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https://www.readbyqxmd.com/read/27936518/computational-investigation-of-proton-transfer-pka-shifts-and-ph-optimum-of-protein-dna-and-protein-rna-complexes
#1
Yunhui Peng, Emil Alexov
Protein-nucleic acid interactions play a crucial role in many biological processes. This work investigates the changes of pKa values and protonation states of ionizable groups (including nucleic acid bases) that may occur at protein-nucleic acid binding. Taking advantage of the recently developed pKa calculation tool DelphiPka, we utilize the large protein-nucleic acid interaction database (NPIDB database) to model pKa shifts caused by binding. It has been found that the protein's interfacial basic residues experience favorable electrostatic interactions while the protein acidic residues undergo proton uptake to reduce the energy cost upon the binding...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936407/sentence-context-influences-the-subjective-perception-of-foreign-accents
#2
Sara Incera, Amee P Shah, Conor T McLennan, Matthew T Wetzel
We examined whether sentence context (the predictability of the final word) influences listeners' ratings of foreign-accented words. Previous work has demonstrated that accent manipulations affect listeners' processing of spoken language. We examined the converse of this relationship; whether context manipulations affect listeners' perceptions of accents. If there is a bidirectional relationship, listeners should be more likely to rate an accent as strong when the accented word is not predicted by the sentence...
December 6, 2016: Acta Psychologica
https://www.readbyqxmd.com/read/27936277/algorithm-driven-dosage-decisions-ad3-optimizing-treatment-for-children-with-language-impairment
#3
Laura M Justice, Jessica Logan, Hui Jiang, Mary Beth Schmitt
Background: This study was designed to provide recommended amounts of treatment to achieve the optimal amount of language gain for children with language impairment. Method: The authors retrospectively analyzed treatment outcomes for 233 children for delivered dose, intensity, and cumulative intensity of therapy. The steps of the analytical process they applied to arrive at algorithms for recommended amounts of treatment were (1) multilevel modeling to predict children's language gains from the 3 intensity parameters and (2) extraction of regression weights to create a recommended amount of treatment...
December 9, 2016: American Journal of Speech-language Pathology
https://www.readbyqxmd.com/read/27936217/quantum-decision-theory-in-simple-risky-choices
#4
Maroussia Favre, Amrei Wittwer, Hans Rudolf Heinimann, Vyacheslav I Yukalov, Didier Sornette
Quantum decision theory (QDT) is a recently developed theory of decision making based on the mathematics of Hilbert spaces, a framework known in physics for its application to quantum mechanics. This framework formalizes the concept of uncertainty and other effects that are particularly manifest in cognitive processes, which makes it well suited for the study of decision making. QDT describes a decision maker's choice as a stochastic event occurring with a probability that is the sum of an objective utility factor and a subjective attraction factor...
2016: PloS One
https://www.readbyqxmd.com/read/27936148/screening-for-dyslexia-using-eye-tracking-during-reading
#5
Mattias Nilsson Benfatto, Gustaf Öqvist Seimyr, Jan Ygge, Tony Pansell, Agneta Rydberg, Christer Jacobson
Dyslexia is a neurodevelopmental reading disability estimated to affect 5-10% of the population. While there is yet no full understanding of the cause of dyslexia, or agreement on its precise definition, it is certain that many individuals suffer persistent problems in learning to read for no apparent reason. Although it is generally agreed that early intervention is the best form of support for children with dyslexia, there is still a lack of efficient and objective means to help identify those at risk during the early years of school...
2016: PloS One
https://www.readbyqxmd.com/read/27936127/interactions-between-thermal-acclimation-growth-rate-and-phylogeny-influence-prochlorococcus-elemental-stoichiometry
#6
Adam C Martiny, Lanying Ma, Céline Mouginot, Jeremy W Chandler, Erik R Zinser
Variability in plankton elemental requirements can be important for global ocean biogeochemistry but we currently have a limited understanding of how ocean temperature influences the plankton C/N/P ratio. Multiple studies have put forward a 'translation-compensation' hypothesis to describe the positive relationship between temperature and plankton N/P or C/P as cells should have lower demand for P-rich ribosomes and associated depressed QP when growing at higher temperature. However, temperature affects many cellular processes beyond translation with unknown outcomes on cellular elemental composition...
