Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiobjective optimization technique based on monitoring information to increase the performance of thread migration on multicores

Multicore systems present on-board memory hierarchies and communication networks that influence their performance when they execute shared memory parallel codes. Characterizing this influence is complex, and understanding the effect of particular hardware configurations on different codes is of paramount importance. In this paper, monitoring information extracted from hardware counters in runtime is used to characterize the behaviour of each thread in the parallel code in terms of three values: the number of floating point operations per second, the operational intensity, and the memory access latency. Note that these values characterize the Roofline Model with the inclusion of additional information about memory access latencies. We propose to use this information to guide thread migration strategies that improve the efficiency of the execution of the code by increasing locality and affinity. The idea behind this proposal is to use these three values as objective functions to be optimized as a multiobjective optimization problem. The proposed technique is an iterative method inspired in evolutive optimization algorithms. To this end, an individual utility function is defined to represent the relative importance of these values. This function is a weighted product that can be considered as representative of the performance of each parallel thread. Different configurations of the SAXPY and SDOT kernels on multicores were used to validate the benefits of the proposed thread migration strategies. The results show that our strategy produces improvements up to 25% in scenarios where locality and affinity are low, and negligible degradation is observed when they are high. The use of hardware counters produces low overheads when extracting monitoring information.
Identifying native‐like protein structures using physics‐based potentials

As the field of structural genomics matures, new methods will be required that can accurately and rapidly distinguish reliable structure predictions from those that are more dubious. We present a method based on the CHARMM gas phase implicit hydrogen force field in conjunction with a generalized Born implicit solvation term that allows one to make such discrimination. We begin by analyzing pairs of threaded structures from the EMBL database, and find that it is possible to identify the misfolded structures with over 90% accuracy. Further, we find that misfolded states are generally favored by the solvation term due to the mispairing of favorable intramolecular ionic contacts. We also examine 29 sets of 29 misfolded globin sequences from Levitt's “Decoys ‘R’ Us” database generated using a sequence homology‐based method. Again, we find that discrimination is possible with approximately 90% accuracy. Also, even in these less distorted structures, mispairing of ionic contacts results in a more favorable solvation energy for misfolded states. This is also found to be the case for collapsed, partially folded conformations of CspA and protein G taken from folding free energy calculations. We also find that the inclusion of the generalized Born solvation term, in postprocess energy evaluation, improves the correlation between structural similarity and energy in the globin database. This significantly improves the reliability of the hypothesis that more energetically favorable structures are also more similar to the native conformation. Additionally, we examine seven extensive collections of misfolded structures created by Park and Levitt using a four‐state reduced model also contained in the “Decoys ‘R’ Us” database. Results from these large databases confirm those obtained in the EMBL and misfolded globin databases concerning predictive accuracy, the energetic advantage of misfolded proteins regarding the solvation component, and the improved correlation between energy and structural similarity due to implicit solvation. Z‐scores computed for these databases are improved by including the generalized Born implicit solvation term, and are found to be comparable to trained and knowledge‐based scoring functions. Finally, we briefly explore the dynamic behavior of a misfolded protein relative to properly folded conformations. We demonstrate that the misfolded conformation diverges quickly from its initial structure while the properly folded states remain stable. Proteins in this study are shown to be more stable than their misfolded counterparts and readily identified based on energetic as well as dynamic criteria. In summary, we demonstrate the utility of physics‐based force fields in identifying native‐like conformations in a variety of preconstructed structural databases. The details of this discrimination are shown to be dependent on the construction of the structural database. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 147–160, 2002
An Improvement of Both Security and Reliability for Keccak Implementations on Smart Card

As the new SHA-3 standard, the security and reliability of Keccak have attracted a lot of attentions. Previous works already show that both software and hardware implementations of Keccak have strong side-channel power (electromagnetic) leakages, and these leakages can be easily used by attackers to recover secret key bits. Meanwhile, Keccak is vulnerable to random errors and injected faults, which will cause errors in the computation results. In this paper, we introduce a scheme based on the round rotation invariance property of Keccak to reduce the side-channel leakages while improve its reliability. The proposed scheme is resource friendly. Side-channel analysis results show that this method can efficiently reduce the side-channel leakages of Keccak implementations. Meanwhile, fault injection simulation results show that the proposed scheme can effectively improve the reliability of Keccak implementation, with error coverage almost 100%.
Robust iterative fitting of multilinear models based on linear programming

