Miracle-dz/UniFAR-FTUs huggingface dataset:
Virtual-GEMS : An Infrastructure To Simulate Virtual Machines

Recently, virtualization has become a hot topic in computer architecture research. The cost reduction and management simplification brought by server consolidation are good reasons why virtualization has become so popular. But there is a lack of tools for researchers to seek new proposals of architectures that improve the performance of virtualized systems. To fill this niche we have developed VirtualGEMS, a multiprocessor simulator that allows us to simulate the behavior of a virtualized system and research new architectures suitable for virtualization. For testing VirtualGEMS, we describe and evaluate some configurations for the shared L2 cache of a 16-core CMP running 4 virtual machines. Our main contribution is the ease of configuration of simulations of virtualized workloads. Virtual-GEMS uses ordinary system checkpoints as virtual machines. This way, it avoids the need to create complex checkpoints including the hypervisor and the images of the virtual machines to simulate.
Atg9 sorting from mitochondria is impaired in early secretion and VFT-complex mutants in Saccharomyces cerevisiae

In eukaryotic cells, the turnover of long-lived proteins and large cytoplasmic structures is mediated by autophagy. Components that have to be eliminated are sequestered into double-membrane vesicles called autophagosomes and delivered into the lysosome or vacuole where they are destroyed by resident hydrolases. The integral membrane protein Atg9 is essential for both autophagy and the cytoplasm-to-vacuole targeting pathway, a selective biosynthetic process in Saccharomyces cerevisiae that is mechanistically and morphologically similar to autophagy. Atg9 cycles between the pre-autophagosomal structure, the putative site of double-membrane vesicle biogenesis and mitochondria. To understand the function of Atg9, and also its trafficking mode between these two locations, we identified mutants that affect specific Atg9 transport steps. We recently reported that five Atg proteins and phosphatidylinositol-3-phosphate regulate Atg9 recycling from the pre-autophagosomal structure. Here, we describe a different category of mutants that blocks Atg9 sorting from mitochondria. All mutants have been previously shown to be required for the normal progression of both the Cvt pathway and autophagy, but their precise role in these transport routes was unknown.
Is Branched-Chain Amino Acids Supplementation an Efficient Nutritional Strategy to Alleviate Skeletal Muscle Damage? A Systematic Review

Amino acids and more precisely, branched-chain amino acids (BCAAs), are usually consumed as nutritional supplements by many athletes and people involved in regular and moderate physical activities regardless of their practice level. BCAAs have been initially shown to increase muscle mass and have also been implicated in the limitation of structural and metabolic alterations associated with exercise damage. This systematic review provides a comprehensive analysis of the literature regarding the beneficial effects of BCAAs supplementation within the context of exercise-induced muscle damage or muscle injury. The potential benefit of a BCAAs supplementation was also analyzed according to the supplementation strategy—amount of BCAAs, frequency and duration of the supplementation—and the extent of muscle damage. The review protocol was registered prospectively with Prospective Register for Systematic Reviews (registration number CRD42017073006) and followed Preferred Reporting Items for Systematic reviews and Meta-Analyses guidelines. Literature search was performed from the date of commencement until August 2017 using four online databases (Medline, Cochrane library, Web of science and ScienceDirect). Original research articles: (i) written in English; (ii) describing experiments performed in Humans who received at least one oral BCAAs supplementation composed of leucine, isoleucine and valine mixture only as a nutritional strategy and (iii) reporting a follow-up of at least one day after exercise-induced muscle damage, were included in the systematic review analysis. Quality assessment was undertaken independently using the Quality Criteria Checklist for Primary Research. Changes in indirect markers of muscle damage were considered as primary outcome measures. Secondary outcome measures were the extent of change in indirect markers of muscle damage. In total, 11 studies were included in the analysis. A high heterogeneity was found regarding the different outcomes of these studies. The risk of bias was moderate considering the quality ratings were positive for six and neutral for three. Although a small number of studies were included, BCAAs supplementation can be efficacious on outcomes of exercise-induced muscle damage, as long as the extent of muscle damage was low-to-moderate, the supplementation strategy combined a high daily BCAAs intake (>200 mg kg−1 day−1) for a long period of time (>10 days); it was especially effective if taken prior to the damaging exercise.
Complex dynamics in intimate partner violence: a time series study of 16 women.

