RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions

Summary: Several methods have been proposed to detect copy number changes and recurrent regions of copy number variation from aCGH, but few methods return probabilities of alteration explicitly, which are the direct answer to the question ‘is this probe/region altered?’ RJaCGH fits a Non-Homogeneous Hidden Markov model to the aCGH data using Markov Chain Monte Carlo with Reversible Jump, and returns the probability that each probe is gained or lost. Using these probabilites, recurrent regions (over sets of individuals) of copy number alteration can be found

Hydrogen storage properties of magnesium borohydride infiltrated in silica aerogel using solvated and pressure methods

In this work, the polymorphic α-magnesium borohydride form was infiltrated by wet impregnation using tetrahydrofuran (THF) as solvent and subcritical carbon dioxide as innovative drying process. Pressure infiltration at high temperature was also tested as another promising method for confinement. After infiltration, onset decomposition temperature was reduced from 280 °C into 220 °C using high pressure infiltration and down to 100 °C using wet impregnation followed by CO2 drying. Faster kinetics were obtained in both cases due the possible particle size reduction in the precipitation process of the complex hydride and the presence of silica, which could behave as an additive. It is the first time that this complex borohydride is 6.1 wt% H2 reversible performing the rehydrogenation at moderate conditions of 390 °C and 120 bar H2 using silica as support. Different values were obtained after infiltration method due to the different intermediates that were obtained after the first dehydrogenation

Growth of out-of-plane standing MoTe2(1-x)Se2x/MoSe2 composite flake films by sol–gel nucleation of MoOy and isothermal closed space telluro-selenization

This study describes the sol–gel processing of MoOy on Si (1 0 0) to subsequently achieve out-of-plane MoTe2/MoSe2 flake composite films by an isothermal closed space vapor transformation. The oxide precursor films have been prepared from a Mo isopropoxide solution in isopropanol and acid catalysis induced by HCl. Thermal annealing at 200, 400 and 600 °C enhanced the condensation after xerogel formation. An x-ray absorption analysis demonstrates that films condensed at 200 °C are at an intermediate chemical state between MoO3 and MoO2. To achieve MoTe2/MoSe2 composite films, the precursor oxide films were reduced in H2 and exposed to the chalcogenides by isothermal closed space vapor transport at 600 °C. The multilayered nanocomposite films grow with an out-of-plane flake-like structure and an evident integration of Se in the MoTe2 phase according to a MoTe2(1-x)Se2x alloy, with an estimation of x of 0.25. The alloy and the orientation of the flakes are consistent with the bands present in the Raman spectrum. These films are attractive for applications requiring high surface area interfaces favoring gas or ion exchange reactions with transition metal dichalcogenidesThe current research was funded by grant CTQ2017-84309-C2-2-R from Ministerio de Ciencia e Innovación (Spain). The authors acknowledge the ESRF and the Ministerio de Ciencia, Innovación y Universidades (Spain), for provision of synchrotron radiation facilities and the Consejo Superior de Investigaciones Científicas (Spain) financial support for the operation of the beamline under Grant No. PIE 2010 6 OE 01

Functional Massage of the Teres Major Muscle in Patients with Subacromial Impingement Syndrome. A Randomized Controlled Case Series Study.

Objective: the purpose of the present study was to analyze the concurrent validity and reliability of a force platform clinical COBS Feedback® for the estimation of the height of vertical jumps. Design: a cross-sectional correlational and comparative study. Setting: University Human Movement and Physiotherapy Laboratory. Participants: healthy university students (14 female and 13 male) aged between 18 and 25 years old (mean = 20.074 ±1.542). Main Outcome Measures: vertical jump heights, technical error and grade of agreement between methods of measurement. Results: after the 27 subjects performed a total of 135 vertical jumps on COBS Feedback®platform while simultaneously being recorded with a high-speed camera-based method, the intraclass correlation coefficient showed an almost perfect concordance between the two methods (ICC = 0.916, CI95%= 0.882 to 0.940, p<0.001). The technical error of the COBS Feedback® against HSC-Kinovea video analysis was at 0.310±0.223m, being higher in males than in females (t= -2.822, CI95%: -0.376 to -0.574, p=0.001). Conclusions: the COBS Feedback® method provided a valid measurement of the flight times for estimate the vertical jump height as a number of well-known tests and devices.Aims: Subacromial impingement syndrome is the most common shoulder condition. Myofascial trigger points in teres major muscle can be associated with this syndrome. Our objective is to determine whether adding manual therapy specifically for teres major trigger points can produce better results in these patients. Study Design: Randomized controlled case series. Place and Duration of Study: Public Primary Care Center in the Spanish National Health System (Cornellà de Llobregat - Barcelona) and the FREMAP Mutual Society for Work-related Injuries and Occupational Illness (Arnedo - La Rioja), between January and March 2014. Methodology: Fifty-eight people were recruited but 8 subjects were lost during the follow-up period. The sample consisted of 50 patients (17 male and 33 female, age range 23-80 years) randomly assigned to one of two groups: the intervention group or the control group. Both groups received a protocolized physical therapy treatment, while the intervention group also received manual therapy for teres major trigger points. Results: Pain intensity (p=.01) and function (p=.01) showed significant improvement in the control group, whereas pain intensity (p=.01), function (p=.01) and active range of motion (p=.01) showed significant improvement in the intervention group. Between-group differences were statistically significant for abduction (p=.01), extension (p=.02) and lateral rotation (p=.02), and clinically significant (Cohen’s d) for function, flexion, extension, lateral rotation and abduction. Conclusion: Although our findings must be considered as preliminary, they suggest that adding manual therapy to treat teres major trigger points achieves better results in the glenohumeral range of motion