Parallel factor (PARAFAC) analysis is an extension of low-rank matrix decomposition to higher-way arrays. It decomposes a given array in a sum of multilinear terms. PARAFAC analysis generalizes and unifies common array processing models (like joint diagonalization and ESPRIT); it has found numerous applications from blind multiuser detection and multi-dimensional harmonic retrieval to clustering and nuclear magnetic resonance. The prevailing fitting algorithm in all these applications is based on alternating least squares (ALS) optimization, which is matched to Gaussian noise. In many cases, however, measurement errors are far from being Gaussian. We develop an iterative algorithm for least absolute error fitting of general multilinear models, based on efficient interior point methods for linear programming (LP). We also benchmark its performance in Laplacian, Cauchy, and Gaussian noise environments, versus the respective CRBs and the commonly used ALS algorithm.
A Specific A/T Polymorphism in Western Tyrosine Phosphorylation B-Motifs Regulates Helicobacter pylori CagA Epithelial Cell Interactions

Helicobacter pylori persistently colonizes the human stomach, with mixed roles in human health. The CagA protein, a key host-interaction factor, is translocated by a type IV secretion system into host epithelial cells, where its EPIYA tyrosine phosphorylation motifs (TPMs) are recognized by host cell kinases, leading to multiple host cell signaling cascades. The CagA TPMs have been described as type A, B, C or D, each with a specific conserved amino acid sequence surrounding EPIYA. Database searching revealed strong non-random distribution of the B-motifs (including EPIYA and EPIYT) in Western H. pylori isolates. In silico analysis of Western H. pylori CagA sequences provided evidence that the EPIYT B-TPMs are significantly less associated with gastric cancer than the EPIYA B-TPMs. By generating and using a phosphorylated CagA B-TPM-specific antibody, we demonstrated the phosphorylated state of the CagA B-TPM EPIYT during H. pylori co-culture with host cells. We also showed that within host cells, CagA interaction with phosphoinositol 3-kinase (PI3-kinase) was B-TPM tyrosine-phosphorylation-dependent, and the recombinant CagA with EPIYT B-TPM had higher affinity to PI3-kinase and enhanced induction of AKT than the isogenic CagA with EPIYA B-TPM. Structural modeling of the CagA B-TPM motif bound to PI3-kinase indicated that the threonine residue at the pY+1 position forms a side-chain hydrogen bond to N-417 of PI3-kinase, which cannot be formed by alanine. During co-culture with AGS cells, an H. pylori strain with a CagA EPIYT B-TPM had significantly attenuated induction of interleukin-8 and hummingbird phenotype, compared to the isogenic strain with B-TPM EPIYA. These results suggest that the A/T polymorphisms could regulate CagA activity through interfering with host signaling pathways related to carcinogenesis, thus influencing cancer risk.
Flexible Neural Representations of Value in the Primate Brain

Abstract: The amygdala and orbitofrontal cortex (OFC) are often thought of as components of a neural circuit that assigns affective significance—or value—to sensory stimuli so as to anticipate future events and adjust behavioral and physiological responses. Much recent work has been aimed at understanding the distinct contributions of the amygdala and OFC to these processes, but a detailed understanding of the physiological mechanisms underlying learning about value remains lacking. To gain insight into these processes, we have focused initially on characterizing the neural signals of the primate amygdala, and more recently of the primate OFC, during appetitive and aversive reinforcement learning procedures. We have employed a classical conditioning procedure whereby monkeys form associations between visual stimuli and rewards or aversive stimuli. After learning these initial associations, we reverse the stimulus‐reinforcement contingencies, and monkeys learn these new associations. We have discovered that separate populations of neurons in the amygdala represent the positive and negative value of conditioned visual stimuli. This representation of value updates rapidly upon image value reversal, as fast as monkeys learn, often within a single trial. We suggest that representations of value in the amygdala may change through multiple interrelated mechanisms: some that arise from fairly simple Hebbian processes, and others that may involve gated inputs from other brain areas, such as the OFC.
Ad hoc assisted handoff for real-time voice in IEEE 802.11 infrastructure WLANs

IEEE 802.11 WLANs are increasingly used to support real-time services such as voice and video. Reliable portable operation, however, is often difficult due to factors such as imperfect customer access point (AP) installation, unpredictable WLAN coverage, and unexpected co-channel interferers. In this paper we propose and investigate the use of IEEE 802.11 ad hoc-assisted handoff (AAHO). In AAHO, a single additional ad hoc hop may he used by a mobile station (MS) to obtain the range extension or channel quality needed to maintain its real-time voice connection. There are three versions of IEEE 802.11 AAHO. In backward ad hoc assisted handoff (BAAHO), the additional hop uses a relay station which already has an IEEE 802.11 association with the AP that the MS is using. In forward ad hoc assisted handoff (FAAHO) the additional hop uses a relay station whose AP is different from the one that the MS is currently using. Hybrid ad hoc assisted handoff (HAAHO) is a combination of the two and allows an MS to perform either BAAHO or FAAHO. The proposed AAHO designs are backward compatible, and thus can be implemented as a transparent overlay across existing IEEE 802.11 infrastructure deployments. Performance results show that AAHO can greatly improve performance in many practical situations.
An effective post quantization rate estimation for HEVC intra encoder

