Commissioning and performance of the CMS pixel tracker with cosmic ray muons

The pixel detector of the Compact Muon Solenoid experiment consists of three barrel layers and two disks for each endcap. The detector was installed in summer 2008, commissioned with charge injections, and operated in the 3.8 T magnetic field during cosmic ray data taking. This paper reports on the first running experience and presents results on the pixel tracker performance, which are found to be in line with the design specifications of this detector. The transverse impact parameter resolution measured in a sample of high momentum muons is 18 microns. © 2010 IOP Publishing Ltd and SISSA.

Alignment of the CMS silicon tracker during commissioning with cosmic rays

The CMS silicon tracker, consisting of 1440 silicon pixel and 15 148 silicon strip detector modules, has been aligned using more than three million cosmic ray charged particles, with additional information from optical surveys. The positions of the modules were determined with respect to cosmic ray trajectories to an average precision of 3-4 microns RMS in the barrel and 3-14 microns RMS in the endcap in the most sensitive coordinate. The results have been validated by several studies, including laser beam cross-checks, track fit self-consistency, track residuals in overlapping module regions, and track parameter resolution, and are compared with predictions obtained from simulation. Correlated systematic effects have been investigated. The track parameter resolutions obtained with this alignment are close to the design performance. © 2010 IOP Publishing Ltd and SISSA.

Performance and operation of the CMS electromagnetic calorimeter

The operation and general performance of the CMS electromagnetic calorimeter using cosmic-ray muons are described. These muons were recorded after the closure of the CMS detector in late 2008. The calorimeter is made of lead tungstate crystals and the overall status of the 75 848 channels corresponding to the barrel and endcap detectors is reported. The stability of crucial operational parameters, such as high voltage, temperature and electronic noise, is summarised and the performance of the light monitoring system is presented. © 2010 IOP Publishing Ltd and SISSA.

Time reconstruction and performance of the CMS electromagnetic calorimeter

The resolution and the linearity of time measurements made with the CMS electromagnetic calorimeter are studied with samples of data from test beam electrons, cosmic rays, and beam-produced muons. The resulting time resolution measured by lead tungstate crystals is better than 100 ps for energy deposits larger than 10 GeV. Crystal-to-crystal synchronization with a precision of 500 ps is performed using muons produced with the first LHC beams in 2008. © 2010 IOP Publishing Ltd and SISSA.

Performance of the CMS hadron calorimeter with cosmic ray muons and LHC beam data

The CMS Hadron Calorimeter in the barrel, endcap and forward regions is fully commissioned. Cosmic ray data were taken with and without magnetic field at the surface hall and after installation in the experimental hall, hundred meters underground. Various measurements were also performed during the few days of beam in the LHC in September 2008. Calibration parameters were extracted, and the energy response of the HCAL determined from test beam data has been checked. © 2010 IOP Publishing Ltd and SISSA.

Identification and filtering of uncharacteristic noise in the CMS hadron calorimeter

Commissioning studies of the CMS hadron calorimeter have identified sporadic uncharacteristic noise and a small number of malfunctioning calorimeter channels. Algorithms have been developed to identify and address these problems in the data. The methods have been tested on cosmic ray muon data, calorimeter noise data, and single beam data collected with CMS in 2008. The noise rejection algorithms can be applied to LHC collision data at the trigger level or in the offline analysis. The application of the algorithms at the trigger level is shown to remove 90% of noise events with fake missing transverse energy above 100 GeV, which is sufficient for the CMS physics trigger operation. © 2010 IOP Publishing Ltd and SISSA.

Performance of the CMS drift tube chambers with cosmic rays

Studies of the performance of the CMS drift tube barrel muon system are described, with results based on data collected during the CMS Cosmic Run at Four Tesla. For most of these data, the solenoidal magnet was operated with a central field of 3.8 T. The analysis of data from 246 out of a total of 250 chambers indicates a very good muon reconstruction capability, with a coordinate resolution for a single hit of about 260 μm, and a nearly 100% efficiency for the drift tube cells. The resolution of the track direction measured in the bending plane is about 1.8 mrad, and the efficiency to reconstruct a segment in a single chamber is higher than 99%. The CMS simulation of cosmic rays reproduces well the performance of the barrel muon detector. © 2010 IOP Publishing Ltd and SISSA.

Performance study of the CMS barrel resistive plate chambers with cosmic rays

In October and November 2008, the CMS collaboration conducted a programme of cosmic ray data taking, which has recorded about 270 million events. The Resistive Plate Chamber system, which is part of the CMS muon detection system, was successfully operated in the full barrel. More than 98% of the channels were operational during the exercise with typical detection efficiency of 90%. In this paper, the performance of the detector during these dedicated runs is reported. © 2010 IOP Publishing Ltd and SISSA.

Performance of the CMS cathode strip chambers with cosmic rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47μm to 243μm. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns. © 2010 IOP Publishing Ltd and SISSA.

Aligning the CMS muon chambers with the muon alignment system during an extended cosmic ray run

The alignment system for the muon spectrometer of the CMS detector comprises three independent subsystems of optical and analog position sensors. It aligns muon chambers with respect to each other and to the central silicon tracker. System commissioning at full magnetic field began in 2008 during an extended cosmic ray run. The system succeeded in tracking muon detector movements of up to 18 mm and rotations of several milliradians under magnetic forces. Depending on coordinate and subsystem, the system achieved chamber alignment precisions of 140-350 μm and 30-200 μrad, close to the precision requirements of the experiment. Systematic errors on absolute positions are estimated to be 340-590 μm based on comparisons with independent photogrammetry measurements. © 2010 IOP Publishing Ltd and SISSA.

