Miracle-dz/UniFAR-FTUs huggingface dataset:
A Framework to Resource Partitioning and Task Scheduling of Multiple Applications on an MPSoC

In the era of multicore dominance, multi-processor system-on-chips (MPSoCs) are now increasingly utilized as the appropriate platform in complex embedded systems. An MPSoC consists of multiple heterogeneous processing elements, a memory hierarchy, and input/output components linked together by an on-chip interconnect structure. Many embedded systems employ software-managed memories known as scratch-pad memories (SPM). Scratchpad memories, unlike caches, are software-controlled and hence the execution time of applications on such systems can be accurately predicted and controlled. Often multiple embedded applications are utilizing the system at the same time. The proper allocation of system resources to active applications and scheduling of applications tasks are two critical issues in reducing the computation times as well as the communication overhead. In this article, we present effective resource allocation techniques and a memory-aware task scheduling on an MPSoC with multiple embedded applications possibly entering and leaving the system at different times. The objective is to reduce the execution time of all the applications in the system. Results on real life benchmarks show the effectiveness of our techniques.
Thematic Review Series: The Immune System and Atherogenesis. Cytokines affecting endothelial and smooth muscle cells in vascular disease Published, JLR Papers in Press, April 16, 2005. DOI 10.1194/jlr.R500004-JLR200

The cellular and extracellular matrix accumulations that comprise the lesions of atherosclerosis are driven by local release of cytokines at sites of predilection for lesion formation, and by the specific attraction and activation of cells expressing receptors for these cytokines. Although cytokines were originally characterized for their potent effects on immune and inflammatory cells, they also promote endothelial cell dysfunction and alter smooth muscle cell (SMC) phenotype and function, which can contribute to or retard vascular pathologies. This review summarizes in vivo studies that have characterized endothelial- and smooth muscle-specific effects of altering cytokine signaling in vascular disease. Although multiple reports have identified cytokines as pivotal players in endothelial and SMC responses in vascular disease, they also have highlighted the need to delineate the critical genes and specific cellular functions regulated by individual cytokine signaling pathways.
Management of pediatric hypertrophic cardiomyopathy

Purpose of review As the underlying genetic basis of hypertrophic cardiomyopathy is being characterized, there has been increasing recognition of the wide spectrum and variable evolution of this disease within the pediatric age range. This review outlines recent evidence relevant to the diagnosis, management, and prognosis of hypertrophic cardiomyopathy specific to children and adolescents. Recent findings Studies of putative causal genes are leading to the discovery of factors affecting the variability of phenotypic expression and possible avenues for new therapies. Nonetheless, the use of genetic testing currently remains for research purposes only. Echocardiography is the primary means for evaluation, with an increasing focus on diastolic performance. Useful prognostic information can be obtained from the safe performance of cardiopulmonary stress testing. Sudden death can occur in children, although the risk factors are likely different than in adults. The role and mechanisms for possible ischemia remain controversial, and likely differ between individuals. Activity restrictions are recommended, with medical therapy reserved for those who are symptomatic. For those with important left ventricular outflow obstruction, surgical myectomy may be indicated, with little current role for alcohol septal ablation. Advances in implantable defibrillators now make this therapy feasible in younger children. Summary There are important differences from adults in the approach to the diagnosis and management of hypertrophic cardiomyopathy in children and adolescents. Care regarding prognostication and therapy must be taken given the potential life-long implications.
Automated Test Pattern Generation for Quantum Circuits

This work extends a general method used to test classical circuits to quantum circuits. Gate internal errors are address using a discrete fault model. Fault models to represent unwanted nearest neighbor entanglement as well as unwanted qubit rotation are presented. When witnessed, the faults we model are probabilistic, but there is a set of tests with the highest probability of detecting a discrete repetitive fault. A method of probabilistic set covering to identify the minimal set of tests is introduced. A large part of our work consisted of writing a software package that allows us to compare various fault models and test strategies for quantum networks.
Interaction Engineering: Achieving Perfect CSMA Handshakes in Wireless Networks

