Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation

Translation of consecutive prolines causes ribosome stalling, which is alleviated but cannot be fully compensated by the elongation factor P. However, the presence of polyproline motifs in about one third of the E. coli proteins underlines their potential functional importance, which remains largely unexplored. We conducted an evolutionary analysis of polyproline motifs in the proteomes of 43 E. coli strains and found evidence of evolutionary selection against translational stalling, which is especially pronounced in proteins with high translational efficiency. Against the overall trend of polyproline motif loss in evolution, we observed their enrichment in the vicinity of translational start sites, in the inter-domain regions of multi-domain proteins, and downstream of transmembrane helices. Our analysis demonstrates that the time gain caused by ribosome pausing at polyproline motifs might be advantageous in protein regions bracketing domains and transmembrane helices. Polyproline motifs might therefore be crucial for co-translational folding and membrane insertion.
High speed generator in a CHP unit

This paper presents theoretical background and experimental results obtained during development of a car compressor driven by a turbine and a high speed permanent magnet motor. Alternatively, the turbocharger used in combination with an auxiliary boost motor can be used not only in the car, but with some modifications as CHP unit (Combined Heat and Power). The control algorithms for work in infinite grid and off-grid systems and appropriate modification of Permanent Magnet High Speed Generator (PMHSG) controller are discussed. The experimental results and findings are presented.
Immunolocalization of muscarinic M1 receptor in the rat medial prefrontal cortex

The medial prefrontal cortex (mPFC) has been considered to participate in many higher cognitive functions, such as memory formation and spatial navigation. These cognitive functions are modulated by cholinergic afferents via muscarinic acetylcholine receptors. Previous pharmacological studies have strongly suggested that the M1 receptor (M1R) is the most important subtype among muscarinic receptors to perform these cognitive functions. Actually, M1R is abundant in mPFC. However, the proportion of somata containing M1R among cortical cellular types, and the precise intracellular localization of M1R remain unclear. In this study, to clarify the precise immunolocalization of M1R in rat mPFC, we examined three major cellular types, pyramidal neurons, inhibitory neurons, and astrocytes. M1R immunopositivity signals were found in the majority of the somata of both pyramidal neurons and inhibitory neurons. In pyramidal neurons, strong M1R immunopositivity signals were usually found throughout their somata and dendrites including spines. On the other hand, the signal strength of M1R immunopositivity in the somata of inhibitory neurons significantly varied. Some neurons showed strong signals. Whereas about 40% of GAD67‐immunopositive neurons and 30% of parvalbumin‐immunopositive neurons (PV neurons) showed only weak signals. In PV neurons, M1R immunopositivity signals were preferentially distributed in somata. Furthermore, we found that many astrocytes showed substantial M1R immunopositivity signals. These signals were also mainly distributed in their somata. Thus, the distribution pattern of M1R markedly differs between cellular types. This difference might underlie the cholinergic modulation of higher cognitive functions subserved by mPFC.
Stability analysis for weak grids with power electronics interfaces

A novel modelling method and a stability analysis procedure for weak power networks with high penetration of power electronics converters are proposed in this paper. The modeling approach can be applied to any network topology and in order to model of the complete network it introduces small-signal state-space models for each network component including power lines, loads, power converters and their control algorithms. The proposed linearized model was validated by comparing its response with the response of the non-linear model. In order to identify the critical network and control parameters of the weak grid in presence of disturbances the developed small-signal model was then used in the stability analysis based on the frequency response of singular values. Finally, the existence of the identified resonance modes was confirmed by using the original non-linear model of the network.
Stabilization of Neural-Network-Based Control Systems via Event-Triggered Control With Nonperiodic Sampled Data

This paper focuses on a problem of event-triggered stabilization for a class of nonuniformly sampled neural-network-based control systems (NNBCSs). First, a new event-triggered data transmission mechanism is designed based on the nonperiodic sampled data. Different from the previous works, the proposed triggering scheme enables the NNBCSs design to enjoy the advantages of both nonuniform and event-triggered sampling schemes. Second, under the nonperiodic event-triggered data transmission scheme, the nonperiodic sampled-data three-layer fully connected feedforward neural-network (TLFCFFNN)-based event-triggered controller is constructed, and the resulting closed-loop TLFCFFNN-based event-triggered control system is modeled as a state delay system based on time-delay system modeling approach. Then, the stability criteria for the closed-loop system is formulated using Lyapunov–Krasovskii functional approach. Third, the sufficient conditions for the codesign of the TLFCFFNN-based controller and triggering parameters are given in terms of solvability of matrix inequalities to guarantee the asymptotical stability of the closed-loop system and an upper bound on the given cost function while reducing the updates of the controller. Finally, three numerical examples are provided to illustrate the effectiveness and benefits of the proposed results.
Remotely sensed wind speed predicts soaring behaviour in a wide-ranging pelagic seabird

