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"Validation" simulation model

Nidhi Singh, Priyanka Shah, Hemlata Dwivedi, Shikha Mishra, Renu Tripathi, Amogh A Sahasrabuddhe, Mohammad Imran Siddiqi
N-Myristoyltransferase (NMT) catalyzes the transfer of myristate to the amino-terminal glycine of a subset of proteins, a co-translational modification involved in trafficking substrate proteins to membrane locations, stabilization and protein-protein interactions. It is a studied and validated pre-clinical drug target for fungal and parasitic infections. In the present study, a machine learning approach, docking studies and CoMFA analysis have been integrated with the objective of translation of knowledge into a pipelined workflow towards the identification of putative hits through the screening of large compound libraries...
October 21, 2016: Molecular BioSystems
Shehla Akbar, Fazal Subhan, Nasiara Karim, Muhammad Shahid, Nisar Ahmad, Gowhar Ali, Wajahat Mahmood, Khwaja Fawad
BACKGROUND: Diabetic neuropathy is the most prevalent, persistent and debilitating complication of diabetes mellitus often coupled with vulvodynia that may present as an isolated symptom or as a part of constellation of other neuropathic abnormalities. OBJECTIVE: Flavonoids have selective affinity for GABA receptors and 6-methoxyflavanone (6-MeOF) is a positive allosteric modulator of GABA responses at human recombinant GABAA receptors. GABAergic and opioidergic system inhibition have been shown to facilitate neuropathic pain...
October 17, 2016: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Ashish Kumar Singh, Bo-Yang Chen, Vincent B C Tan, Tong-Earn Tay, Heow-Pueh Lee
Linear ultrasonics methods based on the principle of reflection, transmission, dissipation of sound waves have been traditionally used to detect delaminations in composite structures. However, when the delamination is in very early stages such that it is almost closed, or closed due to a compressive load, the linear methods may fail to detect such cases of delaminations. Nonlinear acoustics/ultrasonics have shown potential to identify damages in composite structures which are difficult to detect using conventional linear ultrasonic methods...
October 8, 2016: Ultrasonics
Matthieu Barbier, James R Watson
Predators of all kinds, be they lions hunting in the Serengeti or fishermen searching for their catch, display various collective strategies. A common strategy is to share information about the location of prey. However, depending on the spatial characteristics and mobility of predators and prey, information sharing can either improve or hinder individual success. Here, our goal is to investigate the interacting effects of space and information sharing on predation efficiency, represented by the expected rate at which prey are found and consumed...
October 2016: PLoS Computational Biology
Jacob Herrmann, Merryn H Tawhai, David W Kaczka
Regional ventilation in the injured lung is heterogeneous and frequency-dependent, making it difficult to predict how an oscillatory flow waveform at a specified frequency will be distributed throughout the periphery. To predict the impact of mechanical heterogeneity on regional ventilation distribution and gas transport, we developed a computational model of distributed gas flow and CO2 elimination during oscillatory ventilation from 0.1 to 30 Hz. The model consists of a three dimensional airway network of a canine lung, with heterogeneous parenchymal tissues to mimic effects of gravity and injury...
October 7, 2016: Journal of Applied Physiology
Asanga Bandara, Afra Panahi, George A Pantelopulos, John E Straub
For 40 years, the existence and possible functional importance of cholesterol dimer formation has been discussed. Due to challenges associated with structural studies of membrane lipids, there has as yet been no direct experimental verification of the existence and relevance of the cholesterol dimer. Building on recent advances in lipid force fields for molecular simulation, in this work the structure and stability of the cholesterol dimer is characterized in POPC bilayers in absence and presence of sphingomyelin...
October 20, 2016: Journal of Computational Chemistry
Wei-Tao Wu, Andrea Blue Martin, Alberto Gandini, Nadine Aubry, Mehrdad Massoudi, James F Antaki
This study is motivated by the development of a blood cell filtration device for removal of malaria-infected, parasitized red blood cells (pRBCs). The blood was modeled as a multi-component fluid using the computational fluid dynamics discrete element method (CFD-DEM), wherein plasma was treated as a Newtonian fluid and the red blood cells (RBCs) were modeled as soft-sphere solid particles which move under the influence of drag, collisions with other RBCs, and a magnetic force. The CFD-DEM model was first validated by a comparison with experimental data from Han et al...
