Profiles and Majority Voting-Based Ensemble Method for Protein Secondary Structure Prediction

Machine learning techniques have been widely applied to solve the problem of predicting protein secondary structure from the amino acid sequence. They have gained substantial success in this research area. Many methods have been used including k-Nearest Neighbors (k-NNs), Hidden Markov Models (HMMs), Artificial Neural Networks (ANNs) and Support Vector Machines (SVMs), which have attracted attention recently. Today, the main goal remains to improve the prediction quality of the secondary structure elements. The prediction accuracy has been continuously improved over the years, especially by using hybrid or ensemble methods and incorporating evolutionary information in the form of profiles extracted from alignments of multiple homologous sequences. In this paper, we investigate how best to combine k-NNs, ANNs and Multi-class SVMs (M-SVMs) to improve secondary structure prediction of globular proteins. An ensemble method which combines the outputs of two feed-forward ANNs, k-NN and three M-SVM classifiers has been applied. Ensemble members are combined using two variants of majority voting rule. An heuristic based filter has also been applied to refine the prediction. To investigate how much improvement the general ensemble method can give rather than the individual classifiers that make up the ensemble, we have experimented with the proposed system on the two widely used benchmark datasets RS126 and CB513 using cross-validation tests by including PSI-BLAST position-specific scoring matrix (PSSM) profiles as inputs. The experimental results reveal that the proposed system yields significant performance gains when compared with the best individual classifier

Urgent referral for suspected CNS cancer: which clinical features are associated with a positive predictive value of 3 % or more?

Background Urgent referral for suspected central nervous system (CNS) cancer is recommended, but little analysis of the referral criteria diagnostic performance has been conducted. New 2015 NICE guidance recommends direct brain imaging for patients with symptoms with positive predictive values (PPV) of 3 %, but further guidance is needed. Methods A 12-month retrospective evaluation of 393 patients referred under previous 2005 NICE 2-week rule criteria was conducted. Analysis was based on the three groups of symptoms forming the referral criteria, (1) CNS symptoms, (2) recent onset headaches, (3) rapidly progressive subacute focal deficit/cognitive/behavioural/personality change. Comparison was made with neuroimaging findings. Results Twelve (3.1 %) of 383 patients who attended clinic had CNS cancer suggesting the combination of clinical judgement and application of 2005 criteria matched the 2015 guideline’s PPV threshold. PPVs for the three groups of symptoms were (1) 4.1 % (95 % CIs 2.0 to 7.4 %), (2) 1.2 % (0.1 to 4.3 %) and (3) 3.7 % (0.1 to 19.0 %). Sensitivities were (1) 83.3 % (95 % CIs 51.6 to 97.9 %), (2) 16.7 % (2.1 to 48.4 %), and (3) 8.3 % (0.2 to 38.5 %); specificities were (1) 37.2 % (32.3 to 42.3 %), (2) 55.5 % (50.3 to 60.7 %) and (3) 93.0 % (89.9 to 95.4 %). Of 288 patients who underwent neuroimaging, 59 (20.5 %) had incidental findings, most commonly cerebrovascular disease. Conclusions The 2015 guidance is less prescriptive than previous criteria making clinical judgement more important. CNS symptoms had greatest sensitivity, while PPVs for CNS symptoms and rapidly progressive subacute deficit/cognitive/behavioural/personality change were closest to 3 %. Recent onset headaches had the lowest sensitivity and PPV

A Conceptual Model of Natural and Anthropogenic Drivers and Their Influence on the Prince William Sound, Alaska, Ecosystem

Prince William Sound (PWS) is a semi-enclosed fjord estuary on the coast of Alaska adjoining the northern Gulf of Alaska (GOA). PWS is highly productive and diverse, with primary productivity strongly coupled to nutrient dynamics driven by variability in the climate and oceanography of the GOA and North Pacific Ocean. The pelagic and nearshore primary productivity supports a complex and diverse trophic structure, including large populations of forage and large fish that support many species of marine birds and mammals. High intra-annual, inter-annual, and interdecadal variability in climatic and oceanographic processes as drives high variability in the biological populations. A risk-based conceptual ecosystem model (CEM) is presented describing the natural processes, anthropogenic drivers, and resultant stressors that affect PWS, including stressors caused by the Great Alaska Earthquake of 1964 and the Exxon Valdez oil spill of 1989. A trophodynamic model incorporating PWS valued ecosystem components is integrated into the CEM. By representing the relative strengths of driver/stressors/effects, the CEM graphically demonstrates the fundamental dynamics of the PWS ecosystem, the natural forces that control the ecological condition of the Sound, and the relative contribution of natural processes and human activities to the health of the ecosystem. The CEM illustrates the dominance of natural processes in shaping the structure and functioning of the GOA and PWS ecosystems

