Determination of viral load and integration status of HPV 16 in normal and LSIL exfoliated cervical cells

L’intégration du génome du virus papilloma humain (VPH) a été reconnu jusqu’`a récemment comme étant un événnement fréquent mais pourtant tardif dans la progression de la maladie du col de l’utérus. La perspective temporelle vient, pourtant, d’être mise au défi par la détection de formes intégrées de VPH dans les tissus normaux et dans les lésions prénéoplasiques. Notre objectif était de déterminer la charge virale de VPH-16 et son état physique dans une série de 220 échantillons provenant de cols uterins normaux et avec des lésions de bas-grade. La technique quantitative de PCR en temps réel, méthode Taqman, nous a permis de quantifier le nombre de copies des gènes E6, E2, et de la B-globine, permettant ainsi l’évaluation de la charge virale et le ratio de E6/E2 pour chaque spécimen. Le ratio E6/E2 de 1.2 ou plus était suggestif d’intégration. Par la suite, le site d’intégration du VPH dans le génome humain a été déterminé par la téchnique de RS-PCR. La charge virale moyenne était de 57.5±324.6 copies d'ADN par cellule et le ratio E6/E2 a évalué neuf échantillons avec des formes d’HPV intégrées. Ces intégrants ont été amplifiés par RS-PCR, suivi de séquençage, et l’homologie des amplicons a été déterminée par le programme BLAST de NCBI afin d’identifier les jonctions virales-humaines. On a réussi `a identifier les jonctions humaines-virales pour le contrôle positif, c'est-à-dire les cellules SiHa, pourtant nous n’avons pas detecté d’intégration par la technique de RS-PCR dans les échantillons de cellules cervicales exfoliées provenant de tissus normaux et de lésions de bas-grade. Le VPH-16 est rarement intégré dans les spécimens de jeunes patientes.

On the external validity of laboratory experiments

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

Studies on the Effect of an External Flaw on the Tensile Strength of Short Kevlar Fiber-Thermoplastic Polyurethane Composites

The effect of an external flaw on the tensile strength of short kevlar fiber-thermoplastic composites has been studied with respect to fiber content, fiber orientation, location of the external flaw, and the temperature of test. The composites showed a three-step reduction in tensile strength with increasing flaw size. The critical flaw-length region was shifted to higher flaw-size levels with increasing fiber content. With increasing temperature, the critical flaw length was increased in the case of unfilled TPU, whereas it remained more or less constant in the case of short kevlar fiber-filled-TPU composite.

A new method for load matching in multimode microwave feating applicators based on the use of dielectric layer superposition

Usage of a dielectric multilayer around a dielectric Sample is studied as a means for improving the efficiency in multimode microwave- heating cavities. The results show that by using additional dielectric constant layers the appearance of undesired reflections at the sample-air interface is avoided and higher power -absorption rates within the sample and high -efficiency designs are obtained

OPTIMAL UTILIZATION OF SERVICE FACILITY FOR A k-OUT-OF-n SYSTEM WITH REPAIR BY EXTENDING SERVICE TO EXTERNAL CUSTOMERS IN A RETRIAL QUEUE

In this paper, we study a k-out-of-n system with single server who provides service to external customers also. The system consists of two parts:(i) a main queue consisting of customers (failed components of the k-out-of-n system) and (ii) a pool (of finite capacity M) of external customers together with an orbit for external customers who find the pool full. An external customer who finds the pool full on arrival, joins the orbit with probability and with probability 1− leaves the system forever. An orbital customer, who finds the pool full, at an epoch of repeated attempt, returns to orbit with probability (< 1) and with probability 1 − leaves the system forever. We compute the steady state system size probability. Several performance measures are computed, numerical illustrations are provided.

