Improving sequence-based fold recognition by using 3D model quality assessment

Motivation: The ability of a simple method (MODCHECK) to determine the sequence–structure compatibility of a set of structural models generated by fold recognition is tested in a thorough benchmark analysis. Four Model Quality Assessment Programs (MQAPs) were tested on 188 targets from the latest LiveBench-9 automated structure evaluation experiment. We systematically test and evaluate whether the MQAP methods can successfully detect native-likemodels. Results: We show that compared with the other three methods tested MODCHECK is the most reliable method for consistently performing the best top model selection and for ranking the models. In addition, we show that the choice of model similarity score used to assess a model's similarity to the experimental structure can influence the overall performance of these tools. Although these MQAP methods fail to improve the model selection performance for methods that already incorporate protein three dimension (3D) structural information, an improvement is observed for methods that are purely sequence-based, including the best profile–profile methods. This suggests that even the best sequence-based fold recognition methods can still be improved by taking into account the 3D structural information.

Assessing the quality of modelled 3D protein structures using the ModFOLD server

Model quality assessment programs (MQAPs) aim to assess the quality of modelled 3D protein structures. The provision of quality scores, describing both global and local (per-residue) accuracy are extremely important, as without quality scores we are unable to determine the usefulness of a 3D model for further computational and experimental wet lab studies.Here, we briefly discuss protein tertiary structure prediction, along with the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) competition and their key role in driving the field of protein model quality assessment methods (MQAPs). We also briefly discuss the top MQAPs from the previous CASP competitions. Additionally, we describe our downloadable and webserver-based model quality assessment methods: ModFOLD3, ModFOLDclust, ModFOLDclustQ, ModFOLDclust2, and IntFOLD-QA. We provide a practical step-by-step guide on using our downloadable and webserver-based tools and include examples of their application for improving tertiary structure prediction, ligand binding site residue prediction, and oligomer predictions.

High night temperature induces contrasting responses for spikelet fertility, spikelet tissue temperature, flowering characteristics and grain quality in rice

Climate change is increasing night temperature (NT) more than day temperature (DT) in rice-growing areas. Effects of combinations of NT (24-35°C) from microsporogenesis to anthesis at one or more DT (30 or 35°C) at anthesis on rice spikelet fertility, temperature within spikelets, flowering pattern, grain weight per panicle, amylose content and gel consistency were investigated in contrasting rice cultivars under controlled environments. Cultivars differed in spikelet fertility response to high NT, with higher fertility associated with cooler spikelets (P < 0.01). Flowering dynamics were altered by high NT and a novel high temperature tolerance complementary mechanism, shorter flower open duration in cv. N22, was identified. High NT reduced spikelet fertility, grain weight per panicle, amylose content and gel consistency, whereas high DT reduced only gel consistency. Night temperature >27°C was estimated to reduce grain weight. Generally, high NT was more damaging to grain weight and selected grain quality traits than high DT, with little or no interaction between them. The critical tolerance and escape traits identified, i.e. spikelet cooling, relatively high spikelet fertility, earlier start and peak time of anthesis and shorter spikelet anthesis duration can aid plant breeding programs targeting resilience in warmer climates.

Globalisation and MA TESOL programs in the UK

This article reports the results of a mixed-methods approach to investigating the association between globalisation and MATESOL in UK universities. Qualitative and quantitative data collected from academic staff through eight emails, four interviews and 41 questionnaires indicate that the globalised context of higher education have affected these programmes in a number of ways including an increasing interest in recruiting more international students and a growing awareness about the need for curriculum and content modifications. The analysis of the data suggests that although change has been an inherent characteristic of these MAs over the past decade, it has been implemented gradually and conservatively, often relying on a dialectic relationship between academic staff and universities’ policies. The results imply that factors other than globalisation have also been at work. Many of the participants contend that globalisation has not lowered the quality of these MAs or standards of good practice.

JCML: A specification language for the runtime verification of Java Card programs

COSTA, Umberto Souza; MOREIRA, Anamaria Martins; MUSICANTE, Matin A.; SOUZA NETO, Plácido A. JCML: A specification language for the runtime verification of Java Card programs. Science of Computer Programming. [S.l]: [s.n], 2010.

Specification and Runtime Verification of Java Card Programs

COSTA, Umberto Souza da; MOREIRA, Anamaria Martins; MUSICANTE, Martin A. Specification and Runtime Verification of Java Card Programs. Electronic Notes in Theoretical Computer Science. [S.l:s.n], 2009.

