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https://www.readbyqxmd.com/read/29054096/simplified-autodock-force-field-for-hydrated-binding-sites
#1
Marek Wojciechowski
A set of high quality structures of protein-ligand complexes with experimentally determined binding affinities has been extracted from the Protein Data Bank and used to test and recalibrate AutoDock force field. Since for some binding sites water molecules are crucial for bridging the receptor-ligand interactions, they have to be included in the analysis. To simplify the process of incorporating water molecules into the binding sites and make it less ambiguous, new simple water model was created. After recalibration of the force field on the new dataset much better correlation between the computed and experimentally determined binding affinities was achieved and the quality of pose prediction improved even more...
September 23, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29054039/control-of-brain-energy-supply-by-astrocytes
#2
REVIEW
Ross Nortley, David Attwell
Astrocytes form an anatomical bridge between the vasculature and neuronal synapses. Recent work suggests that they play a key role in regulating brain energy supply by increasing blood flow to regions where neurons are active, and setting the baseline level of blood flow. Controversy persists over whether lactate derived from astrocyte glycolysis is used to power oxidative phosphorylation in neurons, but astrocytes sustain neuronal ATP production by recycling neurotransmitter glutamate that would otherwise need to be resynthesised from glucose, and by providing a short-term energy store in the form of glycogen that can be mobilised when neurons are active...
October 17, 2017: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/29053956/assembly-of-the-whip-trim14-ppp6c-mitochondrial-complex-promotes-rig-i-mediated-antiviral-signaling
#3
Peng Tan, Lian He, Jun Cui, Chen Qian, Xin Cao, Meng Lin, Qingyuan Zhu, Yinyin Li, Changsheng Xing, Xiao Yu, Helen Y Wang, Rong-Fu Wang
Mitochondrial antiviral signaling platform protein (MAVS) acts as a central hub for RIG-I receptor proximal signal propagation. However, key components in the assembly of the MAVS mitochondrial platform that promote RIG-I mitochondrial localization and optimal activation are still largely undefined. Employing pooled RNAi and yeast two-hybrid screenings, we report that the mitochondrial adaptor protein tripartite motif (TRIM)14 provides a docking platform for the assembly of the mitochondrial signaling complex required for maximal activation of RIG-I-mediated signaling, consisting of WHIP and protein phosphatase PPP6C...
October 19, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29053746/external-auditory-exostoses-and-hearing-loss-in-the-shanidar-1-neandertal
#4
Erik Trinkaus, Sébastien Villotte
The Late Pleistocene Shanidar 1 older adult male Neandertal is known for the crushing fracture of his left orbit with a probable reduction in vision, the loss of his right forearm and hand, and evidence of an abnormal gait, as well as probable diffuse idiopathic skeletal hyperostosis. He also exhibits advanced external auditory exostoses in his left auditory meatus and larger ones with complete bridging across the porus in the right meatus (both Grade 3). These growths indicate at least unilateral conductive hearing (CHL) loss, a serious sensory deprivation for a Pleistocene hunter-gatherer...
2017: PloS One
https://www.readbyqxmd.com/read/29053572/monitoring-bridge-dynamic-responses-using-fiber-bragg-grating-tiltmeters
#5
Feng Xiao, Gang S Chen, J Leroy Hulsey
In bridge health monitoring, tiltmeters have been used for measuring rotation and curvature; however, their application in dynamic parameter identification has been lacking. This study installed fiber Bragg grating (FBG) tiltmeters on the bearings of a bridge and monitored the dynamic rotational angle. The dynamic features, including natural frequencies and mode shapes, have been identified successfully. The innovation presented in this paper is the first-time use of FBG tiltmeter readings to identify the natural frequencies of a long-span steel girder bridge...
October 20, 2017: Sensors
https://www.readbyqxmd.com/read/29053560/evaluation-of-human-corneal-lenticule-quality-after-smile-with-different-cap-thicknesses-using-scanning-electron-microscopy
#6
Shengbei Weng, Manli Liu, Xiaonan Yang, Fang Liu, Yugui Zhou, Haiqin Lin, Quan Liu
PURPOSE: To evaluate the surface characteristics of lenticules created by small-incision lenticule extraction (SMILE) with different cap thicknesses. METHODS: This prospective study included 20 consecutive patients who underwent bilateral SMILE. Surface regularity of the extracted corneal lenticule was analyzed using scanning electron microscopy (SEM) combined with 2 methods: qualitative and quantitative regularity. Qualitative regularity of SEM images was graded by masked observers using an established scoring system...
