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.

Performance of CMS muon reconstruction in cosmic-ray events

The performance of muon reconstruction in CMS is evaluated using a large data sample of cosmic-ray muons recorded in 2008. Efficiencies of various high-level trigger, identification, and reconstruction algorithms have been measured for a broad range of muon momenta, and were found to be in good agreement with expectations from Monte Carlo simulation. The relative momentum resolution for muons crossing the barrel part of the detector is better than 1% at 10 GeV/c and is about 8% at 500 GeV/c, the latter being only a factor of two worse than expected with ideal alignment conditions. Muon charge misassignment ranges from less than 0.01% at 10GeV/c to about 1% at 500 GeV/c. © 2010 IOP Publishing Ltd and SISSA.

Evaluation of a digital methodology for human identification using palatal rugoscopy

Palatal rugoscopy, or palatoscopy, is the process by which human identification can be obtained by inspecting the transverse palatal rugae inside the mouth. Aim: This study evaluated a digital method for human identification using palatoscopy, by comparing photographs of the palate against the images of cast models of the maxilla photographed with and without highlighting of the palatal rugae. Methods: Condensation silicone impressions were made from the upper arches of 30 adult subjects of both genders and their palates were then photographed. The first impression was made with heavy silicone, the second impression with light silicone, and then the models were cast in improved type IV dental stone. The casts were photographed, the palatal rugae of each one were highlighted with a pencil, and then the models were photographed again. Using a free image-editing software, the digital photographs were overlapped over the images of the palatal rugae of the models with and without highlighting of the palatal rugae, in order to identify the pairs. Results: The result of overlapping the digital photographs with the images of the models without highlighted palatal rugae resulted in 90% positive identification. For the overlapping of the digital photographs with the images of models with highlighted palatal rugae, there was 100% positive identification. Conclusions: The digital method evaluated in this study was proven effective for human identification.

Characterization of the genetic diversity of Mycobacterium tuberculosis in São Paulo city, Brazil

Background: Tuberculosis is a major health problem in São Paulo, Brazil, which is the most populous and one of the most cosmopolitan cities in South America. To characterize the genetic diversity of Mycobacterium tuberculosis in the population of this city, the genotyping techniques of spoligotyping and MIRU were applied to 93 isolates collected in two consecutive years from 93 different tuberculosis patients residing in São Paulo city and attending the Clemente Ferreira Institute (the reference clinic for the treatment of tuberculosis). Findings. Spoligotyping generated 53 different spoligotype patterns. Fifty-one isolates (54.8%) were grouped into 13 spoligotyping clusters. Seventy- two strains (77.4%) showed spoligotypes described in the international databases (SpolDB4, SITVIT), and 21 (22.6%) showed unidentified patterns. The most frequent spoligotype families were Latin American Mediterranean (LAM) (26 isolates), followed by the T family (24 isolates) and Haarlem (H) (11 isolates), which together accounted for 65.4% of all the isolates. These three families represent the major genotypes found in Africa, Central America, South America and Europe. Six Spoligo-International- types (designated SITs by the database) comprised 51.8% (37/72) of all the identified spoligotypes (SIT53, SIT50, SIT42, SIT60, SIT17 and SIT1). Other SITs found in this study indicated the great genetic diversity of M. tuberculosis, reflecting the remarkable ethnic diversity of São Paulo city inhabitants. The MIRU technique was more discriminatory and did not identify any genetic clusters with 100% similarity among the 93 isolates. The allelic analysis showed that MIRU loci 26, 40, 23 and 10 were the most discriminatory. When MIRU and spoligotyping techniques were combined, all isolates grouped in the 13 spoligotyping clusters were separated. Conclusions: Our data indicated the genomic stability of over 50% of spoligotypes identified in São Paulo and the great genetic diversity of M. tuberculosis isolates in the remaining SITs, reflecting the large ethnic mix of the São Paulo city inhabitants. The results also indicated that in this city, M. tuberculosis isolates acquired drug resistance independently of genotype and that resistance was more dependent on the selective pressure of treatment failure and the environmental circumstances of patients. © 2011 Leite et al; licensee BioMed Central Ltd.

Molecular phylogenetic relationships and phenotypic diversity in miniaturized toadlets, genus Brachycephalus (Amphibia: Anura: Brachycephalidae)

Toadlets of the genus Brachycephalus are endemic to the Atlantic rainforests of southeastern and southern Brazil. The 14 species currently described have snout-vent lengths less than 18. mm and are thought to have evolved through miniaturization: an evolutionary process leading to an extremely small adult body size. Here, we present the first comprehensive phylogenetic analysis for Brachycephalus, using a multilocus approach based on two nuclear (Rag-1 and Tyr) and three mitochondrial (Cyt b, 12S, and 16S rRNA) gene regions. Phylogenetic relationships were inferred using a partitioned Bayesian analysis of concatenated sequences and the hierarchical Bayesian method (BEST) that estimates species trees based on the multispecies coalescent model. Individual gene trees showed conflict and also varied in resolution. With the exception of the mitochondrial gene tree, no gene tree was completely resolved. The concatenated gene tree was completely resolved and is identical in topology and degree of statistical support to the individual mtDNA gene tree. On the other hand, the BEST species tree showed reduced significant node support relative to the concatenate tree and recovered a basal trichotomy, although some bipartitions were significantly supported at the tips of the species tree. Comparison of the log likelihoods for the concatenated and BEST trees suggests that the method implemented in BEST explains the multilocus data for Brachycephalus better than the Bayesian analysis of concatenated data. Landmark-based geometric morphometrics revealed marked variation in cranial shape between the species of Brachycephalus. In addition, a statistically significant association was demonstrated between variation in cranial shape and genetic distances estimated from the mtDNA and nuclear loci. Notably, B. ephippium and B. garbeana that are predicted to be sister-species in the individual and concatenated gene trees and the BEST species tree share an evolutionary novelty, the hyperossified dorsal plate. © 2011 Elsevier Inc.

