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https://www.readbyqxmd.com/read/28918599/optimal-affinity-ranking-for-automated-virtual-screening-validated-in-prospective-d3r-grand-challenges
#1
Bentley M Wingert, Rick Oerlemans, Carlos J Camacho
The goal of virtual screening is to generate a substantially reduced and enriched subset of compounds from a large virtual chemistry space. Critical in these efforts are methods to properly rank the binding affinity of compounds. Prospective evaluations of ranking strategies in the D3R grand challenges show that for targets with deep pockets the best correlations (Spearman ρ ~ 0.5) were obtained by our submissions that docked compounds to the holo-receptors with the most chemically similar ligand. On the other hand, for targets with open pockets using multiple receptor structures is not a good strategy...
September 16, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28918572/spot-light-on-skeletal-muscles-optogenetic-stimulation-to-understand-and-restore-skeletal-muscle-function
#2
Tobias van Bremen, Thorsten Send, Philipp Sasse, Tobias Bruegmann
Damage of peripheral nerves results in paralysis of skeletal muscle. Currently, the only treatment option to restore proper function is electrical stimulation of the innervating nerve or of the skeletal muscles directly. However this approach has low spatial and temporal precision leading to co-activation of antagonistic muscles and lacks cell-type selectivity resulting in pain or discomfort by stimulation of sensible nerves. In contrast to electrical stimulation, optogenetic methods enable spatially confined and cell-type selective stimulation of cells expressing the light sensitive channel Channelrhodopsin-2 with precise temporal control over the membrane potential...
September 16, 2017: Journal of Muscle Research and Cell Motility
https://www.readbyqxmd.com/read/28918374/a-general-strategy-to-fabricate-photonic-crystal-heterostructure-with-programmed-photonic-stopband
#3
Lijing Zhang, Bofan Liu, Jie Wang, Shengyang Tao, Qingfeng Yan
In this paper, we present a general fabrication strategy to achieve the structure control and the flexible photonic stop band regulation of (2+1) D photonic crystal heterostructures (PCHs) by layer-by-layer depositing the annealed colloidal crystal monolayers of different sphere size. The optical properties of the resulting (2+1) DPCHs with different lattice constants were systematically studied and a universal photonic stopband variation rule was proposed, which makes it possible to program any kind of stopband structure as required, such as dual- or multi-stopbands PCH and ultra-wide stopband PCH...
August 24, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28918265/amorphous-liquid-metal-electrodes-enabled-conformable-electrochemical-therapy-of-tumors
#4
Xuyang Sun, Bo Yuan, Wei Rao, Jing Liu
Electrochemical treatment of tumors (EChT) has recently been identified as a very effective way for local tumor therapy. However, hindered by the limited effective area of a single rigid electrode, multiple electrodes are often recruited when tackling large tumors, where too many electrodes not only complicate the clinical procedures but also aggravate patients' pain. Here we present a new conceptual electric stimulation tumor therapy through introducing the injectable liquid metal electrodes, which can adapt to complex tumor shapes so as to achieve desired therapeutic performance...
September 5, 2017: Biomaterials
https://www.readbyqxmd.com/read/28917932/rewiring-neutral-lipids-production-for-the-de-novo-synthesis-of-wax-esters-in-rhodococcus-opacus-pd630
#5
Mariana P Lanfranconi, Héctor M Alvarez
Rhodococcus opacus PD630 accumulates significant amounts of triacylglycerols (TAG), but is not able to de novo synthesize wax esters (WE) from structural unrelated carbon sources, such as gluconate. In this study, strain PD630 was engineered to produce WE by heterologous expression of maqu_2220 gene, which encodes a fatty acyl-CoA reductase for the production of fatty alcohols in Marinobacter hydrocarbonoclasticus. Recombinant cells produced ca. 46% of WE and 54% of TAG (of total WE+TAG) from gluconate compared with the wild type, which produced 100% of TAG...
