Miracle-dz/UniFAR-FTUs huggingface dataset:
WildFire: a scalable path for SMPs

Researchers have searched for scalable alternatives to the symmetric multiprocessor (SMP) architecture since it was first introduced in 1982. The paper introduces an alternative view of the relationship between scalable technologies and SMPs. Instead of replacing large SMPs with scalable technology, we propose new scalable techniques that allow large SMPs to be tied together efficiently, while maintaining the compatibility with, and performance characteristics of, an SMP. The trade-offs of such an architecture differ from those of traditional, scalable, Non-Uniform Memory Architecture (cc-NUMA) approaches. WildFire is a distributed shared memory (DSM) prototype implementation based on large SMPs. It relies on two techniques for creating application-transparent locality: Coherent Memory Replication (CMR), which is a variation of Simple COMA/Reactive NUMA, and Hierarchical Affinity Scheduling (HAS). These two optimizations create extra node locality, which blurs the node boundaries to an application such that SMP-like performance can be achieved with no NUMA-specific optimizations. We present a performance study of a large OLTP benchmark running on DSMs built from various sized nodes and with varying amounts of application-transparent locality. WildFire's measured performance is shown to be more than two times that of an unoptimized NUMA implementation built from small nodes and within 13% of the performance of the ideal implementation: a large SMP with the same access time to its entire shared memory as the local memory access time of WildFire.
Cross‐regulation among arabinose, xylose and rhamnose utilization systems in E. coli

Bacteria frequently encounter multiple sugars in their natural surroundings. While the dynamics of utilization of glucose‐containing sugar mixtures have been well investigated, there are few reports addressing regulation of utilization of glucose‐free mixtures particularly pentoses. These sugars comprise a considerable fraction in hemicellulose which can be converted by suitable biocatalysts to biofuels and other value‐added products. Hence, understanding of transcriptional cross‐regulation among different pentose sugar utilization systems is essential for successful development of industrial strains. In this work, we study mixed‐sugar utilization with respect to three secondary carbon sources — arabinose, xylose and rhamnose at single‐cell resolution in Escherichia coli. Our results reveal that hierarchical utilization among these systems is not strict but rather can be eliminated or reversed by altering the relative ratios of the preferred and nonpreferred sugars. Since transcriptional cross‐regulation among pentose sugar systems operates through competitive binding of noncognate sugar‐regulator complex, altering sugar concentrations is thought to eliminate nonspecific binding by affecting concentration of the regulator — sugar complexes.
Solutions in folded geometries, and associated cloaking due to anomalous resonance

Solutions for the fields in a coated cylinder where the core radius is bigger than the shell radius are seemingly unphysical, but can be given a physical meaning if one transforms to an equivalent problem by unfolding the geometry. In particular, the unfolded material can act as an impedance matched hyperlens, and as the loss in the lens goes to zero finite collections of polarizable line dipoles lying within a critical region surrounding the hyperlens are shown to be cloaked having vanishingly small dipole moments. This cloaking, which occurs both in the folded geometry and the equivalent unfolded one, is due to anomalous resonance, where the collection of dipoles generates an anomalously resonant field, which acts back on the dipoles to essentially cancel the external fields acting on them.
Evidence for a curvilinear relationship between posttraumatic growth and posttrauma depression and PTSD in assault survivors

Two studies of assault survivors (Ns = 180, 70) examined associations between posttraumatic growth (PTG) and posttrauma psychopathology. Both studies found significant curvilinear associations between PTG and posttraumatic stress disorder, whereas only Study 1 found a curvilinear association between PTG and depression symptom severity. Survivors with no or high growth levels reported fewer symptoms than those who reported moderate growth. Study 1 also investigated potential PTG predictors. Non-Caucasian ethnicity, religiousness, peritraumatic fear, shame, and ruminative thinking style, assessed at 2 weeks, predicted growth at 6 months. Posttraumatic growth may thus be most relevant in trauma survivors who attach enduring significance to the trauma for their lives and show initial distress. Moderate levels of PTG do not seem to ameliorate posttrauma psychopathology.
Cost effective traffic grooming in WDM rings

We provide network designs for optical wavelength division multiplexed (OWDM) rings that minimize overall network cost, rather than just the number of wavelengths needed. The network cost includes the cost of the transceivers required at the nodes as well as the number of wavelengths. The transceiver cost includes the cost of terminating equipment as well as higher-layer electronic processing equipment, and in practice, can dominate over the cost of the number of wavelengths in the network. The networks support dynamic (time varying) traffic streams that are at lower rates (e.g., OC-3, 155 Mb/s) than the lightpath capacities (e.g., OC-48, 2.5 Gb/s). A simple OWDM ring is the point-to-point ring, where traffic is transported on WDM links optically, but switched through nodes electronically. Although the network is efficient in using link bandwidth, it has high electronic and opto-electronic processing costs. Two OWDM ring networks are given that have similar performance but are less expensive. Two other OWDM ring networks are considered that are nonblocking, where one has a wide sense nonblocking property and the other has a rearrangeably nonblocking property. All the networks are compared using the cost criteria of number of wavelengths and number of transceivers.
The Hypoxia-inducible Factor Renders Cancer Cells More Sensitive to Vitamin C-induced Toxicity*

