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Simulation AND Virtual

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https://www.readbyqxmd.com/read/28239489/insights-from-molecular-dynamics-simulations-for-computational-protein-design
#1
Matthew Carter Childers, Valerie Daggett
A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics...
February 1, 2017: Molecular Systems Design & Engineering
https://www.readbyqxmd.com/read/28238965/preoperative-planning-for-accurate-glenoid-component-positioning-in-reverse-shoulder-arthroplasty
#2
Julien Berhouet, Lawrence Gulotta, David Dines, Edward Craig, Russell Warren, Daniel Choi, Xiang Chen, Andreas Kontaxis
BACKGROUND: Glenoid component positioning in reverse shoulder arthroplasty (RSA) is challenging. Patient-specific instrumentation (PSI) has been advocated to improve accuracy, and is based on precise preoperative planning. The purpose of this study was to determine the accuracy of glenoid component positioning when only the glenoid surface is visible, compared to when the entire scapula is visible on a 3D virtual model. METHODS: CT scans of 30 arthritic shoulders were reconstructed in 3D models...
February 23, 2017: Orthopaedics & Traumatology, Surgery & Research: OTSR
https://www.readbyqxmd.com/read/28238283/supporting-skill-acquisition-in-cochlear-implant-surgery-through-virtual-reality-simulation
#3
Bridget Copson, Sudanthi Wijewickrema, Yun Zhou, Patorn Piromchai, Robert Briggs, James Bailey, Gregor Kennedy, Stephen O'Leary
OBJECTIVES: To evaluate the effectiveness of a virtual reality (VR) temporal bone simulator in training cochlear implant surgery. METHODS: We compared the performance of 12 otolaryngology registrars conducting simulated cochlear implant surgery before (pre-test) and after (post-tests) receiving training on a VR temporal bone surgery simulator with automated performance feedback. The post-test tasks were two temporal bones, one that was a mirror image of the temporal bone used as a pre-test and the other, a novel temporal bone...
March 2017: Cochlear Implants International
https://www.readbyqxmd.com/read/28237981/ex-vivo-ceftolozane-tazobactam-clearance-during-continuous-renal-replacement-therapy
#4
Weerachai Chaijamorn, Alexander R Shaw, Susan J Lewis, Bruce A Mueller
BACKGROUND/AIMS: To determine ceftolozane/tazobactam transmembrane clearances (CLTM) in continuous hemofiltration (CHF) and continuous hemodialysis (CHD) and to determine optimal ceftolozane/tazobactam dosing regimens for patients receiving continuous renal replacement therapy (CRRT). METHOD: Validated, ex vivo CHF and CHD bovine blood models using polysulfone (HF1400) and AN69 (Multiflow 150-M) hemofilters were used to evaluate adsorption and CLTM at different effluent flow rates...
February 25, 2017: Blood Purification
https://www.readbyqxmd.com/read/28237941/observer-based-fuzzy-adaptive-output-feedback-control-of-stochastic-nonlinear-multiple-time-delay-systems
#5
Huanqing Wang, Peter Xiaoping Liu, Peng Shi
This paper is concerned with the observer-based fuzzy output-feedback control for stochastic nonlinear multiple time-delay systems. On the basis of the consistent form of virtual input signals and increasing characteristics of the system upper bound functions, a variable splitting technique is employed to surmount the difficulty occurred in the nonlower-triangular form. In the controller design procedure, a state observer is first designed, and then an adaptive fuzzy output-feedback control method is presented by combining backstepping design together with fuzzy systems' universal approximation capability...
February 21, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28237939/virtual-network-embedding-via-monte-carlo-tree-search
#6
Soroush Haeri, Ljiljana Trajkovic
Network virtualization helps overcome shortcomings of the current Internet architecture. The virtualized network architecture enables coexistence of multiple virtual networks (VNs) on an existing physical infrastructure. VN embedding (VNE) problem, which deals with the embedding of VN components onto a physical network, is known to be NP-hard. In this paper, we propose two VNE algorithms: MaVEn-M and MaVEn-S. MaVEn-M employs the multicommodity flow algorithm for virtual link mapping while MaVEn-S uses the shortest-path algorithm...
