Prediction of Protein Domain with mRMR Feature Selection and Analysis

The domains are the structural and functional units of proteins. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to develop effective methods for predicting the protein domains according to the sequences information alone, so as to facilitate the structure prediction of proteins and speed up their functional annotation. However, although many efforts have been made in this regard, prediction of protein domains from the sequence information still remains a challenging and elusive problem. Here, a new method was developed by combing the techniques of RF (random forest), mRMR (maximum relevance minimum redundancy), and IFS (incremental feature selection), as well as by incorporating the features of physicochemical and biochemical properties, sequence conservation, residual disorder, secondary structure, and solvent accessibility. The overall success rate achieved by the new method on an independent dataset was around 73%, which was about 28–40% higher than those by the existing method on the same benchmark dataset. Furthermore, it was revealed by an in-depth analysis that the features of evolution, codon diversity, electrostatic charge, and disorder played more important roles than the others in predicting protein domains, quite consistent with experimental observations. It is anticipated that the new method may become a high-throughput tool in annotating protein domains, or may, at the very least, play a complementary role to the existing domain prediction methods, and that the findings about the key features with high impacts to the domain prediction might provide useful insights or clues for further experimental investigations in this area. Finally, it has not escaped our notice that the current approach can also be utilized to study protein signal peptides, B-cell epitopes, HIV protease cleavage sites, among many other important topics in protein science and biomedicine

Automatic lung health screening using respiratory sounds

Significant changes have been made on audio-based technologies over years in several different fields. Healthcare is no exception. One of such avenues is health screening based on respiratory sounds. In this paper, we developed a tool to detect respiratory sounds that come from respiratory infection carrying patients. Linear Predictive Cepstral Coefficient (LPCC)-based features were used to characterize such audio clips. With Multilayer Perceptron (MLP)-based classifier, in our experiment, we achieved the highest possible accuracy of 99.22% that was tested on a publicly available respiratory sounds dataset (ICBHI17) (Rocha et al. Physiol. Meas. 40(3):035,001 20) of size 6800+ clips. In addition to other popular machine learning classifiers, our results outperformed common works that exist in the literature

Incidence and drug treatment of emotional distress after cancer diagnosis : a matched primary care case-control study

Notes This work is published under the standard license to publish agreement. After 12 months the work will become freely available and the license terms will switch to a Creative Commons Attribution-NonCommercial-Share Alike 3.0 Unported License.Peer reviewedPublisher PD

Convergent Surface Water Distributions in U.S. Cities

Earth's surface is rapidly urbanizing, resulting in dramatic changes in the abundance, distribution and character of surface water features in urban landscapes. However, the scope and consequences of surface water redistribution at broad spatial scales are not well understood. We hypothesized that urbanization would lead to convergent surface water abundance and distribution: in other words, cities will gain or lose water such that they become more similar to each other than are their surrounding natural landscapes. Using a database of more than 1 million water bodies and 1 million km of streams, we compared the surface water of 100 US cities with their surrounding undeveloped land. We evaluated differences in areal (A WB) and numeric densities (N WB) of water bodies (lakes, wetlands, and so on), the morphological characteristics of water bodies (size), and the density (D C) of surface flow channels (that is, streams and rivers). The variance of urban A WB, N WB, and D C across the 100 MSAs decreased, by 89, 25, and 71%, respectively, compared to undeveloped land. These data show that many cities are surface water poor relative to undeveloped land; however, in drier landscapes urbanization increases the occurrence of surface water. This convergence pattern strengthened with development intensity, such that high intensity urban development had an areal water body density 98% less than undeveloped lands. Urbanization appears to drive the convergence of hydrological features across the US, such that surface water distributions of cities are more similar to each other than to their surrounding landscapes. © 2014 The Author(s)

Visualisation to enhance biomechanical tuning of ankle-foot orthoses (AFOs) in stroke: study protocol for a randomised controlled trial

There are a number of gaps in the evidence base for the use of ankle-foot orthoses for stroke patients. Three dimensional motion analysis offers an ideal method for objectively obtaining biomechanical gait data from stroke patients, however there are a number of major barriers to its use in routine clinical practice. One significant problem is the way in which the biomechanical data generated by these systems is presented. Through the careful design of bespoke biomechanical visualisation software it may be possible to present such data in novel ways to improve clinical decision making, track progress and increase patient understanding in the context of ankle-foot orthosis tuning

Planning a 'slum free' Trivandrum: housing upgrade and the rescaling of urban governance in India

This paper examines how India’s national urban development agenda is reshaping relationships between national, State and city-level governments. JNNURM, the flagship programme that heralded a new era of urban investment in India, contained a range of key governance aspirations: linking the analysis of urban poverty to city-level planning, developing holistic housing solutions for the urban poor, and above all empowering Urban Local Bodies to re-balance relationships between State and city-level governments in favour of the latter. Here, we trace JNNURM’s implementation in Kerala’s capital city, Trivandrum (Thiruvananthapuram), where the city’s decentralised urban governance structure and use of ‘pro-poor’ institutions to implement housing upgrade programmes could have made it an exemplar of success. In practice, Trivandrum’s ‘city visioning’ exercises and the housing projects it has undertaken have fallen short of JNNURM’s lofty goals. The contradictions between empowering cities and retaining centralised control embedded within this national programme, and the unintended city-level consequences of striving for JNNURM funding success, have reshaped urban governance in ways not envisaged within policy. As a result, JNNURM has been important in rescaling governance relationships through three interlinked dynamics of problem framing, technologies of governance and the scalar strategy of driving reform ‘from above’ that together have ensured the national state’s continued influence over the practices of urban governance in India

Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation

Domestication and selective breeding has resulted in over 1000 extant cattle breeds. Many of these breeds do not excel in important traits but are adapted to local environments. These adaptations are a valuable source of genetic material for efforts to improve commercial breeds. As a step toward this goal we identified candidate regions to be under selection in genomes of nine Russian native cattle breeds adapted to survive in harsh climates. After comparing our data to other breeds of European and Asian origins we found known and novel candidate genes that could potentially be related to domestication, economically important traits and environmental adaptations in cattle. The Russian cattle breed genomes contained regions under putative selection with genes that may be related to adaptations to harsh environments (e.g., AQP5, RAD50, and RETREG1). We found genomic signatures of selective sweeps near key genes related to economically important traits, such as the milk production (e.g., DGAT1, ABCG2), growth (e.g., XKR4), and reproduction (e.g., CSF2). Our data point to candidate genes which should be included in future studies attempting to identify genes to improve the extant breeds and facilitate generation of commercial breeds that fit better into the environments of Russia and other countries with similar climates

Optimal functional outcome measures for assessing treatment for Dupuytren's disease: A systematic review and recommendations for future practice

This article is available through the Brunel Open Access Publishing Fund. Copyright © 2013 Ball et al.; licensee BioMed Central Ltd.Background: Dupuytren's disease of the hand is a common condition affecting the palmar fascia, resulting in progressive flexion deformities of the digits and hence limitation of hand function. The optimal treatment remains unclear as outcomes studies have used a variety of measures for assessment. Methods: A literature search was performed for all publications describing surgical treatment, percutaneous needle aponeurotomy or collagenase injection for primary or recurrent Dupuytren’s disease where outcomes had been monitored using functional measures. Results: Ninety-one studies met the inclusion criteria. Twenty-two studies reported outcomes using patient reported outcome measures (PROMs) ranging from validated questionnaires to self-reported measures for return to work and self-rated disability. The Disability of Arm, Shoulder and Hand (DASH) score was the most utilised patient-reported function measure (n=11). Patient satisfaction was reported by eighteen studies but no single method was used consistently. Range of movement was the most frequent physical measure and was reported in all 91 studies. However, the methods of measurement and reporting varied, with seventeen different techniques being used. Other physical measures included grip and pinch strength and sensibility, again with variations in measurement protocols. The mean follow-up time ranged from 2 weeks to 17 years. Conclusions: There is little consistency in the reporting of outcomes for interventions in patients with Dupuytren’s disease, making it impossible to compare the efficacy of different treatment modalities. Although there are limitations to the existing generic patient reported outcomes measures, a combination of these together with a disease-specific questionnaire, and physical measures of active and passive individual joint Range of movement (ROM), grip and sensibility using standardised protocols should be used for future outcomes studies. As Dupuytren’s disease tends to recur following treatment as well as extend to involve other areas of the hand, follow-up times should be standardised and designed to capture both short and long term outcomes

The heterogeneous coma of comet 67P/Churyumov-Gerasimenko as seen by ROSINA: H <inf>2</inf> O, CO <inf>2</inf>, and CO from September 2014 to February 2016

Context. The ESA Rosetta mission has been investigating the environment of comet 67P/Churyumov-Gerasimenko (67P) since August 2014. Among the experiments on board the spacecraft, the ROSINA experiment (Rosetta Orbiter Spectrometer for Ion and Neutral Analysis) includes two mass spectrometers to analyse the composition of neutrals and ions and a COmet Pressure Sensor (COPS) to monitor the density and velocity of neutrals in the coma. Aims. We study heterogeneities in the coma during three periods starting in October 2014 (summer in the northern hemisphere) and ending in February 2016 (end of winter in the northern hemisphere). We provide a detailed description of the main volatiles dynamics (H2O, CO2, CO) and their abundance ratios. Methods. We analysed and compared the data of the Reflectron-Type Time-Of-Flight (RTOF) mass spectrometer with data from both the Double Focusing Mass Spectrometer (DFMS) and COPS during the comet escort phase. This comparison has demonstrated that the observations performed with each ROSINA sensor are indeed consistent. Furthermore, we used a Direct Simulation Monte Carlo (DSMC) model to compare modelled densitites with in situ detections. Results. Our analysis shows how the active regions of the main volatiles evolve with the seasons with a variability mostly driven by the illumination conditions; this is the case except for an unexpected dichotomy suggesting the presence of a dust layer containing water deposited in the northern hemisphere during previous perihelions hiding the presence of CO2. The influence of various parameters is investigated in detail: distance to the comet, heliocentric distance, longitude and latitude of sub-satellite point, local time, and phase angle