Degree of multicollinearity and variables involved in linear dependence in additive-dominant models

The objective of this work was to assess the degree of multicollinearity and to identify the variables involved in linear dependence relations in additive-dominant models. Data of birth weight (n=141,567), yearling weight (n=58,124), and scrotal circumference (n=20,371) of Montana Tropical composite cattle were used. Diagnosis of multicollinearity was based on the variance inflation factor (VIF) and on the evaluation of the condition indexes and eigenvalues from the correlation matrix among explanatory variables. The first model studied (RM) included the fixed effect of dam age class at calving and the covariates associated to the direct and maternal additive and non-additive effects. The second model (R) included all the effects of the RM model except the maternal additive effects. Multicollinearity was detected in both models for all traits considered, with VIF values of 1.03 - 70.20 for RM and 1.03 - 60.70 for R. Collinearity increased with the increase of variables in the model and the decrease in the number of observations, and it was classified as weak, with condition index values between 10.00 and 26.77. In general, the variables associated with additive and non-additive effects were involved in multicollinearity, partially due to the natural connection between these covariables as fractions of the biological types in breed composition.

Genetic diversity of the Brazilian Creole cattle Pé-duro assessed by microsatellites and mitochondrial DNA

The objective of this study was to describe the genetic diversity and structure of the largest Pé-duro population by assessing variation at ten autosomal microsatellite (STR) loci and mitochondrial DNA (mtDNA) sequences. The mean expected heterozygosity was 0.755, the mean observed heterozygosity was 0.600 and significant inbreeding coefficient (Fis) and deviations from the Hardy-Weinberg equilibrium in most of analyzed loci demonstrate the impact of inbreeding and homozygosis on this population. A more in-depth genetic analysis could be achieved by expanding the STR list. The analysis of mtDNA provided evidence of ancestral African taurine haplotypes in Pé-duro and excluded maternal Zebuine introgression. In this report, the main Pé-duro population is genetically portrayed by sampling approximately 40% of it. As this herd represents the core of the Pé-duro conservation program, these findings are of outstanding value for the management and preservation of this Brazilian 'native' cattle breed.