2016: Microfluidics and Nanofluidics
Fangzhou Shen, Jian Li, Ying Zhu, Zhuo Wang
Cancer cells have different metabolism in contrast to normal cells. The advancement in omics measurement technology enables the genome-wide characterization of altered cellular processes in cancers, but the metabolic flux landscape of cancer is still far from understood. In this study, we compared the well-reconstructed tissue-specific models of five cancers, including breast, liver, lung, renal, and urothelial cancer, and their corresponding normal cells. There are similar patterns in majority of significantly regulated pathways and enriched pathways in correlated reaction sets...
August 29, 2016: Journal of Bioinformatics and Computational Biology
Yunzhu Meng, Wansoo Pak, Berkan Guleyupoglu, Bharath Koya, F Scott Gayzik, Costin D Untaroiu
Child pedestrian protection deserves more attention in vehicle safety design since they are the most vulnerable road users who face the highest mortality rate. Pediatric Finite Element (FE) models could be used to simulate and understand the pedestrian injury mechanisms during crashes in order to mitigate them. Thus, the objective of the study was to develop a computationally efficient (simplified) six-year-old (6YO-PS) pedestrian FE model and validate it based on the latest published pediatric data. The 6YO-PS FE model was developed by morphing the existing GHBMC adult pedestrian model...
October 16, 2016: Accident; Analysis and Prevention
S Negin Mortazavi, Donna Geddes, Fatemeh Hassanipour
This work presents a fluid dynamic study of milk flow in lactating human breast. The motivation for this study is in part to improve the fundamental understanding of transport processes in an important but insufficiently studied human organ, and in part to produce a new methodology for the understanding of the pathologies of lactation, which can have a huge impact on the health and well-being of a significant proportion of the population. This collaborative effort among lactation specialists and fluid dynamic engineers starts with a careful, statistically representative measurement of infant suckling patterns...
October 19, 2016: Journal of Biomechanical Engineering
Vicente Andreu-Fernandez, Maria J García-Murria, Manuel Bañó-Polo, Juliette Martin, Luca Monticelli, Mar Orzáez, Ismael Mingarro
Changes in the equilibrium of pro- and anti-apoptotic members of the B-cell lymphoma-2 (Bcl-2) protein family in the mitochondrial outer membrane (MOM) induce structural changes that commit cells to apoptosis. Bcl-2 homology-3 (BH3)-only proteins participate in this process by either activating pro-apoptotic effectors or inhibiting anti-apoptotic components and by promoting MOM permeabilization. The association of BH3-only proteins with MOMs is necessary for the activation and amplification of death signals; however, the nature of this association remains controversial, as these proteins lack a canonical transmembrane sequence...
October 7, 2016: Journal of Biological Chemistry
M Hiligsmann, N Burlet, P Fardellone, N Al-Daghri, J-Y Reginster
: The recommended intake of vitamin D-fortified dairy products can substantially decrease the burden of osteoporotic fractures and seems an economically beneficial strategy in the general French population aged over 60 years. INTRODUCTION: This study aims to assess the public health and economic impact of vitamin D-fortified dairy products in the general French population aged over 60 years. METHODS: We estimated the lifetime health impacts expressed in number of fractures prevented, life years gained, and quality-adjusted life years (QALY) gained of the recommended intake of dairy products in the general French population over 60 years for 1 year (2015)...
October 18, 2016: Osteoporosis International
T Christian Gasser
Abdominal aortic aneurysm (AAA) rupture is a local event in the aneurysm wall that naturally demands tools to assess the risk for local wall rupture. Consequently, global parameters like the maximum diameter and its expansion over time can only give very rough risk indications; therefore, they frequently fail to predict individual risk for AAA rupture. In contrast, the Biomechanical Rupture Risk Assessment (BRRA) method investigates the wall's risk for local rupture by quantitatively integrating many known AAA rupture risk factors like female sex, large relative expansion, intraluminal thrombus-related wall weakening, and high blood pressure...
April 2016: Aorta (Stamford, Conn.)
Amy J Davis, Mevin B Hooten, Ryan S Miller, Matthew L Farnsworth, Jesse Lewis, Michael Moxcey, Kim M Pepin
Evaluation of the progress of management programs for invasive species is crucial for demonstrating impacts to stakeholders and strategic planning of resource allocation. Estimates of abundance before and after management activities can serve as a useful metric of population management programs. However, many methods of estimating population size are too labor intensive and costly to implement, posing restrictive levels of burden on operational programs. Removal models are a reliable method for estimating abundance before and after management using data from the removal activities exclusively, thus requiring no work in addition to management...
