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https://www.readbyqxmd.com/read/28738655/risk-of-false-decision-on-conformity-of-a-multicomponent-material-when-test-results-of-the-components-content-are-correlated
#1
Ilya Kuselman, Francesca R Pennecchi, Ricardo J N B da Silva, D Brynn Hibbert
The probability of a false decision on conformity of a multicomponent material due to measurement uncertainty is discussed when test results are correlated. Specification limits of the components' content of such a material generate a multivariate specification interval/domain. When true values of components' content and corresponding test results are modelled by multivariate distributions (e.g. by multivariate normal distributions), a total global risk of a false decision on the material conformity can be evaluated based on calculation of integrals of their joint probability density function...
November 1, 2017: Talanta
https://www.readbyqxmd.com/read/28738606/a-label-free-fluorometric-assay-for-actin-detection-based-on-enzyme-responsive-dna-templated-copper-nanoparticles
#2
Quanwei Song, Lixia Yang, Hongkun Chen, Rong Zhang, Na Na, Jin Ouyang
Herein, we develop a fluorescent strategy for label-free detection of actin by the in situ formation of double-stranded DNA (dsDNA) templated copper nanoparticles (CuNPs) and the digestion capability of deoxyribonuclease I (DNase I). In this design, the introduction of actin can effectively hinder the enzymic digestion owing to the exceptional target-mediated conformational structure between actin and DNase I. Consequently, the remaining adenine-thymine-rich dsDNA can act as an efficient template for fluorescent CuNPs (λex = 340nm, λem = 585nm) with a Mega-Stokes shifting (245nm)...
November 1, 2017: Talanta
https://www.readbyqxmd.com/read/28738357/biphasically-modulating-the-activity-of-carboxypeptidase-g2-with-ultrasound
#3
Wanying Ma, Ying Zhang, Xueling Zheng, Tinghe Yu
BACKGROUND/AIMS: Carboxypeptidase G2 (CPG2) has been used for cancer prodrug therapy to realize the targeted release of active drugs, but there yet lacks a means to modulate the CPG2 activity. Here ultrasound was used to modulate the CPG2 activity. METHODS: The activity of insonated CPG2 was determined, and then underlying biochemical (i.e., monomer, dimer and conformation) and ultrasonic (i.e., heat and cavitation) mechanisms were explored. RESULTS: Ultrasound (1...
July 24, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28737940/defining-the-structural-basis-for-allosteric-product-release-from-e-coli-dihydrofolate-reductase-using-nmr-relaxation-dispersion
#4
David Oyen, R Bryn Fenwick, Phillip C Aoto, Robyn L Stanfield, Ian A Wilson, H Jane Dyson, Peter E Wright
The rate-determining step in the catalytic cycle of E.coli dihydrofolate reductase is tetrahydrofolate (THF) product release, which can occur via an allosteric or an intrinsic pathway. The allosteric pathway, which becomes accessible when the reduced cofactor NADPH is bound, involves transient sampling of a higher energy conformational state, greatly increasing the product dissociation rate compared to the intrinsic pathway that obtains when NADPH is absent. Although the kinetics of this process are known, the enzyme structure and the THF product conformation in the transiently formed excited state remains elusive...
July 24, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28737924/linking-ph-temperature-and-k-concentration-for-dna-i-motif-formation
#5
Tra Nguyen, Claudette Fraire, Richard D Sheardy
The conformation a particular DNA segment assumes depends upon its sequence context and the environment under which it is prepared. To complement our findings with G-rich sequences related to the human telomere, we have been investigating the pH induced transition from single strand to i-motif for sequences related to the human telomere C-rich strand. We have carried out titrations of (CCCTAA)4 from pH 7.0 to pH 5.0 at temperatures ranging from 15 to 45 (o)C at 115 mM K(+) and at K(+) concentrations ranging from 15 to 315 mM at 25 (o)C...
