Novel tools for conservation genetics in marine fish: population structure and evolution of the European hake (Merluccius merluccius) inferred by SNP variation and applications to traceability

The research presented in my PhD thesis is part of a wider European project, FishPopTrace, focused on traceability of fish populations and products. My work was aimed at developing and analyzing novel genetic tools for a widely distributed marine fish species, the European hake (Merluccius merluccius), in order to investigate population genetic structure and explore potential applications to traceability scenarios. A total of 395 SNPs (Single Nucleotide Polymorphisms) were discovered from a massive collection of Expressed Sequence Tags, obtained by high-throughput sequencing, and validated on 19 geographic samples from Atlantic and Mediterranean. Genome-scan approaches were applied to identify polymorphisms on genes potentially under divergent selection (outlier SNPs), showing higher genetic differentiation among populations respect to the average observed across loci. Comparative analysis on population structure were carried out on putative neutral and outlier loci at wide (Atlantic and Mediterranean samples) and regional (samples within each basin) spatial scales, to disentangle the effects of demographic and adaptive evolutionary forces on European hake populations genetic structure. Results demonstrated the potential of outlier loci to unveil fine scale genetic structure, possibly identifying locally adapted populations, despite the weak signal showed from putative neutral SNPs. The application of outlier SNPs within the framework of fishery resources management was also explored. A minimum panel of SNP markers showing maximum discriminatory power was selected and applied to a traceability scenario aiming at identifying the basin (and hence the stock) of origin, Atlantic or Mediterranean, of individual fish. This case study illustrates how molecular analytical technologies have operational potential in real-world contexts, and more specifically, potential to support fisheries control and enforcement and fish and fish product traceability.

Measurement of the oscillation frequency of B s mesons in the hadronic decay mode B s pi D s (phi pi) X with the D0 detector at the Fermilab Tevatron collider

The standard model (SM) of particle physics is a theory, describing three out of four fundamental forces. In this model the Cabibbo-Kobayashi-Maskawa (CKM) matrix describes the transformation between the mass and weak eigenstates of quarks. The matrix properties can be visualized as triangles in the complex plane. A precise measurement of all triangle parameters can be used to verify the validity of the SM. The least precisely measured parameter of the triangle is related to the CKM element |Vtd|, accessible through the mixing frequency (oscillation) of neutral B mesons, where mixing is the transition of a neutral meson into its anti-particle and vice versa. It is possible to calculate the CKM element |Vtd| and a related element |Vts| by measuring the mass differences Dmd (Dms ) between neutral Bd and bar{Bd} (Bs and bar{Bs}) meson mass eigenstates. This measurement is accomplished by tagging the initial and final state of decaying B mesons and determining their lifetime. Currently the Fermilab Tevatron Collider (providing pbar{p} collisions at sqrt{s}=1.96 TeV) is the only place, where Bs oscillations can be studied. The first selection of the "golden", fully hadronic decay mode Bs->Ds pi(phi pi)X at DØ is presented in this thesis. All data, taken between April 2002 and August 2007 with the DØ detector, corresponding to an integrated luminosity of int{L}dt=2.8/fb is used. The oscillation frequency Dms and the ratio |Vtd|/|Vts| are determined as Dms = (16.6 +0.5-0.4(stat) +0.4-0.3(sys)) 1/ps, |Vtd|/|Vts| = 0.213 +0.004-0.003(exp)pm 0.008(theor). These results are consistent with the standard model expectations and no evidence for new physics is observable.

Anatomic study of the feline bronchial and vascular structures with a 64 detector-row computed tomography

