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Bounded rationality

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https://www.readbyqxmd.com/read/28530741/thionine-graphene-oxide-covalent-hybrid-and-its-interaction-with-light
#1
Ewelina Krzyszkowska, Justyna Walkowiak-Kulikowska, Sven Stienen, Aleksandra Wojcik
Graphene oxide sheets (GO) were covalently functionalized with thionine molecules. The obtained hybrid material, Th-GO, was characterized by means of scanning electron microscopy (SEM), Auger electron spectroscopy (AES), Fourier transform infrared spectroscopy (FTIR) and Raman spectroscopy. Subsequently, the interaction of light with the free dye molecules and with dye molecules bound to the graphene oxide sheets was probed via UV-Vis spectroscopy, fluorescence spectroscopy and femtosecond pump-probe spectroscopy...
May 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28522117/characterization-of-cu-ii-reconstituted-acc-oxidase-using-experimental-and-theoretical-approaches
#2
Nadia El Bakkali-Tahéri, Sybille Tachon, Maylis Orio, Sylvain Bertaina, Marlène Martinho, Viviane Robert, Marius Réglier, Thierry Tron, Pierre Dorlet, A Jalila Simaan
1-Aminocyclopropane-1-carboxylic acid oxidase (ACCO) is a non heme iron(II) containing enzyme that catalyzes the final step of the ethylene biosynthesis in plants. The iron(II) ion is bound in a facial triad composed of two histidines and one aspartate (H177, D179 and H234). Several active site variants were generated to provide alternate binding motifs and the enzymes were reconstituted with copper(II). Continuous wave (cw) and pulsed Electron Paramagnetic Resonance (EPR) spectroscopies as well as Density Functional Theory (DFT) calculations were performed and models for the copper(II) binding sites were deduced...
May 15, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28511016/structural-and-biochemical-insights-into-dimethylsulfoniopropionate-cleavage-by-cofactor-bound-dddk-from-the-prolific-marine-bacterium-pelagibacter
#3
Nicholas J Schnicker, Saumya M De Silva, Jonathan D Todd, Mishtu Dey
Enormous amounts of the organic osmolyte dimethylsulfoniopropionate (DMSP) are produced in marine environments where bacterial DMSP lyases cleave it yielding acrylate and the climate-active gas dimethylsulfide (DMS). SAR11 bacteria are the most abundant clade of heterotrophic bacteria in the oceans and they play a key role in DMSP catabolism. An important environmental factor affecting DMS generation via DMSP lyases is the availability of metal ions since they are essential cofactors for many of these enzymes...
May 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28505196/unveiling-a-novel-transient-druggable-pocket-in-bace-1-through-molecular-simulations-conformational-analysis-and-binding-mode-of-multisite-inhibitors
#4
Ornella Di Pietro, Jordi Juárez-Jiménez, Diego Muñoz-Torrero, Charles A Laughton, F Javier Luque
The critical role of BACE-1 in the formation of neurotoxic ß-amyloid peptides in the brain makes it an attractive target for an efficacious treatment of Alzheimer's disease. However, the development of clinically useful BACE-1 inhibitors has proven to be extremely challenging. In this study we examine the binding mode of a novel potent inhibitor (compound 1, with IC50 80 nM) designed by synergistic combination of two fragments-huprine and rhein-that individually are endowed with very low activity against BACE-1...
2017: PloS One
https://www.readbyqxmd.com/read/28493700/the-effect-of-fluorination-on-the-competition-of-halogen-bonding-and-hydrogen-bonding-complexes-of-fluoroiodomethane-with-dimethyl-ether-and-trimethylamine
#5
Yannick Geboes, Frank De Proft, Wouter A Herrebout
To further rationalize the competition between halogen and hydrogen bonding, a combined experimental and theoretical study on the weakly bound molecular complexes formed between the combined halogen bond / hydrogen bond donor fluoroiodomethane and the Lewis bases dimethyl ether and trimethylamine (in standard and fully deuterated form) is presented. The experimental data are obtained by recording infrared and Raman spectra of mixtures of the compounds in liquid krypton, at temperatures between 120 K and 156 K...