2016: PloS One
https://www.readbyqxmd.com/read/27936097/petmbase-a-database-of-plant-endogenous-target-mimics-etms
#7
Gökhan Karakülah, Kuaybe Yücebilgili Kurtoğlu, Turgay Unver
MicroRNAs (miRNA) are small endogenous RNA molecules, which regulate target gene expression at post-transcriptional level. Besides, miRNA activity can be controlled by a newly discovered regulatory mechanism called endogenous target mimicry (eTM). In target mimicry, eTMs bind to the corresponding miRNAs to block the binding of specific transcript leading to increase mRNA expression. Thus, miRNA-eTM-target-mRNA regulation modules involving a wide range of biological processes; an increasing need for a comprehensive eTM database arose...
2016: PloS One
https://www.readbyqxmd.com/read/27935944/novel-and-lost-forests-in-the-upper-midwestern-united-states-from-new-estimates-of-settlement-era-composition-stem-density-and-biomass
#8
Simon J Goring, David J Mladenoff, Charles V Cogbill, Sydne Record, Christopher J Paciorek, Stephen T Jackson, Michael C Dietze, Andria Dawson, Jaclyn Hatala Matthes, Jason S McLachlan, John W Williams
BACKGROUND: EuroAmerican land-use and its legacies have transformed forest structure and composition across the United States (US). More accurate reconstructions of historical states are critical to understanding the processes governing past, current, and future forest dynamics. Here we present new gridded (8x8km) reconstructions of pre-settlement (1800s) forest composition and structure from the upper Midwestern US (Minnesota, Wisconsin, and most of Michigan), using 19th Century Public Land Survey System (PLSS), with estimates of relative composition, above-ground biomass, stem density, and basal area for 28 tree types...
2016: PloS One
https://www.readbyqxmd.com/read/27935835/robust-extracellular-ph-modulation-by-candida-albicans-during-growth-in-carboxylic-acids
#9
Heather A Danhof, Slavena Vylkova, Elisa M Vesely, Amy E Ford, Manuel Gonzalez-Garay, Michael C Lorenz
: The opportunistic fungal pathogen Candida albicans thrives within diverse niches in the mammalian host. Among the adaptations that underlie this fitness is an ability to utilize a wide array of nutrients, especially sources of carbon that are disfavored by many other fungi; this contributes to its ability to survive interactions with the phagocytes that serve as key barriers against disseminated infections. We have reported that C. albicans generates ammonia as a byproduct of amino acid catabolism to neutralize the acidic phagolysosome and promote hyphal morphogenesis in a manner dependent on the Stp2 transcription factor...
November 15, 2016: MBio
https://www.readbyqxmd.com/read/27935726/automatic-avoidance-tendencies-for-alcohol-cues-predict-drinking-after-detoxification-treatment-in-alcohol-dependence
#10
Matt Field, Lisa Di Lemma, Paul Christiansen, Joanne Dickson
Alcohol dependence is characterized by conflict between approach and avoidance motivational orientations for alcohol that operate in automatic and controlled processes. This article describes the first study to investigate the predictive validity of these motivational orientations for relapse to drinking after discharge from alcohol detoxification treatment in alcohol-dependent patients. One hundred twenty alcohol-dependent patients who were nearing the end of inpatient detoxification treatment completed measures of self-reported (Approach and Avoidance of Alcohol Questionnaire; AAAQ) and automatic (modified Stimulus-Response Compatibility task) approach and avoidance motivational orientations for alcohol...
December 1, 2016: Psychology of Addictive Behaviors: Journal of the Society of Psychologists in Addictive Behaviors
https://www.readbyqxmd.com/read/27935692/dynamic-and-electrostatic-effects-on-the-reaction-catalyzed-by-hiv-1-protease
#11
Agnieszka Krzemińska, Vicent Moliner, Katarzyna Świderek
HIV-1 Protease (HIV-1 PR) is one of the three enzymes essential for the replication process of HIV-1 virus, which explains why it has been the main target for design of drugs against acquired immunodeficiency syndrome (AIDS). This work is focused on exploring the proteolysis reaction catalyzed by HIV-1 PR, with special attention to the dynamic and electrostatic effects governing its catalytic power. Free energy surfaces for all possible mechanisms have been computed in terms of potentials of mean force (PMFs) within hybrid QM/MM potentials, with the QM subset of atoms described at semiempirical (AM1) and DFT (M06-2X) level...