Bioremediation of PAHs - Limitations and soultions

Introduction 1.1 Occurrence of polycyclic aromatic hydrocarbons (PAH) in the environment Worldwide industrial and agricultural developments have released a large number of natural and synthetic hazardous compounds into the environment due to careless waste disposal, illegal waste dumping and accidental spills. As a result, there are numerous sites in the world that require cleanup of soils and groundwater. Polycyclic aromatic hydrocarbons (PAHs) are one of the major groups of these contaminants (Da Silva et al., 2003). PAHs constitute a diverse class of organic compounds consisting of two or more aromatic rings with various structural configurations (Prabhu and Phale, 2003). Being a derivative of benzene, PAHs are thermodynamically stable. In addition, these chemicals tend to adhere to particle surfaces, such as soils, because of their low water solubility and strong hydrophobicity, and this results in greater persistence under natural conditions. This persistence coupled with their potential carcinogenicity makes PAHs problematic environmental contaminants (Cerniglia, 1992; Sutherland, 1992). PAHs are widely found in high concentrations at many industrial sites, particularly those associated with petroleum, gas production and wood preserving industries (Wilson and Jones, 1993). 1.2 Remediation technologies Conventional techniques used for the remediation of soil polluted with organic contaminants include excavation of the contaminated soil and disposal to a landfill or capping - containment - of the contaminated areas of a site. These methods have some drawbacks. The first method simply moves the contamination elsewhere and may create significant risks in the excavation, handling and transport of hazardous material. Additionally, it is very difficult and increasingly expensive to find new landfill sites for the final disposal of the material. The cap and containment method is only an interim solution since the contamination remains on site, requiring monitoring and maintenance of the isolation barriers long into the future, with all the associated costs and potential liability. A better approach than these traditional methods is to completely destroy the pollutants, if possible, or transform them into harmless substances. Some technologies that have been used are high-temperature incineration and various types of chemical decomposition (for example, base-catalyzed dechlorination, UV oxidation). However, these methods have significant disadvantages, principally their technological complexity, high cost , and the lack of public acceptance. Bioremediation, on the contrast, is a promising option for the complete removal and destruction of contaminants. 1.3 Bioremediation of PAH contaminated soil & groundwater Bioremediation is the use of living organisms, primarily microorganisms, to degrade or detoxify hazardous wastes into harmless substances such as carbon dioxide, water and cell biomass Most PAHs are biodegradable unter natural conditions (Da Silva et al., 2003; Meysami and Baheri, 2003) and bioremediation for cleanup of PAH wastes has been extensively studied at both laboratory and commercial levels- It has been implemented at a number of contaminated sites, including the cleanup of the Exxon Valdez oil spill in Prince William Sound, Alaska in 1989, the Mega Borg spill off the Texas coast in 1990 and the Burgan Oil Field, Kuwait in 1994 (Purwaningsih, 2002). Different strategies for PAH bioremediation, such as in situ , ex situ or on site bioremediation were developed in recent years. In situ bioremediation is a technique that is applied to soil and groundwater at the site without removing the contaminated soil or groundwater, based on the provision of optimum conditions for microbiological contaminant breakdown.. Ex situ bioremediation of PAHs, on the other hand, is a technique applied to soil and groundwater which has been removed from the site via excavation (soil) or pumping (water). Hazardous contaminants are converted in controlled bioreactors into harmless compounds in an efficient manner. 1.4 Bioavailability of PAH in the subsurface Frequently, PAH contamination in the environment is occurs as contaminants that are sorbed onto soilparticles rather than in phase (NAPL, non aqueous phase liquids). It is known that the biodegradation rate of most PAHs sorbed onto soil is far lower than rates measured in solution cultures of microorganisms with pure solid pollutants (Alexander and Scow, 1989; Hamaker, 1972). It is generally believed that only that fraction of PAHs dissolved in the solution can be metabolized by microorganisms in soil. The amount of contaminant that can be readily taken up and degraded by microorganisms is defined as bioavailability (Bosma et al., 1997; Maier, 2000). Two phenomena have been suggested to cause the low bioavailability of PAHs in soil (Danielsson, 2000). The first one is strong adsorption of the contaminants to the soil constituents which then leads to very slow release rates of contaminants to the aqueous phase. Sorption is often well correlated with soil organic matter content (Means, 1980) and significantly reduces biodegradation (Manilal and Alexander, 1991). The second phenomenon is slow mass transfer of pollutants, such as pore diffusion in the soil aggregates or diffusion in the organic matter in the soil. The complex set of these physical, chemical and biological processes is schematically illustrated in Figure 1. As shown in Figure 1, biodegradation processes are taking place in the soil solution while diffusion processes occur in the narrow pores in and between soil aggregates (Danielsson, 2000). Seemingly contradictory studies can be found in the literature that indicate the rate and final extent of metabolism may be either lower or higher for sorbed PAHs by soil than those for pure PAHs (Van Loosdrecht et al., 1990). These contrasting results demonstrate that the bioavailability of organic contaminants sorbed onto soil is far from being well understood. Besides bioavailability, there are several other factors influencing the rate and extent of biodegradation of PAHs in soil including microbial population characteristics, physical and chemical properties of PAHs and environmental factors (temperature, moisture, pH, degree of contamination). Figure 1: Schematic diagram showing possible rate-limiting processes during bioremediation of hydrophobic organic contaminants in a contaminated soil-water system (not to scale) (Danielsson, 2000). 1.5 Increasing the bioavailability of PAH in soil Attempts to improve the biodegradation of PAHs in soil by increasing their bioavailability include the use of surfactants , solvents or solubility enhancers.. However, introduction of synthetic surfactant may result in the addition of one more pollutant. (Wang and Brusseau, 1993).A study conducted by Mulder et al. showed that the introduction of hydropropyl-ß-cyclodextrin (HPCD), a well-known PAH solubility enhancer, significantly increased the solubilization of PAHs although it did not improve the biodegradation rate of PAHs (Mulder et al., 1998), indicating that further research is required in order to develop a feasible and efficient remediation method. Enhancing the extent of PAHs mass transfer from the soil phase to the liquid might prove an efficient and environmentally low-risk alternative way of addressing the problem of slow PAH biodegradation in soil.

Sindrome di Buschke-Ollendorff: clinica e genetica

Buschke Ollendorff syndrome (BOS) is a rare autosomal dominant genodermatosis, with high penetrance and variable expressivity, characterized by the association of connective tissue naevi and osteopoikilosis. Both cutaneous and osseous manifestations are usually asymptomatic. The disease is caused by a loss-of-function mutation in the gene LEMD3, that is located on chromosome 12q13. Differential diagnosis mainly includes pseudoxantoma elasticum, morphea, lipoid proteinosis, papular elastorrhexis, juvenile elastoma, papular mucinosis. The 2 cases of BOS here reported are an example of segmental type 2 autosomal dominant genodermatosis, that is due to the loss of heterozygosity occurring at an early developmental stage in a heterozygous patient, causing a segmental homozygosity. Such patients usually have pronounced segmental lesions in the first years of life and later develop disseminated symmetrical lesions.

