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Bounded rationality

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https://www.readbyqxmd.com/read/28327216/the-expressive-rationality-of-inaccurate-perceptions
#1
Dan M Kahan
This commentary uses the dynamic of identity-protective cognition to pose a friendly challenge to Jussim (2012). Like other forms of information processing, this one is too readily characterized as a bias. It is no mistake, however, to view identity-protective cognition as generating inaccurate perceptions. The "bounded rationality" paradigm incorrectly equates rationality with forming accurate beliefs. But so does Jussim's critique.
January 2017: Behavioral and Brain Sciences
https://www.readbyqxmd.com/read/28326779/illuminating-photochemistry-of-an-excitation-ratiometric-fluorescent-protein-calcium-biosensor
#2
Longteng Tang, Yanli Wang, Weimin Liu, Yongxin Zhao, Robert E Campbell, Chong Fang
Fluorescent protein (FP) based biosensors have become an important and promising tool to track metal ion movement inside living systems. Their working principles after light irradiation, however, remain elusive. To facilitate the rational design of biosensors, we dissect the fluorescence modulation mechanism of a newly developed excitation ratiometric green FP-based Ca(2+) biosensor, GEX-GECO1, using femtosecond stimulated Raman spectroscopy (FSRS) in the electronic excited state. Upon 400 nm photoexcitation, characteristic vibrational marker bands at ~1180 and 1300 cm(-1) show concomitant decay and rise dynamics, probing the progression of an ultrafast excited state proton transfer (ESPT) reaction...
March 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28319400/playing-with-emulsion-formulation-to-control-the-perforation-of-a-freely-expanding-liquid-sheet
#3
Clara Vernay, Laurence Ramos, Alois Würger, Christian Ligoure
A single-drop experiment based on the collision of one drop of liquid on a small solid target is used to produce liquid sheets that are visualized with a fast camera. Upon impact, the drop flattens into a sheet that is bounded by a thicker rim and radially expanding in air. Emulsion-based liquid sheets are destabilized through the nucleation of holes that perforate the sheet during its expansion. The holes grow until they merge together and form a web of ligaments, which are then destabilized into drops. We propose the perforation mechanism as a sequence of two necessary steps...
March 20, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28290497/structural-basis-of-eco1-mediated-cohesin-acetylation
#4
William C H Chao, Benjamin O Wade, Céline Bouchoux, Andrew W Jones, Andrew G Purkiss, Stefania Federico, Nicola O'Reilly, Ambrosius P Snijders, Frank Uhlmann, Martin R Singleton
Sister-chromatid cohesion is established by Eco1-mediated acetylation on two conserved tandem lysines in the cohesin Smc3 subunit. However, the molecular basis of Eco1 substrate recognition and acetylation in cohesion is not fully understood. Here, we discover and rationalize the substrate specificity of Eco1 using mass spectrometry coupled with in-vitro acetylation assays and crystallography. Our structures of the X. laevis Eco2 (xEco2) bound to its primary and secondary Smc3 substrates demonstrate the plasticity of the substrate-binding site, which confers substrate specificity by concerted conformational changes of the central β hairpin and the C-terminal extension...
March 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28288216/rovibrational-spectroscopic-constants-of-the-interaction-between-ammonia-and-metallo-phthalocyanines-a-theoretical-protocol-for-ammonia-sensor-design
#5
Alan R Baggio, Daniel F S Machado, Valter H Carvalho-Silva, Leonardo G Paterno, Heibbe Cristhian B de Oliveira
In the present contribution, we develop an adapted theoretical approach based on DFT calculations (B3LYP functional) and solution of the nuclear Schrödinger equation by using the Discrete Variable Representation method to model the interaction of ammonia with metallo-phthalocyanines (MPcs, where M = Fe(2+), Co(2+), Ni(2+), Cu(2+) or Zn(2+)). This approach is intended to be a general protocol for the rational design of chemical sensors. The as-obtained binding energy curves, obtained from ab initio points, permitted us to calculate rovibrational energies and spectroscopic constants, as well as to establish the relative population of rovibrational states in different types of MPc-NH3 thermodynamic systems...
