Miracle-dz/UniFAR-FTUs huggingface dataset:
Real-time multi-core virtual machine scheduling in Xen

Recent years have witnessed two major trends in the development of complex real-time embedded systems. First, to reduce cost and enhance flexibility, multiple systems are sharing common computing platforms via virtualization technology, instead of being deployed separately on physically isolated hosts. Second, multicore processors are increasingly being used in real-time systems. The integration of real-time systems as virtual machines (VMs) atop common multicore platforms raises significant new research challenges in meeting the real-time performance requirements of multiple systems. This paper advances the state of the art in real-time virtualization by designing and implementing RT-Xen 2.0, a new real-time multicore VM scheduling framework in the popular Xen virtual machine monitor (VMM). RT-Xen 2.0 realizes a suite of real-time VM scheduling policies spanning the design space. We implement both global and partitioned VM schedulers; each scheduler can be configured to support dynamic or static priorities and to run VMs as periodic or deferrable servers. We present a comprehensive experimental evaluation that provides important insights into real-time scheduling on virtualized multicore platforms: (1) both global and partitioned VM scheduling can be implemented in the VMM at moderate overhead; (2) at the VMM level, while compositional scheduling theory shows partitioned EDF (pEDF) is better than global EDF (gEDF) in providing schedulability guarantees, in our experiments their performance is reversed in terms of the fraction of workloads that meet their deadlines on virtualized multicore platforms; (3) at the guest OS level, pEDF requests a smaller total VCPU bandwidth than gEDF based on compositional scheduling analysis, and therefore using pEDF at the guest OS level leads to more schedulable workloads in our experiments; (4) a combination of pEDF in the guest OS and gEDF in the VMM - configured with deferrable server - leads to the highest fraction of schedulable task sets compared to other real-time VM scheduling policies; and (5) on a platform with a shared last-level cache, the benefits of global scheduling outweigh the cache penalty incurred by VM migration.
Semi‐idealized urban heat advection simulations using the Weather Research and Forecasting mesoscale model

Urban heat advection (UHA) can extend the climatic impact of a city into the surrounding countryside. This may lead to an intensification of already well‐documented urban heat island (UHI) impacts on health and infrastructure, and challenge the representativeness of long‐term reference temperature records taken near urban areas. However, previous UHA studies have been unable to accurately quantify surface‐level UHA due to challenges arising from complex urban land‐use patterns. To address this, the numerical Weather Research and Forecasting (WRF) mesoscale model coupled with the Building Energy Parameterization urban canopy scheme is used to simulate meteorological fields for idealized land‐use cases. Hypothetical square cities (up to 32 km in size) are simulated for a year's period. A time‐mean 2‐m temperature field (representing the canopy UHI) shows that the mean UHI intensity (up to 4.3 °C [SD 1.7 °C]), wind speed <3.9 m/s) is linearly related to the logarithm of city size. This finding, entirely derived from numerical modelling, is consistent with the log‐linear relationships previously found in the observational data of many cities in the world. A UHA methodology was then applied to the temperature fields to separate UHA from the UHI, with up to 2.9 °C (SD 1.7 °C) of UHA found downwind of the largest city size. For this hypothetical city size, an UHA intensity of 0.5 °C is found up to 24‐km downwind from the urban boundary. In addition, the UHA‐distance profiles along the central horizontal transect for various urban sizes are found to follow a scaling rule as a good approximation. As a result, the findings of this paper can be used as a starting point for climate impact assessments for areas surrounding urban areas without the need for complex, computation‐intensive simulations.
Conditional Causal Mediation Analysis of Factors Associated With Cover Crop Adoption in Iowa, USA

The Iowa Nutrient Reduction Strategy is a statewide effort that aims to encourage voluntary adoption of conservation practices by farmers to reduce the loss of nitrogen and phosphorus that contribute to water quality impairments in the Upper Midwest and drive hypoxic conditions in the Gulf of Mexico. This work is an analysis of the first 2 years (2015–2016) of a 5‐year survey of Iowa farmers. We employ causal mediation analysis to examine the direct and indirect effects of key explanatory variables (e.g., information sources, nutrient management influences, involvement in watershed management activities, and conservation technical assistance) and two causally ordered mediators (farmers' awareness of and attitudes toward the Nutrient Reduction Strategy) on cover crop use. Results showed that participation in watershed activities and receipt of cost share or technical assistance had positive direct effects on cover crop use, while low levels of perceived nutrient loss mitigation self‐efficacy had a negative direct effect. Information and influence of public sector soil and water conservation entities had positive indirect effects on cover crop use through awareness and attitudes, while influence of private sector agribusiness entities had negative indirect effects through those mediators. These results suggest that current strategies such as engaging farmers in watershed management activities and public sector cost share and technical assistance are increasing adoption of cover crops, but the data also point to a need to increase engagement with private sector actors to help them improve their effectiveness as conservation technical assistance providers.
Body Mass Parameters, Lipid Profiles and Protein Contents of Zebrafish Embryos and Effects of 2,4-Dinitrophenol Exposure

