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https://www.readbyqxmd.com/read/29453083/nonuniform-sampling-by-quantiles
#1
D Levi Craft, Reilly E Sonstrom, Virginia G Rovnyak, David Rovnyak
A flexible strategy for choosing samples nonuniformly from a Nyquist grid using the concept of statistical quantiles is presented for broad classes of NMR experimentation. Quantile-directed scheduling is intuitive and flexible for any weighting function, promotes reproducibility and seed independence, and is generalizable to multiple dimensions. In brief, weighting functions are divided into regions of equal probability, which define the samples to be acquired. Quantile scheduling therefore achieves close adherence to a probability distribution function, thereby minimizing gaps for any given degree of subsampling of the Nyquist grid...
February 13, 2018: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/29451898/integrating-linear-optimization-with-structural-modeling-to-increase-hiv-neutralization-breadth
#2
Alexander M Sevy, Swetasudha Panda, James E Crowe, Jens Meiler, Yevgeniy Vorobeychik
Computational protein design has been successful in modeling fixed backbone proteins in a single conformation. However, when modeling large ensembles of flexible proteins, current methods in protein design have been insufficient. Large barriers in the energy landscape are difficult to traverse while redesigning a protein sequence, and as a result current design methods only sample a fraction of available sequence space. We propose a new computational approach that combines traditional structure-based modeling using the Rosetta software suite with machine learning and integer linear programming to overcome limitations in the Rosetta sampling methods...
February 16, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29451586/virtual-reality-exposure-therapy-for-fear-of-driving-analysis-of-clinical-characteristics-physiological-response-and-sense-of-presence
#3
Rafael T da Costa, Marcele R de Carvalho, Pedro Ribeiro, Antonio E Nardi
OBJECTIVE: To investigate the reactions of women with driving phobia to a therapeutic program of scheduled virtual reality exposure treatment (VRET) sessions. METHODS: The study intervention consisted of a computer game with car-driving scenarios that included several traffic situations. We investigated the participants' sense of presence, subjective distress, and physiological responses during eight virtual-reality exposures. We also evaluated clinical characteristics, driving cognitions, and quality of life in the participants...
February 15, 2018: Revista Brasileira de Psiquiatria
https://www.readbyqxmd.com/read/29450945/clinical-application-of-3d-technology-for-tooth-autotransplantation-a-case-report
#4
Keunhee Kim, Hee-Seung Choi, Nan-Sim Pang
This report presents two cases of tooth autotransplantation using cone-beam computed tomography (CBCT), the three-dimensional (3D) simulation dental planning software and a computer-aided rapid prototyping (CARP) model. Two hopeless teeth of adult patients were replaced as their third molar teeth. Before deciding the autotransplantation, diagnostic CBCT images were acquired and imported to SimPlant software. The SimPlant dental program was used for surgical simulation prior to autotransplantation, which created 3D images of the available donor teeth and recipient site tooth and superimposed the images to display their morphological similarity...
February 16, 2018: Australian Endodontic Journal: the Journal of the Australian Society of Endodontology Inc
https://www.readbyqxmd.com/read/29450404/reengineering-deep-brain-stimulation-for-movement-disorders-emerging-technologies
#5
Aysegul Gunduz, Kelly D Foote, Michael S Okun
Deep brain stimulation (DBS) is a neurosurgical technique, which consists of continuous delivery of an electrical pulse through chronically implanted electrodes connected to a neurostimulator, programmable in amplitude, pulse width, frequency, and stimulation channel. DBS is a promising treatment option for addressing severe and drug-resistant movement disorders. The success of DBS therapy is a combination of surgical implantation techniques, device technology, and clinical programming strategies. Changes in device settings require highly trained and experienced clinicians to achieve maximal therapeutic benefit for each targeted symptom, and optimization of stimulation parameters can take many visits...
