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https://www.readbyqxmd.com/read/29649971/realizing-drug-repositioning-by-adapting-a-recommendation-system-to-handle-the-process
#1
Makbule Guclin Ozsoy, Tansel Özyer, Faruk Polat, Reda Alhajj
BACKGROUND: Drug repositioning is the process of identifying new targets for known drugs. It can be used to overcome problems associated with traditional drug discovery by adapting existing drugs to treat new discovered diseases. Thus, it may reduce associated risk, cost and time required to identify and verify new drugs. Nowadays, drug repositioning has received more attention from industry and academia. To tackle this problem, researchers have applied many different computational methods and have used various features of drugs and diseases...
April 12, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29623088/a-cross-domain-collaborative-filtering-algorithm-based-on-feature-construction-and-locally-weighted-linear-regression
#2
Xu Yu, Jun-Yu Lin, Feng Jiang, Jun-Wei Du, Ji-Zhong Han
Cross-domain collaborative filtering (CDCF) solves the sparsity problem by transferring rating knowledge from auxiliary domains. Obviously, different auxiliary domains have different importance to the target domain. However, previous works cannot evaluate effectively the significance of different auxiliary domains. To overcome this drawback, we propose a cross-domain collaborative filtering algorithm based on Feature Construction and Locally Weighted Linear Regression (FCLWLR). We first construct features in different domains and use these features to represent different auxiliary domains...
2018: Computational Intelligence and Neuroscience
https://www.readbyqxmd.com/read/29610073/a-new-4-d-nonlocal-transform-domain-filter-for-3-d-magnetic-resonance-images-denoising
#3
Zhaoming Kong, Le Han, Xiaolan Liu, Xiaowei Yang
The simultaneous removal of noise and preservation of the integrity of 3-D magnetic resonance (MR) images is a difficult and important task. In this paper, we consider characterizing MR images with 3-D operators, and present a novel 4-D transform-domain method termed 'modified nonlocal tensor-SVD (MNL-tSVD)' for MR image denoising. The proposed method is based on the grouping, hard-thresholding and aggregation paradigms, and can be viewed as a generalized nonlocal extension of tensor-SVD (t-SVD). By keeping MR images in its natural three-dimensional form, and collaboratively filtering similar patches, MNL-tSVD utilizes both the self-similarity property and 3-D structure of MR images to preserve more actual details and minimize the introduction of new artifacts...
April 2018: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/29599954/efficient-oct-image-enhancement-based-on-collaborative-shock-filtering
#4
Guohua Liu, Ziyu Wang, Guoying Mu, Peijin Li
Efficient enhancement of noisy optical coherence tomography (OCT) images is a key task for interpreting them correctly. In this paper, to better enhance details and layered structures of a human retina image, we propose a collaborative shock filtering for OCT image denoising and enhancement. Noisy OCT image is first denoised by a collaborative filtering method with new similarity measure, and then the denoised image is sharpened by a shock-type filtering for edge and detail enhancement. For dim OCT images, in order to improve image contrast for the detection of tiny lesions, a gamma transformation is first used to enhance the images within proper gray levels...
2018: Journal of Healthcare Engineering
https://www.readbyqxmd.com/read/29596782/scalable-open-science-approach-for-mutation-calling-of-tumor-exomes-using-multiple-genomic-pipelines
#5
Kyle Ellrott, Matthew H Bailey, Gordon Saksena, Kyle R Covington, Cyriac Kandoth, Chip Stewart, Julian Hess, Singer Ma, Kami E Chiotti, Michael McLellan, Heidi J Sofia, Carolyn Hutter, Gad Getz, David Wheeler, Li Ding
The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center Mutation Calling in Multiple Cancers project, our effort to generate a comprehensive encyclopedia of somatic mutation calls for the TCGA data to enable robust cross-tumor-type analyses. Our approach accounts for variance and batch effects introduced by the rapid advancement of DNA extraction, hybridization-capture, sequencing, and analysis methods over time...
March 28, 2018: Cell Systems
https://www.readbyqxmd.com/read/29562590/hyra-a-hybrid-recommendation-algorithm-focused-on-smart-poi-ceut%C3%A3-as-a-study-scenario
#6
Joanna Alvarado-Uribe, Andrea Gómez-Oliva, Ari Yair Barrera-Animas, Germán Molina, Miguel Gonzalez-Mendoza, María Concepción Parra-Meroño, Antonio J Jara
Nowadays, Physical Web together with the increase in the use of mobile devices, Global Positioning System (GPS), and Social Networking Sites (SNS) have caused users to share enriched information on the Web such as their tourist experiences. Therefore, an area that has been significantly improved by using the contextual information provided by these technologies is tourism. In this way, the main goals of this work are to propose and develop an algorithm focused on the recommendation of Smart Point of Interaction (Smart POI) for a specific user according to his/her preferences and the Smart POIs' context...