Morphology and physiology of fish embryos undergo dramatic changes during their development until the onset of feeding, supplied only by endogenous yolk reserves. For obtaining an insight how these restructuring processes are reflected by body mass related parameters, dry weights (dw), contents of the elements carbon and nitrogen and lipid and protein levels were quantified in different stages within the first four days of embryo development of the zebrafish (Danio rerio). The data show age dependent changes in tissue composition. Dry weights decreased significantly from 79μgdw/egg at 0hours post fertilization (hpf) to 61 μgdw/egg after 96 hpf. The amounts of total carbon fluctuated between 460 mg g-1 and 540 mg g-1 dw, nitrogen was at about 100 mg g-1 dw and total fatty acids were between 48–73 mg g-1 dw. In contrast to these parameters that remained relatively constant, the protein content, which was 240 mg g-1 at 0 hpf, showed an overall increase of about 40%. Comparisons of intact eggs and dechorionated embryos at stages prior to hatching (24, 30, 48 hpf) showed that the differences seen for dry weight and for carbon and nitrogen contents became smaller at more advanced stages, consistent with transition of material from the chorion to embryo tissue. Further, we determined the effect of 2,4-dinitrophenol at a subacutely toxic concentration (14 μM, LC10) as a model chemical challenge on the examined body mass related parameters. The compound caused significant decreases in phospholipid and glycolipid fatty acid contents along with a decrease in the phospholipid fatty acid unsaturation index. No major changes were observed for the other examined parameters. Lipidomic studies as performed here may thus be useful for determining subacute effects of lipophilic organic compounds on lipid metabolism and on cellular membranes of zebrafish embryos.
Cooperativity To Increase Turing Pattern Space for Synthetic Biology

It is hard to bridge the gap between mathematical formulations and biological implementations of Turing patterns, yet this is necessary for both understanding and engineering these networks with synthetic biology approaches. Here, we model a reaction–diffusion system with two morphogens in a monostable regime, inspired by components that we recently described in a synthetic biology study in mammalian cells.1 The model employs a single promoter to express both the activator and inhibitor genes and produces Turing patterns over large regions of parameter space, using biologically interpretable Hill function reactions. We applied a stability analysis and identified rules for choosing biologically tunable parameter relationships to increase the likelihood of successful patterning. We show how to control Turing pattern sizes and time evolution by manipulating the values for production and degradation relationships. More importantly, our analysis predicts that steep dose–response functions arising from cooperativity are mandatory for Turing patterns. Greater steepness increases parameter space and even reduces the requirement for differential diffusion between activator and inhibitor. These results demonstrate some of the limitations of linear scenarios for reaction–diffusion systems and will help to guide projects to engineer synthetic Turing patterns.
Assessing the Impact of Misclassification Error on an Epidemiological Association between Two Helminthic Infections

Background Polyparasitism can lead to severe disability in endemic populations. Yet, the association between soil-transmitted helminth (STH) and the cumulative incidence of Schistosoma japonicum infection has not been described. The aim of this work was to quantify the effect of misclassification error, which occurs when less than 100% accurate tests are used, in STH and S. japonicum infection status on the estimation of this association. Methodology/Principal Findings Longitudinal data from 2276 participants in 50 villages in Samar province, Philippines treated at baseline for S. japonicum infection and followed for one year, served as the basis for this analysis. Participants provided 1–3 stool samples at baseline and 12 months later (2004–2005) to detect infections with STH and S. japonicum using the Kato-Katz technique. Variation from day-to-day in the excretion of eggs in feces introduces individual variations in the sensitivity and specificity of the Kato-Katz to detect infection. Bayesian logit models were used to take this variation into account and to investigate the impact of misclassification error on the association between these infections. Uniform priors for sensitivity and specificity of the diagnostic test to detect the three STH and S. japonicum were used. All results were adjusted for age, sex, occupation, and village-level clustering. Without correction for misclassification error, the odds ratios (ORs) between hookworm, Ascaris lumbricoides, and Trichuris trichiura, and S. japonicum infections were 1.28 (95% Bayesian credible intervals: 0.93, 1.76), 0.91 (95% BCI: 0.66, 1.26), and 1.11 (95% BCI: 0.80, 1.55), respectively, and 2.13 (95% BCI: 1.16, 4.08), 0.74 (95% BCI: 0.43, 1.25), and 1.32 (95% BCI: 0.80, 2.27), respectively, after correction for misclassification error for both exposure and outcome. Conclusions/Significance The misclassification bias increased with decreasing test accuracy. Hookworm infection was found to be associated with increased 12-month cumulative incidence of S. japonicum infection after correction for misclassification error. Such important associations might be missed in analyses which do not adjust for misclassification errors.
All-optical digital-to-analog conversion using nonlinear optical loop mirrors