February 20, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28231346/in-vitro-three-dimensional-accuracy-of-digital-implant-impressions-the-effect-of-implant-angulation
#7
Vanessa A Chia, Roxanna J Esguerra, Khim Hean Teoh, Juin Wei Teo, Keng Mun Wong, Keson B Tan
PURPOSE: To compare the three-dimensional (3D) accuracy of conventional impressions (CIs) with digital scans (DSs) using an intraoral scanner (IOS) with intraoral scan bodies (SBs) and varying buccolingual interimplant angulations. A secondary aim was to measure the SB machining tolerance and height with and without application of torque. MATERIALS AND METHODS: Three master models (MMs) with two implants simulating an implant-supported three-unit fixed partial denture for bone-level implants were used...
February 23, 2017: International Journal of Oral & Maxillofacial Implants
https://www.readbyqxmd.com/read/28227675/investigating-an-alternative-ring-design-of-transducer-arrays-for-tumor-treating-fields-ttfields
#8
Mario Macedo, Cornelia Wenger, Ricardo Salvador, Sofia R Fernandes, Pedro C Miranda, Mario Macedo, Cornelia Wenger, Ricardo Salvador, Sofia R Fernandes, Pedro C Miranda, Sofia R Fernandes, Pedro C Miranda, Cornelia Wenger, Ricardo Salvador, Mario Macedo
Tumor treating fields (TTFields) is a therapy that inhibits cell proliferation and has been approved by the U.S Food and Drug Administration (FDA) for the treatment of Glioblastoma Multiforme. This anti-mitotic technique works non-invasively and regionally, and is associated with less toxicity and a better quality of life. Currently a device called Optune™ is clinically used which works with two perpendicular and alternating array pairs each consisting of 3×3 transducers. The aim of this study is to investigate a theoretical alternative array design which consists of two rings of 16 transducers and thus permits various field directions...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227154/teaching-cardiopulmonary-auscultation-in-workshops-using-a-virtual-patient-simulation-technology-a-pilot-study
#9
D Pereira, P Gomes, S Faria, R Cruz-Correia, M Coimbra, D Pereira, P Gomes, S Faria, R Cruz-Correia, M Coimbra, P Gomes, R Cruz-Correia, S Faria, M Coimbra, D Pereira
Auscultation is currently both a powerful screening tool, providing a cheap and quick initial assessment of a patient's clinical condition, and a hard skill to master. The teaching of auscultation in Universities is today reduced to an unsuitable number of hours. Virtual patient simulators can potentially mitigate this problem, by providing an interesting high-quality alternative to teaching with real patients or patient simulators. In this paper we evaluate the pedagogical impact of using a virtual patient simulation technology in a short workshop format for medical students, training them to detect cardiac pathologies...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227086/catheter-simulator-software-tool-to-generate-electrograms-of-any-multi-polar-diagnostic-catheter-from-3d-atrial-tissue
#10
Kristina E Shillieto, Prasanth Ganesan, Anthony J Salmin, Elizabeth M Cherry, Arkady M Pertsov, Behnaz Ghoraani, Kristina E Shillieto, Prasanth Ganesan, Anthony J Salmin, Elizabeth M Cherry, Arkady M Pertsov, Behnaz Ghoraani, Arkady M Pertsov, Behnaz Ghoraani, Anthony J Salmin, Kristina E Shillieto, Elizabeth M Cherry, Prasanth Ganesan
Simulations are excellent tools for assessing new therapeutic strategies and are often conducted before implementing new therapy options in a clinical practice. For patients suffering from a heart arrhythmia, the main source of information comes from an intracardiac catheter. One of the common catheters is a Lasso multi-pole diagnostic catheter, which is a catheter that has 20 electrodes in a circular pattern. In this paper, we developed algorithm and simulation software that allows the users to place a multi-pole catheter on the atrial endocardial surface and record electrograms...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227083/creating-virtual-ards-patients
#11
Anup Das, Mainul Haque, Marc Chikhani, Wenfei Wang, Jonathan G Hardman, Declan G Bates, Anup Das, Mainul Haque, Marc Chikhani, Wenfei Wang, Jonathan G Hardman, Declan G Bates, Wenfei Wang, Declan G Bates, Anup Das, Mainul Haque, Marc Chikhani, Jonathan G Hardman
