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Qiaozhen Meng, Zhenling Peng, Jianyi Yang
Motivation: Coenzyme A (CoA)-protein binding plays an important role in various cellular functions and metabolic pathways. However, no computational methods can be employed for CoA-binding residues prediction. Results: We developed three methods for the prediction of CoA- and CoA derivatives-binding residues, including an ab-initio method SVMpred, a template-based method TemPred, and a consensus-based method CoABind. In SVMpred, a comprehensive set of features are designed from two complementary sequence profiles and the predicted secondary structure and solvent accessibility...
March 14, 2018: Bioinformatics
Tristan Pascart, Frédéric Lioté
This review article summarizes the relevant English literature on gout from 2010 through April 2017. It emphasizes that the current epidemiology of gout indicates a rising prevalence worldwide, not only in Western countries but also in Southeast Asia, in close relationship with the obesity and metabolic syndrome epidemics. New pathogenic mechanisms of chronic hyperuricaemia focus on the gut (microbiota, ABCG2 expression) after the kidney. Cardiovascular and renal comorbidities are the key points to consider in terms of management...
March 13, 2018: Rheumatology
Igor Mandric, Sergey Knyazev, Alex Zelikovsky
Summary: Genomic sequences are assembled into a variable, but large number of contigs that should be scaffolded (ordered and oriented) for facilitating comparative or functional analysis. Finding scaffolding is computationally challenging due to misassemblies, inconsistent coverage across the genome, and long repeats. An accurate assessment of scaffolding tools should take into account multiple locations of the same contig on the reference scaffolding rather than matching a repeat to a single best location...
March 14, 2018: Bioinformatics
Kiran T Thakur, Alexandra Boubour, Deanna Saylor, Mitashee Das, David R Bearden, Gretchen L Birbeck
: Neurological conditions associated with HIV remain major contributors to morbidity and mortality and are increasingly recognized in the aging population on long-standing combination antiretroviral therapy (cART). Importantly, growing evidence shows that the CNS may serve as a reservoir for viral replication, which has major implications for HIV eradication strategies. Though there has been major progress in the last decade in our understanding of the pathogenesis, burden, and impact of neurological conditions associated with HIV infection, significant scientific gaps remain...
March 15, 2018: AIDS
Lucia Romero, Jordi Cano, Julio Gomis-Tena, Beatriz Trenor, Ferran Sanz, Manuel Pastor, Javier Saiz
Drug-induced proarrhythmicity is a major concern for regulators and pharmaceutical companies. For novel drug candidates, the standard assessment involves the evaluation of the potassium hERG channels block and the in vivo prolongation of the QT interval. However, this method is known to be too restrictive and to stop the development of potentially valuable therapeutic drugs. The aim of this work is to create an in silico tool for early detection of drug-induced proarrhythmic risk. The system is based on simulations of how different compounds affect the action potential duration (APD) of isolated endocardial, midmyocardial, and epicardial cells as well as the QT prolongation in a virtual tissue...
March 16, 2018: Journal of Chemical Information and Modeling
Yizhi Zhuo, Verner Håkonsen, Zhiwei He, Senbo Xiao, Jianying He, Zhiliang Zhang
Ice accretion presents a severe risk for human safety. Despite great efforts for developing icephobic surfaces (the surface with an ice adhesion strength below 100 kPa) have been devoted, expanding the lifetime of state-of-the-art icephobic surfaces still remains as a critical unsolved issue. Herein, a novel icephobic material is designed by integrating interpenetrating polymer network (IPN) into autonomous self-healing elastomer, and applied in anti-icing for enhancing mechanical durability. The molecular structure, surface morphology, mechanical properties and durable icephobicity of the material were studied...
March 16, 2018: ACS Applied Materials & Interfaces
Rob Smith
Mass spectrometry is an important tool used by many scientists throughout the world. Nonetheless, feedback on the strengths and limitations of current software is often restricted to anecdote rather than formal inquiry. Over the course of 100 interviews over the state of mass spectrometry software, surprising patterns coalesced on several topics: perception of the frontier, perception of software quality, and differences between commercial and non-profit environments. Most notably, interviews suggested a substantial schism between user satisfaction with current software and developer perceptions of software quality...