Global wind patterns affect flight strategies in many birds, including pelagic seabirds, many of which use wind-powered soaring to reduce energy costs during at-sea foraging trips and migration. Such long-distance movement patterns are underpinned by local interactions between wind conditions and flight behaviour, but these fine-scale relationships are far less well understood. Here we show that remotely sensed ocean wind speed and direction are highly significant predictors of soaring behaviour in a migratory pelagic seabird, the Manx shearwater (Puffinus puffinus). We used high-frequency GPS tracking data (10 Hz) and statistical behaviour state classification to identify two energetic modes in at-sea flight, corresponding to flap-like and soar-like flight. We show that soaring is significantly more likely to occur in tailwinds and crosswinds above a wind speed threshold of around 8 m s−1, suggesting that these conditions enable birds to reduce metabolic costs by preferentially soaring over flapping. Our results suggest a behavioural mechanism by which wind conditions may shape foraging and migration ecology in pelagic seabirds, and thus indicate that shifts in wind patterns driven by climate change could impact this and other species. They also emphasize the emerging potential of high-frequency GPS biologgers to provide detailed quantitative insights into fine-scale flight behaviour in free-living animals.
A continuous sliding mode controller for the PMSM speed regulation based on disturbance observer

This paper mainly studies the speed control for a permanent magnet synchronous motor system. The relationship between the reference quadrature axis current and the speed output is approximately considered as a second-order model. Based on this second-order model, a composite control strategy is adopted, where a continuous sliding mode controller is designed for the speed regulation without chattering and a disturbance observer is introduced as a compensator to resist disturbances and to reduce control gains. Simulation results have been presented to illustrate that the proposed method has good responses to reference speed signals with torque load disturbances.
Photomodulating Gene Expression by Using Caged siRNAs with Single‐Aptamer Modification

Caged siRNAs incorporating terminal modification were rationally designed for photochemical regulation of gene silencing induced by RNA interference (RNAi). Through the conjugation of a single oligonucleotide aptamer at the 5′ terminus of the antisense RNA strand, enhancement of the blocking effect for RNA‐induced silencing complex (RISC) formation/processing was expected, due both/either to the aptamers themselves and/or to their interaction with large binding proteins. Two oligonucleotide aptamers (AS1411 and MUC‐1) were chosen for aptamer‐siRNA conjugation through a photolabile linker. This caging strategy was successfully used to photoregulate gene expression both of firefly luciferase and of green fluorescent protein (GFP) in cells. Further patterning experiments revealed that spatial regulation of GFP expression was successfully achieved by using the aptamer‐modified caged siRNA and light activation. We expect that further optimized caged siRNAs featuring aptamer conjugation will be promising for practical applications to spatiotemporal photoregulation of gene expression in the future.
Reliability and minimal detectable change of between-limb synchronization, weight-bearing symmetry, and amplitude of postural sway in individuals with stroke

Introduction: Recently, variables related to between-limb synchronization of the centers of pressure (COP) have been proposed as measures of postural control in post-stroke patients. Although it is crucial in verifying their potential clinical use, the reliability of these variables is unknown. The aim of this work was to determine the reliability and minimal detectable change (MDC) of the peak of synchronization (ρmax) in the anteroposterior (AP) and mediolateral (ML) directions, the time lag for the peak (ρmaxlag), synchronization at lag zero (ρ0), weight-bearing symmetry, and amplitude of postural sway, measured as the root mean square (RMS) values of the COP displacements in both directions (AP and ML COP displacement). Methods: COP data of 16 participants with stroke were collected at quiet standing with two force plates at two sessions separated by 2 to 7 days. The procedure was repeated three times in each session. The within and between sessions reliability was determined by the intraclass correlation coefficient (ICC), and the MDC was obtained from the ICC between sessions. Results: The variables ρmaxlag in the AP and ML directions, as well as ρ0 in the AP direction, exhibited poor within session reliability (ICC ≤ 0.4). The findings revealed excellent within and between sessions reliability (ICC ≥ 0.89) for weight-bearing symmetry and the RMS displacement in the AP direction, with MDC values of 5% and 2.07 mm, respectively. The remaining variables exhibited moderate reliability. Conclusion: Weight-bearing symmetry and AP COP displacement can be considered reliable variables for use in clinical practice.
Genome Sequence of Lactococcus lactis subsp . lactis bv . diacetylactis LD 61 FALENTIN

