Miracle-dz/UniFAR-FTUs huggingface dataset:
Roles of partly unfolded conformations in macromolecular self‐assembly

From genes to cells there are many steps of hierarchical increments in building up complex frameworks that provide intricate networks of macromolecular interactions, through which cellular activities such as gene expression, signal processing, energy transduction and material conversion are dynamically organized and regulated. The self‐assembly of macromolecules into large complexes is one such important step, but this process is by no means a simple aggregation of macromolecules with predefined, rigid complementary structures. In many cases the component molecules undergo either domain rearrangements or folding of disordered portions, which occurs only following binding to their correct partners. The partial disorder is used in some cases to prevent spontaneous assembly at inappropriate times or locations. It is also often used for finely tuning the equilibrium and activation energy of reversible binding. In other cases, such as protein translocation across membranes, an unfolded terminus appears to be the prerequisite for the process as an initiation signal, as well as the physical necessity to be taken into narrow channels. Self‐assembly processes of viruses and bacterial flagella are typical examples where the induced folding of disordered chains plays a key role in regulating the addition of new components to a growing assembly. Various aspects of mechanistic roles of natively unfolded conformations of proteins are overviewed and discussed in this short review.
An evolutionary multiobjective genetic algorithm to solve 0/1 Knapsack Problem

The 0/1 Knapsack Problem is a very well known and it appears in many real life world with different application. The solution to the multi objective 0/1 Knapsack problem can be viewed as the result of a sequence of decisions. The problem is NP - complete and it also generalization of the 0/1 Knapsack problem in which many Knapsack are considered. A evolutionary algorithm for solving multi objective 0/1 Knapsack Problem is introduced in this paper. This algorithm used a genetic algorithm for direct comparison of two solutions. Few numerical experiments are realized using the best and recent algorithm in this paper. Experimental outcome show that the new proposed algorithm out performance the existing evolutionary approach for this problem.
The role of locomotion in psychological development

The psychological revolution that follows the onset of independent locomotion in the latter half of the infant's first year provides one of the best illustrations of the intimate connection between action and psychological processes. In this paper, we document some of the dramatic changes in perception-action coupling, spatial cognition, memory, and social and emotional development that follow the acquisition of independent locomotion. We highlight the range of converging research operations that have been used to examine the relation between locomotor experience and psychological development, and we describe recent attempts to uncover the processes that underlie this relation. Finally, we address three important questions about the relation that have received scant attention in the research literature. These questions include: (1) What changes in the brain occur when infants acquire experience with locomotion? (2) What role does locomotion play in the maintenance of psychological function? (3) What implications do motor disabilities have for psychological development? Seeking the answers to these questions can provide rich insights into the relation between action and psychological processes and the general processes that underlie human development.
Toward Nanoscale Particle Imaging using Near-Field Subwavelength Measurements in a 3-D Cylindrical Array of Nanometer Sized Probes

Rapid identification in parallel of nanometer structural changes, like protein folding, needs a low cost technique to screen many objects at once. This paper presents progress toward development of a near-field imager with a 3-D cylindrical nanometer sized probe array, into which nanoscale objects can be placed to be imaged using subwavelength electromagnetic radiation. Developing such a small probe array device based on sub-micron CMOS technology will allow many parallel devices to be utilized achieving the goal of massively parallel screening, and the imaging of nanoparticles and large molecules. In this paper, scaled probe array designs, fabricated in low cost Printed Wiring Boards (PWBs), and a low cost CMOS process are discussed and tested to verify the probe designs as a step toward fabrication of the final array.
Na+-dependent SR Ca2+ overload induces arrhythmogenic events in mouse cardiomyocytes with a human CPVT mutation.

