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https://www.readbyqxmd.com/read/27914174/mathematical-detection-of-aortic-valve-opening-b-point-in-impedance-cardiography-a-comparison-of-three-popular-algorithms
#1
Javier Rodríguez Árbol, Pandelis Perakakis, Alba Garrido, José Luis Mata, M Carmen Fernández-Santaella, Jaime Vila
The preejection period (PEP) is an index of left ventricle contractility widely used in psychophysiological research. Its computation requires detecting the moment when the aortic valve opens, which coincides with the B point in the first derivative of impedance cardiogram (ICG). Although this operation has been traditionally made via visual inspection, several algorithms based on derivative calculations have been developed to enable an automatic performance of the task. However, despite their popularity, data about their empirical validation are not always available...
December 3, 2016: Psychophysiology
https://www.readbyqxmd.com/read/27914172/cryotherapy-of-renal-lesions-enhancement-on-contrast-enhanced-sonography-on-postoperative-day-1-does-not-imply-viable-tissue-persistence
#2
Michele Bertolotto, Salvatore Siracusano, Calogero Cicero, Mariano Iannelli, Tommaso Silvestri, Antonio Celia, Alessandro Guarise, Fulvio Stacul
OBJECTIVES: To investigate whether persistent enhancement detected on contrast-enhanced sonography at postoperative day 1 (early contrast-enhanced sonography) after cryoablation of renal tumors implies the presence of residual viable tumor tissue, defined as residual enhancing tissue on reference imaging (computed tomography or magnetic resonance imaging) performed 6 months after the procedure. METHODS: Seventy-four patients with percutaneous cryoablation of renal tumors had early contrast-enhanced sonography from November 2011 to August 2015...
December 3, 2016: Journal of Ultrasound in Medicine: Official Journal of the American Institute of Ultrasound in Medicine
https://www.readbyqxmd.com/read/27914171/clinical-feasibility-of-brain-computer-interface-based-on-steady-state-visual-evoked-potential-in-patients-with-locked-in-syndrome-case-studies
#3
Han-Jeong Hwang, Chang-Hee Han, Jeong-Hwan Lim, Yong-Wook Kim, Soo-In Choi, Kwang-Ok An, Jun-Hak Lee, Ho-Seung Cha, Seung Hyun Kim, Chang-Hwan Im
Although the feasibility of brain-computer interface (BCI) systems based on steady-state visual evoked potential (SSVEP) has been extensively investigated, only a few studies have evaluated its clinical feasibility in patients with locked-in syndrome (LIS), who are the main targets of BCI technology. The main objective of this case report was to share our experiences of SSVEP-based BCI experiments involving five patients with LIS, thereby providing researchers with useful information that can potentially help them to design BCI experiments for patients with LIS...
December 3, 2016: Psychophysiology
https://www.readbyqxmd.com/read/27914137/is-vitamin-d-an-independent-risk-factor-of-nonalcoholic-fatty-liver-disease-a-cross-sectional-study-of-the-healthy-population
#4
Danbee Park, Hyuktae Kwon, Seung Won Oh, Hee Kyung Joh, Seung Sik Hwang, Jin Ho Park, Jae Moon Yun, Hyejin Lee, Goh Eun Chung, Sangjoon Ze, Jae Hong Park, Yeseul Bae, Arang Lee
The association between vitamin D levels and nonalcoholic fatty liver disease (NAFLD) has been recognized. However, few studies showed independent associations between vitamin D deficiency and NAFLD after a sex-related adjustment for metabolic factors. We aimed to study whether vitamin D deficiency is an independent risk factor of NAFLD even after controlling for metabolic syndrome and visceral fat in both sexes. In this cross-sectional study, 7,514 Korean adults (5,278 men, 2,236 women) participated in a health check-up program...
