Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic clustering for acoustic target tracking in wireless sensor networks

In the paper, we devise and evaluate a fully decentralized, light-weight, dynamic clustering algorithm for target tracking. Instead of assuming the same role for all the sensors, we envision a hierarchical sensor network that is composed of (a) a static backbone of sparsely placed high-capability sensors which assume the role of a cluster head (CH) upon triggered by certain signal events; and (b) moderately to densely populated low-end sensors whose function is to provide sensor information to CHs upon request. A cluster is formed and a CH becomes active, when the acoustic signal strength detected by the CH exceeds a pre-determined threshold. The active CH then broadcasts an information solicitation packet, asking sensors in its vicinity to join the cluster and provide their sensing information. We address and devise solution approaches (with the use of Voronoi diagram) to realize dynamic clustering: (I1) how CHs cooperate with one another to ensure that for the most of time only one CH (preferably the CH that is closest to the target) is active; (I2) when the active CH solicits for sensor information, instead of having all the sensors in its vicinity reply, only a sufficient number of sensors respond with non-redundant, essential information to determine the target location; and (I3) both packets with which sensors respond to their CHs and packets that CHs report to subscribers do not incur significant collision. Through both probabilistic analysis and ns-2 simulation, we show with the use of Voronoi diagram, the CH that is usually closest to the target is (implicitly) selected as the leader and that the proposed dynamic clustering algorithm effectively eliminates contention among sensors and renders more accurate estimates of target locations as a result of better quality data collected and less collision incurred.
Robust resource management for metacomputers

Presents a robust software infrastructure for metacomputing. The system is intended to be used by others as a building block for large and powerful computational grids. Much effort has been taken to develop a fault-tolerant architecture that does not exhibit a single point of failure. Furthermore, we have designed the system to be modular, lean and portable. It is available as open source code and has been successfully compiled on POSIX- and Microsoft Windows-compliant platforms. The system does not originate from a laboratory environment but has proven its robustness within two large metacomputing installations. It embodies a modular concept which allows easy integration of new or modified components. Hence, it is not necessary to buy into the system as whole. We rather encourage others to use only those components that fit into their specific environments.
Hepatoprotective effect of bis(4‐methylbenzoyl) diselenide against CCl4‐induced oxidative damage in mice

From a pharmacological point of view, organoseleniums are compounds with important and interesting antioxidant and biological activities. The aim of this study was to evaluate the hepatoprotective effect of bis(4‐methylbenzoyl) diselenide (BMD) against carbon tetrachloride (CCl4)–induced oxidative damage in mice. The animals received BMD (25 mg/kg p.o., for 3 days), and after 1 day, CCl4 (1 mg/kg body weight) was administered by intraperitoneal route. One day after the CCl4 exposure, the animals were euthanized for biochemical and histological analysis. Treatment with BMD (25 mg/kg p.o.) protected against aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase, gamma‐glutamyl transferase and lactate dehydrogenase activity increases induced by CCl4 plasma exposure. Treatment with BMD (25 mg/kg) protected against increases in thiobarbituric reactive species and decreasing non‐protein thiols and ascorbic acid levels in liver of mice. Catalase and superoxide dismutase activity inhibition in the liver caused by CCl4 were protected by treatment with BMD (25 mg/kg). Glutathione S‐transferase activity was inhibited by CCl4 and remained unaltered even after treatment with BMD. Sections of liver from CCl4‐exposed mice presented an intense infiltration of inflammatory cells and loss of the cellular architecture. BMD (25 mg/kg) attenuated CCl4‐induced hepatic histological alterations. The results demonstrated the hepatoprotective effects of BMD in the mouse liver, possibly by modulating the antioxidant status. Copyright © 2012 John Wiley & Sons, Ltd.
BSAlign: a rapid graph-based algorithm for detecting ligand-binding sites in protein structures.

Detection of ligand-binding sites in protein structures is a crucial task in structural bioinformatics, and has applications in important areas like drug discovery. Given the knowledge of the site in a particular protein structure that binds to a specific ligand, we can search for similar sites in the other protein structures that the same ligand is likely to bind. In this paper, we propose a new method named "BSAlign" (Binding Site Aligner) for rapid detection of potential binding site(s) in the target protein(s) that is/are similar to the query protein's ligand-binding site. We represent both the binding site and the protein structure as graphs, and employ a subgraph isomorphism algorithm to detect the similarities of the binding sites in a very time-efficient manner. Preliminary experimental results show that the proposed BSAlign binding site detection method is about 14 times faster than a well-known method called SiteEngine, while offering the same level of accuracy. Both BSAlign and SiteEngine achieve 60% search accuracy in finding adenine-binding sites from a data set of 126 proteins. The proposed method can be a useful contribution towards speed-critical applications such as drug discovery in which a large number of proteins are needed to be processed. The program is available for download at: http://www1.i2r. a-star.edu. sg/~azeyar/BSAlign/.
Managing distributed UPS energy for effective power capping in data centers

