Expected performance of the ATLAS experiment - detector, trigger and physics

A detailed study is presented of the expected performance of the ATLAS detector. The reconstruction of tracks, leptons, photons, missing energy and jets is investigated, together with the performance of b-tagging and the trigger. The physics potential for a variety of interesting physics processes, within the Standard Model and beyond, is examined. The study comprises a series of notes based on simulations of the detector and physics processes, with particular emphasis given to the data expected from the first years of operation of the LHC at CERN.

Root Foraging Increases Performance of the Clonal Plant Potentilla reptans in Heterogeneous Nutrient Environments

Background Plastic root-foraging responses have been widely recognized as an important strategy for plants to explore heterogeneously distributed resources. However, the benefits and costs of root foraging have received little attention. Methodology/Principal Findings In a greenhouse experiment, we grew pairs of connected ramets of 22 genotypes of the stoloniferous plant Potentilla reptans in paired pots, between which the contrast in nutrient availability was set as null, medium and high, but with the total nutrient amount kept the same. We calculated root-foraging intensity of each individual ramet pair as the difference in root mass between paired ramets divided by the total root mass. For each genotype, we then calculated root-foraging ability as the slope of the regression of root-foraging intensity against patch contrast. For all genotypes, root-foraging intensity increased with patch contrast and the total biomass and number of offspring ramets were lowest at high patch contrast. Among genotypes, root-foraging intensity was positively related to production of offspring ramets and biomass in the high patch-contrast treatment, which indicates an evolutionary benefit of root foraging in heterogeneous environments. However, we found no significant evidence that the ability of plastic foraging imposes costs under homogeneous conditions (i.e. when foraging is not needed). Conclusions/Significance Our results show that plants of P. reptans adjust their root-foraging intensity according to patch contrast. Moreover, the results show that the root foraging has an evolutionary advantage in heterogeneous environments, while costs of having the ability of plastic root foraging were absent or very small.

Performance of the Hamamatsu R11410 photomultiplier tube in cryogenic xenon environments

The Hamamatsu R11410 photomultiplier, a tube of 3" diameter and with a very low intrinsic radioactivity, is an interesting light sensor candidate for future experiments using liquid xenon (LXe) as target for direct dark matter searches. We have performed several experiments with the R11410 with the goal of testing its performance in environments similar to a dark matter detector setup. In particular, we examined its long-term behavior and stability in LXe and its response in various electric field configurations.

Understanding the performance of the FLake model over two African Great Lakes

The ability of the one-dimensional lake model FLake to represent the mixolimnion temperatures for tropical conditions was tested for three locations in East Africa: Lake Kivu and Lake Tanganyika's northern and southern basins. Meteorological observations from surrounding automatic weather stations were corrected and used to drive FLake, whereas a comprehensive set of water temperature profiles served to evaluate the model at each site. Careful forcing data correction and model configuration made it possible to reproduce the observed mixed layer seasonality at Lake Kivu and Lake Tanganyika (northern and southern basins), with correct representation of both the mixed layer depth and water temperatures. At Lake Kivu, mixolimnion temperatures predicted by FLake were found to be sensitive both to minimal variations in the external parameters and to small changes in the meteorological driving data, in particular wind velocity. In each case, small modifications may lead to a regime switch, from the correctly represented seasonal mixed layer deepening to either completely mixed or permanently stratified conditions from similar to 10 m downwards. In contrast, model temperatures were found to be robust close to the surface, with acceptable predictions of near-surface water temperatures even when the seasonal mixing regime is not reproduced. FLake can thus be a suitable tool to parameterise tropical lake water surface temperatures within atmospheric prediction models. Finally, FLake was used to attribute the seasonal mixing cycle at Lake Kivu to variations in the near-surface meteorological conditions. It was found that the annual mixing down to 60m during the main dry season is primarily due to enhanced lake evaporation and secondarily to the decreased incoming long wave radiation, both causing a significant heat loss from the lake surface and associated mixolimnion cooling.

Performance of the resolute zotarolimus-eluting stent in small vessels.