Spontaneous oxidation of disordered fcc FePt nanoparticles

In this work we present new results on spontaneous oxidation of disordered fcc FePt nanoparticles. The "as-made" oleic acid and oleylamine coated FePt nanoparticles of average size 4 nm synthesized by a high-boiling coordinating solvent method were exposed to air over a period of days and characterized structurally and magnetically by means of different techniques such as XANES, XPS, EXAFS, and SQUID magnetometry. The "as-made" FePt nanoparticles stabilize in the disordered fcc structure and have a very low magnetic saturation (M(s)=11 emu/g) and a huge coercive field (H_(c)=1800 Oe) compared to the low temperature bulk values of the disordered fcc FePt. We observed that the coercive field and the magnetic saturation change with the time the sample is exposed to air and these changes are associated with the oxidation or passivation of the nanoparticle surface that gives place to a core-shell structure. Indeed, the study on the electronic properties of the nanoparticles confirms the magnetic results and indicates that when the nanoparticles are exposed to air, changes in the oxidation state of both Fe and Pt occur, the oxidation state of Fe coming close to hematite. The formation of hematite tends to soften the "as-made" FePt nanoparticles as observed by the reduction of the coercive field to almost one third of the original value. Although the hematite softens the FePt nanoparticles, there is an exchange coupling at the interface of the core-shell characterized by the increase of the coercive field from 300 to 900 Oe when the sample is cooled in an applied field of 50 kOe

Production and economic potentials of cattle in pasture-based systems of the Western Amazon region of Brazil.

Our objectives were to evaluate strategies to improve productivity and economic returns from beef and dual-purpose cattle systems based on data collected on one dual-purpose (Bos taurus × Bos indicus) and two beef (Nellore) cattle farms in the western Amazon region of Brazil. Forage chemical composition and digestion rates of carbohydrate fractions of grazed Brachiaria decumbens and Brachiaria brizantha cv. Marandu grasses and Pueraria phaseoloides (tropical kudzu) legume were measured monthly during a 9-mo period from the end of one dry season to the end of the subsequent rainy season. Measurements of milk and growth responses to grazing these forages were used to predict animal productivity responses to dietary nutrient availability throughout an annual cycle. The ME available for gain in our simulations was always more limiting than metabolizable protein. The predicted ME available for gain was 0.50 kg/d for steers grazing B. brizantha and 0.40 kg/d for finishing steers grazing B. decumbens. Grasses contained more NDF and neutral detergent insoluble protein and less ME (P < 0.05) in the rainiest months than in the less rainy season, which resulted in 20% less predicted weight gain by growing steers (P < 0.05). Supplementation with sorghum grain was required to increase milk production and growth by 25 or 50% per animal, respectively, but this strategy was less profitable than current forage-only diets. Greater productivity of land and labor from higher stocking indicated greater net margins for beef production, but not for milk. This study suggested that more intensive beef production by judicious fertilization of grass-legume pastures and greater stocking density is the preferable strategy for owners of these cattle systems to improve economic returns under current conditions. It also might help decrease the motivation for additional forest clearing

Evaluación de las condiciones de salud para la inclusión de individuos en estudio de niveles de glucemia postprandial

Las condiciones iniciales del individuo son determinantes para la validez de los resultados, por lo que el objetivo general fue seleccionar la muestra verificando determinadas condiciones de inclusión para obtener datos confiables que permitan garantizar el desarrollo eficaz de la etapa posterior del proyecto macro (ingesta de galleta tipo dulce y niveles de glucemia en individuos diabéticos tipo 2 no insulino requirientes). Se diseñó y aplicó una encuesta para la inclusión de los individuos por estudiar, con su previo consentimiento, según Artículo 15 de la Resolución Nº 8430 de 1993; se defi nieron criterios de inclusión, exclusión y estado de salud de los individuos. Se seleccionaron 10 individuos diabéticos Tipo 2 sin terapia farmacológica (Hipoglucemiantes e insulina) que cumplían los criterios de inclusión definidos por conveniencia para observar el comportamiento del alimento estudiado frente a un alimento Standard (pan blanco sin dulce). Se concluyó que la edad promedio de los individuos diabéticos tipo 2 seleccionados fue de 65 años, la mayoría tendiendo a ser obesos por varios factores nutricionales: malos hábitos alimentación, falta control médico y poca actividad física, entre otros

A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145

<p>Abstract</p> <p>Background</p> <p>Yu et al. (BMC Bioinformatics 2007,8: 145+) have recently compared the performance of several methods for the detection of genomic amplification and deletion breakpoints using data from high-density single nucleotide polymorphism arrays. One of the methods compared is our non-homogenous Hidden Markov Model approach. Our approach uses Markov Chain Monte Carlo for inference, but Yu et al. ran the sampler for a severely insufficient number of iterations for a Markov Chain Monte Carlo-based method. Moreover, they did not use the appropriate reference level for the non-altered state.</p> <p>Methods</p> <p>We rerun the analysis in Yu et al. using appropriate settings for both the Markov Chain Monte Carlo iterations and the reference level. Additionally, to show how easy it is to obtain answers to additional specific questions, we have added a new analysis targeted specifically to the detection of breakpoints.</p> <p>Results</p> <p>The reanalysis shows that the performance of our method is comparable to that of the other methods analyzed. In addition, we can provide probabilities of a given spot being a breakpoint, something unique among the methods examined.</p> <p>Conclusion</p> <p>Markov Chain Monte Carlo methods require using a sufficient number of iterations before they can be assumed to yield samples from the distribution of interest. Running our method with too small a number of iterations cannot be representative of its performance. Moreover, our analysis shows how our original approach can be easily adapted to answer specific additional questions (e.g., identify edges).</p