Vulnerability and robustness indices against blackouts in power grids

In this dissertation some novel indices for vulnerability and robustness assessment of power grids are presented. Such indices are mainly defined from the structure of transmission power grids, and with the aim of Blackout (BO) prevention and mitigation. Numerical experiments showing how they could be used alone or in coordination with pre-existing ones to reduce the effects of BOs are discussed. These indices are introduced inside 3 different sujects: The first subject is for taking a look into economical aspects of grids’ operation and their effects in BO propagation. Basically, simulations support that: the determination to operate the grid in the most profitable way could produce an increase in the size or frequency of BOs. Conversely, some uneconomical ways of supplying energy are shown to be less affected by BO phenomena. In the second subject new topological indices are devised to address the question of "which are the best buses to place distributed generation?". The combined use of two indices, is shown as a promising alternative for extracting grid’s significant features regarding robustness against BOs and distributed generation. For this purpose, a new index based on outage shift factors is used along with a previously defined electric centrality index. The third subject is on Static Robustness Analysis of electric networks, from a purely structural point of view. A pair of existing topological indices, (namely degree index and clustering coefficient), are combined to show how degradation of the network structure can be accelerated. Blackout simulations were carried out using the DC Power Flow Method and models of transmission networks from the USA and Europe.

Genexpressionsanalyse boviner mesenchymaler Stammzellen und deren in-vitro-differenzierten Folgelinien