January 2017: Journal of Korean Medical Science
https://www.readbyqxmd.com/read/27914078/computer-vision-based-image-analysis-of-bacteria
#5
Jonas Danielsen, Pontus Nordenfelt
Microscopy is an essential tool for studying bacteria, but is today mostly used in a qualitative or possibly semi-quantitative manner often involving time-consuming manual analysis. It also makes it difficult to assess the importance of individual bacterial phenotypes, especially when there are only subtle differences in features such as shape, size, or signal intensity, which is typically very difficult for the human eye to discern. With computer vision-based image analysis - where computer algorithms interpret image data - it is possible to achieve an objective and reproducible quantification of images in an automated fashion...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914076/reconstructing-the-ancestral-relationships-between-bacterial-pathogen-genomes
#6
Caitlin Collins, Xavier Didelot
Following recent developments in DNA sequencing technology, it is now possible to sequence hundreds of whole genomes from bacterial isolates at relatively low cost. Analyzing this growing wealth of genomic data in terms of ancestral relationships can reveal many interesting aspects of the evolution, ecology, and epidemiology of bacterial pathogens. However, reconstructing the ancestry of a sample of bacteria remains challenging, especially for the majority of species where recombination is frequent. Here, we review and describe the computational techniques currently available to infer ancestral relationships, including phylogenetic methods that either ignore or account for the effect of recombination, as well as model-based and model-free phylogeny-independent approaches...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914075/development-of-a-single-locus-sequence-typing-slst-scheme-for-typing-bacterial-species-directly-from-complex-communities
#7
Christian F P Scholz, Anders Jensen
The protocol describes a computational method to develop a Single Locus Sequence Typing (SLST) scheme for typing bacterial species. The resulting scheme can be used to type bacterial isolates as well as bacterial species directly from complex communities using next-generation sequencing technologies.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914066/computational-tools-for-allosteric-drug-discovery-site-identification-and-focus-library-design
#8
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
#9
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
#10
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
#11
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
#12
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/27914061/probing-oligomerized-conformations-of-defensin-in-the-membrane
#13
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/27914059/evolution-inspired-computational-design-of-symmetric-proteins
#14
Arnout R D Voet, David Simoncini, Jeremy R H Tame, Kam Y J Zhang
Monomeric proteins with a number of identical repeats creating symmetrical structures are potentially very valuable building blocks with a variety of bionanotechnological applications. As such proteins do not occur naturally, the emerging field of computational protein design serves as an excellent tool to create them from nonsymmetrical templates. Existing pseudo-symmetrical proteins are believed to have evolved from oligomeric precursors by duplication and fusion of identical repeats. Here we describe a computational workflow to reverse-engineer this evolutionary process in order to create stable proteins consisting of identical sequence repeats...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914058/osprey-predicts-resistance-mutations-using-positive-and-negative-computational-protein-design
#15
Adegoke Ojewole, Anna Lowegard, Pablo Gainza, Stephanie M Reeve, Ivelin Georgiev, Amy C Anderson, Bruce R Donald
Drug resistance in protein targets is an increasingly common phenomenon that reduces the efficacy of both existing and new antibiotics. However, knowledge of future resistance mutations during pre-clinical phases of drug development would enable the design of novel antibiotics that are robust against not only known resistant mutants, but also against those that have not yet been clinically observed. Computational structure-based protein design (CSPD) is a transformative field that enables the prediction of protein sequences with desired biochemical properties such as binding affinity and specificity to a target...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914056/parallel-computational-protein-design
#16
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/27914055/an-evolution-based-approach-to-de-novo-protein-design
#17
Jeffrey R Brender, David Shultis, Naureen Aslam Khattak, Yang Zhang
EvoDesign is a computational algorithm that allows the rapid creation of new protein sequences that are compatible with specific protein structures. As such, it can be used to optimize protein stability, to resculpt the protein surface to eliminate undesired protein-protein interactions, and to optimize protein-protein binding. A major distinguishing feature of EvoDesign in comparison to other protein design programs is the use of evolutionary information in the design process to guide the sequence search toward native-like sequences known to adopt structurally similar folds as the target...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914054/computational-protein-design-through-grafting-and-stabilization
#18
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/27914053/computational-protein-design-under-a-given-backbone-structure-with-the-abacus-statistical-energy-function
#19
Peng Xiong, Quan Chen, Haiyan Liu
An important objective of computational protein design is to identify amino acid sequences that stably fold into a given backbone structure. A general approach to this problem is to minimize an energy function in the sequence space. We have previously reported a method to derive statistical energies for fixed-backbone protein design and showed that it led to de novo proteins that fold as expected. Here, we present the usage of the program that implements this method, which we now name as ABACUS (A Backbone-based Amino aCid Usage Survey)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914052/applications-of-normal-mode-analysis-methods-in-computational-protein-design
#20
Vincent Frappier, Matthieu Chartier, Rafael Najmanovich
Recent advances in coarse-grained normal mode analysis methods make possible the large-scale prediction of the effect of mutations on protein stability and dynamics as well as the generation of biologically relevant conformational ensembles. Given the interplay between flexibility and enzymatic activity, the combined analysis of stability and dynamics using the Elastic Network Contact Model (ENCoM) method has ample applications in protein engineering in industrial and medical applications such as in computational antibody design...
2017: Methods in Molecular Biology
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