglycerides, lower rates of obesity and lower pulse wave velocity values

    The relationship of the atlantic diet with cardiovascular risk factors and markers of arterial stiffness in adults without cardiovascular disease

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    [EN]Abstract: Background: Studying the adherence of the population to the Atlantic Diet (AD) could be simplified by an easy and quickly applied dietary index. The aim of this study is to analyse the relationship of an index measuring compliance with recommendations regarding the Atlantic diet and physical activity with cardiovascular disease risk factors, cardiovascular risk factors, obesity indexes and arterial stiffness markers. Methods: We included 791 individuals from the EVIDENT study (lifestyles and arterial ageing), (52.3 ± 12 years, 61.7% women) without cardiovascular disease. Compliance with recommendations on AD was collected through the responses to a food frequency questionnaire, while physical activity was measured by accelerometer. The number of recommendations being met was estimated using a global scale between 0 and 14 points (a higher score representing greater adherence). Blood pressure, plasma lipid and glucose values and obesity rates were measured. Cardiovascular risk was estimated with the Framingham equation. Results: In the overall sample, 184 individuals (23.3%) scored between 0–3 on the 14-point index we created, 308 (38.9%) between 4 and 5 points, and 299 (37.8%) 6 or more points. The results of multivariate analysis yield a common tendency in which the group with an adherence score of at least 6 points shows lower figures for total cholesterol (p = 0.007) and triglycerides (p = 0.002). Similarly, overall cardiovascular risk in this group is the lowest (p < 0.001), as is pulse wave velocity (p = 0.050) and the mean values of the obesity indexes studied (p < 0.05 in all cases). Conclusion: The rate of compliance with the Atlantic diet and physical activity shows that greater adherence to these recommendations is linked to lower cardiovascular risk, lower total cholesterol and triglycerides, lower rates of obesity and lower pulse wave velocity values.This study was funded by the Spanish Ministry of Science and Innovation (MICINN) and the Carlos III Health Institute/European Regional Development Fund (ERDF) (FIS: PI13/00618, PI13/01526, PI13/00058, PI13/01635, PI13/02528, PI12/01474; RETICS: RD12/0005, RD16/0007), the Regional Health Administration of Castilla and León (GRS 1191/B/15, GRS 909/B/14, GRS 770/B/13) and the Infosalud Foundation. None of the funders were involved in the design, implementation, analysis or interpretation of the data

    Search for supersymmetry in events with b-quark jets and missing transverse energy in pp collisions at 7 TeV

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    Results are presented from a search for physics beyond the standard model based on events with large missing transverse energy, at least three jets, and at least one, two, or three b-quark jets. The study is performed using a sample of proton-proton collision data collected at sqrt(s) = 7 TeV with the CMS detector at the LHC in 2011. The integrated luminosity of the sample is 4.98 inverse femtobarns. The observed number of events is found to be consistent with the standard model expectation, which is evaluated using control samples in the data. The results are used to constrain cross sections for the production of supersymmetric particles decaying to b-quark-enriched final states in the context of simplified model spectra.Comment: Submitted to Physical Review

    Differential cross section measurements for the production of a W boson in association with jets in proton–proton collisions at √s = 7 TeV

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    Measurements are reported of differential cross sections for the production of a W boson, which decays into a muon and a neutrino, in association with jets, as a function of several variables, including the transverse momenta (pT) and pseudorapidities of the four leading jets, the scalar sum of jet transverse momenta (HT), and the difference in azimuthal angle between the directions of each jet and the muon. The data sample of pp collisions at a centre-of-mass energy of 7 TeV was collected with the CMS detector at the LHC and corresponds to an integrated luminosity of 5.0 fb[superscript −1]. The measured cross sections are compared to predictions from Monte Carlo generators, MadGraph + pythia and sherpa, and to next-to-leading-order calculations from BlackHat + sherpa. The differential cross sections are found to be in agreement with the predictions, apart from the pT distributions of the leading jets at high pT values, the distributions of the HT at high-HT and low jet multiplicity, and the distribution of the difference in azimuthal angle between the leading jet and the muon at low values.United States. Dept. of EnergyNational Science Foundation (U.S.)Alfred P. Sloan Foundatio

