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https://www.readbyqxmd.com/read/28319781/systematic-study-of-imidazoles-inhibiting-ido1-via-the-integration-of-molecular-mechanics-and-quantum-mechanics-calculations
#1
Yi Zou, Fang Wang, Yan Wang, Wenjie Guo, Yihua Zhang, Qiang Xu, Yisheng Lai
Indoleamine 2,3-dioxygenase 1 (IDO1) is regarded as an attractive target for cancer immunotherapy. To rationalize the detailed interactions between IDO1 and its inhibitors at the atomic level, an integrated computational approach by combining molecular mechanics and quantum mechanics methods was employed in this report. Specifically, the binding modes of 20 inhibitors was initially investigated using the induced fit docking (IFD) protocol, which outperformed other two docking protocols in terms of correctly predicting ligand conformations...
March 14, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28319706/fire-spread-predictions-sweeping-uncertainty-under-the-rug
#2
Akli Benali, Ana C L Sá, Ana R Ervilha, Ricardo M Trigo, Paulo M Fernandes, José M C Pereira
Predicting fire spread and behavior correctly is crucial to minimize the dramatic consequences of wildfires. However, our capability of accurately predicting fire spread is still very limited, undermining the utility of such simulations to support decision-making. Improving fire spread predictions for fire management purposes, by using higher quality input data or enhanced models, can be expensive, unfeasible or even impossible. Fire managers would benefit from fast and inexpensive ways of improving their decision-making...
March 15, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28319685/linking-actions-and-objects-context-specific-learning-of-novel-weight-priors
#3
Kevin M Trewartha, J Randall Flanagan
Distinct explicit and implicit memory processes support weight predictions used when lifting objects and making perceptual judgments about weight, respectively. The first time that an object is encountered weight is predicted on the basis of learned associations, or priors, linking size and material to weight. A fundamental question is whether the brain maintains a single, global representation of priors, or multiple representations that can be updated in a context specific way. A second key question is whether the updating of priors, or the ability to scale lifting forces when repeatedly lifting unusually weighted objects requires focused attention...
March 17, 2017: Cognition
https://www.readbyqxmd.com/read/28319649/optimization-of-extraction-of-linarin-from-flos-chrysanthemi-indici-by-response-surface-methodology-and-artificial-neural-network
#4
Hongye Pan, Qing Zhang, Keke Cui, Guoquan Chen, Xuesong Liu, Longhu Wang
The extraction of linarin from Flos chrysanthemi indici by ethanol was investigated. Two modeling techniques, response surface methodology and artificial neural network, were adopted to optimize the process parameters, such as, ethanol concentration, extraction period, extraction frequency, and solvent to material ratio. We showed that both methods provided good predictions, but artificial neural network provided a better and more accurate result. The optimum process parameters include, ethanol concentration of 74%, extraction period of 2 h, extraction three times, solvent to material ratio of 12 mL/g...
March 20, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/28319645/the-atypical-genesis-and-bioavailability-of-the-plant-based-small-rna-mir2911-bulking-up-while-breaking-down
#5
Jian Yang, Natee Kongchan, Cecilia Primo Planta, Joel R Neilson, Kendal D Hirschi
SCOPE: The uptake of dietary plant small RNAs (sRNAs) in consumers remains controversial, which is mainly due to low dietary content in combination with poor fractional absorption. MIR2911, among all the plant sRNAs including microRNAs, has been shown to be one of the most robustly absorbed sRNAs. Here we analyze the unusual abundance and unique genesis of MIR2911 during vegetable processing. METHODS AND RESULTS: Using qRT-PCR, the abundance of MIR2911 increased dramatically in macerated tissues while other microRNAs degraded...
