Miracle-dz/UniFAR-FTUs huggingface dataset:
Global Analysis of Human Nonreceptor Tyrosine Kinase Specificity Using High-Density Peptide Microarrays

Protein kinases phosphorylate substrates in the context of specific phosphorylation site sequence motifs. The knowledge of the specific sequences that are recognized by kinases is useful for mapping sites of phosphorylation in protein substrates and facilitates the generation of model substrates to monitor kinase activity. Here, we have adapted a positional scanning peptide library method to a microarray format that is suitable for the rapid determination of phosphorylation site motifs for tyrosine kinases. Peptide mixtures were immobilized on glass slides through a layer of a tyrosine-free Y33F mutant avidin to facilitate the analysis of phosphorylation by radiolabel assay. A microarray analysis provided qualitatively similar results in comparison with the solution phase peptide library “macroarray” method. However, much smaller quantities of kinases were required to phosphorylate peptides on the microarrays, which thus enabled a proteome scale analysis of kinase specificity. We illustrated this capability by microarray profiling more than 80% of the human nonreceptor tyrosine kinases (NRTKs). Microarray results were used to generate a universal NRTK substrate set of 11 consensus peptides for in vitro kinase assays. Several substrates were highly specific for their cognate kinases, which should facilitate their incorporation into kinase-selective biosensors.
The Near-UV Pulse Profile and Spectrum of the Pulsar PSR B0656+14

We have observed the middle-aged pulsar PSR B0656+14 with the prism and the NUV MAMA detector of the Space Telescope Imaging Spectrograph (STIS) to measure the pulsar spectrum and periodic pulsations in the near-ultraviolet (NUV). The pulsations are clearly detected, double-peaked and very similar to the optical pulse profile. The NUV pulsed fraction is 70 ± 12%. The spectral slope of the dereddened phase-integrated spectrum in the ∼1800-3200 A range is ∼α v = 0.35 ±0.5 which together with the high pulse fraction indicates a non-thermal origin for the NUV emission. The total flux in the range ∼1700-3400 A is estimated to be 3.4 ± 0.3 x 10 -15 erg s -1 cm -2 when corrected for E(B - V) = 0.03 mag. At a distance of 288 pc this corresponds to a luminosity L NUV = 3.4 x 10 28 erg s -1 assuming isotropy of the emission. We compare the NUV pulse profile with observations from radio to gamma-rays. The first NUV sub-pulse is in phase with the gamma-ray pulse marginally detected with EGRET, while the second NUV sub-pulse is similar both in shape and in phase with the non-thermal pulse in hard X-rays. This indicates a single origin of the non-thermal emission in the optical-NUV and in the X-rays. This is also supported by the observed NUV spectral slope, which is compatible with a blackbody plus power-law fit extended from the X-ray range, but dominated by the power-law component in most of the NUV range.
Non-coherent TOA estimation in IR-UWB systems with different signal waveforms

In this paper, signal waveform designs for TOA estimation with non-coherent receivers based on ultrawideband impulse radio are discussed. Four different transmit signal waveforms are analyzed, both with respect to their design constraints, and their precision ranging performance in IEEE 802.15. 4a multipath channels. We introduce novel searchback and thresholding algorithms, and show that the ranging performance can be improved considerably with a-priori knowledge of noise variance. Simulation results show that it is possible to achieve sub-meter ranging accuracy with 90% confidence by using such energy detecting (non-coherent) receivers
Through Wall Surveillance Using Ultrawideband Random Noise Radar