Carrier Sense Multiple Access (CSMA) protocols are unable to effectively arbitrate the medium in wireless networks; problems such as hidden and exposed terminals occur frequently leading to collisions, poor performance and unfairness. CSMA networks can be optimized by careful tuning of transceiver parameters, such as transmission power and carrier sensing threshold, to maximize spatial reuse of wireless channel while minimizing collisions. However, existing studies fail to jointly optimize these parameters to eliminate collisions and maximize spatial reuse. Our approach leverages on the observation that links under CSMA interfere in one of the few discrete interaction modes; each mode leads to different behavior in terms of performance and fairness. The proposed methodology controls the transceiver parameters to convert destructive interaction modes (such as various types of hidden terminals) into constructive ones; we call this approach Interaction Engineering (IE). In this paper, we first formulate a model and centralized algorithm that computes the parameters based on one-to-one interaction between the links. We then develop a distributed IE protocol. We evaluate the protocols under Wireless LAN and multi-hop wireless networks using both simulation and testbed. We show that IE eliminates a vast majority of the collisions and significantly boosts spatial reuse. For example, in the WLAN scenarios, we observed a median improvement of 4x in throughput and more than 2.5x improvement in fairness, and orders of magnitude improvement in connection delay and jitter. IE also shows significant improvements in multi-hop networks, and under different forms of traffic such as video and TCP.
Adding Test Generation to the Teaching Machine

We propose an extension of the Teaching Machine project, called Quiz Generator, that allows instructors to produce assessment quizzes in the field of algorithm and data structures quite easily. This extension makes use of visualization techniques and is based on new features of the Teaching Machine that allow third-party visualizers to be added as plugins and on new scripting capabilities. Using these new capabilities, five quiz types have already been produced, which can be applied to any algorithm and/or data structure for which the necessary visualizer plugins exist.
Categorizing images in Web documents

The Web provides an increasingly powerful and popular publication mechanism. Web documents often contain a large number of images that serve various purposes. Identifying the functional categories of these images is an important task in Web repurposing. This article describes a study on the functional categorization of Web images using data collected from news Web sites. As the popularity of the Web soars, the content on the Web is increasingly accessed from wireless devices that have small screens and different bandwidths. Because many Web documents contain a large number of images serving different purposes, how to identify the function of each image so that it can be handled accordingly is an important issue in Web content repurposing. Much work remains to be done in function-based image classification of all images. Icons that appear regularly on Web sites (for example, newspaper logos) could be classified by analyzing different editions of the pages for repetitions. For the host class, a combination of detecting repetitive images and face recognition should help significantly.
Rab11 polarization of the Drosophila oocyte: a novel link between membrane trafficking, microtubule organization, and oskar mRNA localization and translation.

The Drosophila embryonic body plan is specified by asymmetries that arise in the oocyte during oogenesis. These asymmetries are apparent in the subcellular distribution of key mRNAs and proteins and in the organization of the microtubule cytoskeleton. We present evidence that the Drosophila oocyte also contains important asymmetries in its membrane trafficking pathways. Specifically, we show that alpha-adaptin and Rab11, which function critically in the endocytic pathways of all previously examined animal cells, are localized to neighboring compartments at the posterior pole of stage 8-10 oocytes. Rab11 and alpha-adaptin localization occurs in the absence of a polarized microtubule cytoskeleton, i.e. in grk null mutants, but is later reinforced and/or refined by Osk, the localization of which is microtubule dependent. Analyses of germline clones of a rab11 partial loss-of-function mutation reveal a requirement for Rab11 in endocytic recycling and in the organization of posterior membrane compartments. Such analyses also reveal a requirement for Rab11 in the organization of microtubule plus ends and osk mRNA localization and translation. We propose that microtubule plus ends and, possibly, translation factors for osk mRNA are anchored to posterior membrane compartments that are defined by Rab11-mediated trafficking and reinforced by Rab11-Osk interactions.
The Role of Hemocytes in the Hawaiian Bobtail Squid, Euprymna scolopes: A Model Organism for Studying Beneficial Host–Microbe Interactions