October 17, 2017: Cornea
https://www.readbyqxmd.com/read/29053532/using-a-complex-patient-management-scenario-to-help-bridge-the-education-practice-gap
#7
Adriane Burgess, Hannah Murphy Buc, Janice M Brennan
Preparing nursing students for transition to practice is challenging in light of the increasing complexity of today's health care environment. A clinical simulation was developed to engage senior-level bachelor of science in nursing students in the management of a critically ill patient whose deterioration warranted timely transfer to an intensive care unit. In this fast-paced, highly charged simulation, students were challenged to implement priority setting, delegation, communication methods, and teamwork...
October 20, 2017: Nursing Education Perspectives
https://www.readbyqxmd.com/read/29053443/enhancement-of-intercellular-electrical-synchronization-by-conductive-materials-in-cardiac-tissue-engineering
#8
Yu Wu, Liang Guo
OBJECTIVE: cardiac tissue regeneration for the treatment of cardiovascular diseases has been of great research interest. Under the hypothesis that electrical synchronization of cardiac cells can be aided by conductive materials, electrically conductive scaffolds have been frequently used to improve cardiac tissue regeneration. However, theoretical analysis is presently absent in examining the underlying mechanism and rationally guiding the design of these conductive scaffolds. METHODS: here, equivalent-circuit models are proposed, in which two adjacent groups of cardiomyocytes are grown either on a bulk conductive substrate or around conductive nanostructures...
October 15, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/29053276/atomic-scale-front-propagation-at-the-onset-of-frictional-sliding
#9
Silvia Bonfanti, Alessandro Taloni, Carlotta Negri, Alessandro Sellerio, Nicola Manini, Stefano Zapperi
Macroscopic frictional sliding emerges from atomic-scale interactions and processes at the contact interface, but bridging the gap between micro and macro scales still remains an unsolved challenge. Direct imaging of the contact surface and simultaneous measurement of stress fields during macroscopic frictional slip revealed the formation of crack precursors, questioning the traditional picture of frictional contacts described in terms of a single degree of freedom. Here we study the onset of frictional slip at atomic scale by simulating the motion of an aluminum block pushed by a slider on a copper substrate...
October 20, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29053272/cardiotoxins-functional-role-of-local-conformational-changes
#10
Anastasia G Konshina, Nikolay A Krylov, Roman G Efremov
Cardiotoxins (CTs) from snake venoms are a family of homologous highly basic proteins that have extended hydrophobic patterns on their molecular surfaces. CTs are folded into three β-structured loops stabilized by four disulfide bridges. Being well-structured in aqueous solution, most of these proteins are membrane-active, although the exact molecular mechanisms of CT-induced cell damage are still poorly understood. To elucidate the structure-function relationships in CTs, a detailed knowledge of their spatial organization and local conformational dynamics is required...
October 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29053242/environmental-effects-on-zirconium-hydroxide-nanoparticles-and-chemical-warfare-agent-decomposition-implications-of-atmospheric-water-and-carbon-dioxide
#11
Robert B Balow, Jeffrey G Lundin, Grant C Daniels, Wesley O Gordon, Monica McEntee, Gregory W Peterson, James H Wynne, Pehr E Pehrsson
Zirconium hydroxide (Zr(OH)4) has excellent sorption properties and wide-ranging reactivity towards numerous types of chemical warfare agents (CWAs) and toxic industrial chemicals. Under pristine laboratory conditions, the effectiveness of Zr(OH)4 has been attributed to a combination of diverse surface hydroxyl species and defects; however, atmospheric components (e.g. CO2, H2O, etc.) and trace contaminants can form adsorbates with potentially detrimental impact to the chemical reactivity of Zr(OH)4. Here, we report the hydrolysis of a chemical warfare agent simulant, dimethyl methylphosphonate (DMMP) on Zr(OH)4 determined by gas chromatography mass spectrometry and in situ attenuated total reflectance Fourier transform infrared spectroscopy under ambient conditions...
