Miracle-dz/UniFAR-FTUs huggingface dataset:
Cost-Effective Software Based Fault-Tolerant Routing in Pipelined Networks *

This paper presents a software based approach to fault-tolerant routing in networks using wormhole or virtual cut-through switching. When a message encounters a faulty output link, it is removed from the network by the local router and delivered to the messaging layer of the local node’s operating system. The message passing software can re-route this message, possibly along non-minimal paths. Alternatively the message may be addressed to an intermediate node, which will forward the message to the destination. A message may encounter multiple faults and pass through multiple intermediate nodes. The proposed techniques are applicable to both obliviously and adaptively routed networks. The techniques are specifically targeted towards commercial multiprocessors where the mean time to repair (MTTR) is much smaller than the mean time between router failures (MTBF), i.e., it is sufficient to tolerate a maximum of 2-3 failures. This paper presents requirements for buffer management, deadlock freedom and livelock freedom. Simulation results are presented to evaluate the degradation in latency and throughput as a function of the number and distribution of faults. There are several advantages of such an approach. Router designs are minimally impacted, and thus remain compact and fast. Only messages that encounter faulty components are affected, while the machine is ensured of continued operation until the faulty components can be replaced. The technique leverages existing network technology, and is a good candidate for incorporation into the next generation of multiprocessor networks.
Boron Toxicity Tolerance in Barley through Reduced Expression of the Multifunctional Aquaporin HvNIP2;11[W]

Boron (B) toxicity is a significant limitation to cereal crop production in a number of regions worldwide. Here we describe the cloning of a gene from barley (Hordeum vulgare), underlying the chromosome 6H B toxicity tolerance quantitative trait locus. It is the second B toxicity tolerance gene identified in barley. Previously, we identified the gene Bot1 that functions as an efflux transporter in B toxicity-tolerant barley to move B out of the plant. The gene identified in this work encodes HvNIP2;1, an aquaporin from the nodulin-26-like intrinsic protein (NIP) subfamily that was recently described as a silicon influx transporter in barley and rice (Oryza sativa). Here we show that a rice mutant for this gene also shows reduced B accumulation in leaf blades compared to wild type and that the mutant protein alters growth of yeast (Saccharomyces cerevisiae) under high B. HvNIP2;1 facilitates significant transport of B when expressed in Xenopus oocytes compared to controls and to another NIP (NOD26), and also in yeast plasma membranes that appear to have relatively high B permeability. We propose that tolerance to high soil B is mediated by reduced expression of HvNIP2;1 to limit B uptake, as well as by increased expression of Bot1 to remove B from roots and sensitive tissues. Together with Bot1, the multifunctional aquaporin HvNIP2;1 is an important determinant of B toxicity tolerance in barley.
Coronary artery calcium score prediction of all cause mortality and cardiovascular events in people with type 2 diabetes: systematic review and meta-analysis

Objective To investigate the association of coronary artery calcium score with all cause mortality and cardiovascular events in people with type 2 diabetes. Design Systematic review and meta-analysis of observational studies. Data sources Studies were identified from Embase, PubMed, and abstracts from the 2011 and 2012 annual meetings of the American Diabetes Association, European Association for the Study of Diabetes, American College of Cardiology, and American Heart Association (2011). Eligibility criteria Prospective studies that evaluated baseline coronary artery calcium score in people with type 2 diabetes and subsequent all cause mortality or cardiovascular events (fatal and non-fatal). Data extraction Two independent reviewers extracted the data. The predictive value of the coronary artery calcium score was assessed by random effects model. Results Eight studies were included (n=6521; 802 events; mean follow-up 5.18 years). The relative risk for all cause mortality or cardiovascular events, or both comparing a total coronary artery calcium score of ≥10 with a score of <10 was 5.47 (95% confidence interval 2.59 to 11.53; I2=82.4%, P<0.001). The overall sensitivity of a total coronary artery calcium score of ≥10 for this composite outcome was 94% (95% confidence interval 89% to 96%), with a specificity of 34% (24% to 44%). The positive and negative likelihood ratios were 1.41 (95% confidence interval 1.20 to 1.66) and 0.18 (0.10 to 0.30), respectively. For people with a coronary artery calcium score of <10, the post-test probability of the composite outcome was about 1.8%, representing a 6.8-fold reduction from the pretest probability. Four studies evaluated cardiovascular events as the outcome (n=1805; 351 events). The relative risk for cardiovascular events comparing a total coronary artery calcium score of ≥10 with a score of <10 was 9.22 (2.73 to 31.07; I2=76.7%, P=0.005). The positive and negative likelihood ratios were 1.67 (1.30 to 2.17) and 0.11 (0.04 to 0.29), respectively. Conclusion In people with type 2 diabetes, a coronary artery calcium score of ≥10 predicts all cause mortality or cardiovascular events, or both, and cardiovascular events alone, with high sensitivity but low specificity. Clinically, the finding of a coronary artery calcium score of <10 may facilitate risk stratification by enabling the identification of people at low risk within this high risk population.
A pheromone-based utility model for collaborative foraging

