Miracle-dz/UniFAR-FTUs huggingface dataset:
OUTSTANDING PAPER: Evaluation of Cache Partitioning for Hard Real-Time Systems

In hard real-time systems, cache partitioning is often suggested as a means of increasing the predictability of caches in pre-emptively scheduled systems: when a task is assigned its own cache partition, inter-task cache eviction is avoided, and timing verification is reduced to the standard worst case execution time (WCET) analysis used in non-pre-emptive systems. The downside of cache partitioning is the potential increase in execution times. In this paper, we evaluate cache partitioning for hard real time systems in terms of overall schedulability. To this end, we examine the sensitivity of task execution times to the size of the cache partition allocated and present a cache partitioning algorithm that is optimal with respect to task set schedulability. We then evaluate the performance of cache partitioning compared to state-of-the-art pre-emption cost analysis based on benchmark code and on a large number of synthetic task sets. This allows us to derive general conclusions about the usability of cache partitioning and identify task set and system parameters that influence the relative e effectiveness of cache partitioning.
Local Statistics of Lattice Points on the Sphere

A celebrated result of Legendre and Gauss determines which inte- gers can be represented as a sum of three squares, and for those it is typically the case that there are many ways of doing so. These different representations give collections of points on the unit sphere, and a fundamental result, con- jectured by Linnik, is that under a simple condition these become uniformly distributed on the sphere. In this note we survey some of our recent work, which explores what happens beyond uniform distribution, giving evidence to randomness on smaller scales. We treat the electrostatic energy, local statistics such as the point pair statistic (Ripley's function), nearest neighbour statis- tics, minimum spacing and covering radius. We briefly discuss the situation in other dimensions, which is very different. In an appendix we compute the corresponding quantities for random points.
Inequalities in reported use of breast and cervical screening in Great Britain: analysis of cross sectional survey data

Objective To investigate the relation between women’s reported use of breast and cervical screening and sociodemographic characteristics. Design Cross sectional multipurpose survey. Setting Private households, Great Britain. Population 3185 women aged 40-74 interviewed in the National Statistics Omnibus Survey 2005-7. Main outcome measures Ever had a mammogram, ever had a cervical smear, and, for each, timing of most recent screen. Results 91% (95% confidence interval 90% to 92%) of women aged 40-74 years reported ever having had a cervical smear, and 93% (92% to 94%) of those aged 53-74 years reported ever having had a mammogram; 3% (2% to 4%) of women aged 53-74 years had never had either breast or cervical screening. Women were significantly more likely to have had a mammogram if they lived in households with cars (compared with no car: one car, odds ratio 1.67, 95% confidence interval 1.06 to 2.62; two or more cars, odds ratio 2.65, 1.34 to 5.26), and in owner occupied housing (compared with rented housing: own with mortgage, odds ratio 2.12, 1.12 to 4.00; own outright, odds ratio 2.19, 1.39 to 3.43), but no significant differences by ethnicity, education, occupation, or region were found. For cervical screening, ethnicity was the most important predictor; white British women were significantly more likely to have had a cervical smear than were women of other ethnicity (odds ratio 2.20, 1.41 to 3.42). Uptake of cervical screening was greater among more educated women but was not significantly associated with cars, housing tenure, or region. Conclusions Most (84%) eligible women report having had both breast and cervical screening, but 3% report never having had either. Some inequalities exist in the reported use of screening, which differ by screening type; indicators of wealth were important for breast screening and ethnicity for cervical screening. The routine collection within general practice of additional sociodemographic information would aid monitoring of inequalities in screening coverage and inform policies to correct them.
Evaluation of Wearing Surface Materials for FRP Bridge Decks

The wearing surface on many fiber reinforced polymer (FRP) composite bridge decks have cracked or delaminated after only a short time in service. Consequently, a set of tests were conducted on four wearing surface products in order to select the material with the best performance with respect to service conditions on an FRP deck. The products were evaluated for tensile strength, failure strain, bond strength, and abrasion resistance. Results were summarized in a ranking matrix, which showed Urefast PF60 should provide the best performance of the products tested.
Adding force feedback to graphics systems: issues and solutions