Multidetector row computed tomography over the last decade is commonly used in veterinary medicine. This new technology has an increased spatial and temporal resolution, could evaluate wider scanning range in shorter scanning time, providing an advanced imaging modality. Computed tomography angiographic studies are commonly used in veterinary medicine in order to evaluate vascular structures of the abdomen and the thorax. Pulmonary pathology in feline patients is a very common condition and usually is further evaluating with computed tomography. Up to date few references of the normal computed tomographic aspects of the feline thorax are reported. In this study a computed tomographic pulmonary angiography (CTPA) protocol is reported in normal cats and is compared with the up to date anatomical references. A CTPA protocol using a 64 MDCT in our study achieved high resolution images of the pulmonary arteries, pulmonary veins and bronchial lumen till the level of minor segmental branches. Feline pulmonary bronchial parenchyma demonstrates an architecture of mixed type with a monopedial model observed in the most anatomical parts and the dichotomic aspect is seen at the accessory lobe. The arterial and venous architecture is similar to the bronchial. Statistical analysis demonstrates the linear correlation of tracheal diameter to the felines weight. Vascular variations were noticed. The pulmonary venous system enters into the left atrium through three ostia (left cranial ostia: consisted of the anastomosis of the cranial and caudal portion of the left cranial pulmonary vein; right ostia: consisted of the anastomosis of the right cranial and middle pulmonary vein; and the caudal ostia: consisted of the anastomosis of the right and left caudal pulmonary vein). In conclusion CTPA is applicable in feline patients and provides an excellent imaging of the pulmonary arterial, venous and bronchial system till the level of minor segmental branches.

Ability of the PM3 Quantum Mechanical Method to Model Intermolecular Hydrogen Bonding between Neutral Molecules

The PM3 semiempirical quantum-mechanical method was found to systematically describe intermolecular hydrogen bonding in small polar molecules. PM3 shows charge transfer from the donor to acceptor molecules on the order of 0.02-0.06 units of charge when strong hydrogen bonds are formed. The PM3 method is predictive; calculated hydrogen bond energies with an absolute magnitude greater than 2 kcal mol-' suggest that the global minimum is a hydrogen bonded complex; absolute energies less than 2 kcal mol-' imply that other van der Waals complexes are more stable. The geometries of the PM3 hydrogen bonded complexes agree with high-resolution spectroscopic observations, gas electron diffraction data, and high-level ab initio calculations. The main limitations in the PM3 method are the underestimation of hydrogen bond lengths by 0.1-0.2 for some systems and the underestimation of reliable experimental hydrogen bond energies by approximately 1-2 kcal mol-l. The PM3 method predicts that ammonia is a good hydrogen bond acceptor and a poor hydrogen donor when interacting with neutral molecules. Electronegativity differences between F, N, and 0 predict that donor strength follows the order F > 0 > N and acceptor strength follows the order N > 0 > F. In the calculations presented in this article, the PM3 method mirrors these electronegativity differences, predicting the F-H- - -N bond to be the strongest and the N-H- - -F bond the weakest. It appears that the PM3 Hamiltonian is able to model hydrogen bonding because of the reduction of two-center repulsive forces brought about by the parameterization of the Gaussian core-core interactions. The ability of the PM3 method to model intermolecular hydrogen bonding means reasonably accurate quantum-mechanical calculations can be applied to small biologic systems.

ESC/EAS Guidelines for the management of dyslipidaemias: the Task Force for the management of dyslipidaemias of the European Society of Cardiology (ESC) and the European Atherosclerosis Society (EAS)

Cardiovascular disease (CVD) due to atherosclerosis of the arterial vessel wall and to thrombosis is the foremost cause of premature mortality and of disability-adjusted life years (DALYs) in Europe, and is also increasingly common in developing countries.1 In the European Union, the economic cost of CVD represents annually E192 billion1 in direct and indirect healthcare costs. The main clinical entities are coronary artery disease (CAD), ischaemic stroke, and peripheral arterial disease (PAD). The causes of these CVDs are multifactorial. Some of these factors relate to lifestyles, such as tobacco smoking, lack of physical activity, and dietary habits, and are thus modifiable. Other risk factors are also modifiable, such as elevated blood pressure, type 2 diabetes, and dyslipidaemias, or non-modifiable, such as age and male gender. These guidelines deal with the management of dyslipidaemias as an essential and integral part of CVD prevention. Prevention and treatment of dyslipidaemias should always be considered within the broader framework of CVD prevention, which is addressed in guidelines of the Joint European Societies’ Task forces on CVD prevention in clinical practice.2 – 5 The latest version of these guidelines was published in 20075; an update will become available in 2012. These Joint ESC/European Atherosclerosis Society (EAS) guidelines on the management of dyslipidaemias are complementary to the guidelines on CVD prevention in clinical practice and address not only physicians [e.g. general practitioners (GPs) and cardiologists] interested in CVD prevention, but also specialists from lipid clinics or metabolic units who are dealing with dyslipidaemias that are more difficult to classify and treat.

