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https://www.readbyqxmd.com/read/28330175/exploration-of-the-binding-modes-of-l-asparaginase-complexed-with-its-amino-acid-substrates-by-molecular-docking-dynamics-and-simulation
#1
Erva Rajeswara Reddy, Rajulapati Satish Babu, Potla Durthi Chandrasai, Pola Madhuri
Acute lymphocytic leukemia (ALL) is an outrageous disease worldwide. L-Asparagine (L-Asn) and L-glutamine (L-Gln) deamination plays crucial role in ALL treatment. Role of Erwinaze(®) (L-asparaginase from Erwinia chrysanthemi) in regulation of L-Asn and L-Gln has been confirmed by the experimental studies. Therapeutic research against ALL remained elusive with the lack of structural information on Erwinaze(®) enzyme. In this present study, homology model of the Erwinaze(®) was developed using MODELLER and the same was validated by various quality indexing tools...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330111/effect-of-stat3-inhibitor-in-chronic-myeloid-leukemia-associated-signaling-pathway-a-mathematical-modeling-simulation-and-systems-biology-study
#2
Himansu Kumar, Swapnil Tichkule, Utkarsh Raj, Saurabh Gupta, Swati Srivastava, Pritish Kumar Varadwaj
Chronic myeloid leukemia (CML) is a hematopoietic stem-cell disorder which proliferates due to abnormal growth of basophil cells. Several proangiogenic molecules have been reported to be associated in CML progression, including the hepatocyte growth factor (HGF). However, detail mechanism about the cellular distribution and function of HGF in CML is yet to be revealed. The proliferation of hematopoietic cells are regulated by some of the growth factors like interleukin 3 (IL-3), IL-6, erythropoietin, thrombopoietin, etc...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329429/racial-disparity-in-life-expectancies-and-life-years-lost-associated-with-multiple-obesity-related-chronic-conditions
#3
Su-Hsin Chang, Yao-Chi Yu, Nils P Carlsson, Xiaoyan Liu, Graham A Colditz
OBJECTIVE: This study investigated racial disparity in life expectancies (LEs) and life years lost (LYL) associated with multiple obesity-related chronic conditions (OCCs). METHODS: Data from the Medical Expenditure Panel Survey, 2008-2012, were used. Four OCCs were studied: diabetes, hypertension, coronary heart disease (CHD), and stroke. LE for each subpopulation was simulated by Markov modelling. LYL associated with a disease for a subpopulation was computed by taking the difference between LEs for members of that subpopulation without disease and LEs for members of that subpopulation who had that disease...
March 22, 2017: Obesity
https://www.readbyqxmd.com/read/28329208/differentiated-hiv-rna-viral-load-monitoring-in-resource-limited-settings-an-economic-analysis
#4
Diana M Negoescu, Zhenhuan Zhang, Heiner C Bucher, Eran Bendavid
Background: Viral load (VL) monitoring for patients receiving antiretroviral therapy (ART) is recommended worldwide. However, the costs of frequent monitoring are a barrier to implementation in resource-limited settings. The extent to which personalized monitoring frequencies may be cost-effective is unknown. Methods: We created a simulation model parameterized using person-level longitudinal data to assess the benefits of flexible monitoring frequencies. Our data-driven model tracked HIV+ individuals for 10 years following ART initiation...
March 1, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28329034/use-of-pfhrp2-only-rdts-rapidly-select-for-pfhrp2-negative-parasites-with-serious-implications-for-malaria-case-management-and-control
#5
Michelle L Gatton, Jessica Dunn, Alisha Chaudhry, Sadmir Ciketic, Jane Cunningham, Qin Cheng
Background: Rapid diagnostic tests (RDTs) are an important tool for malaria diagnosis, with most utilising antibodies against histidine-rich protein 2 (PfHRP2). Reports of Plasmodium falciparum lacking this protein are increasing, creating a problem for diagnosis of falciparum malaria in locations without quality microscopy. Methods: An agent-based stochastic simulation model of P.falciparum transmission was used to investigate the selective pressure exerted on parasite populations by use of RDTs for diagnosis of symptomatic cases...
March 8, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28328984/using-simulation-to-aid-trial-design-ring-vaccination-trials
#6
Matt David Thomas Hitchings, Rebecca Freeman Grais, Marc Lipsitch
BACKGROUND: The 2014-6 West African Ebola epidemic highlights the need for rigorous, rapid clinical trial methods for vaccines. A challenge for trial design is making sample size calculations based on incidence within the trial, total vaccine effect, and intracluster correlation, when these parameters are uncertain in the presence of indirect effects of vaccination. METHODS AND FINDINGS: We present a stochastic, compartmental model for a ring vaccination trial. After identification of an index case, a ring of contacts is recruited and either vaccinated immediately or after 21 days...
March 22, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28328943/structurally-detailed-coarse-grained-model-for-sec-facilitated-co-translational-protein-translocation-and-membrane-integration
#7
Michiel J M Niesen, Connie Y Wang, Reid C Van Lehn, Thomas F Miller
We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations...
