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Brian simulator

Junghyun L Suh, Brian Watts, Jacob I Stuckey, Jacqueline L Norris-Drouin, Stephanie H Cholensky, Bradley M Dickson, Yi An, Sebastian Mathea, Eidarus Salah, Stefan Knapp, Abid Khan, Alexander T Adams, Brian D Strahl, Cari A Sagum, Mark T Bedford, Lindsey I James, Dmitri B Kireev, Stephen V Frye
Multivalent binding is an efficient means to enhance the affinity and specificity of chemical probes targeting multi-domain proteins in order to study their function and role in disease. While the theory of multivalent binding is straightforward, physical and structural characterization of bivalent binding encounters multiple technical difficulties. We present a case study where a combination of experimental techniques and computational simulations was used to comprehensively characterize the binding and structure-affinity relationships for a series of Bromosporine-based bivalent bromodomain ligands with a bivalent protein, Transcription Initiation Factor TFIID subunit 1 (TAF1)...
March 20, 2018: Biochemistry
Oguzhan Alagoz, Mehmet Ali Ergun, Mucahit Cevik, Brian L Sprague, Dennis G Fryback, Ronald E Gangnon, John M Hampton, Natasha K Stout, Amy Trentham-Dietz
The University of Wisconsin Breast Cancer Epidemiology Simulation Model (UWBCS), also referred to as Model W, is a discrete-event microsimulation model that uses a systems engineering approach to replicate breast cancer epidemiology in the US over time. This population-based model simulates the lifetimes of individual women through 4 main model components: breast cancer natural history, detection, treatment, and mortality. A key feature of the UWBCS is that, in addition to specifying a population distribution in tumor growth rates, the model allows for heterogeneity in tumor behavior, with some tumors having limited malignant potential (i...
April 2018: Medical Decision Making: An International Journal of the Society for Medical Decision Making
Ronald E Gangnon, Natasha K Stout, Oguzhan Alagoz, John M Hampton, Brian L Sprague, Amy Trentham-Dietz
OBJECTIVE: Breast cancer simulation models must take changing mortality rates into account to evaluate the potential impact of cancer control interventions. We estimated mortality rates due to breast cancer and all other causes combined to determine their impact on overall mortality by year, age, and birth cohort. METHODS: Based on mortality rates from publicly available datasets, an age-period-cohort model was used to estimate the proportion of deaths due to breast cancer for US women aged 0 to 119 years, with birth years 1900 to 2000...
April 2018: Medical Decision Making: An International Journal of the Society for Medical Decision Making
Aimee H Fullerton, Brian J Burke, Joshua J Lawler, Christian E Torgersen, Joseph L Ebersole, Scott G Leibowitz
It is generally accepted that climate change will stress coldwater species like Pacific salmon. However, it is unclear what aspect of altered thermal regimes (e.g., warmer winters, springs, summers, or increased variability) will have the greatest effect, and what role the spatial properties of river networks play. Thermally diverse habitats may afford protection from climate change by providing opportunities for aquatic organisms to find and use habitats with optimal conditions for growth. We hypothesized that climate-altered thermal regimes will change growth and timing of life history events such as emergence or migration but that changes will be moderated in topologically complex stream networks where opportunities to thermoregulate are more readily available to mobile animals...
December 22, 2017: Ecosphere
Junichi Tokuda, Laurent Chauvin, Brian Ninni, Takahisa Kato, Franklin King, Kemal Tuncali, Nobuhiko Hata
Patient-mounted needle guide devices for
 percutaneous ablations are vulnerable to patient motion. The objective of this study is to develop and evaluate a software system for MRI-compatible patient-mounted needle guide device that can adaptively compensate for the displacement of the device due to the patient motion using a novel image-based automatic device-to-image registration.
 Materials and Methods. We developed a software system for an MRI-compatible patient-mounted needle guide device for percutaneous ablations...
March 16, 2018: Physics in Medicine and Biology
Shuai Zhang, Qinfu Liu, Hongfei Cheng, Feng Gao, Cun Liu, Brian J Teppen
Intercalation is the promising strategy to expand the interlayer region of kaolinite for their further applications. Herein, the adaptive biasing force (ABF) accelerated molecular dynamics simulations were performed to calculate the free energies involved in the kaolinite intercalation by dimethyl sulfoxide (DMSO). Additionally, the classical all atom molecular dynamics simulations were carried out to calculate the interfacial interactions between kaolinite interlayer surfaces and DMSO with the aim at exploring the underlying force that drives the DMSO to enter the interlayer space...
