Protein Secondary Structure Prediction Using Support Vector Machines, Nueral Networks and Genetic Algorithms

Bioinformatics techniques to protein secondary structure prediction mostly depend on the information available in amino acid sequence. Support vector machines (SVM) have shown strong generalization ability in a number of application areas, including protein structure prediction. In this study, a new sliding window scheme is introduced with multiple windows to form the protein data for training and testing SVM. Orthogonal encoding scheme coupled with BLOSUM62 matrix is used to make the prediction. First the prediction of binary classifiers using multiple windows is compared with single window scheme, the results shows single window not to be good in all cases. Two new classifiers are introduced for effective tertiary classification. This new classifiers use neural networks and genetic algorithms to optimize the accuracy of the tertiary classifier. The accuracy level of the new architectures are determined and compared with other studies. The tertiary architecture is better than most available techniques

Protocol for a randomised control trial of methylnaltrexone for the treatment of opioid-induced constipation and gastrointestinal stasis in intensive care patients (MOTION)

Gastrointestinal dysmotility and constipation are common problems in intensive care patients. The majority of critical care patients are sedated with opioids to facilitate tolerance of endotracheal tubes and mechanical ventilation, which inhibit gastrointestinal motility and lead to adverse outcomes. Methylnaltrexone is a peripheral opioid antagonist that does not cross the blood-brain barrier and can reverse the peripheral side effects of opioids without affecting the desired central properties. This trial will investigate whether methylnaltrexone can reverse opioid-induced constipation and gastrointestinal dysmotility.This is a single-centre, multisite, double-blind, randomised, placebo-controlled trial. 84 patients will be recruited from 4 intensive care units (ICUs) within Imperial College Healthcare NHS Trust. Patients will receive intravenous methylnaltrexone or placebo on a daily basis if they are receiving opioid infusion to facilitate mechanical ventilation and have not opened their bowels for 48 hours. All patients will receive standard laxatives as per the clinical ICU bowel protocol prior to randomisation. The primary outcome of the trial will be time to significant rescue-free laxation following randomisation. Secondary outcomes will include tolerance of enteral feed, gastric residual volumes, incidence of pneumonia, blood stream and Clostridium difficile infection, and any reversal of central opioid effects.The trial protocol, the patient/legal representative information sheets and consent forms have been reviewed and approved by the Harrow Research Ethics Committee (REC Reference 14/LO/2004). An independent Trial Steering Committee and Data Monitoring Committee are in place, with patient representation. On completion, the trial results will be published in peer-reviewed journals and presented at national and international scientific meetings.2014-004687-37; Pre-results

XMM-Newton Observations of the Cataclysmic Variable GW Lib

XMM-Newton observations of the accreting, pulsating white dwarf in the quiescent dwarf nova GW Librae were conducted to determine if the non-radial pulsations present in previous UV and optical data affect the X-ray emission. The non-radial pulsations are evident in the simultaneous Optical Monitor data but are not detected in X-ray with an upper limit on the pulsation amplitude of 0.092 mags. The best fits to the X-ray spectrum are with a low temperature diffuse gas model or a multi-temperature cooling flow model, with a strong OVIII line, similar to other short period dwarf novae, but with a lower temperature range than evident in normal short period dwarf novae. The lack of pulsations and the spectrum likely indicate that the boundary layer does not extend to the surface of the white dwarf.Comment: 16 pages, 4 figures; accepted for publication in A

Explaining deep neural networks: A survey on the global interpretation methods

A substantial amount of research has been carried out in Explainable Artificial Intelligence (XAI) models, especially in those which explain the deep architectures of neural networks. A number of XAI approaches have been proposed to achieve trust in Artificial Intelligence (AI) models as well as provide explainability of specific decisions made within these models. Among these approaches, global interpretation methods have emerged as the prominent methods of explainability because they have the strength to explain every feature and the structure of the model. This survey attempts to provide a comprehensive review of global interpretation methods that completely explain the behaviour of the AI models. We present a taxonomy of the available global interpretations models and systematically highlight the critical features and algorithms that differentiate them from local as well as hybrid models of explainability. Through examples and case studies from the literature, we evaluate the strengths and weaknesses of the global interpretation models and assess challenges when these methods are put into practice. We conclude the paper by providing the future directions of research in how the existing challenges in global interpretation methods could be addressed and what values and opportunities could be realized by the resolution of these challenges

Self-perceived barriers to eye care in a hard-to-reach population: The Karachi marine fishing communities eye and general health survey

