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https://www.readbyqxmd.com/read/27914065/computational-design-of-membrane-curvature-sensing-peptides
#1
Armando Jerome de Jesus, Hang Yin
Computer simulations have become an indispensable tool in studying molecular biological systems. The unmatched spatial and temporal resolution that it offers enables for microscopic-level views into the dynamics and mechanics of biological systems. Recent advances in hardware resources have also opened up to computer simulations the investigation of longer timescale biological processes and larger systems. The study of membrane proteins or peptides especially benefits from simulations due to difficulties related to crystallization of such proteins in a membrane environment...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914061/probing-oligomerized-conformations-of-defensin-in-the-membrane
#2
Wenxun Gan, Dina Schneidman, Ning Zhang, Buyong Ma, Ruth Nussinov
Computational prediction and design of membrane protein-protein interactions facilitate biomedical engineering and biotechnological applications. Due to their antimicrobial activity, human defensins play an important role in the innate immune system. Human defensins are attractive pharmaceutical targets due to their small size, broad activity spectrum, reduced immunogenicity, and resistance to proteolysis. Protein engineering based modification of defensins can improve their pharmaceutical properties. Here we present an approach to computationally probe defensins' oligomerization states in the membrane...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914051/integration-of-molecular-dynamics-based-predictions-into-the-optimization-of-de-novo-protein-designs-limitations-and-benefits
#3
Henrique F Carvalho, Arménio J M Barbosa, Ana C A Roque, Olga Iranzo, Ricardo J F Branco
Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914048/geometric-potentials-for-computational-protein-sequence-design
#4
Jie Li, Patrice Koehl
Computational protein sequence design is the rational design based on computer simulation of new protein molecules to fold to target three-dimensional structures, with the ultimate goal of designing novel functions. It requires a good understanding of the thermodynamic equilibrium properties of the protein of interest. Here, we consider the contribution of the solvent to the stability of the protein. We describe implicit solvent models, focusing on approximations of their nonpolar components using geometric potentials...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914041/paliperidone-loaded-nanolipomer-system-for-sustained-delivery-and-enhanced-intestinal-permeation-superiority-to-polymeric-and-solid-lipid-nanoparticles
#5
Hala Mahmoud Helal, Sana Mohamed Mortada, Marwa Ahmed Sallam
Paliperidone (PPD) is the most recent second-generation atypical antipsychotic approved for the treatment of schizophrenia. An immediate release dose causes extrapyramidal side effects. In this work, a novel nanolipomer carrier system for PPD with enhanced intestinal permeability and sustained release properties has been developed and optimized. PPD was successfully encapsulated into a lipomer consisting of a specific combination of biocompatible materials including poly-ε-caprolactone as a polymeric core, Lipoid S75, and Gelucire® 50/13 as a lipid shell and polyvinyl alcohol as a stabilizing agent...
December 2, 2016: AAPS PharmSciTech
https://www.readbyqxmd.com/read/27914012/biomechanical-investigation-of-titanium-elastic-nail-prebending-for-treating-diaphyseal-long-bone-fractures
#6
Yen-Nien Chen, Pei-Yuan Lee, Chih-Wei Chang, Yi-Hung Ho, Yao-Te Peng, Chih-Han Chang, Chun-Ting Li
This study numerically investigated the deformation of titanium elastic nails prebent at various degrees during implantation into the intramedullary canal of fractured bones and the mechanism by which this prebending influenced the stability of the fractured bone. Three degrees of prebending the implanted portions of the nails were used: equal to, two times, and three times the diameter of the intramedullary canal. Furthermore, a simulated diaphyseal fracture with a 5-mm gap was created in the middle shaft portion of the bone fixed with two elastic nails in a double C-type configuration...
December 2, 2016: Australasian Physical & Engineering Sciences in Medicine
https://www.readbyqxmd.com/read/27913989/cost-effectiveness-analysis-of-isavuconazole-vs-voriconazole-as-first-line-treatment-for-invasive-aspergillosis
#7
Rachel Harrington, Edward Lee, Hongbo Yang, Jin Wei, Andrew Messali, Nkechi Azie, Eric Q Wu, James Spalding
INTRODUCTION: Invasive aspergillosis (IA) is associated with a significant clinical and economic burden. The phase III SECURE trial demonstrated non-inferiority in clinical efficacy between isavuconazole and voriconazole. No studies have evaluated the cost-effectiveness of isavuconazole compared to voriconazole. The objective of this study was to evaluate the costs and cost-effectiveness of isavuconazole vs. voriconazole for the first-line treatment of IA from the US hospital perspective...