July 24, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28737917/antagonistic-interplay-between-an-intermolecular-ch%C3%A2-%C3%A2-%C3%A2-o-and-an-intramolecular-oh%C3%A2-%C3%A2-%C3%A2-o-hydrogen-bond-in-a-1-1-complex-between-1-2-cyclohexanedione-and-chloroform-a-combined-matrix-isolation-infrared-and-quantum-chemistry-study
#6
Amit Kumar Samanta, Pujarini Banerjee, Biman Bandyopadhyay, Prasenjit Pandey, Tapas Chakraborty
Matrix isolation infrared spectra of a weak C-H•••O hydrogen bonded complex between the keto-enol form of 1,2-cyclohexanedione (HCHD) and chloroform have been measured. The spectra reveal that the intramolecular O-H•••O H-bond of HCHD is weakened as a result of complex formation, manifesting in prominent blue shift (~23 cm-1) of the νO-H band and red shifts (~7 cm-1) of νC=O bands of the acceptor (HCHD). The νC-H band of donor CHCl3 undergoes a large red shift of ~33 cm-1. Very similar spectral effects are also observed for formation of the complex in CCl4 solution at room temperature...
July 24, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28737912/molecular-structure-equilibrium-conformation-and-ring-puckering-motion-in-1-1-3-3-tetramethylcyclobutane-an-electron-diffraction-investigation-augmented-by-molecular-orbital-and-normal-coordinate-calculations
#7
Kenneth Hedberg, Lise Hedberg, Jason Sandwich
The molecule cyclobutane (CB) has a non-planar carbon skeleton folded around a line connecting diagonally opposite atoms. The puckering angle (the change from planarity) of about 30° is generally attributed to steric repulsion between the four sets of adjacent methylene groups which would be opposed in a planar ring and is relieved by the puckering. According to this criterion, a similar molecule, 1,1,3,3-tetramethylcyclobutene (TMCB), in which adjacent methylene groups do not exist, would be expected to have a planar ring in the equilibrium form...
July 24, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28737816/protein-stability-and-dynamics-influenced-by-ligands-in-extremophilic-complexes-a-molecular-dynamics-investigation
#8
Sara Khan, Umar Farooq, Maria Kurnikova
In this study, we explore the structural and dynamic adaptations of the Tryptophan synthase α-subunit in a ligand bound state in psychrophilic, mesophilic and hyperthermophilic organisms at different temperatures by MD simulations. We quantify the global and local fluctuations in the 40 ns time scale by analyzing the root mean square deviation/fluctuations. The distinct behavior of the active site and loop 6 is observed with the elevation of temperature. Protein stability relies more on electrostatic interactions, and these interactions might be responsible for the stability of varying temperature evolved proteins...
July 24, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28737807/npy-binds-with-heme-to-form-a-npy-heme-complex-enhancing-peroxidase-activity-in-free-heme-and-promoting-npy-nitration-and-inactivation
#9
Huixian Ye, Zhen Yang, Hailing Li, Zhonghong Gao
Neuropeptide Y (NPY) is a member of the pancreatic peptide family of neuropeptides that play a crucial role in numerous central and peripheral nervous system responses. Recently, it has been shown that NPY protects cells against neurotoxic damage from β-amyloid peptides (Aβ) in Alzheimer's disease (AD). Heme is a common factor linking several metabolic perturbations in AD and altered heme metabolism has been shown to be related to the pathologies of AD. Thus, heme may have a chance to act on NPY and potentially counteract its function...
July 24, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28737804/modulation-of-in-out-and-out-out-conformations-in-x-x-x-phosphatranes-by-lewis-acids
#10
Goar Sánchez-Sanz, Cristina Trujillo, Ibon Alkorta, José Elguero
A theoretical study of [X.X'.X'']phosphatrane:Lewis acid complexes has been carried out in order to analyze how the in:out and out:out conformations can be modulated by the interaction with Lewis acids (LA). It has been found that in:out structures are more stable in larger systems i.e. in [4.4.3]:LA and [4.4.4]:LA than in [3.3.3]:LA and [4.3.3]:LA. The results obtained for the relative energies in conjunction with electron density properties showed that upon complexation, in:out conformers become more stable with the increasing acidity of the corresponding Lewis acid...