    Penilaian Kinerja Keuangan Koperasi di Kabupaten Pelalawan

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    This paper describe development and financial performance of cooperative in District Pelalawan among 2007 - 2008. Studies on primary and secondary cooperative in 12 sub-districts. Method in this stady use performance measuring of productivity, efficiency, growth, liquidity, and solvability of cooperative. Productivity of cooperative in Pelalawan was highly but efficiency still low. Profit and income were highly, even liquidity of cooperative very high, and solvability was good

    Juxtaposing BTE and ATE – on the role of the European insurance industry in funding civil litigation

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    One of the ways in which legal services are financed, and indeed shaped, is through private insurance arrangement. Two contrasting types of legal expenses insurance contracts (LEI) seem to dominate in Europe: before the event (BTE) and after the event (ATE) legal expenses insurance. Notwithstanding institutional differences between different legal systems, BTE and ATE insurance arrangements may be instrumental if government policy is geared towards strengthening a market-oriented system of financing access to justice for individuals and business. At the same time, emphasizing the role of a private industry as a keeper of the gates to justice raises issues of accountability and transparency, not readily reconcilable with demands of competition. Moreover, multiple actors (clients, lawyers, courts, insurers) are involved, causing behavioural dynamics which are not easily predicted or influenced. Against this background, this paper looks into BTE and ATE arrangements by analysing the particularities of BTE and ATE arrangements currently available in some European jurisdictions and by painting a picture of their respective markets and legal contexts. This allows for some reflection on the performance of BTE and ATE providers as both financiers and keepers. Two issues emerge from the analysis that are worthy of some further reflection. Firstly, there is the problematic long-term sustainability of some ATE products. Secondly, the challenges faced by policymakers that would like to nudge consumers into voluntarily taking out BTE LEI

    Search for stop and higgsino production using diphoton Higgs boson decays

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    Results are presented of a search for a "natural" supersymmetry scenario with gauge mediated symmetry breaking. It is assumed that only the supersymmetric partners of the top-quark (stop) and the Higgs boson (higgsino) are accessible. Events are examined in which there are two photons forming a Higgs boson candidate, and at least two b-quark jets. In 19.7 inverse femtobarns of proton-proton collision data at sqrt(s) = 8 TeV, recorded in the CMS experiment, no evidence of a signal is found and lower limits at the 95% confidence level are set, excluding the stop mass below 360 to 410 GeV, depending on the higgsino mass

    Impacts of the Tropical Pacific/Indian Oceans on the Seasonal Cycle of the West African Monsoon

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    The current consensus is that drought has developed in the Sahel during the second half of the twentieth century as a result of remote effects of oceanic anomalies amplified by local land–atmosphere interactions. This paper focuses on the impacts of oceanic anomalies upon West African climate and specifically aims to identify those from SST anomalies in the Pacific/Indian Oceans during spring and summer seasons, when they were significant. Idealized sensitivity experiments are performed with four atmospheric general circulation models (AGCMs). The prescribed SST patterns used in the AGCMs are based on the leading mode of covariability between SST anomalies over the Pacific/Indian Oceans and summer rainfall over West Africa. The results show that such oceanic anomalies in the Pacific/Indian Ocean lead to a northward shift of an anomalous dry belt from the Gulf of Guinea to the Sahel as the season advances. In the Sahel, the magnitude of rainfall anomalies is comparable to that obtained by other authors using SST anomalies confined to the proximity of the Atlantic Ocean. The mechanism connecting the Pacific/Indian SST anomalies with West African rainfall has a strong seasonal cycle. In spring (May and June), anomalous subsidence develops over both the Maritime Continent and the equatorial Atlantic in response to the enhanced equatorial heating. Precipitation increases over continental West Africa in association with stronger zonal convergence of moisture. In addition, precipitation decreases over the Gulf of Guinea. During the monsoon peak (July and August), the SST anomalies move westward over the equatorial Pacific and the two regions where subsidence occurred earlier in the seasons merge over West Africa. The monsoon weakens and rainfall decreases over the Sahel, especially in August.Peer reviewe
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