Transcriptome architecture across tissues in the pig

Background: Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask: How relevant is tissue in terms of total transcriptome variability? Which are the genes most distinctly expressed between tissues? Does breed or sex equally affect the transcriptome across tissues?Results: In order to gain insight on these issues, we conducted microarray expression profiling of 16 different tissues from four animals of two extreme pig breeds, Large White and Iberian, two males and two females. Mixed model analysis and neighbor - joining trees showed that tissues with similar developmental origin clustered closer than those with different embryonic origins. Often a sound biological interpretation was possible for overrepresented gene ontology categories within differentially expressed genes between groups of tissues. For instance, an excess of nervous system or muscle development genes were found among tissues of ectoderm or mesoderm origins, respectively. Tissue accounted for similar to 11 times more variability than sex or breed. Nevertheless, we were able to confidently identify genes with differential expression across tissues between breeds (33 genes) and between sexes (19 genes). The genes primarily affected by sex were overall different than those affected by breed or tissue. Interaction with tissue can be important for differentially expressed genes between breeds but not so much for genes whose expression differ between sexes.Conclusion: Embryonic development leaves an enduring footprint on the transcriptome. The interaction in gene x tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome.

Energy and angular momentum of the gravitational field in the teleparallel geometry

The Hamiltonian formulation of the teleparallel equivalent of general relativity is considered. Definitions of energy, momentum and angular momentum of the gravitational field arise from the integral form of the constraint equations of the theory. In particular, the gravitational energy-momentum is given by the integral of scalar densities over a three-dimensional spacelike hypersurface. The definition for the gravitational energy is investigated in the context of the Kerr black hole. In the evaluation of the energy contained within the external event horizon of the Kerr black hole, we obtain a value strikingly close to the irreducible mass of the latter. The gravitational angular momentum is evaluated for the gravitational field of a thin, slowly rotating mass shell. © 2002 The American Physical Society.

Gravitational energy of Kerr and Kerr anti-de Sitter space-times in the teleparallel geometry

In the context of the hamiltonian formulation of the teleparallel equivalent of general relativity we compute the gravitational energy of Kerr and Kerr Anti-de Sitter (Kerr-AdS) space-times. The present calculation is carried out by means of an expression for the energy of the gravitational field that naturally arises from the integral form of the constraint equations of the formalism. In each case, the energy is exactly computed for finite and arbitrary spacelike two-spheres, without any restriction on the metric parameters. In particular, we evaluate the energy at the outer event horizon of the black holes. © SISSA/ISAS 2003.

Diferentes níveis de torta de nabo forrageiro (Raphanus sativus) como aditivo na silagem de capim elefante

The aim of the study was to evaluate the effects of the inclusion of different levels of turnip cake (TNF) on the chemical composition, digestibility and quality of elephant grass silage. Due to the quality of the oil extracted from the seeds, the turnip is being considered as an important option for the biodiesel industry in Brazil. The turnip cake is obtained from the mechanical pressing of the seeds to produce oil, and it differs from the meal by the content of fat. In the meal the fat is less than 1%, due to the use of solvents for the oil extraction. Experimental silos were used in a completely randomized design, in factorial arrangement 2 x 3 (two types of material and four levels of inclusion). The materials were represented for original material (fresh) and ensiled material, with four levels of inclusion of TNF (0, 3, 6, and 9%). Dry matter (DM), ether extract (EE), crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), nitrogen indigestible neutral detergent (NIDN), nitrogen indigestible acid detergent (NIDA), ash (MM), lignin (LIG), buffer power (PT), calcium (Ca), phosphorus (P) and in vitro dry matter digestibility (IVDDM) were determined in all materials. In silage, additionally, were determined pH and amoniacal nitrogen (NH3-N). There were effects of inclusion of TNF and the type of material on the DM, CP, ADF, NIDA, P, and MM contents and on IVDDM. The interaction of the two factors was observed to the contents of CP, NDF, ADF, NIDA, Ca and IVDDM. In silage, the DM levels were lower (P < 0.05) than in original material. The values of DM were increased linearly as increased levels of inclusion of TNF. The fibrous components, including NIDN and NIDA, decreased linearly when the TNF increased. In all treatments, values of pH and N-NH3 considered ideal for good silage were observed. The IVDDM was reduced, linearly, with the addition of increasing levels of TNF. A negative correlation (-0.95) between IVDDM and content of EE may explain the tendency of this variable, due to the EE content increased linearly with the addition of TNF. The addition of TNF as an additive in silage of elephant diminished IVDDM. Considering the changes observed in the chemical composition and digestibility of elephant grass silage with TNF as additive, suggests that this should not be included at levels exceeding 3%. On the other hand, the silages with TNF as additive showed appropriate fermentation characteristics.