Multi-agent research often borrows from biology, where remarkable examples of collective intelligence may be found. One interesting example is ant colonies¿ use of pheromones as a joint communication mechanism. In this paper we propose two pheromone-based algorithms for artificial agent foraging, trail-creation, and other tasks. Whereas practically all previous work in this area has focused on biologically-plausible but ad-hoc single pheromone models, we have developed a formalism which uses multiple pheromones to guide cooperative tasks. This model bears some similarity to reinforcement learning. However, our model takes advantage of symmetries common to foraging environments which enables it to achieve much faster reward propagation than reinforcement learning does. Using this approach we demonstrate cooperative behaviors well beyond the previous ant-foraging work, including the ability to create optimal foraging paths in the presence of obstacles, to cope with dynamic environments, and to follow tours with multiple waypoints.We believe that this model may be used for more complex problems still.
A search for distant radio galaxies from SUMSS and NVSS ¿ II. Optical spectroscopy

This is the second in a series of papers presenting observations and results for a sample of 76 ultra-steep-spectrum (USS) radio sources in the southern hemisphere designed to nd galaxies at high redshift. Here we focus on the optical spectroscopy program for 53 galaxies in the sample. We report 35 spectroscopic redshifts, based on observations with the Very Large Telescope (VLT), the New Technology Telescope (NTT) and the Australian National University’s 2.3m telescope; they include v e radio galaxies with z > 3. Spectroscopic redshifts for the remaining 18 galaxies could not be conrmed: three are occulted by Galactic stars, eight show continuum emission but no discernible spectral lines, whilst the remaining seven galaxies are undetected in medium-deep VLT integrations. The latter are either at very high redshift (z > 7) or heavily obscured by dust. A discussion of the eciency of the USS technique is presented. Based on the similar space density of z > 3 radio galaxies in our sample compared with other USS-selected samples, we argue that USS selection at 843{1400MHz is an ecien t and reliable technique for nding distant radio galaxies.
Age-Related Changes in the Global DNA Methylation Profile of Leukocytes Are Linked to Nutrition but Are Not Associated with the MTHFR C677T Genotype or to Functional Capacities

Global DNA methylation of peripheral blood leukocytes has been recently proposed as a potential biomarker for disease risk. However, the amplitude of the changes in DNA methylation associated with normal aging and the impacts of environmental changes on this variation are still unclear. In this context, we evaluated the association of global DNA methylation with nutritional habits, tobacco smoking, body mass index (BMI), clinical laboratory parameters, polymorphism C677T MTHFR, functional cognition and the daily practice of physical activity in a cancer-free older population. Leukocyte global DNA methylation from 126 older individuals was quantified using a high-throughput ELISA-based method. Global DNA hypomethylation was observed in older individuals when compared to a younger population (p = 0.0469), confirming changes in DNA methylation in the aging process. Furthermore, the methylation profile of elders was correlated with the daily ingestion of carbohydrates (p = 0.0494), lipids (p = 0.0494), vitamin B6 (p = 0.0421), magnesium (p = 0.0302), and also to the serum levels of total protein (p = 0.0004), alpha 2 globulin (p = 0.0013) and albumin (p = 0.0015). No statistically significant difference was observed when global DNA methylation were stratified according to C677T MTHFR genotypes (p = 0.7200), BMI (p = 0.1170), smoking habit (p = 0.4382), physical activity in daily life (p = 0.8492), scored cognitive function (p = 0.7229) or depression state (p = 0.8301). Our data indicate that age-related variations in the global DNA methylation profile of leukocytes might be modulated by the daily intake of carbohydrates, lipids, vitamin B6, and magnesium and be associated with serum protein levels, however it is independent of C677T MTHFR genotype and not correlated with BMI, smoking habit, cognitive function or the routine physical activities.
Application of adsorption on activated carbons and natural zeolite for the removal of lincomycin from wastewater of swine production industry