December 2, 2016: Advances in Therapy
https://www.readbyqxmd.com/read/27913950/mechanics-reveals-the-biological-trigger-in-wrinkly-fingers
#8
P Sáez, A M Zöllner
Fingertips wrinkle due to long exposure to water. The biological reason for this morphological change is unclear and still not fully understood. There are two main hypotheses for the underlying mechanism of fingertip wrinkling: the 'shrink' model (in which the wrinkling is driven by the contraction of the lower layers of skin, associated with the shrinking of the underlying vasculature), and the 'swell' model (in which the wrinkling is driven by the swelling of the upper layers of the skin, associated with osmosis)...
December 2, 2016: Annals of Biomedical Engineering
https://www.readbyqxmd.com/read/27913943/the-cost-effectiveness-of-interventions-targeting-lifestyle-change-for-the-prevention-of-diabetes-in-a-swedish-primary-care-and-community-based-prevention-program
#9
Anne Neumann, Lars Lindholm, Margareta Norberg, Olaf Schoffer, Stefanie J Klug, Fredrik Norström
BACKGROUND: Policymakers need to know the cost-effectiveness of interventions to prevent type 2 diabetes (T2D). The objective of this study was to estimate the cost-effectiveness of a T2D prevention initiative targeting weight reduction, increased physical activity and healthier diet in persons in pre-diabetic states by comparing a hypothetical intervention versus no intervention in a Swedish setting. METHODS: A Markov model was used to study the cost-effectiveness of a T2D prevention program based on lifestyle change versus a control group where no prevention was applied...
December 2, 2016: European Journal of Health Economics: HEPAC: Health Economics in Prevention and Care
https://www.readbyqxmd.com/read/27913901/3d-active-passive-response-of-human-knee-joint-in-gait-is-markedly-altered-when-simulated-as-a-planar-2d-joint
#10
H Marouane, A Shirazi-Adl, M Adouni
Musculoskeletal models of the lower extremity make a number of important assumptions when attempting to estimate muscle forces and tibiofemoral compartmental loads in activities such as gait. The knee is commonly idealized as a planar 2D joint in the sagittal plane with no consideration of motions and equilibrium in remaining planes. With muscle forces predicted, the static equilibrium in the frontal plane is then used to estimate compartmental loads neglecting also joint passive resistance and assuming condylar contact centers...
December 2, 2016: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/27913840/finding-direction-in-the-search-for-selection
#11
Grant Thiltgen, Mario Dos Reis, Richard A Goldstein
Tests for positive selection have mostly been developed to look for diversifying selection where change away from the current amino acid is often favorable. However, in many cases we are interested in directional selection where there is a shift toward specific amino acids, resulting in increased fitness in the species. Recently, a few methods have been developed to detect and characterize directional selection on a molecular level. Using the results of evolutionary simulations as well as HIV drug resistance data as models of directional selection, we compare two such methods with each other, as well as against a standard method for detecting diversifying selection...
December 2, 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27913823/mathematical-models-suggest-facilitated-fatty-acids-crossing-of-the-luminal-membrane-in-the-cardiac-muscle
#12
Efrath Barta
Long-chain fatty acids cross a few membranes on their way from the capillary blood to the cardiomyocyte cytosol, where they are utilized as an essential source of energy. Details of the transport mechanism across those membranes remained elusive despite decades of laboratory and theoretical work. Here we inspect several optional scenarios for the crossing of the luminal membrane of the endothelial cell, the first barrier that should be crossed: a passive diffusion, facilitation by receptors for albumin and facilitation by fatty acids transporters...
December 3, 2016: Journal of Membrane Biology
https://www.readbyqxmd.com/read/27913731/disentangling-polydispersity-in-the-pcna-p15paf-complex-a-disordered-transient-and-multivalent-macromolecular-assembly
#13
Tiago N Cordeiro, Po-Chia Chen, Alfredo De Biasio, Nathalie Sibille, Francisco J Blanco, Jochen S Hub, Ramon Crehuet, Pau Bernadó
The intrinsically disordered p15(PAF) regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15(PAF) and trimeric PCNA is of low affinity, forming a transient complex that is difficult to characterize at a structural level due to its inherent polydispersity. We have determined the structure, conformational fluctuations, and relative population of the five species that coexist in solution by combining small-angle X-ray scattering (SAXS) with molecular modelling...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913617/evaluating-sequence-based-genomic-prediction-with-an-efficient-new-simulator
#14
Miguel Pérez-Enciso, Natalia Forneris, Gustavo de Los Campos, Andrés Legarra
The vast amount of sequence data to analyze complex traits is posing new challenges in terms of analysis and interpretation of the results. Although simulation is a fundamental tool to investigate the reliability of genomic analyses and to optimize experimental design, existing software cannot simulate complete genomes realistically. To remedy this, we have developed a new strategy (Sequence Based Virtual Breeding, SBVB) that consists of using real sequence data and simulating new offspring genomes and phenotypes in a very efficient and flexible manner...
