Haplotyping via minimum recombinant paradigm

<p>Abstract</p> <p>Background</p> <p>Haplotypes can increase the power of gene detection over genotypes and are essential to estimate linkage disequilibrium.</p> <p>Methods</p> <p>Haplotyping was based on the minimum recombinant paradigm, whereby a phase is obtained only if it uniquely minimises the number of recombinants within a full sib family. Performance of this method was tested across three different data sets, consisting of genotypes and pedigree.</p> <p>Results</p> <p>The percentage of phased alleles ranged from ~80% to ~95%, and the percentage of correct phases reached ~99% in all cases. A measure of uncertainty was obtained via simulations. A partial haplotyping algorithm consisting of four deterministic rules was almost as effective as a full one consisting of six deterministic rules, and took up to 5 times less time to compute.</p> <p>Conclusion</p> <p>Haplotyping via the minimum recombinant paradigm is consistently reliable and computationally efficient. A single simulation is enough to produce a population-wide uncertainty estimate associated with a set of all reconstructed haplotypes.</p

Comparative Evaluation of Action Recognition Methods via Riemannian Manifolds, Fisher Vectors and GMMs: Ideal and Challenging Conditions

We present a comparative evaluation of various techniques for action recognition while keeping as many variables as possible controlled. We employ two categories of Riemannian manifolds: symmetric positive definite matrices and linear subspaces. For both categories we use their corresponding nearest neighbour classifiers, kernels, and recent kernelised sparse representations. We compare against traditional action recognition techniques based on Gaussian mixture models and Fisher vectors (FVs). We evaluate these action recognition techniques under ideal conditions, as well as their sensitivity in more challenging conditions (variations in scale and translation). Despite recent advancements for handling manifolds, manifold based techniques obtain the lowest performance and their kernel representations are more unstable in the presence of challenging conditions. The FV approach obtains the highest accuracy under ideal conditions. Moreover, FV best deals with moderate scale and translation changes

Predicting the onset and persistence of episodes of depression in primary health care. The predictD-Spain study: Methodology

Background: The effects of putative risk factors on the onset and/or persistence of depression remain unclear. We aim to develop comprehensive models to predict the onset and persistence of episodes of depression in primary care. Here we explain the general methodology of the predictD-Spain study and evaluate the reliability of the questionnaires used. Methods: This is a prospective cohort study. A systematic random sample of general practice attendees aged 18 to 75 has been recruited in seven Spanish provinces. Depression is being measured with the CIDI at baseline, and at 6, 12, 24 and 36 months. A set of individual, environmental, genetic, professional and organizational risk factors are to be assessed at each follow-up point. In a separate reliability study, a proportional random sample of 401 participants completed the test-retest (251 researcher-administered and 150 self-administered) between October 2005 and February 2006. We have also checked 118,398 items for data entry from a random sample of 480 patients stratified by province. Results: All items and questionnaires had good test-retest reliability for both methods of administration, except for the use of recreational drugs over the previous six months. Cronbach's alphas were good and their factorial analyses coherent for the three scales evaluated (social support from family and friends, dissatisfaction with paid work, and dissatisfaction with unpaid work). There were 191 (0.16%) data entry errors. Conclusion: The items and questionnaires were reliable and data quality control was excellent. When we eventually obtain our risk index for the onset and persistence of depression, we will be able to determine the individual risk of each patient evaluated in primary health car

New methods for the assessment of Parkinson’s Disease (2005 to 2015): a systematic review

"BACKGROUND: The past decade has witnessed a highly dynamic and growing expansion of novel methods aimed at improving the assessment of Parkinson's disease with technology (NAM-PD) in laboratory, clinical, and home environments. However, the current state of NAM-PD regarding their maturity, feasibility, and usefulness in assessing the main PD features has not been systematically evaluated. METHODS: A systematic review of articles published in the field from 2005 to 2015 was performed. Of 9,503 publications identified in PubMed and the Web of Science, 848 full papers were evaluated, and 588 original articles were assessed to evaluate the technological, demographic, clinimetric, and technology transfer readiness parameters of NAM-PD. RESULTS: Of the studies, 65% included fewer than 30 patients, < 50% employed a standard methodology to validate diagnostic tests, 8% confirmed their results in a different dataset, and 87% occurred in a clinic or lab. The axial features domain was the most frequently studied, followed by bradykinesia. Rigidity and nonmotor domains were rarely investigated. Only 6% of the systems reached a technology level that justified the hope of being included in clinical assessments in a useful time period. CONCLUSIONS: This systematic evaluation provides an overview of the current options for quantitative assessment of PD and what can be expected in the near future. There is a particular need for standardized and collaborative studies to confirm the results of preliminary initiatives, assess domains that are currently underinvestigated, and better validate the existing and upcoming NAM-PD. © 2016 International Parkinson and Movement Disorder Society."Funding agency: The research leading to these results has received funding from “Consejería de Educación, Juventud y Deporte of Comunidad de Madrid” and the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant 291820.info:eu-repo/semantics/acceptedVersio

The GUAPOS project: III. Characterization of the O- and N-bearing complex organic molecules content and search for chemical differentiation