BACKGROUND Drug eluting stents for the treatment of small vessel coronary artery disease have traditionally yielded inferior clinical outcomes compared to the use of DES in large vessels. The benefit of the second-generation Resolute zotarolimus-eluting stent (R-ZES) in small vessels was examined. METHODS Two-year clinical outcomes from five combined R-ZES studies were compared between patients with small (reference vessel diameter [RVD] ≤2.5 mm; n = 1,956) and large (RVD >2.5 mm; n = 3174) vessels. RESULTS Despite a higher incidence of comorbidities in the small vessel group, there was no significant difference in target lesion failure (TLF) (10.1% vs. 8.7%; P = 0.54) at 2 years. When the subgroup of patients with diabetes was examined (n = 1,553) there was no significant difference in 2-year TLF in small compared to large vessels (11.2% vs. 11.1%; P = 0.17). Similarly, within the small vessel cohort, no significant difference was seen regarding TLF at 2 years between people with and without diabetes (11.2% vs 9.6%; P = 0.28). CONCLUSION When used for the treatment of small vessels, the R-ZES appears to provide acceptable clinical results at 2 years when compared to its performance in large vessels.

Measurement of the muon reconstruction performance of the ATLAS detector using 2011 and 2012 LHC proton-proton collision data

This paper presents the performance of the ATLAS muon reconstruction during the LHC run with pp collisions at √s = 7–8 TeV in 2011–2012, focusing mainly on data collected in 2012. Measurements of the reconstruction efficiency and of the momentum scale and resolution, based on large reference samples of J/ψ → μμ, Z → μμ and ϒ → μμ decays, are presented and compared to Monte Carlo simulations. Corrections to the simulation, to be used in physics analysis, are provided. Over most of the covered phase space (muon |η| < 2.7 and 5 ≲ pT ≲ 100 GeV) the efficiency is above 99% and is measured with per-mille precision. The momentum resolution ranges from 1.7% at central rapidity and for transverse momentum pT ≅ 10 GeV, to 4% at large rapidity and pT ≅ 100 GeV. The momentum scale is known with an uncertainty of 0.05% to 0.2% depending on rapidity. A method for the recovery of final state radiation from the muons is also presented.

Low current performance of the Bern medical cyclotron down to the pA range

A medical cyclotron accelerating H- ions to 18 MeV is in operation at the Bern University Hospital (Inselspital). It is the commercial IBA 18/18 cyclotron equipped with a specifically conceived 6 m long external beam line ending in a separate bunker. This feature is unique for a hospital-based facility and makes it possible to conduct routine radioisotope production for PET diagnostics in parallel with multidisciplinary research activities, among which are novel particle detectors, radiation biophysics, radioprotection, radiochemistry and radiopharmacy developments. Several of these activities, such as radiobiology experiments for example, require low current beams down to the pA range, while medical cyclotrons are designed for high current operation above 10 μA. In this paper, we present the first results on the low current performance of a PET medical cyclotron obtained by ion source, radio-frequency and main coil tuning. With this method, stable beam currents down to (1.5+/- 0.5 ) pA were obtained and measured with a high-sensitivity Faraday cup located at the end of the beam transport line.

In situ cardiac performance of Atlantic cod (Gadus morhua) at cold temperatures: long-term acclimation, acute thermal challenge and the role of adrenaline

The resting and maximum in situ cardiac performance of Newfoundland Atlantic cod (Gadus morhua) acclimated to 10, 4 and 0°C were measured at their respective acclimation temperatures, and when acutely exposed to temperature changes: i.e. hearts from 10°C fish cooled to 4°C, and hearts from 4°C fish measured at 10 and 0°C. Intrinsic heart rate (f(H)) decreased from 41 beats min(-1) at 10°C to 33 beats min(-1) at 4°C and 25 beats min(-1) at 0°C. However, this degree of thermal dependency was not reflected in maximal cardiac output (Q(max) values were ~44, ~37 and ~34 ml min(-1) kg(-1) at 10, 4 and 0°C, respectively). Further, cardiac scope showed a slight positive compensation between 4 and 0°C (Q(10)=1.7), and full, if not a slight over compensation between 10 and 4°C (Q(10)=0.9). The maximal performance of hearts exposed to an acute decrease in temperature (i.e. from 10 to 4°C and 4 to 0°C) was comparable to that measured for hearts from 4°C- and 0°C-acclimated fish, respectively. In contrast, 4°C-acclimated hearts significantly out-performed 10°C-acclimated hearts when tested at a common temperature of 10°C (in terms of both Q(max) and power output). Only minimal differences in cardiac function were seen between hearts stimulated with basal (5 nmol l(-1)) versus maximal (200 nmol l(-1)) levels of adrenaline, the effects of which were not temperature dependent. These results: (1) show that maximum performance of the isolated cod heart is not compromised by exposure to cold temperatures; and (2) support data from other studies, which show that, in contrast to salmonids, cod cardiac performance/myocardial contractility is not dependent upon humoral adrenergic stimulation.