Most, if not all, animals engage in associations with bacterial symbionts. Understanding the mechanisms by which host immune systems and beneficial bacteria communicate is a fundamental question in the fields of immunology and symbiosis. The Hawaiian bobtail squid (Euprymna scolopes) engages in two known symbioses; a binary relationship with the light organ symbiont Vibrio fischeri, and a bacterial consortium within a specialized organ of the female reproductive system, the accessory nidamental gland (ANG). E. scolopes has a well-developed circulatory system that allows immune cells (hemocytes) to migrate into tissues, including the light organ and ANG. In the association with V. fischeri, hemocytes are thought to have a number of roles in the management of symbiosis, including the recognition of non-symbiotic bacteria and the contribution of chitin as a nutrient source for V. fischeri. Hemocytes are hypothesized to recognize bacteria through interactions between pattern recognition receptors and microbe-associated molecular patterns. Colonization by V. fischeri has been shown to affect the bacteria-binding behavior, gene expression, and proteome of hemocytes, indicating that the symbiont can modulate host immune function. In the ANG, hemocytes have also been observed interacting with the residing bacterial community. As a model host, E. scolopes offers a unique opportunity to study how the innate immune system interacts with both a binary and consortial symbiosis. This mini review will recapitulate what is known about the role of hemocytes in the light organ association and offer future directions for understanding how these immune cells interact with multiple types of symbioses.
Dynamics of soil exploration by fine roots down to a depth of 10 m throughout the entire rotation in Eucalyptus grandis plantations

Although highly weathered soils cover considerable areas in tropical regions, little is known about exploration by roots in deep soil layers. Intensively managed Eucalyptus plantations are simple forest ecosystems that can provide an insight into the belowground growth strategy of fast-growing tropical trees. Fast exploration of deep soil layers by eucalypt fine roots may contribute to achieving a gross primary production that is among the highest in the world for forests. Soil exploration by fine roots down to a depth of 10 m was studied throughout the complete cycle in Eucalyptus grandis plantations managed in short rotation. Intersects of fine roots, less than 1 mm in diameter, and medium-sized roots, 1–3 mm in diameter, were counted on trench walls in a chronosequence of 1-, 2-, 3.5-, and 6-year-old plantations on a sandy soil, as well as in an adjacent 6-year-old stand growing in a clayey soil. Two soil profiles were studied down to a depth of 10 m in each stand (down to 6 m at ages 1 and 2 years) and 4 soil profiles down to 1.5–3.0 m deep. The root intersects were counted on 224 m2 of trench walls in 15 pits. Monitoring the soil water content showed that, after clear-cutting, almost all the available water stored down to a depth of 7 m was taken up by tree roots within 1.1 year of planting. The soil space was explored intensively by fine roots down to a depth of 3 m from 1 year after planting, with an increase in anisotropy in the upper layers throughout the rotation. About 60% of fine root intersects were found at a depth of more than 1 m, irrespective of stand age. The root distribution was isotropic in deep soil layers and kriged maps showed fine root clumping. A considerable volume of soil was explored by fine roots in eucalypt plantations on deep tropical soils, which might prevent water and nutrient losses by deep drainage after canopy closure and contribute to maximizing resource uses.
Brain and Muscle Redox Imbalance Elicited by Acute Ethylmalonic Acid Administration