Mesenchymale Stamzellen (MSC) sind Vertreter der adulten Stammzellen. Sie bergen durch ihre große Plastizität ein immenses Potential für die klinische Nutzung in Form von Stammzelltherapien. Zellen dieses Typs kommen vornehmlich im Knochenmark der großen Röhrenknochen vor und können zu Knochen, Knorpel und Fettzellen differenzieren. MSC leisten einen wichtigen Beitrag im Rahmen regenerativer Prozesse, beispielsweise zur Heilung von Frakturen. Breite Studien demonstrieren bereits jetzt auch bei komplexeren Erkrankungen (z.B. Osteoporose) therapeutisch vielversprechende Einsatzmöglichkeiten. Oft kommen hierbei aus MSC gezielt differenzierte Folgelinien aus Zellkulturen zum Einsatz. Dies bedingt eine kontrollierte Steuerung der Differenzierungsprozesse in vitro. Der Differenzierung einer Stammzelle liegt eine komplexe Veränderung ihrer Genexpression zugrunde. Genexpressionsmuster zur Erhaltung und Proliferation der Stammzellen müssen durch solche, die der linienspezifischen Differenzierung dienen, ersetzt werden. Die mit der Differenzierung einhergehende, transkriptomische Neuausrichtung ist für das Verständnis der Prozesse grundlegend und wurde bislang nur unzureichend untersucht. Ziel der vorliegenden Arbeit ist eine transkriptomweite und vergleichende Genexpressionsanalyse Mesenchymaler Stammzellen und deren in vitro differenzierten Folgelinien mittels Plasmid - DNA Microarrays und Sequenziertechniken der nächsten Generation (RNA-Seq, Illumina Plattform). In dieser Arbeit diente das Hausrind (Bos taurus) als Modellorganismus, da es genetisch betrachtet eine hohe Ähnlichkeit zum Menschen aufweist und Knochenmark als Quelle von MSC gut verfügbar ist. Primärkulturen Mesenchymaler Stammzellen konnten aus dem Knochenmark von Rindern erfolgreich isoliert werden. Es wurden in vitro Zellkultur - Versuche durchgeführt, um die Zellen zu Osteoblasten, Chondrozyten und Adipozyten zu differenzieren. Zur Genexpressionsanalyse wurde RNA aus jungen MSC und einer MSC Langzeitkultur („alte MSC“), sowie aus den differenzierten Zelllinien isoliert und für nachfolgende Experimente wo nötig amplifiziert. Der Erfolg der Differenzierungen konnte anhand der Genexpression von spezifischen Markergenen und mittels histologischer Färbungen belegt werden. Hierbei zeigte sich die Differenzierung zu Osteoblasten und Adipozyten erfolgreich, während die Differenzierung zu Chondrozyten trotz diverser Modifikationen am Protokoll nicht erfolgreich durchgeführt werden konnte. Eine vergleichende Hybridisierung zur Bestimmung differentieller Genexpression (MSC vs. Differenzierung) mittels selbst hergestellter Plasmid - DNA Microarrays ergab für die Osteogenese mit Genen wie destrin und enpp1, für die undifferenzierten MSC mit dem Gen sema3c neue Kandidatengene, deren biologische Funktion aufzuklären in zukünftigen Experimenten vielversprechende Ergebnisse liefern sollte. Die Analyse der transkriptomweiten Genexpression mittels NGS lieferte einen noch umfangreicheren Einblick ins Differenzierungsgeschehen. Es zeigte sich eine hohe Ähnlichkeit im Expressionsprofil von jungen MSC und Adipozyten, sowie zwischen den Profilen der alten MSC (eine Langzeitkultur) und Osteoblasten. Die alten MSC wiesen deutliche Anzeichen für eine spontane Differenzierung in die osteogene Richtung auf. Durch Analyse der 100 am stärksten exprimierten Gene jeder Zelllinie ließen sich für junge MSC und Adipozyten besonders Gene der extrazellulären Matrix (z.B col1a1,6 ; fn1 uvm.) auffinden. Sowohl Osteoblasten, als auch die alten MSC exprimieren hingegen verstärkt Gene mit Bezug zur oxidativen Phosphorylierung, sowie ribosomale Proteine. Eine Betrachtung der differentiellen Genexpression (junge MSC vs. Differenzierung) mit anschließender Pathway Analyse und Genontologie Anreicherungsstatistik unterstützt diese Ergebnisse vor allem bei Osteoblasten, wo nun jedoch zusätzlich auch Gene zur Regulation der Knochenentwicklung und Mineralisierung in den Vordergrund treten. Für Adipozyten konnte mit Genen des „Jak-STAT signaling pathway“, der Fokalen Adhäsion, sowie Genen des „Cytokine-cytokine receptor interaction pathway“ sehr spannende Einsichten in die Biologie dieses Zelltyps erlangt werden, die sicher weiterer Untersuchungen bedürfen. In undifferenzierten MSC konnte durch differentielle Genexpressionsanalyse die Rolle des nicht kanonischen Teils des WNT Signalweges als für die Aufrechterhaltung des Stammzellstatus potentiell äußerst einflussreich ermittelt werden. Die hier diskutierten Ergebnisse zeigen beispielhaft, dass besonders mittels Genexpressionsanalyse im Hochdurchsatzverfahren wertvolle Einblicke in die komplexe Biologie der Stammzelldifferenzierung möglich sind. Als Grundlage für nachfolgende Arbeiten konnten interessante Gene ermittelt und Hypothesen zu deren Einfluss auf Stammzelleigenschaften und Differenzierungsprozesse aufgestellt werden. Um einen besseren Einblick in den Differenzierungsverlauf zu ermöglichen, könnten künftig NGS Analysen zu unterschiedlichen Differenzierungszeitpunkten durchgeführt werden. Zudem wären weitere Anstrengungen zur erfolgreichen Etablierung der chondrogenen Differenzierung zur vollständigen Analyse der Genexpression des trilinearen Differenzierungspotentials von MSC wünschenswert.

Socio-Spatial Relationships in Dairy Cows

Farm animals may serve as models for evaluating social networks in a controlled environment. We used an automated system to track, at fine temporal and spatial resolution (once per minute, +/- 50 cm) every individual in six herds of dairy cows (Bos taurus). We then analysed the data using social network analyses. Relationships were based on non-random attachment and avoidance relationships in respect to synchronous use and distances observed in three different functional areas (activity, feeding and lying). We found that neither synchrony nor distance between cows was strongly predictable among the three functional areas. The emerging social networks were tightly knit for attachment relationships and less dense for avoidance relationships. These networks loosened up from the feeding and lying area to the activity area, and were less dense for relationships based on synchronicity than on median distance with respect to node degree, relative size of the largest cluster, density and diameter of the network. In addition, synchronicity was higher in dyads of dairy cows that had grown up together and shared their last dry period. This last effect disappeared with increasing herd size. Dairy herds can be characterized by one strongly clustered network including most of the herd members with many non-random attachment and avoidance relationships. Closely synchronous dyads were composed of cows with more intense previous contact. The automatic tracking of a large number of individuals proved promising in acquiring the data necessary for tackling social network analyses.