ii ACKNOWLEDGEMENTS . iv DEDICATION . v TABLE OF CONTENTS . vi LIST OF TABLES . xi LIST OF FIGURES . xiii NOMENCLATURE AND ABBREVIATIONS. xv Chapter
A method to predict fatigue crack initiation in metals using dislocation dynamics

Abstract A theory is proposed to predict the initiation of fatigue cracks using cyclic dislocation dynamics (DD) simulations. The evolution of dislocation networks in a grain is simulated over several cycles. It is shown that the dislocation density and the energy stored in the dislocation networks increase with the number of cycles. The results of the DD simulations are used to construct an energy balance expression for crack initiation. A hypothetical crack is inserted into the grain, and the Gibbs energy consisting of the energy of the dislocation structure, the surface energy of the hypothetical crack, and the reduction in continuum energy is evaluated. Once the Gibbs energy attains a maximum, the dislocation structure becomes unstable, and it becomes energetically more favorable to form a real crack. The proposed method is applied to oxygen-free high conductivity copper, and the results are compared against experiments. Finally, it is shown how the method can be amended to account for environmental effects.
Switching between executive and default mode networks in posttraumatic stress disorder: alterations in functional connectivity.

UNLABELLED Working memory processing and resting-state connectivity in the default mode network are altered in patients with posttraumatic stress disorder (PTSD). Because the ability to effortlessly switch between concentration on a task and an idling state during rest is implicated in both these alterations, we undertook a functional magnetic resonance imaging study with a block design to analyze task-induced modulations in connectivity. METHODS We performed a working memory task and psychophysiologic interaction analyses with the posterior cingulate cortex and the medial prefrontal cortex as seed regions during fixation in 12 patients with severe, chronic PTSD and 12 healthy controls. RESULTS During the working memory task, the control group showed significantly stronger connectivity with areas implicated in the salience and executive networks, including the right inferior frontal gyrus and the right inferior parietal lobule. The PTSD group showed stronger connectivity with areas implicated in the default mode network, namely enhanced connectivity between the posterior cingulate cortex and the right superior frontal gyrus and between the medial prefrontal cortex and the left parahippocampal gyrus. LIMITATIONS Because we were studying alterations in patients with severe, chronic PTSD, we could not exclude patients taking medication. The small sample size may have limited the power of our analyses. To avoid multiple testing in a small sample, we only used 2 seed regions for our analyses. CONCLUSION The different patterns of connectivity imply significant group differences with task-induced switches (i.e., engaging and disengaging the default mode network and the central-executive network).
Spatial and temporal profile of apoptosis following lateral fluid percussion brain injury.

OBJECTIVE To investigate the spatial and temporal profile of neural cell apoptosis following traumatic brain injury (TBI). METHODS In addition to morphological evidence of apoptosis, TUNEL histochemistry assay was used to identify DNA fragmentation in situ at both light and electron microscopic levels, whereas characteristic internucleosomal DNA fragmentation of apoptosis was demonstrated by DNA gel electrophoresis. RESULTS Using TUNEL method, we detected massive cells with extensive DNA fragmentation in different regions of the brains of rats subjected to experimental traumatic brain injury. Compared with the sham controls, in the injured cortex, the apoptotic cells were detectable for up to 24 h and reached a peak at 1 week after injury. The number of apoptotic cells in the white matter h ad a significant increase as early as 12 h after injury and peaked at 1 wee k. The number of apoptotic cells increased in the hippocampus at 72 h, whereas i n the thalamus, the peak of apoptotic cells was at 2 weeks after injury. The number of apoptotic cells in most regions returned to sham values 2 months after in jury. Gel electrophoresis of DNA extracted from affected areas of the injured br ain revealed only internucleosomal fragmentation at 185-bp intervals, a feature originally described in apoptotic cell death. And no DNA ladder was detectable in the cortex and hippocampus contralateral to the injured hemisphere. CONCLUSIONS These data suggest that in addition to the well described necrotic cell death, a temporal course of apoptotic cell death is initiated after brain trauma in selected brain regions.
Role of vav1 in the Lipopolysaccharide-Mediated Upregulation of Inducible Nitric Oxide Synthase Production and Nuclear Factor for Interleukin-6 Expression Activity in Murine Macrophages