Recent terrorist activities and law-enforcement situations involving hostage situations underscore the need for effective through-wall detection. Current building interior imaging systems are based on short-pulse waveforms, which require specially designed antennas to subdue unwanted ringing. In addition, periodically transmitted pulses of energy are easily recognizable by the intelligent adversary who may employ appropriate countermeasures to confound detection. A non-coherent polarimetric random noise radar architecture is being developed based on ultrawideband (UWB) technology and software defined radio, which has great promise in its ability to covertly detect obscured targets. The main advantages of the random noise radar lie in two aspects: first, random noise waveform has an ideal " thumbtack " ambiguity function, i.e., its down range and cross range resolution can be separately controlled, thus providing unambiguous high resolution imaging at any distance; second, random noise waveform is inherently low probability of intercept (LPI) and low probability of detection (LPD), i.e., it is immune from detection, jamming, and interference. Thus, it is an ideal candidate sensor for covert imaging of obscured regions in hostile environments. Other than those advantages, we also suffer some real problems that we lack of the back scattering information in the strong clutter and interference environment and most of the previous through wall studies are based on the research of light cluttered environment. This paper presents the radar system design, simulation study, measurements, and data analysis.
Weighted energy linear quadratic regulator vibration control of piezoelectric composite plates

In this paper on finite element linear quadratic regulator (LQR) vibration control of smart piezoelectric composite plates, we propose the use of the total weighted energy method to select the weighting matrices. By constructing the optimal performance function as a relative measure of the total kinetic energy, strain energy and input energy of the system, only three design variables need to be considered to achieve a balance between the desired higher damping effect and lower input cost. Modal control analysis is used to interpret the effects of three energy weight factors on the damping ratios and modal voltages and it is shown that the modal damping effect will increase with the kinetic energy weight factor, approaching √2/2 as the strain energy weight factor increases and decrease with the input energy weight factor. Numerical results agree well with those from the modal control analysis. Since the control problem is simplified to three design variables only, the computational cost will be greatly reduced and a more accurate structural control analysis becomes more attractive for large systems.
XPED2: A Passive Exoskeleton with Artificial Tendons

Wearable exoskeletons might reduce human effort during walking. However, many of the current exoskeletons rely on heavy actuators and/or external power supplies; this has a negative impact on their efficiency and operation range. As an alternative, (quasi)passive exoskeletons have been developed. One of the proposed passive exoskeleton concepts is the exotendon concept of van den Bogert [1]. In this concept, long elastic cables span multiple joints. The cables can temporarily store and transfer energy between joints. In simulation, the average absolute joint torque can be reduced by 71%. The simulations are based on the hypotheses 1) that the exoskeleton does not influence the joint angles and 2) the total joint torques and a reduction in the human joint torques results in a reduction in the metabolic cost of walking. The goal of this article is to experimentally evaluate the exotendon concept and test the hypotheses underlying it. We implemented the exotendon concept in a lightweight exoskeleton. Experimental results show that the exotendons indeed reduced the average absolute joint torques. However, the exotendons also influenced the joint kinematics, and the metabolic cost of walking did not decrease. Therefore, the underlying assumptions of the exotendon concept are invalid. We also found that, in practice, the amount of support given by the exotendons is limited to about 35% of the theoretical optimal support. For higher levels of support, the motion is hindered and the support is experienced as uncomfortable by the users of the exoskeleton.
Regulation of Penicillinase Synthesis: a Mutation in Staphylococcus aureus Unlinked to the Penicillinase Plasmid That Reduces Penicillinase Inducibility

A mutant of Staphylococcus aureus strain 655 was isolated that is restricted in penicillinase induction. Wild-type plasmids that bear penicillinase determinants could not be fully induced in this mutant, 655par-1; hence, the responsible mutation is not located on the plasmid. Mutant plasmid PI258penI443, which produces penicillinase constitutively in wild-type cells, was fully constitutive for penicillinase production when it was harbored by mutant 655par-1. Therefore, the bacterial mutation does not interfere directly with the transcription of the penZ gene or translation of the penicillinase messenger ribonucleic acid. Mutant plasmid PII147penI220 was fully inducible in the mutant bacterium, even though the wild-type plasmid PII147 was only partially inducible in the par-1 mutant. Thus, in the presence of inducer, complementation appears to occur between the product of the par-1 gene and the product of the penI220 gene. These results suggest that the par-1 gene codes for a penicillinase antire-pressor.
Computational efficiency improvements for image colorization