March 20, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28319380/evaluation-and-characterization-of-trk-kinase-inhibitors-for-the-treatment-of-pain-reliable-binding-affinity-predictions-from-theory-and-computation
#6
Shunzhou Wan, Agastya P Bhati, Sarah Skerratt, Kiyoyuki Omoto, Veerabahu Shanmugasundaram, Sharan K Bagal, Peter Vivian Coveney
Optimisation of ligand binding affinity to the target protein of interest is a primary objective in small-molecule drug discovery. Until now, the prediction of binding affinities by computational methods has not been widely applied in the drug discovery process, mainly due to its lack of accuracy and reproducibility, as well as the long turnaround times required to obtain results. Herein, we report on a collaborative study that compares tropomyosin receptor kinase A (TrkA) binding affinity predictions using two recently formulated fast computational approaches - namely ESMACS (Enhanced Sampling of Molecular dynamics with Approximation of Continuum Solvent) and TIES (Thermodynamic Integration with Enhanced Sampling) - to experimentally derived TrkA binding affinities for a set of Pfizer pan-Trk compounds...
March 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28319268/developmental-changes-in-feeding-behaviors-of-infant-chimpanzees-at-mahale-tanzania-implications-for-nutritional-independence-long-before-cessation-of-nipple-contact
#7
Takuya Matsumoto
OBJECTIVES: Weaning of chimpanzees is considered to occur at 4-5-years-old with complete cessation of nipple contact and timing of reconception calculated by inter-birth interval minus gestation length. This is also the basis of "early weaning" in humans (i.e., approximately 2.5-years-old). However, recent studies of the survival of orphans and the first molar (M1) eruption in wild chimpanzees have predicted that infants move toward nutritional independence at 3-years-old. Therefore, this study aimed to investigate ontogeny of feeding behavior at around 3-years-old in wild infant chimpanzees...
March 20, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28318972/persistent-single-neuron-activity-during-working-memory-in-the-human-medial-temporal-lobe
#8
Simon Kornblith, Rodrigo Quian Quiroga, Christof Koch, Itzhak Fried, Florian Mormann
Working memory is an essential component of human cognition. Persistent activity related to working memory has been reported in many brain areas, including the inferior temporal and prefrontal cortex [1-8]. The medial temporal lobe (MTL) contains "concept cells" that respond invariantly to specific individuals or places whether presented as images, text, or speech [9, 10]. It is unknown, however, whether the MTL also participates in working memory processes. We thus sought to determine whether human MTL neurons respond to images held in working memory...
March 15, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28318826/modelling-pollutant-emissions-in-diesel-engines-influence-of-biofuel-on-pollutant-formation
#9
Zvonimir Petranović, Tibor Bešenić, Milan Vujanović, Neven Duić
In order to reduce the harmful effect on the environment, European Union allowed using the biofuel blends as fuel for the internal combustion engines. Experimental studies have been carried on, dealing with the biodiesel influence on the emission concentrations, showing inconclusive results. In this paper numerical model for pollutant prediction in internal combustion engines is presented. It describes the processes leading towards the pollutant emissions, such as spray particles model, fuel disintegration and evaporation model, combustion and the chemical model for pollutant formation...
March 16, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28318762/gene-expression-profiling-reveals-genes-and-transcription-factors-associated-with-dilated-and-ischemic-cardiomyopathies
#10
Aiqing Qiao, Zhenying Zhao, Hui Zhang, Zhenyu Sun, Xiao Cui
AIMS: Dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM) can cause heart failure, and this study aims to identify genes and transcription factors (TFs) associated with DCM and ICM. METHODS: Gene expression dataset GSE42955 was generated from GEO database, and it contained 12 DCM, 12 ICM, and 5 control samples. Differentially expressed genes (DEGs) were identified between DCM (or ICM) and controls. Gene functions were investigated, and their associations were analyzed using Enrichmentmap plugin in Cytoscape...