OBJECTIVE Three theories attempt to explain the dynamics of intimate partner violence, each representing a different dynamic pattern of violence: periodic, chaotic, and random. But few studies assess violence and its potential predictors in real time or permit assessment of the dynamics of violence. The purpose of this exploratory study was to estimate the degree of complexity in patterns of violence and identify predictors of violent events. METHOD This time series study was conducted between September 2006 and April 2007 among 16 adult women presenting to a university-affiliated family health center who had experienced violence within the past month. Women completed a daily telephone assessment of household environment and marital relationship for 2 months. To assess the degree of complexity, 3 different measures were used. Lyapunov exponents and saturation of correlation dimension were used to approximate dynamic patterns. Vector autoregression identified prior-week predictors of violence. Results were pooled across the 16 subjects who provided daily reports using meta-analytic techniques. RESULTS Most relationships exhibited complex dynamics, with all 3 distinct dynamic patterns found. The longer the relationship had lasted, the more predictable and periodic were its dynamics. The more frequent the violence, the more complex and sensitive to change were its dynamics. Comparing dynamic patterns, 3 distinct combinations of significant prior-day and prior-week associations were found. CONCLUSIONS Although complex dynamics were unrelated to duration of violence, there was a dynamic tension between (1) the duration of the relationship and its periodic temporal patterns and (2) the frequency of violence and its complex dynamics. Identification of dynamic patterns may aid understanding of the phenomena of intimate partner violence and lead to novel targeted screening, monitoring, and intervention/treatment approaches.
A METHOD FOR THE QUANTITATIVE ESTIMATION OF CYTOPLASMIC STRUCTURES

A sampling procedure and calculations are described by which electron micrographs of cytoplasmic structures may be quantitatively analyzed. The relative areas occupied by formed bodies and by the "membrane space," the remainder of the cytoplasm, are evaluated. A method for making a measurement of the quantity of endoplasmic reticulum or other membrane profiles is described. The technic and results are illustrated with normal rat liver cells.
Inotropic Effects of Electric Currents

I. Tension was recorded from a segment of a thin bundle of calf or sheep ventricular fibers in which the membrane potential could be changed electrically, using a sucrose-gap technique. After reversal of membrane potential and consequent contracture for 2 to 3 seconds, a positive inotropic effect 2 to 12 times that which occurred during paired-pulse stimulation was obtained. The decay of this potentiated state was slow in resting preparations (average half-life, 95 seconds), but was determined by the number of beats in driven preparations (about eight beats to return to control amplitude). Lengthening consecutive action potentials by subthreshold constant depolarizing currents or 5-mv shifts in the membrane potential by 50-msec current pulses during the plateau phase of successive action potentials caused positive inotropic effects, attaining a steady state in about eight beats. Reversing the polarity of such currents (hyperpolarization) caused negative inotropic effects with the same phase dependency as for depolarizing currents. These negative inotropic effects attained a steady state in six to eight beats. The first action potential after cessation of these currents was close to normal, whereas return to control tension required six to eight beats. The half-life of decay of these negative inotropic states at rest was similar to that of positive inotropic states. Decay of inotropic states in contracting preparations was phase dependent, occurring only during the rapid depolarization and plateau phases of the action potential. II. These and other strength-interval effects on cardiac contractility in a constant chemical and physical environment are consistent with two hypotheses. (1) The presystolic level of intracellular calcium bound to specific (rapid release) sites on the sarcoplasmic reticulum, the inner surfaces of the sarcolemma and T tubules, is a major determinant of the level of [Ca2+]1 attained during the initial phase of an action potential and hence the tension developed by mammalian cardiac muscle (that is, its inotropic state) at that particular instant. (2) The amount of intracellular calcium present at these sites at any instant after an action potential (that is, the moment-to-moment inotropic state of the muscle) is predetermined in the inverse direction of the intersystolic intervals of prior systoles and in the positive direction by the duration and magnitude of the plateau phases of prior action potentials and (for rest periods as long as 10 seconds) the elapsed time, in an exponentially decreasing fashion, since termination of the last absolute refractory period.
Fatigue Life Evaluation of Concrete Bridge Deck Slabs Reinforced with Glass FRP Composite Bars

As bridge deck slabs directly sustain repeated moving wheel loads, they are among the bridge elements most susceptible to fatigue failure. Recently, glass fiber-reinforced polymer (FRP) composites have been widely used as internal reinforcement for concrete bridge deck slabs because they are less expensive as compared to other kinds of FRPs (carbon and aramid). However, there is still a lack of information on the performance of FRP–reinforced concrete elements subjected to cyclic fatigue loading. This paper investigates fatigue behavior and fatigue life of concrete bridge deck slabs reinforced with glass FRP bars. A total of 5 full-scale deck slabs were constructed and tested under concentrated cyclic loading until failure. Different reinforcement types (steel and glass FRP), ratios, and configurations were used. Different schemes of cyclic loading (accelerated variable amplitude fatigue loading) were applied. Results are presented in terms of deflections, strains in concrete and FRP bars, and crack widths at various levels of cyclic loading. The results show the superior fatigue performance and longer fatigue life of concrete bridge deck slabs reinforced with glass FRP composite bars.
Chapter 3 Interaction Between the Immune System and Melanoma