March 16, 2018: Journal of Proteome Research
Yupeng Shen, Fancy Qian Wang, Jie Liu, Yaguang Guo, Xiaoyin Li, Guangzhao Qin, Ming Hu, Qian Wang
A new two-dimensional (2D) carbon allotrope, Hexa-C20, composed of C20 fullerene is proposed. State-of-the-art first principles calculations combined with solving the linearized phonon Boltzmann transport equation confirm that the new carbon structure is not only dynamically and thermally stable, but also can withstand temperatures as high as 1500 K. Hexa-C20 possesses a quasi-direct band gap of 3.28 eV, close to that of bulk ZnO and GaN. The intrinsic lattice thermal conductivity κlat of Hexa-C20 is 1132 W m-1 K-1 at room temperature, which is much larger than those of most carbon materials such as graphyne (82...
March 16, 2018: Nanoscale
Jose M Sanchez Bornot, KongFatt Wong-Lin, Alwani Liyana Ahmad, Girijesh Prasad
The brain's functional connectivity (FC) estimated at sensor level from electromagnetic (EEG/MEG) signals can provide quick and useful information towards understanding cognition and brain disorders. Volume conduction (VC) is a fundamental issue in FC analysis due to the effects of instantaneous correlations. FC methods based on the imaginary part of the coherence (iCOH) of any two signals are readily robust to VC effects, but neglecting the real part of the coherence leads to negligible FC when the processes are truly connected but with zero or π-phase (modulus 2π) interaction...
March 15, 2018: Brain Topography
Wail Alkashkari, Amani Alsubei, Ziyad M Hijazi
PURPOSE OF REVIEW: The past couple of decades have brought tremendous advances to the field of pediatric and adult congenital heart disease (CHD). Percutaneous valve interventions are now a cornerstone of not just the congenital cardiologist treating patients with congenital heart disease, but also-and numerically more importantly-for adult interventional cardiologists treating patients with acquired heart valve disease. Transcatheter pulmonary valve replacement (tPVR) is one of the most exciting recent developments in the treatment of CHD and has evolved to become an attractive alternative to surgery in patients with right ventricular outflow tract (RVOT) dysfunction...
March 15, 2018: Current Cardiology Reports
Jinkwon Jun, Soyoung Yoo
Neuroscientific imaging evidence (NIE) has become an integral part of the criminal justice system in the United States. However, in most legal cases, NIE is submitted and used only to mitigate penalties because the court does not recognize it as substantial evidence, considering its lack of reliability. Nevertheless, we here discuss how neuroscience is expected to improve the use of NIE in the legal system. For this purpose, we classified the efforts of neuroscientists into three research strategies: cognitive subtraction, the data-driven approach, and the brain-manipulation approach...
2018: Frontiers in Neuroscience
Dezső Ribli, Anna Horváth, Zsuzsa Unger, Péter Pollner, István Csabai
In the last two decades, Computer Aided Detection (CAD) systems were developed to help radiologists analyse screening mammograms, however benefits of current CAD technologies appear to be contradictory, therefore they should be improved to be ultimately considered useful. Since 2012, deep convolutional neural networks (CNN) have been a tremendous success in image recognition, reaching human performance. These methods have greatly surpassed the traditional approaches, which are similar to currently used CAD solutions...
March 15, 2018: Scientific Reports
Sara Moccia, Elena De Momi, Sara El Hadji, Leonardo S Mattos
BACKGROUND: Blood vessel segmentation is a topic of high interest in medical image analysis since the analysis of vessels is crucial for diagnosis, treatment planning and execution, and evaluation of clinical outcomes in different fields, including laryngology, neurosurgery and ophthalmology. Automatic or semi-automatic vessel segmentation can support clinicians in performing these tasks. Different medical imaging techniques are currently used in clinical practice and an appropriate choice of the segmentation algorithm is mandatory to deal with the adopted imaging technique characteristics (e...
May 2018: Computer Methods and Programs in Biomedicine
Shuchao Pang, Mehmet A Orgun, Zhezhou Yu
BACKGROUND AND OBJECTIVES: The traditional biomedical image retrieval methods as well as content-based image retrieval (CBIR) methods originally designed for non-biomedical images either only consider using pixel and low-level features to describe an image or use deep features to describe images but still leave a lot of room for improving both accuracy and efficiency. In this work, we propose a new approach, which exploits deep learning technology to extract the high-level and compact features from biomedical images...