Analytical Investigations 0n Collapse of Cylindrical Submarine Shells

Submarine hull structure is a watertight envelope, under hydrostatic pressure when in operation. Stiffened cylindrical shells constitute the major portion of these submarine hulls and these thin shells under compression are susceptible to buckling failure. Normally loss of stability occurs at the limit point rather than at the bifurcation point and the stability analysis has to consider the change in geometry at each load step. Hence geometric nonlinear analysis of the shell forms becomes. a necessity. External hydrostatic pressure will follow the deformed configuration of the shell and hence follower force effect has to be accounted for. Computer codes have been developed based on all-cubic axisymmetric cylindrical shell finite element and discrete ring stiffener element for linear elastic, linear buckling and geometric nonIinear analysis of stiffened cylindrical shells. These analysis programs have the capability to treat hydrostatic pressure as a radial load and as a follower force. Analytical investigations are carried out on two attack submarine cylindrical hull models besides standard benchmark problems. In each case, the analysis has been carried out for interstiffener, interdeepframe and interbulkhead configurations. The shell stiffener attachment in each of this configuration has been represented by the simply supported-simply supported, clamped-clamped and fixed-fixed boundary conditions in this study. The results of the analytical investigations have been discussed and the observations and conclusions are described. Rotation restraint at the ends is influential for interstiffener and interbulkhead configurations and the significance of axial restraint becomes predominant in the interbulkhead configuration. The follower force effect of hydrostatic pressure is not significant in interstiffener and interdeepframe configurations where as it has very high detrimental effect on buckling pressure on interbulkhead configuration. The geometric nonlinear interbulkhead analysis incorporating follower force effect gives the critical value of buckling pressure and this analysis is recommended for the determination of collapse pressure of stiffened cylindrical submarine shells.

Studies on the dynamics and rheology of dilute suspensions of Brownian particles in simple shear flow under the action of an external force

We present a novel approach to computing the orientation moments and rheological properties of a dilute suspension of spheroids in a simple shear flow at arbitrary Peclct number based on a generalised Langevin equation method. This method differs from the diffusion equation method which is commonly used to model similar systems in that the actual equations of motion for the orientations of the individual particles are used in the computations, instead of a solution of the diffusion equation of the system. It also differs from the method of 'Brownian dynamics simulations' in that the equations used for the simulations are deterministic differential equations even in the presence of noise, and not stochastic differential equations as in Brownian dynamics simulations. One advantage of the present approach over the Fokker-Planck equation formalism is that it employs a common strategy that can be applied across a wide range of shear and diffusion parameters. Also, since deterministic differential equations are easier to simulate than stochastic differential equations, the Langevin equation method presented in this work is more efficient and less computationally intensive than Brownian dynamics simulations.We derive the Langevin equations governing the orientations of the particles in the suspension and evolve a procedure for obtaining the equation of motion for any orientation moment. A computational technique is described for simulating the orientation moments dynamically from a set of time-averaged Langevin equations, which can be used to obtain the moments when the governing equations are harder to solve analytically. The results obtained using this method are in good agreement with those available in the literature.The above computational method is also used to investigate the effect of rotational Brownian motion on the rheology of the suspension under the action of an external force field. The force field is assumed to be either constant or periodic. In the case of con- I stant external fields earlier results in the literature are reproduced, while for the case of periodic forcing certain parametric regimes corresponding to weak Brownian diffusion are identified where the rheological parameters evolve chaotically and settle onto a low dimensional attractor. The response of the system to variations in the magnitude and orientation of the force field and strength of diffusion is also analyzed through numerical experiments. It is also demonstrated that the aperiodic behaviour exhibited by the system could not have been picked up by the diffusion equation approach as presently used in the literature.The main contributions of this work include the preparation of the basic framework for applying the Langevin method to standard flow problems, quantification of rotary Brownian effects by using the new method, the paired-moment scheme for computing the moments and its use in solving an otherwise intractable problem especially in the limit of small Brownian motion where the problem becomes singular, and a demonstration of how systems governed by a Fokker-Planck equation can be explored for possible chaotic behaviour.

