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https://www.readbyqxmd.com/read/27914062/computational-design-of-ligand-binding-proteins
#1
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
#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/27914058/osprey-predicts-resistance-mutations-using-positive-and-negative-computational-protein-design
#3
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/27914057/bindml-bindml-detecting-protein-protein-interaction-interface-propensity-from-amino-acid-substitution-patterns
#4
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/27914052/applications-of-normal-mode-analysis-methods-in-computational-protein-design
#5
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
https://www.readbyqxmd.com/read/27914014/experimental-and-theoretical-investigation-of-sodiated-multimers-of-steroid-epimers-with-ion-mobility-mass-spectrometry
#6
Christopher D Chouinard, Vinícius Wilian D Cruzeiro, Adrian E Roitberg, Richard A Yost
Ion mobility-mass spectrometry (IM-MS) has recently seen increased use in the analysis of small molecules, especially in the field of metabolomics, for increased breadth of information and improved separation of isomers. In this study, steroid epimers androsterone and trans-androsterone were analyzed with IM-MS to investigate differences in their relative mobilities. Although sodiated monomers exhibited very similar collision cross-sections (CCS), baseline separation was observed for the sodiated dimer species (RS = 1...
December 2, 2016: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/27913961/prediction-of-postoperative-clinical-recovery-of-drop-foot-attributable-to-lumbar-degenerative-diseases-via-a-bayesian-network
#7
Shota Takenaka, Hiroyuki Aono
BACKGROUND: Drop foot resulting from degenerative lumbar diseases can impair activities of daily living. Therefore, predictors of recovery of this symptom have been investigated using univariate or/and multivariate analyses. However, the conclusions have been somewhat controversial. Bayesian network models, which are graphic and intuitive to the clinician, may facilitate understanding of the prognosis of drop foot resulting from degenerative lumbar diseases. QUESTIONS/PURPOSES: (1) To show a layered correlation among predictors of recovery from drop foot resulting from degenerative lumbar diseases; and (2) to develop support tools for clinical decisions to treat drop foot resulting from lumbar degenerative diseases...
December 2, 2016: Clinical Orthopaedics and related Research
https://www.readbyqxmd.com/read/27913921/language-difficulty-at-school-entry-and-the-trajectories-of-hyperactivity-inattention-problems-from-ages-4-to-11-evidence-from-a-population-representative-cohort-study
#8
Shaun Goh Kok Yew, Richard O'Kearney
Latent growth curve modelling was used to contrast the developmental trajectories of hyperactivity-inattention (H-I) problems across childhood for children with a language difficulty at the start of school and those with typical language and to examine if the presence of a language difficulty moderates the associations of child, parent and peer predictors with these trajectories. Unconditional and language-status conditional latent growth curves of H-I problems were estimated for a large nationally representative cohort of children, comprising 1627 boys (280 - language difficulty) and 1609 girls (159 - language difficulty) measured at age 4 to 5, 6 to 7, 8 to 9 and 10 to 11...
December 3, 2016: Journal of Abnormal Child Psychology
https://www.readbyqxmd.com/read/27913902/a-new-multiscale-micromechanical-model-of-vertebral-trabecular-bones
#9
Rami Haj-Ali, Eyass Massarwa, Jacob Aboudi, Fabio Galbusera, Uwe Wolfram, Hans-Joachim Wilke
A new three-dimensional (3D) multiscale micromechanical model has been suggested as adept at predicting the overall linear anisotropic mechanical properties of a vertebral trabecular bone (VTB) highly porous microstructure. A nested 3D modeling analysis framework spanning the multiscale nature of the VTB is presented herein. This hierarchical analysis framework employs the following micromechanical methods: the 3D parametric high-fidelity generalized method of cells (HFGMC) as well as the 3D sublaminate model...
