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https://www.readbyqxmd.com/read/29150626/constructing-genetic-networks-using-biomedical-literature-and-rare-event-classification
#1
Amira Al-Aamri, Kamal Taha, Yousof Al-Hammadi, Maher Maalouf, Dirar Homouz
Text mining has become an important tool in bioinformatics research with the massive growth in the biomedical literature over the past decade. Mining the biomedical literature has resulted in an incredible number of computational algorithms that assist many bioinformatics researchers. In this paper, we present a text mining system called Gene Interaction Rare Event Miner (GIREM) that constructs gene-gene-interaction networks for human genome using information extracted from biomedical literature. GIREM identifies functionally related genes based on their co-occurrences in the abstracts of biomedical literature...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29148892/impact-of-prognostic-discussions-on-the-patient-physician-relationship-prospective-cohort-study
#2
Joshua J Fenton, Paul R Duberstein, Richard L Kravitz, Guibo Xing, Daniel J Tancredi, Kevin Fiscella, Supriya Mohile, Ronald M Epstein
Purpose Some research has suggested that discussion of prognosis can disrupt the patient-physician relationship. This study assessed whether physician discussion of prognosis is associated with detrimental changes in measures of the strength of the patient-physician relationship. Methods This was a longitudinal cohort study of 265 adult patients with advanced cancer who visited 38 oncologists within community- and hospital-based cancer clinics in Western New York and Northern California. Prognostic discussion was assessed by coding transcribed audio-recorded visits using the Prognostic and Treatment Choices (PTCC) scale and by patient survey at 3 months after the clinic visit...
November 17, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/29147132/numerical-investigation-of-pulse-wave-propagation-in-arteries-using-fluid-structure-interaction-capabilities
#3
Hisham Elkenani, Essam Al-Bahkali, Mhamed Souli
The aim of this study is to present a reliable computational scheme to serve in pulse wave velocity (PWV) assessment in large arteries. Clinicians considered it as an indication of human blood vessels' stiffness. The simulation of PWV was conducted using a 3D elastic tube representing an artery. The constitutive material model specific for vascular applications was applied to the tube material. The fluid was defined with an equation of state representing the blood material. The onset of a velocity pulse was applied at the tube inlet to produce wave propagation...
2017: Computational and Mathematical Methods in Medicine
https://www.readbyqxmd.com/read/29145931/in-vitro-and-in-silico-approaches-to-study-cytochrome-p450-mediated-interactions
#4
Boon Hooi Tan, Yan Pan, Amelia Nathania Dong, Chin Eng Ong
In vitro and in silico models of drug metabolism are utilized regularly in the drug research and development as tools for assessing pharmacokinetic variability and drug-drug interaction risk. The use of in vitro and in silico predictive approaches offers advantages including guiding rational design of clinical drug-drug interaction studies, minimization of human risk in the clinical trials, as well as cost and time savings due to lesser attrition during compound development process. This article gives a review of some of the current in vitro and in silico methods used to characterize cytochrome P450(CYP)-mediated drug metabolism for estimating pharmacokinetic variability and the magnitude of drug-drug interactions...
2017: Journal of Pharmacy & Pharmaceutical Sciences: a Publication of the Canadian Society for Pharmaceutical Sciences
https://www.readbyqxmd.com/read/29143250/cliques-and-cavities-in-the-human-connectome
#5
Ann E Sizemore, Chad Giusti, Ari Kahn, Jean M Vettel, Richard F Betzel, Danielle S Bassett
Encoding brain regions and their connections as a network of nodes and edges captures many of the possible paths along which information can be transmitted as humans process and perform complex behaviors. Because cognitive processes involve large, distributed networks of brain areas, principled examinations of multi-node routes within larger connection patterns can offer fundamental insights into the complexities of brain function. Here, we investigate both densely connected groups of nodes that could perform local computations as well as larger patterns of interactions that would allow for parallel processing...
November 16, 2017: Journal of Computational Neuroscience
https://www.readbyqxmd.com/read/29141584/sprint-ultrafast-protein-protein-interaction-prediction-of-the-entire-human-interactome
#6
Yiwei Li, Lucian Ilie
BACKGROUND: Proteins perform their functions usually by interacting with other proteins. Predicting which proteins interact is a fundamental problem. Experimental methods are slow, expensive, and have a high rate of error. Many computational methods have been proposed among which sequence-based ones are very promising. However, so far no such method is able to predict effectively the entire human interactome: they require too much time or memory. RESULTS: We present SPRINT (Scoring PRotein INTeractions), a new sequence-based algorithm and tool for predicting protein-protein interactions...
November 15, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29140779/experiencing-the-sights-smells-sounds-and-climate-of-southern-italy-in-vr
#7
Vito M Manghisi, Michele Fiorentino, Michele Gattullo, Antonio Boccaccio, Vitoantonio Bevilacqua, Giuseppe L Cascella, Michele Dassisti, Antonio E Uva
This article explores what it takes to make interactive computer graphics and VR attractive as a promotional vehicle, from the points of view of tourism agencies and the tourists themselves. The authors exploited current VR and human-machine interface (HMI) technologies to develop an interactive, innovative, and attractive user experience called the Multisensory Apulia Touristic Experience (MATE). The MATE system implements a natural gesture-based interface and multisensory stimuli, including visuals, audio, smells, and climate effects...