Depth wise variation of microbial load in the soils of midland region of Kerala: a function of important soil physicochemical characteristics and nutrients

Soil microorganisms play a main part in organic matter decomposition and are consequently necessary to soil ecosystem processes maintaining primary productivity of plants. In light of current concerns about the impact of cultivation and climate change on biodiversity and ecosystem performance, it is vital to expand a complete understanding of the microbial community ecology in our soils. In the present study we measured the depth wise profile of microbial load in relation with important soil physicochemical characteristics (soil temperature, soil pH, moisture content, organic carbon and available NPK) of the soil samples collected from Mahatma Gandhi University Campus, Kottayam (midland region of Kerala). Soil cores (30 cm deep) were taken and the cores were separated into three 10-cm depths to examine depth wise distribution. In the present study, bacterial load ranged from 141×105 to 271×105 CFU/g (10cm depth), from 80×105 to 131×105 CFU/g (20cm depth) and from 260×104 to 47×105 CFU/g (30cm depth). Fungal load varies from 124×103 to 27×104 CFU/g, from 61×103 to110×103 CFU/g and from 16×103 to 49×103 CFU/g at 10, 20 and 30 cm respectively. Actinomycetes count ranged from 129×103 to 60×104 CFU/g (10cm), from 70×103 to 31×104 CFU/g (20cm) and from 14×103 to 66×103 CFU/g (30cm). The study revealed that there was a significant difference in the depthwise distribution of microbial load and soil physico-chemical properties. Bacterial, fungal and actinomycetes load showed a decreasing trend with increasing depth at all the sites. Except pH all other physicochemical properties showed decreasing trend with increasing depth. The vertical profile of total microbial load was well matched with the depthwise profiles of soil nutrients and organic carbon that is microbial load was highest at the soil surface where organics and nutrients were highest

Acoustic Structure Interaction For Floating Structure Under Moving Load

The present thesis concentrates largely on sound radiation from floating structure due to moving load

Reducing Vibrio load in Artemia nauplii usingantimicrobial photodynamic therapy: a promising strategy to reduce antibiotic application in shrimp larviculture

We propose antimicrobial photodynamic therapy (aPDT) as an alternative strategy to reduce the use of antibiotics in shrimp larviculture systems. The growth of a multiple antibiotic resistant Vibrio harveyi strain was effectively controlled by treating the cells with Rose Bengal and photosensitizing for 30 min using a halogen lamp. This resulted in the death of > 50% of the cells within the first 10 min of exposure and the 50% reduction in the cell wall integrity after 30 min could be attributed to the destruction of outer membrane protein of V. harveyi by reactive oxygen intermediates produced during the photosensitization. Further, mesocosm experiments with V. harveyi and Artemia nauplii demonstrated that in 30 min, the aPDT could kill 78.9% and 91.2% of heterotrophic bacterial and Vibrio population respectively. In conclusion, the study demonstrated that aPDT with its rapid action and as yet unreported resistance development possibilities could be a propitious strategy to reduce the use of antibiotics in shrimp larviculture systems and thereby, avoid their hazardous effects on human health and the ecosystem at large.

Short-Term Load Forecast Of A Low Loadfactor Power System For Optimization Of Merit Order Dispatch Using Adaptive Learning Algorithm

Short term load forecasting is one of the key inputs to optimize the management of power system. Almost 60-65% of revenue expenditure of a distribution company is against power purchase. Cost of power depends on source of power. Hence any optimization strategy involves optimization in scheduling power from various sources. As the scheduling involves many technical and commercial considerations and constraints, the efficiency in scheduling depends on the accuracy of load forecast. Load forecasting is a topic much visited in research world and a number of papers using different techniques are already presented. The accuracy of forecast for the purpose of merit order dispatch decisions depends on the extent of the permissible variation in generation limits. For a system with low load factor, the peak and the off peak trough are prominent and the forecast should be able to identify these points to more accuracy rather than minimizing the error in the energy content. In this paper an attempt is made to apply Artificial Neural Network (ANN) with supervised learning based approach to make short term load forecasting for a power system with comparatively low load factor. Such power systems are usual in tropical areas with concentrated rainy season for a considerable period of the year