Ethylmalonic acid (EMA) accumulates in tissues and biological fluids of patients affected by short-chain acyl-CoA dehydrogenase deficiency (SCADD) and ethylmalonic encephalopathy, illnesses characterized by neurological and muscular symptoms. Considering that the mechanisms responsible for the brain and skeletal muscle damage in these diseases are poorly known, in the present work we investigated the effects of acute EMA administration on redox status parameters in cerebral cortex and skeletal muscle from 30-day-old rats. Animals received three subcutaneous injections of EMA (6 μmol/g; 90 min interval between injections) and were killed 1 h after the last administration. Control animals received saline in the same volumes. EMA administration significantly increased thiobarbituric acid-reactive substances levels in cerebral cortex and skeletal muscle, indicating increased lipid peroxidation. In addition, carbonyl content was increased in EMA-treated animal skeletal muscle when compared to the saline group. EMA administration also significantly increased 2’,7’-dihydrodichlorofluorescein oxidation and superoxide production (reactive species markers), and decreased glutathione peroxidase activity in cerebral cortex, while glutathione levels were decreased only in skeletal muscle. On the other hand, respiratory chain complex I-III activity was altered by acute EMA administration neither in cerebral cortex nor in skeletal muscle. The present results show that acute EMA administration elicits oxidative stress in rat brain and skeletal muscle, suggesting that oxidative damage may be involved in the pathophysiology of the brain and muscle symptoms found in patients affected by SCADD and ethylmalonic encephalopathy.
Optimal hard fusion strategies for cognitive radio networks

Optimization of hard fusion spectrum sensing using the k-out-of-N rule is considered. Two different setups are used to derive the optimal k. A throughput optimization setup is defined by minimizing the probability of false alarm subject to a probability of detection constraint representing the interference of a cognitive radio with the primary user, and an interference management setup is considered by maximizing the probability of detection subject to a false alarm rate constraint. It is shown that the underlying problems can be simplified to equality constrained optimization problems and an algorithm to solve them is presented. We show the throughput optimization and interference management setups are dual. The simulation results show the majority rule is optimal or near optimal for the desirable range of false alarm and detection rates for a cognitive radio network. Furthermore, an energy efficient setup is considered where the number of cognitive radios is to be minimized for the AND and the OR rule and a certain probability of detection and false alarm constraint. The simulation results show that the OR rule outperforms the AND rule in terms of energy efficiency.
Nicardipine-Induced Acute Pulmonary Edema: A Rare but Severe Complication of Tocolysis

We report four cases of acute pulmonary edema that occurred during treatment by intravenous tocolysis using nicardipine in pregnancy patients with no previous heart problems. Clinical severity justified hospitalization in intensive care unit (ICU) each time. Acute dyspnea has begun at an average of 63 hours after initiation of treatment. For all patients, the first diagnosis suspected was pulmonary embolism. The patients' condition improved rapidly with appropriate diuretic treatment and by modifying the tocolysis. The use of intravenous nicardipine is widely used for tocolysis in France even if its prescription does not have a marketing authorization. The pathophysiological mechanisms of this complication remain unclear. The main reported risk factors are spontaneous preterm labor, multiple pregnancy, concomitant obstetrical disease, association with beta-agonists, and fetal lung maturation corticotherapy. A better knowledge of this rare but serious adverse event should improve the management of patients. Nifedipine or atosiban, the efficiency of which tocolysis was also studied, could be an alternative.
Masking within and across visual dimensions: Psychophysical evidence for perceptual segregation of color and motion

Abstract Visual masking can result from the interference of perceptual signals. According to the principle of functional specialization, interference should be greatest when signal and mask belong to the same visual attribute (e.g., color or motion) and least when they belong to different ones. We provide evidence to support this view and show that the time course of masking is visual attribute specific. First, we show that a color target is masked most effectively by color (homogeneous target-mask pair) and least effectively by motion (heterogeneous pair) and vice versa for a motion target. Second, we show that the time at which the mask is most effective depends strongly on the target-mask pairing. Heterogeneous masking is strongest when the mask is presented before the target (forward masking) but this is not true of homogeneous masking. This finding supports a delayed cross-feature interaction due to segregated processing sites. Third, lengthening the stimulus onset asynchrony between target and mask leads to a faster improvement in color than in motion detectability, lending support for a faster color processing system and consistent with reports of perceptual asynchrony in vision. In summary, we present three lines of psychophysical evidence, all of which support a segregated neural coding scheme for color and motion in the human brain.
Mean value conjectures for rational maps

