Spatial visualization of DNA in solution.

An image analysis method is presented which allows for the reconstruction of the three-dimensional path of filamentous objects from two of their projections. Starting with stereo pairs, this method is used to trace the trajectory of DNA molecules embedded in vitreous ice and leads to a faithful representation of their three-dimensional shape in solution. This computer-aided reconstruction is superior to the subjective three-dimensional impression generated by observation of stereo pairs of micrographs because it enables one to look at the reconstructed molecules from any chosen direction and distance and allows quantitative analysis such as determination of distances, curvature, persistence length, and writhe of DNA molecules in solution.

Development and Evaluation of a Portable Device for Measuring Curling and Warping in Concrete Pavements, 2016

Portland cement concrete (PCC) pavement undergoes repeated environmental load-related deflection resulting from temperature and moisture variations across pavement depth. This has been recognized as resulting in PCC pavement curling and warping since the mid-1920s. Slab curvature can be further magnified under repeated traffic loads and may ultimately lead to fatigue failures, including top-down and bottom-up transverse, longitudinal, and corner cracking. It is therefore significant to measure the “true” degree of curling and warping in PCC pavements, not only for quality control (QC) and quality assurance (QA) purposes, but also for better understanding of its relationship to long-term pavement performance. Although several approaches and devices—including linear variable differential transducers (LVDTs), digital indicators, and some profilers—have been proposed for measuring curling and warping, their application in the field is subject to cost, inconvenience, and complexity of operation. This research therefore explores developing an economical and simple device for measuring curling and warping in concrete pavements with accuracy comparable to or better than existing methodologies. Technical requirements were identified to establish assessment criteria for development, and field tests were conducted to modify the device to further enhancement. The finalized device is about 12 inches in height and 18 pounds in weight, and its manufacturing cost is just $320. Detailed development procedures and evaluation results for the new curling and warping measuring device are presented and discussed, with a focus on achieving reliable curling and warping measurements in a cost effective manner.

Transjugular liver biopsy: prospective evaluation of the angle formed between the hepatic veins and the vena cava main axis and modification of a semi-automated biopsy device in cases of an unfavorable angle.

In cases of transjugular liver biopsies, the venous angle formed between the chosen hepatic vein and the vena cava main axis in a frontal plane can be large, leading to technical difficulties. In a prospective study including 139 consecutive patients who underwent transjugular liver biopsy using the Quick-Core biopsy set, the mean venous angle was equal to 49.6 degrees. For 21.1% of the patients, two attempts at hepatic venous catheterization failed because the venous angle was too large, with a mean of 69.7 degrees. In all of these patients, manual reshaping of the distal curvature of the stiffening metallic cannula, by forming a new mean angle equal to 48 degrees , allowed successful completion of the procedure in less than 10 min.

Metal surface and subsurface inspection using nondestructive optical methods

This thesis considers nondestructive optical methods for metal surface and subsurface inspection. The main purpose of this thesis was to study some optical methods in order to find out their applicability to industrial measurements. In laboratory testing the simplest light scattering approach, measurement of specular reflectance, was used for surface roughness evaluation. Surface roughness, curvature and finishing process of metal sheets were determined by specular reflectance measurements. Using a fixed angleof incidence, the specular reflectance method might be automated for industrialinspection. For defect detection holographic interferometry and thermography were compared. Using either holographic interferometry or thermography, relativelysmall-size defects in metal plates could be revealed. Holographic techniques have some limitations for industrial measurements. On the contrary, thermography has excellent prospects for on-line inspection, especially with scanning techniques.

A founder CEP120 mutation in Jeune asphyxiating thoracic dystrophy expands the role of centriolar proteins in skeletal ciliopathies.