Measurement of the W+ W- cross section in sqrt(s) = 7 TeV pp collisions with ATLAS

This Letter presents a measurement of the W+ W- production cross section in sqrt(s) = 7  TeV pp collisions by the ATLAS experiment, using 34  pb(-1) of integrated luminosity produced by the Large Hadron Collider at CERN. Selecting events with two isolated leptons, each either an electron or a muon, 8 candidate events are observed with an expected background of 1.7 ± 0.6 events. The measured cross section is 41(-16)(+20)(stat) ± 5(syst)±1(lumi)  pb, which is consistent with the standard model prediction of 44 ± 3  pb calculated at next-to-leading order in QCD.

Search for a heavy particle decaying into an electron and a muon with the ATLAS detector in sqrt[s] = 7 TeV pp collisions at the LHC

This Letter presents the first search for a heavy particle decaying into an e ± μ(-/+) final state in sqrt[s] = 7 TeV pp collisions at the LHC. The data were recorded by the ATLAS detector during 2010 and correspond to a total integrated luminosity of 35 pb(-1). No excess above the standard model background expectation is observed. Exclusions at 95% confidence level are placed on two representative models. In an R-parity violating supersymmetric model, tau sneutrinos with a mass below 0.75 TeV are excluded, assuming all R-parity violating couplings are zero except λ(311)' = 0.11 and λ312 = 0.07. In a lepton flavor violating model, a Z'-like vector boson with masses of 0.70-1.00 TeV and corresponding cross sections times branching ratios of 0.175-0.183 pb is excluded. These results extend to higher mass R-parity violating sneutrinos and lepton flavor violating Z's than previous constraints from the Tevatron.

Measurement of dijet azimuthal decorrelations in pp collisions at sqrt(s)=7 TeV

Azimuthal decorrelations between the two central jets with the largest transverse momenta are sensitive to the dynamics of events with multiple jets. We present a measurement of the normalized differential cross section based on the full data set (∫Ldt=36  pb(-1)) acquired by the ATLAS detector during the 2010 sqrt(s)=7  TeV proton-proton run of the LHC. The measured distributions include jets with transverse momenta up to 1.3 TeV, probing perturbative QCD in a high-energy regime.

Search for supersymmetry using final states with one lepton, jets, and missing transverse momentum with the ATLAS detector in √s=7 TeV pp collisions

This Letter presents the first search for supersymmetry in final states containing one isolated electron or muon, jets, and missing transverse momentum from √s=7  TeV proton-proton collisions at the LHC. The data were recorded by the ATLAS experiment during 2010 and correspond to a total integrated luminosity of 35  pb(-1). No excess above the standard model background expectation is observed. Limits are set on the parameters of the minimal supergravity framework, extending previous limits. Within this framework, for A(0)=0 GeV, tanβ=3, and μ>0 and for equal squark and gluino masses, gluino masses below 700 GeV are excluded at 95% confidence level.

Search for diphoton events with large missing transverse energy in 7 TeV proton-proton collisions with the ATLAS detector

A search for diphoton events with large missing transverse energy is presented. The data were collected with the ATLAS detector in proton-proton collisions at √s=7 TeV at the CERN Large Hadron Collider and correspond to an integrated luminosity of 3.1 pb⁻¹. No excess of such events is observed above the standard model background prediction. In the context of a specific model with one universal extra dimension with compactification radius R and gravity-induced decays, values of 1/R<729 GeV are excluded at 95% C. L., providing the most sensitive limit on this model to date.

Search for a standard model Higgs boson in the H→ZZ→ℓ(+)ℓ(-)νν decay channel with the ATLAS detector

A search for a heavy standard model Higgs boson decaying via H→ZZ→→ℓ(+)ℓ(-)νν, where ℓ=e, μ, is presented. It is based on proton-proton collision data at √s=7 TeV, collected by the ATLAS experiment at the LHC in the first half of 2011 and corresponding to an integrated luminosity of 1.04 fb(-1). The data are compared to the expected standard model backgrounds. The data and the background expectations are found to be in agreement and upper limits are placed on the Higgs boson production cross section over the entire mass window considered; in particular, the production of a standard model Higgs boson is excluded in the region 340