July 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28737800/c-h-addition-reactivity-of-2-phenylpyridine-and-2-2-bipyridine-with-pentaphenylborole
#11
Venkata A K Adiraju, Caleb D Martin
The reactions of pentaphenylborole with pyridines with a pendent aryl group in the 2-position, specifically 2-phenylpyridine and 2,2'-bipyridine, readily afforded adducts. Upon thermolysis, the adducts converted to ortho C-H addition products with the two substituents introduced onto the diene on the boracyclic carbon atoms adjacent to boron in a syn fashion. Photolysis of the syn 2-phenypyridine product led to isomerization to the anti conformer which did not readily occur for the 2,2'-bipyridine complex. Such C-H bond reactivity is uncommon for main group elements and provides insight into methodologies to access boron frameworks...
July 24, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28737791/aqueous-ionic-liquids-and-their-influence-on-peptide-conformations-denaturation-and-dehydration-mechanisms
#12
Diddo Diddens, Volker Lesch, Andreas Heuer, Jens Smiatek
Low concentrated aqueous ionic liquids (ILs) and their influence on protein structures have attracted a lot of interest over the last few years. This can be mostly attributed to the fact that aqueous ILs, depending on the ion species involved, can be used as protein protectants or protein denaturants. Atomistic molecular dynamics (MD) simulations are performed in order to study the influence of different aprotic ILs on the properties of a short hairpin peptide. Our results reveal distinct binding and denaturation effects for 1-ethyl-3-methylimidazolium (EMIM) in combination with different anions, namely, chloride (CL), tetrafluoroborate (BF4) and acetate (ACE)...
July 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28737760/channel-opening-and-gating-mechanism-in-ampa-subtype-glutamate-receptors
#13
Edward C Twomey, Maria V Yelshanskaya, Robert A Grassucci, Joachim Frank, Alexander I Sobolevsky
AMPA-subtype ionotropic glutamate receptors mediate fast excitatory neurotransmission throughout the central nervous system. Gated by the neurotransmitter glutamate, AMPA receptors are critical for synaptic strength and dysregulation of AMPA receptor-mediated signalling is linked to numerous neurological diseases. Here, we use cryo-electron microscopy to solve the structures of AMPA receptor-auxiliary subunit complexes in the apo, antagonist and agonist-bound states and elucidate the iris-like mechanism of ion channel opening...
July 24, 2017: Nature
https://www.readbyqxmd.com/read/28737397/conformational-nonequilibrium-enzyme-kinetics-generalized-michaelis-menten-equation
#14
D Evan Piephoff, Jianlan Wu, Jianshu Cao
In a conformational nonequilibrium steady state (cNESS), enzyme turnover is modulated by the underlying conformational dynamics. On the basis of a discrete kinetic network model, we use an integrated probability flux balance method to derive the cNESS turnover rate for a conformation-modulated enzymatic reaction. The traditional Michaelis-Menten (MM) rate equation is extended to a generalized form, which includes non-MM corrections induced by conformational population currents within combined cyclic kinetic loops...
July 24, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28737392/ligand-strain-and-entropic-effects-on-the-binding-of-macrocyclic-and-linear-inhibitors-molecular-modelling-of-penicillopepsin-complexes
#15
Dimas Suarez, Natalia Diaz
Using extensive molecular dynamics simulations, we investigate the structure and dynamics of the complexes formed between penicillopepsin and two peptidomimetic inhibitors: a linear compound, isovaleryl(P4)-valine(P3)-asparagine(P2)-leucine(P1)-phosphonate-phenilalanine(P1'), and its macrocylic analog that includes a methylene bridge between the Asn(P2) and Phe(P1') side chains. The macrocyclic inhibitor, which has a 420-fold larger affinity than that of the acyclic one, has been considered to lower the entropic penalty for binding...