Integrating force feedback with a complete real-time virtual environment system presents problems which are more difficult than those encountered in building simpler forcefeedback systems. In particular, lengthy computations for graphics or simulation require a decoupling of the haptic servo loop from the main application loop if high-quality forces are to be produced. We present some approaches to these problems and describe our force-feedback software library which implements these techniques and provides other benefits including haptic-textured surfaces, device independence, distributed operation and easy enhancement.
WSMX - a semantic service-oriented architecture

Web services offer an interoperability model that abstracts from the idiosyncrasies of specific implementations; they were introduced to address the increasing need for seamless interoperability between systems in the business-to-business domain. We analyse the requirements from this domain and show that to fully address interoperability demands we need to make use of semantic descriptions of Web services. We therefore introduce the Web service execution environment (WSMX), at software system that enables the creation and execution of semantic Web services based on the Web service modelling ontology. Providers can use it to register and offer their services and requesters can use it to dynamically discover and invoke relevant services. WSMX allows a requester to discover, mediate and invoke Web services in order to carry out its tasks, based on services available on the Internet.
A Rigorous Forest Scattering Model Validation through Comparison with Indoor Bistatic Scattering Measurements

In this paper, we present numerical simulations and indoor bistatic scattering measurements on scaled targets. The targets are vertical and/or tilted dielectric parallelepipeds representing the main forest elements (tree-trunks and primary branches) at VHF and low- UHF frequencies. They are placed above an aluminum circular plate to simulate a ∞at ground. The measurements have been conducted in the anechoic chamber of the \Centre Commun de Ressources Micro- ondes" (CCRM) in Marseille, France. A 3D forest scattering model using a Method of Moments (MoM) is deployed to simulate the electric flelds scattered by these targets. Two radar geometric, azimuthal and zenithal, bistatic conflgurations with special attention to the specular direction have been considered. Simulation results and experimental data are confronted for both V V - and HH-polarizations in order to evaluate the accuracy of our model. We have obtained a very good agreement between theoretical and experimental scattered flelds for both the magnitude and phase.
Phosphorylation Dependence and Stoichiometry of the Complex Formed by Tyrosine Hydroxylase and 14-3-3γ*

Phosphorylated tyrosine hydroxylase (TH) can form complexes with 14-3-3 proteins, resulting in enzyme activation and stabilization. Although TH was among the first binding partners identified for these ubiquitous regulatory proteins, the binding stoichiometry and the activation mechanism remain unknown. To address this, we performed native mass spectrometry analyses of human TH (nonphosphorylated or phosphorylated on Ser19 (TH-pS19), Ser40 (TH-pS40), or Ser19 and Ser40 (TH-pS19pS40)) alone and together with 14-3-3γ. Tetrameric TH-pS19 (224 kDa) bound 14-3-3γ (58.3 kDa) with high affinity (Kd = 3.2 nM), generating complexes containing either one (282.4 kDa) or two (340.8 kDa) dimers of 14-3-3. Electron microscopy also revealed one major population of an asymmetric complex, consistent with one TH tetramer and one 14-3-3 dimer, and a minor population of a symmetric complex of one TH tetramer with two 14-3-3 dimers. Lower phosphorylation stoichiometries (0.15–0.54 phosphate/monomer) produced moderate changes in binding kinetics, but native MS detected much less of the symmetric TH:14-3-3γ complex. Interestingly, dephosphorylation of [32P]-TH-pS19 was mono-exponential for low phosphorylation stoichiometries (0.18–0.52), and addition of phosphatase accelerated the dissociation of the TH-pS19:14-3-3γ complex 3- to 4-fold. All together this is consistent with a model in which the pS19 residues in the TH tetramer contribute differently in the association to 14-3-3γ. Complex formation between TH-pS40 and 14-3-3γ was not detected via native MS, and surface plasmon resonance showed that the interaction was very weak. Furthermore, TH-pS19pS40 behaved similarly to TH-pS19 in terms of binding stoichiometry and affinity (Kd = 2.1 nM). However, we found that 14-3-3γ inhibited the phosphorylation rate of TH-pS19 by PKA (3.5-fold) on Ser40. We therefore conclude that Ser40 does not significantly contribute to the binding of 14-3-3γ, and rather has reduced accessibility in the TH:14-3-3γ complex. This adds to our understanding of the fine-tuned physiological regulation of TH, including hierarchical phosphorylation at multiple sites.
HapCUT: an efficient and accurate algorithm for the haplotype assembly problem