December 2, 2016: Biomechanics and Modeling in Mechanobiology
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/27913862/prognostic-impact-of-her3-based-on-protein-and-mrna-expression-in-high-grade-serous-ovarian-carcinoma
#11
Ulrike Unger, Carsten Denkert, Ioana Braicu, Jalid Sehouli, Manfred Dietel, Sibylle Loibl, Silvia Darb-Esfahani
HER3 is a member of the epidermal growth factor family and was predominantly described as a negative prognostic factor in various solid tumors as well as in ovarian cancer. In this study, we investigated HER3 on protein and mRNA expression in histologically defined subtypes of ovarian cancer looking for an influence on patient's survival. Altogether, we examined HER3 in ovarian high-grade serous (HGSC, n = 320), low-grade serous (LGSC, n = 55), endometrioid (EC, n = 33), and clear cell (CCC, n = 48) carcinomas using immunohistochemistry (IHC) and quantitative real-time reverse transcription PCR (qRT-PCR)...
December 2, 2016: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/27913614/relationship-between-employment-histories-and-frailty-trajectories-in-later-life-evidence-from-the-english-longitudinal-study-of-ageing
#12
Wentian Lu, Rebecca Benson, Karen Glaser, Loretta G Platts, Laurie M Corna, Diana Worts, Peggy McDonough, Giorgio Di Gessa, Debora Price, Amanda Sacker
BACKGROUND: Given the acceleration of population ageing and policy changes to extend working lives, evidence is needed on the ability of older adults to work for longer. To understand more about the health impacts of work, this study examined the relationship between employment histories before retirement and trajectories of frailty thereafter. METHODS: The sample comprised 2765 women and 1621 men from the English Longitudinal Study of Ageing. We used gendered typologies of life-time employment and a frailty index (FI)...
December 2, 2016: Journal of Epidemiology and Community Health
https://www.readbyqxmd.com/read/27913613/socioeconomic-differences-in-health-check-ups-and-medically-certified-sickness-absence-a-10-year-follow-up-among-middle-aged-municipal-employees-in-finland
#13
Kustaa Piha, Hilla Sumanen, Eero Lahelma, Ossi Rahkonen
BACKGROUND: There is contradictory evidence on the association between health check-ups and future morbidity. Among the general population, those with high socioeconomic position participate more often in health check-ups. The main aims of this study were to analyse if attendance to health check-ups are socioeconomically patterned and affect sickness absence over a 10-year follow-up. METHODS: This register-based follow-up study included municipal employees of the City of Helsinki...
December 2, 2016: Journal of Epidemiology and Community Health
https://www.readbyqxmd.com/read/27913585/the-influence-of-placental-metabolism-on-fatty-acid-transfer-to-the-fetus
#14
Simone Perazzolo, Birgit Hirschmugl, Christian Wadsack, Gernot Desoye, Rohan M Lewis, Bram G Sengers
The factors determining Fatty acid transfer across the placenta are not fully understood. This study used a combined experimental and computational modelling approach to explore placental transfer of non-esterified fatty acids and identify rate-determining processes. The isolated perfused human placenta was used to study the uptake and transfer of [(13)C]-fatty acids and the release of endogenous fatty acids. Only 6.2 ± 0.8% of the maternal (13)C-fatty acids taken up by the placenta was delivered to the fetal circulation...
December 2, 2016: Journal of Lipid Research
https://www.readbyqxmd.com/read/27913508/risk-stratification-and-management-of-acute-pulmonary-embolism
#15
Cecilia Becattini, Giancarlo Agnelli
The clinical management of patients with acute pulmonary embolism is rapidly changing over the years. The widening spectrum of clinical management strategies for these patients requires effective tools for risk stratification. Patients at low risk for death could be candidates for home treatment or early discharge. Clinical models with high negative predictive value have been validated that could be used to select patients at low risk for death. In a major study and in several meta-analyses, thrombolysis in hemodynamically stable patients was associated with unacceptably high risk for major bleeding complications or intracranial hemorrhage...