Jeune asphyxiating thoracic dystrophy (JATD) is a skeletal dysplasia characterized by a small thoracic cage and a range of skeletal and extra-skeletal anomalies. JATD is genetically heterogeneous with at least nine genes identified, all encoding ciliary proteins, hence the classification of JATD as a skeletal ciliopathy. Consistent with the observation that the heterogeneous molecular basis of JATD has not been fully determined yet, we have identified two consanguineous Saudi families segregating JATD who share a single identical ancestral homozygous haplotype among the affected members. Whole-exome sequencing revealed a single novel variant within the disease haplotype in CEP120, which encodes a core centriolar protein. Subsequent targeted sequencing of CEP120 in Saudi and European JATD cohorts identified two additional families with the same missense mutation. Combining the four families in linkage analysis confirmed a significant genome-wide linkage signal at the CEP120 locus. This missense change alters a highly conserved amino acid within CEP120 (p.Ala199Pro). In addition, we show marked reduction of cilia and abnormal number of centrioles in fibroblasts from one affected individual. Inhibition of the CEP120 ortholog in zebrafish produced pleiotropic phenotypes characteristic of cilia defects including abnormal body curvature, hydrocephalus, otolith defects and abnormal renal, head and craniofacial development. We also demonstrate that in CEP120 morphants, cilia are shortened in the neural tube and disorganized in the pronephros. These results are consistent with aberrant CEP120 being implicated in the pathogenesis of JATD and expand the role of centriolar proteins in skeletal ciliopathies.

Soluble models in two-dimensional dilaton gravity

A one-parameter class of simple models of two-dimensional dilaton gravity, which can be exactly solved including back-reaction effects, is investigated at both classical and quantum levels. This family contains the RST model as a special case, and it continuously interpolates between models having a flat (Rindler) geometry and a constant curvature metric with a nontrivial dilaton field. The processes of formation of black hole singularities from collapsing matter and Hawking evaporation are considered in detail. Various physical aspects of these geometries are discussed, including the cosmological interpretation.

Absoluuttisten solmukoordinaattien menetelmä kuorimaisten kappaleiden mallinnuksessa

Työn tavoitteena oli kehittää nopeasti konvergoiva kuorielementti epälineaarisesti joustavien kappaleiden analysointiin. Kuorielementti perustuu absoluuttisten solmukoordinaattien menetelmään ja se hyödyntää kaarevuuden kuvausta elastisten voimien määrityksessä. Kehitettyä elementtiä verrattiin kontinuumimekaniikalla kehitettyyn kuorielementtiin ja kaupallisen elementtimenetelmän kuorielementtiin. Yksinkertaisimman kuormitustapauksen tuloksia verrattiin teknisen taivutusteorian mukaiseen analyyttiseen ratkaisuun. Staattisten testien tulokset tässä työssä kehitetyllä kuorielementillä vastasivat hyvin kaupallisella elementtimenetelmällä saatuja tuloksia. Deformaatioiden ollessa geometrisesti lineaarisella alueella, kehitetyllä kuorielementillä saadut tulokset vastasivat paremmin sekä analyyttistä ratkaisua että kaupallisella elementtimenetelmällä saatuja tuloksia kuin aiemman kontinuumimekaniikkaan perustuvan kuorielementin tulokset. Kehitetyn kuorielementin ongelmana verrattuna kontinuumimekaniikkaan perustuvaan elementtiin on monimutkaisempi kinematiikan kuvaus. Tästä on seurauksena laskenta-ajan huomattava kasvaminen. Jatkossa kannattaisi keskittyä numeeristen ratkaisumenetelmien kehittämiseen.

Very high-resolution digital elevation models: are multi-scale-derived variables ecologically relevant?