March 13, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28283570/stabilization-of-a-soluble-native-like-trimeric-form-of-an-efficiently-cleaved-indian-hiv-1-clade-c-envelope-glycoprotein
#6
Shubbir Ahmed, Tripti Shrivastava, Naresh Kumar, Gabriel Ozorowski, Andrew B Ward, Bimal K Chakrabarti
Designing an effective HIV-1 envelope glycoprotein (Env) immunogen for elicitation of broadly neutralizing antibodies (bNAbs) is a challenging task owing to the high sequence diversity, heavy glycosylation and inherent meta-stability of Env. Based on the antigenic profile of recently isolated bNAbs, the rational approach to immunogen design is to make a stable version of the Env trimer, which mimics the native trimeric Env present on the viral surface. The SOSIP.664 form of a clade A Env, BG505, yields a homogeneous and well-ordered pre-fusion trimeric form, which maintains structural integrity and desired antigenicity...
March 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28282057/adsorbate-mediated-strong-metal-support-interactions-in-oxide-supported-rh-catalysts
#7
John C Matsubu, Shuyi Zhang, Leo DeRita, Nebojsa S Marinkovic, Jingguang G Chen, George W Graham, Xiaoqing Pan, Phillip Christopher
The optimization of supported metal catalysts predominantly focuses on engineering the metal site, for which physical insights based on extensive theoretical and experimental contributions have enabled the rational design of active sites. Although it is well known that supports can influence the catalytic properties of metals, insights into how metal-support interactions can be exploited to optimize metal active-site properties are lacking. Here we utilize in situ spectroscopy and microscopy to identify and characterize a support effect in oxide-supported heterogeneous Rh catalysts...
February 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28279557/rational-design-and-studies-of-excimer-forming-novel-dual-probes-to-target-rna
#8
O A Krasheninina, A A Lomzov, V S Fishman, D S Novopashina, A G Venyaminova
In this paper, we report structure-based rational design and physico-chemical and biological studies of novel pyrene excimer forming dual probes for visualization of intracellular RNAs. Herein, the probes based on 2'-O-methyl RNA with linkers of different structure and length between pyrene moiety and ribose are studied with respect to their hybridization and spectral properties. We found optimal linkers that provide more intense excimer emission (at ∼480nm) of RNA-bound probes; particularly, the length of the linker arm of the 3'-component of dual probes plays a key role in formation of pyrene excimer...
February 27, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28276656/a-dimeric-bis-melamine-substituted-bispidine-for-efficient-transmembrane-h-cl-cotransport
#9
Sopan Valiba Shinde, Pinaki Talukdar
A 3,7-diazabicyclo[3.3.1]nonane linking to two melamines is a unique transmembrane H(+) /Cl(-) carrier. In the solid state, the V-shaped compound forms a HCl-bound zig-zag network through cooperative protonation and hydrogen bond interactions. In the lipid membrane, the receptor forms a dimeric self-assembly involving multiple H(+) and Cl(-) leading to the efficient transport of the acid. The pH-dependent Cl(-) efflux observed for the compound was rationalized based on a gradual protonation model that confers an active transmembrane carrier at physiological pH...
March 9, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28251414/molecular-dynamics-simulations-and-molecular-flooding-studies-of-the-retinoid-x-receptor-ligand-binding-domain
#10
Geoffrey M Gray, Ning Ma, Carl E Wagner, Arjan van der Vaart
Bexarotene is an FDA approved retinoid X-receptor (RXR) agonist for the treatment of cutaneous T-cell lymphoma, and its use in other cancers and Alzheimer's disease is being investigated. The drug causes serious side effects, which might be reduced by chemical modifications of the molecule. To rationalize known agonists and to help identify sites for potential substitutions we present molecular simulations in which the RXR ligand-binding domain was flooded with a large number of drug-like molecules, and molecular dynamics simulations of a series of bexarotene-like ligands bound to the RXR ligand-binding domain...
March 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28202514/mcl-1-degradation-is-required-for-targeted-therapeutics-to-eradicate-colon-cancer-cells
#11
Jingshan Tong, Peng Wang, Shuai Tan, Dongshi Chen, Zaneta Nikolovska-Coleska, Fangdong Zou, Jian Yu, Lin Zhang
The Bcl-2 family protein Mcl-1 is often degraded in cancer cells subjected to effective therapeutic treatment, and defective Mcl-1 degradation has been associated with intrinsic and acquired drug resistance. However, a causal relationship between Mcl-1 degradation and anticancer drug responses has not been directly established, especially in solid tumor cells where Mcl-1 inhibition alone is insufficient to trigger cell death. In this study, we present evidence that Mcl-1 participates directly in determining effective therapeutic responses in colon cancer cells...
