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https://www.readbyqxmd.com/read/27914055/an-evolution-based-approach-to-de-novo-protein-design
#1
Jeffrey R Brender, David Shultis, Naureen Aslam Khattak, Yang Zhang
EvoDesign is a computational algorithm that allows the rapid creation of new protein sequences that are compatible with specific protein structures. As such, it can be used to optimize protein stability, to resculpt the protein surface to eliminate undesired protein-protein interactions, and to optimize protein-protein binding. A major distinguishing feature of EvoDesign in comparison to other protein design programs is the use of evolutionary information in the design process to guide the sequence search toward native-like sequences known to adopt structurally similar folds as the target...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914048/geometric-potentials-for-computational-protein-sequence-design
#2
Jie Li, Patrice Koehl
Computational protein sequence design is the rational design based on computer simulation of new protein molecules to fold to target three-dimensional structures, with the ultimate goal of designing novel functions. It requires a good understanding of the thermodynamic equilibrium properties of the protein of interest. Here, we consider the contribution of the solvent to the stability of the protein. We describe implicit solvent models, focusing on approximations of their nonpolar components using geometric potentials...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913928/coordination-complexes-of-4-methylimidazole-with-zn-ii-and-cu-ii-in-gas-phase-and-in-water-a-dft-study
#3
Malek Boukallaba, Boutheïna Kerkeni, Christine Lepetit, Dorothée Berthomieu
A quantum chemistry study of mononuclear metal coordination with four 4-methylimidazole ligands (4-MeIm) was investigated. The four complexes [Cu(4-MeIm)4](2+), [Cu(4-MeIm)4, H2O](2+), [Zn(4-MeIm)4](2+) and [Zn(4-MeIm)4, H2O](2+) were studied with particular attention to the Nπ or Nτ possible coordinations of the 4-MeIm ring with the metals, using different DFT methods. The results suggest that the Nτ coordination of 4-MeIm ring to Zn(II) or Cu(II) is more favorable whatever the level of calculation. In contrast, the addition of one water molecule in the first coordination sphere of the metal ions provides five-coordinated complexes showing no Nπ or Nτ preferences...
December 2016: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/27911892/authorization-of-animal-experiments-is-based-on-confidence-rather-than-evidence-of-scientific-rigor
#4
Lucile Vogt, Thomas S Reichlin, Christina Nathues, Hanno Würbel
Accumulating evidence indicates high risk of bias in preclinical animal research, questioning the scientific validity and reproducibility of published research findings. Systematic reviews found low rates of reporting of measures against risks of bias in the published literature (e.g., randomization, blinding, sample size calculation) and a correlation between low reporting rates and inflated treatment effects. That most animal research undergoes peer review or ethical review would offer the possibility to detect risks of bias at an earlier stage, before the research has been conducted...
December 2016: PLoS Biology
https://www.readbyqxmd.com/read/27909466/illusory-temporal-binding-in-meditators
#5
Peter Lush, Jim Parkinson, Zoltan Dienes
We investigate conditions in which more accurate metacognition may lead to greater susceptibility to illusion and thus conditions under which mindfulness meditation may lead to less accurate perceptions. Specifically, greater awareness of intentions may lead to an illusory compression of time between a voluntary action and its outcome ("intentional binding"). Here, we report that experienced Buddhist mindfulness meditators rather than non-meditators display a greater illusory shift of the timing of an outcome toward an intentional action...
2016: Mindfulness
https://www.readbyqxmd.com/read/27909401/implicit-learning-in-transient-global-amnesia-and-the-role-of-stress
#6
Frauke Nees, Martin Griebe, Anne Ebert, Michaela Ruttorf, Benjamin Gerber, Oliver T Wolf, Lothar R Schad, Achim Gass, Kristina Szabo
Transient global amnesia (TGA) is a disorder with reversible anterograde disturbance of explicit memory, frequently preceded by an emotionally or physically stressful event. By using magnetic resonance imaging (MRI) following an episode of TGA, small hippocampal lesions have been observed. Hence it has been postulated that the disorder is caused by the stress-related transient inhibition of memory formation in the hippocampus. In experimental studies, stress has been shown to affect both explicit and implicit learning-the latter defined as learning and memory processes that lack conscious awareness of the information acquired...
2016: Frontiers in Behavioral Neuroscience
https://www.readbyqxmd.com/read/27908145/electrolyte-decomposition-on-li-metal-surfaces-from-first-principles-theory
#7
Mahsa Ebadi, Daniel Brandell, C Moyses Araujo
An important feature in Li batteries is the formation of a solid electrolyte interphase (SEI) on the surface of the anode. This film can have a profound effect on the stability and the performance of the device. In this work, we have employed density functional theory combined with implicit solvation models to study the inner layer of SEI formation from the reduction of common organic carbonate electrolyte solvents (ethylene carbonate, propylene carbonate, dimethyl carbonate, and diethyl carbonate) on a Li metal anode surface...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27908017/symmetry-restoring-bifurcations-and-quasiperiodic-chaos-induced-by-a-new-intermittency-in-a-vibro-impact-system
#8
Yuan Yue, Pengcheng Miao, Jianhua Xie, Grebogi Celso
Quasiperiodic chaos (QC), which is a combination of quasiperiodic sets and a chaotic set, is uncovered in the six dimensional Poincaré map of a symmetric three-degree of freedom vibro-impact system. Accompanied by symmetry restoring bifurcation, this QC is the consequence of a novel intermittency that occurs between two conjugate quasiperiodic sets and a chaotic set. The six dimensional Poincaré map P is the 2-fold composition of another virtual implicit map Q, yielding the symmetry of the system. Map Q can capture two conjugate attractors, which is at the core of the dynamics of the vibro-impact system...
November 2016: Chaos
https://www.readbyqxmd.com/read/27907879/language-production-in-a-shared-task-cumulative-semantic-interference-from-self-and-other-produced-context-words
#9
Renske S Hoedemaker, Jessica Ernst, Antje S Meyer, Eva Belke
This study assessed the effects of semantic context in the form of self-produced and other-produced words on subsequent language production. Pairs of participants performed a joint picture naming task, taking turns while naming a continuous series of pictures. In the single-speaker version of this paradigm, naming latencies have been found to increase for successive presentations of exemplars from the same category, a phenomenon known as Cumulative Semantic Interference (CSI). As expected, the joint-naming task showed a within-speaker CSI effect, such that naming latencies increased as a function of the number of category exemplars named previously by the participant (self-produced items)...
November 28, 2016: Acta Psychologica
https://www.readbyqxmd.com/read/27906526/statistical-learning-a-powerful-mechanism-that-operates-by-mere-exposure
#10
REVIEW
Richard N Aslin
How do infants learn so rapidly and with little apparent effort? In 1996, Saffran, Aslin, and Newport reported that 8-month-old human infants could learn the underlying temporal structure of a stream of speech syllables after only 2 min of passive listening. This demonstration of what was called statistical learning, involving no instruction, reinforcement, or feedback, led to dozens of confirmations of this powerful mechanism of implicit learning in a variety of modalities, domains, and species. These findings reveal that infants are not nearly as dependent on explicit forms of instruction as we might have assumed from studies of learning in which children or adults are taught facts such as math or problem solving skills...
December 1, 2016: Wiley Interdisciplinary Reviews. Cognitive Science
https://www.readbyqxmd.com/read/27906288/eigen-energy-effects-and-non-orthogonality-in-the-quasi-normal-mode-expansion-of-maxwell-equations
#11
Mathias Perrin
We derive a quasi-normal mode theory for three-dimensional scatterers, taking care to remove an hypothesis of weakly dispersive materials implicitely used in previous works. In our approach, the normalized modes remain unchanged, but the analytic expansion coefficients onto the set of QNM are modified. In particular, we take into account in a simple way the non-orthogonality of the modes, and we set up a rigourous frame, to treat the case where several QNMs are excited. Eventally, the complex concept of PML integration, previously introduced, becomes unnecessary, even to compute the QNM mode volume...
November 28, 2016: Optics Express
https://www.readbyqxmd.com/read/27906266/a-population-based-approach-to-point-sampling-spatial-color-algorithms
#12
Gabriele Gianini, Michela Lecca, Alessandro Rizzi
Inspired by the behavior of the human visual system, spatial color algorithms perform image enhancement by correcting the pixel channel lightness based on the spatial distribution of the intensities in the surrounding area. The two visual contrast enhancement algorithms RSR and STRESS belong to this family of models: they rescale the input based on local reference values, which are determined by exploring the image by means of random point samples, called sprays. Due to the use of sampling, they may yield a noisy output...
December 1, 2016: Journal of the Optical Society of America. A, Optics, Image Science, and Vision
https://www.readbyqxmd.com/read/27902832/association-of-irritability-and-anxiety-with-the-neural-mechanisms-of-implicit-face-emotion-processing-in-youths-with-psychopathology
#13
Joel Stoddard, Wan-Ling Tseng, Pilyoung Kim, Gang Chen, Jennifer Yi, Laura Donahue, Melissa A Brotman, Kenneth E Towbin, Daniel S Pine, Ellen Leibenluft
Importance: Psychiatric comorbidity complicates clinical care and confounds efforts to elucidate the pathophysiology of commonly occurring symptoms in youths. To our knowledge, few studies have simultaneously assessed the effect of 2 continuously distributed traits on brain-behavior relationships in children with psychopathology. Objective: To determine shared and unique effects of 2 major dimensions of child psychopathology, irritability and anxiety, on neural responses to facial emotions during functional magnetic resonance imaging...
November 30, 2016: JAMA Psychiatry
https://www.readbyqxmd.com/read/27900585/divided-attention-reduces-resistance-to-distraction-at-encoding-but-not-retrieval
#14
Jennifer C Weeks, Lynn Hasher
Older adults show implicit memory for previously seen distraction, an effect attributed to poor attentional control. It is unclear whether this effect results from lack of control over encoding during the distraction task, lack of retrieval constraint during the test task, or both. In the present study, we simulated poor distraction control in young adults using divided attention at encoding, at retrieval, at both times, or not at all. The encoding task was a 1-back task on pictures with distracting superimposed letter strings, some of which were words...
November 29, 2016: Psychonomic Bulletin & Review
https://www.readbyqxmd.com/read/27898705/the-role-of-the-amygdala-in-facial-trustworthiness-processing-a-systematic-review-and-meta-analyses-of-fmri-studies
#15
Sara Santos, Inês Almeida, Bárbara Oliveiros, Miguel Castelo-Branco
BACKGROUND: Faces play a key role in signaling social cues such as signals of trustworthiness. Although several studies identify the amygdala as a core brain region in social cognition, quantitative approaches evaluating its role are scarce. OBJECTIVES: This review aimed to assess the role of the amygdala in the processing of facial trustworthiness, by analyzing its amplitude BOLD response polarity to untrustworthy versus trustworthy facial signals under fMRI tasks through a Meta-analysis of effect sizes (MA)...
2016: PloS One
https://www.readbyqxmd.com/read/27898381/error-bounded-and-feature-preserving-surface-remeshing-with-minimal-angle-improvement
#16
Kaimo Hu, Dong-Ming Yan, David Bommes, Pierre Alliez, Bedrich Benes
The typical goal of surface remeshing consists in finding a mesh that is (1) geometrically faithful to the original geometry, (2) as coarse as possible to obtain a low-complexity representation and (3) free of bad elements that would hamper the desired application. In this paper, we design an algorithm to address all three optimization goals simultaneously. The user specifies desired bounds on approximation error , minimal interior angle and maximum mesh complexity N (number of vertices). Since such a desired mesh might not even exist, our optimization framework treats only the approximation error bound as a hard constraint and the other two criteria as optimization goals...
November 24, 2016: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/27896539/why-health-and-social-care-support-for-people-with-long-term-conditions-should-be-oriented-towards-enabling-them-to-live-well
#17
Vikki A Entwistle, Alan Cribb, John Owens
There are various reasons why efforts to promote "support for self-management" have rarely delivered the kinds of sustainable improvements in healthcare experiences, health and wellbeing that policy leaders internationally have hoped for. This paper explains how the basis of failure is in some respects built into the ideas that underpin many of these efforts. When (the promotion of) support for self-management is narrowly oriented towards educating and motivating patients to adopt the behaviours recommended for disease control, it implicitly reflects and perpetuates limited and somewhat instrumental views of patients...
November 28, 2016: Health Care Analysis: HCA: Journal of Health Philosophy and Policy
https://www.readbyqxmd.com/read/27895607/caffeine-enhances-memory-performance-in-young-adults-during-their-non-optimal-time-of-day
#18
Stephanie M Sherman, Timothy P Buckley, Elsa Baena, Lee Ryan
Many college students struggle to perform well on exams in the early morning. Although students drink caffeinated beverages to feel more awake, it is unclear whether these actually improve performance. After consuming coffee (caffeinated or decaffeinated), college-age adults completed implicit and explicit memory tasks in the early morning and late afternoon (Experiment 1). During the morning, participants ingesting caffeine demonstrated a striking improvement in explicit memory, but not implicit memory. Caffeine did not alter memory performance in the afternoon...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27894467/association-between-hair-cortisol-concentration-and-perceived-stress-in-female-methamphetamine-addicts
#19
Liuna Geng, Peng Xiang, Jin Yang, Hui Shen, Zhiqin Sang
OBJECTIVE: The present study aims to explore whether hair cortisol concentration is associated with explicit stress or implicit stress in female methamphetamine addicts. METHODS: Hair samples were collected from 51 female methamphetamine addicts from inpatient addiction treatment programs. Perceived stress was assessed by both explicit and implicit measures through the Perceived Stress Scale (PSS) and the Implicit Association Test (IAT), respectively. RESULTS: The positive relationship between hair cortisol concentration with D-scores of the IAT reached statistically significant difference...
December 2016: Journal of Psychosomatic Research
https://www.readbyqxmd.com/read/27894378/an-experimental-approach-to-linguistic-representation
#20
Holly P Branigan, Martin J Pickering
Within the cognitive sciences, most researchers assume that it is the job of linguists to investigate how language is represented, and that they do so largely by building theories based on explicit judgments about patterns of acceptability - whereas it is the task of psychologists to determine how language is processed, and that in doing so, they do not typically question the linguists' representational assumptions. We challenge this division of labor, by arguing that structural priming provides an implicit method of investigating linguistic representations that should end the current reliance on acceptability judgments...
November 29, 2016: Behavioral and Brain Sciences
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