Lactococcus lactis is widely used in the dairy industry. We report the draft genome sequence of L. lactis subsp. lactis bv. diacetylactis LD61, an industrial and extensively studied strain. In contrast to the closely related and plasmidless strain IL1403, LD61 contains 6 plasmids, and the genome sequence provides additional information related to adaptation to the dairy
The GSK3 kinase inhibitor lithium produces unexpected hyperphosphorylation of β-catenin, a GSK3 substrate, in human glioblastoma cells

ABSTRACT Lithium salt is a classic glycogen synthase kinase 3 (GSK3) inhibitor. Beryllium is a structurally related inhibitor that is more potent but relatively uncharacterized. This study examined the effects of these inhibitors on the phosphorylation of endogenous GSK3 substrates. In NIH-3T3 cells, both salts caused a decrease in phosphorylated glycogen synthase, as expected. GSK3 inhibitors produce enhanced phosphorylation of Ser9 of GSK3β via a positive feedback mechanism, and both salts elicited this enhancement. Another GSK3 substrate is β-catenin, which has a central role in Wnt signaling. In A172 human glioblastoma cells, lithium treatment caused a surprising increase in phospho-Ser33/Ser37-β-catenin, which was quantified using an antibody-coupled capillary electrophoresis method. The β-catenin hyperphosphorylation was unaffected by p53 RNAi knockdown, indicating that p53 is not involved in the mechanism of this response. Lithium caused a decrease in the abundance of axin, a component of the β-catenin destruction complex that has a role in coordinating β-catenin ubiquitination and protein turnover. The axin and phospho-β-catenin results were reproduced in U251 and U87MG glioblastoma cell lines. These observations run contrary to the conventional view of the canonical Wnt signaling pathway, in which a GSK3 inhibitor would be expected to decrease, not increase, phospho-β-catenin levels. This article has an associated First Person interview with the first author of the paper. Summary: GSK3 inhibitors have potential use against Alzheimer's disease and other conditions. In this study, a classic inhibitor produced unexpected molecular effects on key components of the Wnt signaling pathway.
Design and Characterization of Electroresponsive Polymers Based on the Johnsen-Rahbek Effect

Electroactive polymers (EAPs) are synthetic materials that react to an electrical stimulus by altering one or more of their properties and have been of much interest in the fields of electrochemical actuation and electroadhesion. The majority of electroadhesive devices employing EAPs are governed by coulombic forces generated when an electric potential is applied across a dielectric polymer. Typically these devices are comprised of a stack of two composites, each consisting of a dielectric bound to an electrode, in which the dielectric layers are in contact. The coulombic force generated across the electroactive layers electrostatically adheres the composite together. However, there exists another electroadhesive force, the Johnsen-Rahbek (JR) force, which is expressed in the case of imperfectly insulating materials such as ion-containing polymers. Whereas coulombic electroadhesive systems have been studied extensively, materials that exhibit the JR force have received much less attention. Herein, the synthesis and characterization of structures composed poly(ethylene-co-acrylic acid) polymers with tetraalkylammonium counterions is described. A structure-activity relationship between the identity of the counterion and the thermal, electrical, mechanical, and electroresponsive attributes of the material is presented. The alkyl chain length of the quaternary ammonium counterions is found to influence the properties such that longer chain lengths result in both a lower initial modulus and a higher percentage change in modulus under an applied voltage.
Motion Estimation from Tagged MR Images and Application to Cardiac Strain Evaluation and Functional Analysis of Ocular Tissues

Tagged MRI is a magnetic resonance imaging technique that has been widely applied to tissue functional evaluation, especially the myocardium. Unlike traditional anatomical imaging methods, tagged MRI spatially encodes the motion of underlying tissue by modulating the longitudinal magnetization periodically before deformation. The visual appearance is dark strips or grids that follow along with the tissue motion. Therefore, by investigating the apparent changing of the tag pattern, one can estimate the deformation pattern and mechanical properties of the target tissue. Previous motion estimation methods either manually or automatically reconstruct the deformation field from tagged MRI. However, most of them have limitations such as low computational efficiency or accuracy, or the inability to reconstruct a 3D deformation. In this dissertation, we develop three motion estimation methods that reduce manual intervention rate and computation time, while retaining a relatively high accuracy. The first introduced method improves a previous unwrapped phase-based method by automatically optimizing the branch cut configuration using simulated annealing. Then a quality-guided phase unwrapping follows after the application of branch cuts to unwrap the harmonic phase image. The unwrapped phase values provide displacement measurement and can be used to reconstruct a 3D deformation field. Although this method reduces manual intervention greatly compared to the previous manual method, it is time consuming. Then, we introduce a second method, which unwraps the harmonic phase image using integer optimization with graph cuts. The resulting unwrapped phase is both spatially and temporally smooth, as we assume the underlying deformation is continuous and smooth. We also use a dynamic model with a Kalman filter to improve the performance on biventricular studies. This method largely reduces the computation time and is highly automated. The third
Building Evaluation Dataset for Textual Entailment in Czech

