Calibration and Alignment of the CMS Silicon Tracking Detector

The Large Hadron Collider (LHC) will dominate the high energy physics program in the coming decade. The discovery of the standard model Higgs boson and the discovery of super-symmetric particles are within the reach at the energy scale explored by the LHC. However, the high luminosity and the high energy of the colliding protons lead to challenging demands on the detectors. The hostile radiation environment requires irradiation hard detectors, where the innermost subdetectors, consisting of silicon modules, are most affected. This thesis is devoted to the calibration and alignment of the silicon tracking detector. Electron test beam data, taken at DESY, have been used to investigate the performance of detector modules which previously were irradiated with protons up to a dose expected after 10 years of operation. The irradiated sensors turned out to be still better than required. The performance of the inner tracking systems will be dominated by the degree to which the positions of the sensors can be determined. Only a track based alignment procedure can reach the required precision. Such an alignment procedure is a major challenge given that about 50000 geometry constants need to be measured. Making use of the novel minimization program Millepede II an alignment strategy has been developed in which all detector components are aligned simultaneously, as many sources of information as possible are used, and all correlations between the position parameters of the detectors are taken into account. Utilizing simulated data, a proof of concept of the alignment strategy is shown

Correction: Benchmarking tools for the alignment of functional noncoding DNA

AbstractIn follow-up studies to this work [1], we have identified an error in a single line of code responsible for parsing BLASTZ [2] alignments that affects our previously published results for this alignment tool. This error resulted in a reduction in overall alignment coverage, with a concomitant underestimation of alignment sensitivity and overestimation of alignment specificity. As BLASTZ is an important and widely used alignment tool, we present here the revised results of our performance evaluations for BLASTZ together with previously reported results for the other alignment tools studied, which have been subsequently verified (Figures 1-4). The general conclusions presented in [1] remain unchanged, although the following sections concerning BLASTZ performance must be modified in light of our recent findings. The true overall alignment coverage for BLASTZ with and without insertion/deletion evolution and with and without blocks of constraint is shown in Figure 1, and reveals increased overall coverage in the presence of constrained blocks for intermediate to high divergence distances (Figures 1C & 1D) relative to previous results ([1] Figures 3C & 3D). As a consequence, the true overall sensitivity for BLASTZ is increased for intermediate to high divergence distances, especially in the presence of insertion/deletion evolution and constrained blocks (Figure 2D) relative to previous results ([1] Figure 4D). The most important revisions to [1] concern BLASTZ performance in interspersed blocks of constrained sequences (Figures 3, 4). Figure 3 shows that the true constraint coverage, and therefore constraint sensitivity, of BLASTZ is much improved relative to previous results for intermediate to high divergence distances ([1], Figure 5). Thus BLASTZ has increased constraint coverage relative to overall coverage (cp. Figures 1C & 1D with 3A & 3B), indicating that BLASTZ local alignments preferentially occur in constrained sequences for intermediate to high divergence distances, overturning claims on page 6 of [1] to the contrary. Likewise, the claim that BLASTZ has a "dramatic decrease in constraint sensitivity in the presence of indel evolution" on page 10 of [1] is incorrect. The increase in overall coverage, however, decreases the constraint specificity of BLASTZ for intermediate to high divergence distances (Figure 4A & 4B) relative to previous results ([1] Figure 6A & 6B). This decrease in constraint specificity requires reconsideration of the use of BLASTZ local alignments as specific detectors of constrained noncoding sequences discussed page 10 of [1]. Revised performance statistics for BLASTZ are posted along with previous results at [3]. We apologize for any misconception or inconvenience this error may have caused. References: 1. Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB: Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 2004, 5:6. 2. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W: Human-mouse alignments with BLASTZ. Genome Res 2003, 13:103-7. 3. AlignmentBenchmarking [http://rana.lbl.gov/AlignmentBenchmarking

Public Hospital Spending in England: Evidence from National Health Service Administrative Records

© 2016 The Authors. Fiscal Studies published by John Wiley & Sons Ltd. on behalf of Institute for Fiscal StudiesHealth spending per capita in England has almost doubled since 1997, yet relatively little is known about how that spending is distributed across the population. This paper uses administrative National Health Service (NHS) hospital records to examine key features of public hospital spending in England. We describe how costs vary across the life cycle, and the concentration of spending among people and over time. We find that costs per person start to increase after age 50 and escalate after age 70. Spending is highly concentrated in a small section of the population, but the degree of concentration is lower for older age groups. For those aged 25 and under, a third of all hospital spending is accounted for by 1 per cent of the population under 25 and a fifth of spending is accounted for by 1 per cent of patients under 25. For those aged 65 and over, these figures fall to 22 and 13 per cent, respectively. There is persistence in spending over time, with patients with high spending more likely to have spending in subsequent years and those with zero expenditures more likely to remain out of hospital

Signal-to-Noise Measurements on Irradiated CMS Tracker Detector Modules in an Electron Testbeam