We propose an efficient algorithm for colorization of greyscale images. As in prior work, colorization is posed as an optimization problem: a user specifies the color for a few scribbles drawn on the greyscale image and the color image is obtained by propagating color information from the scribbles to surrounding regions, while maximizing the local smoothness of colors. In this formulation, colorization is obtained by solving a large sparse linear system, which normally requires substantial computation and memory resources. Our algorithm improves the computational performance through three innovations over prior colorization implementations. First, the linear system is solved iteratively without explicitly constructing the sparse matrix, which significantly reduces the required memory. Second, we formulate each iteration in terms of integral images obtained by dynamic programming, reducing repetitive computation. Third, we use a coarseto- fine framework, where a lower resolution subsampled image is first colorized and this low resolution color image is upsampled to initialize the colorization process for the fine level. The improvements we develop provide significant speedup and memory savings compared to the conventional approach of solving the linear system directly using off-the-shelf sparse solvers, and allow us to colorize images with typical sizes encountered in realistic applications on typical commodity computing platforms.
Scheduling of QR Factorization Algorithms on SMP and Multi-Core Architectures

This paper examines the scalable parallel implementation of the QR factorization of a general matrix, targeting SMP and multi-core architectures. Two implementations of algorithms-by-blocks are presented. Each implementation views a block of a matrix as the fundamental unit of data, and likewise, operations over these blocks as the primary unit of computation. The first is a conventional blocked algorithm similar to those included in libFLAME and LAPACK but expressed in a way that allows operations in the so-called critical path of execution to be computed as soon as their dependencies are satisfied. The second algorithm captures a higher degree of parallelism with an approach based on Givens rotations while preserving the performance benefits of algorithms based on blocked Householder transformations. We show that the implementation effort is greatly simplified by expressing the algorithms in code with the FLAME/FLASH API, which allows matrices stored by blocks to be viewed and managed as matrices of matrix blocks. The SuperMatrix run-time system utilizes FLASH to assemble and represent matrices but also provides out-of-order scheduling of operations that is transparent to the programmer. Scalability of the solution is demonstrated on ccNUMA platform with 16 processors and an SMP architecture with 16 cores.
Reliability of estimating active drag in swimming using the assisted towing method with fluctuating speed

Abstract The reliability of active drag values was examined using a method that compared free swim speed with measurements taken by towing swimmers slightly faster than their maximum swim speed, while allowing their intra-stroke speed fluctuations. Twelve national age and open level swimmers were tested on two alternate days (Day 1 and Day 2). All participants completed four maximum swim speed, three passive drag and five active drag trials on each of the days. The reliability was determined using within-participant intra-class correlation coefficients (ICC) within each day and between the days. The ICCs for Day 1 and Day 2 were 0.82 and 0.85, respectively, while the comparison of the mean active drag values between days was 0.93. The data showed that the assisted towing method (ATM) with fluctuating speed was only moderately reliable within a single test. However, this method was more reliable when using the average value of active drag from both days (ICC = 0.93). This study identified that the ATM method with fluctuating speed had moderate reliability within-participant trials on values in a single day but high reliability for the average active drag values across different days.
Fast and Robust 2 D Parametric Image Registration

Camera stabilization is an important task for video analysis. In this report, we describe a method for estimating and stabilizing camera motion between two images via 2D image registration. Our approach is based on a pair-wise registration of images parameterized by 2D affine or projective transformation. Pair-wise image registration estimates transformation parameters for each pair of consecutive frames, and the transformation between arbitrary frames is computed by the concatenation of the pair-wise transformations. Pair-wise registration is based on 1) hierarchical parameter estimation and refinement 2) feature-matching 3) FFT(Fast Fourier Transformation)-based global matching 4) RANSAC-based parameter estimation.
Development of suitable interatomic potentials for simulation of liquid and amorphous Cu–Zr alloys