ABSTRACT vav1 has been shown to play a key role in lymphocyte development and activation, but its potential importance in macrophage activation has received little attention. We have previously reported that exposure of macrophages to bacterial lipopolysaccharide (LPS) leads to increased activity of hck and other src-related tyrosine kinases and to the prompt phosphorylation of vav1 on tyrosine. In this study, we tested the role of vav1 in macrophage responses to LPS, focusing on the upregulation of nuclear factor for interleukin-6 expression (NF-IL-6) activity and inducible nitric oxide synthase (iNOS) protein accumulation in RAW-TT10 murine macrophages. We established a series of stable cell lines expressing three mutant forms of vav1 in a tetracycline-regulatable fashion: (i) a form producing a truncated protein, vavC; (ii) a form containing a point mutation in the regulatory tyrosine residue, vavYF174; and (iii) a form with an in-frame deletion of 6 amino acids required for the guanidine nucleotide exchange factor (GEF) activity of vav1 for rac family GTPases, vavGEFmt. Expression of the truncated mutant (but not the other two mutants) has been reported to interfere with T-cell activation. In contrast, we now demonstrate that expression of any of the three mutant forms of vav1 in RAW-TT10 cells consistently inhibited LPS-mediated increases in iNOS protein accumulation and NF-IL-6 activity. These data provide direct evidence for a role for vav1 in LPS-mediated macrophage activation and iNOS production and suggest that vav1 functions in part via activation of NF-IL-6. Furthermore, these findings indicate that the GEF activity of vav1 is required for its ability to mediate macrophage activation by LPS.
A Comparison of Biomechanical Parameters between Two Methods of Countermovement Jump

The purpose of the present study was to compare of biomechanical parameters between countermovement jump with arm swing and countermovement jump no arm swing, and investigate the effect of arm swing to enhance the performance of countermovement jump. Five male high level athletes participated in this study were volleyball players (age: 20.2 ± 1.06 years; body mass: 82.77 ± 19.3 kg; height: 189.6 ± 9.34 cm). The two methods of countermovement jumps were performed on a strain gage force platform, high-speed motion capture system at a frequency of 250 Hz, video point v 2.5 2D motion analysis for kinematic parameters, and the integration was calculated by OriginPro 8.5 SR1 Data Analysis and Graphing Software. The following variables were analyzed: Maximum height, Low point, Height at TO, Maximum force, Velocity at TO, Kinetic Energy at TO, Potential Energy at TO, Impulse at TO, and the angles of lower limb at low point and take off. To examine the importance of biomechanical parameters on countermovement jump, a comparison between countermovement with arm swing and countermovement no arm swing and a correlations between arm swing and biomechanical parameters were used. The results showed, the performance (countermovement) was better among CMJ arm swing than CMJ no arm swing, of the parameters (Maximum height, Maximum force, Velocity at TO, Kinetic Energy at TO, Potential Energy at TO), and Arm swing was strongly correlated with Maximum force, Velocity at TO, Kinetic Energy at TO, Potential Energy at TO, and Knee angle at Low point. And Maximum height was strongly correlated with Height at TO, Maximum force, Velocity at TO, Kinetic Energy at TO, Potential Energy at TO and Impulse at TO. Finally, the percentage contribution arm swing in improving jump height was noted that arm swing led to an improvement in the CMJ arm swing by 27.08%.
Explicit Linear Kernels via Dynamic Programming

