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Feature selection

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
Silvia Salerno, Aída Nelly García-Argáez, Elisabetta Barresi, Sabrina Taliani, Francesca Simorini, Concettina La Motta, Giorgio Amendola, Stefano Tomassi, Sandro Cosconati, Ettore Novellino, Federico Da Settimo, Anna Maria Marini, Lisa Dalla Via
Inhibition of angiogenesis via blocking vascular endothelial growth factor receptor (VEGFR) signaling pathway emerged as an established approach in anticancer therapy. So far, many monoclonal antibodies and ATP-competitive small molecule inhibitors have been clinically validated and approved. In this study, structure-activity relationships (SAR) within the 2-phenylamino-substituted benzothiopyrano[4,3-d]pyrimidine class of kinase inhibitors were further refined by the synthesis and biological evaluation of new compounds 1-21 featuring different substitution patterns on the pendant phenyl moiety, combined with H, OCH3 , or Cl at 8-position...
March 7, 2018: European Journal of Medicinal Chemistry
Ariana Sherdil, Stéphan Chabardès, Isabelle Guillemain, Sandrine Michallat, Shivadatta Prabhu, Karine Pernet-Gallay, Olivier David, Brigitte Piallat
PURPOSE: Our objective was to propose a new on demand non-human primate model of mesial temporal lobe seizures suitable for pre-clinical innovative therapeutic research. METHODS: Five macaques were stereotaxically implanted unilaterally with a deep recording electrode in the hippocampus. For each experiment, penicillin was injected into the hippocampus and animals were monitored during five consecutive hours. A total of 12-27 experiments with a mean cumulative dose of 162644 ± 70190 UI of penicillin have been performed per animal Injections were repeated at least once a week over a period of 98-276 days...
March 9, 2018: Epilepsy Research
William W L Sampson, Sara A Khan, Eric J Nisenbaum, Jerald D Kralik
Abstraction allows us to discern regularities beyond the specific instances we encounter. It also promotes creative problem-solving by enabling us to consider unconventional problem solutions. However, the mechanisms by which this occurs are not well understood. Because it is often difficult to isolate human high-level cognitive processes, we utilized a nonhuman primate model, in which rhesus monkeys appear to use similar processes to consider an unconventional solution to the difficult reverse-reward problem: i...
March 13, 2018: Cognition
Martin A Bewley, Richard C Budd, Eilise Ryan, Joby Cole, Paul Collini, Jennifer Marshall, Umme Kolsum, Gussie Beech, Richard D Emes, Irina Tcherniaeva, Guy A M Berbers, Sarah R Walmsley, Gavin Donaldson, Jadwiga A Wedzicha, Iain Kilty, William Rumsey, Yolanda Sanchez, Christopher E Brightling, Louise E Donnelly, Peter J Barnes, Dave Singh, Moira K B Whyte, David H Dockrell
RATIONALE: Previous studies have identified defects in bacterial phagocytosis by alveolar macrophages (AM) in patients with chronic obstructive pulmonary disease (COPD) but the mechanisms and clinical consequences remain incompletely defined. OBJECTIVES: To examine the effect of COPD on AM phagocytic responses and identify the mechanisms, clinical consequences and potential for therapeutic manipulation of these defects. METHODS: We isolated alveolar macrophages (AM) and monocyte-derived macrophages (MDM) from a cohort of COPD patients and controls within the MRC COPD-MAP consortium and measured phagocytosis of bacteria in relation to opsonic conditions and clinical features...
March 16, 2018: American Journal of Respiratory and Critical Care Medicine
Eloisa Basile, Giulio Russo, Antonio M Leone
It is essential to understand the pathophysiology of cardiogenic shock and the possible deterioration of contractile function during high-risk PCI in order to select those patients who could benefit from mechanical support thus choosing the most suitable device in every situation. Percutaneous Ventricular Assist Devices (pVAD) provide hemodynamic support by improving cardiac output and mean arterial pressure, but their specific features result in different hemodynamic effects and degrees of myocardial ischemic protection and LV unloading...
March 15, 2018: Minerva Cardioangiologica
Jyoti Singh Kirar, R K Agrawal
This paper presents a novel algorithm (CVSTSCSP) for determining discriminative features from an optimal combination of temporal, spectral and spatial information for motor imagery brain computer interfaces. The proposed method involves four phases. In the first phase, EEG signal is segmented into overlapping time segments and bandpass filtered through frequency filter bank of variable size subbands. In the next phase, features are extracted from the segmented and filtered data using stationary common spatial pattern technique (SCSP) that can handle the non- stationarity and artifacts of EEG signal...