Background: There is renewed interest in the possibility of using Vc as an anticancer agent. Results: Activation of HIF triggers a Warburg effect that renders cancer cells more sensitive to Vc-induced toxicity. Conclusion: These results provide a link between the metabolic state and the susceptibility to Vc. Significance: Our work helps to understand the preferential toxicity of Vc toward cancer cells. Megadose vitamin C (Vc) is one of the most enduring alternative treatments for diverse human diseases and is deeply engrafted in popular culture. Preliminary studies in the 1970s described potent effects of Vc on prolonging the survival of patients with terminal cancer, but these claims were later criticized. An improved knowledge of the pharmacokinetics of Vc and recent reports using cancer cell lines have renewed the interest in this subject. Despite these findings, using Vc as an adjuvant for anticancer therapy remains questionable, among other things because there is no proper mechanistic understanding. Here, we show that a Warburg effect triggered by activation of the hypoxia-inducible factor (HIF) pathway greatly enhances Vc-induced toxicity in multiple cancer cell lines, including von Hippel-Lindau (VHL)-defective renal cancer cells. HIF increases the intracellular uptake of oxidized Vc through its transcriptional target glucose transporter 1 (GLUT1), synergizing with the uptake of its reduced form through sodium-dependent Vc transporters. The resulting high levels of intracellular Vc induce oxidative stress and massive DNA damage, which then causes metabolic exhaustion by depleting cellular ATP reserves. HIF-positive cells are particularly sensitive to Vc-induced ATP reduction because they mostly rely on the rather inefficient glycolytic pathway for energy production. Thus, our experiments link Vc-induced toxicity and cancer metabolism, providing a new explanation for the preferential effect of Vc on cancer cells.
A Phase I/II trial design when response is unobserved in subjects with dose-limiting toxicity

We propose a Phase I/II trial design in which subjects with dose-limiting toxicity are not followed for response, leading to three possible outcomes for each subject: dose-limiting toxicity, absence of therapeutic response without dose-limiting toxicity, and presence of therapeutic response without dose-limiting toxicity. We define the latter outcome as a ‘success,’ and the goal of the trial is to identify the dose with the largest probability of success. This dose is commonly referred to as the most successful dose. We propose a design that accumulates information on subjects with regard to both dose-limiting toxicity and response conditional on no dose-limiting toxicity. Bayesian methods are used to update the estimates of dose-limiting toxicity and response probabilities when each subject is enrolled, and we use these methods to determine the dose level assigned to each subject. Due to the need to explore doses more fully, each subject is not necessarily assigned the current estimate of the most successful dose; our algorithm may instead assign a dose that is in a neighborhood of the current most successful dose. We examine the ability of our design to correctly identify the most successful dose in a variety of settings via simulation and compare the performance of our design to that of competing approaches.
On the explanation of spatial smoothing in MUSIC algorithm for coherent sources

This paper presents the necessity analysis and the sufficiency analysis of DOA estimation in coherent situation by means of three different aspects respectively, including the rank of covariance matrix, the correlation coefficient and the phase difference between coherent sources. The analyses explain how spatial smoothing decorrelates the coherent sources and how many times of spatial smoothing are needed to decorrelate completely. Simulation results illustrate the sensitivity of the MUSIC algorithm to the number of spatial smoothing.
Theoretical improvements in the stability analysis of a new class of model-free visual servoing methods

This paper concerns the stability analysis of a new class of model-free visual servoing methods. These methods are "model-free" since they are based on the estimation of the relative camera orientation between two views of an object without knowing its 3-D model. The visual servoing is decoupled by controlling the rotation of the camera separately from the rest of the system. The way the remaining degrees of freedom are controlled differentiates the methods within the class. For all the methods of the class, the robustness with respect to both camera and hand-eye calibration errors can be analytically studied. In some cases, necessary and sufficient conditions can be found not only for the local asymptotic stability but also for the global asymptotic stability. In the other cases, simple conditions on the calibration errors are sufficient to ensure the global asymptotic stability of the control law. In addition to the theoretical proof of the stability, the experimental results prove the validity of the control strategy proposed in the paper.
Medical and Surgical Advances in Intracerebral Hemorrhage and Intraventricular Hemorrhage