Radiographic study of the mandibular retromolar canal: an anatomic structure with clinical importance

The retromolar canal is an anatomic structure of the mandible with clinical importance. This canal branches off from the mandibular canal behind the third molar and travels to the retromolar foramen in the retromolar fossa. The retromolar canal might conduct accessory innervation to the mandibular molars or contain an aberrant buccal nerve.

Proposal of Bisgaardia hudsonensis gen. nov., sp. nov. and an additional genomospecies, isolated from seals, as new members of the family Pasteurellaceae

Phenotypic and phylogenetic studies were performed on eight Gram-negative-staining, rod-shaped bacteria isolated from seals. Biochemical and physiological studies showed identical profiles for all of the isolates and indicated that they were related to the family Pasteurellaceae. 16S rRNA gene sequencing demonstrated that the organism represented a distinct cluster with two sublines within the family Pasteurellaceae with <96% sequence similarity to any recognized species. Multilocus sequence analysis (MLSA) including rpoB, infB and recN genes further confirmed these findings with the eight isolates forming a genus-like cluster with two branches. Genome relatedness as deduced from recN gene sequences suggested that the isolates represented a new genus with two species. On the basis of the results of the phylogenetic analysis and phenotypic criteria, it is proposed that these bacteria from seals are classified as Bisgaardia hudsonensis gen. nov., sp. nov. (the type species) and Bisgaardia genomospecies 1. The G+C content of the DNA was 39.5 mol%. The type strain of Bisgaardia hudsonensis gen. nov., sp. nov. is M327/99/2(T) (=CCUG 43067(T)=NCTC 13475(T)=98-D-690B(T)) and the reference strain of Bisgaardia genomospecies 1 is M1765/96/5 (=CCUG 59551=NCTC 13474).

Effect of the Various Degrees of Stress on Childrens Art Expression Through Drawings

One of the aims of this project was to understand the way in which external environment or situation affects children's behaviour. Emotional experiences are developed and acquired under the influence of the environment, and a good family relationship is necessary for young people to grow, develop and socialise at all ages. Stress causes specific negative emotions, including concern, anxiety, sorrow and hostility. A pathologic environment in childhood forces the development of special abilities, both creative and destructive, It supports the development of an abnormal state of mind in which the usual relations between body and mind, reality and imagination, knowledge and memory are changed. Here the environment considered was that of the war and aggression in Bosnia & Herzegovina, where children, particularly those from Podrinje, witnessed arrests, killing, deforming and slaughtering of adults and children, in many cases members of their immediate families. Sehovic analysed the content of drawings by children exposed to various degrees of stress, to discover how these indicate various degrees of stress with the aim of using these as a projective technique in diagnostic work with children. The sample included around 600 children expelled from their homes, of both sexes aged between 6 and 12.

Hemodynamic Modeling of the Intrarenal Circulation

Three dimensional, time dependent numerical simulations of healthy and pathological conditions in a model kidney were performed. Blood flow in a kidney is not commonly investigated by computational approach, in contrast for example, to the flow in a heart. The flow in a kidney is characterized by relatively small Reynolds number (100 < Re < 0.01-laminar regime). The presented results give insight into the structure of such flow, which is hard to measure in vivo. The simulations have suggested that venous thrombosis is more likely than arterial thrombosis-higher shear rate observed. The obtained maximum velocity, as a result of the simulations, agrees with the observed in vivo measurements. The time dependent simulations show separation regimes present in the vicinity of the maximum pressure value. The pathological constriction introduced to the arterial geometry leads to the changes in separation structures. The constriction of a single vessel affects flow in the whole kidney. Pathology results in different flow rate values in healthy and affected branches, as well as, different pulsate cycle characteristic for the whole system.