December 2017: Current Opinion in Biomedical Engineering
https://www.readbyqxmd.com/read/29449204/national-food-nutrition-and-physical-activity-survey-of-the-portuguese-general-population-2015-2016-protocol-for-design-and-development
#6
Carla Lopes, Duarte Torres, Andreia Oliveira, Milton Severo, Sofia Guiomar, Violeta Alarcão, Elisabete Ramos, Sara Rodrigues, Sofia Vilela, Luísa Oliveira, Jorge Mota, Pedro J Teixeira, Paulo J Nicola, Simão Soares, Lene Frost Andersen
BACKGROUND: The assessment of food consumption data using harmonized methodologies at the European level is fundamental to support the development of public policies. Portugal is one of the countries with the most outdated information on individual food consumption. OBJECTIVE: The objective of this study was to describe the design and methodology of the National Food, Nutrition and Physical Activity Survey, 2015-2016, developed to collect national and regional data on dietary habits, physical activity (PA), and nutritional status, in a representative sample of the Portuguese general population (3 months-84 years)...
February 15, 2018: JMIR Research Protocols
https://www.readbyqxmd.com/read/29449199/implementation-of-digital-awareness-strategies-to-engage-patients-and-providers-in-a-lung-cancer-screening-program-retrospective-study
#7
Dana L Jessup, McKinley Glover Iv, Dania Daye, Lynda Banzi, Philip Jones, Garry Choy, Jo-Anne O Shepard, Efrén J Flores
BACKGROUND: Lung cancer is the leading cause of cancer-related deaths in the United States. Despite mandated insurance coverage for eligible patients, lung cancer screening rates remain low. Digital platforms, including social media, provide a potentially valuable tool to enhance health promotion and patient engagement related to lung cancer screening (LCS). OBJECTIVE: The aim was to assess the effectiveness of LCS digital awareness campaigns on utilization of low-dose computed tomography (LDCT) and visits to institutional online educational content...
February 15, 2018: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/29449083/three-dimensional-scapular-dyskinesis-in-hook-plated-acromioclavicular-dislocation-including-hook-motion
#8
Eugene Kim, Seunghee Lee, Hwa-Jae Jeong, Jai Hyung Park, Se-Jin Park, Jaewook Lee, Woosub Kim, Hee Jin Park, So Yeon Lee, Tsuyoshi Murase, Kazuomi Sugamoto, Sumika Ikemoto
BACKGROUND: The purpose of this study is to analyze the 3-dimensional scapular dyskinesis and the kinematics of a hook plate relative to the acromion after hook-plated acromioclavicular dislocation in vivo. Reported complications of acromioclavicular reduction using a hook plate include subacromial erosion and impingement. However, there are few reports of the 3-dimensional kinematics of the hook and scapula after the aforementioned surgical procedure. METHODS: We studied 15 cases of acromioclavicular dislocation treated with a hook plate and 15 contralateral normal shoulders using computed tomography in the neutral and full forward flexion positions...
February 13, 2018: Journal of Shoulder and Elbow Surgery
https://www.readbyqxmd.com/read/29449001/balance-assessment-during-squatting-exercise-a-comparison-between-laboratory-grade-force-plate-and-a-commercial-low-cost-device
#9
Alessandro Mengarelli, Federica Verdini, Stefano Cardarelli, Francesco Di Nardo, Laura Burattini, Sandro Fioretti
Testing balance through squatting exercise is a central part of many rehabilitation programs and sports and plays also an important role in clinical evaluation of residual motor ability. The assessment of center of pressure (CoP) displacement and its parametrization is commonly used to describe and analyze squat movement and the laboratory-grade force plates (FP) are the gold standard for measuring balance performances from a dynamic view-point. However, the Nintendo Wii Balance Board (NWBB) has been recently proposed as an inexpensive and easily available device for measuring ground reaction force and CoP displacement in standing balance tasks...
February 5, 2018: Journal of Biomechanics
https://www.readbyqxmd.com/read/29448909/a-preliminary-investigation-into-a-range-of-implicit-and-explicit-offense-supportive-cognitions-in-perpetrators-of-physical-intimate-partner-violence
#10
Chrisa D Pornari, Louise Dixon, Glyn W Humphreys
The current study assessed a wide range of offense supportive cognitions in relation to the perpetration of physical intimate partner violence (IPV). This research used both implicit and explicit measures in a U.K. sample of 19 male IPV perpetrators recruited from a community-based IPV intervention program and 20 men from the community with no history of IPV. The study also explored the ability of the implicit measures to differentiate between the two groups. The cognitions assessed included gender-role stereotype, attitudes condoning violence against a partner, attitudes condoning violence in general, hostile attitudes toward women, sense of entitlement in the relationship and over the intimate partner (control and dominance), and general sense of entitlement...