AIMS Mutations in the cardiac ryanodine receptor Ca(2+) release channel, RyR2, underlie catecholaminergic polymorphic ventricular tachycardia (CPVT), an inherited life-threatening arrhythmia. CPVT is triggered by spontaneous RyR2-mediated sarcoplasmic reticulum (SR) Ca(2+) release in response to SR Ca(2+) overload during beta-adrenergic stimulation. However, whether elevated SR Ca(2+) content--in the absence of protein kinase A activation--affects RyR2 function and arrhythmogenesis in CPVT remains elusive. METHODS AND RESULTS Isolated murine ventricular myocytes harbouring a human RyR2 mutation (RyR2(R4496C+/-)) associated with CPVT were investigated in the absence and presence of 1 micromol/L JTV-519 (RyR2 stabilizer) followed by 100 micromol/L ouabain intervention to increase cytosolic [Na(+)] and SR Ca(2+) load. Changes in membrane potential and intracellular [Ca(2+)] were monitored with whole-cell patch-clamping and confocal Ca(2+) imaging, respectively. At baseline, action potentials (APs), Ca(2+) transients, fractional SR Ca(2+) release, and SR Ca(2+) load were comparable in wild-type (WT) and RyR2(R4496C+/-) myocytes. Ouabain evoked significant increases in diastolic [Ca(2+)], peak systolic [Ca(2+)], fractional SR Ca(2+) release, and SR Ca(2+) content that were quantitatively similar in WT and RyR2(R4496C+/-) myocytes. Ouabain also induced arrhythmogenic events, i.e. spontaneous Ca(2+) waves, delayed afterdepolarizations and spontaneous APs, in both groups. However, the ouabain-induced increase in the frequency of arrhythmogenic events was dramatically larger in RyR2(R4496C+/-) when compared with WT myocytes. JTV-519 greatly reduced the frequency of ouabain-induced arrhythmogenic events. CONCLUSION The elevation of SR Ca(2+) load--in the absence of beta-adrenergic stimulation--is sufficient to increase the propensity for triggered arrhythmias in RyR2(R4496C+/-) cardiomyocytes. Stabilization of RyR2 by JTV-519 effectively reduces these triggered arrhythmias.
Spatial clustering method for geographic data

In the process of visualizing quantitative spatial data, it is necessary to classify attribute values into some class divisions. In a previous paper, the author proposed a classification method for minimizing the loss of information contained in original data. This method can be considered as a kind of smoothing method that neglects the characteristics of spatial distribution. In order to understand the spatial structure of data, it is also necessary to construct another smoothing method considering the characteristics of the distribution of the spatial data. In this paper, a spatial clustering method based on Akaike’s Information Criterion is proposed. Furthermore, numerical examples of its application are shown using actual spatial data for the Tokyo Metropolitan area.
A Phonological Phrase Sequence Modelling Approach for Resource Efficient and Robust Real-Time Punctuation Recovery

For the automatic punctuation of Automatic Speech Recognition (ASR) output, both prosodic and text based features are used, often in combination. Pure prosody based approaches usually have low computation needs, introduce little latency (delay) and they are also more robust to ASR errors. Text based approaches usually yield better performance, they are however resource demanding (both regarding their training and computational needs), often introduce high time latency and are more sensitive to ASR errors. The present paper proposes a lightweight prosody based punctuation approach following a new paradigm: we argue in favour of an all-inclusive modelling of speech prosody instead of just relying on distinct acoustic markers: first, the entire phonological phrase structure is reconstructed, then its close correlation with punctuations is exploited in a sequence modelling approach with recurrent neural networks. With this tiny and easy to implement model we reach performance in Hungarian punctuation comparable to large, text based models for other languages by keeping resource requirements minimal and suitable for real-time operation with low latency.
Superefficiency in blind source separation

Blind source separation is the problem of extracting independent signals from their mixtures without knowing the mixing coefficients nor the probability distributions of source signals and may be applied to EEG and MEG imaging of the brain. It is already known that certain algorithms work well for the extraction of independent components. The present paper is concerned with superefficiency of these based on the statistical and dynamical analysis. In a statistical estimation using t examples, the covariance of any two extracted independent signals converges to 0 of the order of 1/t. On-line dynamics shows that the covariance is of the order of /spl eta/ when the learning rate /spl eta/ is fixed to a small constant. In contrast with the above general properties, a surprising superefficiency holds in blind source separation under certain conditions where superefficiency implies that covariance decreases in the order of 1/t/sup 2/ or of /spl eta//sup 2/. The paper uses the natural gradient learning algorithm and method of estimating functions to obtain superefficient procedures for both batch estimation and on-line learning. A standardized estimating function is introduced to this end. Superefficiency does not imply that the error variances of the extracted signals decrease in the order of 1/t/sup 2/ or /spl eta//sup 2/ but implies that their covariances (and independencies) do.
Noise-robust speech recognition with exemplar-based sparse representations using Alpha-Beta divergence

In this paper, we investigate the performance of a noise-robust sparse representations (SR)-based recognizer using the Alpha-Beta (AB)-divergence to compare the noisy speech segments and exemplars. The baseline recognizer, which approximates noisy speech segments as a linear combination of speech and noise exemplars of variable length, uses the generalized Kullback-Leibler divergence to quantify the approximation quality. Incorporating a reconstruction error-based back-end, the recognition performance highly depends on the congruence of the divergence measure and used speech features. Having two tuning parameters, namely α and β, the AB-divergence provides improved robustness against background noise and outliers. These parameters can be adjusted for better performance depending on the distribution of speech and noise exemplars in the high-dimensional feature space. Moreover, various well-known distance/divergence measures such as the Euclidean distance, generalized Kullback-Leibler divergence, Itakura-Saito divergence and Hellinger distance are special cases of the AB-divergence for different (α, β) values. The goal of this work is to investigate the optimal divergence for mel-scaled magnitude spectral features by performing recognition experiments at several SNR levels using different (α, β) pairs. The results demonstrate the effectiveness of the AB-divergence compared to the generalized Kullback-Leibler divergence especially at the lower SNR levels.
Recombinant Expression and Characterization of Human and Murine ACE2: Species-Specific Activation of the Alternative Renin-Angiotensin-System