Peri-orbital bone dimensional analysis using computed tomography for placement of osseointegrated implants

Craniofacial osseointegrated implants enabled producing implant-retained facial prosthesis, namely the orbital prosthesis. Aim: To evaluate the length and width of the bone structure of the peri-orbital region and to present the method validation. Methods: Computed tomography scans of 30 dry human skulls were obtained in order to register linear length and width measurements of the periorbital region. Two examiners made the measurements twice with intervals of at least 7 days between them. Data were analyzed by descriptive statistics and the paired Student's t-test was used as inferential technique (SAS, α =0.05). Results: In most cases, the intra- and inter-examiner variations were not significant (p>0.05). Therefore, the method proposed was considered as precise and valid for the measurement of the peri-orbital region. The measured points correspond to the hours of a clock. The major lengths were observed at 1 h (18.32 mm) for the left peri-orbital bone and at 11h (19.28 mm) for the right peri-orbital bone, followed by the points situated at 2h (13.05 mm) and 12h (11.37 mm) for the left side and at 10 h (12.34 mm) and 12 h (11.56 mm) for the right side. It was verified that the three points with lowest values followed the same anatomical sequence in the supraorbital rim for the right and left orbits, showing compatibility with the insertion of the intraoral osseointegrated implants. The medial wall of both orbits did not present sufficient length to allow the insertion of intraoral or craniofacial implants. Conclusions: The largest width points were observed in the supraorbital rim and in the infralateral region of both orbits and those of smallest width were found in the supralateral region of both orbits.

A new species of miniaturized toadlet, genus Brachycephalus (Anura: Brachycephalidae), from the atlantic forest of southeastern Brazil

A new species of miniaturized froglet (genus Brachycephalus) is described from Morro Prumirim in the municipality of Ubatuba, São Paulo, southeastern Brazil. Specimens were collected from the leaf litter at approximately 800 m above sea level. The new species is distinguished from all its congeners by the combination of the following characters: snout-vent length 8.7-13.4 mm; skin on head and dorsum with dermal ossification; general color orange, with a narrow brownish vertebral stripe and belly without spots; and skull, spinal processes of sacral and pre-sacral vertebrae, and process of the fourth vertebra hyperossified. Canonical variates analysis of linear body measurement demonstrates that the new species is easily discriminated from other Brachycephalus species with which it shares an intermediate condition of hyperossification. © 2012 by The Herpetologists League, Inc.

Origin and impact of the oldest metazoan bioclastic sediments

The emergence of soft-bodied metazoans and the radiation of the earliest skeletal organisms substantially changed the ecological dynamics of Ediacaran environments, leading to the genesis of biogenic hard-part deposits for the fi rst time in Earth's history. The impact of bioclast origin on sedimentary processes is analyzed herein, focusing on the sedimentology and taphonomy of shell concentrations dominated by the Ediacaran index fossil Cloudina from the Itapucumí Group, Paraguay. Skeletal concentrations include both dense accumulations of parautochthonous, disarticulated specimens (Type 1 deposits) and in situ specimens preserved as loosely packed assemblages (Type 2 deposits). At that time, Cloudina was the critical source of durable biomineralized hard parts in an environment nearly free of other bioclasts. The simple fabric and geometry of these accumulations are typical of Cambrian-style shell beds. Despite their Precambrian age, these deposits indicate that the establishment of the Phanerozoic style of marine substrates and preservation in early shell beds was determined more by the acquisition of hard parts than by environmental changes. © 2013 Geological Society of America.

Is characterizing the digital forensic facial reconstruction with hair necessary? A familiar assessors' analysis

Background: In the international scientific literature, there are few studies that emphasize the presence or absence of hair in forensic facial reconstructions. There are neither Brazilian studies concerning digital facial reconstructions without hair, nor research comparing recognition tests between digital facial reconstructions with hair and without hair. The miscegenation of Brazilian people is considerable. Brazilian people, and, in particular, Brazilian women, even if considered as Caucasoid, may present the hair in very different ways: curly, wavy or straight, blonde, red, brown or black, long or short, etc. For this reason, it is difficult to find a correct type of hair for facial reconstruction (unless, in real cases, some hair is recovered with the skeletal remains). Aims and methods: This study focuses on the performance of three different digital forensic facial reconstructions, without hair, of a Brazilian female subject (based on one international database and two Brazilian databases for soft facial-tissue thickness) and evaluates the digital forensic facial reconstructions comparing them to photographs of the target individual and nine other subjects, employing the recognition method. A total of 22 assessors participated in the recognition process; all of them were familiar with the 10 individuals who composed the face pool. Results and conclusions: The target subject was correctly recognized by 41% of the 22 examiners in the International Pattern, by 32% in the Brazilian Magnetic Resonance Pattern and by 32% in the Brazilian Fresh Cadavers Pattern. The facial reconstructions without hair were correctly recognized using the three databases of facial soft-tissue thickness. The observed results were higher than the results obtained using facial reconstructions with hair, from the same skull, which can indicate that it is better to not use hair, at least when there is no information concerning its characteristics. © 2013 Elsevier B.V. All rights reserved.