March 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28328937/efficient-occupancy-model-fitting-for-extensive-citizen-science-data
#8
Emily B Dennis, Byron J T Morgan, Stephen N Freeman, Martin S Ridout, Tom M Brereton, Richard Fox, Gary D Powney, David B Roy
Appropriate large-scale citizen-science data present important new opportunities for biodiversity modelling, due in part to the wide spatial coverage of information. Recently proposed occupancy modelling approaches naturally incorporate random effects in order to account for annual variation in the composition of sites surveyed. In turn this leads to Bayesian analysis and model fitting, which are typically extremely time consuming. Motivated by presence-only records of occurrence from the UK Butterflies for the New Millennium data base, we present an alternative approach, in which site variation is described in a standard way through logistic regression on relevant environmental covariates...
2017: PloS One
https://www.readbyqxmd.com/read/28328758/posttransfusion-increase-of-hematocrit-per-se-does-not-improve-circulatory-oxygen-delivery-due-to-increased-blood-viscosity
#9
Robert Zimmerman, Amy G Tsai, Beatriz Y Salazar Vázquez, Pedro Cabrales, Axel Hofmann, Jens Meier, Aryeh Shander, Donat R Spahn, Joel M Friedman, Daniel M Tartakovsky, Marcos Intaglietta
BACKGROUND: Blood transfusion is used to treat acute anemia with the goal of increasing blood oxygen-carrying capacity as determined by hematocrit (Hct) and oxygen delivery (DO2). However, increasing Hct also increases blood viscosity, which may thus lower DO2 if the arterial circulation is a rigid hydraulic system as the resistance to blood flow will increase. The net effect of transfusion on DO2 in this system can be analyzed by using the relationship between Hct and systemic blood viscosity of circulating blood at the posttransfusion Hct to calculate DO2 and comparing this value with pretransfusion DO2...
March 21, 2017: Anesthesia and Analgesia
https://www.readbyqxmd.com/read/28328516/anrad-a-neuromorphic-anomaly-detection-framework-for-massive-concurrent-data-streams
#10
Qiuwen Chen, Ryan Luley, Qing Wu, Morgan Bishop, Richard W Linderman, Qinru Qiu
The evolution of high performance computing technologies has enabled the large-scale implementation of neuromorphic models and pushed the research in computational intelligence into a new era. Among the machine learning applications, unsupervised detection of anomalous streams is especially challenging due to the requirements of detection accuracy and real-time performance. Designing a computing framework that harnesses the growing computing power of the multicore systems while maintaining high sensitivity and specificity to the anomalies is an urgent research topic...
March 17, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28328510/investigation-and-modeling-of-capacitive-human-body-communication
#11
Xiao-Qi Zhu, Yong-Xin Guo, Wen Wu
This paper presents a systematic investigation of the capacitive human body communication (HBC). The measurement of HBC channels is performed using a novel battery-powered system to eliminate the effects of baluns, cables and instruments. To verify the measured results, a numerical model incorporating the entire HBC system is established. Besides, it is demonstrated that both the impedance and path gain bandwidths of HBC channels is affected by the electrode configuration. Based on the analysis of the simulated electric field distribution, an equivalent circuit model is proposed and the circuit parameters are extracted using the finite element method...
March 16, 2017: IEEE Transactions on Biomedical Circuits and Systems
https://www.readbyqxmd.com/read/28328501/monte-carlo-simulations-of-diffusion-weighted-mri-in-myocardium-validation-and-sensitivity-analysis
#12
Joanne Bates, Darryl McClymont, Irvin Teh, Peter Kohl, Jurgen Schneider, Vicente Grau
A model of cardiac microstructure and diffusion MRI is presented, and compared with experimental data from ex vivo rat hearts. The model includes a simplified representation of individual cells, with physiologically correct cell size and orientation, as well as intra- to extracellular volume ratio. Diffusion MRI is simulated using a Monte Carlo model and realistic MRI sequences. The results show good correspondence between the simulated and experimental MRI signals. Similar patterns are observed in the eigenvalues of the diffusion tensor, the mean diffusivity (MD) and the fractional anisotropy (FA)...
March 10, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28328394/proposing-telecardiology-services-on-cloud-for-different-medical-institutions-a-model-of-reference
#13
Isabel De la Torre-Díez, Begoña Garcia-Zapirain, Miguel López-Coronado, Joel J P C Rodrigues
INTRODUCTION: For a cloud-based telecardiology solution to be established in any scenario, it is necessary to ensure optimum levels of security, as patient's data will not be in the same place from where access is gained. The main objective of this article is to present a secure, cloud-based solution for a telecardiology service in different scenarios: a hospital, a health center in a city, and a group of health centers in a rural area. METHODS: iCanCloud software is used to simulate the scenarios...