The influence of PVC wrapping on the performance of two laser fluorescence devices on occlusal surfaces in vitro

OBJECTIVE: The aim of this study was to determine the influence of polyvinyl chloride (PVC) wrapping on the performance of two laser fluorescence devices (LF and LFpen) by assessing tooth occlusal surfaces. BACKGROUND DATA: Protection of their tips may influence LF measurements. To date there are no studies evaluating the influence of this protection on the performance of the LFpen on permanent teeth, or comparing it to the original LF device. MATERIALS AND METHODS: One hundred nineteen permanent molars were assessed by two experienced dentists using the LF and the LFpen devices, both with and without PVC wrapping. The teeth were histologically prepared and assessed for caries extension. RESULTS: The LF values with and without PVC wrapping were significantly different. For both LF devices, the sensitivity and accuracy were lower when the PVC wrapping was used. The specificity was statistically significantly higher for the LFpen with PVC. No difference was found between the areas under the ROC curves with and without PVC wrapping. The ICC showed excellent interexaminer agreement. The Bland and Altman method showed a range between the upper and the lower limits of agreement of 63.4 and 57.8 units for the LF device, and 49.4 and 74.2 for the LFpen device, with and without PVC wrapping, respectively. CONCLUSIONS: We found an influence of the PVC wrapping on the performance of the LF and LFpen devices. However, since its influence on detection of occlusal caries lesions is considered for, the use of one PVC layer is suggested to avoid cross-contamination in clinical practice.

New insights into the performance of human whole-exome capture platforms.

Whole exome sequencing (WES) is increasingly used in research and diagnostics. WES users expect coverage of the entire coding region of known genes as well as sufficient read depth for the covered regions. It is, however, unknown which recent WES platform is most suitable to meet these expectations. We present insights into the performance of the most recent standard exome enrichment platforms from Agilent, NimbleGen and Illumina applied to six different DNA samples by two sequencing vendors per platform. Our results suggest that both Agilent and NimbleGen overall perform better than Illumina and that the high enrichment performance of Agilent is stable among samples and between vendors, whereas NimbleGen is only able to achieve vendor- and sample-specific best exome coverage. Moreover, the recent Agilent platform overall captures more coding exons with sufficient read depth than NimbleGen and Illumina. Due to considerable gaps in effective exome coverage, however, the three platforms cannot capture all known coding exons alone or in combination, requiring improvement. Our data emphasize the importance of evaluation of updated platform versions and suggest that enrichment-free whole genome sequencing can overcome the limitations of WES in sufficiently covering coding exons, especially GC-rich regions, and in characterizing structural variants.

Influence of contact points on the performance of caries detection methods in approximal surfaces of primary molars: an in vivo study