September 13, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28917921/effect-of-oxidized-chitin-nanocrystals-isolated-by-ammonium-persulfate-method-on-the-properties-of-carboxymethyl-cellulose-based-films
#6
Ahmed A Oun, Jong-Whan Rhim
Oxidized chitin nanocrystals (ChNCs) were isolated from crab shell chitin using ammonium persulfate (APS) method. The oxidized ChNCs were in needle shape with a diameter of 15nm, the length of 400-500nm, and crystallinity index of 93.5%. Carboxymethyl cellulose (CMC)-based films reinforced with the ChNCs (0, 1, 5, and 10wt.%) were flexible and transparent. The mechanical strength of the CMC film increased significantly (p<0.05) after blending with the ChNCs. The tensile strength (TS) and elastic modulus (EM) increased by 88% and 243% when 10wt...
November 1, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28917893/carboxymethyl-cyclosophoraoses-as-a-flexible-ph-responsive-solubilizer-for-pindolol
#7
Yiluo Hu, Hwanhee Kim, Vijay Vilas Shinde, Daham Jeong, Youngjin Choi, Eunae Cho, Seunho Jung
In the present study, cyclosophoraoses (CyS) (β-1,2 linked cyclic glucans, with glucopyranose units ranging from 17 to 23) isolated from Rhizobium leguminosarum biovar viciae VF-39 were modified with carboxymethyl (CM) groups, and the pH-sensitive complexation of CM CyS with pindolol was investigated. The solubility of pindolol increased 32-fold by its complexation with 5mM CM CyS at pH 10, whereas it shows no significant change at pH 3. Pindolol, a β-adrenergic blocking agent, has a hydrophobic nature at non-ionized state, and CM CyS could solubilize efficiently pindolol in a high alkaline solution...
November 1, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28917849/understanding-the-microstructure-and-absorption-rate-of-starch-based-superabsorbent-polymers-prepared-under-high-starch-concentration
#8
Dongling Qiao, Long Yu, Xianyang Bao, Binjia Zhang, Fatang Jiang
From a microstructural view, the focus of this work was on the water absorption rate of starch-based superabsorbent polymers (starch-SAPs) prepared under high starch concentration (0.27:1w/w starch:water). The effects of starch amylose/amylopectin ratio were disclosed. The increase in amylopectin reduced the amount (CPAM) of polyacrylamide (PAM) in starch-SAPs but increased the ratio of starch carbons grafted with PAM, which eventually decreased the average length (LPAM) of PAM chains. The shorter PAM chains could reduce starch-SAP chain flexibility, thus inducing larger mass fractal gels in swollen starch-SAPs...
November 1, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28917799/a-reagentless-and-reusable-electrochemical-aptamer-based-sensor-for-rapid-detection-of-ampicillin-in-complex-samples
#9
Zhi-Gang Yu, Rebecca Y Lai
We report the design and fabrication of a "signal-on" electrochemical aptamer-based (E-AB) sensor for detection of ampicillin. The signaling of the sensor is based on target binding-induced changes in the conformation and flexibility of the methylene blue-modified aptamer probe. The sensor's response is fast; signal saturation can be reached in ~ 200s. Since all the sensor components are surface-immobilized, it is regenerable and can be reused for at least three times. It has demonstrated good specificity and is capable of differentiating between ampicillin and structurally similar antibiotics such as amoxicillin...
January 1, 2018: Talanta
https://www.readbyqxmd.com/read/28917793/multi-elemental-nd-sm-eu-gd-isotope-ratio-measurements-by-stop-flow-isotachophoresis-coupled-to-mc-icpms
#10
L Vio, B Martelat, H Isnard, A Nonell, F Chartier
In this study, a new analytical procedure based on isotachophoresis (ITP) coupled to a multi collector inductively coupled plasma mass spectrometer named Stop-Flow-ITP-MC-ICPMS is developed for exhaustive and high-precision multi-elemental isotopic characterization. We demonstrate that Stop-Flow-ITP makes it possible to stop the analytes migration several times for a duration compatible with the detector configuration changes without losing the separation performance. With this procedure, isotope ratio measurements of four lanthanides of interest for nuclear applications (Nd, Sm, Eu and Gd) were obtained with a reproducibility better than 0...