MOTIVATION The goal of the haplotype assembly problem is to reconstruct the two haplotypes (chromosomes) for an individual using a mix of sequenced fragments from the two chromosomes. This problem has been shown to be computationally intractable for various optimization criteria. Polynomial time algorithms have been proposed for restricted versions of the problem. In this article, we consider the haplotype assembly problem in the most general setting, i.e. fragments of any length and with an arbitrary number of gaps. RESULTS We describe a novel combinatorial approach for the haplotype assembly problem based on computing max-cuts in certain graphs derived from the sequenced fragments. Levy et al. have sequenced the complete genome of a human individual and used a greedy heuristic to assemble the haplotypes for this individual. We have applied our method HapCUTto infer haplotypes from this data and demonstrate that the haplotypes inferred using HapCUT are significantly more accurate (20-25% lower maximum error correction scores for all chromosomes) than the greedy heuristic and a previously published method, Fast Hare. We also describe a maximum likelihood based estimator of the absolute accuracy of the sequence-based haplotypes using population haplotypes from the International HapMap project. AVAILABILITY A program implementing HapCUT is available on request.
Expression Profiling of Major Histocompatibility and Natural Killer Complex Genes Reveals Candidates for Controlling Risk of Graft versus Host Disease

Background The major histocompatibility complex (MHC) is the most important genomic region that contributes to the risk of graft versus host disease (GVHD) after haematopoietic stem cell transplantation. Matching of MHC class I and II genes is essential for the success of transplantation. However, the MHC contains additional genes that also contribute to the risk of developing acute GVHD. It is difficult to identify these genes by genetic association studies alone due to linkage disequilibrium in this region. Therefore, we aimed to identify MHC genes and other genes involved in the pathophysiology of GVHD by mRNA expression profiling. Methodology/Principal Findings To reduce the complexity of the task, we used genetically well-defined rat inbred strains and a rat skin explant assay, an in-vitro-model of the graft versus host reaction (GVHR), to analyze the expression of MHC, natural killer complex (NKC), and other genes in cutaneous GVHR. We observed a statistically significant and strong up or down regulation of 11 MHC, 6 NKC, and 168 genes encoded in other genomic regions, i.e. 4.9%, 14.0%, and 2.6% of the tested genes respectively. The regulation of 7 selected MHC and 3 NKC genes was confirmed by quantitative real-time PCR and in independent skin explant assays. In addition, similar regulations of most of the selected genes were observed in GVHD-affected skin lesions of transplanted rats and in human skin explant assays. Conclusions/Significance We identified rat and human MHC and NKC genes that are regulated during GVHR in skin explant assays and could therefore serve as biomarkers for GVHD. Several of the respective human genes, including HLA-DMB, C2, AIF1, SPR1, UBD, and OLR1, are polymorphic. These candidates may therefore contribute to the genetic risk of GVHD in patients.
High Prevalence of High Grade Anal Intraepithelial Neoplasia in HIV-Infected Women Screened for Anal Cancer

Abstract:There is no consensus on optimal screening for anal cancer (AC) in HIV+ women. Seven hundred fifteen unique asymptomatic women in a high-prevalence HIV+ community were screened for AC with anal cytology and triage to high-resolution anoscopy after routine screening was implemented in a large urban hospital system. Of these, 75 (10.5%) had an abnormal anal cytology and 29 (38.7%) of those with an abnormality had high-grade anal intraepithelial neoplasia (AIN). Women with poorly controlled HIV were significantly more likely to have high-grade AIN (P = 0.03). Given the high rate of AIN in screened HIV-infected women, routine AC screening in all HIV-infected women should be strongly considered.
Interventions for minimal change disease in adults with nephrotic syndrome.