Endoscopic ultrasound of the canine abdomen

The aim of this study was to develop a standardized procedure for examination of the canine abdomen using endoscopic ultrasound and to describe the organs and structures that could be identified transgastrically. The abdomen of four healthy dogs and two cadavers were examined with endoscopic ultrasound. Five anatomic landmarks were used for standardized imaging of the cranial abdomen. These were the portal vein, splenic head and body, duodenum, left kidney, and aorta. High-resolution images of the following organs and structures could be made: distal esophagus, gastric wall from the cardia to the pylorus, liver, caudal vena cava, hepatic lymph nodes, liver hilus, and associated vessels, trifurcation of the celiac artery as well as the path of its branches and the left pancreatic limb and body. Structures that were more difficult to image were the distal duodenum and right pancreatic limb, the entire jejunum, ileum, and cecum as well as the tail of the spleen. Endoscopic ultrasound allowed excellent visualization of the gastric wall and regional structures without interference with gas artefacts. Centrally located organs such as the pancreas could be well examined transgastrically with endoscopic ultrasound without interference by overlying intestinal segments as is common with transabdominal ultrasound.

Assessment of the optimal temporal window for intravenous CT cholangiography

The optimal temporal window of intravenous (IV) computed tomography (CT) cholangiography was prospectively determined. Fifteen volunteers (eight women, seven men; mean age, 38 years) underwent dynamic CT cholangiography. Two unenhanced images were acquired at the porta hepatis. Starting 5 min after initiation of IV contrast infusion (20 ml iodipamide meglumine 52%), 15 pairs of images at 5-min intervals were obtained. Attenuation of the extrahepatic bile duct (EBD) and the liver parenchyma was measured. Two readers graded visualization of the higher-order biliary branches. The first biliary opacification in the EBD occurred between 15 and 25 min (mean, 22.3 min +/- 3.2) after initiation of the contrast agent. Biliary attenuation plateaued between the 35- and the 75-min time points. Maximum hepatic parenchymal enhancement was 18.5 HU +/- 2.7. Twelve subjects demonstrated poor or non-visualization of higher-order biliary branches; three showed good or excellent visualization. Body weight and both biliary attenuation and visualization of the higher-order biliary branches correlated significantly (P<0.05). For peak enhancement of the biliary tree, CT cholangiography should be performed no earlier than 35 min after initiation of IV infusion. For a fixed contrast dose, superior visualization of the biliary system is achieved in subjects with lower body weight.

Influence of suture tension to the tearing characteristics of the soft tissues: an in vitro experiment

OBJECTIVES: To evaluate the influence of flap tension on the tearing characteristics of mucosal tissue samples in relation to various suture and needle characteristics. MATERIAL AND METHODS: Lining and masticatory mucosal tissue samples obtained from pig jaws were prepared for in vitro testing. Tension tearing diagrams of 60 experiments were traced for 3-0, 5-0 and 7-0 sutures with applied forces up to 20 N. In the second part, the same experiments were repeated with 100 diagrams to test the influence of needle characteristics with 5-0 and 6-0 sutures using only gingival tissue samples. RESULTS: 3-0 sutures mainly lead to tissue breakage at an average of 13.4 N. In contrast, 7-0 sutures only resulted in breakage of the thread at a mean applied force of 3.7 N. With 5-0 sutures, both events occurred at random at a mean force of 14.6 N. Irrespective of the needle characteristics, the mean breaking force for gingival samples with 5-0 and 6-0 sutures was approximately 10 N. CONCLUSIONS: Tissue trauma may be reduced by choosing finer suture diameters, because thinner (6-0, 7-0) sutures lead to thread breakage rather than tissue breakage.

Governmentality in higher education : a critical analysis of the National Survey of Student Engagement (NSSE)

In this dissertation, the National Survey of Student Engagement (NSSE) serves as a nodal point through which to examine the power relations shaping the direction and practices of higher education in the twenty-first century. Theoretically, my analysis is informed by Foucault’s concept of governmentality, briefly defined as a technology of power that influences or shapes behavior from a distance. This form of governance operates through apparatuses of security, which include higher education. Foucault identified three essential characteristics of an apparatus—the market, the milieu, and the processes of normalization—through which administrative mechanisms and practices operate and govern populations. In this project, my primary focus is on the governance of faculty and administrators, as a population, at residential colleges and universities. I argue that the existing milieu of accountability is one dominated by the neoliberal assumption that all activity—including higher education—works best when governed by market forces alone, reducing higher education to a market-mediated private good. Under these conditions, what many in the academy believe is an essential purpose of higher education—to educate students broadly, to contribute knowledge for the public good, and to serve as society’s critic and social conscience (Washburn 227)—is being eroded. Although NSSE emerged as a form of resistance to commercial college rankings, it did not challenge the forces that empowered the rankings in the first place. Indeed, NSSE data are now being used to make institutions even more responsive to market forces. Furthermore, NSSE’s use has a normalizing effect that tends to homogenize classroom practices and erode the autonomy of faculty in the educational process. It also positions students as part of the system of surveillance. In the end, if aspects of higher education that are essential to maintaining a civil society are left to be defined solely in market terms, the result may be a less vibrant and, ultimately, a less just society.