Ein Beitrag zur realitätsnahen Modellierung und Analyse von stahlfaserverstärkten Stahlbeton- und Stahlbetonflächentragwerken

Das Werkstoffverhalten von stahlfaserfreiem bzw. stahlfaserverstärktem Stahlbeton unter biaxialle Druck- Zugbeanspruchung wurde experimentell und theoretisch untersucht. Die Basis der experimentellen Untersuchungen waren zahlreiche Versuche, die in der Vergangenheit an faserfreiem Stahlbetonscheiben zur Bestimmung des Werkstoffverhaltens von gerissenem Stahlbeton im ebenen Spannungszustand durchgeführt wurden. Bei diesen Untersuchungen wurde festgestellt, dass infolge einer Querzugbeanspruchung eine Abminderung der biaxialen Druckfestigkeit entsteht. Unter Berücksichtigung dieser Erkenntnisse sind zur Verbesserung der Werkstoffeigenschaften des Betons, Stahlbetonscheiben aus stahlfaserverstärktem Beton hergestellt worden. Die aus der Literatur bekannten Werkstoffmodelle für Beton sowie Stahlbeton, im ungerissenen und gerissenen Zustand wurden hinsichtlich der in der Vergangenheit ermittelten Materialeigenschaften des Betons bzw. Stahlbetons unter proportionalen sowie nichtproportionalen äußeren Belastungen erklärt und kritisch untersucht. In den frischen Beton wurden Stahlfasern hinzugegeben. Dadurch konnte die Festigkeits- und die Materialsteifigkeitsabminderung infolge Rissbildung, die zur Schädigung des Verbundwerkstoffs Beton führt, reduziert werden. Man konnte sehen, dass der Druckfestigkeitsabminderungsfaktor und insbesondere die zur maximal aufnehmbaren Zylinderdruckfestigkeit gehörende Stauchung, durch Zugabe von Stahlfasern besser begrenzt wird. Die experimentelle Untersuchungen wurden an sechs faserfreien und sieben stahlfaserverstärkten Stahlbetonscheiben unter Druck-Zugbelastung zur Bestimmung des Verhaltens des gerissenen faserfreien und stahlfaserverstärkten Stahlbetons durchgeführt. Die aus eigenen Versuchen ermittelten Materialeigenschaften des Betons, des stahlfaserverstärkten Betons und Stahlbetons im gerissenen Zustand wurden dargelegt und diskutiert. Bei der Rissbildung des quasi- spröden Werkstoffs Beton und dem stahlfaserverstärkten Beton wurde neben dem plastischen Fließen, auch die Abnahme des Elastizitätsmoduls festgestellt. Die Abminderung der aufnehmbaren Festigkeit und der zugehörigen Verzerrung lässt sich nicht mit der klassischen Fließtheorie der Plastizität ohne Modifizierung des Verfestigungsgesetzes erfassen. Es wurden auf elasto-plastischen Werkstoffmodellen basierende konstitutive Beziehungen für den faserfreien sowie den stahlfaserverstärkten Beton vorgeschlagen. Darüber hinaus wurde in der vorliegenden Arbeit eine auf dem elasto-plastischen Werkstoffmodell basierende konstitutive Beziehung für Beton und den stahlfaser-verstärkten Beton im gerissenen Zustand formuliert. Die formulierten Werkstoffmodelle wurden mittels dem in einer modularen Form aufgebauten nichtlinearen Finite Elemente Programm DIANA zu numerischen Untersuchungen an ausgewählten experimentell untersuchten Flächentragwerken, wie scheibenartigen-, plattenartigen- und Schalentragwerken aus faserfreiem sowie stahlfaserverstärktem Beton verwendet. Das entwickelte elasto-plastische Modell ermöglichte durch eine modifizierte effektive Spannungs-Verzerrungs-Beziehung für das Verfestigungsmodell, nicht nur die Erfassung des plastischen Fließens sondern auch die Berücksichtigung der Schädigung der Elastizitätsmodule infolge Mikrorissen sowie Makrorissen im Hauptzugspannungs-Hauptdruckspannungs-Bereich. Es wurde bei den numerischen Untersuchungen zur Ermittlung des Last-Verformungsverhaltens von scheibenartigen, plattenartigen- und Schalentragwerken aus faserfreiem und stahlfaserverstärktem Stahlbeton, im Vergleich mit den aus Versuchen ermittelten Ergebnissen, eine gute Übereinstimmung festgestellt.