October 20, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29052991/transition-metal-single-molecule-magnets-a-mn31-nano-sized-cluster-with-a-large-energy-barrier-of-60-k-and-magnetic-hysteresis-at-5-k
#12
Parisa Abbasi, Kevan Quinn, Dimitris I Alexandropoulos, Marko Damjanović, Wolfgang Wernsdorfer, Albert Escuer, Julia Mayans, Melanie Pilkington, Theocharis C Stamatatos
The first {Mn31} cluster (1) has been prepared from carboxylate ions and the chelating/bridging ligand α-methyl-2-pyridine-methanol. Compound 1 possesses a unique nano-sized structural topology with one of the largest energy barriers reported to-date for high-nuclearity 3d-metal clusters. Single-crystal magnetic hysteresis studies reveal the presence of hysteresis loops below 5 K, one of the highest temperatures below which molecular hysteresis has been observed for 3d-based SMMs.
October 20, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29052990/spatial-screening-of-hemagglutinin-on-influenza-a-virus-particles-sialyl-lacnac-displays-on-dna-and-peg-scaffolds-reveal-the-requirements-for-bivalency-enhanced-interactions-with-weak-monovalent-binders
#13
Victor Bandlow, Susanne Liese, Daniel Lauster, Kai Ludwig, Roland R Netz, Andreas Herrmann, Oliver Seitz
Attachment of the Influenza A virus onto host cells involves multivalent interactions between virus surface hemagglutinin (HA) and sialoside-containing glyco ligands. Despite the development of extremely powerful multivalent bind-ers of the Influenza virus and other viruses, comparably little is known about the optimal spacing of HA ligands, which ought to bridge binding sites within or across the trimeric HA molecules. To explore the criteria for ligand economical high affinity binding, we systematically probed distance-affinity relationships by means of two differently behaving scaffold types based on i) flexible polyethylene glycol (PEG) conjugates and ii) rigid self-assembled DNA·PNA complexes...
October 20, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29052984/complex-structural-landscape-of-titanium-organophosphonates-isolation-of-structurally-related-ti4-ti5-and-ti6-species-and-mechanistic-insights
#14
Kamna Sharma, Rajendran Antony, Alok Ch Kalita, Sandeep Kumar Gupta, Paul Davis, Ramaswamy Murugavel
[Ti(acac)2(O(i)Pr)2] reacts with tert-butylphosphonic acid to yield a series of titanium organophosphonates such as tetranuclear [Ti4(acac)4(μ-O)2(μ-(t)BuPO3)2(μ-(t)BuPO3H)4]·2CH3CN (1), pentanuclear [Ti5(acac)5(μ-O)2(O(i)Pr)(μ-(t)BuPO3)4(μ-(t)BuPO3H)2] (2), hexanuclear [Ti6(acac)6(μ-O)2(O(i)Pr)2(μ-(t)BuPO3)6] (3), or [Ti6(acac)6(μ-O)3(O(i)Pr)(μ-(t)BuPO3)5(μ-(t)BuPO3H)]·2CH3CN (4). The isolation of each of these products in pure form depends on the molar ratio of the reactants or the solvent medium...
October 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/29052981/cation-induced-dimerization-of-crown-substituted-phthalocyanines-by-complexation-with-rubidium-nicotinate-as-revealed-by-x-ray-structural-data
#15
Lyudmila A Lapkina, Vladimir E Larchenko, Gayane A Kirakosyan, Aslan Yu Tsivadze, Sergey I Troyanov, Yulia G Gorbunova
The supramolecular dimeric complex [(μ-oxo)bis(tetra-15-crown-5-phthalocyaninato)(nicotinato)aluminum(III)]tetra(rubidium) bis(nicotinate) was prepared by addition of an excess of a methanol solution of rubidium nicotinate to a chloroform solution of the aluminum crown-phthalocyaninate, [(HO)Al(15C5)4Pc]. A single-crystal X-ray diffraction study of {[Rb4(NicAl(15C5)4Pc)2(μ-O)](2+)(Nic(-))2}·2.36HNic·11H2O demonstrated that two molecules of the aluminum crown-phthalocyaninate nicotinate are connected through an Al-O-Al bridge supported by sandwiching of crown ether moieties by Rb(+) cations...
