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https://www.readbyqxmd.com/read/27914125/having-a-physician-rather-than-a-place-as-a-usual-source-of-care-would-be-better-from-2012-korea-health-panel-data
#1
Kyeong Min Kim, Hyunsoo Jeon, Jae Ho Lee
A usual source of care (USC) in primary care improves health care quality and can result in improved health. However, current research about the type of USC (place only vs. physician with a place) is insufficient as an evidence to support the value of primary care. We analyzed data from the 2012 Korea Health Panel survey of adults aged 18 years or older (n = 11,873) who reported whether having a USC or not to compare the effects by type of USC on medical care use and out-of-pocket costs. Descriptive analysis showed significant differences in the distributions of sociodemographic and health status factors except frequency of outpatient visit by type of USC...
January 2017: Journal of Korean Medical Science
https://www.readbyqxmd.com/read/27914066/computational-tools-for-allosteric-drug-discovery-site-identification-and-focus-library-design
#2
Wenkang Huang, Ruth Nussinov, Jian Zhang
Allostery is an intrinsic phenomenon of biological macromolecules involving regulation and/or signal transduction induced by a ligand binding to an allosteric site distinct from a molecule's active site. Allosteric drugs are currently receiving increased attention in drug discovery because drugs that target allosteric sites can provide important advantages over the corresponding orthosteric drugs including specific subtype selectivity within receptor families. Consequently, targeting allosteric sites, instead of orthosteric sites, can reduce drug-related side effects and toxicity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914065/computational-design-of-membrane-curvature-sensing-peptides
#3
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/27914064/computational-tools-for-aiding-rational-antibody-design
#4
Konrad Krawczyk, James Dunbar, Charlotte M Deane
Antibodies are a group of proteins responsible for mediating immune reactions in vertebrates. They are able to bind a variety of structural motifs on noxious molecules tagging them for elimination from the organism. As a result of their versatile binding properties, antibodies are currently one of the most important classes of biopharmaceuticals. In this chapter, we discuss how knowledge-based computational methods can aid experimentalists in the development of potent antibodies. When using common experimental methods for antibody development, we often know the sequence of an antibody that binds to our molecule, antigen, of interest...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914063/episweep-computationally-driven-reengineering-of-therapeutic-proteins-to-reduce-immunogenicity-while-maintaining-function
#5
Yoonjoo Choi, Deeptak Verma, Karl E Griswold, Chris Bailey-Kellogg
Therapeutic proteins are yielding ever more advanced and efficacious new drugs, but the biological origins of these highly effective therapeutics render them subject to immune surveillance within the patient's body. When recognized by the immune system as a foreign agent, protein drugs elicit a coordinated response that can manifest a range of clinical complications including rapid drug clearance, loss of functionality and efficacy, delayed infusion-like allergic reactions, more serious anaphylactic shock, and even induced auto-immunity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914062/computational-design-of-ligand-binding-proteins
#6
Christine E Tinberg, Sagar D Khare
The ability to design novel small-molecule binding sites in proteins is a stringent test of our understanding of the principles of molecular recognition, and would have many practical applications, in synthetic biology and medicine. Here, we describe a computational method in the context of the macromolecular modeling suite Rosetta to designing proteins with sites featuring predetermined interactions to ligands of choice. The required inputs for the method are a model of the small molecule and the desired interactions (e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914060/a-protocol-for-the-design-of-protein-and-peptide-nanostructure-self-assemblies-exploiting-synthetic-amino-acids
#7
Nurit Haspel, Jie Zheng, Carlos Aleman, David Zanuy, Ruth Nussinov
In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914057/bindml-bindml-detecting-protein-protein-interaction-interface-propensity-from-amino-acid-substitution-patterns
#8
Qing Wei, David La, Daisuke Kihara
Prediction of protein-protein interaction sites in a protein structure provides important information for elucidating the mechanism of protein function and can also be useful in guiding a modeling or design procedures of protein complex structures. Since prediction methods essentially assess the propensity of amino acids that are likely to be part of a protein docking interface, they can help in designing protein-protein interactions. Here, we introduce BindML and BindML+ protein-protein interaction sites prediction methods...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914056/parallel-computational-protein-design
#9
Yichao Zhou, Bruce R Donald, Jianyang Zeng