Angiotensin-converting enzyme 2 (ACE2) is a monocarboxypeptidase of the renin-angiotensin-system (RAS) which is known to cleave several substrates among vasoactive peptides. Its preferred substrate is Angiotensin II, which is tightly involved in the regulation of important physiological functions including fluid homeostasis and blood pressure. Ang 1–7, the main enzymatic product of ACE2, became increasingly important in the literature in recent years, as it was reported to counteract hypertensive and fibrotic actions of Angiotensin II via the MAS receptor. The functional connection of ACE2, Ang 1–7, and the MAS receptor is also referred to as the alternative axis of the RAS. In the present paper, we describe the recombinant expression and purification of human and murine ACE2 (rhACE2 and rmACE2). Furthermore, we determined the conversion rates of rhACE2 and rmACE2 for different natural peptide substrates in plasma samples and discovered species-specific differences in substrate specificities, probably leading to functional differences in the alternative axis of the RAS. In particular, conversion rates of Ang 1–10 to Ang 1–9 were found to be substantially different when applying rhACE2 or rmACE2 in vitro. In contrast to rhACE2, rm ACE2 is substantially less potent in transformation of Ang 1–10 to Ang 1–9.
Discrete logarithm computations over finite fields using Reed-Solomon codes

Cheng and Wan have related the decoding of Reed-Solomon codes to the computation of discrete logarithms over finite fields, with the aim of proving the hardness of their decoding. In this work, we experiment with solving the discrete logarithm over GF(q^h) using Reed-Solomon decoding. For fixed h and q going to infinity, we introduce an algorithm (RSDL) needing O~(h! q^2) operations over GF(q), operating on a q x q matrix with (h+2) q non-zero coefficients. We give faster variants including an incremental version and another one that uses auxiliary finite fields that need not be subfields of GF(q^h); this variant is very practical for moderate values of q and h. We include some numerical results of our first implementations.
Hebbian learning analysis of a grid cell based cognitive mapping system

It is believed that animals sense the environment by encoding the spatial information into an internal representation. Grid cells in the rat entorhinal cortex are found with periodic firing fields and have been hypothesized as the basis for the `cognitive map'. This paper presents a grid-cell based computational model for cognitive map building together with an analysis of the learning from grid cells to place cells. Experiment results demonstrate that the learning from grid cells to place cells plays an important role affecting the performance of map building and that the proposed computational model provides an alternative approach for robot mapping.
LIMITS and Applications of Group Algebras for Parameterized Problems

The fastest known randomized algorithms for several parameterized problems use reductions to the k-MlD problem: detection of multilinear monomials of degree k in polynomials presented as circuits. The fastest known algorithm for k-MlD is based on 2k evaluations of the circuit over a suitable algebra. We use communication complexity to show that it is essentially optimal within this evaluation framework. On the positive side, we give additional applications of the method: finding a copy of a given tree on k nodes, a minimum set of nodes that dominate at least t nodes, and an m-dimensional k-matching. In each case, we achieve a faster algorithm than what was known before. We also apply the algebraic method to problems in exact counting. Among other results, we show that a variation of it can break the trivial upper bounds for the disjoint summation problem.
Economics of location : A selective survey q

We present a selective survey of the main results obtained in spatial economic theory. Our focus is on "rm location. We start with the simplest location problem and proceed to recent models of industrial location in general equilibrium. The middle section is a review of what has been accomplished in the literature on spatial pricing and spatial competition. We conclude with a discussion of recent models of economic geography which explain the uneven spatial distribution of economic activity. ( 1999 Elsevier Science Ltd. All rights
Measuring Media Compliance and Divergence in the Nondemocratic Press System

This study examined the flow of government messages through Iran's nondemocratic press system by measuring the exchange of news frames from the national media apparatus, the Islamic Republic News Agency (IRNA), onto two commercial sources: ultra-conservative newspaper, Jomhuri-ye Eslami, and rare reformist daily, Aftab-e Yazd. This mixed-methods research compared the news coverage of Iran's nuclear program and subsequent conflicts with the United States and Israel. The findings revealed Jomhuri-ye Eslami's characteristic reflection of government policy messages (91% rhetoric-reception), signifying what this research calls the model of media compliance. Conversely, Aftab-e Yazd rejected the majority of IRNA (Government) frames (55% rhetoric-rejection), demonstrating not only an extraordinary breach in media compliance, but also the rare indications of anti-government/antiwar sentiments growing inside the Islamic Republic.
Pelvis and Torso Kinematics and Their Relationship to Shoulder Kinematics in High-School Baseball Pitchers