March 17, 2018: Sensors
https://www.readbyqxmd.com/read/29554288/ti-workbench-an-integrated-software-package-for-electrophysiology-and-imaging
#7
Takafumi Inoue
TI Workbench is a software package that serves as a control and analysis center for cellular imaging and electrophysiological experiments. It is unique among general-purpose software packages where it integrates the control of cellular imaging and electrophysiological devices, as well as sophisticated data analyses, which provides superior usability in imaging experiments combined with electrophysiology. During the development over the last 20 years, the range of supported image acquisition devices has expanded from cooled charge-coupled device (CCD) cameras to multi-photon microscope systems...
March 15, 2018: Microscopy
https://www.readbyqxmd.com/read/29503650/dried-blood-spots-an-affordable-tool-to-collect-ship-and-sequence-gdna-from-patients-with-an-x-linked-agammaglobulinemia-phenotype-residing-in-a-developing-country
#8
Gesmar R S Segundo, Anh T V Nguyen, Huyen T Thuc, Le N Q Nguyen, Roger H Kobayashi, Hai T Le, Huong T M Le, Troy R Torgerson, Hans D Ochs
Background: New sequencing techniques have revolutionized the identification of the molecular basis of primary immunodeficiency disorders (PID) not only by establishing a gene-based diagnosis but also by facilitating defect-specific treatment strategies, improving quality of life and survival, and allowing factual genetic counseling. Because these techniques are generally not available for physicians and their patients residing in developing countries, collaboration with overseas laboratories has been explored as a possible, albeit cumbersome, strategy...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29431865/refinement-of-mlc-modelling-improves-comercial-qa-dosimetry-system-for-srs-and-sbrt-patient-specific-qa
#9
Yair Hillman, Josh Kim, Indrin Chetty, Ning Wen
PURPOSE: Mobius 3D (M3D) provides a volumetric dose verification of the treatment planning system's calculated dose using an independent beam model and a collapsed cone convolution superposition algorithm. However, there is a lack of investigation into M3D's accuracy and effectiveness for stereotactic radiosurgery (SRS) and stereotactic body radiotherapy (SBRT) quality assurance (QA). Here, we collaborated with the vendor to develop a revised M3D beam model for SRS/SBRT cases treated with a 6X Flattening Filter Free (FFF) beam and high definition multiple leaf collimator (HDMLC) on an Edge linear accelerator...
February 12, 2018: Medical Physics
https://www.readbyqxmd.com/read/29416294/online-graph-completion-multivariate-signal-recovery-in-computer-vision
#10
Won Hwa Kim, Mona Jalal, Seongjae Hwang, Sterling C Johnson, Vikas Singh
The adoption of "human-in-the-loop" paradigms in computer vision and machine learning is leading to various applications where the actual data acquisition (e.g., human supervision) and the underlying inference algorithms are closely interwined. While classical work in active learning provides effective solutions when the learning module involves classification and regression tasks, many practical issues such as partially observed measurements, financial constraints and even additional distributional or structural aspects of the data typically fall outside the scope of this treatment...
July 2017: Proceedings
https://www.readbyqxmd.com/read/29396321/conceptual-endophentoypes-a-strategy-to-advance-the-impact-of-psychoneuroendocrinology-in-precision-medicine
#11
REVIEW
Dirk Hellhammer, Gunther Meinlschmidt, Jens C Pruessner
Psychobiological research has generated a tremendous amount of findings on the psychological, neuroendocrine, molecular and environmental processes that are directly relevant for mental and physical health, but have overwhelmed our capacity to meaningfully absorb, integrate, and utilize this knowledge base. Here, we reflect about suitable strategies to improve the translational success of psychoneuroendocrinological research in the era of precision medicine. Following a strategy advocated by the National Research Council and the tradition of endophenotype-based research, we advance here a new approach, termed "conceptual endophenotypes"...
January 9, 2018: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/29297351/probability-based-collaborative-filtering-model-for-predicting-gene-disease-associations
#12
Xiangxiang Zeng, Ningxiang Ding, Alfonso Rodríguez-Patón, Quan Zou
BACKGROUND: Accurately predicting pathogenic human genes has been challenging in recent research. Considering extensive gene-disease data verified by biological experiments, we can apply computational methods to perform accurate predictions with reduced time and expenses. METHODS: We propose a probability-based collaborative filtering model (PCFM) to predict pathogenic human genes. Several kinds of data sets, containing data of humans and data of other nonhuman species, are integrated in our model...
December 28, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29283007/how-to-write-a-systematic-review-of-the-literature
#13
Debajyoti Pati, Lesa N Lorusso
This article provides a step-by-step approach to conducting and reporting systematic literature reviews (SLRs) in the domain of healthcare design and discusses some of the key quality issues associated with SLRs. SLR, as the name implies, is a systematic way of collecting, critically evaluating, integrating, and presenting findings from across multiple research studies on a research question or topic of interest. SLR provides a way to assess the quality level and magnitude of existing evidence on a question or topic of interest...