No scientist can escape being fascinated by the complexity of the interplay between innate and adaptive immunity in order to monitor tissue homeostasis, to protect against infectious pathogens and to eliminate damaged cells. One of the most important tasks of the Immune System is to distinguish between “self” and “foreign”. Cancer is formed of cells that suffer several mutations but form still part of the individual body. All types of cancer are caused by the progressive growth of the progeny of a single transformed cell. Curing this disease requires that all the malignant cells have to be removed or destroyed without damaging the patient. To achieve this task the own body has to distinguish between the cells of “the tumor” and their “other cellular” counterparts.
Activation of mitogen‐activated protein kinase cascades during priming of human neutrophils by TNF‐α and GM‐CSF

The signal transduction pathways activated by tumor necrosis factor α (TNF‐α) and granulocyte‐macrophage colony‐stimulating factor (GM‐CSF) that lead to priming of polymorphonuclear leukocytes (PMNs) are unknown. The hypotheses that these cytokines stimulate multiple mitogen‐activated protein kinase (MAPK) cascades, including extracellular signal‐regulated kinases (ERKs), c‐Jun amino‐terminal kinases (JNKs), and p38 MAPK, and that these MAPKs participate in priming of human PMNs were examined. TNF‐α stimulated a dose‐dependent increase in ERK and p38 MAPK activities that was maximal at 10 min. JNKs were not stimulated by TNF‐α or GM‐CSF. GM‐CSF stimulated ERK activity comparable to that of TNF‐α, but GM‐CSF was a less potent stimulus of p38 MAPK activity. The tyrosine kinase inhibitor, genistein, inhibited ERK and p38 MAPK stimulation by both cytokines. The phosphatidylinositol 3‐kinase inhibitor, wortmannin, attenuated stimulation of ERKs and p38 MAPK by GM‐CSF, but not TNF‐α. GM‐CSF, but not TNF‐α, stimulated wortmannin‐sensitive activation of Raf‐1. TNF‐α and GM‐CSF priming of superoxide release stimulated by N‐formyl‐methionyl‐leucyl‐phenylalanine was significantly attenuated by the MEK inhibitor, PD098059, and the p38 MAPK inhibitor, SB203580. Incubation with both MAPK inhibitors produced an additive effect. Our data suggest that TNF‐α and GM‐CSF activate ERKs and p38 MAPK by different signal transduction pathways. Both ERK and p38 MAPK cascades contribute to the ability of TNF‐α and GM‐CSF to prime the respiratory burst response in human PMNs. J. Leukoc. Biol. 64: 537–545; 1998.
Recognizing Multiple Ingredients in Food Images Using a Single-Ingredient Classification Model

Recognizing food images presents unique challenges due to the variable spatial layout and shape changes of ingredients with different cooking and cutting methods. This study introduces an advanced approach for recognizing ingredients segmented from food images. The method localizes the candidate regions of the ingredients using the locating and sliding window techniques. Then, these regions are assigned into ingredient classes using a CNN (Convolutional Neural Network)-based single-ingredient classification model trained on a dataset of single-ingredient images. To address the challenge of processing speed in multi-ingredient recognition, a novel model pruning method is proposed that enhances the efficiency of the classification model. Subsequently, the multi-ingredient identification is achieved through a decision-making scheme, incorporating two novel algorithms. The single-ingredient image dataset, designed in accordance with the book entitled"New Food Ingredients List FOODS 2021", encompasses 9982 images across 110 diverse categories, emphasizing variety in ingredient shapes. In addition, a multi-ingredient image dataset is developed to rigorously evaluate the performance of our approach. Experimental results validate the effectiveness of our method, particularly highlighting its improved capability in recognizing multiple ingredients. This marks a significant advancement in the field of food image analysis.
Point-process high-resolution representations of heartbeat dynamics for multiscale analysis: A CHF survivor prediction study

Multiscale analysis of human heartbeat dynamics has been proved effective in characterizeing cardiovascular control physiology in health and disease. However, estimation of multiscale properties can be affected by the interpolation procedure used to preprocess the unevenly sampled R-R intervals derived from the ECG. To this extent, in this study we propose the estimation of wavelet coefficients and wavelet leaders on the output of inhomogeneous point process models of heartbeat dynamics. The RR interval series is modeled using probability density functions (pdfs) characterizing and predicting the time until the next heartbeat event occurs, as a linear function of the past history. Multiscale analysis is then applied to the pdfs' instantaneous first order moment. The proposed approach is tested on experimental data gathered from 57 congestive heart failure (CHF) patients by evaluating the recognition accuracy in predicting survivor and non-survivor patients, and by comparing performances from the informative point-process based interpolation and non-informative spline-based interpolation. Results demonstrate that multiscale analysis of point-process high-resolution representations achieves the highest prediction accuracy of 65.45%, proving our method as a promising tool to assess risk prediction in CHF patients.
Numerical Predictions and Experimental Verifications for Hydrodynamic Performance of Tidal Stream Turbine