November 2017: IEEE Computer Graphics and Applications
https://www.readbyqxmd.com/read/29140409/ebolavirus-interferon-antagonists-protein-interaction-perspectives-to-combat-pathogenesis
#8
Anupam Banerjee, Abantika Pal, Debnath Pal, Pralay Mitra
Zaire ebolavirus, one of the most pathogenic species of Ebolavirus, is a significant threat to the human community being both highly infectious and lethal. The viral proteins (VPs), specifically VP24 and VP35, antagonize the interferon (IFN) proteins accountable for human immune response. Several efforts have been made to design vaccines and therapeutics drugs. However, the success is not encouraging because of limited knowledge about the binding site information of the VPs. Such limitations stem largely from the highly infectious nature of the virus that requires specialized personnel and biosafety laboratories...
November 13, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29140311/scene-aware-adaptive-updating-for-visual-tracking-via-correlation-filters
#9
Fan Li, Sirou Zhang, Xiaoya Qiao
In recent years, visual object tracking has been widely used in military guidance, human-computer interaction, road traffic, scene monitoring and many other fields. The tracking algorithms based on correlation filters have shown good performance in terms of accuracy and tracking speed. However, their performance is not satisfactory in scenes with scale variation, deformation, and occlusion. In this paper, we propose a scene-aware adaptive updating mechanism for visual tracking via a kernel correlation filter (KCF)...
November 15, 2017: Sensors
https://www.readbyqxmd.com/read/29138087/beyond-modularity-fine-scale-mechanisms-and-rules-for-brain-network-reconfiguration
#10
Ankit N Khambhati, Marcelo G Mattar, Nicholas F Wymbs, Scott T Grafton, Danielle S Bassett
The human brain is in constant flux, as distinct areas engage in transient communication to support basic behaviors as well as complex cognition. The collection of interactions between cortical and subcortical areas forms a functional brain network whose topology evolves with time. Despite the nontrivial dynamics that are germane to this networked system, experimental evidence demonstrates that functional interactions organize into putative brain systems that facilitate different facets of cognitive computation...
November 11, 2017: NeuroImage
https://www.readbyqxmd.com/read/29134429/self-driving-cars-and-engineering-ethics-the-need-for-a-system-level-analysis
#11
Jason Borenstein, Joseph R Herkert, Keith W Miller
The literature on self-driving cars and ethics continues to grow. Yet much of it focuses on ethical complexities emerging from an individual vehicle. That is an important but insufficient step towards determining how the technology will impact human lives and society more generally. What must complement ongoing discussions is a broader, system level of analysis that engages with the interactions and effects that these cars will have on one another and on the socio-technical systems in which they are embedded...
November 13, 2017: Science and Engineering Ethics
https://www.readbyqxmd.com/read/29134168/anatomical-region-segmentation-for-objective-surgical-skill-assessment-with-operating-room-motion-data
#12
Yangming Li, Randall A Bly, R Alex Harbison, Ian M Humphreys, Mark E Whipple, Blake Hannaford, Kris S Moe
Background  Most existing objective surgical motion analysis schemes are limited to structured surgical tasks or recognition of motion patterns for certain categories of surgeries. Analyzing instrument motion data with respect to anatomical structures can break the limit, and an anatomical region segmentation algorithm is required for the analysis. Methods  An atlas was generated by manually segmenting the skull base into nine regions, including left/right anterior/posterior ethmoid sinuses, frontal sinus, left and right maxillary sinuses, nasal airway, and sphenoid sinus...
December 2017: Journal of Neurological Surgery. Part B, Skull Base
https://www.readbyqxmd.com/read/29131383/rational-optimization-of-tumor-suppressor-derived-peptide-inhibitor-selectivity-between-oncogene-tyrosine-kinases-erbb1-and-erbb2
#13
Yilin Deng, Jian Li
The tumor-suppressor protein Mig-6 has been found to directly target and inhibit the human ErbB receptor tyrosine kinases ErbB1 and ErbB2. Despite their highly homologous nature, these two kinases are separately involved in the development of different types of human cancer. Here, we utilized a rational strategy to iteratively optimize the interaction specificity of the two kinases with a Mig-6 derived peptide by exploiting structural diversity space. Instead of traditionally improving the peptide binding potency, the optimization attempts to maximize the affinity difference between peptides binding to ErbB1 and ErbB2...
November 13, 2017: Archiv der Pharmazie
https://www.readbyqxmd.com/read/29128889/the-role-of-neuron-glia-interactions-in-the-emergence-of-ultra-slow-oscillations
#14
Siow-Cheng Chan, Siew-Ying Mok, Danny Wee-Kiat Ng, Sing-Yau Goh
Ultra-slow cortical oscillatory activity of 1-100 mHz has been recorded in human by electroencephalography and in dissociated cultures of cortical rat neurons, but the underlying mechanisms remain to be elucidated. This study presents a computational model of ultra-slow oscillatory activity based on the interaction between neurons and astrocytes. We predict that the frequency of these oscillations closely depends on activation of astrocytes in the network, which is reflected by oscillations of their intracellular calcium concentrations with periods between tens of seconds and minutes...
