The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC

Positive selection is widely estimated from protein coding sequence alignments by the nonsynonymous-to-synonymous ratio omega. Increasingly elaborate codon models are used in a likelihood framework for this estimation. Although there is widespread concern about the robustness of the estimation of the omega ratio, more efforts are needed to estimate this robustness, especially in the context of complex models. Here, we focused on the branch-site codon model. We investigated its robustness on a large set of simulated data. First, we investigated the impact of sequence divergence. We found evidence of underestimation of the synonymous substitution rate for values as small as 0.5, with a slight increase in false positives for the branch-site test. When dS increases further, underestimation of dS is worse, but false positives decrease. Interestingly, the detection of true positives follows a similar distribution, with a maximum for intermediary values of dS. Thus, high dS is more of a concern for a loss of power (false negatives) than for false positives of the test. Second, we investigated the impact of GC content. We showed that there is no significant difference of false positives between high GC (up to similar to 80%) and low GC (similar to 30%) genes. Moreover, neither shifts of GC content on a specific branch nor major shifts in GC along the gene sequence generate many false positives. Our results confirm that the branch-site is a very conservative test.

The effect of test meal monounsaturated fatty acid: saturated fatty acid ratio on postprandial lipid metabolism

Epidemiological evidence shows that a diet high in monounsaturated fatty acids (MUFA) but low in saturated fatty acids (SFA) is associated with reduced risk of CHD. The hypocholesterolaemic effect of MUFA is known but there has been little research on the effect of test meal MUFA and SFA composition on postprandial lipid metabolism. The present study investigated the effect of meals containing different proportions of MUFA and SFA on postprandial triacylglycerol and non-esterified fatty acid (NEFA) metabolism. Thirty healthy male volunteers consumed three meals containing equal amounts of fat (40 g), but different proportions of MUFA (12, 17 and 24% energy) in random order. Postprandial plasma triacylglycerol, apolipoprotein B-48, cholesterol, HDL-cholesterol, glucose and insulin concentrations and lipoprotein lipase (EC 3.1.1.34) activity were not significantly different following the three meals which varied in their levels of SFA and MUFA. There was a significant difference in the postprandial NEFA response between meals. The incremental area under the curve of postprandial plasma NEFA concentrations was significantly (P = 0.03) lower following the high-MUFA meal. Regression analysis showed that the non-significant difference in fasting NEFA concentrations was the most important factor determining difference between meals, and that the test meal MUFA content had only a minor effect. In conclusion, varying the levels of MUFA and SFA in test meals has little or no effect on postprandial lipid metabolism.

Biomechanical influence of crown-to-implant ratio on stress distribution over internal hexagon short implant: 3-D finite element analysis with statistical test

The study of short implants is relevant to the biomechanics of dental implants, and research on crown increase has implications for the daily clinic. The aim of this study was to analyze the biomechanical interactions of a singular implant-supported prosthesis of different crown heights under vertical and oblique force, using the 3-D finite element method. Six 3-D models were designed with Invesalius 3.0, Rhinoceros 3D 4.0, and Solidworks 2010 software. Each model was constructed with a mandibular segment of bone block, including an implant supporting a screwed metal-ceramic crown. The crown height was set at 10, 12.5, and 15 mm. The applied force was 200 N (axial) and 100 N (oblique). We performed an ANOVA statistical test and Tukey tests; p < 0.05 was considered statistically significant. The increase of crown height did not influence the stress distribution on screw prosthetic (p > 0.05) under axial load. However, crown heights of 12.5 and 15 mm caused statistically significant damage to the stress distribution of screws and to the cortical bone (p <0.001) under oblique load. High crown to implant (C/I) ratio harmed microstrain distribution on bone tissue under axial and oblique loads (p < 0.001). Crown increase was a possible deleterious factor to the screws and to the different regions of bone tissue. (C) 2014 Elsevier Ltd. All rights reserved.

Normative reference values for the 20-meter shuttlerun test in a population-based sample of schoolchildren in Bogota, Colombia: The FUPRECOL Study

Our aim was to determine the normative reference values of cardiorespiratory fitness (CRF) and to establish the proportion of subjects with low CRF suggestive of future cardio-metabolic risk.

Comparison between the 1% and 2% ibopamine provocative test in primary open-angle glaucoma patients: sensitivity, specificity and tolerability

PURPOSE: To compare intraocular pressure (IOP) rise in normal individuals and primary open-angle glaucoma patients and the safety and efficacy of ibopamine eye drops in different concentrations as a provocative test for glaucoma. METHODS: Glaucoma patients underwent (same eye) the ibopamine provocative test with two concentrations, 1% and 2%, in a random sequence at least 3 weeks apart, but not more than 3 months. The normal individuals were randomly submitted to one of the concentrations of ibopamine (1% and 2%). The test was considered positive if there was an IOP rise greater than 3 or 4 mmHg at 30 or 45 minutes to test which subset of the test has the best sensitivity (Se)/specificity (Sp). RESULTS: There was no statistically significant difference in any of the IOP measurements, comparing 1% with 2% ibopamine. The IOP was significantly higher at 30 and 45 minutes with both concentrations (p<0.001). The best sensitivity/specificity ratio was achieved with the cutoff point set as greater than 3 mmHg at 45 minutes with 2% ibopamine (area under the ROC curve: 0.864, Se: 84.6%; Sp:73.3%). All patients described a slight burning after ibopamine's instillation. CONCLUSION: 2% ibopamine is recommended as a provocative test for glaucoma. Because both concentrations have similar ability to rise IOP, 1% ibopamine may be used to treat ocular hypotony.