1. Digital elevation models (DEMs) are often used in landscape ecology to retrieve elevation or first derivative terrain attributes such as slope or aspect in the context of species distribution modelling. However, DEM-derived variables are scale-dependent and, given the increasing availability of very high-resolution (VHR) DEMs, their ecological relevancemust be assessed for different spatial resolutions. 2. In a study area located in the Swiss Western Alps, we computed VHR DEMs-derived variables related to morphometry, hydrology and solar radiation. Based on an original spatial resolution of 0.5 m, we generated DEM-derived variables at 1, 2 and 4 mspatial resolutions, applying a Gaussian Pyramid. Their associations with local climatic factors, measured by sensors (direct and ambient air temperature, air humidity and soil moisture) as well as ecological indicators derived fromspecies composition, were assessed with multivariate generalized linearmodels (GLM) andmixed models (GLMM). 3. Specific VHR DEM-derived variables showed significant associations with climatic factors. In addition to slope, aspect and curvature, the underused wetness and ruggedness indices modelledmeasured ambient humidity and soilmoisture, respectively. Remarkably, spatial resolution of VHR DEM-derived variables had a significant influence on models' strength, with coefficients of determination decreasing with coarser resolutions or showing a local optimumwith a 2 mresolution, depending on the variable considered. 4. These results support the relevance of using multi-scale DEM variables to provide surrogates for important climatic variables such as humidity, moisture and temperature, offering suitable alternatives to direct measurements for evolutionary ecology studies at a local scale.

Modeling the transport phenomena within arterial wall: porous media approach

The transport of macromolecules, such as low-density lipoprotein (LDL), and their accumulation in the layers of the arterial wall play a critical role in the creation and development of atherosclerosis. Atherosclerosis is a disease of large arteries e.g., the aorta, coronary, carotid, and other proximal arteries that involves a distinctive accumulation of LDL and other lipid-bearing materials in the arterial wall. Over time, plaque hardens and narrows the arteries. The flow of oxygen-rich blood to organs and other parts of the body is reduced. This can lead to serious problems, including heart attack, stroke, or even death. It has been proven that the accumulation of macromolecules in the arterial wall depends not only on the ease with which materials enter the wall, but also on the hindrance to the passage of materials out of the wall posed by underlying layers. Therefore, attention was drawn to the fact that the wall structure of large arteries is different than other vessels which are disease-resistant. Atherosclerosis tends to be localized in regions of curvature and branching in arteries where fluid shear stress (shear rate) and other fluid mechanical characteristics deviate from their normal spatial and temporal distribution patterns in straight vessels. On the other hand, the smooth muscle cells (SMCs) residing in the media layer of the arterial wall respond to mechanical stimuli, such as shear stress. Shear stress may affect SMC proliferation and migration from the media layer to intima. This occurs in atherosclerosis and intimal hyperplasia. The study of blood flow and other body fluids and of heat transport through the arterial wall is one of the advanced applications of porous media in recent years. The arterial wall may be modeled in both macroscopic (as a continuous porous medium) and microscopic scales (as a heterogeneous porous medium). In the present study, the governing equations of mass, heat and momentum transport have been solved for different species and interstitial fluid within the arterial wall by means of computational fluid dynamics (CFD). Simulation models are based on the finite element (FE) and finite volume (FV) methods. The wall structure has been modeled by assuming the wall layers as porous media with different properties. In order to study the heat transport through human tissues, the simulations have been carried out for a non-homogeneous model of porous media. The tissue is composed of blood vessels, cells, and an interstitium. The interstitium consists of interstitial fluid and extracellular fibers. Numerical simulations are performed in a two-dimensional (2D) model to realize the effect of the shape and configuration of the discrete phase on the convective and conductive features of heat transfer, e.g. the interstitium of biological tissues. On the other hand, the governing equations of momentum and mass transport have been solved in the heterogeneous porous media model of the media layer, which has a major role in the transport and accumulation of solutes across the arterial wall. The transport of Adenosine 5´-triphosphate (ATP) is simulated across the media layer as a benchmark to observe how SMCs affect on the species mass transport. In addition, the transport of interstitial fluid has been simulated while the deformation of the media layer (due to high blood pressure) and its constituents such as SMCs are also involved in the model. In this context, the effect of pressure variation on shear stress is investigated over SMCs induced by the interstitial flow both in 2D and three-dimensional (3D) geometries for the media layer. The influence of hypertension (high pressure) on the transport of lowdensity lipoprotein (LDL) through deformable arterial wall layers is also studied. This is due to the pressure-driven convective flow across the arterial wall. The intima and media layers are assumed as homogeneous porous media. The results of the present study reveal that ATP concentration over the surface of SMCs and within the bulk of the media layer is significantly dependent on the distribution of cells. Moreover, the shear stress magnitude and distribution over the SMC surface are affected by transmural pressure and the deformation of the media layer of the aorta wall. This work reflects the fact that the second or even subsequent layers of SMCs may bear shear stresses of the same order of magnitude as the first layer does if cells are arranged in an arbitrary manner. This study has brought new insights into the simulation of the arterial wall, as the previous simplifications have been ignored. The configurations of SMCs used here with elliptic cross sections of SMCs closely resemble the physiological conditions of cells. Moreover, the deformation of SMCs with high transmural pressure which follows the media layer compaction has been studied for the first time. On the other hand, results demonstrate that LDL concentration through the intima and media layers changes significantly as wall layers compress with transmural pressure. It was also noticed that the fraction of leaky junctions across the endothelial cells and the area fraction of fenestral pores over the internal elastic lamina affect the LDL distribution dramatically through the thoracic aorta wall. The simulation techniques introduced in this work can also trigger new ideas for simulating porous media involved in any biomedical, biomechanical, chemical, and environmental engineering applications.