January 2018: HERD
https://www.readbyqxmd.com/read/29273285/the-danish-head-and-neck-cancer-fast-track-program-a-tertiary-cancer-centre-experience
#14
Anders B Roennegaard, Tine Rosenberg, Kristine Bjørndal, Jens Ahm Sørensen, Jørgen Johansen, Christian Godballe
INTRODUCTION: During the 1990s, all Nordic countries except for Denmark experienced a general increase in 5-year survival rates for cancer patients. In 2007, the Danish National Board of Health in collaboration with national multidisciplinary cancer groups and the Danish regions initiated fast-track clinical pathway solutions. OBJECTIVES: The objectives of this study were 1) to present the setup of the head and neck cancer (HNC) fast-track program at Odense University Hospital (OUH) as an example of the Danish model and 2) to present patient characteristics, diagnostic outcome, cancer detection rate, and duration of the fast-track patient courses...
February 2018: European Journal of Cancer
https://www.readbyqxmd.com/read/29204108/cross-dependency-inference-in-multi-layered-networks-a-collaborative-filtering-perspective
#15
Chen Chen, Hanghang Tong, Lei Xie, Lei Ying, Qing He
The increasingly connected world has catalyzed the fusion of networks from different domains, which facilitates the emergence of a new network model-multi-layered networks. Examples of such kind of network systems include critical infrastructure networks, biological systems, organization-level collaborations, cross-platform e-commerce, and so forth. One crucial structure that distances multi-layered network from other network models is its cross-layer dependency, which describes the associations between the nodes from different layers...
August 2017: ACM Transactions on Knowledge Discovery From Data
https://www.readbyqxmd.com/read/29203067/personalized-prediction-of-glaucoma-progression-under-different-target-intraocular-pressure-levels-using-filtered-forecasting-methods
#16
Pooyan Kazemian, Mariel S Lavieri, Mark P Van Oyen, Chris Andrews, Joshua D Stein
PURPOSE: To generate personalized forecasts of how patients with open-angle glaucoma (OAG) experience disease progression at different intraocular pressure (IOP) levels to aid clinicians with setting personalized target IOPs. DESIGN: Secondary analyses using longitudinal data from 2 randomized controlled trials. PARTICIPANTS: Participants with moderate or advanced OAG from the Collaborative Initial Glaucoma Treatment Study (CIGTS) or the Advanced Glaucoma Intervention Study (AGIS)...
December 1, 2017: Ophthalmology
https://www.readbyqxmd.com/read/29194368/vitamin-d-moving-forward-to-address-emerging-science
#17
REVIEW
Christine L Taylor, Christopher T Sempos, Cindy D Davis, Patsy M Brannon
The science surrounding vitamin D presents both challenges and opportunities. Although many uncertainties are associated with the understandings concerning vitamin D, including its physiological function, the effects of excessive intake, and its role in health, it is at the same time a major interest in the research and health communities. The approach to evaluating and interpreting the available evidence about vitamin D should be founded on the quality of the data and on the conclusions that take into account the totality of the evidence...
December 1, 2017: Nutrients
https://www.readbyqxmd.com/read/29188764/assessing-the-performance-of-methodological-search-filters-to-improve-the-efficiency-of-evidence-information-retrieval-five-literature-reviews-and-a-qualitative-study
#18
Carol Lefebvre, Julie Glanville, Sophie Beale, Charles Boachie, Steven Duffy, Cynthia Fraser, Jenny Harbour, Rachael McCool, Lynne Smith
BACKGROUND: Effective study identification is essential for conducting health research, developing clinical guidance and health policy and supporting health-care decision-making. Methodological search filters (combinations of search terms to capture a specific study design) can assist in searching to achieve this. OBJECTIVES: This project investigated the methods used to assess the performance of methodological search filters, the information that searchers require when choosing search filters and how that information could be better provided...
November 2017: Health Technology Assessment: HTA
https://www.readbyqxmd.com/read/29187898/precisely-enumerating-circulating-tumor-cells-utilizing-a-multi-functional-microfluidic-chip-and-unique-image-interpretation-algorithm
#19
Mingxing Zhou, Hui Zheng, Zhaoba Wang, Ren Li, Xiaoran Liu, Weikai Zhang, Zihua Wang, Huiping Li, Zewen Wei, Zhiyuan Hu
Enumerating circulating tumor cells (CTCs) has been demonstrably useful in cancer treatment. Although there are several approaches that have proved effective in isolating CTC-like cells, the crucial identification of CTCs continues to rely on the manual interpretation of immunofluorescence images of all cells that have been isolated. This procedure is time consuming and more importantly, CTC identification relies on subjective criteria that may differ between examiners. In this study, we describe the design, testing, and verification of a microfluidic platform that provides accurate and automated CTC enumeration using a common objective criterion...
2017: Theranostics
https://www.readbyqxmd.com/read/29187342/assessing-the-efficacy-of-mobile-health-apps-using-the-basic-principles-of-cognitive-behavioral-therapy-systematic-review
#20
REVIEW
Amy Leigh Rathbone, Laura Clarry, Julie Prescott
BACKGROUND: Cognitive behavioral therapy (CBT) in its basic principle has developed itself as a stand-alone, substantial method of therapy. With effective application in therapy for a range of mental health issues, the spread of CBT methods to Web-based therapy sources is evident. The development of mobile phone apps using CBT principles is increasing within the research area. Despite the move to Web-based methods of therapy, it is argued that these methods lack the same efficacy of face-to-face therapy sessions...
November 28, 2017: Journal of Medical Internet Research
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