Abstract Purpose.: We examined self-reported barriers to eye care among marginalized, hard-to-reach fishing communities in Karachi, Pakistan. Methods.: The Karachi Marine Fishing Communities Eye and General Health Survey was a cross-sectional survey conducted between March 2009 and April 2010 in fishing communities in Keamari, Karachi, located on the coast of the Arabian Sea. Adults aged ≥50 years living on seven islands and coastal areas were interviewed regarding sociodemographic background, experience of eye problems, eye care use, and barriers to access. They also were examined to determine visual acuity with a reduced logMAR chart and underwent a detailed eye examination. Results.: Of 700 people planned to be included in the study, 638 (91.1%) were interviewed and examined. Of these participants, 599 (93.9%) lived in extreme poverty and 84.3% had no school-based education, and 349 (54.7%; 95% confidence interval [CI], 50.8–58.6) of them had never had an eye examination. The common barriers to access identified included a perceived lack of or low need (176/349 or 50.4%), financial hardships (36.4%), “fears” (8.6%), and social support constraints (6.3%). Of those reporting a “lack of need,” 21.9% had significant visual loss. Financial hardships, “fears,” and social support constraints were more prevalent among women than men. Bengalis compared to Kutchis and Sindhis, and individuals with “poor/fragile” household financial status (self-reported) compared to those with “fine” status, were more likely to cite financial hardships. Conclusions.: Access to eye care in this marginalized population is substantially hindered by perceived lack of need, financial hardships, and a range of “fears” and anxieties, despite a large unmet need. These barriers should be addressed while paying particular attention to gender, and ethnic and socioeconomic differences

Effect of microneedling by dermaroller on acne scars: an observational study at tertiary care hospital

Background: Post acne facial scar is very distressing phenomenon. There are many treatment options like laser resurfacing, dermabrasion, microdermabrasion and non-ablative laser resurfacing but it may cause adverse effects and interference with the daily activities of the patient. Microneedling or dermaroller therapy is newer modality in management of acne scars with satisfactory improvement and no significant side effect. Objective of our study was to evaluate efficacy and safety of microneedling in the treatment of atrophic facial acne scars. Methods: Twenty-eight patients of Fitzpatrick skin type IV to V having atrophic facial acne scars and fulfilling inclusion criteria were treated with multiple sittings of microneedling (dermaroller) treatment at monthly interval. Goodman and Baron’s qualitative and quantitative acne scar grading system was used for assessment. Patients were evaluated clinically and by serial photography. Presence of any active infection, active acne, wounds, blisters, keloids, taking some medications like Accutane, antihypertensives, anticoagulants, systemic retinoids, topical retinoids, those undergoing cosmetic procedures, treatment with injecting fillers or ablative or non-ablative laser resurfacing, diabetes, collagen diseases and those who do not agree to participate in study were excluded. Results: Any change in the grading of scars after the end of treatment and follow-up period was noted. Efficacy and improvement of dermaroller treatment was assessed by Goodman and Baron’s global acne scarring system. Out of 18 patients (of total 28) with Goodman and Baron’s qualitative grade-4, 16 (88.90%) patients reduced to grade-1. 21 out of 28 patients achieved ‘excellent’ response. Adverse effects were limited to transient erythema and post inflammatory hyperpigmentation. Conclusions: Microneedling therapy seems to be simple, safe and efficacious for the management of atrophic facial acne scars

A semantic rule based digital fraud detection

Digital fraud has immensely affected ordinary consumers and the finance industry. Our dependence on internet banking has made digital fraud a substantial problem. Financial institutions across the globe are trying to improve their digital fraud detection and deterrence capabilities. Fraud detection is a reactive process, and it usually incurs a cost to save the system from an ongoing malicious activity. Fraud deterrence is the capability of a system to withstand any fraudulent attempts. Fraud deterrence is a challenging task and researchers across the globe are proposing new solutions to improve deterrence capabilities. In this work, we focus on the very important problem of fraud deterrence. Our proposed work uses an Intimation Rule Based (IRB) alert generation algorithm. These IRB alerts are classified based on severity levels. Our proposed solution uses a richer domain knowledge base and rule-based reasoning. In this work, we propose an ontology-based financial fraud detection and deterrence model

Production of sensitive gas sensors using CuO/SnO2 nanoparticles

Metal oxide nanoparticles, such as CuO and SnO2, are outstanding systems for H2S gas sensing in air. In this work, those nanoparticles were deposited with different mixing percentages on substrates to form percolating networks of nanoparticles. Electrical electrodes were deposited on the nanoparticles’ films to investigate their gas sensing response against H2 and H2S, and their electrical characteristics. The sensor devices based on CuO–SnO2 nanoparticles revealed enhanced sensing characteristics against H2S with a sensitivity of 10 ppm. The enhanced sensing characteristics could be attributed to the formation of PN-junctions among CuO and SnO2 nanoparticles. The reasonable production cost (due to simple structure and cheap used materials), low power consumption ( ~ 1 µW for H2S at room temperature), high sensitivity, high response, and reasonable response time of the present sensors qualify them for practical implementation in portable gas sensing devices with enhanced characteristics.Open Access funding provided by the Qatar National Library. This work was supported by both Qatar National Research Fund (QNRF) under a Grant Number UREP21-035-2-013, and Qatar University fund under a Grant Number QUCG-CAS-20182019-1. The SEM/EDS measurements were accomplished in the Central Laboratories unit at Qatar University. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations