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Recent advances in machine learning techniques have led to development of a number of protein design and engineering approaches. One of them, ProteinMPNN, predicts an amino acid sequence that would fold and match user‐defined backbone structure. Its performance was previously tested for proteins composed of standard amino acids, as well as for peptide‐ and protein‐binding proteins. In this short report, we test whether ProteinMPNN can be used to reengineer a non‐proteinaceous ligand‐binding protein, flavin‐based fluorescent protein CagFbFP. We fixed the native backbone conformation and the identity of 20 amino acids interacting with the chromophore (flavin mononucleotide, FMN) while letting ProteinMPNN predict the rest of the sequence. The software package suggested replacing 36–48 out of the remaining 86 amino acids so that the resulting sequences are 55%–66% identical to the original one. The three designs that we tested experimentally displayed different expression levels, yet all were able to bind FMN and displayed fluorescence, thermal stability, and other properties similar to those of CagFbFP. Our results demonstrate that ProteinMPNN can be used to generate diverging unnatural variants of fluorescent proteins, and, more generally, to reengineer proteins without losing their ligand‐binding capabilities. [ABSTRACT FROM AUTHOR]

Flavins such as flavin mononucleotide or flavin adenine dinucleotide are bound by diverse proteins, yet have very similar spectra when in the oxidized state. Recently, we developed new variants of flavin‐binding protein CagFbFP exhibiting notable blue (Q148V) or red (I52V A85Q) shifts of fluorescence emission maxima. Here, we use time‐resolved and low‐temperature spectroscopy to show that whereas the chromophore environment is static in Q148V, an additional protein‐flavin hydrogen bond is formed upon photoexcitation in the I52V A85Q variant. Consequently, in Q148V, excitation, emission, and phosphorescence spectra are shifted, whereas in I52V A85Q, excitation and low‐temperature phosphorescence spectra are relatively unchanged, while emission spectrum is altered. We also determine the x‐ray structures of the two variants to reveal the flavin environment and complement the spectroscopy data. Our findings illustrate two distinct color‐tuning mechanisms of flavin‐binding proteins and could be helpful for the engineering of new variants with improved optical properties. [ABSTRACT FROM AUTHOR]

STAC-A2™ is a compute and memory intensive industry benchmark in the field of market risk analysis. The benchmark specifications were created by the Securities Technology Analysis Center (STAC®), and are based on the inputs collected from the leading trading companies, universities, and high performance computing vendors. The specifications describe models that represent realistic market risk analysis workloads. In this paper, we discuss the development steps that lead to the competitive performance of the STAC-A2 benchmark executed on systems consisting of Intel® Xeon® processors and an Intel® Xeon Phi™ coprocessor. We show the importance of the utilization of all parallel resources available on Intel architectures to achieve maximum performance. We demonstrate that the offload extension supported by Intel® Composer XE minimizes the efforts required to create accelerated applications by using only C/C++ language. With Intel's latest implementation of the STAC-A2 benchmark, we were able to achieve a significant (800%) performance gain by using a heterogeneous approach running on two Intel Xeon E5-2699 v3 processors and a single Intel® Xeon Phi™ 7120A card, compared with earlier version running on only two Intel Xeon E5-2697 v2 processors. Copyright © 2016 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Let $G$ be a non-elementary hyperbolic group. Let $w$ be a proper group word. We show that the width of the verbal subgroup $w(G)=\langle w[G]\rangle$ is infinite. That is, there is no $l\in \mathbb Z$ such that any $g\in w(G)$ can be represented as a product of at most $l$ values of $w$ and their inverses. As a consequence, we obtain the same result for a wide class of relatively hyperbolic groups. [ABSTRACT FROM PUBLISHER]

In this study we investigate the possibility of a-GaN ELOG process and its peculiarities for stripes of various orientations. It is shown that stripe orientation allows governing such important parameters of ELOG-process as lateral growth rate, voids high, fast growth direction. The intermediate orientations of stripe windows (differ from conventional (0001) and (1-100)) can be effectively used for double-cross ELOG process. (© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [ABSTRACT FROM AUTHOR]

Phase patterns of human scalp alpha EEG activity show spontaneous transitions between different globally phase-synchronized states. We studied the dynamical properties of these transitions using the method of symbolic dynamics. We found greater predictability (deterministicity) and heterogeneity in the dynamics than what was expected from corresponding surrogate series in which linear correlations are retained. A possible explanation of these observations within the framework of chaotic itinerancy is discussed. Hum Brain Mapp, 2007. © 2007 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

Dimensional complexity (DCx) is an EEG measure derived from nonlinear systems theory that can be indicative of the global dynamical complexity of electrocortical activity. This study examined developmental changes in DCx, as well as the effects of cognitive tasks, gender, and brain topography, and compared DCx with traditional spectral power measures. EEG was recorded in three groups of children at mean age of 7.5 (n = 37), 13.8 (n = 42), and 16.4 (n = 56) years at rest and during the performance of verbal and spatial cognitive tasks. DCx measured both at rest and during tasks increased with age. Specific effects of brain topography, condition, and gender became stronger with age, suggesting an increase in structural and functional differentiation of the cortex. Hemispheric asymmetry of DCx recorded during tasks also increased with age, with the task-induced DCx reduction being stronger in the left hemisphere. Gender differences in DCx suggested faster cerebral maturation in girls over late adolescence. Relationships between DCx and spectral power varied as a function of tasks and scalp locations, suggesting that these EEG measures can reflect different aspects of cortical functioning. © 2000 John Wiley & Sons, Inc. Dev Psychobiol 36: 9–22, 2000 [ABSTRACT FROM AUTHOR]

While viewing a scene, the eyes are attracted to salient stimuli. We set out to identify the brain signals controlling this process. In a contour integration task, in which participants searched for a collinear contour in a field of randomly oriented Gabor elements, a previously established model was applied to calculate a visual saliency value for each fixation location. We studied brain activity related to the modeled saliency values, using coregistered eye tracking and EEG. To disentangle EEG signals reflecting salience in free viewing from overlapping EEG responses to sequential eye movements, we adopted generalized additive mixed modeling (GAMM) to single epochs of saccade‐related EEG. We found that, when saliency at the next fixation location was high, amplitude of the presaccadic EEG activity was low. Since presaccadic activity reflects covert attention to the saccade target, our results indicate that larger attentional effort is needed for selecting less salient saccade targets than more salient ones. This effect was prominent in contour‐present conditions (half of the trials), but ambiguous in the contour‐absent condition. Presaccadic EEG activity may thus be indicative of bottom‐up factors in saccade guidance. The results underscore the utility of GAMM for EEG—eye movement coregistration research. [ABSTRACT FROM AUTHOR]