February 1, 2018: Journal of Interpersonal Violence
https://www.readbyqxmd.com/read/29447345/the-biocyc-collection-of-microbial-genomes-and-metabolic-pathways
#11
Peter D Karp, Richard Billington, Ron Caspi, Carol A Fulcher, Mario Latendresse, Anamika Kothari, Ingrid M Keseler, Markus Krummenacker, Peter E Midford, Quang Ong, Wai Kit Ong, Suzanne M Paley, Pallavi Subhraveti
BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of query tools, visualization services and analysis software. Recent advances in BioCyc include an expansion in the content of BioCyc in terms of both the number of genomes and the types of information available for each genome; an expansion in the amount of curated content within BioCyc; and new developments in the BioCyc software tools including redesigned gene/protein pages and metabolite pages; new search tools; a new sequence-alignment tool; a new tool for visualizing groups of related metabolic pathways; and a facility called SmartTables, which enables biologists to perform analyses that previously would have required a programmer's assistance...
August 17, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29446725/mapping-of-protein-protein-interactions-web-based-resources-for-revealing-interactomes
#12
Branislava Gemovic, Neven Sumonja, Radoslav Davidovic, Vladimir Perovic, Nevena Veljkovic
BACKGROUND: The significant number of protein-protein interactions (PPIs) discovered by harnessing concomitant advances in the fields of sequencing, crystallography, spectrometry and two-hybrid screening suggests astonishing prospects for remodelling drug discovery. The PPI space which includes up to 650 000 entities is a remarkable reservoir of potential therapeutic targets for every human disease. In order to allow modern drug discovery programs to leverage this we should be able to discern complete PPI maps associated with a specific disorder and corresponding normal physiology...
February 13, 2018: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/29446082/development-of-a-dual-energy-computed-tomography-quality-control-program-characterization-of-scanner-response-and-definition-of-relevant-parameters-for-a-fast-kvp-switching-dect-system
#13
Jessica L Nute, Megan C Jacobsen, Wolfgang Stefan, Wei Wei, Dianna D Cody
PURPOSE: A prototype QC phantom system and analysis process were developed to characterize the spectral capabilities of a fast kV-switching dual-energy computed tomography (DECT) scanner. This work addresses the current lack of quantitative oversight for this technology, with the goal of identifying relevant scan parameters and test metrics instrumental to the development of a dual-energy quality control (DEQC). METHODS: A prototype elliptical phantom (effective diameter: 35 cm) was designed with multiple material inserts for DECT imaging...
February 15, 2018: Medical Physics
https://www.readbyqxmd.com/read/29444993/a-novel-method-for-qualification-of-a-potency-assay-through-partial-computer-simulation
#14
Steven Novick, Perceval Sondag, Tim Schofield, Kenneth Miller
For biotherapeutics and vaccines, potency is measured in a bioassay which compares the concentration-response curves of a new batch to that of a reference standard. Acceptable accuracy and precision of potency measurement is critical to the manufacturing of these products. These characteristics of a bioassay are typically assessed in a procedure which is carried out with samples spanning the acceptable range for the product. During early development, however, a full validation study such as that which is carried out in late development can be costly as it relates to the likelihood of eventual program success...
February 14, 2018: PDA Journal of Pharmaceutical Science and Technology
https://www.readbyqxmd.com/read/29444815/molecular-mechanisms-of-missense-mutations-that-generate-ectopic-n-glycosylation-sites-in-coagulation-factor-viii
#15
Wei Wei, Saurav Misra, Matthew V Cannon, Renchi Yang, Xiaofan Zhu, Reid Gilmore, Min Zhu, Bin Zhang
N-glycosylation is a common posttranslational modification of secreted and membrane proteins, catalyzed by the two enzymatic isoforms of the oligosaccharyltransferase, STT3A and STT3B. Missense mutations are the most common mutations in inherited diseases, however, missense mutations that generate extra, non-native N-glycosylation sites have not been well characterized. Coagulation factor VIII (FVIII) contains five consensus N-glycosylation sites outside its functionally dispensable B domain. We developed a computer program that identified hemophilia A mutations in FVIII that can potentially create ectopic glycosylation sites...