December 9, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27935683/structural-regulation-of-pdcu2-nanoparticles-and-their-electrocatalytic-performance-for-ethanol-oxidation
#12
Jing Xue, Guangting Han, Wanneng Ye, Yutao Sang, Hongliang Li, Peizhi Guo, X S Zhao
Two types of PdCu2 nanoparticles were prepared through one-pot synthesis and a two-step reducing process, named as PdCu2-1 and PdCu2-2, respectively. The morphology and structure of as-prepared samples were investigated by transmission electron microscopy, high-resolution transmission electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy, and inductively coupled plasma-optical emission spectrometry. Results showed that more Pd atoms were buried in the inside of PdCu2-1, whereas more available Pd sites were distributed on the surface of PdCu2-2...
December 9, 2016: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/27935640/the-basis-function-approach-for-modeling-autocorrelation-in-ecological-data
#13
Trevor J Hefley, Kristin M Broms, Brian M Brost, Frances E Buderman, Shannon L Kay, Henry R Scharf, John R Tipton, Perry J Williams, Mevin B Hooten
Analyzing ecological data often requires modeling the autocorrelation created by spatial and temporal processes. Many seemingly disparate statistical methods used to account for autocorrelation can be expressed as regression models that include basis functions. Basis functions also enable ecologists to modify a wide range of existing ecological models in order to account for autocorrelation, which can improve inference and predictive accuracy.Furthermore, understanding the properties of basis functions is essential for evaluating the fit of spatial or time-series models, detecting a hidden form of collinearity, and analyzing large data sets...
December 9, 2016: Ecology
https://www.readbyqxmd.com/read/27935592/molecular-insights-into-a-dinoflagellate-bloom
#14
Weida Gong, Jamie Browne, Nathan Hall, David Schruth, Hans Paerl, Adrian Marchetti
In coastal waters worldwide, an increase in frequency and intensity of algal blooms has been attributed to eutrophication, with further increases predicted because of climate change. Yet, the cellular-level changes that occur in blooming algae remain largely unknown. Comparative metatranscriptomics was used to investigate the underlying molecular mechanisms associated with a dinoflagellate bloom in a eutrophied estuary. Here we show that under bloom conditions, there is increased expression of metabolic pathways indicative of rapidly growing cells, including energy production, carbon metabolism, transporters and synthesis of cellular membrane components...
December 9, 2016: ISME Journal
https://www.readbyqxmd.com/read/27935316/rapid-synthesis-of-sub-5-nm-sized-cubic-boron-nitride-nanocrystals-with-high-piezoelectric-behavior-via-electrochemical-shock
#15
Zhigang Chen, Lianhui Li, Shan Cong, Jinnan Xuan, Dengsong Zhang, Fengxia Geng, Ting Zhang, Zhigang Zhao
A key challenge in current superhard materials research is the design of novel superhard nanocrystals (NCs) whereby new and unexpected properties may be predicted. Cubic boron nitride (c-BN) is a superhard material which ranks next to diamond; however, downsizing c-BN material below the 10 nm scale is rather challenging, and the interesting new properties of c-BN NCs remain unexplored and wide open. Herein we report an electrochemical shock method to prepare uniform c-BN NCs with a lateral size of only 3.4 ± 0...
December 9, 2016: Nano Letters
https://www.readbyqxmd.com/read/27935297/probing-the-soft-and-nanoductile-mechanical-nature-of-single-and-polycrystalline-organic-inorganic-hybrid-perovskites-for-flexible-functional-devices
#16
Jingui Yu, Mingchao Wang, Shangchao Lin
Although organic-inorganic hybrid perovskites have been extensively investigated for promising applications in energy-related devices, their mechanical properties, which restrict their practical deployment as flexible and wearable devices, have been largely unexplored at the atomistic level. Toward this level of understanding, we predict the elastic constant matrix and various elastic properties of CH3NH3PbI3 (MAPbI3) using atomistic simulations. We find that single-crystalline MAPbI3 is much stiffer and exhibits higher ultimate tensile strength than polycrystalline samples, but the latter exhibit unexpected, greatly enhanced nanoductility and fracture toughness, resulting from the extensive amorphization during the yielding process...