Measurement of the charge ratio of atmospheric muons with the CMS detector

We present a measurement of the ratio of positive to negative muon fluxes from cosmic ray interactions in the atmosphere, using data collected by the CMS detector both at ground level and in the underground experimental cavern at the CERN LHC. Muons were detected in the momentum range from 5 GeV/. c to 1 TeV/. c. The surface flux ratio is measured to be 1.2766±0.0032(stat.)±0.0032(syst.), independent of the muon momentum, below 100 GeV/. c. This is the most precise measurement to date. At higher momenta the data are consistent with an increase of the charge ratio, in agreement with cosmic ray shower models and compatible with previous measurements by deep-underground experiments. © 2010.

Measurement of the muon stopping power in lead tungstate

A large sample of cosmic ray events collected by the CMS detector is exploited to measure the specific energy loss of muons in the lead tungstate (PbWO4) of the electromagnetic calorimeter. The measurement spans a momentum range from 5 GeV/c to 1 TeV/c. The results are consistent with the expectations over the entire range. The calorimeter energy scale, set with 120 GeV/c electrons, is validated down to the sub-GeV region using energy deposits, of order 100 MeV, associated with low-momentum muons. The muon critical energy in PbWO4 is measured to be 160+5 -68 GeV, in agreement with expectations. This is the first experimental determination of muon critical energy. © 2010 IOP Publishing Ltd and SISSA.

Commissioning of the CMS experiment and the cosmic run at four tesla

The CMS Collaboration conducted a month-long data-taking exercise known as the Cosmic Run At Four Tesla in late 2008 in order to complete the commissioning of the experiment for extended operation. The operational lessons resulting from this exercise were addressed in the subsequent shutdown to better prepare CMS for LHC beams in 2009. The cosmic data collected have been invaluable to study the performance of the detectors, to commission the alignment and calibration techniques, and to make several cosmic ray measurements. The experimental setup, conditions, and principal achievements from this data-taking exercise are described along with a review of the preceding integration activities. © 2010 IOP Publishing Ltd and SISSA.

Performance of the CMS Level-1 trigger during commissioning with cosmic ray muons and LHC beams

The CMS Level-1 trigger was used to select cosmic ray muons and LHC beam events during data-taking runs in 2008, and to estimate the level of detector noise. This paper describes the trigger components used, the algorithms that were executed, and the trigger synchronisation. Using data from extended cosmic ray runs, the muon, electron/photon, and jet triggers have been validated, and their performance evaluated. Efficiencies were found to be high, resolutions were found to be good, and rates as expected. © 2010 IOP Publishing Ltd and SISSA.

Performance of the CMS drift-tube chamber local trigger with cosmic rays

The performance of the Local Trigger based on the drift-tube system of the CMS experiment has been studied using muons from cosmic ray events collected during the commissioning of the detector in 2008. The properties of the system are extensively tested and compared with the simulation. The effect of the random arrival time of the cosmic rays on the trigger performance is reported, and the results are compared with the design expectations for proton-proton collisions and with previous measurements obtained with muon beams. © 2010 IOP Publishing Ltd and SISSA.

Fine synchronization of the CMS muon drift-tube local trigger using cosmic rays

The CMS experiment uses self-triggering arrays of drift tubes in the barrel muon trigger to perform the identification of the correct bunch crossing. The identification is unique only if the trigger chain is correctly synchronized. In this paper, the synchronization performed during an extended cosmic ray run is described and the results are reported. The random arrival time of cosmic ray muons allowed several synchronization aspects to be studied and a simple method for the fine synchronization of the Drift Tube Local Trigger at LHC to be developed. © 2010 IOP Publishing Ltd and SISSA.

Commissioning of the CMS High-Level Trigger with cosmic rays

The CMS High-Level Trigger (HLT) is responsible for ensuring that data samples with potentially interesting events are recorded with high efficiency and good quality. This paper gives an overview of the HLT and focuses on its commissioning using cosmic rays. The selection of triggers that were deployed is presented and the online grouping of triggered events into streams and primary datasets is discussed. Tools for online and offline data quality monitoring for the HLT are described, and the operational performance of the muon HLT algorithms is reviewed. The average time taken for the HLT selection and its dependence on detector and operating conditions are presented. The HLT performed reliably and helped provide a large dataset. This dataset has proven to be invaluable for understanding the performance of the trigger and the CMS experiment as a whole. © 2010 IOP Publishing Ltd and SISSA.

CMS data processing workflows during an extended cosmic ray run

The CMS Collaboration conducted a month-long data taking exercise, the Cosmic Run At Four Tesla, during October-November 2008, with the goal of commissioning the experiment for extended operation. With all installed detector systems participating, CMS recorded 270 million cosmic ray events with the solenoid at a magnetic field strength of 3.8 T. This paper describes the data flow from the detector through the various online and offline computing systems, as well as the workflows used for recording the data, for aligning and calibrating the detector, and for analysis of the data. © 2010 IOP Publishing Ltd and SISSA.

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.