October 2016: Ecological Applications: a Publication of the Ecological Society of America
John S Nemer, Gavriel D Kohlberg, Dean M Mancuso, Brianna M Griffin, Michael V Certo, Stephanie Y Chen, Michael B Chun, Jaclyn B Spitzer, Anil K Lalwani
OBJECTIVE: Cochlear implantation is associated with poor music perception and enjoyment. Reducing music complexity has been shown to enhance music enjoyment in cochlear implant (CI) recipients. In this study, we assess the impact of harmonic series reduction on music enjoyment. STUDY DESIGN: Prospective analysis of music enjoyment in normal-hearing (NH) individuals and CI recipients. SETTING: Single tertiary academic medical center. PATIENTS: NH adults (N = 20) and CI users (N = 8) rated the Happy Birthday song on three validated enjoyment modalities-musicality, pleasantness, and naturalness...
October 12, 2016: Otology & Neurotology
Karl Stoffel, Ivan Zderic, Florian Gras, Christoph Sommer, Ursula Eberli, David Mueller, Martin Oswald, Boyko Gueorguiev
OBJECTIVES: To evaluate the biomechanical performance of Femoral Neck System (FNS) in comparison to established methods for fixation of femoral neck fractures in a cadaveric model. METHODS: Twenty pairs of fresh-frozen human cadaveric femora were instrumented either with DHS-Screw, DHS-Blade, 3CS or with FNS in a partially paired design. The specimens were randomized to two paired treatment groups based on the BMD, namely DHS-Screw/DHS-Blade and FNS/3CS. A reduced unstable femoral neck fracture with postero-caudal comminution, AO/OTA 31-B2...
October 13, 2016: Journal of Orthopaedic Trauma
Guangpu Zhu, Jun Yao, Lei Zhang, Hai Sun, Aifen Li
A large amount of residual oil, which exists as isolated oil slugs, remains trapped in reservoirs after water flooding. Numerous numerical studies are performed to investigate the fundamental flow mechanism of oil slugs to improve flooding efficiency. Dynamic contact angle models are usually introduced to simulate an accurate contact angle and meniscus displacement of oil slug under a high capillary number. Nevertheless, in the oil slug flow simulation process, it is unnecessary to introduce the dynamic contact angle model due to a negligible change of meniscus displacement after using the dynamic contact angle model when the capillary number is small...
October 18, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
Sheng Luo, Jodie L Lutkenhaus, Hadi Nasrabadi
For over a century, the phase behavior of bulk fluids has been described as PVT (pressure-volume-temperature) three-dimensional properties, but it has become increasingly clear that the liquid-vapor phase behavior in confined geometries is significantly altered from the bulk. Efforts have been devoted to accessing confined phase transitions using sorption, molecular simulations and theoretical methods. However, a comprehensive picture of PVT relationships for confined hydrocarbons remains uncertain. Herein, we introduce d (confining pore diameter) as a fourth dimension, and we present PVT-d behavior of confined fluids in nanopores...
October 18, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
Dejan Agić, Hrvoje Brkić, Sanja Tomić, Zrinka Karačić, Marija Špoljarević, Miroslav Lisjak, Drago Bešlo, Marija Abramić
Fifteen flavonoids were studied for their inhibitory activity against human dipeptidyl peptidase III (hDPP III) combining an in vitro assay with an in silico molecular modeling study. All analyzed flavonoids showed inhibitory effects against hDPP III with the IC50 values ranging from 22.0 to 437.2 μM. Our 3D QSAR studies indicate that the presence of hydrophilic regions at a flavonoid molecule increases its inhibitory activity while the higher percentage of hydrophobic surfaces have negative impact on enzyme inhibition...
October 18, 2016: Chemical Biology & Drug Design
Tim Friede, Christian Röver, Simon Wandel, Beat Neuenschwander
Random-effects meta-analyses are used to combine evidence of treatment effects from multiple studies. Since treatment effects may vary across trials due to differences in study characteristics, heterogeneity in treatment effects between studies must be accounted for to achieve valid inference. The standard model for random-effects meta-analysis assumes approximately normal effect estimates and a normal random-effects model. However, standard methods based on this model ignore the uncertainty in estimating the between-trial heterogeneity...
October 18, 2016: Biometrical Journal. Biometrische Zeitschrift
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