December 9, 2016: ACS Nano
https://www.readbyqxmd.com/read/27935083/endometrial-cancer-risk-prediction-including-serum-based-biomarkers-results-from-the-epic-cohort
#17
Renée T Fortner, Anika Hüsing, Tilman Kühn, Meric Konar, Kim Overvad, Anne Tjønneland, Louise Hansen, Marie-Christine Boutron-Ruault, Gianluca Severi, Agnès Fournier, Heiner Boeing, Antonia Trichopoulou, Vasiliki Benetou, Philippos Orfanos, Giovanna Masala, Claudia Agnoli, Amalia Mattiello, Rosario Tumino, Carlotta Sacerdote, H B As Bueno-de-Mesquita, Petra H M Peeters, Elisabete Weiderpass, Inger T Gram, Oxana Gavrilyuk, J Ramón Quirós, José Maria Huerta, Eva Ardanaz, Nerea Larrañaga, Leila Lujan-Barroso, Emilio Sánchez-Cantalejo, Salma Tunå Butt, Signe Borgquist, Annika Idahl, Eva Lundin, Kay-Tee Khaw, Naomi E Allen, Sabina Rinaldi, Laure Dossus, Marc Gunter, Melissa A Merritt, Ioanna Tzoulaki, Elio Riboli, Rudolf Kaaks
Endometrial cancer risk prediction models including lifestyle, anthropometric, and reproductive factors have limited discrimination. Adding biomarker data to these models may improve predictive capacity; to our knowledge, this has not been investigated for endometrial cancer. Using a nested case-control study within the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort, we investigated the improvement in discrimination gained by adding serum biomarker concentrations to risk estimates derived from an existing risk prediction model based on epidemiologic factors...
December 9, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27935034/integrated-analysis-and-microrna-expression-profiling-identified-seven-mirnas-associated-with-progression-of-oral-squamous-cell-carcinoma
#18
Zhong-Yi Yan, Zhi-Qing Luo, Lai-Jian Zhang, Jia Li, Jia-Qiang Liu
MicroRNAs have been used as diagnostic and prognostic biomarkers for many cancers including oral squamous cell carcinoma (OSCC). Several studies have been shown that microRNA (miRNA) play important roles during the progression of OSCC. However, the results vary largely in different studies due to different platforms and sample sizes. In this study, we systematically evaluated a large scale of miRNA profiles from current qualified OSCC samples, and further investigated the functions of genes regulated by these key miRNAs as well as the signaling pathways through which these miRNA effect carcinogenesis...
December 9, 2016: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/27934638/comparative-evaluation-of-dehydroepiandrosterone-sulfate-dheas-potential-to-predict-hepatic-oatp-transporter-based-drug-drug-interactions
#19
Kei Nishizawa, Takeo Nakanishi, Ikumi Tamai
Pharmacokinetic drug-drug interactions (DDIs) on hepatic organic anion transporting polypeptides (OATPs) are important clinical issues. Previously we reported that plasma dehydroepiandrosterone sulfate (DHEAS) could serve as an endogenous probe to predict OATP-based DDIs in monkeys using rifampicin as an OATP inhibitor. However, since the contribution of hepatic OATPs to the changes of plasma DHEAS by rifampicin remains unclear, here, we evaluated by an in vivo pharmacokinetic study. Since plasma DHEAS concentrations were unexpectedly low in our rat model, disposition of externally administered DHEAS was evaluated...
December 1, 2016: Drug Metabolism and Disposition: the Biological Fate of Chemicals
https://www.readbyqxmd.com/read/27934172/crystal-engineering-for-low-defect-density-and-high-efficiency-hybrid-chemical-vapor-deposition-grown-perovskite-solar-cells
#20
Annie Ng, Zhiwei Ren, Qian Shen, Sin Hang Cheung, Huseyin Cem Gokkaya, Shu Kong So, Aleksandra B Djurišić, Yangyang Wan, Xiaojun Wu, Charles Surya
Synthesis of high quality perovskite absorber is a key factor in determining the performance of the solar cells. We demonstrate that hybrid chemical vapor deposition (HCVD) growth technique can provide high level of versatility and repeatability to ensure the optimal conditions for the growth of the perovskite films as well as potential for batch processing. It is found that the growth ambient and degree of crystallization of CH3NH3PbI3 (MAPI) have strong impact on the defect density of MAPI. We demonstrate that HCVD process with slow postdeposition cooling rate can significantly reduce the density of shallow and deep traps in the MAPI due to enhanced material crystallization, while a mixed O2/N2 carrier gas is effective in passivating both shallow and deep traps...
December 7, 2016: ACS Applied Materials & Interfaces
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