Context. The G31.41+0.31 Unbiased ALMA sPectral Observational Survey (GUAPOS) project targets the hot molecular core (HMC) G31.41+0.31 (G31) to reveal the complex chemistry of one of the most chemically rich high-mass star-forming regions outside the Galactic center (GC). Aims. In the third paper of the project we present a study of nine O-bearing (CH3OH, 13CH3OH, CH318OH, CH3CHO, CH3OCH3, CH3COCH3, C2H5OH, aGg′-(CH2OH)2, and gGg′-(CH2OH)2) and six N-bearing (CH3CN,13CH3CN, CH313CN, C2H3CN, C2H5CN, and C2H513CN) complex organic molecules toward G31. The aim of this work is to characterize the abundances in G31 and to compare them with the values estimated in other sources. Moreover, we searched for a possible chemical segregation between O-bearing and N-bearing species in G31, which hosts four compact sources as seen with higher angular resolution data. In the discussion we also include the three isomers of C2H4O2 and the O- and N-bearing molecular species NH2CHO, CH3NCO, CH3C(O)CH2, and CH3NHCHO, which were analyzed in previous GUAPOS papers. Methods. Observations were carried out with the interferometer ALMA and cover the entire Band 3 from 84 to 116 GHz (∼32 GHz bandwidth) with an angular resolution of 1.2″ × 1.2″ (∼4400 au × 4400 au) and a spectral resolution of ∼0.488 MHz (∼1.3- 1.7 km s-1). The transitions of the 14 molecular species were analyzed with the tool SLIM of MADCUBA to determine the physical parameters of the emitting gas. Moreover, we analyzed the morphology of the emission of the molecular species. Results. The values of abundances with respect to H2 in G31 range from 10-6 to 10-10 for the different species. We compared the abundances with respect to methanol of O-bearing, N-bearing, and O- and N-bearing COMs in G31 with 27 other sources, including other hot molecular cores inside and outside the GC, hot corinos, shocked regions, envelopes around young stellar objects, and quiescent molecular clouds, and with chemical models. Conclusions. From the comparison with other sources there is not a unique template for the abundances in hot molecular cores, pointing toward the importance of the thermal history for the chemistry of the various sources. The abundances derived from the chemical models are in good agreement, within a factor of 10, with those of G31. From the analysis of the maps we derived the peak positions of all the molecular species toward G31. Different species peak at slightly different positions, and this, together with the different central velocities of the lines obtained from the spectral fitting, point to chemical differentiation of selected O-bearing species

A smog chamber comparison of a microfluidic derivatisation measurement of gas-phase glyoxal and methylglyoxal with other analytical techniques

A microfluidic lab-on-a-chip derivatisation technique has been developed to measure part per billion (ppbV) mixing ratios of gaseous glyoxal (GLY) and methylglyoxal (MGLY), and the method is compared with other techniques in a smog chamber experiment. The method uses-(2, 3, 4, 5, 6-pentafluorobenzyl) hydroxylamine (PFBHA) as a derivatisation reagent and a microfabricated planar glass micro-reactor comprising an inlet, gas and fluid splitting and combining channels, mixing junctions, and a heated capillary reaction microchannel. The enhanced phase contact area-to-volume ratio and the high heat transfer rate in the micro-reactor resulted in a fast and highly efficient derivatisation reaction, generating an effluent stream ready for direct introduction to a gas chromatograph-mass spectrometer (GC-MS). A linear response for GLY was observed over a calibration range 0.7 to 400 ppbV, and for MGLY of 1.2 to 300 ppbV, when derivatised under optimal reaction conditions. The analytical performance shows good accuracy (6.6% for GLY and 7.5% for MGLY), suitable precision (<12.0%) with method detection limits (MDLs) of 75 pptV for GLY and 185 pptV for MGLY, with a time resolution of 30 min. These MDLs are below or close to typical concentrations of these compounds observed in ambient air. The feasibility of the technique was assessed by applying the methodology to quantify α-dicarbonyls formed during the photo-oxidation of isoprene in the EUPHORE chamber. Good correlations were found between microfluidic measurements and Fourier Transform InfraRed spectroscopy (FTIR) with a correlation coefficient (2) of 0.84, Broadband Cavity Enhanced Absorption Spectroscopy (BBCEAS) (2 Combining double low line 0.75), solid phase micro extraction (SPME) (2 Combining double low line 0.89), and a photochemical chamber box modelling calculation (2 Combining double low line 0.79) for GLY measurements. For MGLY measurements, the microfluidic technique showed good agreement with BBCEAS (2 Combining double low line 0.87), SPME (2 Combining double low line 0.76), and the modeling simulation (2 Combining double low line 0.83), FTIR (2 Combining double low line 0.72) but displayed a discrepancy with Proton-Transfer Reaction Time-of-Flight Mass Spectrometry (PTR-ToF-MS) with 2 value of 0.39

Beyond carbon and nitrogen: how the microbial energy economy couples elemental cycles in diverse ecosystems

Microbial metabolism couples elemental reactions, driving biogeochemical cycles. Assimilatory coupling of elemental cycles, such as the carbon (C), nitrogen (N), and phosphorus cycles, occurs when these elements are incorporated into biomass or released through its decomposition. In addition, many microbes are capable of dissimilatory coupling, catalyzing energy-releasing reactions linked to transformations in the oxidation state of elements, and releasing the transformed elements to the environment. Different inorganic elements provide varying amounts of energy yield, and the interaction of these processes creates a microbial energy economy. Dissimilatory reactions involving C, N, iron, and sulfur provide particularly important examples where microbially mediated oxidation–reduction (redox) transformations affect nutrient availability for net primary production, greenhouse-gas emissions, levels of contaminants and natural toxic factors, and other ecosystem dynamics. Recent discoveries of previously unrecognized microbial dissimilatory processes are leading to reevaluation of traditional perceptions of biogeochemical cycles