The CMS experiment at the Large Hadron Collider at CERN is in the last phase of its construction. The harsh radiation environment at LHC will put strong demands in radiation hardness to the innermost parts of the detector. To assess the performance of irradiated microstrip detector modules, a testbeam was conducted at the Testbeam 22 facility of the DESY research center. The primary objective was the signal-to-noise measurement of irradiated CMS Tracker modules to ensure their functionality up to 10 years of LHC operation. The paper briefly summarises the basic setup at the facility and the hardware and software used to collect and analyse the data. Some interesting subsidiary results are shown, which confirm the expected behaviour of the detector with respect to the signal-to-noise performance over the active detector area and for different electron energies. The main focus of the paper are the results of the signal-to-noise measurements for CMS Tracker Modules which were exposed to different radiation doses

A Minimal Periods Algorithm with Applications

Kosaraju in ``Computation of squares in a string'' briefly described a linear-time algorithm for computing the minimal squares starting at each position in a word. Using the same construction of suffix trees, we generalize his result and describe in detail how to compute in O(k|w|)-time the minimal k-th power, with period of length larger than s, starting at each position in a word w for arbitrary exponent $k\geq2$ and integer $s\geq0$. We provide the complete proof of correctness of the algorithm, which is somehow not completely clear in Kosaraju's original paper. The algorithm can be used as a sub-routine to detect certain types of pseudo-patterns in words, which is our original intention to study the generalization.Comment: 14 page

Louse (Insecta : Phthiraptera) mitochondrial 12S rRNA secondary structure is highly variable

Lice are ectoparasitic insects hosted by birds and mammals. Mitochondrial 12S rRNA sequences obtained from lice show considerable length variation and are very difficult to align. We show that the louse 12S rRNA domain III secondary structure displays considerable variation compared to other insects, in both the shape and number of stems and loops. Phylogenetic trees constructed from tree edit distances between louse 12S rRNA structures do not closely resemble trees constructed from sequence data, suggesting that at least some of this structural variation has arisen independently in different louse lineages. Taken together with previous work on mitochondrial gene order and elevated rates of substitution in louse mitochondrial sequences, the structural variation in louse 12S rRNA confirms the highly distinctive nature of molecular evolution in these insects

Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners and help detect systematic errors in alignments, a number of benchmarking strategies have been pursued. Here we present an overview of the main strategies--based on simulation, consistency, protein structure, and phylogeny--and discuss their different advantages and associated risks. We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application--with a keen awareness of the assumptions underlying each benchmarking strategy.Comment: Revie

Cleaning of soft-solid soil layers on vertical and horizontal surfaces by stationary coherent impinging liquid jets

The cleaning action of stationary coherent liquid jets impinging (a) vertically downwards on horizontal plates, and (b) horizontally on vertical plates, was investigated using three soft-solid model soil layers: (i) PVA glue on glass and polymethylmethacrylate (Perspex) substrates; (ii) Xanthan gum on stainless steel; and (iii) petroleum jelly on glass. The liquid stream nozzle sizes, mass and volumetric flow rates and mean jet velocities investigated were: PVA, 2 mm, 17-50 g s^-1 (0.06-0.139 m^3 h^-1), 5.3-15.9 m s^-1; Xanthan gum, 0.39-3.3 mm, 2.1-148 g s^-1 (0.008-0.53 m^3 h^-1); 4.5-31.7 m s^-1; petroleum jelly, 2 mm, 7.8-50 g s^-1 (0.06-0.139 m^3 h^-1); 2.5-15.9 m s^-1. For all three soils, rapid initial removal of soil from the jet footprint was followed by the growth of a nearly circular, clean region centred at the point of jet impingement. The rate of removal of soil decreased sharply when the cleaning front reached the hydraulic or film jump. The data for the radial growth removal stage were compared with a mathematical model describing removal of the adhesive soil layer, where the force on the cleaning front was evaluated using the result reported by Wilson et al. (2011): their theory gave the momentum of the liquid film; this momentum was balanced against the soil strength, giving a simple relation between the cleaned radius and time. All three soils showed reasonable agreement with the model, across the range of flow rates and temperatures studied. The kinetic constant in the model was sensitive to soil layer thickness and the nature of the soil. Cleaning tests on the petroleum jelly soils at different temperatures, and separate rheological measurements, showed that the kinetic time constant for coating removal was proportional to the (critical shear stress)^-1.8. There was good agreement between results obtained with vertical and horizontal plates for the PVA and Xanthan gum soil layers. The petroleum jelly results differed, which is partly attributed to differences in preparing the layers of this rheologically complex material.This is the author's accepted manuscript and is under embargo until 3/2/16. The final published version can be found in Chemical Engineering Science here: http://www.sciencedirect.com/science/article/pii/S000925091400044X

SUSY searches at CMS

This article summarizes searches for supersymmetry at the CMS detector performed in 2011 at the LHC with pp collisions energies of 7TeV. For several leptonic and photonic supersymmetry searches results are presented with an integrated luminosity of approximately 5 fb−1 that are shown for the first time in public at this conference. In none of the searches a potential supersymmetry signal has been observed and within the CMSSM gluiono masses below ∼ 750 and first generation squarks masses below ∼ 1250 GeV have been excluded. Finally an outlook on the focus of supersymmetry related activities at the CMS detector in the near future is given