We present a new semi-empirical potential suitable for molecular dynamics simulations of liquid and amorphous Cu–Zr alloys. To provide input data for developing the potential, new experimental measurements of the structure factors for amorphous Cu64.5Zr35. 5 alloy were performed. In this work, we propose a new method to include diffraction data in the potential development procedure, which also includes fitting to first-principles and liquid density and enthalpy of mixing data. To refine the new potential, we used first-principles and liquid enthalpy of mixing data published earlier combined with the densities of liquid Cu64.5Zr35. 5 measured over a range of temperatures. We show that the potential predicts a liquid-to-glass transition temperature that agrees reasonably well with experimental data. Finally, we compare the new potential with two previously developed semi-empirical potentials for Cu–Zr alloys and examine their comparative and contrasting descriptions of structure and properties for Cu64.5Zr35. 5 liquids and glasses.
A Parallel Approach to HRTF Approximation and Interpolation Based on a Parametric Filter Model

Spatial audio-rendering techniques using head-related transfer functions (HRTFs) are currently used in many different contexts such as immersive teleconferencing systems, gaming, or 3-D audio reproduction. Since all these applications usually involve real-time constraints, efficient processing structures for HRTF modeling and interpolation are necessary for providing real-time binaural audio solutions. This letter presents a parametric parallel model that allows us to perform HRTF filtering and interpolation efficiently from an input HRTF dataset. The resulting model, which is an adaptation from a recently proposed modeling technique, not only reduces the size of HRTF datasets significantly, but also allows for simplified interpolation and real-time computation over parallel processors. In order to discuss the suitability of this new model, an implementation over a graphic processing unit is presented.
Factors affecting sulfate resistance of mortars

Abstract : The ability of a mortar made using portland cement, fine aggregate, and water to resist attack by sulfates is affected by the proportions of the mortar (water-cement ratio and cement content), by the maturity, by the amount of tricalcium aluminate in the portland cement, by the presence of tricalcium aluminate-sodium oxide solid solutions with different structures and reactivities, and by the composition, reactivity, and amount of pozzolan used together with the portland cement. Cements investigated included: portland cements of Types (I-III), and V meeting ASTM C 150; blended cements including Type IP's meeting ASTM C 595 that were made from the same clinkers as the Type I's; and Type I's blended with pozzolans including fly ashes produced by burning bituminous, subbitumous, and lignitic coals, calcined natural volcanic glass high in silica, and silica fume. Silica fume forms glassy microspheres that may contain over 90% SiO2; it is a by-product of the production of silicon metal. Some of the fly ashes produced from subbituminous and lignitic coals replacing 30% by volume of cements increased the expansion of mortars containing the blends when stored in sulfate solutions. This behavior reflects SiO2 below 50%, Al2O3 16 to 26%, and CaO 5 to 30%. Al2O3 and CaO in the fly ash glass are readily available to combine with sulfate to form ettringite. With cement of lower C3A content, some of the subbituminous and lignitic fly ash blends improved the sulfate resistance of mortars, except when SiO2 in the fly ashes was 38% or less.
Extended Kalman Filter Based Learning Algorithm for Type-2 Fuzzy Logic Systems and Its Experimental Evaluation

In this paper, the use of extended Kalman filter for the optimization of the parameters of type-2 fuzzy logic systems is proposed. The type-2 fuzzy logic system considered in this study benefits from a novel type-2 fuzzy membership function which has certain values on both ends of the support and the kernel, and uncertain values on other parts of the support. To have a comparison of the extended Kalman filter with other existing methods in the literature, particle swarm optimization and gradient descent-based methods are used. The proposed type-2 fuzzy neuro structure is tested on different noisy input-output data sets, and it is shown that extended Kalman filter has a better performance as compared to the gradient descent-based methods. Although the performance of the proposed method is comparable with the particle swarm optimization method, it is faster and more efficient than the particle swarm optimization method. Moreover, the simulation results show that the proposed novel type-2 fuzzy membership function with the extended Kalman filter has noise rejection property. Kalman filter is also used to train the parameters of type-2 fuzzy logic system in a feedback error learning scheme. Then, it is used to control a real-time laboratory setup ABS and satisfactory results are obtained.
3D Alignment and Change Detection from Uncalibrated Eye Images