January 1, 2018: Talanta
https://www.readbyqxmd.com/read/28917725/a-computational-approach-for-phenotypic-comparisons-of-cell-populations-in-high-dimensional-cytometry-data
#11
Ludovic Platon, David Pejoski, Guillaume Gautreau, Brice Targat, Roger Le Grand, Anne-Sophie Beignon, Nicolas Tchitchek
BACKGROUND: Cytometry is an experimental technique used to measure molecules expressed by cells at a single cell resolution. Recently, several technological improvements have made possible to increase greatly the number of cell markers that can be simultaneously measured. Many computational methods have been proposed to identify clusters of cells having similar phenotypes. Nevertheless, only a limited number of computational methods exist to compare the phenotypes of the cell clusters identified by different clustering approaches...
September 13, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28917130/bending-behaviors-of-fully-covered-biodegradable-polydioxanone-biliary-stent-for-human-body-by-finite-element-method
#12
Yanhui Liu, Guoqing Zhu, Huazhe Yang, Conger Wang, Peihua Zhang, Guangting Han
This paper presents a study of the bending flexibility of fully covered biodegradable polydioxanone biliary stents (FCBPBs) developed for human body. To investigate the relationship between the bending load and structure parameter (monofilament diameter and braid-pin number), biodegradable polydioxanone biliary stents derived from braiding method were covered with membrane prepared via electrospinning method, and nine FCBPBSs were then obtained for bending test to evaluate the bending flexibility. In addition, by the finite element method, nine numerical models based on actual biliary stent were established and the bending load was calculated through the finite element method...
August 24, 2017: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/28917105/optimal-conditions-for-flexible-methane-production-in-a-demand-based-operation-of-biogas-plants
#13
W Laperrière, B Barry, M Torrijos, B Pechiné, N Bernet, J P Steyer
The aim of the presented work was to study the methane production limits and to determine optimal conditions for flexible operation of an anaerobic reactor in order to set up an operational strategy. Punctual overloads were conducted in a laboratory-scale anaerobic reactor with readily biodegradable solid substrates, and the influences of overload intensity, baseload value and substrate used were investigated. A maximal daily value around 1000mL/L of reactor for methane production has been assessed. This value did not evolve significantly during experiment time, and conditioned the persistence of overloads as well as the flexibility margin on the reactor, which ranged from +25% to +140% on daily production...
September 5, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28917095/turning-movements-vehicle-offsets-and-ageing-drivers-driving-behaviour-at-channelized-and-unchannelized-intersections
#14
Jaisung Choi, Richard Tay, Sangyoup Kim, Seungwon Jeong
Ageing drivers experience a higher risk of intersection crashes because of their decrease in driving efficiency, including the decline in cognitive ability, head and neck flexibility, and visual acuity. Although several studies have been conducted to examine the factors associated with ageing driver crashes at intersections, little research has been conducted to examine the differences in the factors related to ageing drivers' turning paths and intersection geometric features. This study aims to improve the safety of ageing drivers at intersections by identifying the maneuvers that are risky for them and tracking their turning movements at selected intersections...
September 13, 2017: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/28916960/a-novel-approach-using-the-enhanced-view-totally-extraperitoneal-etep-technique-for-laparoscopic-retromuscular-hernia-repair
#15
Igor Belyansky, Jorge Daes, Victor Gheorghe Radu, Ramana Balasubramanian, H Reza Zahiri, Adam S Weltz, Udai S Sibia, Adrian Park, Yuri Novitsky
BACKGROUND: The enhanced-view totally extraperitoneal (eTEP) technique has been previously described for Laparoscopic Inguinal Hernia Repair. We present a novel application of the eTEP access technique for the repair of ventral and incisional hernias. METHODS: Retrospective review of consecutive laparoscopic retromuscular hernia repair cases utilizing the eTEP access approach from five hernia centers between August 2015 and October 2016 was conducted. Patient demographics, hernia characteristics, operative details, perioperative complications, and quality of life outcomes utilizing the Carolina's Comfort Scale (CCS) were included in our data analysis...