We propose a novel ultrafast all-optical digital-to-analog conversion (DAC) scheme consisting of nonlinear optical loop mirrors, which can be applied to both a standard binary code and a Gray code. We conducted a proof-of-principle experiment and successfully demonstrated a 2-bit all-optical DAC with a Gray code, which indicates that the proposed scheme is feasible.
Three single nucleotide polymorphisms of the vascular endothelial growth factor (VEGF) gene and glioma risk in a Chinese population

Objective To investigate the association between three single nucleotide polymorphisms (SNPs) of the vascular endothelial growth factor (VEGF) gene and the risk of glioma in a Han Chinese population. Methods This hospital-based case–control study used polymerase chain reaction–restriction fragment length polymorphism analysis to detect three SNPs (−634 G/C, +936 C/T and +1612 G/A) of the VEGF gene in patients with glioma compared with healthy control subjects. Results The study investigated 880 patients with gliomas and 880 age- and sex-matched healthy control subjects. Patients with gliomas had a significantly higher frequency of the −634 CC genotype (odds ratio [OR] 1.35, 95% confidence interval [CI] 1.05, 1.75) and the +936 TT (OR 1.73, 95% CI 1.20, 2.48) genotype compared with the control subjects. Patients with glioblastomas had a significantly higher frequency of the −634 CC and +936 TT genotypes. Patients with grade IV gliomas had a significantly higher frequency of the −634 CC and +936 TT genotypes. The +1612 G/A polymorphisms were not associated with glioma risk. Conclusion The VEGF − 634 CC and +936 TT genotypes were associated with a higher risk of glioma in a Han Chinese population.
Vascular Health and Risk Management Dovepress Impact of a Diabetic Foot Care Education Program on Lower Limb Amputation Rate

Background: Diabetic foot complications are a leading cause of lower extremity amputation. With the increasing incidence of diabetes mellitus in the Arab world, specifically in the Kingdom of Saudi Arabia, the rate of amputation will rise significantly. A diabetic foot care program was implemented at King Abdulaziz Medical City in Riyadh, Saudi Arabia, in 2002. The program was directed at health care staff and patients to increase their awareness about diabetic foot care and prevention of complications. The purpose of this study was to perform a primary evaluation of the program's impact on the rate of lower extremity amputation due to diabetic foot complications. Method: This pilot study was the first analysis of the diabetic foot care program and examined two groups of participants for comparison, ie, a " before " group having had diabetic foot ulcers managed between 1983, when the hospital was first established, and 2002 when the program began and an " after group " having had foot ulcers managed between 2002 and 2004, in the program's initial phase. A total of 41 charts were randomly chosen retrospectively. A data sheet containing age, gender, medical data, and the presentation, management, and outcome of diabetic foot cases was used for the analysis. Results: The before group contained 20 patients (17 males) and the after group contained 21 patients (16 males). There was no difference between the two groups with regard to age and comorbidities. The rate of amputation was 70% in the before group and 61.9% in the after group. There was a decrease in the percentage of toe amputation in the after group and an increase in the percentage of below-knee amputation in the before group. However, these changes were not significant. Conclusion: The program, although evaluated at an early stage, has increased the awareness of both patients and health care staff about the prevention and management of diabetic foot disease, and decreased the rate of lower extremity amputation. We believe that the statistical proof of its impact will be evident in the final evaluation.
Quantification of group A colicin import sites

Pore-forming colicins are soluble bacteriocins which form voltage-gated ion channels in the inner membrane of Escherichia coli. To reach their target, these colicins first bind to a receptor located on the outer membrane and then are translocated through the envelope. Colicins are subdivided into two groups according to the envelope proteins involved in their translocation: group A colicins use the Tol proteins; group B colicins use the proteins TonB, ExbB, and ExbD. We have previously shown that a double-cysteine colicin A mutant which possesses a disulfide bond in its pore-forming domain is translocated through the envelope but is unable to form a channel in the inner membrane (D. Duché, D. Baty, M. Chartier, and L. Letellier, J. Biol. Chem. 269:24820-24825, 1994). Measurements of colicin-induced K+ efflux reveal that preincubation of the cells with the double-cysteine mutant prevents binding of colicins of group A but not of group B. Moreover, we show that the mutant is still in contact with its receptor and import machinery when it interacts with the inner membrane. From these competition experiments, we conclude that each Escherichia coli cell contains approximately 400 and 1,000 colicin A receptors and translocation sites, respectively.
Role Induced Bias in Court: An Experimental Analysis