Development of beam and plate finite elements based on the absolute nodal coordinate formulation

The focus of this dissertation is to develop finite elements based on the absolute nodal coordinate formulation. The absolute nodal coordinate formulation is a nonlinear finite element formulation, which is introduced for special requirements in the field of flexible multibody dynamics. In this formulation, a special definition for the rotation of elements is employed to ensure the formulation will not suffer from singularities due to large rotations. The absolute nodal coordinate formulation can be used for analyzing the dynamics of beam, plate and shell type structures. The improvements of the formulation are mainly concentrated towards the description of transverse shear deformation. Additionally, the formulation is verified by using conventional iso-parametric solid finite element and geometrically exact beam theory. Previous claims about especially high eigenfrequencies are studied by introducing beam elements based on the absolute nodal coordinate formulation in the framework of the large rotation vector approach. Additionally, the same high eigenfrequency problem is studied by using constraints for transverse deformation. It was determined that the improvements for shear deformation in the transverse direction lead to clear improvements in computational efficiency. This was especially true when comparative stress must be defined, for example when using elasto-plastic material. Furthermore, the developed plate element can be used to avoid certain numerical problems, such as shear and curvature lockings. In addition, it was shown that when compared to conventional solid elements, or elements based on nonlinear beam theory, elements based on the absolute nodal coordinate formulation do not lead to an especially stiff system for the equations of motion.

Resultados científicos do cruzeiro do "Baependi" e do "Vega" à Ilha da Trindade: Hydrozoa

In Anis paper are listed 19 different species of Hydrozca collected during a trip to the oceanic island of Trindade, located at lat. 20º 30' 00" S. and long. 29º 22' 00" W., 600 miles off the brazilian coast. During the trip hawls and dredges were done at different points of the island and of banks that exist between the coast and the island. Of the 19 listed species one is here considered new to science: Hebellopsis besnardi (p. 83), characterized by having thecae with a single curvature and a strongly everted margin. Its measures are intermediate between those os H. hartmeyeri and H. sinuosa, which are its closest allies. H. besnardi was found epizoic on D. quadridentata. Of the remainder 18, 14 were already known from the brazilian coast. Of these 14, 4 were previously known only from the coast south of Cabo Frio, and 10 are at present known only from the region north of Cabo Frio. Five species are found both north and south of this Cape. As a whole, 5 species are recorded now for the first time on the brazilian coast, of these are given a full description and figures. This paper has the purpose of increasing the faunistical knowledge of this region of the Atlantic Ocean as a first step towards the understanding of the zoogeographical relationships with the other oceans and the establishment of the zoogeographical regions of this coast.