September 15, 2017: Surgical Endoscopy
https://www.readbyqxmd.com/read/28916858/an-endoscopic-mucosal-grading-system-is-predictive-of-leak-in-stapled-rectal-anastomoses
#16
Sarath Sujatha-Bhaskar, Mehraneh D Jafari, Mark Hanna, Christina Y Koh, Colette S Inaba, Steven D Mills, Joseph C Carmichael, Ninh T Nguyen, Michael J Stamos, Alessio Pigazzi
BACKGROUND: Anastomotic leak is a devastating postoperative complication following rectal anastomoses associated with significant clinical and oncological implications. As a result, there is a need for novel intraoperative methods that will help predict anastomotic leak. METHODS: From 2011 to 2014, patient undergoing rectal anastomoses by colorectal surgeons at our institution underwent prospective application of intraoperative flexible endoscopy with mucosal grading...
September 15, 2017: Surgical Endoscopy
https://www.readbyqxmd.com/read/28916841/some-liked-it-hot-a-hypothesis-regarding-establishment-of-the-proto-mitochondrial-endosymbiont-during-eukaryogenesis
#17
Cory D Dunn
Eukaryotic cells are characterized by a considerable increase in subcellular compartmentalization when compared to prokaryotes. Most evidence suggests that the earliest eukaryotes consisted of mitochondria derived from an α-proteobacterial ancestor enclosed within an archaeal host cell. However, what benefits the archaeal host and the proto-mitochondrial endosymbiont might have obtained at the beginning of this endosymbiotic relationship remains unclear. In this work, I argue that heat generated by the proto-mitochondrion initially permitted an archaeon living at high temperatures to colonize a cooler environment, thereby removing apparent limitations on cellular complexity...
September 15, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28916808/the-effects-of-domestication-and-ontogeny-on-cognition-in-dogs-and-wolves
#18
Michelle Lampe, Juliane Bräuer, Juliane Kaminski, Zsófia Virányi
Cognition is one of the most flexible tools enabling adaptation to environmental variation. Living close to humans is thought to influence social as well as physical cognition of animals throughout domestication and ontogeny. Here, we investigated to what extent physical cognition and two domains of social cognition of dogs have been affected by domestication and ontogeny. To address the effects of domestication, we compared captive wolves (n = 12) and dogs (n = 14) living in packs under the same conditions...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916761/chronic-interfacing-with-the-autonomic-nervous-system-using-carbon-nanotube-cnt-yarn-electrodes
#19
Grant A McCallum, Xiaohong Sui, Chen Qiu, Joseph Marmerstein, Yang Zheng, Thomas E Eggers, Chuangang Hu, Liming Dai, Dominique M Durand
The ability to reliably and safely communicate chronically with small diameter (100-300 µm) autonomic nerves could have a significant impact in fundamental biomedical research and clinical applications. However, this ability has remained elusive with existing neural interface technologies. Here we show a new chronic nerve interface using highly flexible materials with axon-like dimensions. The interface was implemented with carbon nanotube (CNT) yarn electrodes to chronically record neural activity from two separate autonomic nerves: the glossopharyngeal and vagus nerves...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916680/variation-in-developmental-trajectories-of-physiological-and-somatic-traits-in-a-common-songbird-approaching-fledging
#20
Allison Cornell, Tony D Williams
In avian species, little is known about the development of physiological traits in the days preceding fledging, a critical life history transition marked by a high mortality rate. Developmental trajectory during this period may be flexible based on ecological context or hardwired, with potential costs for variation in growth in the form of oxidative stress. Patterns in development are likely to relate to variation in life history, for which seabirds and aerial insectivores have been well studied, while our focal species is a grassland ground forager, the European starling (Sturnus vulgaris)...
September 15, 2017: Journal of Experimental Biology
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