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Piotr Klukowski, Michal Augoff, Maciej Zieba, Maciej Drwal, Adam Gonczarek, Michal J Walczak
Motivation: Automated selection of signals in protein NMR spectra, known as peak picking, has been studied for over 20 years, nevertheless existing peak picking methods are still largely deficient. Accurate and precise automated peak picking would accelerate the structure calculation, and analysis of dynamics and interactions of macromolecules. Recent advancement in handling big data, together with an outburst of machine learning techniques, offer an opportunity to tackle the peak picking problem substantially faster than manual picking and on par with human accuracy...
March 14, 2018: Bioinformatics
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
M Martínez-García, J Vargas-Barrón, F Bañuelos-Téllez, H González-Pacheco, C Fresno, E Hernández-Lemus, M A Martínez-Ríos, M Vallejo
OBJECTIVE: ST-segment elevation myocardial infarction (STEMI) has an important economic burden that poised the urgent need to evaluate its catastrophic medical expense. This study evaluates the first 5 years of the national health initiative called Popular Insurance (PI) at the National Institute of Cardiology in Mexico. STUDY DESIGN: Retrospective data analysis. METHODS: STEMI patients with (n=317) and without (n=260) PI were selected. Analysed variables included socio-economical context, management care, cost evaluation and three outcomes (mortality, hospital readmission and therapeutic adherence)...
March 13, 2018: Public Health
Cheng Jin, Jianjiang Feng, Lei Wang, Heng Yu, Jiang Liu, Jiwen Lu, Jie Zhou
In this paper, we present an approach for left atrial appendage (LAA) multi-phase fast segmentation and quantitative assisted diagnosis of atrial fibrillation (AF) based on 4D-CT data. We take full advantage of the temporal dimension information to segment the living, flailed LAA based on a parametric max-flow method and graph-cut approach to build 3-D model of each phase. To assist the diagnosis of AF, we calculate the volumes of 3-D models, and then generate a "volume-phase" curve to calculate the important dynamic metrics: ejection fraction, filling flux, and emptying flux of the LAA's blood by volume...
March 9, 2018: Computers in Biology and Medicine
Hendrik Göddeke, M Hadi Timachi, Cedric A Hutter, Laura Galazzo, Markus A Seeger, Mikko Karttunen, Enrica Bordignon, Lars V Schäfer
ATP-binding cassette (ABC) transporters are ATP-driven molecular machines, in which ATP binding and hydrolysis in the nucleotide-binding domains (NBDs) is chemo-mechanically coupled to large-scale, alternating access conformational changes in the transmembrane domains (TMDs), ultimately leading to the translocation of substrates across biological membranes. The precise nature of the structural dynamics behind the large-scale conformational transition as well as the coupling of NBD and TMD motions is still unresolved...
March 16, 2018: Journal of the American Chemical Society
Shanon Seger, Manuel Stritt, Enrico Vezzali, Oliver Nayler, Patrick Hess, Peter M A Groenen, Anna K Stalder
Intratracheal administration of bleomycin induces fibrosis in the lung, which is mainly assessed by histopathological grading that is subjective. Current literature highlights the need of reproducible and quantitative pulmonary fibrosis analysis. If some quantitative studies looked at fibrosis parameters separately, none of them quantitatively assessed both aspects: lung tissue remodeling and collagenization. To ensure reliable quantification, support vector machine learning was used on digitalized images to design a fully automated method that analyzes two important aspects of lung fibrosis: (i) areas having substantial tissue remodeling with appearance of dense fibrotic masses and (ii) collagen deposition...
2018: PloS One
Andrew McDowell, Neeraj Raizada, Sunil D Khaparde, Raghuram Rao, Sanjay Sarin, Aakshi Kalra, Virender Singh Salhotra, Sreenivas Achuthan Nair, Catharina Boehme, Claudia M Denkinger
BACKGROUND: Diagnosing tuberculosis (TB) in children presents considerable challenges. Upfront testing on Xpert® MTB/RIF ('Xpert')-a rapid molecular assay with high sensitivity and specificity-for pediatric presumptive TB patients, as recommended by India's Revised National Tuberculosis Control Program (RNTCP), can pave the way for early TB diagnosis. As part of an ongoing project implemented by Foundation for Innovative New Diagnostics (FIND) dedicated to providing upfront free-of-cost (FOC) Xpert testing to children seeking care in the public and private sectors, a qualitative assessment was designed to understand how national guidelines on TB diagnosis and Xpert technology have been integrated into the pediatric TB care practices of different health providers...
2018: PloS One
Aïsha Sahaï, Elisabeth Pacherie, Ouriel Grynszpan, Bruno Berberian
[This corrects the article on p. 52 in vol. 11, PMID: 29081744.].
2018: Frontiers in Neurorobotics
Jing Zhang, Siyue Li, Ruozhu Dong, Changsheng Jiang
The Three Gorges Reservoir (TGR) is one of the largest hydropower reservoirs in the world. However, changes of the important physical characteristics of the reservoir covering pre-, during-, and post- dam have not been well studied. This study analyzed the lengths and water surface areas of the TGR using advanced support vector machine method (SVM) combined Landsat images with the Shuttle Radar Topography Mission (SRTM) digital elevation model (DEM), which showed an increasing trend of lengths and surface areas with variable growth rates from pre-dam period to post-dam period...