BACKGROUND Steroids have been used widely since the early 1970s for the treatment of adult-onset minimal change disease. The response rates to immunosuppressive agents in adult minimal change disease, especially steroids, are more variable than in children. The optimal agent, dose, and duration of treatment for the first episode of nephrotic syndrome, or for disease relapse(s) has not been determined. OBJECTIVES To determine the benefits and harms of interventions for the nephrotic syndrome in adults caused by minimal change disease. SEARCH STRATEGY We searched the Cochrane Central Register of Controlled Trials, MEDLINE, EMBASE, reference articles and abstracts from conference proceedings, without language restriction. Search date: January 2007. SELECTION CRITERIA Randomised controlled trials (RCTs) and quasi-RCTs of any intervention for minimal change disease in adults over 18 years with the nephrotic syndrome were included. Studies comparing different routes, frequencies, and duration of immunosuppressive agents were selected. Studies comparing non-immunosuppressive agents were also assessed. DATA COLLECTION AND ANALYSIS Two authors independently assessed study quality and extracted data. Statistical analyses were performed using the random effects model and results were expressed as a relative risk (RR) for dichotomous outcomes, or mean difference (WMD) for continuous data with 95% confidence intervals (CI). MAIN RESULTS Three RCTs (68 participants) were identified. All treatment comparisons contained only one study. No significant difference was found between prednisone compared with placebo for complete (RR 1.44, CI 0.95 to 2.19) and partial remission (RR 1.00, CI 0.07 to 14.45) of the nephrotic syndrome due to minimal change disease. There was no difference between intravenous methylprednisolone plus oral prednisone compared with oral prednisone alone for complete remission (RR 0.74, CI 0.50 to 1.08). Prednisone, compared with short-course intravenous methylprednisolone, increased the number of subjects who achieved complete remission (RR 4.95, CI 1.15 to 21.26). The lack of statistical evidence of efficacy associated with prednisone therapy was based on data derived from a single study that compared 'alternate-day prednisone' to no immunosuppression' with only a small number of participants in each group. No RCTs were identified comparing regimens in adults with a steroid-dependent or relapsing disease course or comparing treatments comprising alkylating agents, cyclosporine, tacrolimus, levamisole, or mycophenolate mofetil. AUTHORS' CONCLUSIONS Further comparative studies are required to examine the efficacy of immunosuppressive agents for achievement of sustained remission of nephrotic syndrome caused by minimal change disease. Studies are also needed to evaluate treatments for adults with steroid-dependent or relapsing disease.
Aminoglycosides Are Captured from both Periplasm and Cytoplasm by the AcrD Multidrug Efflux Transporter of Escherichia coli

ABSTRACT To understand better the mechanisms of resistance-nodulation-division (RND)-type multidrug efflux pumps, we examined the Escherichia coli AcrD pump, whose typical substrates, aminoglycosides, are not expected to diffuse spontaneously across the lipid bilayer. The hexahistidine-tagged AcrD protein was purified and reconstituted into unilamellar proteoliposomes. Its activity was measured by the proton flux accompanying substrate transport. When the interior of the proteoliposomes was acidified, the addition of aminoglycosides to the external medium stimulated proton efflux and the intravesicular accumulation of radiolabeled gentamicin, suggesting that aminoglycosides can be captured and transported from the external medium in this system (corresponding to cytosol). This activity required the presence of AcrA within the proteoliposomes. Interestingly, the increase in proton efflux also occurred when aminoglycosides were present only in the intravesicular space. This result suggested that AcrD can also capture aminoglycosides from the periplasm to extrude them into the medium in intact cells, acting as a “periplasmic vacuum cleaner. ”
A PVS-Simulink Integrated Environment for Model-Based Analysis of Cyber-Physical Systems

