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https://www.readbyqxmd.com/read/27914354/3d-qsar-predictions-for-%C3%AE-cyclodextrin-binding-constants-using-quantum-mechanically-based-descriptors
#1
Lukas Linden, Kai-Uwe Goss, Satoshi Endo
Binding of organic chemicals to α-cyclodextrin (αCD) is a typical example for host-guest complexation that is influenced by the 3D-structure of both the binding site (host) and the solute (guest). Prediction of the binding constant is challenging and requires a successful representation of the binding site-solute interactions in the 3D-space. In this study, we tested if a 3D quantitative structure activity relationship (3D-QSAR) model with quantum mechanically based local sigma profiles (LSPs) derived from the COSMOsar3D method is capable of predicting αCD binding constants from the most recent literature and how the model performs in comparison to a standard comparative molecular field analysis and to a reference 2D-QSAR...
November 30, 2016: Chemosphere
https://www.readbyqxmd.com/read/27914353/two-liquid-phase-system-a-promising-technique-for-predicting-bioavailability-of-polycyclic-aromatic-hydrocarbons-in-long-term-contaminated-soils
#2
Congying Wang, Ziyu Wang, Zengbo Li, Riaz Ahmad
A two-liquid-phase system (TLPS), which consisted of soil slurry and silicone oil, was employed to extract polycyclic aromatic hydrocarbons (PAHs) in four long-term contaminated soils in order to assess the bioavailability of PAHs. Extraction kinetics of six PAHs viz. phenanthrene, fluoranthene, pyrene, benzo(a)anthracene, benzo(a)pyrene, dibenzo(a,h)anthrancene were selected to investigate as they covered the susceptible and recalcitrant PAHs in soil. A parallel experiments were also carried out on the microbial degradation of these PAHs in soil with and without biostimulation (by adding (NH4)2HPO4)...
November 30, 2016: Chemosphere
https://www.readbyqxmd.com/read/27914310/electrical-potentials-measured-on-the-surface-of-the-knee-reflect-the-changes-of-the-contact-force-in-the-knee-joint-produced-by-postural-sway
#3
Lin Zhu, Martin Garon, Éric Quenneville, Michael D Buschmann, Pierre Savard
Electroarthrography (EAG) is a novel technique for recording potentials on the knee surface that are generated by the compression of articular cartilage and that reflect both compression force and cartilage quality. The mechanical loading of the knee is achieved by transferring the subject's body weight from a bipedal stance to a unipedal stance. We hypothesized that EAG potentials change with postural sway. The study was performed on 20 normal subjects (10 male, 10 female; age 29±10.5 yrs.; mass 68.8±14...
October 18, 2016: Gait & Posture
https://www.readbyqxmd.com/read/27914278/fdstools-a-software-package-for-analysis-of-massively-parallel-sequencing-data-with-the-ability-to-recognise-and-correct-str-stutter-and-other-pcr-or-sequencing-noise
#4
Jerry Hoogenboom, Kristiaan J van der Gaag, Rick H de Leeuw, Titia Sijen, Peter de Knijff, Jeroen F J Laros
Massively parallel sequencing (MPS) is on the advent of a broad scale application in forensic research and casework. The improved capabilities to analyse evidentiary traces representing unbalanced mixtures is often mentioned as one of the major advantages of this technique. However, most of the available software packages that analyse forensic short tandem repeat (STR) sequencing data are not well suited for high throughput analysis of such mixed traces. The largest challenge is the presence of stutter artefacts in STR amplifications, which are not readily discerned from minor contributions...
November 27, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27914234/food-gastrointestinal-ph-and-models-of-oral-drug-absorption
#5
REVIEW
Ahmad Y Abuhelwa, Desmond B Williams, Richard N Upton, David J R Foster
This article reviews the major physiological and physicochemical principles of the effect of food and gastrointestinal (GI) pH on the absorption and bioavailability of oral drugs, and the various absorption models that are used to describe/predict oral drug absorption. The rate and extent of oral drug absorption is determined by a complex interaction between a drug's physicochemical properties, GI physiologic factors, and the nature of the formulation administered. GI pH is an important factor that can markedly affect oral drug absorption and bioavailability as it may have significant influence on drug dissolution & solubility, drug release, drug stability, and intestinal permeability...
November 30, 2016: European Journal of Pharmaceutics and Biopharmaceutics
https://www.readbyqxmd.com/read/27914200/assembling-the-tat-protein-translocase
#6
Felicity Alcock, Phillip J Stansfeld, Hajra Basit, Johann Habersetzer, Matthew Ab Baker, Tracy Palmer, Mark I Wallace, Ben C Berks
The twin-arginine protein translocation system (Tat) transports folded proteins across the bacterial cytoplasmic membrane and the thylakoid membranes of plant chloroplasts. The Tat transporter is assembled from multiple copies of the membrane proteins TatA, TatB, and TatC. We combine sequence co-evolution analysis, molecular simulations, and experimentation to define the interactions between the Tat proteins of Escherichia coli at molecular-level resolution. In the TatBC receptor complex the transmembrane helix of each TatB molecule is sandwiched between two TatC molecules, with one of the inter-subunit interfaces incorporating a functionally important cluster of interacting polar residues...
December 3, 2016: ELife
https://www.readbyqxmd.com/read/27914062/computational-design-of-ligand-binding-proteins
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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