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We describe the new CDF Level 2 Trigger, which was commissioned during Spring 2005. The upgrade was necessitated by several factors that included increased bandwidth requirements, in view of the growing instantaneous luminosity of the Tevatron, and the need for a more robust system, since the older system was reaching the limits of maintainability. The challenges in designing the new system were interfacing with many different upstream detector subsystems, processing larger volumes of data at higher speed, and minimizing the impact on running the CDF experiment during the system commissioning phase. To meet these challenges, the new system was designed around a general purpose motherboard, the PULSAR, which is instrumented with powerful FPGAs and modern SRAMs, and which uses mezzanine cards to interface with upstream detector components and an industry standard data link (S-LINK) within the system. Index Terms--FPGA based hardware, real-time systems, trigger.

We present a comprehensive simulation study on the solid-liquid phase transition of the ionic liquid 1,3-dimethylimidazolium chloride in terms of the changes in the atomic structure and their effect on the Compton profile. The structures were obtained by using ab initio molecular dynamics simulations. Chosen radial distribution functions of the liquid structure are presented and found generally to be in good agreement with previous ab initio molecular dynamics and neutron scattering studies. The main contributions to the predicted difference Compton profile are found to arise from intermolecular changes in the phase transition. This prediction can be used for interpreting future experiments. [ABSTRACT FROM AUTHOR]

The isomers of small molecule alcohols propanol (PrOH) and butanol (BuOH) are studied by x-ray Compton scattering experiments with synchrotron radiation and density-functional theory calculations. The lineshape of the measured spectra, i.e., the Compton profile, is a momentum-space property, and its changes reflect changes in the electronic charge density between the isomers. Compared to the linear alcohols (n-PrOH and n-BuOH), the Compton profiles of the branched alcohols (iso-PrOH, iso-BuOH, sec-BuOH) are found to be narrower, which indicates a more delocalized charge for the latter. The calculations are performed for systems consisting of one to three monomer units and are found to reproduce reasonably the experimental spectral features. The influence of the basis set and exchange-correlation scheme is studied in more detail. The results provide new insight into the isomeric differences in small molecule alcohols and show that quantum chemical calculations can be increasingly tested against the x-ray Compton scattering data. [ABSTRACT FROM AUTHOR]

The isotope quantum effects in the ground-state electron momentum density of water are studied at temperatures ranging from 5 to 90 °C by combining Compton scattering experiments utilizing synchrotron radiation and computational analysis within density functional theory. We observe clear differences in the momentum density between normal and heavy water at room temperature, which are interpreted as predominantly reflecting intramolecular structural differences. The changes in the momentum density upon increasing the temperature are found to be larger for heavy than for normal water, which is attributed primarily to temperature-induced intramolecular structural effects. Both model computations and an ab initio approach qualitatively reproduce the changes in the momentum density as a function of temperature. [ABSTRACT FROM AUTHOR]

The temperature-dependent hydrogen-bond geometry in liquid water is studied by x-ray Compton scattering using synchrotron radiation combined with density functional theory analysis. Systematic changes, related to the weakening of hydrogen bonding, are observed in the shape of the Compton profile upon increasing the temperature. Using model calculations and published distribution functions of hydrogen-bond geometries obtained from a NMR study we find a significant correlation between the hydrogen-bond length and angle. This imposes a new constraint on the possible local structure distributions in liquid water. In particular, the angular distortions of the short hydrogen bonds are significantly restricted. [ABSTRACT FROM AUTHOR]

We have performed first principles calculations to investigate the structure and electronic properties of several different Si–HfOx interfaces. The atomic structure has been obtained by growing HfOx layer by layer on top of the Si(100) surface and repeatedly annealing the structure using ab initio molecular dynamics. The interfaces are characterized via their geometric and electronic properties, and also using electron transport calculations implementing a finite element based Green’s function method. We find that in all interfaces, oxygen diffuses towards the interface to form a silicon dioxide layer. This results in the formation of dangling Hf bonds in the oxide, which are saturated either by hafnium diffusion or Hf–Si bonds. The generally poor performance of these interfaces suggests that it is important to stabilize the system with respect to lattice oxygen diffusion. [ABSTRACT FROM AUTHOR]

We have modeled transport properties of nanostructures using Green’s-function method within the framework of the density-functional theory. The scheme is computationally demanding, so numerical methods have to be chosen carefully. A typical solution to the numerical burden is to use a special basis-function set, which is tailored to the problem in question, for example, the atomic-orbital basis. In this paper we present our solution to the problem. We have used the finite-element method with a hierarchical high-order polynomial basis, the so-called p elements. This method allows the discretation error to be controlled in a systematic way. The p elements work so efficiently that they can be used to solve interesting nanosystems described by nonlocal pseudopotentials. We demonstrate the potential of the implementation with two different systems. As a test system a simple Na-atom chain between two leads is modeled and the results are compared with several previous calculations. Secondly, we consider a thin hafnium dioxide (HfO2) layer on a silicon surface as a model for a gate structure of the next generation of microelectronics. [ABSTRACT FROM AUTHOR]