November 11, 2017: Biological Cybernetics
https://www.readbyqxmd.com/read/29127346/microelectrode-implantation-in-motor-cortex-causes-fine-motor-deficit-implications-on-potential-considerations-to-brain-computer-interfacing-and-human-augmentation
#15
Monika Goss-Varley, Keith R Dona, Justin A McMahon, Andrew J Shoffstall, Evon S Ereifej, Sydney C Lindner, Jeffrey R Capadona
Intracortical microelectrodes have shown great success in enabling locked-in patients to interact with computers, robotic limbs, and their own electrically driven limbs. The recent advances have inspired world-wide enthusiasm resulting in billions of dollars invested in federal and industrial sponsorships to understanding the brain for rehabilitative applications. Additionally, private philanthropists have also demonstrated excitement in the field by investing in the use of brain interfacing technologies as a means to human augmentation...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29126115/hominid-a-framework-for-identifying-associations-between-host-genetic-variation-and-microbiome-composition
#16
Joshua Lynch, Karen Tang, Sambhawa Priya, Joanna Sands, Margaret Sands, Evan Tang, Sayan Mukherjee, Dan Knights, Ran Blekhman
Recent studies have uncovered a strong effect of host genetic variation on the composition of host-associated microbiota. Here, we present HOMINID, a computational approach based on Lasso linear regression, that given host genetic variation and microbiome taxonomic composition data, identifies host SNPs that are correlated with microbial taxa abundances. Using simulated data we show that HOMINID has accuracy in identifying associated SNPs, and performs better compared to existing methods. We also show that HOMINID can accurately identify the microbial taxa that are correlated with associated SNPs...
November 8, 2017: GigaScience
https://www.readbyqxmd.com/read/29125134/implicit-relevance-feedback-from-electroencephalography-and-eye-tracking-in-image-search
#17
Jan Eike Golenia, Markus Andreas Wenzel, Mihail Bogojeski, Benjamin Blankertz
OBJECTIVE: Methods from brain-computer interfacing (BCI) open a direct access to the mental processes of computer users, which offers particular benefits in comparison to standard methods for inferring user-related information. The signals can be recorded unobtrusively in the background, which circumvents the time-consuming and distracting need for the users to give explicit feedback to questions concerning the individual interest. The obtained implicit information makes it possible to create dynamic user interest profiles in real-time, that can be taken into account by novel types of adaptive, personalised software...
November 10, 2017: Journal of Neural Engineering
https://www.readbyqxmd.com/read/29123330/markov-logic-networks-for-adverse-drug-event-extraction-from-text
#18
Sriraam Natarajan, Vishal Bangera, Tushar Khot, Jose Picado, Anurag Wazalwar, Vitor Santos Costa, David Page, Michael Caldwell
Adverse drug events (ADEs) are a major concern and point of emphasis for the medical profession, government, and society. A diverse set of techniques from epidemiology, statistics, and computer science are being proposed and studied for ADE discovery from observational health data (e.g., EHR and claims data), social network data (e.g., Google and Twitter posts), and other information sources. Methodologies are needed for evaluating, quantitatively measuring, and comparing the ability of these various approaches to accurately discover ADEs...
May 2017: Knowledge and Information Systems
https://www.readbyqxmd.com/read/29120797/interaction-of-chromium-iii-or-chromium-vi-with-catalase-and-its-effect-on-the-structure-and-function-of-catalase-an-in-vitro-study
#19
Linfeng Chen, Jing Zhang, Yaxian Zhu, Yong Zhang
Heavy metal chromium (Cr) poses a severe health risk to humans via food chain contamination. In this study, the interactions of either trivalent chromium (Cr(III)) or hexavalent chromium (Cr(VI)) with catalase (CAT) were investigated via multi-spectroscopic studies and computational simulations. The fluorescence analysis showed that Cr(III) and Cr(VI) quenched the fluorescence of CAT through a dynamic and a static quenching mechanism, respectively. The binding constant of Cr(VI) with CAT was 3.44×10(4)lmol(-1) at 298K...
April 1, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29119617/computer-aided-design-of-human-sialyltransferase-inhibitors-of-hst8sia-iii
#20
Christopher Dobie, Andrew P Montgomery, Rémi Szabo, Danielle Skropeta, Haibo Yu
Sialyltransferase (ST) upregulation and the resultant hypersialylation of tumour cell surfaces is an established hallmark of many cancers including lung, breast, ovarian, pancreatic and prostate cancer. The role of ST enzymes in tumour cell growth and metastasis, as well as links to multi-drug resistance, has seen ST inhibition emerge as a target for potential antimetastatic cancer treatments. The most potent of these reported inhibitors are transition-state analogues. Although there are several examples of these in the literature, many have suspected poor pharmacokinetic properties and are not readily synthetically accessible...
November 9, 2017: Journal of Molecular Recognition: JMR
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