Let p be a polynomial in one complex variable. Smale's mean value conjecture estimates |p′(z)| in terms of the gradient of a chord from (z, p(z)) to some stationary point on the graph of p. The conjecture does not immediately generalize to rational maps since its formulation is invariant under the group of affine maps, not the full Möbius group. Here we give two possible generalizations to rational maps, both of which are Möbius invariant. In both cases we prove a version with a weaker constant, in parallel to the situation for Smale's mean value conjecture. Finally, we discuss some candidate extremal rational maps, namely rational maps all of whose critical points are fixed points.
The pricing of discretely sampled Asian and lookback options: a change of numeraire approach

This paper considers the pricing of discretely sampled Asian and lookback options with floating and fixed strikes. In the modelling framework of Black and Scholes (1973), it is shown that a change of numeraire of the martingale measure can be used to reduce the dimension of these path-dependent option pricing problems to one in addition time. This means that the pricing problems can be solved by numerically solving onedimensional partial differential equations. The author demonstrates how a Crank‐ Nicolson scheme can be applied to the numerical solution. Finally, the methodology is extended to the case when the underlying stock exhibits discontinuous returns, and it is shown that in this case the Asian and lookback option pricing problems can be solved by numerically solving one-dimensional partial integrodifferential equations.
Features of ChIP-seq data peak calling algorithms with good operating characteristics

Author description Reuben Thomas is a Staff Research Scientist in the Bioinformatics Core at Gladstone Institutes Sean Thomas is a Staff Research Scientist in the Bioinformatics Core at Gladstone Institutes Alisha K Holloway is the Director of Bioinformatics at Phylos Biosciences, visiting scientist at Gladstone Institutes and Adjunct Assistant Professor in Biostatistics at the University of California, San Francisco. Katherine S Pollard is a Senior Investigator at Gladstone Institutes and Professor of Biostatistics at University of California, San Francisco. Key Points Peak-calling using Chip-seq data consists of two sub-problems: identifying candidate peaks and testing candidate peaks for statistical significance. Twelve features of the two sub-problems of peak-calling methods are identified. Methods that explicitly combine the signals from ChIP and input samples are less powerful than methods that do not. Methods that use windows of different sizes to scan the genome for potential peaks are more powerful than ones that do not. Methods that use a Poisson test to rank their candidate peaks are more powerful than those that use a Binomial test. Abstract Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is an important tool for studying gene regulatory proteins, such as transcription factors and histones. Peak calling is one of the first steps in analysis of these data. Peak-calling consists of two sub-problems: identifying candidate peaks and testing candidate peaks for statistical significance. We surveyed 30 methods and identified 12 features of the two sub-problems that distinguish methods from each other. We picked six methods (GEM, MACS2, MUSIC, BCP, TM and ZINBA) that span this feature space and used a combination of 300 simulated ChIP-seq data sets, 3 real data sets and mathematical analyses to identify features of methods that allow some to perform better than others. We prove that methods that explicitly combine the signals from ChIP and input samples are less powerful than methods that do not. Methods that use windows of different sizes are more powerful than ones that do not. For statistical testing of candidate peaks, methods that use a Poisson test to rank their candidate peaks are more powerful than those that use a Binomial test. BCP and MACS2 have the best operating characteristics on simulated transcription factor binding data. GEM has the highest fraction of the top 500 peaks containing the binding motif of the immunoprecipitated factor, with 50% of its peaks within 10 base pairs (bp) of a motif. BCP and MUSIC perform best on histone data. These findings provide guidance and rationale for selecting the best peak caller for a given application.