This paper presents the methodology used in patient-specific calibration of a novel highly integrated model of the cardiovascular and pulmonary pathophysiology associated with Acute Respiratory Distress Syndrome (ARDS). We focus on data from previously published clinical trials on the static and dynamic cardio-pulmonary responses of three ARDS patients to changes in ventilator settings. From this data, the parameters of the integrated model were identified using an optimization-based methodology in multiple stages...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227051/optimal-decision-support-rules-improve-personalize-warfarin-treatment-outcomes
#12
Chih-Lin Chi, Kourosh Ravvaz, John Weissert, Peter J Tonellato, Chih-Lin Chi, Kourosh Ravvaz, John Weissert, Peter J Tonellato, Chih-Lin Chi, Kourosh Ravvaz, John Weissert, Peter J Tonellato
We tested optimization-based approaches to generate decision support rules used to improve personalized warfarin treatment based on clinical and genetic characteristics. Our approach simulated warfarin treatment outcomes using five existing treatment plans for clinical avatars (virtual patients). We used individual clinical avatar Time-in-Therapeutic-Range to represent the two-sided adverse risk to bleeding (over dosed - above therapeutic range) and thrombosis (under dosed - below therapeutic range) and as the objective function in the optimization to minimize overall risk...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226972/design-of-a-dual-hormone-model-predictive-control-for-artificial-pancreas-with-exercise-model
#13
Navid Resalat, Joseph El Youssef, Ravi Reddy, Peter G Jacobs, Navid Resalat, Joseph El Youssef, Ravi Reddy, Peter G Jacobs, Navid Resalat, Joseph El Youssef, Peter G Jacobs, Ravi Reddy
The Artificial Pancreas (AP) is a new technology for helping people with type 1 diabetes to better control their glucose levels through automated delivery of insulin and optionally glucagon in response to sensed glucose levels. In a dual hormone AP, insulin and glucagon are delivered automatically to the body based on glucose sensor measurements using a control algorithm that calculates the amount of hormones to be infused. A dual-hormone MPC may deliver insulin continuously; however, it must avoid continuous delivery of glucagon because nausea can occur from too much glucagon...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226944/3d-force-torque-characterization-of-emergency-cricothyroidotomy-procedure-using-an-instrumented-scalpel
#14
Adam Ryason, Ganesh Sankaranarayanan, Kathryn L Butler, Marc DeMoya, Suvranu De, Adam Ryason, Ganesh Sankaranarayanan, Kathryn L Butler, Marc DeMoya, Suvranu De, Suvranu De, Marc DeMoya, Kathryn L Butler, Ganesh Sankaranarayanan, Adam Ryason
Emergency Cricothyroidotomy (CCT) is a surgical procedure performed to secure a patient's airway. This high-stakes, but seldom-performed procedure is an ideal candidate for a virtual reality simulator to enhance physician training. For the first time, this study characterizes the force/torque characteristics of the cricothyroidotomy procedure, to guide development of a virtual reality CCT simulator for use in medical training. We analyze the upper force and torque thresholds experienced at the human-scalpel interface...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28222783/walking-in-fully-immersive-virtual-environments-an-evaluation-of-potential-adverse-effects-in-older-adults-and-individuals-with-parkinson-s-disease
#15
Aram Kim, Nora Darakjian, James M Finley
BACKGROUND: Virtual reality (VR) has recently been explored as a tool for neurorehabilitation to enable individuals with Parkinson's disease (PD) to practice challenging skills in a safe environment. Current technological advances have enabled the use of affordable, fully immersive head-mounted displays (HMDs) for potential therapeutic applications. However, while previous studies have used HMDs in individuals with PD, these were only used for short bouts of walking. Clinical applications of VR for gait training would likely involve an extended exposure to the virtual environment, which has the potential to cause individuals with PD to experience simulator-related adverse effects due to their age or pathology...