Population structure and effects of inbreeding on milk yield and quality of Murrah buffaloes

To provide data for conservation, selection, and expansion programs of buffalo herds, this study evaluated the history of a population of Murrah buffaloes based on population structure and the effect of inbreeding on accumulated 305-d milk yield (MY), fat yield (FY), protein yield (PY), mozzarella production (MProd), and somatic cell score (SCS). The usefulness of including the individual inbreeding coefficient (F) or individual increase in inbreeding coefficient (Delta F) in the model to describe inbreeding depression was evaluated. Pedigree information from 8,054 animals born between 1976 and 2008 and 4,497 lactation records obtained from 12 herds were used. The realized effective population size was 40.10 +/- 1.27, and the mean F of the entire population was 2.14%. The ratio between the number of founders and ancestors demonstrated the existence of a bottleneck in the pedigree of this population, which may contribute to a reduction of genetic diversity. The effect of F on MY, FY, PY, MProd, and SCS was -1.005 kg, -0.299 kg, -0.246 kg, -1.201 kg, and -0.002 units, and the effect of Delta F transformed to equivalent F (%) for a mean of 2.57 equivalent generations was -4.287 kg, -0.581 kg, -0.383 kg, -2.001 kg, and -0.007 units, respectively. The inbreeding depression observed may have important economic repercussions for production systems. The Delta F can be considered the better of the two indicators of inbreeding depression due to its properties that prevent underestimation of this effect. A designed mating system to avoid inbreeding may be applied to this population to maintain genetic diversity.

Strategies to promote farm animal welfare in Latin America and their effects on carcass and meat quality traits

Several initiatives, including research and development, increasing stakeholders' awareness and application of legislation and recommendation, have been carried out in Latin America to promote animal welfare and meat quality. Most activities focused on the impact of pre-slaughter conditions (facilities, equipment and handling procedures) on animal welfare and meat quality. The results are encouraging; data from Brazil, Chile and Uruguay showed that the application of the improved pre-slaughter handling practices reduced aggressive handling and the incidence of bruised carcasses at slaughter in cattle and pigs. These outcomes stimulated some to apply animal welfare concepts in livestock handling within the meat production chain as shown by the increasing demand for personnel training on the best. To attend this demand is important to expand local studies on farm animal welfare and to set up (or maintain) an efficient system for knowledge transfer to all stakeholders in the Latin America meat production chains. However, it is clear that to promote the long-term progress in this field is important to deliver practical solutions, assuring that they match the technical and financial conditions of those who are the target of training programs. (C) 2012 Elsevier Ltd. All rights reserved.

Diagnosis of Public Programs focused on Herbal Medicines in Brazil

The present study is aimed to diagnose the current public programs focused on herbal medicine in Brazil where the following results can be observed. The main purpose of implementation of these programs was the demand of the users of medicinal plants and herbal medicines. The initiative of the implementation of these programs was related to the managers (58%). The difficulties in this implementation were due to lack of funding (90%) of the programs. In 80% of the programs, the physicians did not adhere to herbal medicine services due to lack of knowledge in the subject. Training courses were proposed (70%) to increase the adhesion of prescribers to the system. Some municipalities use information obtained from patients to assess the therapeutic efficiency of medicinal plants and herbal medicines. of the programs underway, cultivation of medicinal plants was observed in 50%, and 67% of the programs adopted quality control. In most programs, this control is not performed in accordance with the legal requirements.

Quality of life and its association with cardiovascular risk factors in a community health care program population

OBJECTIVE: To evaluate quality of life in a population that attended a specific community event on health care education, and to investigate the association of their quality of life with the presence of cardiovascular risk factors INTRODUCTION: Interest in health-related quality of life is growing worldwide as a consequence of increasing rates of chronic disease. However, little is known about the association between quality of life and cardiovascular risk factors. METHODS: This study included 332 individuals. Demographics, blood pressure, body mass index, and casual glycemia were evaluated. The brief version of the World Health Organization Quality of Life questionnaire on quality of life was given to them. The medians of the scores obtained for the physical, psychological, emotional, and environmental domains were used as cutoffs to define higher and lower scores. A multinomial logistic regression model was used to define the parameters associated with lower scores. RESULTS: Diabetes mellitus, dyslipidemia, and obesity were associated with lower scores in the physical domain. Dyslipidemia was also associeted with lower scores in the psychological domain. Male gender and regular physical activity had protective effects on quality of life. Aging was inversely associated with decreased quality of life in the environmental domain. CONCLUSION: The presence of cardiovascular risk factors is related to a decreased quality of life. Conversely, male gender and regular physical activity had protective effects on quality of life. These findings suggest that exercising should be further promoted by health-related public programs, with a special focus on women.