Criminal procedure is organized as a tournament with predefined roles. We show that assuming the role of a defense counsel or prosecutor leads to role induced bias even if participants are asked to predict a court ruling after they have ceased to act in that role, and if they expect a substantial financial incentive for being accurate. The bias is not removed either if participants are instructed to predict the court ruling in preparation of plea bargaining. In line with parallel constraint satisfaction models for legal decision making, findings indicate that role induced bias is driven by coherence effects (Simon, 2004), that is, systematic information distortions in support of the favored option. This is mainly achieved by downplaying the importance of conflicting evidence. These distortions seem to stabilize interpretations, and people do not correct for this bias. Implications for legal procedure are briefly discussed.
Stabilization of expansive soils using alkali activated fly ash

This research work presents the efficacy of sodium based alkaline activators and class F fly ash as an additive in improving the engineering characteristics of expansive Black cotton soils. Sodium hydroxide concentrations of 10, 12.5 and 15 molal along with 1 Molar solution of sodium silicate were used as activators. The activator to ash ratios was kept between between 1 and 2.5 and ash percentages of 20, 30 and 40 %, relatively to the total solids. The effectiveness of this binder is tested by conducting the Unconfined compressive strength (UCS) at curing periods of 3,7 and 28 days and is compared with that of a common fly ash based binder, also the most effective mixtures were analysed for mineralogy with XRD. Suitability of alkaline activated fly ash mix as a grouting material is also ascertained by studying the rheological properties of the grout such as, setting time, density and viscosity and is compared with that of common cement grouts. Results shows that the fluidity of the grouts correlate very well with UCS, with an increase in the former resulting in a decrease in the latter.
Krylov-Schur-Type Restarts for the Two-Sided Arnoldi Method

We consider the two-sided Arnoldi method and propose a two-sided Krylov--Schur-type restarting method. We discuss the restart for standard Rayleigh--Ritz extraction as well as harmonic Rayleigh--Ritz extraction. Additionally, we provide error bounds for Ritz values and Ritz vectors in the context of oblique projections and present generalizations of, e.g., the Bauer--Fike theorem and Saad's theorem. Applications of the two-sided Krylov--Schur method include the simultaneous computation of left and right eigenvectors and the computation of eigenvalue condition numbers. We demonstrate how the method can be used to find the least sensitive eigenvalues of a nonnormal matrix and how to approximate pseudospectra by using left and right shift-invariant subspaces. The results demonstrate that significant improvements in quality can be obtained over approximations with the (one-sided) Krylov--Schur method.
Circulating microRNA profiles in human patients with acetaminophen hepatotoxicity or ischemic hepatitis

Significance Hundreds of microRNAs become dramatically elevated in the plasma or serum of acetaminophen (APAP) overdose patients and then recover back toward normal during successful treatment with the APAP antidote, N-acetyl cysteine (NAC). Importantly, the elevation of these circulating miRNAs can precede the rise in the standard biomarker, alanine aminotransferase (ALT), and the recovery of these miRNAs during NAC treatment is more rapid than ALT. We identify a set of 11 miRNAs whose profiles and dynamics in circulation during NAC treatment can discriminate APAP hepatotoxicity from another common hepatotoxic condition, ischemic hepatitis. These findings suggest that miRNAs are sensitive diagnostic and prognostic biomarkers for liver injury with broad potential for use in monitoring drug-induced liver injury in clinical and research contexts. We have identified, by quantitative real-time PCR, hundreds of miRNAs that are dramatically elevated in the plasma or serum of acetaminophen (APAP) overdose patients. Most of these circulating microRNAs decrease toward normal levels during treatment with N-acetyl cysteine (NAC). We identified a set of 11 miRNAs whose profiles and dynamics in the circulation during NAC treatment can discriminate APAP hepatotoxicity from ischemic hepatitis. The elevation of certain miRNAs can precede the dramatic rise in the standard biomarker, alanine aminotransferase (ALT), and these miRNAs also respond more rapidly than ALT to successful treatment. Our results suggest that miRNAs can serve as sensitive diagnostic and prognostic clinical tools for severe liver injury and could be useful for monitoring drug-induced liver injury during drug discovery.
In Search of Our True Selves: Feedback as a Path to Self-Knowledge

How can self-knowledge of personality be improved? What path is the most fruitful source for learning about our true selves? Previous research has noted two main avenues for learning about the self: looking inward (e.g., introspection) and looking outward (e.g., feedback). Although most of the literature on these topics does not directly measure the accuracy of self-perceptions (i.e., self-knowledge), we review these paths and their potential for improving self-knowledge. We come to the conclusion that explicit feedback, a largely unexamined path, is likely a fruitful avenue for learning about one’s own personality. Specifically, we suggest that self-knowledge might be fully realized through the use of explicit feedback from close, knowledgeable others. As such, we conclude that the road to self-knowledge likely cannot be traveled alone but must be traveled with close others who can help shed light on our blind spots.