Power over-subscription can reduce costs for modern data centers. However, designing the power infrastructure for a lower operating power point than the aggregated peak power of all servers requires dynamic techniques to avoid high peak power costs and, even worse, tripping circuit breakers. This work presents an architecture for distributed per-server UPSs that stores energy during low activity periods and uses this energy during power spikes. This work leverages the distributed nature of the UPS batteries and develops policies that prolong the duration of their usage. The specific approach shaves 19.4% of the peak power for modern servers, at no cost in performance, allowing the installation of 24% more servers within the same power budget. More servers amortize infrastructure costs better and, hence, reduce total cost of ownership per server by 6.3%.
Active Sample Learning and Feature Selection: A Unified Approach

This paper focuses on the problem of simultaneous sample and feature selection for machine learning in a fully unsupervised setting. Though most existing works tackle these two problems separately that derives two well-studied sub-areas namely active learning and feature selection, a unified approach is inspirational since they are often interleaved with each other. Noisy and high-dimensional features will bring adverse effect on sample selection, while `good' samples will be beneficial to feature selection. We present a unified framework to conduct active learning and feature selection simultaneously. From the data reconstruction perspective, both the selected samples and features can best approximate the original dataset respectively, such that the selected samples characterized by the selected features are very representative. Additionally our method is one-shot without iteratively selecting samples for progressive labeling. Thus our model is especially suitable when the initial labeled samples are scarce or totally absent, which existing works hardly address particularly for simultaneous feature selection. To alleviate the NP-hardness of the raw problem, the proposed formulation involves a convex but non-smooth optimization problem. We solve it efficiently by an iterative algorithm, and prove its global convergence. Experiments on publicly available datasets validate that our method is promising compared with the state-of-the-arts.
Using Video as an Advance Organizer to a Written Passage in the FLES Classroom

We compared the effects of two visual advance organizers on comprehension and retention of a written passage in a FLES (Foreign Language in the Elementary School) Program: (a) Video and (b) Pictures + Teacher Narrative. Sixty-two English-speaking students enrolled in fifth grade in a parochial elementary school served as subjects. Investigators randomly assigned students to one of two conditions. Students in both conditions read 12 identical passages in French. The two groups differed only in their introduction to the passages. For students in the video group, a short video clip presented the narration of the advance organizer while for the comparative group, the teacher presented the identical narration by reading it aloud and showing four pictures related in context. Findings indicated that Video was a more effective advance organizer than Pictures + Teacher Narrative. The investigators interpreted these results as evidence of video's potential to enhance comprehension and enrich instruction.
Growth differentiation factor 15 in different stages of heart failure: potential screening implications

Identification of individuals in the early stage of heart failure (HF) may allow earlier initiation of disease-modifying treatment. We evaluated concentrations of the growth differentiation factor (GDF)-15at different stages and its potential screening value in 208 subjects. Plasma GDF-15 was measured by using an enzyme-linked immunosorbent assay. GDF-15 was positively correlated with the stages of HF (r=0.804, p<0.001). In distinguishing patients with stage B HF, the area under the curve was 0.873 (p<0.001). These findings indicate that GDF-15 concentration was elevated with the progressing stages of HFand might have potential screening implications for stage B HF.
Formalisation of product requirements: from natural language descriptions to formal specifications

In engineering design, customers usually provide product requirements in the form of a natural language while computer-aided design systems may prefer more formal and structured specifications. In this paper, a formalisation process is proposed to transform product requirements from its natural language descriptions to a formal specification. The formal specification is based on the product environment and the formulation of design problem, which identifies the components included in a design problem in terms of the product environment. Through the lexical, syntactic, and structure analysis of natural language descriptions of a design problem, the formalisation process identifies the product to be designed, its environment components, and their relations. A software prototype is developed to validate the formalisation process. An example of rivet setting tool design shows that both the formalisation process and software prototype are feasible.
Quantification of collagen alteration in mid-dermis of skin lesion with mucinosis using second harmonic generation imaging

Cutaneous mucinoses are a heterogeneous group of diseases characterized by abnormal deposition of dermal mucin. Considering the collagen disorder due to the mucin deposition, collagen microstructure was visualized by second harmonic generation (SHG) microscopy to gain structural and diagnostic information. High resolution images of collagen in the dermis of skin lesion with mucinosis and healthy skin showed differences in their microstructures. SHG density as well as depth dependant decay coefficient was analyzed to quantitatively characterize the microstructure. Our results demonstrated the possibility of SHG imaging to in vivo tracking the pathological process of mucinoses and evaluate the therapeutic efficacy.
The glutamate transporter EAAT2 is transiently expressed in developing human cerebral white matter