Effect of three exercise programs on patients with chronic obstructive pulmonary disease

We compared the effect of three different exercise programs on patients with chronic obstructive pulmonary disease including strength training at 50_80% of one-repetition maximum (1-RM) (ST; N = 11), low-intensity general training (LGT; N = 13), or combined training groups (CT; N = 11). Body composition, muscle strength, treadmill endurance test (TEnd), 6-min walk test (6MWT), Saint George's Respiratory Questionnaire (SGRQ), and baseline dyspnea (BDI) were assessed prior to and after the training programs (12 weeks). The training modalities showed similar improvements (P > 0.05) in SGRQ-total (ST = 13 ± 14%; CT = 12 ± 14%; LGT = 11 ± 10%), BDI (ST = 1.8 ± 4; CT = 1.8 ± 3; LGT = 1 ± 2), 6MWT (ST = 43 ± 51 m; CT = 48 ± 50 m; LGT = 31 ± 75 m), and TEnd (ST = 11 ± 20 min; CT = 11 ± 11 min; LGT = 7 ± 5 min). In the ST and CT groups, an additional improvement in 1-RM values was shown (P < 0.05) compared to the LGT group (ST = 10 ± 6 to 57 ± 36 kg; CT = 6 ± 2 to 38 ± 16 kg; LGT = 1 ± 2 to 16 ± 12 kg). The addition of strength training to our current training program increased muscle strength; however, it produced no additional improvement in walking endurance, dyspnea or quality of life. A simple combined training program provides benefits without increasing the duration of the training sessions.

Health related quality of life among the elderly: a population-based study using SF-36 survey

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Production performance and egg quality of quails (Coturnix japonica) during several periods of the day

Three experiments were carried out to analyze the performance and egg quality of Japanese quails throughout the day when submitted to different lighting programs. In each experiment, birds were submitted to a period of 28 days for adaptation to the lighting program. During the following three days, each day - from 7 am to 7 pm or 9 pm - was divided into six or seven periods of two hours each, and the remaining hours corresponded to another single period. All birds were submitted to the same management practices, and received water and feed ad libitum. The experimental diet was formulated according to NRC (1994) standards. It was observed lower feed intake in the period of 9 pm to 7 am, and a higher incidence of lay from 3 pm to 7 pm, as opposite to hens, which peak of egg laying occurs during the morning. Some controversial results were found among experiments as to eggshell quality during the different periods of the day. Variation on the lighting program had little influence on the other performance and egg quality parameters.

Screening Brazilian commercial gasoline quality by hydrogen nuclear magnetic resonance spectroscopic fingerprintings and pattern-recognition multivariate chemometric analysis

The identification of gasoline adulteration by organic solvents is not an easy task, because compounds that constitute the solvents are already in gasoline composition. In this work, the combination of Hydrogen Nuclear Magnetic Resonance ((1)H NMR) spectroscopic fingerprintings with pattern-recognition multivariate Soft Independent Modeling of Class Analogy (SIMCA) chemometric analysis provides an original and alternative approach to screening Brazilian commercial gasoline quality in a Monitoring Program for Quality Control of Automotive Fuels. SIMCA was performed on spectroscopic fingerprints to classify the quality of representative commercial gasoline samples selected by Hierarchical Cluster Analysis (HCA) and collected over a 6-month period from different gas stations in the São Paulo state, Brazil. Following optimized the (1)H NMR-SIMCA algorithm, it was possible to correctly classify 92.0% of commercial gasoline samples, which is considered acceptable. The chemometric method is recommended for routine applications in Quality-Control Monitoring Programs, since its measurements are fast and can be easily automated. Also, police laboratories could employ this method for rapid screening analysis to discourage adulteration practices. (C) 2010 Elsevier B.V. All rights reserved.

Stream fish, water and habitat quality in a pasture dominated basin, southeastern Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)