Protein Folding Simulations: Confinement, External Fields and Sequence Design

The present Thesis looks at the problem of protein folding using Monte Carlo and Langevin simulations, three topics in protein folding have been studied: 1) the effect of confining potential barriers, 2) the effect of a static external field and 3) the design of amino acid sequences which fold in a short time and which have a stable native state (global minimum). Regarding the first topic, we studied the confinement of a small protein of 16 amino acids known as 1NJ0 (PDB code) which has a beta-sheet structure as a native state. The confinement of proteins occurs frequently in the cell environment. Some molecules called Chaperones, present in the cytoplasm, capture the unfolded proteins in their interior and avoid the formation of aggregates and misfolded proteins. This mechanism of confinement mediated by Chaperones is not yet well understood. In the present work we considered two kinds of potential barriers which try to mimic the confinement induced by a Chaperon molecule. The first kind of potential was a purely repulsive barrier whose only effect is to create a cavity where the protein folds up correctly. The second kind of potential was a barrier which includes both attractive and repulsive effects. We performed Wang-Landau simulations to calculate the thermodynamical properties of 1NJ0. From the free energy landscape plot we found that 1NJ0 has two intermediate states in the bulk (without confinement) which are clearly separated from the native and the unfolded states. For the case of the purely repulsive barrier we found that the intermediate states get closer to each other in the free energy landscape plot and eventually they collapse into a single intermediate state. The unfolded state is more compact, compared to that in the bulk, as the size of the barrier decreases. For an attractive barrier modifications of the states (native, unfolded and intermediates) are observed depending on the degree of attraction between the protein and the walls of the barrier. The strength of the attraction is measured by the parameter $\epsilon$. A purely repulsive barrier is obtained for $\epsilon=0$ and a purely attractive barrier for $\epsilon=1$. The states are changed slightly for magnitudes of the attraction up to $\epsilon=0.4$. The disappearance of the intermediate states of 1NJ0 is already observed for $\epsilon =0.6$. A very high attractive barrier ($\epsilon \sim 1.0$) produces a completely denatured state. In the second topic of this Thesis we dealt with the interaction of a protein with an external electric field. We demonstrated by means of computer simulations, specifically by using the Wang-Landau algorithm, that the folded, unfolded, and intermediate states can be modified by means of a field. We have found that an external field can induce several modifications in the thermodynamics of these states: for relatively low magnitudes of the field ($<2.06 \times 10^8$ V/m) no major changes in the states are observed. However, for higher magnitudes than ($6.19 \times 10^8$ V/m) one observes the appearance of a new native state which exhibits a helix-like structure. In contrast, the original native state is a $\beta$-sheet structure. In the new native state all the dipoles in the backbone structure are aligned parallel to the field. The design of amino acid sequences constitutes the third topic of the present work. We have tested the Rate of Convergence criterion proposed by D. Gridnev and M. Garcia ({\it work unpublished}). We applied it to the study of off-lattice models. The Rate of Convergence criterion is used to decide if a certain sequence will fold up correctly within a relatively short time. Before the present work, the common way to decide if a certain sequence was a good/bad folder was by performing the whole dynamics until the sequence got its native state (if it existed), or by studying the curvature of the potential energy surface. There are some difficulties in the last two approaches. In the first approach, performing the complete dynamics for hundreds of sequences is a rather challenging task because of the CPU time needed. In the second approach, calculating the curvature of the potential energy surface is possible only for very smooth surfaces. The Rate of Convergence criterion seems to avoid the previous difficulties. With this criterion one does not need to perform the complete dynamics to find the good and bad sequences. Also, the criterion does not depend on the kind of force field used and therefore it can be used even for very rugged energy surfaces.