December 29, 2016: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28318643/cxcl10-alters-the-tumour-immune-microenvironment-and-disease-progression-in-a-syngeneic-murine-model-of-high-grade-serous-ovarian-cancer
#11
Katrina K Au, Nichole Peterson, Peter Truesdell, Gillian Reid-Schachter, Kasra Khalaj, Runhan Ren, Julie-Ann Francis, Charles H Graham, Andrew W Craig, Madhuri Koti
OBJECTIVE: We recently established that high STAT1 expression and associated T helper type I tumour immune microenvironment (TME) are prognostic and chemotherapy response predictive biomarkers in high-grade serous ovarian cancer (HGSC). STAT1 induced chemokine CXCL10 is key to the recruitment of lymphocytes in the TME and is significantly highly expressed in the tumours from patients with longer survival. In the current study we therefore aimed to elucidate the role CXCL10 in disease progression and tumour immune transcriptomic alterations using the ID8 syngeneic murine model of HGSC...
March 16, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/28318559/screening-level-risk-assessment-applied-to-dredging-of-polluted-sediments-from-guanabara-bay-rio-de-janeiro-brazil
#12
Ana Elisa F Silveira, Juliana R Nascimento, Elisamara Sabadini-Santos, Edison D Bidone
Guanabara Bay is characterized by predominant eutrophication and anoxic sediments with a mixture of pollutants. The risk prognosis associated with the dumping of its dredged sediments into the open ocean was addressed by our algorithm. Our algorithm could prioritize areas, characterize major processes related to dredging, measure the potential risk of sediments, and predict the effects of sediment mixing. The estimated risk of dredged sediment was >10-fold than that of ocean sediments. Among metals, mercury represented 50-90% of the total risk...
March 16, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/28318468/understanding-adolescent-personality-pathology-from-growth-trajectories-of-childhood-oddity
#13
Barbara De Clercq, Lize Verbeke, Elien De Caluwé, Tom Vercruysse, Joeri Hofmans
Research on developmental trajectories of early maladaptive features for understanding later personality disorders (PDs) is increasingly recognized as an important study area. The course of early odd features is highly relevant in this regard, as only a few researchers have addressed childhood oddity in the context of emerging PDs. Using latent growth modeling, the current study explores growth parameters of odd features in a mixed sample of Flemish community and referred children (N = 485) across three measurement waves with 1-year time intervals...
March 20, 2017: Development and Psychopathology
https://www.readbyqxmd.com/read/28318367/combinatorial-control-of-messenger-rnas-by-pumilio-nanos-and-brain-tumor-proteins
#14
René M Arvola, Chase A Weidmann, Traci M Tanaka Hall, Aaron C Goldstrohm
Eukaryotes possess a vast array of RNA-binding proteins (RBPs) that affect mRNAs in diverse ways to control protein expression. Combinatorial regulation of mRNAs by RBPs is emerging as the rule. No example illustrates this as vividly as the partnership of three Drosophila RBPs, Pumilio, Nanos and Brain Tumor, which have overlapping functions in development, stem cell maintenance and differentiation, fertility and neurological processes. Here we synthesize thirty years of research with new insights into their molecular functions and mechanisms of action...
March 20, 2017: RNA Biology
https://www.readbyqxmd.com/read/28318336/are-tumor-infiltrating-lymphocytes-protagonists-or-background-actors-in-patient-selection-for-cancer-immunotherapy
#15
Federica Zito Marino, Paolo Antonio Ascierto, Giulio Rossi, Stefania Staibano, Marco Montella, Daniela Russo, Roberto Alfano, Alessandro Morabito, Gerardo Botti, Renato Franco
Tumor-infiltrating lymphocytes (TILs) are frequently observed in several tumors, reflecting the dynamic process of ''cancer immunoediting''. Prognostic and predictive values of TILs have been demonstrated in different cancers, proving their pivotal role in clinical outcome. In recent years, new therapies targeting immune checkpoint inhibitors, especially CTLA-4 and PD-1/PDL-1 pathways, have been introduced into clinical practice. In this context, TILs may even have a possible utility as a predictive biomarker for immunotherapy response...