Computational structure-based protein design (CSPD) is an important problem in computational biology, which aims to design or improve a prescribed protein function based on a protein structure template. It provides a practical tool for real-world protein engineering applications. A popular CSPD method that guarantees to find the global minimum energy solution (GMEC) is to combine both dead-end elimination (DEE) and A* tree search algorithms. However, in this framework, the A* search algorithm can run in exponential time in the worst case, which may become the computation bottleneck of large-scale computational protein design process...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914054/computational-protein-design-through-grafting-and-stabilization
#10
Cheng Zhu, David D Mowrey, Nikolay V Dokholyan
Computational grafting of target residues onto existing protein scaffolds is a powerful method for the design of proteins with novel function. In the grafting method side chain mutations are introduced into a preexisting protein scaffold to recreate a target functional motif. The success of this approach relies on two primary criteria: (1) the availability of compatible structural scaffolds, and (2) the introduction of mutations that do not affect the protein structure or stability. To identify compatible structural motifs we use the Erebus webserver, to search the protein data bank (PDB) for user-defined structural scaffolds...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914049/modeling-binding-affinity-of-pathological-mutations-for-computational-protein-design
#11
Miguel Romero-Durana, Chiara Pallara, Fabian Glaser, Juan Fernández-Recio
An important aspect of protein functionality is the formation of specific complexes with other proteins, which are involved in the majority of biological processes. The functional characterization of such interactions at molecular level is necessary, not only to understand biological and pathological phenomena but also to design improved, or even new interfaces, or to develop new therapeutic approaches. X-ray crystallography and NMR spectroscopy have increased the number of 3D protein complex structures deposited in the Protein Data Bank (PDB)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914047/deterministic-search-methods-for-computational-protein-design
#12
Seydou Traoré, David Allouche, Isabelle André, Thomas Schiex, Sophie Barbe
One main challenge in Computational Protein Design (CPD) lies in the exploration of the amino-acid sequence space, while considering, to some extent, side chain flexibility. The exorbitant size of the search space urges for the development of efficient exact deterministic search methods enabling identification of low-energy sequence-conformation models, corresponding either to the global minimum energy conformation (GMEC) or an ensemble of guaranteed near-optimal solutions. In contrast to stochastic local search methods that are not guaranteed to find the GMEC, exact deterministic approaches always identify the GMEC and prove its optimality in finite but exponential worst-case time...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914045/achievements-and-challenges-in-computational-protein-design
#13
Ilan Samish
Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth and maturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a "CPD 101". These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of high- and low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions, (5) assessment of shape-complementarity, electrostatics and solvation effects, (6) integration of thermal plasticity and functional dynamics, (7) negative design, (8) systematic integration of experimental approaches, (9) objective cross-assessment of methods, and (10) successful ranking of potential designs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914044/the-framework-of-computational-protein-design
#14
Ilan Samish
Computational protein design (CPD) has established itself as a leading field in basic and applied science with a strong coupling between the two. Proteins are computationally designed from the level of amino acids to the level of a functional protein complex. Design targets range from increased thermo- (or other) stability to specific requested reactions such as protein-protein binding, enzymatic reactions, or nanotechnology applications. The design scheme may encompass small regions of the proteins or the entire protein...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914016/ms-ms-assisted-design-of-sequence-controlled-synthetic-polymers-for-improved-reading-of-encoded-information
#15
Laurence Charles, Gianni Cavallo, Valérie Monnier, Laurence Oswald, Roza Szweda, Jean-François Lutz
In order to improve their MS/MS sequencing, structure of sequence-controlled synthetic polymers can be optimized based on considerations regarding their fragmentation behavior in collision-induced dissociation conditions, as demonstrated here for two digitally encoded polymer families. In poly(triazole amide)s, the main dissociation route proceeded via cleavage of the amide bond in each monomer, hence allowing the chains to be safely sequenced. However, a competitive cleavage of an ether bond in a tri(ethylene glycol) spacer placed between each coding moiety complicated MS/MS spectra while not bringing new structural information...