Oliver, GD and Keeley, DW. Pelvis and torso kinematics and their relationship to shoulder kinematics in high-school baseball pitchers. J Strength Cond Res 24(12): 3241-3246, 2010-It was the purpose of our study to examine the kinematics of the pelvis and torso and determine their relationship to the kinematics of the shoulder in high-school baseball pitchers. A single group, repeated-measures design was used to collect pelvis, torso, and shoulder kinematics throughout the pitching motion. Subjects threw a series of maximal effort fastballs to a catcher located the regulation distance (18.44m) from the pitching mound, and those data from the fastest pitch passing through the strike zone were analyzed. After test trials, kinematic data were analyzed using a series of descriptive statistics to identify outliers and determine the nature of the distribution before testing for the presence of relationships between the various parameters. Results indicated that for several parameters, the actions at and about the shoulder are strongly related to the actions of the pelvis and torso throughout the pitching motion. However, although pelvis and torso kinematics throughout the pitching motion were inversely related to both shoulder elevation and the plane of shoulder elevation, only the rate of axial torso rotation was significantly related to these shoulder parameters. More importantly, the rate of axial torso rotation is significantly related to these shoulder parameters in a way that may help explain the high rate of shoulder injury in high-school pitchers. Therefore, strength training should focus on developing a strong stable core including the gluteal musculature in an attempt to control the rate of torso rotation during the pitch.
A New Two-Component Regulatory System Involved in Adhesion, Autolysis, and Extracellular Proteolytic Activity ofStaphylococcus aureus

ABSTRACT A transposition mutant of Staphylococcus aureus was selected from the parent strain MT23142, a derivative of strain 8325. The site of transposition was near the 5′ terminus of the genearlS. ArlS exhibits strong similarities with histidine protein kinases. Sequence analysis suggested that arlSforms an operon with upstream gene arlR. The predicted product of arlR is a member of the OmpR-PhoB family of response regulators. The arlS mutant formed a biofilm on a polystyrene surface unlike the parent strain and the complemented mutant. Biofilm formation was associated with increased primary adherence to polystyrene, whereas cellular adhesion was only slightly decreased. In addition, the arlS mutant exhibited increased autolysis and altered peptidoglycan hydrolase activity compared to the parental strain and to the complemented mutant. As it has been shown for coagulase-negative staphylococci that some autolysins are able to bind polymer surfaces, these data suggest that the two-component regulatory system ArlS-ArlR may control attachment to polymer surfaces by affecting secreted peptidoglycan hydrolase activity. Finally, thearlS mutant showed a dramatic decrease of extracellular proteolytic activity, including serine protease activity, in comparison to the wild-type strain and the complemented mutant, and cells grown in the presence of phenylmethylsulfonyl fluoride (a serine protease inhibitor) showed an increased autolysin activity. Since the locusarlR-arlS strikingly modifies extracellular proteolytic activity, this locus might also be involved in the virulence ofS. aureus.
Don't look at me that way!: Understanding User Attitudes Towards Data Glasses Usage

Data glasses do carry promising potential for hands-free interaction, but also raise various concerns amongst their potential users. In order to gain insights into the nature of those concerns, we investigate how potential usage scenarios are perceived by device users and their peers. We present results of a two-step approach: a focus group discussion with 7 participants, and a user study with 38 participants. In particular, we look into differences between the usage of data glasses and more established devices such as smart phones. We provide quantitative measures for scenario-related social acceptability and point out factors that can influence user attitudes. Based on our quantitative and qualitative results, we derive design implications that might support the development of head-worn devices and applications with an improved social acceptability.
Feature Subset Selection Based on Bayesian Networks

Bayesian network is a powerful tool of feature subset selection. Feature subset selection based on Bayesian network is to build the Markov blanket of class variable. In this paper, feature subset selection is done based on local dependency analysis method. First, basic dependency relationships between variables, basic structures between nodes, dependency separation criterion and the Markov blanket are analyzed. Then the Markov blanket of class variables is learned by dependency analysis. Finally, it is proved that learned feature subset is the Markov blanket of class variables under some assumptions. Experiments show that the method is more flexible, efficient and reliable than existing feature subset selection based on Bayesian network.
Directed Self-Assembly Using Graph Grammars

In this paper we describe the graph grammar approach to modeling self-assembly. The approach is used to describe how the topology of an assembling aggregate changes as it grows. The main purpose of the paper is to demonstrate the utility of the approach by giving detailed examples. We also describe the beginnings of our approach to physically embedding graph grammar assembly rules in physical settings, focusing on macroand micro-scale programmable parts and a simulation environment.