Analyzing change in the 3D structure of the optic disc over time has long been recognized as central to the diagnosis of glaucoma but has been inadequately addressed by computer vision methods. Currently, clinicians examine stereo pairs from different time instants for interval changes indicative of glaucoma. Due to the clinical procedures in capturing optic disc images, these stereo pairs are usually completely uncalibrated - the camera intrinsics and extrinsics are unknown. Clinicians have to account for these unknown factors and hence their diagnoses of optic disc stability or change are subjective. Changes in the 3D structure of the optic disc are typically accompanied by changes in the 3D structure of blood vessels in that region. Therefore, change in the 3D structure of blood vessels can be used for glaucoma diagnosis. In this paper, we introduce a projective geometry based approach that reconstructs and aligns 3D blood vessel networks given two stereo pairs of optic disc images. We demonstrate that this alignment can identify regions where the vessel structure has changed. Since calibration is unavailable, the 3D structures and the alignment have a projective ambiguity, and hence, we cannot use an absolute threshold on the alignment error to automatically identify change. We have therefore developed an interactive tool that highlights regions with the largest alignment errors. This tool demonstrates the utility of our approach and also can guide clinical observers to optic disc regions where they should look for changes. We believe that our approach can serve as a platform to develop much needed novel tools for glaucoma diagnosis.
Hierarchical Path Metric in Multi-Hop Wireless Networks

In a large mobile ad hoc network, nodes may be organized by a hierarchical address system that reflects the organizational structure of the users within the network. This is typical for many mission-critical applications such as military networks. For such applications, it is important to keep cross-organization data transfer at the lowest possible level for minimal disruption of the traffic within each organization and for security reasons. To measure the degree that a multi-hop path conforms to this "level constraint", we propose a new link metric to quantify the "distance" between two neighboring nodes in terms of their hierarchical addresses. Using this metric, we discover that existing routing protocols that are not aware of the level preference in routing tend to find routes that violate the level constraint frequently. On the other hand, a direct adoption of the distance metric in existing routing protocols produces significant route detours. To deal with this situation, we need to design a new routing protocol to balance the level preference and the topological shortness of routes.
Correlation between the Trofile test and virological response to a short-term maraviroc exposure in HIV-infected patients.

OBJECTIVES The current validated assay to determine tropism of HIV variants is Trofile, which has some limitations. The aim of this work was to correlate the virological response to a short-term maraviroc exposure with Trofile. METHODS From 1 July 2008 to 1 March 2009, 34 consecutive HIV-infected patients with detectable viral load during the last 6 months began an 8 day exposure to maraviroc (MCT group); six HIV-infected patients without antiretroviral therapy received no treatment (control group). Plasma viral load was evaluated on days 0, 2, 5 and 8. Baseline Trofile was performed in MCT group patients. The maraviroc clinical test (MCT) was considered positive if viral load was undetectable (< 40 HIV-RNA copies/mL) or a reduction > or = 1 log(10) HIV-RNA copies/mL was achieved after 8 days of maraviroc exposure. RESULTS Global concordance between MCT and Trofile was 93.5%. In patients with R5 virus according to Trofile, MCT was positive in 19/20 (concordance 95%); in patients with dual/mixed virus, MCT was negative in 10/11 (concordance 90.9%). An additional phenotypic tropism assay was performed in patients with discordance between MCT and Trofile, being concordant with MCT in both cases. Three patients showed a non-reportable Trofile result, and all of them achieved undetectability after MCT. CONCLUSIONS A clinical approach like short-term maraviroc exposure could be an additional resource to genetic and phenotypic HIV tropism assays. This clinical approach shows high concordance with Trofile, and could allow patients with non-reportable results by Trofile to benefit from maraviroc therapy.