Pulsatile Blood Flow Simulations in Computed Tomography(CT) Scan-Based and Idealized Geometries of Human Aorta

Blood flow in human aorta is an unsteady and complex phenomenon. The complex patterns are related to the geometrical features like curvature, bends, and branching and pulsatile nature of flow from left ventricle of heart. The aim of this work was to understand the effect of aorta geometry on the flow dynamics. To achieve this, 3D realistic and idealized models of descending aorta were reconstructed from Computed Tomography (CT) images of a female patient. The geometries were reconstructed using medical image processing code. The blood flow in aorta was assumed to be laminar and incompressible and the blood was assumed to be Newtonian fluid. A time dependent pulsatile and parabolic boundary condition was deployed at inlet. Steady and unsteady blood flow simulations were performed in real and idealized geometries of descending aorta using a Finite Volume Method (FVM) code. Analysis of Wall Shear Stress (WSS) distribution, pressure distribution, and axial velocity profiles were carried out in both geometries at steady and unsteady state conditions. The results obtained in thesis work reveal that the idealization of geometry underestimates the values of WSS especially near the region with sudden change of diameter. However, the resultant pressure and velocity in idealized geometry are close to those in real geometry

Application of Computational Fluid Dynamics in Modeling Blood Flow in Human Thoracic Aorta

The aim of this study was to simulate blood flow in thoracic human aorta and understand the role of flow dynamics in the initialization and localization of atherosclerotic plaque in human thoracic aorta. The blood flow dynamics in idealized and realistic models of human thoracic aorta were numerically simulated in three idealized and two realistic thoracic aorta models. The idealized models of thoracic aorta were reconstructed with measurements available from literature, and the realistic models of thoracic aorta were constructed by image processing Computed Tomographic (CT) images. The CT images were made available by South Karelia Central Hospital in Lappeenranta. The reconstruction of thoracic aorta consisted of operations, such as contrast adjustment, image segmentations, and 3D surface rendering. Additional design operations were performed to make the aorta model compatible for the numerical method based computer code. The image processing and design operations were performed with specialized medical image processing software. Pulsatile pressure and velocity boundary conditions were deployed as inlet boundary conditions. The blood flow was assumed homogeneous and incompressible. The blood was assumed to be a Newtonian fluid. The simulations with idealized models of thoracic aorta were carried out with Finite Element Method based computer code, while the simulations with realistic models of thoracic aorta were carried out with Finite Volume Method based computer code. Simulations were carried out for four cardiac cycles. The distribution of flow, pressure and Wall Shear Stress (WSS) observed during the fourth cardiac cycle were extensively analyzed. The aim of carrying out the simulations with idealized model was to get an estimate of flow dynamics in a realistic aorta model. The motive behind the choice of three aorta models with distinct features was to understand the dependence of flow dynamics on aorta anatomy. Highly disturbed and nonuniform distribution of velocity and WSS was observed in aortic arch, near brachiocephalic, left common artery, and left subclavian artery. On the other hand, the WSS profiles at the roots of branches show significant differences with geometry variation of aorta and branches. The comparison of instantaneous WSS profiles revealed that the model with straight branching arteries had relatively lower WSS compared to that in the aorta model with curved branches. In addition to this, significant differences were observed in the spatial and temporal profiles of WSS, flow, and pressure. The study with idealized model was extended to study blood flow in thoracic aorta under the effects of hypertension and hypotension. One of the idealized aorta models was modified along with the boundary conditions to mimic the thoracic aorta under the effects of hypertension and hypotension. The results of simulations with realistic models extracted from CT scans demonstrated more realistic flow dynamics than that in the idealized models. During systole, the velocity in ascending aorta was skewed towards the outer wall of aortic arch. The flow develops secondary flow patterns as it moves downstream towards aortic arch. Unlike idealized models, the distribution of flow was nonplanar and heavily guided by the artery anatomy. Flow cavitation was observed in the aorta model which was imaged giving longer branches. This could not be properly observed in the model with imaging containing a shorter length for aortic branches. The flow circulation was also observed in the inner wall of the aortic arch. However, during the diastole, the flow profiles were almost flat and regular due the acceleration of flow at the inlet. The flow profiles were weakly turbulent during the flow reversal. The complex flow patterns caused a non-uniform distribution of WSS. High WSS was distributed at the junction of branches and aortic arch. Low WSS was distributed at the proximal part of the junction, while intermedium WSS was distributed in the distal part of the junction. The pulsatile nature of the inflow caused oscillating WSS at the branch entry region and inner curvature of aortic arch. Based on the WSS distribution in the realistic model, one of the aorta models was altered to induce artificial atherosclerotic plaque at the branch entry region and inner curvature of aortic arch. Atherosclerotic plaque causing 50% blockage of lumen was introduced in brachiocephalic artery, common carotid artery, left subclavian artery, and aortic arch. The aim of this part of the study was first to study the effect of stenosis on flow and WSS distribution, understand the effect of shape of atherosclerotic plaque on flow and WSS distribution, and finally to investigate the effect of lumen blockage severity on flow and WSS distributions. The results revealed that the distribution of WSS is significantly affected by plaque with mere 50% stenosis. The asymmetric shape of stenosis causes higher WSS in branching arteries than in the cases with symmetric plaque. The flow dynamics within thoracic aorta models has been extensively studied and reported here. The effects of pressure and arterial anatomy on the flow dynamic were investigated. The distribution of complex flow and WSS is correlated with the localization of atherosclerosis. With the available results we can conclude that the thoracic aorta, with complex anatomy is the most vulnerable artery for the localization and development of atherosclerosis. The flow dynamics and arterial anatomy play a role in the localization of atherosclerosis. The patient specific image based models can be used to diagnose the locations in the aorta vulnerable to the development of arterial diseases such as atherosclerosis.