February 21, 2017: Journal of Neuroengineering and Rehabilitation
https://www.readbyqxmd.com/read/28221037/computational-investigation-of-ligand-binding-to-the-peripheral-site-in-cyp3a4-conformational-dynamics-and-inhibitor-discovery
#16
Hanwen Du, Junhao Li, Yingchun Cai, Hongxiao Zhang, Guixia Liu, Yun Tang, Weihua Li
Human cytochrome P450 3A4 (CYP3A4) is a major drug-metabolizing enzyme responsible for the metabolism of ~50% of clinically used drugs and is often involved in drug-drug interactions. It exhibits atypical binding and kinetic behavior towards many ligands. Binding of ligands to CYP3A4 is a complex process. Recent studies from both crystallography and biochemistry suggested the existence of a peripheral ligand-binding site at the enzyme surface. However, the stability of ligand bound at this peripheral site and the possibility of discovering new CYP3A4 ligands based on this site remain unclear...
February 21, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28220440/quantum-probability-ranking-principle-for-ligand-based-virtual-screening
#17
Mohammed Mumtaz Al-Dabbagh, Naomie Salim, Mubarak Himmat, Ali Ahmed, Faisal Saeed
Chemical libraries contain thousands of compounds that need screening, which increases the need for computational methods that can rank or prioritize compounds. The tools of virtual screening are widely exploited to enhance the cost effectiveness of lead drug discovery programs by ranking chemical compounds databases in decreasing probability of biological activity based upon probability ranking principle (PRP). In this paper, we developed a novel ranking approach for molecular compounds inspired by quantum mechanics, called quantum probability ranking principle (QPRP)...
February 20, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28220273/numerical-and-experimental-investigations-of-the-flow-pressure-relation-in-multiple-sequential-stenoses-coronary-artery
#18
S Li, Cheng Chin, Vikas Thondapu, Eric K W Poon, Jason P Monty, Yingguang Li, Andrew S H Ooi, Shengxian Tu, Peter Barlis
Virtual fractional flow reserve (vFFR) has been evaluated as an adjunct to invasive fractional flow reserve (FFR) in the light of its operational and economic benefits. The accuracy of vFFR and the complexity of hyperemic flow simulation are still not clearly understood. This study investigates the flow-pressure relation in an idealised multiple sequential stenoses coronary artery model via numerical and experimental approaches. Pressure drop is linearly correlated with flow rate irrespective of the number of stenosis...
February 20, 2017: International Journal of Cardiovascular Imaging
https://www.readbyqxmd.com/read/28217660/reverse-total-shoulder-arthroplasty-research-models
#19
Stefano Petrillo, Umile Giuseppe Longo, Lawrence V Gulotta, Alessandra Berton, Andreas Kontaxis, Timothy Wright, Vincenzo Denaro
PURPOSE: the past decade has seen a considerable increase in the use of research models to study reverse total shoulder arthroplasty (RTSA). Nevertheless, none of these models has been shown to completely reflect real in vivo conditions. METHODS: we performed a systematic review of the literature matching the following key words: "reverse total shoulder arthroplasty" or "reverse total shoulder replacement" or "reverse total shoulder prosthesis" and "research models" or "biomechanical models" or "physical simulators" or "virtual simulators"...
October 2016: Joints
https://www.readbyqxmd.com/read/28217038/prediction-of-pest-pressure-on-corn-root-nodes-the-popp-corn-model
#20
Annika Agatz, Roman Ashauer, Paul Sweeney, Colin D Brown
A model for the corn rootworm Diabrotica spp. combined with a temporally explicit model for development of corn roots across the soil profile was developed to link pest ecology, root damage and yield loss. Development of the model focused on simulating root damage from rootworm feeding in accordance with observations in the field to allow the virtual testing of efficacy from management interventions in the future. We present the model and demonstrate its applicability for simulating root damage by comparison between observed and simulated pest development and root damage (assessed according to the node injury scale from 0 to 3) for field studies from the literature conducted in Urbana, Illinois (US), between 1991 and 2014...
2017: Journal of Pest Science
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