In high efficiency video coding (HEVC), the encoder employs a flexible quad-tree coding structure as well as a large number of prediction modes. For each size of coding unit (CU), transform unit (TU) and each prediction mode, the rate distortion optimization (RDO) is performed to select the best CU, TU and the best prediction mode. Although better coding efficiency is achieved, the computational complexity increases dramatically. In order to reduce the burden of RDO in the HEVC intra encoder, in this paper, we propose an effective approach, which is based on the generalized Gaussian distribution (GGD) model, to estimate the block level bit-rate. The weaknesses of the conventional GGD model are analyzed and relevant improvements are exploited. Our experiments show that, compared with the original RDO procedure in HM16.0, the proposed algorithm reduces RDO time by 37.7% with 0.64% BD-rate loss.
Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China

A novel Gram-negative bacterium, designated ZWT, was isolated from a soil sample of the Western Desert of China, and its phenotypic properties and phylogenetic position were investigated using a polyphasic approach. Growth occurred on TGY medium at 5–42°C with an optimum of 30°C, and at pH 7.0–11.0 with an optimum of pH 9.0. The predominant cellular fatty acids were summed feature 3 (C16:1 ω7c/C16:1 ω6c or C16:1 ω6c/C16:1 ω7c) (39.22%), iso-C15:0 (27.91%), iso-C17:0 3OH (15.21%), C16:0 (4.98%), iso-C15:0 3OH (3.03%), C16:0 3OH (5.39%) and C14:0 (1.74%). The major polar lipid of strain ZWT is phosphatidylethanolamine. The only menaquinone observed was MK-7. The GC content of the DNA of strain ZWT is 44.9 mol%. rDNA phylogeny, genome relatedness and chemotaxonomic characteristics all indicate that strain ZWT represents a novel species of the genus Sphingobacterium. We propose the name S. deserti sp. nov., with ZWT (= KCTC 32092T = ACCC 05744T) as the type strain. Whole genome optical mapping and next-generation sequencing was used to derive a finished genome sequence for strain ZWT, consisting of a circular chromosome of 4,615,818 bp in size. The genome of strain ZWT features 3,391 protein-encoding and 48 tRNA-encoding genes. Comparison of the predicted proteome of ZWT with those of other sphingobacteria identified 925 species-unique proteins that may contribute to the adaptation of ZWT to its native, extremely arid and inhospitable environment. As the first finished genome sequence for any Sphingobacterium, our work will serve as a useful reference for subsequent sequencing and mapping efforts for additional strains and species within this genus.
Soft vs. hard antenna selection based on the minimum distance for MIMO systems

Assuming that channel state information (CSI) can be available at the transmitter, we provide a simplified representation of multi-input multi-output (MIMO) systems and derive a new precoder which maximizes the smallest distance between the received symbols. When the number of transmit antennas, n/sub T/, is greater than the number of transmit data streams, b, R.W. Heath and A. Paulraj (see Proc. ICC 2001) have proposed a "hard" antenna selection (or switch precoder) which consists in choosing the best b (among n/sub T/) antennas of the transmitter according to a criterion based on the minimum distance. Using the same criterion, we propose a "soft" (or linear) precoder that performs power allocation among the transmit antennas. Comparisons in term of bit error rate (BER) between switch and linear precoders are performed considering b=2 independent data streams, a QPSK modulation and the maximum likelihood (ML) receiver.
MODELING INDIVIDUAL DIFFERENCES 1 Modeling Individual Differences In Negative Information Processing Biases

Research on depression and research on personality have long been very different fields. Research on personality and individual differences has concentrated on figuring out why individuals respond differently to similar stimuli, process similar information differently, and act differently in similar social situations. It has often focused on understanding differences between individuals who are considered “normal”. In contrast, research on depression has focused on commonalties among people who are considered depressed. Questions such as why depressed people respond similarly to negative stimuli and why depressed people appear similarly biased in their processing of negative information have pervaded this literature. The disciplines of studying differences among otherwise similar people and similarities between groups of very different people have recently begun to converge as theory begins to suggest that depressed people differ qualitatively on a number of trait-like dimensions, and that mood may affect the expression of individual differences other than depression itself. For example Klein, Wonderlich, and Shea (1992) suggest that enduring personality characteristics such as dependency and perfectionism appear to be associated with qualitative differences in the expression of depression. Similarly, researchers such as Persons and Miranda (1992) have found that biased memory for negative things, which was once thought to be trait-like, appear to vary with affective state. These paths have begun to suggest that depression can affect the assessment of personality, and that personality is intimately associated with the onset, maintenance, and recovery from depression. An area in which this synthesis has been extremely productive regards the mediating role of personality variables upon biased information processing in dysphoric individuals. Some dysphoric individuals appear to systematically attend to negative over positive or neutral information (MacLeod & Mathews, 1991), remember disproportionate amounts of negative information (Blaney, 1986), and engage in excessive processing of negative information or “rumination”. Such information processing biases have been linked by numerous researchers to a vulnerability for depression (e.g., Ingram, 1984). Other dysphoric and even clinically depressed individuals do not appear to show these biases (e.g., Siegle, Ingram, & Matt, 1996a). To the extent that personality and individual difference variables may mediate these biases, it will be important to understand their role in depression. Such variables may be particularly valuable in predicting who will and will not be vulnerable to depression after a period of dysphoria. The goal of this chapter is to illustrate some of the ways in which personality factors might help to explain variation in information processing in dysphoric and depressed individuals.
Generalized Fokker-Planck Theory for Electron and Photon Transport in Biological Tissues: Application to Radiotherapy