Abstract In recent decades, the medical and surgical treatment of intracerebral hemorrhage (ICH) have become the focus of a number of scientific investigations. This effort has been led by an international group of neurologists and neurosurgeons with the goal of studying functional recovery and developing new medical and surgical treatments to facilitate improved clinical outcomes. Currently, two of the most pressing ICH investigational goals are (1) early blood pressure control, and (2) safe hematoma volume reduction. Answering these questions would support decision-making, level-of-care choices, and the global research strategy of developing biologically informed treatments. The authors review the contemporary medical management and the conventional and minimally invasive surgical approaches to spontaneous ICH, as well as discuss the scope of the problem, recent clinical trials, management issues, and relevant questions for future research. They propose the hypothesis that strategies using minimally invasive techniques, including clot aspiration with stereotactic guidance, may give better results with improved clinical outcomes compared with standard open surgical approaches. They also discuss the level of evidence for the variously known approaches.
A Review of Genetic Algorithm application for Image Segmentation

Image segmentation is an important technique of Image Processing. It is a difficult task of image processing and the subsequent tasks including object detection, feature extraction, object recognition and classification depend on the quality of segmentation process. However there is no general way to successfully segment all images. The image segmentation problem can be characterized by several factors which make the parameter selection problem difficult. The segmentation problem is formulated as an optimization problem and Genetic Algorithm efficiently locate the global maximum in a search space and solves the problem of parameter selection in image segmentation. The aim of this paper is to review Genetic Algorithm applications for image segmentation.
AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast

Genome-wide assays and screens typically result in large lists of genes or proteins. Enrichments of functional or other biological properties within such lists can provide valuable insights and testable hypotheses. To systematically detect these enrichments can be challenging and time-consuming, because relevant data to compare against query gene lists are spread over many different sources. We have developed AnGeLi (Analysis of Gene Lists), an intuitive, integrated web-tool for comprehensive and customized interrogation of gene lists from the fission yeast, Schizosaccharomyces pombe. AnGeLi searches for significant enrichments among multiple qualitative and quantitative information sources, including gene and phenotype ontologies, genetic and protein interactions, numerous features of genes, transcripts, translation, and proteins such as copy numbers, chromosomal positions, genetic diversity, RNA polymerase II and ribosome occupancy, localization, conservation, half-lives, domains, and molecular weight among others, as well as diverse sets of genes that are co-regulated or lead to the same phenotypes when mutated. AnGeLi uses robust statistics which can be tailored to specific needs. It also provides the option to upload user-defined gene sets to compare against the query list. Through an integrated data submission form, AnGeLi encourages the community to contribute additional curated gene lists to further increase the usefulness of this resource and to get the most from the ever increasing large-scale experiments. AnGeLi offers a rigorous yet flexible statistical analysis platform for rich insights into functional enrichments and biological context for query gene lists, thus providing a powerful exploratory tool through which S. pombe researchers can uncover fresh perspectives and unexpected connections from genomic data. AnGeLi is freely available at: www.bahlerlab. info/AnGeLi
Leisure-Time Spent Sitting and Site-Specific Cancer Incidence in a Large U.S. Cohort

Background: Time spent sitting is distinctly different from accumulating too little physical activity and may have independent deleterious effects. Few studies have examined the association between sitting time and site-specific cancer incidence. Methods: Among 69,260 men and 77,462 women who were cancer-free and enrolled in the American Cancer Society Cancer Prevention Study II Nutrition Cohort, 18,555 men and 12,236 women were diagnosed with cancer between 1992 and 2009. Extended Cox proportional hazards regression was used to estimate multivariable-adjusted relative risks (RR) and 95% confidence intervals (CI) of leisure-time spent sitting with total and site-specific cancer incidence. Results: Longer leisure-time spent sitting, after adjustment for physical activity, BMI, and other factors, was associated with risk of total cancer in women (RR = 1.10; 95% CI, 1.04–1.17 for ≥6 hours vs. <3 hours per day), but not men (RR = 1.00; 95% CI, 0.96–1.05). In women, sitting time was associated with risk of multiple myeloma (RR = 1.65; 95% CI, 1.07–2.54), invasive breast cancer (RR = 1.10; 95% CI, 1.00–1.21), and ovarian cancer (RR = 1.43; 95% CI, 1.10–1.87). There were no associations between sitting time and site-specific cancers in men. Conclusion: Longer leisure-time spent sitting was associated with a higher risk of total cancer risk in women, and specifically with multiple myeloma, breast, and ovarian cancers, but sitting time was not associated with cancer risk in men. Further research is warranted to better understand the differences in associations between men and women. Impact: For women, these findings support American Cancer Society guidelines for cancer prevention to reduce sitting time when possible. Cancer Epidemiol Biomarkers Prev; 24(9); 1350–9. ©2015 AACR.
Testing the role of dopamine in olfactory sensitivity and learning in the entorhinal cortex