The major brain abnormality underlying cerebral palsy in premature infants is periventricular leukomalacia (PVL), a lesion of the immature cerebral white matter. Oligodendrocyte precursors (pre‐OLs; O4+O1−) predominate in human cerebral white matter during the peak time frame for PVL (24–32 gestational weeks) and are vulnerable to excitotoxicity. We hypothesize that PVL reflects, in part, excitotoxicity to pre‐OLs resulting from cerebral ischemia/reperfusion. Reversal of glutamate transport in the setting of energy failure is a major source of pathologic accumulation of extracellular glutamate. Here, we identify and localize the glutamate transporters in human cerebral white matter during the age range of PVL. In situ hybridization was performed with digoxigenin‐labeled probes directed against the full‐length coding regions of EAAT1, EAAT2, and EAAT3. EAAT2 mRNA was abundant in human fetal white matter during the period of peak incidence of PVL and virtually disappeared by 2 postnatal months. Its developmental profile differed significantly from that of both EAAT1 and EAAT3 mRNA. Immunoblotting demonstrated that EAAT2 protein was highly expressed in early development relative to adult values. Double‐label immunocytochemistry detected EAAT2 in OLs but not astrocytes or axons in the human fetal white matter. We conclude that transient expression of EAAT2 occurs during the window of peak vulnerability for PVL, suggesting that this developmentally up‐regulated transporter may be a major source of extracellular glutamate in ischemic injury to the cerebral white matter of the preterm infant. J. Comp. Neurol. 501:879–890, 2007. © 2007 Wiley‐Liss, Inc.
How Functional Connectivity between Emotion Regulation Structures Can Be Disrupted: Preliminary Evidence from Adolescents with Moderate to Severe Traumatic Brain Injury

Abstract Outcome of moderate to severe traumatic brain injury (TBI) includes impaired emotion regulation. Emotion regulation has been associated with amygdala and rostral anterior cingulate (rACC). However, functional connectivity between the two structures after injury has not been reported. A preliminary examination of functional connectivity of rACC and right amygdala was conducted in adolescents 2 to 3 years after moderate to severe TBI and in typically developing (TD) control adolescents, with the hypothesis that the TBI adolescents would demonstrate altered functional connectivity in the two regions. Functional connectivity was determined by correlating fluctuations in the blood oxygen level dependent (BOLD) signal of the rACC and right amygdala with that of other brain regions. In the TBI adolescents, the rACC was found to be significantly less functionally connected to medial prefrontal cortices and to right temporal regions near the amygdala (height threshold T = 2.5, cluster level p < .05, FDR corrected), while the right amygdala showed a trend in reduced functional connectivity with the rACC (height threshold T = 2.5, cluster level p = .06, FDR corrected). Data suggest disrupted functional connectivity in emotion regulation regions. Limitations include small sample sizes. Studies with larger sample sizes are necessary to characterize the persistent neural damage resulting from moderate to severe TBI during development. (JINS, 2013, 19, 1–14)
Effect of taphonomic processes on dental microwear.

Taphonomic processes have the potential to affect microscopic wear on teeth and to modify the wear patterns so as to confound dietary reconstructions based on dental microwear which was formed during the lifetime of an animal. This study describes a series of experiments which were conducted to simulate various taphonomic agents and to record their effect on dental microwear. Three types of experiment were carried out in order to explain anomalous microscopic wear that had been found on the dentition of several hominoid specimens from the 15 M.a. site of Pasalar in Turkey. The effect of two different acids-citric and hydrochloric acid-on dental microwear was investigated. Modification to microscopic wear caused by alkali (carbonatite ash) was examined in the second set of experiments. Lastly, the effect of abrasion by three different size classes of sediment from the site of Pasalar-quartz pebbles (grain size varied from 2,000-11,000 microm), coarse sand (grain size ranged from 500-1,000 microm), and medium-sized sand (grain diameters were between 250 and 500 microm)-was investigated. Results confirm previous findings that the taphonomic modification of dental microwear is readily identifiable and causes the obliteration rather than secondary alteration of microwear features. The experiments show that both citric and hydrochloric acid affect dental microwear but to varying degrees, whereas alkali did not cause any modification of microscopic features. The different size classes of sediment also had different effects on the dental microwear. The largest size sediment (quartz pebbles) polished the enamel and removed finer microwear features. The coarse sand, however, did not have any effect on the microwear. The greatest amount of abrasion was caused by the smallest sediment particles -the medium-sized sand. Several hominoid dental specimens from Pasalar display similar microscopic wear to the two types of acid erosion and the abrasion caused by the medium-sized sands.
Adaptive local multigrid methods for solving time-harmonic eddy-current problems