March 20, 2017: Expert Opinion on Biological Therapy
https://www.readbyqxmd.com/read/28318265/cytoskeletal-like-filaments-of-camkii-are-formed-in-a-regulated-and-zn2-dependent-manner
#16
Laurel Hoffman, Lin Li, Emil Alexov, Hugo Sanabria, Melvin Neal Waxham
Ca2+-Calmodulin-dependent protein kinase II (CaMKII) is highly abundant in neurons, where its concentration reaches that typically found for cytoskeletal proteins. Functional reasons for such a high concentration are not known, but given the multitude of known binding partners for CaMKII, a role as a scaffolding molecule has been proposed. In this report, we provide experimental evidence that demonstrates a novel structural role for CaMKII. We discovered that CaMKII forms filaments that can extend for several microns in the presence of certain divalent cations (Zn2+, Cd2+ and Cu2+) but not with others (Ca2+, Mg2+, Co2+ and Ni2+)...
March 20, 2017: Biochemistry
https://www.readbyqxmd.com/read/28318252/molecular-dynamics-in-mixed-solvents-reveals-protein-ligand-interactions-improves-docking-and-allows-accurate-binding-free-energy-predictions
#17
Juan Pablo Arcon, Lucas A Alfredo Defelipe, Carlos Pablo Modenutti, Elias Daniel Lopez, Daniel Alvarez-Garcia, Xavier Barril, Adrian Gustavo Turjanski, Marcelo A Marti
One of the most important biological processes at the molecular level is the formation of protein-ligand complexes. Therefore, determining their structure and underlying key interactions is of paramount relevance and has direct applications in drug development. Due to its low cost relative to its experimental sibling, Molecular Dynamics (MD) simulations in the presence of different solvent probes mimicking specific type of interactions have been increasingly used to analyze protein binding sites and reveal protein-ligand interaction hot spots...
March 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28318028/study-of-the-cold-charge-transfer-state-separation-at-the-tq1-pc71-bm-interface
#18
Riccardo Volpi, Mathieu Linares
Charge transfer (CT) state separation is one of the most critical processes in the functioning of an organic solar cell. In this article, we study a bilayer of TQ1 and PC71 BM molecules presenting disorder at the interface, obtained by means of Molecular Dynamics. The study of the CT state splitting can be first analyzed through the CT state splitting diagram, introduced in a previous work. Through this analysis, we identify the possibility of CT state splitting within Marcus Theory in function of the electric field...
March 20, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28318023/therapeutic-disasters-that-hastened-safety-testing-of-new-drugs
#19
EDITORIAL
M F Paine
New drugs were not required to undergo premarket safety testing in the United States until 1938, when a therapeutic disaster-the Elixir Sulfanilamide tragedy-prompted Congress to pass a bill mandating this now-routine process. History repeated itself nearly 25 years later, when another therapeutic disaster-the thalidomide tragedy-led to passage of new amendments in 1962 to ensure drug efficacy and greater drug safety. As is typical with historical events, critical information was gained that led to novel approaches for understanding, predicting, diagnosing, and managing drug-induced toxicities...
April 2017: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/28317947/parietal-operculum-and-motor-cortex-activities-predict-motor-recovery-in-moderate-to-severe-stroke
#20
Firdaus Fabrice Hannanu, Thomas A Zeffiro, Laurent Lamalle, Olivier Heck, Félix Renard, Antoine Thuriot, Alexandre Krainik, Marc Hommel, Olivier Detante, Assia Jaillard
While motor recovery following mild stroke has been extensively studied with neuroimaging, mechanisms of recovery after moderate to severe strokes of the types that are often the focus for novel restorative therapies remain obscure. We used fMRI to: 1) characterize reorganization occurring after moderate to severe subacute stroke, 2) identify brain regions associated with motor recovery and 3) to test whether brain activity associated with passive movement measured in the subacute period could predict motor outcome six months later...
2017: NeuroImage: Clinical
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