Fault current test of a bifilar Bi-2212 bulk coil

A bifilar Bi-2212 bulk coil with parallel shunt resistor was tested under fault current condition using a 3 MVA single-phase transformer in a 220 V-60 Hz line achieving fault current peak of 8 kA. The fault current tests are performed from steady state peak current of 200 A by applying controlled short circuits up to 8 kA varying the time period from one to six cycles. The test results show the function of the shunt resistor providing homogeneous quench behavior of the HTS coil besides its intrinsic stabilizing role. The limiting current ratio achieves a factor 4.2 during 5 cycles without any degradation.

Test of a Modular Fault Current Limiter for 220 V Line Using YBCO Coated Conductor Tapes With Shunt Protection

A modular superconducting fault current limiter (SFCL) consisting of 16 elements was constructed and tested in a 220 V line for a fault current between 1 kA to 7.4 kA. The elements are made up of second generation (2G) YBCO-coated conductor tapes with stainless steel reinforcement. For each element four tapes were electrically connected in parallel with effective length of 0.4 m per element, totaling 16 elements connected in series. The evaluation of SFCL performance was carried out under DC and AC tests. The DC test was performed through pulsed current tests and its recovery characteristics under load current were analysed by changing the shunt resistor value. The AC test performed using a 3 MVA/220 V/60 Hz transformer has shown the current limiting ratio achieved a factor higher than 10 during fault of up to five cycles without conductor degradation. The measurement of the voltage for each element during the AC test showed that in this modular SFCL the quench is homogeneous and the transition occurs similarly in all the elements.

Influence of aggregates grading and water/cement ratio in workability and hardened properties of mortars

Mortar is the material responsible for the distribution of stresses in masonry structures. The knowledge about the fresh and hardened properties of mortar is fundamental to ensure a good performance of masonry walls. Water/cement ratio and aggregates grading are among several variables that influence physical and mechanical behaviour of mortars. An experimental program is presented in order to evaluate the influence of aggregates grading and water/cement ratio in workability and hardened properties of mortars. Eighteen compositions of mortar are prepared using three relations cement:lime:sand, two types of sand and three water/cement ratios. Specimens are analyzed through flow table test, compressive and flexural strength tests. Results indicate that the increase of water/cement ratio reduces the values of hardened properties and increases the workability. Besides, sands grading has no influence in compressive strength. On the other hand, significant differences in deformation capacity of mortars were verified with the variation of the type of sand. Finally, some correlations are presented among hardened properties and the compressive strength. (C) 2010 Elsevier Ltd. All rights reserved.

Slip ratio in dispersed viscous oil-water pipe flow

In this article, dispersed flow of viscous oil and water is investigated. The experimental work was performed in a 26.2-mm-i.d. 12-m-long horizontal glass pipe using water and oil (viscosity of 100 mPa s and density of 860 kg/m(3)) as test fluids. High-speed video recording and a new wire-mesh sensor based on capacitance (permittivity) measurements were used to characterize the flow. Furthermore, holdup data were obtained using quick-closing-valves technique (QCV). An interesting finding was the oil-water slip ratio greater than one for dispersed flow at high Reynolds number. Chordal phase fraction distribution diagrams and images of the holdup distribution over the pipe cross-section obtained via wire-mesh sensor indicated a significant amount of water near to the pipe wall for the three different dispersed flow patterns identified in this study: oil-in-water homogeneous dispersion (o/w H), oil-in-water non-homogeneous dispersion (o/w NH) and Dual continuous (Do/w & Dw/o). The phase slip might be explained by the existence of a water film surrounding the homogeneous mixture of oil-in-water in a hidrofilic-oilfobic pipe. (C) 2010 Elsevier Inc. All rights reserved.

Random regression models to estimate test-day milk yield genetic parameters Holstein cows in Southeastern Brazil

A total of 152,145 weekly test-day milk yield records from 7317 first lactations of Holstein cows distributed in 93 herds in southeastern Brazil were analyzed. Test-day milk yields were classified into 44 weekly classes of DIM. The contemporary groups were defined as herd-year-week of test-day. The model included direct additive genetic, permanent environmental and residual effects as random and fixed effects of contemporary group and age of cow at calving as covariable, linear and quadratic effects. Mean trends were modeled by a cubic regression on orthogonal polynomials of DIM. Additive genetic and permanent environmental random effects were estimated by random regression on orthogonal Legendre polynomials. Residual variances were modeled using third to seventh-order variance functions or a step function with 1, 6,13,17 and 44 variance classes. Results from Akaike`s and Schwarz`s Bayesian information criterion suggested that a model considering a 7th-order Legendre polynomial for additive effect, a 12th-order polynomial for permanent environment effect and a step function with 6 classes for residual variances, fitted best. However, a parsimonious model, with a 6th-order Legendre polynomial for additive effects and a 7th-order polynomial for permanent environmental effects, yielded very similar genetic parameter estimates. (C) 2008 Elsevier B.V. All rights reserved.