July 24, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28737286/unexpected-chiro-thermoresponsive-behavior-of-helical-poly-phenylacetylene-s-bearing-elastin-based-side-chains
#16
Sandra Arias, Felix Freire, Marcelo Calderon, Julian Bergueiro
The thermoresponsive behavior of an elastin based polymer can be altered by the polymeric macromolecular conformation. Thus, when the elastin basic amino-acid sequence VPGVG is used as a pendant group of a poly(phenylacetylene) (PPA) its thermoresponsivity in water can be remotely detected due to conformational changes on the formed helix. Circular dichroism at different temperatures show an inversion of the first Cotton effect (450 nm) at 25.8 ºC that matches with the cloud point temperature. Interestingly, this elastin-based side-chain PPA shows an upper critical solution temperature with low pH and concentration dependency, not expected in elastin based polymers...
July 24, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28736824/evaluation-of-lumazine-synthase-from-bacillus-anthracis-as-a-presentation-platform-for-polyvalent-antigen-display
#17
Yangjie Wei, Newton Wahome, Greta VanSlyke, Neal Whitaker, Prashant Kumar, Michael L Barta, Wendy L Picking, David B Volkin, Nicholas J Mantis, C Russell Middaugh
Polyvalent antigen display is an effective strategy to enhance the immunogenicity of subunit vaccines by clustering them in an array-like manner on a scaffold system. This strategy results in a higher local density of antigens, increased high avidity interactions with B cells and other antigen presenting cells, and therefore a more effective presentation of vaccine antigens. In the present study, we used lumazine synthase (LS), an icosahedral symmetry capsid derived from Bacillus anthracis, as a scaffold to present 60 copies of a linear B cell epitope (PB10) from the ricin toxin fused to the C terminus of LS via four different linkers...
July 24, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28736439/genome-organization-tracking-chromosomal-conformation-through-the-cell-cycle
#18
Carolina Perdigoto
No abstract text is available yet for this article.
July 24, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28736392/-i-am-treated-well-if-i-adhere-to-my-hiv-medication-putting-patient-provider-interactions-in-context-through-insights-from-qualitative-research-in-five-sub-saharan-african-countries
#19
Ken Ondenge, Jenny Renju, Oliver Bonnington, Mosa Moshabela, Joyce Wamoyi, Constance Nyamukapa, Janet Seeley, Alison Wringe, Morten Skovdal
OBJECTIVES: The nature of patient-provider interactions and communication is widely documented to significantly impact on patient experiences, treatment adherence and health outcomes. Yet little is known about the broader contextual factors and dynamics that shape patient-provider interactions in high HIV prevalence and limited-resource settings. Drawing on qualitative research from five sub-Saharan African countries, we seek to unpack local dynamics that serve to hinder or facilitate productive patient-provider interactions...
July 2017: Sexually Transmitted Infections
https://www.readbyqxmd.com/read/28736124/implications-of-three-dimensional-modeling-of-the-proximal-femur-for-cephalomedullary-nailing-an-asian-cadaver-study
#20
Chang-Soo Chon, Bokku Kang, Han Sung Kim, Gu-Hee Jung
PURPOSE: To determine the variability in the ideal entry point of cephalomedullary (CM) nail around the greater trochanter (GT) and the consequent conformity with the proximal femur by analyzing three-dimensional (3D) modeling and virtual implantation MATERIALS AND METHODS: A total of 105 cadaveric femurs (50 males and 55 females) underwent continuous 1.0mm slice computed tomography (CT) scans. CT images imported into Mimics(®) software to reconstruct the 3D model of the proximal femur and medullary canal...
July 11, 2017: Injury
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