Several algorithmic meta-theorems on kernelization have appeared in the last years, starting with the result [Bodlaender et al., FOCS 2009] on graphs of bounded genus, then generalized by [Fomin et al., SODA 2010] to graphs excluding a fixed minor, and by [Kim et al., ICALP 2013] to graphs excluding a fixed topological minor. Typically, these results guarantee the existence of linear or polynomial kernels on sparse graph classes for problems satisfying some generic conditions but, mainly due to their generality, it is not clear how to derive from them constructive kernels with explicit constants. In this paper we make a step toward a fully constructive meta-kernelization theory on sparse graphs. Our approach is based on a more explicit protrusion replacement machinery that, instead of expressibility in CMSO logic, uses dynamic programming, which allows us to find an explicit upper bound on the size of the derived kernels. We demonstrate the usefulness of our techniques by providing the first explicit linear kernels for r-Dominating Set and r-Scattered Set on apex-minor-free graphs, and for Planar-F-Deletion on graphs excluding a fixed (topological) minor in the case where all the graphs in F are connected.
Quantitative Assessment of the Association between rs2046210 at 6q25.1 and Breast Cancer Risk

Genome-wide association studies (GWAS) have identified several genetic susceptibility loci for breast cancer (BC). One of them, conducted among Chinese women, found an association of rs2046210 at 6q25.1 with the risk of BC recently. Since then, numerous association studies have been carried out to investigate the relationship between this polymorphism and BC risk in various populations. However, these have yielded contradictory results. We therefore performed a meta-analysis to clarify this inconsistency. Overall, a total of 235003 subjects based on 13 studies were included in our study. Significantly increased BC risk was detected in the pooled analysis [allele contrast: OR = 1.13, 95%CI = 1.10–1.17, P(Z) <10−5, P(Q) <10−4; dominant model: OR = 1.21, 95%CI = 1.14–1.27, P(Z) <10−5, P(Q) <10−4; recessive model: OR = 1.18, 95%CI = 1.12–1.24, P(Z) <10−5, P(Q) = 0.04]. In addition, our data revealed that rs2046210 conferred greater risk in estrogen receptor (ER)-negative tumors [OR = 1.27, 95%CI = 1.15–1.40, P(Z) <10−5, P(Q) <10−4] than in ER-positive ones [OR = 1.18, 95%CI = 1.09–1.28, P(Z) <10−4, P(Q) = 0.0003]. When stratified by ethnicity, significant associations were found in Caucasian and Asian populations, but not detected among Africans. There was evidence of heterogeneity (P<0.05), however, the heterogeneity largely disappeared after stratification by ethnicity. The present meta-analysis demonstrated that the rs2046210 polymorphism may be associated with increased BC susceptibility, but this association varies in different ethnicities.
Driving DNA transposition by lentiviral protein transduction

Gene vectors derived from DNA transposable elements have become powerful molecular tools in biomedical research and are slowly moving into the clinic as carriers of therapeutic genes. Conventional uses of DNA transposon-based gene vehicles rely on the intracellular production of the transposase protein from transfected nucleic acids. The transposase mediates mobilization of the DNA transposon, which is typically provided in the context of plasmid DNA. In recent work, we established lentiviral protein transduction from Gag precursors as a new strategy for direct delivery of the transposase protein. Inspired by the natural properties of infecting viruses to carry their own enzymes, we loaded lentivirus-derived particles not only with vector genomes carrying the DNA transposon vector but also with hundreds of transposase subunits. Such particles were found to drive efficient transposition of the piggyBac transposable element in a range of different cell types, including primary cells, and offer a new transposase delivery approach that guarantees short-term activity and limits potential cytotoxicity. DNA transposon vectors, originally developed and launched as a non-viral alternative to viral integrating vectors, have truly become viral. Here, we briefly review our findings and speculate on the perspectives and potential advantages of transposase delivery by lentiviral protein transduction.
Reply to “Comments on ‘A New Feedforward Hybrid Active Noise Control System’”

In this reply, we first provide a MATLAB program used in our simulations and clarify our claim regarding the occurrence of the so-called “firework” noise in the broadband active noise control (BANC) system. Next, we present some simulation results of the BANC using the FXLMS and the normalized FXLMS (NFXLMS) algorithms in the presence of a real noise signal generated by a large-scale rotating machine. The real noise is a mixture of several low-frequency sinusoids and a wideband noise component. The existence of “firework” noise is again confirmed in the BANC system when it is made to converge relatively fast.