This in vivo study aimed to evaluate the influence of contact points on the approximal caries detection in primary molars, by comparing the performance of the DIAGNOdent pen and visual-tactile examination after tooth separation to bitewing radiography (BW). A total of 112 children were examined and 33 children were selected. In three periods (a, b, and c), 209 approximal surfaces were examined: (a) examiner 1 performed visual-tactile examination using the Nyvad criteria (EX1); examiner 2 used DIAGNOdent pen (LF1) and took BW; (b) 1 week later, after tooth separation, examiner 1 performed the second visual-tactile examination (EX2) and examiner 2 used DIAGNOdent again (LF2); (c) after tooth exfoliation, surfaces were directly examined using DIAGNOdent (LF3). Teeth were examined by computed microtomography as a reference standard. Analyses were based on diagnostic thresholds: D1: D 0 = health, D 1 –D 4 = disease; D2: D 0 , D 1 = health, D 2 –D 4 = disease; D3: D 0 –D 2 = health, D 3 , D 4 = disease. At D1, the highest sensitivity/specificity were observed for EX1 (1.00)/LF3 (0.68), respectively. At D2, the highest sensitivity/ specificity were observed for LF3 (0.69)/BW (1.00), respectively. At D3, the highest sensitivity/specificity were observed for LF3 (0.78)/EX1, EX2 and BW (1.00). EX1 showed higher accuracy values than LF1, and EX2 showed similar values to LF2. We concluded that the visual-tactile examination showed better results in detecting sound surfaces and approximal caries lesions without tooth separation. However, the effectiveness of approximal caries lesion detection of both methods was increased by the absence of contact points. Therefore, regardless of the method of detection, orthodontic separating elastics should be used as a complementary tool for the diagnosis of approximal noncavitated lesions in primary molars.

Numerical model of the human cornea based on stromal microstructure: identification of mechanical properties for two age groups

The optical quality of the human eye mainly depends on the refractive performance of the cornea. The shape of the cornea is a mechanical balance between intraocular pressure and tissue intrinsic stiffness. Several surgical procedures in ophthalmology alter the biomechanics of the cornea to provoke local or global curvature changes for vision correction. Legitimated by the large number of surgical interventions performed every day, the demand for a deeper understanding of corneal biomechanics is rising to improve the safety of procedures and medical devices. The aim of our work is to propose a numerical model of corneal biomechanics, based on the stromal microstructure. Our novel anisotropic constitutive material law features a probabilistic weighting approach to model collagen fiber distribution as observed on human cornea by Xray scattering analysis (Aghamohammadzadeh et. al., Structure, February 2004). Furthermore, collagen cross-linking was explicitly included in the strain energy function. Results showed that the proposed model is able to successfully reproduce both inflation and extensiometry experimental data (Elsheikh et. al., Curr Eye Res, 2007; Elsheikh et. al., Exp Eye Res, May 2008). In addition, the mechanical properties calculated for patients of different age groups (Group A: 65-79 years; Group B: 80-95 years) demonstrate an increased collagen cross-linking, and a decrease in collagen fiber elasticity from younger to older specimen. These findings correspond to what is known about maturing fibrous biological tissue. Since the presented model can handle different loading situations and includes the anisotropic distribution of collagen fibers, it has the potential to simulate clinical procedures involving nonsymmetrical tissue interventions. In the future, such mechanical model can be used to improve surgical planning and the design of next generation ophthalmic devices.

A comparison of the original and simplified Pulmonary Embolism Severity Index

The Pulmonary Embolism Severity Index (PESI) is a validated clinical prognostic model for patients with pulmonary embolism (PE). Recently, a simplified version of the PESI was developed. We sought to compare the prognostic performance of the original and simplified PESI. Using data from 15,531 patients with PE, we compared the proportions of patients classified as low versus higher risk between the original and simplified PESI and estimated 30-day mortality within each risk group. To assess the models' accuracy to predict mortality, we calculated sensitivity, specificity, and predictive values and likelihood ratios for low- versus higher-risk patients. We also compared the models' discriminative power by calculating the area under the receiver-operating characteristic curve. The overall 30-day mortality was 9.3%. The original PESI classified a significantly greater proportion of patients as low-risk than the simplified PESI (40.9% vs. 36.8%; p<0.001). Low-risk patients based on the original and simplified PESI had a mortality of 2.3% and 2.7%, respectively. The original and simplified PESI had similar sensitivities (90% vs. 89%), negative predictive values (98% vs. 97%), and negative likelihood ratios (0.23 vs. 0.28) for predicting mortality. The original PESI had a significantly greater discriminatory power than the simplified PESI (area under the ROC curve 0.78 [95% CI: 0.77-0.79] vs. 0.72 [95% CI: 0.71-0.74]; p<0.001). In conclusion, even though the simplified PESI accurately identified patients at low-risk of adverse outcomes, the original PESI classified a higher proportion of patients as low-risk and had a greater discriminatory power than the simplified PESI.