Critical values for unit root and cointegration test statistics - the use of response surface equations

This note considers the value of surface response equations which can be used to calculate critical values for a range of unit root and cointegration tests popular in applied economic research.

High HIV incidence and prevalence among young women in rural South Africa: Developing a cohort for intervention trials

Objective: To measure prevalence and model incidence of HIV infection. Setting: 2013 consecutive pregnant women attending public sector antenatal clinics in 1997 in Hlabisa health district, South Africa. Historical seroprevalence data, 1992-1995. Methods: Serum remaining from syphilis testing was tested anonymously for antibodies to HIV to determine seroprevalence. Two models, allowing for differential mortality between HIV-positive and HIV-negative people, were used. The first used serial seroprevalence data to estimate trends in annual incidence. The second, a maximum likelihood model, took account of changing force of infection and age-dependent risk of infection, to estimate age-specific HIV incidence in 1997. Multiple logistic regression provided adjusted odds ratios (OR) for risk factors for prevalent HIV infection. Results: Estimated annual HIV incidence increased from 4% in 1992/1993 to 10% in 1996/1997. In 1997, highest age-specific incidence was 16% among women aged between 20 and 24 years. in 1997, overall prevalence was 26% (95% confidence interval [CI], 24%-28%) and at 34% was highest among women aged between 20 and 24 years. Young age (<30 years; odds ratio [OR], 2.1; p = .001), unmarried status (OR 2.2; p = .001) and living in less remote parts of the district (OR 1.5; p = .002) were associated with HIV prevalence in univariate analysis. Associations were less strong in multivariate analysis. Partner's migration status was not associated with HIV infection. Substantial heterogeneity of HIV prevalence by clinic was observed (range 17%-31%; test for trend, p = .001). Conclusions: This community is experiencing an explosive HIV epidemic. Young, single women in the more developed parts of the district would form an appropriate cohort to test, and benefit from, interventions such as vaginal microbicides and HIV vaccines.

A reassessment of the in vitro RBC haemolysis assay with defibrinated sheep blood for the determination of the ocular irritation potential of cosmetic products: Comparison with the in vivo Draize rabbit test

We examined the correlation between results obtained from the in vivo Draize test for ocular irritation and in vitro results obtained from the sheep red blood cell (RBC) haemolytic assay, which assesses haemolysis and protein denaturation in erythrocytes, induced by cosmetic products. We sought to validate the haemolytic assay as a preliminary test for identifying highly-irritative products, and also to evaluate the in vitro test as alternative assay for replacement of the in vivo test. In vitro and in vivo analyses were carried out on 19 cosmetic products, in order to correlate the lesions in the ocular structures with three in vitro parameters: (i) the extent of haemolysis (H50); (ii) the protein denaturation index (131); and (iii) the H50/DI ratio, which reflects the irritation potential (IP). There was significant correlation between maximum average scores (MAS) and the parameters determined in vitro (r = 0.752-0.764). These results indicate that the RBC assay is a useful and rapid test for use as a screening method to assess the IP of cosmetic products, and for predicting the IP value with a high level of concordance (94.7%). The assay showed high sensitivity and specificity rates of 91.6% and 100%, respectively.

BisGMA/TEGDMA ratio and filler content effects on shrinkage stress

Objective. To investigate the contributions of BisGMA:TEGDMA and filler content on polymerization stress, along with the influence of variables associated with stress development, namely, degree of conversion, reaction rate, shrinkage, elastic modulus and loss tangent for a series of experimental dental composites. Methods. Twenty formulations with BisGMA: TEGDMA ratios of 3: 7, 4: 6, 5: 5, 6: 4 and 7: 3 and barium glass filler levels of 40, 50, 60 or 70 wt% were studied. Polymerization stress was determined in a tensilometer, inserting the composite between acrylic rods fixed to clamps of a universal test machine and dividing the maximum load recorded by the rods cross-sectional area. Conversion and reaction rate were determined by infra-red spectroscopy. Shrinkage was measured by mercury dilatometer. Modulus was obtained by three-point bending. Loss tangent was determined by dynamic nanoindentation. Regression analyses were performed to estimate the effect of organic and inorganic contents on each studied variable, while a stepwise forward regression identified significant variables for polymerization stress. Results. All variables showed dependence on inorganic concentration and monomeric content. The resin matrix showed a stronger influence on polymerization stress, conversion and reaction rate, whereas filler fraction showed a stronger influence on shrinkage, modulus and loss tangent. Shrinkage and conversion were significantly related to polymerization stress. Significance. Both the inorganic filler concentration and monomeric content affect polymerization stress, but the stronger influence of the resin matrix suggests that it may be possible to reduce stress by modifying resin composition without sacrificing filler content. The main challenge is to develop formulations with low shrinkage without sacrificing degree of conversion. (C) 2011 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.