Precise mapping of the magnetic field in the CMS barrel yoke using cosmic rays

The CMS detector is designed around a large 4 T superconducting solenoid, enclosed in a 12 000-tonne steel return yoke. A detailed map of the magnetic field is required for the accurate simulation and reconstruction of physics events in the CMS detector, not only in the inner tracking region inside the solenoid but also in the large and complex structure of the steel yoke, which is instrumented with muon chambers. Using a large sample of cosmic muon events collected by CMS in 2008, the field in the steel of the barrel yoke has been determined with a precision of 3 to 8% depending on the location. © 2010 IOP Publishing Ltd and SISSA.

First measurement of the underlying event activity at the LHC with √ = 0.9 TeV

A measurement of the underlying activity in scattering processes with pT scale in the GeV region is performed in proton-proton collisions at √ = 0.9 TeV, using data collected by the CMS experiment at the LHC. Charged particle production is studied with reference to the direction of a leading object, either a charged particle or a set of charged particles forming a jet. Predictions of several QCD-inspired models as implemented in PYTHIA are compared, after full detector simulation, to the data. The models generally predict too little production of charged particles with pseudorapidity {pipe}η{pipe} < 2, pT > 0.5 GeV/c, and azimuthal direction transverse to that of the leading object. © 2010 CERN for benefit of the CMS collaboration.

Chemical and biological characterization of four new linear cationic α-helical peptides from the venoms of two solitary eumenine wasps

Four novel peptides were isolated from the venoms of the solitary eumenine wasps Eumenes rubrofemoratus and Eumenes fraterculus. Their sequences were determined by MALDI-TOF/TOF (matrix assisted laser desorption/ionization time-of-flight mass spectrometry) analysis, Edman degradation and solid-phase synthesis. Two of them, eumenitin-R (LNLKGLIKKVASLLN) and eumenitin-F (LNLKGLFKKVASLLT), are highly homologous to eumenitin, an antimicrobial peptide from a solitary eumenine wasp, whereas the other two, EMP-ER (FDIMGLIKKVAGAL-NH 2) and EMP-EF (FDVMGIIKKIAGAL-NH 2), are similar to eumenine mastoparan-AF (EMP-AF), a mast cell degranulating peptide from a solitary eumenine wasp. These sequences have the characteristic features of linear cationic cytolytic peptides; rich in hydrophobic and basic amino acids with no disulfide bond, and accordingly, they can be predicted to adopt an amphipathic α-helix secondary structure. In fact, the CD (circular dichroism) spectra of these peptides showed significant α-helical conformation content in the presence of TFE (trifluoroethanol), SDS (sodium dodecylsulfate) and asolectin vesicles. In the biological evaluation, all the peptides exhibited a significant broad-spectrum antimicrobial activity, and moderate mast cell degranulation and leishmanicidal activities, but showed virtually no hemolytic activity. © 2011 Elsevier Ltd.

Morphological and molecular analysis of the collagen fibers in inflammatory process

Collagen makes up one third of the total protein in humans, being formed by the connection of three polypeptide chains arranged in a triple helix. This protein has fundamental importance in the formation of extracellular matrix of connective tissue. This study aimed to analyze the structural changes of collagen, which are resulting from inflammatory processes in oral mucosa, and to make the comparative analysis between the histopathology and the Raman spectra. The samples of tissues with inflammatory fibrous hyperplasia (IFH) and normal mucosa (NM) were evaluated by Raman Spectroscopy, hematoxylin-eosin and Massons trichrome stain. The histological analysis in both stains showed differences in collagen fibers, which was presented as thin fibers and arranged in parallel direction in NM and as collagen fibers are thick, mature and not organized, showing that these types of stain show morphological changes of collagen in IFH. The Raman Spectroscopy discriminate the groups of NM and IFH based on vibrational modes of proline, hydroxiproline and CH3, CH2. The histological stains only shows information from morphological data, and can be complemented by Raman spectra. This technique could demonstrate that inflammatory process caused some changes in collagen structure which is related to aminoacids such as proline and hidroxyproline. © 2011 SPIE-OSA.

Chemometric analysis of Hymenoptera toxins and defensins: A model for predicting the biological activity of novel peptides from venoms and hemolymph

When searching for prospective novel peptides, it is difficult to determine the biological activity of a peptide based only on its sequence. The trial and error approach is generally laborious, expensive and time consuming due to the large number of different experimental setups required to cover a reasonable number of biological assays. To simulate a virtual model for Hymenoptera insects, 166 peptides were selected from the venoms and hemolymphs of wasps, bees and ants and applied to a mathematical model of multivariate analysis, with nine different chemometric components: GRAVY, aliphaticity index, number of disulfide bonds, total residues, net charge, pI value, Boman index, percentage of alpha helix, and flexibility prediction. Principal component analysis (PCA) with non-linear iterative projections by alternating least-squares (NIPALS) algorithm was performed, without including any information about the biological activity of the peptides. This analysis permitted the grouping of peptides in a way that strongly correlated to the biological function of the peptides. Six different groupings were observed, which seemed to correspond to the following groups: chemotactic peptides, mastoparans, tachykinins, kinins, antibiotic peptides, and a group of long peptides with one or two disulfide bonds and with biological activities that are not yet clearly defined. The partial overlap between the mastoparans group and the chemotactic peptides, tachykinins, kinins and antibiotic peptides in the PCA score plot may be used to explain the frequent reports in the literature about the multifunctionality of some of these peptides. The mathematical model used in the present investigation can be used to predict the biological activities of novel peptides in this system, and it may also be easily applied to other biological systems. © 2011 Elsevier Inc.