March 15, 2018: Environmental Science and Pollution Research International
Li Zhang, Jiasheng Chen, Chunming Gao, Chuanmiao Liu, Kuihua Xu
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide. The early diagnosis of HCC is greatly helpful to achieve long-term disease-free survival. However, HCC is usually difficult to be diagnosed at an early stage. The aim of this study was to create the prediction model to diagnose HCC based on gene expression programming (GEP). GEP is an evolutionary algorithm and a domain-independent problem-solving technique. Clinical data show that six serum biomarkers, including gamma-glutamyl transferase, C-reaction protein, carcinoembryonic antigen, alpha-fetoprotein, carbohydrate antigen 153, and carbohydrate antigen 199, are related to HCC characteristics...
March 16, 2018: Medical & Biological Engineering & Computing
Runyu Jing, Yu Liang, Yi Ran, Shengzhong Feng, Yanjie Wei, Li He
In genetic data modeling, the use of a limited number of samples for modeling and predicting, especially well below the attribute number, is difficult due to the enormous number of genes detected by a sequencing platform. In addition, many studies commonly use machine learning methods to evaluate genetic datasets to identify potential disease-related genes and drug targets, but to the best of our knowledge, the information associated with the selected gene set was not thoroughly elucidated in previous studies...
2018: International Journal of Genomics
Florian Ferreri, Alexis Bourla, Stephane Mouchabac, Laurent Karila
Background: New technologies can profoundly change the way we understand psychiatric pathologies and addictive disorders. New concepts are emerging with the development of more accurate means of collecting live data, computerized questionnaires, and the use of passive data. Digital phenotyping , a paradigmatic example, refers to the use of computerized measurement tools to capture the characteristics of different psychiatric disorders. Similarly, machine learning-a form of artificial intelligence-can improve the classification of patients based on patterns that clinicians have not always considered in the past...
2018: Frontiers in Psychiatry
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
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
Yoonjin Nah, Na-Young Shin, Sehjung Yi, Seung-Koo Lee, Sanghoon Han
Numerous studies have suggested that postpartum women show a decline in cognitive abilities. However, to date, no study has investigated the presence of qualitative alterations in recognition memory processes in postpartum women that may lead to a decline in cognitive ability. To address this issue, we employed the Remember/Know procedure and functional magnetic resonance imaging (fMRI). Behavioral results demonstrated that compared with the matched control (CTRL) group, the postpartum (PP) group endorsed "Remember" less and "Know" more to old items...
March 12, 2018: Neurobiology of Learning and Memory
Brendan Joyce, Danny Lee, Alex Rubio, Aleksey Ogurtsov, Gelio Alves, Yi-Kuo Yu
OBJECTIVE: RAId is a software package that has been actively developed for the past 10 years for computationally and visually analyzing MS/MS data. Founded on rigorous statistical methods, RAId's core program computes accurate E-values for peptides and proteins identified during database searches. Making this robust tool readily accessible for the proteomics community by developing a graphical user interface (GUI) is our main goal here. RESULTS: We have constructed a graphical user interface to facilitate the use of RAId on users' local machines...
March 15, 2018: BMC Research Notes
Florian Lamping, Thomas Jack, Nicole Rübsamen, Michael Sasse, Philipp Beerbaum, Rafael T Mikolajczyk, Martin Boehne, André Karch
BACKGROUND: Since early antimicrobial therapy is mandatory in septic patients, immediate diagnosis and distinction from non-infectious SIRS is essential but hampered by the similarity of symptoms between both entities. We aimed to develop a diagnostic model for differentiation of sepsis and non-infectious SIRS in critically ill children based on routinely available parameters (baseline characteristics, clinical/laboratory parameters, technical/medical support). METHODS: This is a secondary analysis of a randomized controlled trial conducted at a German tertiary-care pediatric intensive care unit (PICU)...
March 15, 2018: BMC Pediatrics
K Beltako, F Michelini, N Cavassilas, L Raymond
Nanoscale molecular-electronic devices and machines are emerging as promising functional elements, naturally flexible and efficient, for next-generation technologies. A deeper understanding of carrier dynamics in molecular junctions is expected to benefit many fields of nanoelectronics and power devices. We determine time-resolved charge current flowing at the donor-acceptor interface in molecular junctions connected to metallic electrodes by means of quantum transport simulations. The current is induced by the interaction of the donor with a Gaussian-shape femtosecond laser pulse...
March 14, 2018: Journal of Chemical Physics
Irene Fondón, Auxiliadora Sarmiento, Ana Isabel García, María Silvestre, Catarina Eloy, António Polónia, Paulo Aguiar
Breast cancer is the second leading cause of cancer death among women. Its early diagnosis is extremely important to prevent avoidable deaths. However, malignancy assessment of tissue biopsies is complex and dependent on observer subjectivity. Moreover, hematoxylin and eosin (H&E)-stained histological images exhibit a highly variable appearance, even within the same malignancy level. In this paper, we propose a computer-aided diagnosis (CAD) tool for automated malignancy assessment of breast tissue samples based on the processing of histological images...
March 8, 2018: Computers in Biology and Medicine
Sheng Yan, Yuxing Li, Yuanqing Zhu, Minsu Liu, Qianbin Zhao, Dan Yuan, Guolin Yun, Shiwu Zhang, Weijia Wen, Shi-Yang Tang, Weihua Li
This work presents a simple, low-cost method to fabricate semi-circular channels using solder paste, which can amalgamate the cooper surface to form a half-cylinder mould using the surface tension of Sn-Pd alloy (the main component in solder paste). This technique enables semi-circular channels to be manufactured with different dimensions. These semi-circular channels will then be integrated with a polymethylmethacrylate (PMMA) frame and machine screws to create miniaturised, portable microfluidic valves for sequential liquid delivery and particle synthesis...
March 15, 2018: Electrophoresis
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