March 16, 2018: Journal of Medical Systems
Marcela Ewing, Peter Naredi, Chenyang Zhang, Jörgen Månsson
Background: Many patients with common cancers are late diagnosed. Objectives: Identify consultation profiles and clinical features in patients with the seven most common cancers, who had consulted a general practitioner (GP) frequently before their cancer diagnosis. Methods: A case-control study was conducted in Region Västra Götaland, Sweden. A total of 2570 patients, diagnosed in 2011 with prostate, breast, colorectal, lung, gynaecological and skin cancers including malignant melanoma, and 9424 controls were selected from the Swedish Cancer Register and a regional health care database...
March 13, 2018: Family Practice
Long Chen, Yifeng Jiang, Zhen Du
Although previous studies have demonstrated that dental pulp stem cells (DPSCs) from mature and immature teeth exhibit potential for multi-directional differentiation, the molecular and biological difference between the DPSCs from mature and immature permanent teeth has not been fully investigated. In the present study, 500 differentially expressed genes from dental pulp cells (DPCs) in mature and immature permanent teeth were obtained from the Gene Expression Omnibus online database. Based on bioinformatics analysis using the Database for Annotation, Visualization and Integrated Discovery, these genes were divided into a number of subgroups associated with immunity, inflammation and cell signaling...
April 2018: Experimental and Therapeutic Medicine
Peter L Cummins, Babu Kannappan, Jill E Gready
The ubiquitous enzyme Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) fixes atmospheric carbon dioxide within the Calvin-Benson cycle that is utilized by most photosynthetic organisms. Despite this central role, RuBisCO's efficiency surprisingly struggles, with both a very slow turnover rate to products and also impaired substrate specificity, features that have long been an enigma as it would be assumed that its efficiency was under strong evolutionary pressure. RuBisCO's substrate specificity is compromised as it catalyzes a side-fixation reaction with atmospheric oxygen; empirical kinetic results show a trend to tradeoff between relative specificity and low catalytic turnover rate...
2018: Frontiers in Plant Science
Carlos Perez-Sánchez, Iván Arias-de la Rosa, María Ángeles Aguirre, María Luque-Tévar, Patricia Ruiz-Limón, Nuria Barbarroja, Yolanda Jiménez-Gómez, María Carmen Ábalos-Aguilera, Eduardo Collantes-Estévez, Pedro Segui, Francisco Velasco, María Teresa Herranz, Jesús Lozano-Herrero, María Julia Hernandez-Vidal, Constantino Martínez, Rocío González-Conejero, Massimo Radin, Savino Sciascia, Irene Cecchi, María José Cuadrado, Chary López-Pedrera
The present study aimed at identifying the plasma miRNA profile of antiphospholipid syndrome patients and to investigate the potential role of specific circulating miRNAs as non-invasive disease biomarkers. Ninety antiphospholipid syndrome patients and 42 healthy donors were recruited. Profiling of miRNAs by PCR-array in plasma of antiphospholipid syndrome patients allowed identifying a set of miRNAs differentially expressed and collectively involved in clinical features. Logistic Regression and ROC-curve analyses identified a signature of 10 miRNA ratios as biomarkers of disease...
March 15, 2018: Haematologica
Hisao Tsukamoto, Masahiro Higashi, Hideyoshi Motoki, Hiroki Watanabe, Christian Ganser, Koichi Nakajo, Yoshihiro Kubo, Takayuki Uchihashi, Yuji Furutani
Canonical K+ channels are tetrameric and highly K+ selective, whereas two-pore domain K+ (K2P) channels form dimers, but with a similar pore architecture. A two-pore domain potassium channel TWIK1 (KCNK1 or K2P1) allows permeation of Na+ and other monovalent ions, resulting mainly from the presence of Thr118 in the P1 domain. However, the mechanistic basis for this reduced selectivity is unclear. Using ion-exchange-induced difference infrared spectroscopy, we analyzed WT TWIK1 and T118I (highly K+ selective) and L228F (substitution in the P2 domain) TWIK1 variants and found that in the presence of K+ ions, WT and both variants exhibit an amide-I band at 1680 cm-1 This band corresponds to interactions of the backbone carbonyls in the selectivity filter with K+ , a feature very similar to that of the canonical K+ channel KcsA...