The efficient computation of large eddy-current problems with finite elements requires adaptive methods and fast optimal iterative solvers such as multigrid methods. This paper provides an overview of the most important implementation aspects of an adaptive multigrid scheme for time-harmonic eddy currents. Numerical experiments show that the standard multigrid scheme can be modified to yield an O(N) complexity even for general adaptive refinement strategies, where the number of unknowns N can grow slowly from one to the next refinement level. Algorithmic details and numerical examples are given.
PIPS Is not (just) Polyhedral Software Adding GPU Code Generation in PIPS

Parallel and heterogeneous computing are growing in audience thanks to the increased performance brought by ubiquitous manycores and GPUs. However, available programming models, like OPENCL or CUDA, are far from being straightforward to use. As a consequence, several automated or semi-automated approaches have been proposed to automatically generate hardware-level codes from high-level sequential sources. Polyhedral models are becoming more popular because of their combination of expressiveness, compactness, and accurate abstraction of the data-parallel behaviour of programs. These models provide automatic or semi-automatic parallelization and code transformation capabilities that target such modern parallel architectures. PIPS is a quarter-century old source-to-source transformation framework that initially targeted parallel machines but then evolved to include other targets. PIPS uses abstract interpretation on an integer polyhedral lattice to represent program code, allowing linear relation analysis on integer variables in an interprocedural way. The same representation is used for the dependence test and the convex array region analysis. The polyhedral model is also more classically used to schedule code from linear constraints. In this paper, we illustrate the features of this compiler infrastructure on an hypothetical input code, demonstrating the combination of polyhedral and non polyhedral transformations. PIPS interprocedural polyhedral analyses are used to generate data transfers and are combined with non-polyhedral transformations to achieve efficient CUDA code generation.
Decarbamoyl mitomycin C (DMC) activates p53-independent ataxia telangiectasia and rad3 related protein (ATR) chromatin eviction

Interstrand crosslinks induce DNA replication fork stalling that in turn activates the ATR-dependent checkpoint and DNA repair on nuclear chromatin. Mitomycin C (MC) and Decarbamoyl Mitomycin C (DMC) induce different types of DNA crosslinks with DMC being a more cytotoxic agent. We previously reported that the novel DMC induced β–interstrand DNA crosslinks induce a p53-independent form of cell death. The p53-independent DMC cytotoxicity associates with the activation, and subsequent depletion, of Chk1. In this study we further dissect the novel DMC signal transduction pathway and asked how it influences chromatin-associated proteins. We found that treatment with DMC, but not MC, stimulated the disassociation of ATR from chromatin and re-localization of ATR to the cytoplasm. The chromatin eviction of ATR was coupled with the formation of nuclear Rad51 foci and the phosphorylation of Chk1. Furthermore, DMC but not MC, activated expression of gadd45α mRNA. Importantly, knocking down p53 via shRNA did not inhibit the DMC-induced disassociation of ATR from chromatin or reduce the activation of transcription of gadd45α. Our results suggest that DMC induces a p53-independent disassociation of ATR from chromatin that facilitates Chk1 checkpoint activation and Rad51 chromatin recruitment. Our findings provide evidence that ATR chromatin eviction in breast cancer cells is an area of study that should be focused on for inducing p53-independent cell death.
Susceptibility to tumors induced by polyoma virus is conferred by an endogenous mouse mammary tumor virus superantigen

A dominant gene carried in certain inbred mouse strains confers susceptibility to tumors induced by polyoma virus. This gene, designated Pyvs, was defined in crosses between the highly susceptible C3H/BiDa strain and the highly resistant but H-2k-identical C57BR/cdJ strain. The resistance of C57BR/cdJ mice is overcome by irradiation, indicating an immunological basis. In F1 x C57BR/cdJ backcross mice, tumor susceptibility cosegregates with Mtv-7, a mouse mammary tumor provirus carried by the C3H/BiDa strain. This suggests that Pyvs might encode the Mtv-7 superantigen (SAG) and abrogate polyoma tumor immunosurveillance through elimination of T cells bearing specific V beta domains. DNA typing of 110 backcross mice showed no evidence of recombination between Pyvs and Mtv-7. Strongly biased usage of V beta 6 by polyoma virus-specific CD8+ cytotoxic T lymphocytes in C57BR/cdJ mice implicates T cells bearing this Mtv-7 SAG-reactive V beta domain as critical anti-polyoma tumor effector cells in vivo. These results indicate identity between Pyvs and Mtv-7 sag, and demonstrate a novel mechanism of inherited susceptibility to virus-induced tumors based on effects of an endogenous superantigen on the host's T cell repertoire.