CD-Systems of Stateless Deterministic R(1)-Automata Governed by an External Pushdown Store

We study cooperating distributed systems (CD-systems) of stateless deterministic restarting automata with window size 1 that are governed by an external pushdown store. In this way we obtain an automata-theoretical characterization for the class of context-free trace languages.

Analyse selbsterregter Strömungsfelder im Verdichter-Leitrad durch Kopplung von Particle Image Velocimetry und Hitzdrahtanemometrie mittels Fast Fourier Transformation

Der Einsatz der Particle Image Velocimetry (PIV) zur Analyse selbsterregter Strömungsphänomene und das dafür notwendige Auswerteverfahren werden in dieser Arbeit beschrieben. Zur Untersuchung von solchen Mechanismen, die in Turbo-Verdichtern als Rotierende Instabilitäten in Erscheinung treten, wird auf Datensätze zurückgegriffen, die anhand experimenteller Untersuchungen an einem ringförmigen Verdichter-Leitrad gewonnen wurden. Die Rotierenden Instabilitäten sind zeitabhängige Strömungsphänomene, die bei hohen aerodynamischen Belastungen in Verdichtergittern auftreten können. Aufgrund der fehlenden Phaseninformation kann diese instationäre Strömung mit konventionellen PIV-Systemen nicht erfasst werden. Die Kármánsche Wirbelstraße und Rotierende Instabilitäten stellen beide selbsterregte Strömungsvorgänge dar. Die Ähnlichkeit wird genutzt um die Funktionalität des Verfahrens anhand der Kármánschen Wirbelstraße nachzuweisen. Der mittels PIV zu visualisierende Wirbeltransport erfordert ein besonderes Verfahren, da ein externes Signal zur Festlegung des Phasenwinkels dieser selbsterregten Strömung nicht zur Verfügung steht. Die Methodik basiert auf der Kopplung der PIV-Technik mit der Hitzdrahtanemometrie. Die gleichzeitige Messung mittels einer zeitlich hochaufgelösten Hitzdraht-Messung ermöglicht den Zeitpunkten der PIV-Bilder einen Phasenwinkel zuzuordnen. Hierzu wird das Hitzdrahtsignal mit einem FFT-Verfahren analysiert, um die PIV-Bilder entsprechend ihrer Phasenwinkel zu gruppieren. Dafür werden die aufgenommenen Bilder auf der Zeitachse der Hitzdrahtmessungen markiert. Eine systematische Analyse des Hitzdrahtsignals in der Umgebung der PIV-Messung liefert Daten zur Festlegung der Grundfrequenz und erlaubt es, der markierten PIV-Position einen Phasenwinkel zuzuordnen. Die sich aus den PIV-Bildern einer Klasse ergebenden Geschwindigkeitskomponenten werden anschließend gemittelt. Aus den resultierenden Bildern jeder Klasse ergibt sich das zweidimensionale zeitabhängige Geschwindigkeitsfeld, in dem die Wirbelwanderung der Kármánschen Wirbelstraße ersichtlich wird. In hierauf aufbauenden Untersuchungen werden Zeitsignale aus Messungen in einem Verdichterringgitter analysiert. Dabei zeigt sich, dass zusätzlich Filterfunktionen erforderlich sind. Im Ergebnis wird schließlich deutlich, dass die Übertragung der anhand der Kármánschen Wirbelstraße entwickelten Methode nur teilweise gelingt und weitere Forschungsarbeiten erforderlich sind.