March 15, 2018: Journal of Biological Chemistry
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
Krzysztof Slosarek, Barbara Bekman, Jacek Wendykier, Aleksandra Grządziel, Antonella Fogliata, Luca Cozzi
BACKGROUND: To appraise the dosimetric features and the quality of the treatment plan for radiosurgery of multiple brain metastases optimized with a novel automated engine and to compare with plans optimized for robotic-based delivery. METHODS: A set of 15 patients with multiple brain metastases was selected for this in silico study. The technique under investigation is the recently introduced HyperArc. For all patients, three treatment plans were computed and compared: i: a HyperArc; ii: a standard VMAT; iii) a CyberKnife...
March 15, 2018: Radiation Oncology
Godwin U Ebiloma, Teresa Díaz Ayuga, Emmanuel O Balogun, Lucía Abad Gil, Anne Donachie, Marcel Kaiser, Tomás Herraiz, Daniel K Inaoka, Tomoo Shiba, Shigeharu Harada, Kiyoshi Kita, Harry P de Koning, Christophe Dardonville
African trypanosomiasis is a neglected parasitic disease that is still of great public health relevance, and a severe impediment to agriculture in endemic areas. The pathogens possess certain unique metabolic features that can be exploited for the development of new drugs. Notably, they rely on an essential, mitochondrially-localized enzyme, Trypanosome Alternative Oxidase (TAO) for their energy metabolism, which is absent in the mammalian hosts and therefore an attractive target for the design of safe drugs...
February 26, 2018: European Journal of Medicinal Chemistry
Qiang Wang, Feiyang Liu, Shuang Qi, Ziping Qi, Xiao-E Yan, Beilei Wang, Aoli Wang, Wei Wang, Cheng Chen, Xiaochuan Liu, Zongru Jiang, Zhenquan Hu, Li Wang, Wenchao Wang, Tao Ren, Shanchun Zhang, Cai-Hong Yun, Qingsong Liu, Jing Liu
Through exploration of the non-highly conserved allosteric hydrophobic pocket generated by DFG-out shifting in the inactive conformation, we discovered a highly selective type II PDGFRα kinase inhibitor 15i (CHMFL-PDGFRα-159), which exhibited strong potency against purified PDGFRα (IC50 : 132 nM) but not structurally similar PDGFRβ, ABL, c-KIT and VEGFR2 kinases. In addition, it displayed a high selectivity profile (S score (10) = 0.02) at the concentration of 1 μM among 468 kinases/mutants in the KINOMEscan profiling...
March 12, 2018: European Journal of Medicinal Chemistry
Samane Zare, Mehdi Nemati, Yuqing Zheng
OBJECTIVE: Systematic review of research examining consumer preference for the main electronic cigarette (e-cigarette) attributes namely flavor, nicotine strength, and type. METHOD: A systematic search of peer-reviewed articles resulted in a pool of 12,933 articles. We included only articles that meet all the selection criteria: (1) peer-reviewed, (2) written in English, and (3) addressed consumer preference for one or more of the e-cigarette attributes including flavor, strength, and type...
2018: PloS One
Peng Li, Chandan Karmakar, John Yearwood, Svetha Venkatesh, Marimuthu Palaniswami, Changchun Liu
Entropy measures that assess signals' complexity have drawn increasing attention recently in biomedical field, as they have shown the ability of capturing unique features that are intrinsic and physiologically meaningful. In this study, we applied entropy analysis to electroencephalogram (EEG) data to examine its performance in epilepsy detection based on short-term EEG, aiming at establishing a short-term analysis protocol with optimal seizure detection performance. Two classification problems were considered, i...
2018: PloS One
Ahmed M Megreya, Markus Bindemann
Identity comparisons of photographs of unfamiliar faces are prone to error but important for applied settings, such as person identification at passport control. Finding techniques to improve face-matching accuracy is therefore an important contemporary research topic. This study investigated whether matching accuracy can be improved by instruction to attend to specific facial features. Experiment 1 showed that instruction to attend to the eyebrows enhanced matching accuracy for optimized same-day same-race face pairs but not for other-race faces...
2018: PloS One
Han Sun, Xiong Zhang, Yacong Zhao, Yu Zhang, Xuefei Zhong, Zhaowen Fan
The novel human-computer interface (HCI) using bioelectrical signals as input is a valuable tool to improve the lives of people with disabilities. In this paper, surface electromyography (sEMG) signals induced by four classes of wrist movements were acquired from four sites on the lower arm with our designed system. Forty-two features were extracted from the time, frequency and time-frequency domains. Optimal channels were determined from single-channel classification performance rank. The optimal-feature selection was according to a modified entropy criteria (EC) and Fisher discrimination (FD) criteria...
March 15, 2018: Sensors
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