Blade element momentum (BEM) theory is used to design the tidal stream turbine in this paper. ANSYS-CFX and numeca are used to predict the hydrodynamic performance of the turbine. The power coefficient of the turbine obtained by CFD is 39.36% at the design tip speed ratio. A 300mm diameter scale turbine has been built, and the tests were carried out in the circulating water channel, the power coefficient can reach 40.5% at the design tip speed ratio. Through the comparisons between experimental results and CFD results, it proves the application of the numerical method for blade design, and the distributions of the pressure and axial velocity near the blade are analyzed at the end of the paper.
Thermodynamic and experimental study of role of sintering atmospheres and graphite additions on oxide reduction in Astaloy CrM powder compacts

Abstract Several atmospheres based on N2–H2 gaseous mixtures, with occasional additions of CH4 were used to study the sintering behaviour of Astaloy CrM at temperatures of 1100 and 1240°C. Theoretical thermodynamic calculations and sintering experiments, with and without admixed graphite additions, were carried out devoting particular attention to the oxide reduction reactions. The role of carbon in the reduction of oxides is discussed with reference to Boudouard's reaction, proposing the indirect carbothermal reduction as the controlling mechanism. The microstructural characterisation of the material included inspection of the powder particles as well as sintered specimens. It was established that the Astaloy CrM particles contain two distinct types of oxides. One associated with the particle surface and another, mainly constituted by Cr, forming a dispersion of internal oxides. These internal oxides were microstructurally characterised, both directly and by carbon extraction replicas. A selection of powder mixtures containing 0 and 0.4%C additions were used for obtaining tensile specimens in order to assess neck development, by the strength and elongation obtained under various atmospheres and temperature combinations.
The iron-sensing aconitase B binds its own mRNA to prevent sRNA-induced mRNA cleavage

Aconitase is an iron–sulfur protein and a major enzyme of the TCA cycle that catalyzes the conversion of citrate to isocitrate under iron-rich conditions. In Escherichia coli, aconitase B (AcnB) is a typical moonlighting protein that can switch to its apo form (apo-AcnB) which favors binding its own mRNA 3′UTR and stabilize it when intracellular iron become scarce. The small regulatory RNA (sRNA) RyhB has previously been shown to promote RNase E-dependent degradation of acnB mRNA when it was expressed from an ectopic arabinose-dependent promoter, independently of intracellular iron levels. In marked contrast, we report here that expression of RyhB under low-iron conditions did not result in acnB mRNA degradation even when RyhB was bound to acnB ribosome binding site (RBS). Genetic and biochemical evidence suggested that, under low-iron conditions, apo-AcnB bound to acnB 3′UTR close to a RNase E cleavage site that is essential for RyhB-induced acnB mRNA degradation. Whereas RyhB can block acnB translation initiation, RNase E-dependent degradation of acnB was prevented by apo-AcnB binding close to the cleavage site. This previously uncharacterized regulation suggests an intricate post-transcriptional mechanism that represses protein expression while insuring mRNA stability.
Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome

The continuous integration of experimental data into coherent models of the brain is an increasing challenge of modern neuroscience. Such models provide a bridge between structure and activity, and identify the mechanisms giving rise to experimental observations. Nevertheless, structurally realistic network models of spiking neurons are necessarily underconstrained even if experimental data on brain connectivity are incorporated to the best of our knowledge. Guided by physiological observations, any model must therefore explore the parameter ranges within the uncertainty of the data. Based on simulation results alone, however, the mechanisms underlying stable and physiologically realistic activity often remain obscure. We here employ a mean-field reduction of the dynamics, which allows us to include activity constraints into the process of model construction. We shape the phase space of a multi-scale network model of the vision-related areas of macaque cortex by systematically refining its connectivity. Fundamental constraints on the activity, i.e., prohibiting quiescence and requiring global stability, prove sufficient to obtain realistic layer- and area-specific activity. Only small adaptations of the structure are required, showing that the network operates close to an instability. The procedure identifies components of the network critical to its collective dynamics and creates hypotheses for structural data and future experiments. The method can be applied to networks involving any neuron model with a known gain function.