May 11, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28488849/solution-conformations-and-dynamics-of-substrate-bound-cytochrome-p450-mycg
#6
Drew R Tietz, Larissa M Podust, David H Sherman, Thomas C Pochapsky
MycG is a P450 monooxygenase that catalyzes the sequential hydroxylation and epoxidation of mycinamicin IV (M-IV), the last two steps in the biosynthesis of mycinamicin II, a macrolide antibiotic isolated from Micromonospora griseorubida. The crystal structure of MycG with M-IV bound was previously determined but showed the bound substrate in an orientation that did not rationalize the observed regiochemistry of M-IV hydroxylation. Nuclear magnetic resonance paramagnetic relaxation enhancements provided evidence of an orientation of M-IV in the MycG active site more compatible with the observed chemistry, but substrate-induced changes in the enzyme structure were not characterized...
May 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28485587/strategic-design-of-2-2-bipyridine-derivatives-to-modulate-metal-amyloid-%C3%AE-aggregation
#7
Yonghwan Ji, Hyuck Jin Lee, Minjeong Kim, Geewoo Nam, Shin Jung C Lee, Jaeheung Cho, Cheol-Min Park, Mi Hee Lim
The complexity of Alzheimer's disease (AD) stems from the inter-relation of multiple pathological factors upon initiation and progression of the disease. To identify the involvement of metal-bound amyloid-β (metal-Aβ) aggregation in AD pathology, among the pathogenic features found in the AD-affected brain, small molecules as chemical tools capable of controlling metal-Aβ aggregation were developed. Herein, we report a new class of 2,2'-bipyridine (bpy) derivatives (1-4) rationally designed to be chemical modulators toward metal-Aβ aggregation over metal-free Aβ analogue...
May 9, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28484972/radical-generation-from-the-gas-phase-activation-of-ionized-lipid-ozonides
#8
Shane R Ellis, Huong T Pham, Marc In Het Panhuis, Adam J Trevitt, Todd W Mitchell, Stephen J Blanksby
Reaction products from the ozonolysis of unsaturated lipids at gas-liquid interfaces have the potential to significantly influence the chemical and physical properties of organic aerosols in the atmosphere. In this study, the gas-phase dissociation behavior of lipid secondary ozonides is investigated using ion-trap mass spectrometry. Secondary ozonides were formed by reaction between a thin film of unsaturated lipids (fatty acid methyl esters or phospholipids) with ozone before being transferred to the gas phase as [M + Na](+) ions by electrospray ionization...
May 8, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28484952/the-anchoring-bias-reflects-rational-use-of-cognitive-resources
#9
REVIEW
Falk Lieder, Thomas L Griffiths, Quentin J M Huys, Noah D Goodman
Cognitive biases, such as the anchoring bias, pose a serious challenge to rational accounts of human cognition. We investigate whether rational theories can meet this challenge by taking into account the mind's bounded cognitive resources. We asked what reasoning under uncertainty would look like if people made rational use of their finite time and limited cognitive resources. To answer this question, we applied a mathematical theory of bounded rationality to the problem of numerical estimation. Our analysis led to a rational process model that can be interpreted in terms of anchoring-and-adjustment...
May 8, 2017: Psychonomic Bulletin & Review
https://www.readbyqxmd.com/read/28475327/development-of-dna-nanostructures-for-high-affinity-binding-to-human-serum-albumin
#10
Aurélie Lacroix, Thomas G W Edwardson, Mark A Hancock, Michael D Dore, Hanadi F Sleiman
The development of nucleic acid therapeutics has been hampered by issues associated with their stability and in vivo delivery. To address these challenges, we describe a new strategy to engineer DNA structures with strong binding affinity to human serum albumin (HSA). HSA is the most abundant protein in the blood and has a long circulation half-life (19 days). It has been shown to hinder phagocytosis, is retained in tumors, and aids in cellular penetration. Indeed, HSA has already been successfully used for the delivery of small-molecule drugs and nanoparticles...