December 2, 2016: Genetics
https://www.readbyqxmd.com/read/27913434/a-study-of-tp53-rna-splicing-illustrates-pitfalls-of-rna-seq-methodology
#15
Sunali Mehta, Peter Tsai, Annette Lasham, Hamish Campbell, Roger Reddel, Antony Braithwaite, Cristin Print
TP53 undergoes multiple RNA-splicing events, resulting in at least nine mRNA transcripts encoding at least 12 functionally different protein isoforms. Antibodies specific to p53 protein isoforms have proven difficult to develop, thus researchers must rely on the transcript information to infer isoform abundance. In this study, we used deep RNA-seq, droplet digital PCR (ddPCR), and real-time quantitative reverse transcriptase PCR (RT-qPCR) from nine human cell lines and RNA-seq data available for tumors in The Cancer Genome Atlas to analyze TP53 splice variant expression...
October 20, 2016: Cancer Research
https://www.readbyqxmd.com/read/27913359/network-unfolding-map-by-vertex-edge-dynamics-modeling
#16
Filipe Alves Neto Verri, Paulo Roberto Urio, Liang Zhao
The emergence of collective dynamics in neural networks is a mechanism of the animal and human brain for information processing. In this paper, we develop a computational technique using distributed processing elements in a complex network, which are called particles, to solve semisupervised learning problems. Three actions govern the particles' dynamics: generation, walking, and absorption. Labeled vertices generate new particles that compete against rival particles for edge domination. Active particles randomly walk in the network until they are absorbed by either a rival vertex or an edge currently dominated by rival particles...
November 29, 2016: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/27913347/tree-structure-sparsity-pattern-guided-convex-optimization-for-compressive-sensing-of-large-scale-images
#17
Wei-Jie Liang, Gang-Xuan Lin, Chun-Shien Lu
Cost-efficient compressive sensing of large-scale images with quickly reconstructed high-quality results is very challenging. In this paper, we present an algorithm to solve convex optimization via the tree structure sparsity pattern, which can be run in the operator to reduce computation cost and maintain good quality, especially for large-scale images. We also provide convergence analysis and convergence rate analysis for the proposed method. The feasibility of our method is verified through simulations and comparison with state-of-theart algorithms...
December 1, 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/27913342/efficient-strategies-for-estimating-the-spatial-coherence-of-backscatter
#18
Dongwoon Hyun, Anna Lisa C Crowley, Jeremy J Dahl
The spatial coherence of ultrasound backscatter has been proposed to reduce clutter in medical imaging, to measure the anisotropy of the scattering source, and to improve the detection of blood flow. These techniques rely on correlation estimates that are obtained using computationally expensive strategies. In this study, we assess existing spatial coherence estimation methods and propose three computationally efficient modifications: a reduced kernel, a downsampled receive aperture, and the use of an ensemble correlation coefficient...
December 1, 2016: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/27913340/efficient-3d-reconstruction-in-ultrasound-elastography-via-a-sparse-iteration-based-on-markov-random-fields
#19
Atul Ingle, Tomy Varghese, William Sethares
Percutaneous needle-based liver ablation procedures are becoming increasingly common for treatment of small isolated tumors in hepatocellular carcinoma patients who are not candidates for surgery. Rapid three dimensional visualization of liver ablations has potential clinical value because it can enable interventional radiologists to plan and execute needle-based ablation procedures with real time feedback. Ensuring the right volume of tissue is ablated is desirable to avoid recurrence of tumors from residual untreated cancerous cells...
November 29, 2016: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/27913339/a-parametric-study-for-the-design-of-an-optimized-ultrasonic-percussive-planetary-drill-tool
#20
Xuan Li, Patrick Harkness, Kevin Worrall, Ryan Timoney, Margaret Lucas
Traditional rotary drilling for planetary rock sampling, in-situ analysis and sample return, is challenging because the axial force and holding torque requirements are not necessarily compatible with lightweight spacecraft architectures in low-gravity environments. This article seeks to optimize an ultrasonic-percussive drill tool to achieve rock penetration with lower reacted force requirements, with a strategic view towards building an Ultrasonic Planetary Core Drill (UPCD) device. The UPCD is a descendant of the Ultrasonic/Sonic Driller/Corer (USDC) technique...
November 29, 2016: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
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