December 2, 2016: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/27913959/reaction-of-complement-factors-and-proteasomes-in-experimental-encephalitis
#16
Stefan Lange, Tomas Bergström, Ewa Johansson, Merna Oshalim, Ivar Lönnroth
Herpes simplex virus type 1 (HSV-1) encephalitis causes a deleterious inflammation and elevated intracranial pressure. As a step towards examining the origin of the inflammation, we here report the response of circulating proteasomes and complement factors in blood and cerebrospinal fluid (CSF) in rats infected with HSV-1. Infection was via the nasal route, with 1.1 × 10(4) plaque-forming units of HSV-1 strain 2762 given in one or both nostrils. A sandwich enzyme-linked immunosorbent assay was used to study the level of 26S proteasomes and their complex formation with complement factors 3 and 4...
December 2, 2016: Journal of Neurovirology
https://www.readbyqxmd.com/read/27913951/stereolithography-based-3d-printed-pillar-plates-that-minimizes-fluid-transfers-during-enzyme-linked-immunosorbent-assays
#17
Justin D McCallen, Alison Schaefer, Phoebe Lee, Loretta Hing, Samuel K Lai
Enzyme linked immunosorbent assay (ELISA) is one of the most popular and indispensable tools in molecular biology. Despite numerous advances in ELISA methods that markedly improve the sensitivity and throughput of detection, a hallmark of all ELISA continues to be repeated pipetting of fluids that is not only cumbersome but can easily introduce errors or contaminations. Robotics, despite obvious advantages, remains expensive. Here, we designed and produced cheap "pillar plates" using stereolithography-based 3D printing that can be readily inserted into conventional 96- and 384- well plates and serve as the substrate for ELISA...
December 2, 2016: Annals of Biomedical Engineering
https://www.readbyqxmd.com/read/27913945/the-effect-of-prophylactic-central-neck-dissection-on-locoregional-recurrence-in-papillary-thyroid-cancer-after-total-thyroidectomy-a-systematic-review-and-meta-analysis-pcnd-for-the-locoregional-recurrence-of-papillary-thyroid-cancer
#18
Wenjing Zhao, Lei You, Xianming Hou, Shaobo Chen, Xiaoxia Ren, Ge Chen, Yupei Zhao
BACKGROUND: The use of prophylactic central neck dissection (pCND) for papillary thyroid cancer (PTC) without clinical evidence of nodal metastasis (cN0) remains controversial. This study was designed to examine whether pCND for PTC affected locoregional recurrence (LRR). METHODS: A systematic review was performed to compare the LRR between patients with PTC who underwent total thyroidectomy (TT) and pCND and those who underwent TT alone. The primary outcome was LRR...
December 2, 2016: Annals of Surgical Oncology
https://www.readbyqxmd.com/read/27913910/a-randomized-trial-of-displaying-paid-price-information-on-imaging-study-and-procedure-ordering-rates
#19
Alyna T Chien, Lisa Soleymani Lehmann, Laura A Hatfield, Kate E Koplan, Carter R Petty, Anna D Sinaiko, Meredith B Rosenthal, Thomas D Sequist
BACKGROUND: Prior studies have demonstrated how price transparency lowers the test-ordering rates of trainees in hospitals, and physician-targeted price transparency efforts have been viewed as a promising cost-controlling strategy. OBJECTIVE: To examine the effect of displaying paid-price information on test-ordering rates for common imaging studies and procedures within an accountable care organization (ACO). DESIGN: Block randomized controlled trial for 1 year...
December 2, 2016: Journal of General Internal Medicine
https://www.readbyqxmd.com/read/27913891/biotransformation-of-2-4-dinitroanisole-by-a-fungal-penicillium-sp
#20
Hunter W Schroer, Kathryn L Langenfeld, Xueshu Li, Hans-Joachim Lehmler, Craig L Just
Insensitive munitions explosives are new formulations that are less prone to unintended detonation compared to traditional explosives. While these formulations have safety benefits, the individual constituents, such as 2,4-dinitroanisole (DNAN), have an unknown ecosystem fate with potentially toxic impacts to flora and fauna exposed to DNAN and/or its metabolites. Fungi may be useful in remediation and have been shown to degrade traditional nitroaromatic explosives, such as 2,4,6-trinitrotoluene and 2,4-dinitrotoluene, that are structurally similar to DNAN...
December 2, 2016: Biodegradation
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