May 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28474020/characterization-of-the-structure-dynamics-and-allosteric-pathways-of-human-npp1-in-its-free-form-and-substrate-bound-complex-from-molecular-modeling
#11
Xavier Barbeau, Patrick Mathieu, Jean-François Paquin, Patrick Lagüe
The ectonucleotide phosphodiesterase/pyrophosphatase-1 (NPP1) is a type II transmembrane glycoprotein that regulates extracellular inorganic purine nucleotide and inorganic diphosphate levels through the hydrolysis of ATP into AMP and diphosphate. NPP1 is a promising drug target as it plays a role in several disorders. In the present work, we report the 3D structure modeling and extensive molecular dynamics simulations of NPP1-h, both in its free and ATP-bound forms. We identified the key residues involved in the binding of the ATP and the binding modes...
May 5, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28471355/structure-of-nadp-bound-7%C3%AE-hydroxysteroid-dehydrogenase-reveals-two-cofactor-binding-modes
#12
Rui Wang, Jiaquan Wu, David Kin Jin, Yali Chen, Zhijia Lv, Qian Chen, Qiwei Miao, Xiaoyu Huo, Feng Wang
In mammals, bile acids/salts and their glycine and taurine conjugates are effectively recycled through enterohepatic circulation. 7β-Hydroxysteroid dehydrogenases (7β-HSDHs; EC 1.1.1.201), including that from the intestinal microbe Collinsella aerofaciens, catalyse the NADPH-dependent reversible oxidation of secondary bile-acid products to avoid potential toxicity. Here, the first structure of NADP(+) bound to dimeric 7β-HSDH is presented. In one active site, NADP(+) adopts a conventional binding mode similar to that displayed in related enzyme structures...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28450783/vancomycin-modified-fe3o4-sio2-ag-microflowers-as-effective-antimicrobial-agents
#13
Chongwen Wang, Kehan Zhang, Zhe Zhou, Qingjun Li, Liting Shao, Rong Zhang Hao, Rui Xiao, Shengqi Wang
Nanomaterials combined with antibiotics exhibit synergistic effects and have gained increasing interest as promising antimicrobial agents. In this study, vancomycin-modified magnetic-based silver microflowers (Van/Fe3O4@SiO2@Ag microflowers) were rationally designed and prepared to achieve strong bactericidal ability, a wide antimicrobial spectrum, and good recyclability. High-performance Fe3O4@SiO2@Ag microflowers served as a multifunction-supporting matrix and exhibited sufficient magnetic response property due to their 200 nm Fe3O4 core...
2017: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/28450533/mctbi-a-web-server-for-predicting-metal-ion-effects-in-rna-structures
#14
Lizhen Sun, Jingxiang Zhang, Shi-Jie Chen
Metal ions play critical roles in RNA structure and function. However, web servers and software packages for predicting ion effects in RNA structures is notably scarce. Furthermore, the existing web servers and software packages mainly neglect ion correlation and fluctuation effects, which are potentially important for RNAs. We here report a new web server, MCTBI server (http://rna.physics.missouri.edu/MCTBI), for the prediction of ion effects for RNA structures. The server is based on the recently developed MCTBI, a model that can account for ion correlation and fluctuation effects for nucleic acids structures and can provide improved predictions for the effects of metal ions, especially for multivalent ions such as Mg2+ effects, as shown by extensive theory-experiment test results...
April 27, 2017: RNA
https://www.readbyqxmd.com/read/28444039/the-health-regionalization-process-from-the-perspective-of-the-transation-cost-theory
#15
Leyla Gomes Sancho, Daniela Savi Geremia, Sulamis Dain, Fabiano Geremia, Cláudio José Silva Leão
This study analyzes the incidence of transaction costs in the regionalization process of health policies in the Brazilian federal system. In this work, regionalized health actions contracted and agreed between federal agencies have assumed a transactional nature. A conceptual theoretical essay of reflective nature was prepared with the purpose of questioning and proposing new approaches to improve the health regionalization process. The main considerations suggest that institutional management tools proposed by the standards and regulations of the Unified Health System have a low potential to reduce transaction costs, especially due to hardships in reconciling common goals among the entities, environment surrounded by uncertainty, asymmetries and incomplete information, bounded rationality and conflict of interest...