Views and Experiences of Sex, Sexuality and Relationships Following Spinal Cord Injury: A Systematic Review and Narrative Synthesis of the Qualitative Literature

Research examining the effects of spinal cord injury on sexuality has largely focused on physiological functioning and quantification of dysfunction following injury. This paper reports a systematic review of qualitative research that focused on the views and experiences of people with spinal cord injury on sex and relationships. The review addressed the following research question: What are the views and experiences of people with spinal cord injury of sex, sexuality and relationships following injury? Five databases were relevant and employed in the review: CINAHL (1989-2016 only), PsychInfo, PubMed, Scopus and Web of Science, for research published between 1 January 1980 and 30 November 2019. After removing duplicates, 257 records remained and were screened using a two-stage approach to inclusion and quality appraisal. Following screening, 27 met the criteria for inclusion and are reported in the paper. The review includes studies from fifteen countries across five continents. Two main approaches to data analysis summary and thematic synthesis were undertaken to analyze the qualitative data reported in the papers. The analysis revealed four main themes: sexual identity; significant and generalized others, sexual embodiment; and; sexual rehabilitation and education

Developmental Exposure to a Toxic Spill Compromises Long-Term Reproductive Performance in a Wild, Long-Lived Bird: The White Stork (Ciconia ciconia)

Background/Objective: Exposure to environmental contaminants may result in reduced reproductive success and long- lasting population declines in vertebrates. Emerging data from laboratory studies on model species suggest that certain life- stages, such as development, should be of special concern. However, detailed investigations of long-term consequences of developmental exposure to environmental chemicals on breeding performance are currently lacking in wild populations of long-lived vertebrates. Here, we studied how the developmental exposure to a mine spill (Aznalco´ llar, SW Spain, April 1998) may affect fitness under natural conditions in a long-lived bird, the White Stork (Ciconia ciconia). Methodology: The reproductive performance of individually-banded storks that were or not developmentally exposed to the spill (i.e. hatched before or after the spill) was compared when these individuals were simultaneously breeding during the seven years after the spill occurred (1999–2005). Principal Findings: Female storks developmentally exposed to the spill experienced a premature breeding senescence compared with their non-developmentally exposed counterparts, doing so after departing from an unusually higher productivity in their early reproductive life (non-developmentally exposed females: 0.560.33SE fledglings/year at 3-yr old vs. 1.3860.31SE at 6–7 yr old; developmentally exposed females: 1.560.30SE fledglings/year at 3-yr old vs. 0.8660.25SE at 6– 7 yr old). Conclusions/Significance: Following life-history theory, we propose that costly sub-lethal effects reported in stork nestlings after low-level exposure to the spill-derived contaminants might play an important role in shaping this pattern of reproduction, with a clear potential impact on population dynamics. Overall, our study provides evidence that environmental disasters can have long-term, multigenerational consequences on wildlife, particularly when affecting developing individuals, and warns about the risk of widespread low-level contamination in realistic scenarios.Peer reviewe

Life Expectancy at Birth for People with Serious Mental Illness and Other Major Disorders from a Secondary Mental Health Care Case Register in London

Despite improving healthcare, the gap in mortality between people with serious mental illness (SMI) and general population persists, especially for younger age groups. The electronic database from a large and comprehensive secondary mental healthcare provider in London was utilized to assess the impact of SMI diagnoses on life expectancy at birth.People who were diagnosed with SMI (schizophrenia, schizoaffective disorder, bipolar disorder), substance use disorder, and depressive episode/disorder before the end of 2009 and under active review by the South London and Maudsley NHS Foundation Trust (SLAM) in southeast London during 2007-09 comprised the sample, retrieved by the SLAM Case Register Interactive Search (CRIS) system. We estimated life expectancy at birth for people with SMI and each diagnosis, from national mortality returns between 2007-09, using a life table method.A total of 31,719 eligible people, aged 15 years or older, with SMI were analyzed. Among them, 1,370 died during 2007-09. Compared to national figures, all disorders were associated with substantially lower life expectancy: 8.0 to 14.6 life years lost for men and 9.8 to 17.5 life years lost for women. Highest reductions were found for men with schizophrenia (14.6 years lost) and women with schizoaffective disorders (17.5 years lost).The impact of serious mental illness on life expectancy is marked and generally higher than similarly calculated impacts of well-recognised adverse exposures such as smoking, diabetes and obesity. Strategies to identify and prevent causes of premature death are urgently required