February 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28195463/target-elucidation-by-cocrystal-structures-of-nadh-ubiquinone-oxidoreductase-of-plasmodium-falciparum-pfndh2-with-small-molecule-to-eliminate-drug-resistant-malaria
#12
Yiqing Yang, You Yu, Xiaolu Li, Jing Li, Yue Wu, Jie Yu, Jingpeng Ge, Zhenghui Huang, Lubin Jiang, Yu Rao, Maojun Yang
Drug-resistant malarial strains have been continuously emerging recently, which posts a great challenge for the global health. Therefore, new antimalarial drugs with novel targeting mechanisms are urgently needed for fighting drug-resistant malaria. NADH-ubiquinone oxidoreductase of Plasmodium falciparum (PfNDH2) represents a viable target for antimalarial drug development. However, the absence of structural information on PfNDH2 limited rational drug design and further development. Herein, we report high resolution crystal structures of the PfNDH2 protein for the first time in Apo-, NADH-, and RYL-552 (a new inhibitor)-bound states...
February 22, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28194151/structure-and-dynamics-of-antigenic-peptides-in-complex-with-tap
#13
REVIEW
Elisa Lehnert, Robert Tampé
The transporter associated with antigen processing (TAP) selectively translocates antigenic peptides into the endoplasmic reticulum. Loading onto major histocompatibility complex class I molecules and proofreading of these bound epitopes are orchestrated within the macromolecular peptide-loading complex, which assembles on TAP. This heterodimeric ABC-binding cassette (ABC) transport complex is therefore a major component in the adaptive immune response against virally or malignantly transformed cells. Its pivotal role predestines TAP as a target for infectious diseases and malignant disorders...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28159622/the-discovery-complex-crystal-structure-and-recognition-mechanism-of-a-novel-natural-pde4-inhibitor-from-selaginella-pulvinata
#14
Yiyou Huang, Xin Liu, Deyan Wu, Guihua Tang, Zengwei Lai, Xuehua Zheng, Sheng Yin, Hai-Bin Luo
Phosphodiesterase-4 (PDE4) is an important drug target for treatment of inflammation-related diseases. Till now, natural PDE4 inhibitors are rare and their co-crystal structures with PDE4 are hardly available. In the present study, selaginpulvilins K and L (1 and 2), two novel fluorene derivatives, were isolated from a traditional Chinese medicine Selaginella pulvinata and exhibited remarkable inhibition against phosphodiesterase-4D (PDE4D) at IC50 11nM and 90nM, respectively. Compound 1 also showed a good selectivity across PDE families with the selective fold ranging from 30 to 909...
January 31, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28157330/low-threshold-multiexciton-optical-gain-in-colloidal-cdse-cdte-core-crown-type-ii-nanoplatelet-heterostructures
#15
Qiuyang Li, Zihao Xu, James R McBride, Tianquan Lian
Colloidal cadmium chalcogenide core/crown type-II nanoplatelet heterostructures, such as CdSe/CdTe, are promising materials for lasing and light-emitting applications. Their rational design and improvement requires the understanding of the nature of single- and multiexciton states. Using pump fluence and wavelength-dependent ultrafast transient absorption spectroscopy, we have identified three spatially and energetically distinct excitons (in the order of increasing energy): interface-localized charge transfer exciton (XCT, with electron in the CdSe core bound to the hole in the CdTe crown), and CdTe crown-localized XCdTe and CdSe core-localized XCdSe excitons...
February 7, 2017: ACS Nano
https://www.readbyqxmd.com/read/28157128/cobalt-ii-chloride-adducts-with-acetonitrile-propan-2-ol-and-tetrahydrofuran-considerations-on-nuclearity-reactivity-and-synthetic-applications
#16
Danilo Stinghen, André Luis Rüdiger, Siddhartha O K Giese, Giovana G Nunes, Jaísa F Soares, David L Hughes
High-spin cobalt(II) complexes are considered useful building blocks for the synthesis of single-molecule magnets (SMM) because of their intrinsic magnetic anisotropy. In this work, three new cobalt(II) chloride adducts with labile ligands have been synthesized from anhydrous CoCl2, to be subsequently employed as starting materials for heterobimetallic compounds. The products were characterized by elemental, spectroscopic (EPR and FT-IR) and single-crystal X-ray diffraction analyses. trans-Tetrakis(acetonitrile-κN)bis(tetrahydrofuran-κO)cobalt(II) bis[(acetonitrile-κN)trichloridocobaltate(II)], [Co(C2H3N)4(C4H8O)2][CoCl3(C2H3N)]2, (1), comprises mononuclear ions and contains both acetonitrile and tetrahydrofuran (thf) ligands, The coordination polymer catena-poly[[tetrakis(propan-2-ol-κO)cobalt(II)]-μ-chlorido-[dichloridocobalt(II)]-μ-chlorido], [Co2Cl4(C3H8O)4], (2'), was prepared by direct reaction between anhydrous CoCl2 and propan-2-ol in an attempt to rationalize the formation of the CoCl2-alcohol adduct (2), probably CoCl2(HO(i)Pr)m...