May 2018: Computer Methods and Programs in Biomedicine
Sara Moccia, Gabriele O Vanone, Elena De Momi, Andrea Laborai, Luca Guastini, Giorgio Peretti, Leonardo S Mattos
BACKGROUND AND OBJECTIVE: Early-stage diagnosis of laryngeal cancer is of primary importance to reduce patient morbidity. Narrow-band imaging (NBI) endoscopy is commonly used for screening purposes, reducing the risks linked to a biopsy but at the cost of some drawbacks, such as large amount of data to review to make the diagnosis. The purpose of this paper is to present a strategy to perform automatic selection of informative endoscopic video frames, which can reduce the amount of data to process and potentially increase diagnosis performance...
May 2018: Computer Methods and Programs in Biomedicine
Piotr Chudzik, Somshubra Majumdar, Francesco Calivá, Bashir Al-Diri, Andrew Hunter
BACKROUND AND OBJECTIVES: Diabetic retinopathy is a microvascular complication of diabetes that can lead to sight loss if treated not early enough. Microaneurysms are the earliest clinical signs of diabetic retinopathy. This paper presents an automatic method for detecting microaneurysms in fundus photographies. METHODS: A novel patch-based fully convolutional neural network with batch normalization layers and Dice loss function is proposed. Compared to other methods that require up to five processing stages, it requires only three...
May 2018: Computer Methods and Programs in Biomedicine
Long Chen, Wen Tang, Nigel W John, Tao Ruan Wan, Jian Jun Zhang
BACKGROUND AND OBJECTIVE: While Minimally Invasive Surgery (MIS) offers considerable benefits to patients, it also imposes big challenges on a surgeon's performance due to well-known issues and restrictions associated with the field of view (FOV), hand-eye misalignment and disorientation, as well as the lack of stereoscopic depth perception in monocular endoscopy. Augmented Reality (AR) technology can help to overcome these limitations by augmenting the real scene with annotations, labels, tumour measurements or even a 3D reconstruction of anatomy structures at the target surgical locations...
May 2018: Computer Methods and Programs in Biomedicine
Amit Acharyya, Pranit N Jadhav, Valentina Bono, Koushik Maharatna, Ganesh R Naik
BACKGROUND AND OBJECTIVE: EEG is a non-invasive tool for neuro-developmental disorder diagnosis and treatment. However, EEG signal is mixed with other biological signals including Ocular and Muscular artifacts making it difficult to extract the diagnostic features. Therefore, the contaminated EEG channels are often discarded by the medical practitioners which may result in less accurate diagnosis. Many existing methods require reference electrodes, which will create discomfort to the patient/children and cause hindrance to the diagnosis of the neuro-developmental disorder and Brain Computer Interface in the pervasive environment...
May 2018: Computer Methods and Programs in Biomedicine
Jun Hao, Xinpei Ci, Hui Xue, Rebecca Wu, Xin Dong, Stephen Yiu Chuen Choi, Haiqing He, Yu Wang, Fang Zhang, Sifeng Qu, Fan Zhang, Anne M Haegert, Peter W Gout, Amina Zoubeidi, Colin Collins, Martin E Gleave, Dong Lin, Yuzhuo Wang
BACKGROUND: Although androgen deprivation therapy is initially effective in controlling growth of hormone-naive prostate cancers (HNPCs) in patients, currently incurable castration-resistant prostate cancer (CRPC) inevitably develops. OBJECTIVE: To identify CRPC driver genes that may provide new targets to enhance CRPC therapy. DESIGN, SETTING, AND PARTICIPANTS: Patient-derived xenografts (PDXs) of HNPCs that develop CRPC following host castration were examined for changes in expression of genes at various time points after castration using transcriptome profiling analysis; particular attention was given to pre-CRPC changes in expression indicative of genes acting as potential CRPC drivers...
March 12, 2018: European Urology
Irini A Doytchinova, Darren R Flower
Cancer kills 8 million annually worldwide. Although survival rates in prevalent cancers continue to increase, many cancers have no effective treatment, prompting the search for new and improved protocols. Immunotherapy is a new and exciting addition to the anti-cancer arsenal. The successful and accurate identification of aberrant host proteins acting as antigens for vaccination and immunotherapy is a key aspiration for both experimental and computational research. Here we describe key elements of in silico prediction, including databases of cancer antigens and bleeding-edge methodology for their prediction...
March 15, 2018: BMC Immunology
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