April 2017: Ciência & Saúde Coletiva
https://www.readbyqxmd.com/read/28437629/design-and-development-of-benzoxazole-derivatives-with-toll-like-receptor-9-antagonism
#16
Swarnali Roy, Ayan Mukherjee, Barnali Paul, Oindrila Rahaman, Shounak Roy, Gundaram Maithri, Bandaru Ramya, Sourav Pal, Dipyaman Ganguly, Arindam Talukdar
Toll-like receptor 9 (TLR9) is a major therapeutic target for numerous inflammatory disorders. Development of small molecule inhibitors for TLR9 remains largely empirical due to lack of structural understanding of potential TLR9 antagonism by small molecules and due to the unusual topology of the ligand binding surface of the receptor. To develop a structural model for rational design of small molecule TLR9 antagonists, an enhanced homology model of human TLR9 (hTLR9) was constructed. Binding mode analysis of a series of molecules having characteristic molecular geometry, flexibility and basicity was conducted based on crystal structure of the inhibitory DNA (iDNA) bound to horse and bovine TLR9...
April 5, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28436898/extended-polynomial-growth-transforms-for-design-and-training-of-generalized-support-vector-machines
#17
Ahana Gangopadhyay, Oindrila Chatterjee, Shantanu Chakrabartty
Growth transformations constitute a class of fixed-point multiplicative update algorithms that were originally proposed for optimizing polynomial and rational functions over a domain of probability measures. In this paper, we extend this framework to the domain of bounded real variables which can be applied towards optimizing the dual cost function of a generic support vector machine (SVM). The approach can, therefore, not only be used to train traditional soft-margin binary SVMs, one-class SVMs, and probabilistic SVMs but can also be used to design novel variants of SVMs with different types of convex and quasi-convex loss functions...
April 17, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28433015/probing-the-effects-of-surface-hydrophobicity-and-tether-orientation-on-antibody-antigen-binding
#18
Derek B Bush, Thomas A Knotts
Antibody microarrays have the potential to revolutionize molecular detection for many applications, but their current use is limited by poor reliability, and efforts to change this have not yielded fruitful results. One difficulty which limits the rational engineering of next-generation devices is that little is known, at the molecular level, about the antibody-antigen binding process near solid surfaces. Atomic-level structural information is scant because typical experimental techniques (X-ray crystallography and NMR) cannot be used to image proteins bound to surfaces...
April 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28416110/structural-basis-for-kinase-mediated-macrolide-antibiotic-resistance
#19
Desiree H Fong, David L Burk, Jonathan Blanchet, Amy Y Yan, Albert M Berghuis
The macrolides are a class of antibiotic, characterized by a large macrocyclic lactone ring that can be inactivated by macrolide phosphotransferase enzymes. We present structures for MPH(2')-I and MPH(2')-II in the apo state, and in complex with GTP analogs and six different macrolides. These represent the first structures from the two main classes of macrolide phosphotransferases. The structures show that the enzymes are related to the aminoglycoside phosphotransferases, but are distinguished from them by the presence of a large interdomain linker that contributes to an expanded antibiotic binding pocket...
May 2, 2017: Structure
https://www.readbyqxmd.com/read/28406014/sequence-modulated-interactions-between-single-multivalent-dna-conjugated-gold-nanoparticles
#20
Chunyan Qiao, Jia Wu, Zhenrong Huang, Xuan Cao, Jiayu Liu, Bin Xiong, Yan He, Edward S Yeung
DNA-conjugated gold nanoparticle (AuNP) is an attractive building block to construct elegant plasmonic nanomaterials by self-assembly but the complicated interaction between multivalent nanoconjugates governing the assembly process and the properties of assembled structures remains poorly understood. Herein, with an in situ kinetic single-particle imaging method, we report the dynamic interaction between single multivalent DNA-conjugated AuNPs quantitatively depends on the nucleic acid sequence in nanoconjugates...
April 26, 2017: Analytical Chemistry
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