October 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/29052979/tetranuclear-fe-clusters-with-a-varied-interstitial-ligand-effects-on-the-structure-redox-properties-and-nitric-oxide-activation
#16
Christopher J Reed, Theodor Agapie
A new series of tetranuclear Fe clusters displaying an interstitial μ4-F ligand was prepared for a comparison to previously reported μ4-O analogues. With a single nitric oxide (NO) coordinated as a reporter of small-molecule activation, the μ4-F clusters were characterized in five redox states, from Fe(II)3{FeNO}(8) to Fe(III)3{FeNO}(7), with NO stretching frequencies ranging from 1680 to 1855 cm(-1), respectively. Despite accessing more reduced states with an F(-) bridge, a two-electron reduction of the distal Fe centers is necessary for the μ4-F clusters to activate NO to the same degree as the μ4-O system; consequently, NO reactivity is observed at more positive potentials with μ4-O than μ4-F...
October 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/29052937/targeting-of-c-type-lectin-like-receptor-2-or-p2y12-for-the-prevention-of-platelet-activation-by-immunotherapeutic-cpg-oligodeoxynucleotides-comment
#17
U Flierl, T L Nero, B Lim, R K Andrews, M W Parker, E E Gardiner, K Peter
We read with great interest the article by Delierneux et al. [1] in the Journal of Thrombosis and Haemostasis. The authors elegantly describe a mechanism of platelet activation by CpG oligodeoxynucleotides (ODNs) through CLEC-2 mediated binding and uptake. This is the second platelet activation mechanism to be attributed to CpG ODNs, the first being the one described by our group involving platelet-specific collagen receptor glycoprotein VI (GPVI) [2]. CpG ODNs are short single-stranded DNA molecules resembling bacterial DNA and they were developed as potential drug candidates, largely due to their immunostimulatory properties via activation of toll-like receptor 9 (TLR9) [3]...
October 20, 2017: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/29052799/treatment-and-outcome-of-subdural-hematoma-in-patients-with-spontaneous-intracranial-hypotension-a-report-of-35-cases
#18
Enrico Ferrante, Fabio Rubino, Federica Beretta, Caroline Regna-Gladin, M Mirko Ferrante
Spontaneous intracranial hypotension (SIH) is characterized by orthostatic headache, low CSF pressure and diffuse pachymeningeal enhancement on brain MRI. SIH results from spontaneous CSF leakage leading to brain sag. Sometimes, tearing of bridging veins may produce subdural hematomas (SDHs). Patients with SDH were identified retrospectively from 212 consecutive SIH patients. Data were collected on demographics, clinical courses, neuroimaging findings, treatment and outcome of SDH. Thirty-five patients (16%), (6 women, 29 men; aged 33-68; mean, 50 years) with SDH were recruited...
October 20, 2017: Acta Neurologica Belgica
https://www.readbyqxmd.com/read/29052747/angiosomal-radiopathologic-analysis-of-transarterial-radioembolization%C3%A2-for-the-treatment-of-hepatocellular-carcinoma
#19
Altan F Ahmed, Naziya Samreen, Joseph R Grajo, Ivan Zendejas, Chris L Sistrom, Amy Collinsworth, Ashwini Esnakula, Jehan L Shah, Roniel Cabrera, Brian S Geller, Beau B Toskich
PURPOSE: To assess the radiopathologic correlation following Yttrium-90 transarterial radioembolization (TARE) of hepatocellular carcinoma (HCC) using variable radiodosimetry to identify imaging surrogates of histologic response. METHODS: Twelve patients with HCC underwent ablative (≥ 190 Gy) and/or non-ablative (< 190 Gy) TARE delivered in a segmental, lobar, or combined fashion as a surgical neoadjuvant or bridge to transplantation. Both targeted tumor and treatment angiosome were analyzed before and after TARE utilizing hepatocyte-specific contrast-enhanced MRI or contrast-enhanced CT...
October 20, 2017: Abdominal Radiology
https://www.readbyqxmd.com/read/29052677/silylene-assisted-hydride-transfer-to-co2-and-cs2-at-a-p2si-ru-pincer-type-complex
#20
Matthew T Whited, Jia Zhang, Senjie Ma, Binh D Nguyen, Daron E Janzen
The synthesis and characterization of base-stabilized and base-free pincer-type bis(phosphine)/silylene [P2Si]Ru complexes are reported. The base-free complex readily reduces CO2 and CS2via silylene-assisted hydride transfer, affording structurally distinct products with silicon-to-ruthenium formate and dithioformate bridges.
October 20, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
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