December 2, 2016: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/27913438/quantifying-the-dynamics-of-field-cancerization-in-tobacco-related-head-and-neck-cancer-a-multiscale-modeling-approach
#16
Marc D Ryser, Walter T Lee, Neal E Ready, Kevin Z Leder, Jasmine Foo
High rates of local recurrence in tobacco-related head and neck squamous cell carcinoma (HNSCC) are commonly attributed to unresected fields of precancerous tissue. Because they are not easily detectable at the time of surgery without additional biopsies, there is a need for noninvasive methods to predict the extent and dynamics of these fields. Here, we developed a spatial stochastic model of tobacco-related HNSCC at the tissue level and calibrated the model using a Bayesian framework and population-level incidence data from the Surveillance, Epidemiology, and End Results (SEER) registry...
October 20, 2016: Cancer Research
https://www.readbyqxmd.com/read/27913367/a-new-method-for-self-estimation-of-the-severity-of-obstructive-sleep-apnea-using-easily-available-measurements-and-neural-fuzzy-evaluation-system
#17
Ming-Feng Wu, Wei-Chang Huang, Chia-Feng Juang, Kai-Ming Chang, Chih-Yu Wen, Yu-Hsuan Chen, Ching-Yi Lin, Yi-Chan Chen, Ching-Cheng Lin
This paper proposes a neural fuzzy evaluation system (NFES) with significant variables selected from stepwise regression to predict apnea-hypopnea index (AHI) for evaluating obstructive sleep apnea (OSA). The variables considered are the change statuses of blood pressure (BP) before going to sleep and early in the morning as well as other five easily available measurements (age, body mass index (BMI) etc.) so that users can use the system for self-evaluation of OSA. A total of 150 subjects are reviewed retrospectively and categorized as training (120 subjects) and validation (30 subjects) sets by a five-fold cross validation scheme with stratified sampling based on the OSA severity...
December 1, 2016: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/27913362/learning-to-predict-eye-fixations-via-multiresolution-convolutional-neural-networks
#18
Nian Liu, Junwei Han, Tianming Liu, Xuelong Li
Eye movements in the case of freely viewing natural scenes are believed to be guided by local contrast, global contrast, and top-down visual factors. Although a lot of previous works have explored these three saliency cues for several years, there still exists much room for improvement on how to model them and integrate them effectively. This paper proposes a novel computation model to predict eye fixations, which adopts a multiresolution convolutional neural network (Mr-CNN) to infer these three types of saliency cues from raw image data simultaneously...
November 29, 2016: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/27913178/estimating-the-material-properties-of-heel-pad-sub-layers-using-inverse-finite-element-analysis
#19
Nafiseh Ahanchian, Christopher J Nester, David Howard, Lei Ren, Daniel Parker
Detailed information about the biomechanical behaviour of plantar heel pad tissue contributes to our understanding of load transfer when the foot impacts the ground. The objective of this work was to obtain the hyperelastic and viscoelastic material properties of heel pad sub-layers (skin, micro-chamber and macro-chamber layers) in-vivo. An anatomically detailed 3D Finite Element model of the human heel was used to derive the sub-layer material properties. A combined ultrasound imaging and motorised platform system was used to compress heel pad and to create input data for the Finite Element model...
November 29, 2016: Medical Engineering & Physics
https://www.readbyqxmd.com/read/27913131/using-phenomenological-models-for-forecasting-the-2015-ebola-challenge
#20
Bruce Pell, Yang Kuang, Cecile Viboud, Gerardo Chowell
BACKGROUND: The rising number of novel pathogens threatening the human population has motivated the application of mathematical modeling for forecasting the trajectory and size of epidemics. MATERIALS AND METHODS: We summarize the real-time forecasting results of the logistic equation during the 2015 Ebola challenge focused on predicting synthetic data derived from a detailed individual-based model of Ebola transmission dynamics and control. We also carry out a post-challenge comparison of two simple phenomenological models...
November 19, 2016: Epidemics
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