January 2018: Applied Clay Science
Brian D Segal, Thomas Braun, Michael R Elliott, Hui Jiang
Researchers in genetics and other life sciences commonly use permutation tests to evaluate differences between groups. Permutation tests have desirable properties, including exactness if data are exchangeable, and are applicable even when the distribution of the test statistic is analytically intractable. However, permutation tests can be computationally intensive. We propose both an asymptotic approximation and a resampling algorithm for quickly estimating small permutation p-values (e.g., <10-6) for the difference and ratio of means in two-sample tests...
March 2018: Biometrics
Samir S Soneji, Hai-Yen Sung, Brian A Primack, John P Pierce, James D Sargent
BACKGROUND: Electronic cigarettes (e-cigarettes) may help cigarette smokers quit smoking, yet they may also facilitate cigarette smoking for never-smokers. We quantify the balance of health benefits and harms associated with e-cigarette use at the population level. METHODS AND FINDINGS: Monte Carlo stochastic simulation model. Model parameters were drawn from census counts, national health and tobacco use surveys, and published literature. We calculate the expected years of life gained or lost from the impact of e-cigarette use on smoking cessation among current smokers and transition to long-term cigarette smoking among never smokers for the 2014 US population cohort...
2018: PloS One
Barry James McDermott, Emily Porter, Marggie Jones, Brian McGinley, Martin O'Halloran
OBJECTIVE: The theoretical basis, experimental implementation, and proof of concept of a novel Electrical Impedance Tomography (EIT) imaging technique, called Symmetry Difference EIT, is described. This technique is applicable in situations where there is inherent symmetry in the region being imaged. METHODS: The sample scenario of the human head is used to describe the technique. The head is largely symmetrical across the sagittal plane. A unilateral lesion such as a haemorrhage or region of ischaemia distorts that symmetry...
March 13, 2018: Physiological Measurement
Brian Folt, Maureen A Donnelly, Craig Guyer
The conspecific attraction hypothesis predicts that individuals are attracted to conspecifics because conspecifics may be cues to quality habitat and/or colonists may benefit from living in aggregations. Poison frogs (Dendrobatidae) are aposematic, territorial, and visually oriented-three characteristics which make dendrobatids an appropriate model to test for conspecific attraction. In this study, we tested this hypothesis using an extensive mark-recapture dataset of the strawberry poison frog ( Oophaga pumilio ) from La Selva Biological Station, Costa Rica...
March 2018: Ecology and Evolution
M Montero, Brian D VanScoy, Carla López-Causapé, Haley Conde, Jonathan Adams, Concepción Segura, Laura Zamorano, Antonio Oliver, Juan P Horcajada, Paul G Ambrose
The aim of this study was to investigate the efficacy of ceftolozane-tazobactam in combination with meropenem against an extensively drug-resistant (XDR) Pseudomonas aeruginosa high-risk clone, ST175, isolated in a Spanish university hospital. A 14-day hollow-fiber infection model was used to simulate clinical exposure of the 2 drug regimens alone and in combination, and serial samples were collected to determine drug concentrations and colony-forming unit (CFU) counts. The untreated control failed, as did each study regimen when administered alone...
March 12, 2018: Antimicrobial Agents and Chemotherapy
Brian Appleton, Taylor Hubbard, Andreu Glasmann, Enrico Bellotti
We report on the modulation transfer function (MTF) in short-wave infrared indium gallium arsenide (InGaAs) on indium phosphide (InP) planar photodetector arrays. Our two-dimensional numerical method consists of optical simulations using the finite-difference time domain method and drift-diffusion simulations using the finite-element method. This parametric study investigates MTF dependence on pitch, the addition of refractive microlenses, the thickness of the InGaAs absorber, and the doping concentration of the InGaAs absorber...
March 5, 2018: Optics Express
Camden Cheek, Huiyong Zheng, Brian R Hallstrom, Richard E Hughes
Improving the quality of care for hip arthroplasty (replacement) patients requires the systematic evaluation of clinical performance of implants and the identification of "outlier" devices that have an especially high risk of reoperation ("revision"). Postmarket surveillance of arthroplasty implants, which rests on the analysis of large patient registries, has been effective in identifying outlier implants such as the ASR metal-on-metal hip resurfacing device that was recalled. Although identifying an implant as an outlier implies a causal relationship between the implant and revision risk, traditional signal detection methods use classical biostatistical methods...