This paper presents a methodology, with supporting tool, for formal modeling and analysis of software components in cyber-physical systems. Using our approach, developers can integrate a simulation of logic-based specifications of software components and Simulink models of continuous processes. The integrated simulation is useful to validate the characteristics of discrete system components early in the development process. The same logic-based specifications can also be formally verified using the Prototype Verification System (PVS), to gain additional confidence that the software design complies with specific safety requirements. Modeling patterns are defined for generating the logic-based specifications from the more familiar automata-based formalism. The ultimate aim of this work is to facilitate the introduction of formal verification technologies in the software development process of cyber-physical systems, which typically requires the integrated use of different formalisms and tools. A case study from the medical domain is used to illustrate the approach. A PVS model of a pacemaker is interfaced with a Simulink model of the human heart. The overall cyber-physical system is co-simulated to validate design requirements through exploration of relevant test scenarios. Formal verification with the PVS theorem prover is demonstrated for the pacemaker model for specific safety aspects of the pacemaker design.
Examining Childhood Abuse Patterns and Sensitive Periods in Juvenile Sexual Offenders

Findings in the sexual aggression literature on the link between childhood sexual abuse and future sexual coercion have been inconsistent. In adult sexual offenders, studies have found that the relation of sexual abuse to sexual coercion is mediated by sexually related deviant cognitions, but this mediation is not found when replicated on juvenile sexual offenders. In this study it is hypothesized that this link will be found in juvenile sexual offenders when their sexual abuse history is stratified into discrete developmental epochs. It is further hypothesized that the age range of 3 to 7 years, when children rapidly acquire inhibition and cognitive flexibility skills, will be the most potent predictor. A sample of 193 juvenile sexual offenders is used to examine whether sexual abuse specifically in this discrete period, as opposed to other periods, predicts subsequent sexual fantasy. The results confirm that sexual abuse correlates with later adolescent sexual fantasy only during the 3- to 7-year epoch.
Pili-Induced Clustering of N. gonorrhoeae Bacteria

Type IV pili (Tfp) are prokaryotic retractable appendages known to mediate surface attachment, motility, and subsequent clustering of cells. Tfp are the main means of motility for Neisseria gonorrhoeae, the causative agent of gonorrhea. Tfp are also involved in formation of the microcolonies, which play a crucial role in the progression of the disease. While motility of individual cells is relatively well understood, little is known about the dynamics of N. gonorrhoeae aggregation. We investigate how individual N. gonorrhoeae cells, initially uniformly dispersed on flat plastic or glass surfaces, agglomerate into spherical microcolonies within hours. We quantify the clustering process by measuring the area fraction covered by the cells, number of cell aggregates, and their average size as a function of time. We observe that the microcolonies are also able to move but their mobility rapidly vanishes as the size of the colony increases. After a certain critical size they become immobile. We propose a simple theoretical model which assumes a pili-pili interaction of cells as the main clustering mechanism. Numerical simulations of the model quantitatively reproduce the experimental data on clustering and thus suggest that the agglomeration process can be entirely explained by the Tfp-mediated interactions. In agreement with this hypothesis mutants lacking pili are not able to form colonies. Moreover, cells with deficient quorum sensing mechanism show similar aggregation as the wild-type bacteria. Therefore, our results demonstrate that pili provide an essential mechanism for colony formation, while additional chemical cues, for example quorum sensing, might be of secondary importance.
EPMA and EBSD analysis of the chemical and structural changes in 16 wt% chromium stainless steel during deformation

In this study, four AISI 430 (EN 1.4016) steel samples of different initial composition and annealing treatment were submitted to uni-axial tension deformation. The as-supplied and deformed materials were characterized by electron channelling contrast imaging, electron backscatter diffraction and electron probe microanalysis. The results show a clear correlation between chemical composition, annealing treatment and strain level obtained until fracture.