The position effect of structural Eucalyptus round timber on the flexural modulus of elasticity

Round timber has great use in civil construction, performing the function of beams, columns, foundations, poles for power distribution among others, with the advantage of not being processed, such as lumber. The structural design of round timber requires determining the elastic properties, mainly the modulus of elasticity. The Brazilian standards responsible for the stiffness and strength determination of round timber are in effect for over twenty years with no technical review. Round timber, for generally present an axis with non-zero curvature according to the position of the element in the bending test, may exhibit different values of modulus of elasticity. This study aims to analyze the position effect of Eucalyptus grandis round timber on the flexural modulus of elasticity. The three-point bending test was evaluated in two different positions based on the longitudinal rotation of the round timber element. The results revealed that at least two different positions of the round timber element are desired to obtain significant modulus of elasticity.

Ressecção videolaparoscópica de hemangiopericitoma do estômago

In the present case (77 years-old woman), the diagnosis on an extramucosal lesion by endosonography was leiomyoma or schwanoma. Radiological exam of the upper digestive tract with barium and abdominal computed tomography confirmed the site of the lesion at the level of the lesser curvature. The operative technique followed the steps of the laparoscopic partial gastric resection (wedge resection) for gastric mesenchymal tumours, described elsewhere. The Endo-GIA stapler was introduced through the 12mm port in the right upper quadrant. Proper positioning of the stapler over the lesser curvature and a satisfactory margin of tissue around the mass were attained. Nine sequential firings of the Endo-GIA 30 were needed to completely surround the mass. Histopathological diagnosis was a spindle-cell tumour measuring 3cm in diameter. Mitotic index was measured at almost null. The neoplastic cells were strongly reactive for vimentine and CD34 and negative for the immunohistochemical markers S-100 protein, muscle actin, desmin and Ag linked to VIII factor. There was a slight reaction with keratin (+/+++). The XIIIA factor reaction revealed less than 5% of dendritic elements. These data favour a vascular cell origin better than smooth muscle cell origin. In conclusion it was a gastric hemangiopericytoma. Follow-up showed no recurrence at seven years.