February 14, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/29444634/evaluation-of-reaction-gap-filling-accuracy-by-randomization
#16
Mario Latendresse, Peter D Karp
BACKGROUND: Completion of genome-scale flux-balance models using computational reaction gap-filling is a widely used approach, but its accuracy is not well known. RESULTS: We report on computational experiments of reaction gap filling in which we generated degraded versions of the EcoCyc-20.0-GEM model by randomly removing flux-carrying reactions from a growing model. We gap-filled the degraded models and compared the resulting gap-filled models with the original model...
February 14, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29444233/betaserpentine-a-bioinformatics-tool-for-reconstruction-of-amyloid-structures
#17
Stanislav A Bondarev, Olga V Bondareva, Galina A Zhouravleva, Andrey V Kajava, Alfonso Valencia
Motivation: Numerous experimental studies have suggested that polypeptide chains of large amyloidogenic regions zig-zag in β-serpentine arrangements. These β-serpentines are stacked axially and form the superpleated β-structure. Despite this progress in the understanding of amyloid folds, the determination of their 3D structure at the atomic level is still a problem due to the polymorphism of these fibrils and incompleteness of experimental structural data. Today, the way to get insight into the atomic structure of amyloids is a combination of experimental studies with bioinformatics...
February 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29444205/ssbio-a-python-framework-for-structural-systems-biology
#18
Nathan Mih, Elizabeth Brunk, Ke Chen, Edward Catoiu, Anand Sastry, Erol Kavvas, Jonathan M Monk, Zhen Zhang, Bernhard O Palsson, Alfonso Valencia
Summary: Working with protein structures at the genome-scale has been challenging in a variety of ways. Here, we present ssbio, a Python package that provides a framework to easily work with structural information in the context of genome-scale network reconstructions, which can contain thousands of individual proteins. The ssbio package provides an automated pipeline to construct high quality genomescale models with protein structures (GEM-PROs), wrappers to popular third-party programs to compute associated protein properties, and methods to visualize and annotate structures directly in Jupyter notebooks, thus lowering the barrier of linking 3D structural data with established systems workflows...
February 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29444133/a-long-term-mechanistic-computational-model-of-physiological-factors-driving-the-onset-of-type-2-diabetes-in-an-individual
#19
Joydeep Sarkar, Gaurav Dwivedi, Qian Chen, Iris E Sheu, Mark Paich, Colleen M Chelini, Paul M D'Alessandro, Samuel P Burns
A computational model of the physiological mechanisms driving an individual's health towards onset of type 2 diabetes (T2D) is described, calibrated and validated using data from the Diabetes Prevention Program (DPP). The objective of this model is to quantify the factors that can be used for prevention of T2D. The model is energy and mass balanced and continuously simulates trajectories of variables including body weight components, fasting plasma glucose, insulin, and glycosylated hemoglobin among others on the time-scale of years...
2018: PloS One
https://www.readbyqxmd.com/read/29442253/socioeconomic-inequality-in-screen-time-frequency-in-children-and-adolescents-the-weight-disorders-survey-of-the-caspian-iv-study
#20
Ramin Heshmat, Mostafa Qorbani, Nafiseh Mozaffarian, Shirin Djalalinia, Ali Sheidaei, Mohammad Esmaeil Motlagh, Saeid Safiri, Kimia Gohari, Asal Ataie-Jafari, Gelayol Ardalan, Hamid Asayesh, Morteza Mansourian, Roya Kelishadi
BACKGROUND: This study aimed to assess the socioeconomic inequality and determinants of screen time (ST) frequency in Iranian children and adolescents. METHODS: This nationwide study was conducted as part of a national school-based surveillance program among 36,486 students consisting of 50.79% boys and 74.23% urban inhabitants, aged 6-18 years, living in urban and rural areas of 30 provinces of Iran. Socioeconomic inequality in ST, including the time spent for ST, watching TV and leisure-time working with computer, was assessed across quintiles of SES using concentration index (C) and slope index of inequality (SII)...
February 13, 2018: World Journal of Pediatrics: WJP
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