Quantification of relativistic perturbation forces on spacecraft trajectories

The intent of the work presented in this thesis is to show that relativistic perturbations should be considered in the same manner as well known perturbations currently taken into account in planet-satellite systems. It is also the aim of this research to show that relativistic perturbations are comparable to standard perturbations in speciffc force magnitude and effects. This work would have been regarded as little more then a curiosity to most engineers until recent advancements in space propulsion methods { e.g. the creation of a artiffcial neutron stars, light sails, and continuous propulsion techniques. These cutting-edge technologies have the potential to thrust the human race into interstellar, and hopefully intergalactic, travel in the not so distant future. The relativistic perturbations were simulated on two orbit cases: (1) a general orbit and (2) a Molniya type orbit. The simulations were completed using Matlab's ODE45 integration scheme. The methods used to organize, execute, and analyze these simulations are explained in detail. The results of the simulations are presented in graphical and statistical form. The simulation data reveals that the speciffc forces that arise from the relativistic perturbations do manifest as variations in the classical orbital elements. It is also apparent from the simulated data that the speciffc forces do exhibit similar magnitudes and effects that materialize from commonly considered perturbations that are used in trajectory design, optimization, and maintenance. Due to the similarities in behavior of relativistic versus non-relativistic perturbations, a case is made for the development of a fully relativistic formulation for the trajectory design and trajectory optimization problems. This new framework would afford the possibility of illuminating new more optimal solutions to the aforementioned problems that do not arise in current formulations. This type of reformulation has already showed promise when the previously unknown Space Superhighways arose as a optimal solution when classical astrodynamics was reformulated using geometric mechanics.

Slope stability analysis of the Pacaya Volcano, Guatemala, using limit equilibrium and finite element method

The Pacaya volcanic complex is part of the Central American volcanic arc, which is associated with the subduction of the Cocos tectonic plate under the Caribbean plate. Located 30 km south of Guatemala City, Pacaya is situated on the southern rim of the Amatitlan Caldera. It is the largest post-caldera volcano, and has been one of Central America’s most active volcanoes over the last 500 years. Between 400 and 2000 years B.P, the Pacaya volcano had experienced a huge collapse, which resulted in the formation of horseshoe-shaped scarp that is still visible. In the recent years, several smaller collapses have been associated with the activity of the volcano (in 1961 and 2010) affecting its northwestern flanks, which are likely to be induced by the local and regional stress changes. The similar orientation of dry and volcanic fissures and the distribution of new vents would likely explain the reactivation of the pre-existing stress configuration responsible for the old-collapse. This paper presents the first stability analysis of the Pacaya volcanic flank. The inputs for the geological and geotechnical models were defined based on the stratigraphical, lithological, structural data, and material properties obtained from field survey and lab tests. According to the mechanical characteristics, three lithotechnical units were defined: Lava, Lava-Breccia and Breccia-Lava. The Hoek and Brown’s failure criterion was applied for each lithotechnical unit and the rock mass friction angle, apparent cohesion, and strength and deformation characteristics were computed in a specified stress range. Further, the stability of the volcano was evaluated by two-dimensional analysis performed by Limit Equilibrium (LEM, ROCSCIENCE) and Finite Element Method (FEM, PHASE 2 7.0). The stability analysis mainly focused on the modern Pacaya volcano built inside the collapse amphitheatre of “Old Pacaya”. The volcanic instability was assessed based on the variability of safety factor using deterministic, sensitivity, and probabilistic analysis considering the gravitational instability and the effects of external forces such as magma pressure and seismicity as potential triggering mechanisms of lateral collapse. The preliminary results from the analysis provide two insights: first, the least stable sector is on the south-western flank of the volcano; second, the lowest safety factor value suggests that the edifice is stable under gravity alone, and the external triggering mechanism can represent a likely destabilizing factor.