Recognizing textual entailment (RTE) is a subfield of natural language processing (NLP). Currently several RTE systems exist in which some of the subtasks are language independent but some are not. Moreover, large datasets for evaluation are prepared almost exclusively for English language. In this paper we describe methods for obtaining test dataset for RTE in Czech. We have used methods for extracting facts from texts based on corpus templates as well as syntactic parser. Moreover, we have used reading comprehension tests for children and students. The main contribution of this article is the classification of “difficulty levels” for particular RTE questions.
Asymptotic Optimality in Sampling-based Motion Planning

Although one of the fundamental problems in robotics, the motion planning problem is inherently hard from a computational point of view. In particular, the piano movers’ problem [1], [2] is known to be PSPACE-hard, which implies that any algorithm aimed to solve this problem (with completeness guarantees) is expected not to scale well with increasing number of dimensions of the configuration space. In fact, the computation time required by well-known complete algorithms scale exponentially with the dimensionality of the configuration space in the worst case [3], which makes them impractical, e.g., in motion planning problems for robotic arms with several joints. The optimal motion planning problem is known to be significantly harder computationally when compared to finding just a feasible solution, even when the dimensionality of the configuration space is fixed. In particular, it is known that the optimal motion planning problem is NP-hard for a point mass moving among polygonal obstacles in a three dimensional configuration space [4]. Early research on motion planning during 1980s has involved optimal motion planning algorithms only with limited success [5], [6], [7]. However, especially after the emergence of a deeper understanding of the computational complexity of the problem during the late 1980s, the community shifted towards designing algorithms that can quickly find feasible solutions, usually with no optimality guarantees.
Alleviate Similar Object in Visual Tracking via Online Learning Interference-Target Spatial Structure

Correlation Filter (CF) based trackers have demonstrated superior performance to many complex scenes in smart and autonomous systems, but similar object interference is still a challenge. When the target is occluded by a similar object, they not only have similar appearance feature but also are in same surrounding context. Existing CF tracking models only consider the target’s appearance information and its surrounding context, and have insufficient discrimination to address the problem. We propose an approach that integrates interference-target spatial structure (ITSS) constraints into existing CF model to alleviate similar object interference. Our approach manages a dynamic graph of ITSS online, and jointly learns the target appearance model, similar object appearance model and the spatial structure between them to improve the discrimination between the target and a similar object. Experimental results on large benchmark datasets OTB-2013 and OTB-2015 show that the proposed approach achieves state-of-the-art performance.
Differential Regulation of Bladder Pain and Voiding Function by Sensory Afferent Populations Revealed by Selective Optogenetic Activation

Bladder-innervating primary sensory neurons mediate reflex-driven bladder function under normal conditions, and contribute to debilitating bladder pain and/or overactivity in pathological states. The goal of this study was to examine the respective roles of defined subtypes of afferent neurons in bladder sensation and function in vivo via direct optogenetic activation. To accomplish this goal, we generated transgenic lines that express a Channelrhodopsin-2-eYFP fusion protein (ChR2-eYFP) in two distinct populations of sensory neurons: TRPV1-lineage neurons (Trpv1Cre;Ai32, the majority of nociceptors) and Nav1.8+ neurons (Scn10aCre;Ai32, nociceptors and some mechanosensitive fibers). In spinal cord, eYFP+ fibers in Trpv1Cre;Ai32 mice were observed predominantly in dorsal horn (DH) laminae I-II, while in Scn10aCre;Ai32 mice they extended throughout the DH, including a dense projection to lamina X. Fiber density correlated with number of retrogradely-labeled eYFP+ dorsal root ganglion neurons (82.2% Scn10aCre;Ai32 vs. 62% Trpv1Cre;Ai32) and degree of DH excitatory synaptic transmission. Photostimulation of peripheral afferent terminals significantly increased visceromotor responses to noxious bladder distension (30–50 mmHg) in both transgenic lines, and to non-noxious distension (20 mmHg) in Scn10aCre;Ai32 mice. Depolarization of ChR2+ afferents in Scn10aCre;Ai32 mice produced low- and high-amplitude bladder contractions respectively in 53% and 27% of stimulation trials, and frequency of high-amplitude contractions increased to 60% after engagement of low threshold (LT) mechanoreceptors by bladder filling. In Trpv1Cre;Ai32 mice, low-amplitude contractions occurred in 27% of trials before bladder filling, which was pre-requisite for light-evoked high-amplitude contractions (observed in 53.3% of trials). Potential explanations for these observations include physiological differences in the thresholds of stimulated fibers and their connectivity to spinal circuits.