2018: Biomedical Engineering and Computational Biology
Alan Y Chiang, Brian D Guth, Michael K Pugsley, C Michael Foley, Jennifer M Doyle, Michael J Engwall, John E Koerner, Stanley T Parish, R Dustan Sarazan
INTRODUCTION: The sensitivity of a given test to detect a treatment-induced effect in a variable of interest is intrinsically related to the variability of that variable observed without treatment and the number of observations made in the study (i.e. number of animals). To evaluate test sensitivity to detect drug-induced changes in myocardial contractility using the variable LVdP/dtmax , a HESI-supported consortium designed and conducted studies in chronically instrumented, conscious dogs using telemetry...
March 2, 2018: Journal of Pharmacological and Toxicological Methods
Vikram Ravi, Allan H Gao, Natalie B Martinkus, Michael P Wolcott, Brian K Lamb
Forest residue is a major potential feedstock for second generation biofuel, however little knowledge exists about environmental impacts of development and production of biofuel from such a feedstock. Using a high-resolution regional air quality model, we estimate the air quality impacts of an aviation biofuel supply chain scenario in the Pacific Northwest of the United States that uses forest residue as the feedstock. Pollutant emissions for the major supply chain components including feedstock harvesting, transportation, and biorefinery operations were compiled...
March 5, 2018: Environmental Science & Technology
Einav Nachman, Peter Clemensen, Katheryn Santos, Alexis R Cole, Brian D Polizzotti, Grace Hofmann, Kristen T Leeman, Sarah J van den Bosch, John N Kheir
BACKGROUND: The accurate measurement of oxygen consumption (VO2) and energy expenditure (EE) may be helpful to optimize the treatment of critically ill patients. However, current techniques are limited in their ability to accurately quantify these end points in infants due to a low VO2, low tidal volume, and rapid respiratory rate. This study describes and validates a new device intended to perform in this size range. METHODS: We created a customized device that quantifies inspiratory volume using a pneumotachometer and concentrations of oxygen and carbon dioxide gas in the inspiratory and expiratory limbs...
March 1, 2018: Anesthesia and Analgesia
Maarten Timmers, Vikash Sinha, Borje Darpo, Brian Smith, Randy Brown, Hongqi Xue, Georg Ferber, Johannes Streffer, Alberto Russu, Luc Tritsmans, Bhavna Solanki, Jennifer Bogert, Luc Van Nueten, Giacomo Salvadore, Partha Nandy
Nonclinical assays with JNJ-54861911, a β-secretase 1 inhibitor have indicated that at high concentrations, it may delay cardiac repolarization. A 4-way crossover thorough QT (TQT) study was performed in 64 healthy subjects with 50 and 150 mg JNJ-54861911 once daily for 7 days, placebo, and 400 mg moxifloxacin. Retrospective high-precision QT (HPQT) analysis was performed on serial elecrocardiograms extracted from first-in-human single-ascending dose (SAD) and multiple-ascending dose (MAD) studies to evaluate if early studies could detect and predict QT effect...
March 5, 2018: Journal of Clinical Pharmacology
Abdulrahman M Jabour, Brian E Dixon, Josette F Jones, David A Haggstrom
BACKGROUND: Cancer registries systematically collect cancer-related data to support cancer surveillance activities. However, cancer data are often unavailable for months to years after diagnosis, limiting its utility. OBJECTIVE: The objective of this study was to identify the barriers to rapid cancer reporting and identify ways to shorten the turnaround time. METHODS: Certified cancer registrars reporting to the Indiana State Department of Health cancer registry participated in a semistructured interview...
March 1, 2018: JMIR Cancer
Zackery P Bulman, Miao Zhao, Michael J Satlin, Liang Chen, Barry N Kreiswirth, Thomas J Walsh, Roger L Nation, Jian Li, Brian T Tsuji
Polymyxin B and fosfomycin are two 'old' antibiotics that consistently maintain activity against Klebsiella pneumoniae carbapenemase (KPC)-producing organisms based on in vitro susceptibility testing. However, each antibiotic's use in monotherapy has been associated with high rates of treatment failure. Therefore, our objective was to investigate the combinatorial pharmacodynamics of polymyxin B and fosfomycin against KPC-producing K. pneumoniae. Polymyxin B front-loading (3.33 mg/kg for 1 dose followed by 1...
February 24, 2018: International Journal of Antimicrobial Agents
John A Ruder, Brian K Brighton, Kelly L Vander Have, Blake R Turvey, Joseph R Hsu, Brian P Scannell
OBJECTIVE: The purpose of this study is to determine if an educational model during a surgical skills laboratory results in a significant reduction in cast saw blade temperatures generated during cast removal. DESIGN: As part of an orthopedic resident surgical skills laboratory an Institutional Review Board-approved study was performed. A total of 17 study subjects applied a short arm cast. Everyone removed 1 short arm cast with temperatures recorded on the saw blade...
February 23, 2018: Journal of Surgical Education
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