Dopaminergic innervation of the entorhinal cortex may contribute to the integration and encoding of sensory information. The primary olfactory cortex (piriform cortex) projects to the superficial layers of the entorhinal cortex, and converging dopaminergic inputs from the ventral tegmental area may modulate processes in the entorhinal cortex related to the salience of olfactory stimuli. In the current study, food-restricted rats were trained to dig in cups filled with scented sand and to discriminate between two different odours to obtain a buried food-reward which was always associated with one odour (CS+). Upon reaching criterion performance on this task, animals underwent sham surgery or 6-hydroxydopamine lesions of the entorhinal cortex. After retraining on the original discrimination rule, olfactory sensitivity was tested using cups containing decreasing amounts of the original CS+ odour. Animals showed graded decrements in response accuracy as the concentration of odorant was reduced, but no significant differences were observed between control and lesioned animals. In addition, lesioned animals did not differ in their ability to learn to perform the discrimination task with a new odour pair at low concentrations, and did not show differences in their ability to respond accurately to either the initial or novel odour pair after a delay of two weeks. These findings show that scented sand can be used as an effective stimulus to assess the sensitivity to olfactory stimuli in the rat, but do not provide evidence for deficits in olfactory sensitivity or memory performance in animals with 6-OHDA lesions of the entorhinal cortex.
Age and CD4 count at initiation of antiretroviral therapy in HIV-infected children: effects on long-term T-cell reconstitution.

BACKGROUND Effective therapies and reduced AIDS-related morbidity and mortality have shifted the focus in pediatric human immunodeficiency virus (HIV) from minimizing short-term disease progression to maintaining optimal long-term health. We describe the effects of children's age and pre-antiretroviral therapy (ART) CD4 count on long-term CD4 T-cell reconstitution. METHODS CD4 counts in perinatally HIV-infected, therapy-naive children in the Paediatric European Network for the Treatment of AIDS 5 trial were monitored following initiation of ART for a median 5.7 years. In a substudy, naive and memory CD4 counts were recorded. Age-standardized measurements were analyzed using monophasic, asymptotic nonlinear mixed-effects models. RESULTS One hundred twenty-seven children were studied. Older children had lower age-adjusted CD4 counts in the long term and at treatment initiation (P < .001). At all ages, lower counts before treatment were associated with impaired recovery (P < .001). Age-adjusted naive CD4 counts increased on a timescale comparable to overall CD4 T-cell reconstitution, whereas age-adjusted memory CD4 counts increased less, albeit on a faster timescale. CONCLUSIONS It appears the immature immune system can recover well from HIV infection via the naive pool. However, this potential is progressively damaged with age and/or duration of infection. Current guidelines may therefore not optimize long-term immunological health.
Brain White Matter Development Is Associated with a Human-Specific Haplotype Increasing the Synthesis of Long Chain Fatty Acids

The genetic and molecular pathways driving human brain white matter (WM) development are only beginning to be discovered. Long chain polyunsaturated fatty acids (LC-PUFAs) have been implicated in myelination in animal models and humans. The biosynthesis of LC-PUFAs is regulated by the fatty acid desaturase (FADS) genes, of which a human-specific haplotype is strongly associated with ω-3 and ω-6 LC-PUFA concentrations in blood. To investigate the relationship between LC-PUFA synthesis and human brain WM development, we examined whether this FADS haplotype is associated with age-related WM differences across the life span in healthy individuals 9–86 years of age (n = 207). Diffusion tensor imaging was performed to measure fractional anisotropy (FA), a putative measure of myelination, of the cerebral WM tracts. FADS haplotype status was determined with a single nucleotide polymorphism (rs174583) that tags this haplotype. Overall, normal age-related WM differences were observed, including higher FA values in early adulthood compared with childhood, followed by lower FA values across older age ranges. However, individuals homozygous for the minor allele (associated with lower LC-PUFA concentrations) did not display these normal age-related WM differences (significant age × genotype interactions, pcorrected < 0.05). These findings suggest that LC-PUFAs are involved in human brain WM development from childhood into adulthood. This haplotype and LC-PUFAs may play a role in myelin-related disorders of neurodevelopmental origin.
The End-Organ Impairment in Liver Cirrhosis: Appointments for Critical Care

Liver cirrhosis (LC) can lead to a clinical state of liver failure, which can exacerbate through the course of the disease. New therapies aimed to control the diverse etiologies are now more effective, although the disease may result in advanced stages of liver failure, where liver transplantation (LT) remains the most effective treatment. The extended lifespan of these patients and the extended possibilities of liver support devices make their admission to an intensive care unit (ICU) more probable. In this paper the LC is approached from the point of view of the pathophysiological alterations present in LC patients previous to ICU admission, particularly cardiovascular, but also renal, coagulopathic, and encephalopathic. Infections and available liver detoxifications devices also deserve mentioning. We intend to contribute towards ICU physician readiness to the care for this particular type of patients, possibly in dedicated ICUs.