In this paper, we study a deterministic method for particle transport in biological tissues. The method is specifically developed for dose calculations in cancer therapy and for radiological imaging. Generalized Fokker-Planck (GFP) theory [Leakeas and Larsen, Nucl. Sci. Eng. 137 (2001), pp. 236-250] has been developed to improve the Fokker-Planck (FP) equation in cases where scattering is forward-peaked and where there is a sufficient amount of large-angle scattering. We compare grid-based numerical solutions to FP and GFP in realistic medical applications. First, electron dose calculations in heterogeneous parts of the human body are performed. Therefore, accurate electron scattering cross sections are included and their incorporation into our model is extensively described. Second, we solve GFP approximations of the radiative transport equation to investigate reflectance and transmittance of light in biological tissues. All results are compared with either Monte Carlo or discrete-ordinates transport solutions.
A GRID FOCUSED COMMUNITY CRAWLING ARCHITECTURE FOR MEDICAL INFORMATION RETRIEVAL SERVICES

This paper describes a GRID focused community crawling architecture and its possible adoption in a medical information domain. This architecture has been designed for handling a retrieval information service to individuals that are entitled to access the highly distributed computational power of the GRID, eliminating the need of a central authority/repository such as a unique search engine. In addition, Portals and Directory Services could use GRID focused crawlers to automatically monitor and populate large fresh repositories on a variety of topics. A focused crawler surfs the Web and gathers documents on a specific topic. It can be used like a search engine getting further and faster information, by narrowing its crawl to specific subjects. For a particular topic, the focused crawler results contain many more relevant documents than the collection returned by the generic search engine. In this paper a three tier model architecture is presented, with particular emphasis to the core of the system placed on the middle layer. This tier has been implemented using a general-purpose parallel programming environment for the development of distributed and high-performance applications, together with C++ and Java programming languages.
‘Direction of Arrival’ Estimation Algorithm: Direction Lock Loop

In this paper, a new direction of arrival (DOA) estimation algorithm, direction lock loop (DiLL), is proposed. It has a similar concept to the delay lock loop (DLL) that is used for synchronization. It estimates the DOA of a signal by iterations, and can track the DOA of a moving source. The DiLL scheme is found to track better than the DOA estimation scheme based on the PASTd, and its performance is less sensitive to the DOA of a signal than that of the DOA estimation scheme based on the PASTd. The DOA estimation accuracy and the tracking capability are demonstrated by analysis and computer simulations.
A Pervasive Way : Elderly People Falling Detection and Ambient Intelligence

A stairway falling detection prototype is designed to warn when elderly people fall on the stairs and also accumulatively and unobtrusively study elderly people’s walking patterns. With this prototype, we try to demo a new design strategy, a pervasive way, to facilitate developing proper algorithms and living patterns for elderly people at home. Evaluation of the implicit interactions and potential cooperations with other research domains are then discussed.
USING THE WAVEGUIDE MESH IN MODELLING 3D RESONATORS

Most of the results found by several researchers, during these years, in physical modelling of two dimensional (2D) resonators by means of waveguide meshes, extend without too much difficultyto the three dimensional (3D) case. Important parameters such as the dispersion error, the spatial bandwidth, and the sampling efficiency, which characterize the behavior and the performance of a waveguide mesh, can be reformulated in the 3D case, giving the possibility to design mesh geometries supported by a consistent theory. A comparison between different geometries can be carried out in a theoretical context. Here, we emphasize the use of the waveguide meshes as efficienttools for the analysis of resonances in 3D resonators of various shapes. For this purpose, several mesh geometries have been implemented into an application running on a PC, provided with a graphical interface that allows an easy input of the parameters and a simple observation of the consequent system evolution and the output data. This application is especially expected to give information on the modes resonating in generic 3D shapes, where a theoretical prediction of the modal frequencies is hard to do.