March 1, 2017: Telemedicine Journal and E-health: the Official Journal of the American Telemedicine Association
https://www.readbyqxmd.com/read/28328286/identification-of-the-minimum-effective-dose-for-normally-distributed-data-using-a-bayesian-variable-selection-approach
#14
Martin Otava, Ziv Shkedy, Ludwig A Hothorn, Willem Talloen, Daniel Gerhard, Adetayo Kasim
The identification of the minimum effective dose is of high importance in the drug development process. In early stage screening experiments, establishing the minimum effective dose can be translated into a model selection based on information criteria. The presented alternative, Bayesian variable selection approach, allows for selection of the minimum effective dose, while taking into account model uncertainty. The performance of Bayesian variable selection is compared with the generalized order restricted information criterion on two dose-response experiments and through the simulations study...
February 16, 2017: Journal of Biopharmaceutical Statistics
https://www.readbyqxmd.com/read/28328281/educational-role-for-an-advanced-suturing-task-in-the-pediatric-laparoscopic-surgery-simulator
#15
Maeve O'Neill Trudeau, Brian Carrillo, Ahmed Nasr, Justin T Gerstle, Georges Azzie
BACKGROUND: Laparoscopic models are recognized as important training tools. Lower fidelity systems are used mainly for simpler tasks; an advanced suturing task may allow for additional training of experts. The purpose of this study was to explore the educational role of an advanced suturing task using motion analysis and establish the task's construct validity. METHODS: The pediatric laparoscopic surgery (PLS) simulator was customized with motion-tracking hardware and software...
March 22, 2017: Journal of Laparoendoscopic & Advanced Surgical Techniques. Part A
https://www.readbyqxmd.com/read/28328280/assessment-of-differential-rater-functioning-in-latent-classes-with-new-mixture-facets-models
#16
Kuan-Yu Jin, Wen-Chung Wang
Multifaceted data are very common in the human sciences. For example, test takers' responses to essay items are marked by raters. If multifaceted data are analyzed with standard facets models, it is assumed there is no interaction between facets. In reality, an interaction between facets can occur, referred to as differential facet functioning. A special case of differential facet functioning is the interaction between ratees and raters, referred to as differential rater functioning (DRF). In existing DRF studies, the group membership of ratees is known, such as gender or ethnicity...
March 22, 2017: Multivariate Behavioral Research
https://www.readbyqxmd.com/read/28328194/self-assembly-of-large-gold-nanoparticles-for-surface-enhanced-raman-spectroscopy
#17
Guang Yang, Jagjit Nanda, Boya Wang, Gang Chen, Daniel T Hallinan
Performance of portable technologies from mobile phones to electric vehicles is currently limited by the energy density and lifetime of lithium batteries. Expanding the limits of battery technology requires in situ detection of trace components at electrode-electrolyte interphases. Surface-enhance Raman spectroscopy could satisfy this need if a robust and reproducible substrate were available. Gold nanoparticles (Au NPs) larger than 20 nm diameter are expected to greatly enhance Raman intensity if they can be assembled into ordered monolayers...
March 22, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28328070/modeling-and-simulation-of-dielectrophoretic-collective-dynamics-in-a-suspension-of-polarizable-particles-under-the-action-of-a-gradient-ac-electric-field
#18
Shigeru Tada, Yan Shen, Zhiyong Qiu
When a suspension of polarizable particles is subjected to a gradient AC electric field, the particles exhibit collective motion due to an interaction between the dipole induced in the particles and the spatial gradient of the electric field; this is known as dielectrophoresis. In the present study, the collective dynamics of suspended particles in a parallel-plate electric chamber was investigated by simulating numerically the trajectories of individual particles under the action of combined dielectrophoretic and dipole-dipole interparticle forces...
March 22, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28328067/diminishing-returns-limit-energetic-costs-of-climate-change
#19
Ofir Levy, Jason D Borchert, Travis W Rusch, Lauren B Buckley, Michael J Angilletta
Changes in the time available for organisms to maintain physiologically preferred temperatures (thermal opportunity) is a primary mechanism by which climate change impacts the fitness and population dynamics of organisms. Yet, it is unclear whether losses or gains in thermal opportunity result in proportional changes in rates of energy procurement and use. We experimentally quantified lizard food consumption and energy assimilation at different durations of thermal opportunity. We incorporated these data in an individual-based model of foraging and digestion in lizards to explore the implications of nonlinear responses to shifts in thermal opportunity across a wide geographic range...
March 22, 2017: Ecology
https://www.readbyqxmd.com/read/28327957/nanosim-nanopore-sequence-read-simulator-based-on-statistical-characterization
#20
Chen Yang, Justin Chu, René L Warren, Inanç Birol
Background: The MinION sequencing instrument from Oxford Nanopore Technologies (ONT) produces long read lengths from single-molecule sequencing - valuable features for detailed genome characterization. To realize the potential of this platform, a number of groups are developing bioinformatics tools tuned for the unique characteristics of its data. We note that these development efforts would benefit from a simulator software, output of which could be used to benchmark analysis tools. Findings: Here, we introduce NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology...
February 24, 2017: GigaScience
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