February 1, 2017: Acta Crystallographica. Section C, Structural Chemistry
https://www.readbyqxmd.com/read/28130301/structural-and-biochemical-studies-of-novel-aldo-keto-reductases-for-the-biocatalytic-conversion-of-3-hydroxybutanal-to-1-3-butanediol
#17
Taeho Kim, Robert Flick, Joseph Brunzelle, Alex Singer, Elena Evdokimova, Greg Brown, Jeong Chan Joo, George A Minasov, Wayne F Anderson, Radhakrishnan Mahadevan, Alexei Savchenko, Alexander F Yakunin
The non-natural alcohol 1,3-butanediol (1,3-BDO) is a valuable building block for the synthesis of various polymers. One of the potential pathways for the biosynthesis of 1,3-BDO includes the biotransformation of acetaldehyde to 1,3-BDO via 3-hydroxybutanal (3-HB) using aldolases and aldo-keto reductases. This pathway requires an aldo-keto reductase (AKR) selective for 3-HB, but inactive toward acetaldehyde, so it can be used for one pot synthesis. In this work, we screened over 20 purified uncharacterized AKRs for 3-HB reduction and identified 10 enzymes with significant activity and nine proteins with detectable activity...
January 27, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28126742/binding-of-nadp-triggers-an-open-to-closed-transition-in-a-mycobacterial-fabg-%C3%AE-ketoacyl-acp-reductase
#18
Mickael Blaise, Niel Van Wyk, Francoise Banères-Roquet, Yann Guérardel, Laurent Kremer
The ketoacyl-acyl carrier protein (ACP) reductase FabG catalyzes the NADPH/NADH-dependent reduction of b-ketoacyl-ACP substrates to b-hydroxyacyl-ACP products, the first reductive step in the fatty acid biosynthesis elongation cycle. FabG proteins are ubiquitous in bacteria and are part of the type II fatty acid synthase system (FAS-II). Mining the Mycobacterium smegmatis genome uncovered several putative FabG-like proteins. Among them, we identified MSMEG_6753 whose gene was found adjacent to MSMEG_6754 , encoding a recently characterized enoyl-CoA dehydratase and to MSMEG_6755 , encoding another potential reductase...
January 26, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28118518/pentagonal-bipyramid-fe-ii-complexes-robust-ising-spin-units-towards-heteropolynuclear-nano-magnets
#19
Arun Kumar Bar, Nayanmoni Gogoi, Céline Pichon, Durga Prasad Goli, Mehrez Thlijeni, Carine Duhayon, Nicolas Suaud, Nathalie Guihéry, Anne-Laure Barra, S Ramasesha, Jean-Pascal Sutter
Pentagonal bipyramid Fe(II) complexes have been investigated in order to evaluate their potential as Ising-spin building units for the preparation of hetero-polynuclear species likely to behave as SMMs. The monometallic complexes result from association of a divalent metal ion with pentadentate ligands having 2,6-diacetylpyridine bis(hydrazone) core. Their magnetic anisotropy established by magnetometry revealed zero-field splitting (ZFS) parameter D ranging between -4 and -13 cm-1 which was found to be modulated by the apical ligands (ROH versus Cl)...
January 24, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28117977/interactions-and-attachment-pathways-between-functionalized-gold-nanorods
#20
Shu Fen Tan, Utkarsh Anand, Utkur Mirsaidov
Nanoparticle (NP) self-assembly has been recognized as an important technological process for forming ordered nanostructures. However, the detailed dynamics of the assembly processes remain poorly understood. Using in situ liquid cell transmission electron microscopy, we describe the assembly modes of gold (Au) nanorods (NRs) in solution mediated by hydrogen bonding between NR-bound cysteamine linker molecules. Our observations reveal that by tuning the linker concentration, two different NR assembly modes can be achieved...
February 28, 2017: ACS Nano
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