The native defects in GaSb have been studied with first-principles total-energy calculations. We report the structures and the formation energies of the stable defects and estimate the defect concentrations under different growth conditions. The most important native defect is the Ga[sub Sb] antisite, which acts as an acceptor. The other important defects are the acceptor-type Ga vacancy and the donor-type Ga interstitial. The Sb vacancies and interstitials are found to have much higher formation energies. A metastable state is observed for the Sb[sub Ga] antisite. The significantly larger concentrations of the Ga vacancies and interstitials compared to the corresponding Sb defects is in accordance with the asymmetric self-diffusion behavior in GaSb. The data supports the next-nearest-neighbor model for the self-diffusion, in which the migration occurs independently in the different sublattices. Self-diffusion is dominated by moving Ga atoms. © 2002 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Objectives: Self-rated health (SRH) is a well-known overall health status measure used in the general population but it is rarely examined in a clinical setting. We assessed SRH-related factors in clinic-based patients with rheumatoid arthritis (RA).Method: The study included 123 consecutive outpatients treated in 1998-1999. Patient questionnaires, including a single SRH item, sociodemographics, the Health Assessment Questionnaire (HAQ) for functional ability, and the Nottingham Health Profile (NHP) for health-related quality of life (QoL), were collected at baseline. Comorbidities were measured by the Charlson Comorbidity Index (CCI) and data on the use of drugs and surgery for RA were verified from medical records and by querying patients. Factors associated with SRH were examined using regression models with the propensity score as the covariate. Mortality rates were collected up to 31 December 2014. Hazard ratios (HRs) were used to estimate SRH-associated mortality.Results: In univariate analysis, poor SRH was associated with higher age and poorer patient-reported outcomes (PROs) but not with gender and clinical variables. After adjustment for the propensity score, the NHP dimensions for pain, energy, emotional reactions, and mobility remained significantly associated with SRH. The age- and sex-adjusted HR for death was 2.38 [95% confidence interval (CI) 1.13-5.04, p = 0.034] for the patients with poor vs. good SRH. The propensity score-adjusted HR for death was 1.69 (95% CI 0.74-3.86, p = 0.21). Conclusions  In patients with RA, SRH was associated with health-related QoL dimensions, reflecting patients' well-being rather than clinical factors. During the 16 years of follow-up, SRH had no independent association with mortality. [ABSTRACT FROM AUTHOR]

Objectives: Better treatment strategies and therapeutic options have changed the treatment of rheumatoid arthritis (RA) during the past decade. Our objective was to examine clinical and patient-reported outcomes in patients with RA treated in 1998–99 and 2011–12. Method: The cross-sectional observational study included 303 consecutive outpatients (n = 103 in 1998–99 and n = 200 in 2011–12) from the same outpatient clinic. Patient questionnaires included patients’ sociodemographics, the Health Assessment Questionnaire (HAQ) for functional ability, the Nottingham Health Profile (NHP) for health-related quality of life (HRQoL), self-reported general health (GH), and operations performed due to RA. A clinical examination was conducted for all patients. Comorbidities according to the Charlson Comorbidity Index (CCI), anti-rheumatic drugs and medications were recorded and the HAQ and NHP dimensions calculated. The results from these two patient cohorts were compared. Results: The cohorts were comparable with regard to age, sex, and RA duration while the patients in the 2011–12 cohort were less often seropositive for rheumatoid factor (RF), had a better socioeconomic situation, better functional and working ability, and a decreased rate of RA surgery. The patients in 2011–12 had higher comorbidities and poorer GH while the HRQoL dimensions did not differ between the cohorts except for better mobility in 2011–12. Methotrexate (MTX) and combinations of conventional anti-rheumatic drugs were more frequently used in 2011–12. Biologicals were used only in 2011–12. Conclusions: According to our results, more active anti-rheumatic therapy coincides with better RA-related outcomes. However, the result was the opposite with regard to overall health and comorbidities. Is this a new challenge in the treatment RA? [ABSTRACT FROM AUTHOR]

Objective We describe the epidemiological and microbiological process in the clearing of a foodborne outbreak of O:1 linked to Yersinia pseudotuberculosis raw carrots and frequency of the associated reactive extra-gastrointestinal manifestations. Methods The patient samples were investigated by routine culture or antibody testing methods. The real-time bacterial PCR was used to detect Y pseudotuberculosis in samples from the grated carrots and in those taken from the carrot storage. Genotype of bacterial isolates was determined by pulsed-field gel electrophoresis. For case identification, we retrospectively looked over the laboratory les of the central hospital focusing on the time period of the outbreak. Results Altogether 49 case patients were identified. Y pseudotuberculosis was detected by real-time PCR analysis in samples taken from grated carrots and from the carrot distributor. Bacterial isolates originating from the farm environment showed identical serotype (O:1) and genotype (S12) with the patients' isolates. Among 37 adults, reactive arthritis (ReA) was found in 8 (22%) and three adults had probable ReA. Six (67%) out of nine human leucocyte antigen (HLA) typed patients with ReA were HLA-B27 positive. Erythema nodosum was found in 42% of the 12 children, whereas none of them had definite ReA. Conclusions In this outbreak, Y pseudotuberculosis was for the first time detected in both patient and food samples. ReA was more common than earlier reported in the outbreaks associated with this pathogen; the reason may be that the previous outbreaks have occurred among children. HLA-B27 frequency was higher than usually reported in single-source outbreaks of ReA. [ABSTRACT FROM AUTHOR]