Methodological issues in quantifying the magnitude of the tuberculosis problem in a prison population

SETTING: Correctional settings and remand prisons. OBJECTIVE: To critically discuss calculations for epidemiological indicators of the tuberculosis (TB) burden in prisons and to provide recommendations to improve study comparability. METHODS: A hypothetical data set illustrates issues in determining incidence and prevalence. The appropriate calculation of the incidence rate is presented and problems arising from cross-sectional surveys are clarifi ed. RESULTS: Cases recognized during the fi rst 3 months should be classifi ed as prevalent at entry and excluded from any incidence rate calculation. The numerator for the incidence rate includes persons detected as having developed TB during a specifi ed period of time subsequent to the initial 3 months. The denominator is persontime at risk from 3 months onward to the end point (TB or end of the observation period). Preferably, entry time, exit time and event time are known for each inmate to determine person-time at risk. Failing that, an approximation consists of the sum of monthly head counts, excluding prevalent cases and those persons no longer at risk from both the numerator and the denominator. CONCLUSIONS: The varying durations of inmate incarceration in prisons pose challenges for quantifying the magnitude of the TB problem in the inmate population. Recommendations are made to measure incidence and prevalence.

Uncovering the dynamics of cardiac systems using stochastic pacing and frequency domain analyses

Alternans of cardiac action potential duration (APD) is a well-known arrhythmogenic mechanism which results from dynamical instabilities. The propensity to alternans is classically investigated by examining APD restitution and by deriving APD restitution slopes as predictive markers. However, experiments have shown that such markers are not always accurate for the prediction of alternans. Using a mathematical ventricular cell model known to exhibit unstable dynamics of both membrane potential and Ca2+ cycling, we demonstrate that an accurate marker can be obtained by pacing at cycle lengths (CLs) varying randomly around a basic CL (BCL) and by evaluating the transfer function between the time series of CLs and APDs using an autoregressive-moving-average (ARMA) model. The first pole of this transfer function corresponds to the eigenvalue (λalt) of the dominant eigenmode of the cardiac system, which predicts that alternans occurs when λalt≤−1. For different BCLs, control values of λalt were obtained using eigenmode analysis and compared to the first pole of the transfer function estimated using ARMA model fitting in simulations of random pacing protocols. In all versions of the cell model, this pole provided an accurate estimation of λalt. Furthermore, during slow ramp decreases of BCL or simulated drug application, this approach predicted the onset of alternans by extrapolating the time course of the estimated λalt. In conclusion, stochastic pacing and ARMA model identification represents a novel approach to predict alternans without making any assumptions about its ionic mechanisms. It should therefore be applicable experimentally for any type of myocardial cell.

Macro Monte Carlo for dose calculation of proton beams

Although the Monte Carlo (MC) method allows accurate dose calculation for proton radiotherapy, its usage is limited due to long computing time. In order to gain efficiency, a new macro MC (MMC) technique for proton dose calculations has been developed. The basic principle of the MMC transport is a local to global MC approach. The local simulations using GEANT4 consist of mono-energetic proton pencil beams impinging perpendicularly on slabs of different thicknesses and different materials (water, air, lung, adipose, muscle, spongiosa, cortical bone). During the local simulation multiple scattering, ionization as well as elastic and inelastic interactions have been taken into account and the physical characteristics such as lateral displacement, direction distributions and energy loss have been scored for primary and secondary particles. The scored data from appropriate slabs is then used for the stepwise transport of the protons in the MMC simulation while calculating the energy loss along the path between entrance and exit position. Additionally, based on local simulations the radiation transport of neutrons and the generated ions are included into the MMC simulations for the dose calculations. In order to validate the MMC transport, calculated dose distributions using the MMC transport and GEANT4 have been compared for different mono-energetic proton pencil beams impinging on different phantoms including homogeneous and inhomogeneous situations as well as on a patient CT scan. The agreement of calculated integral depth dose curves is better than 1% or 1 mm for all pencil beams and phantoms considered. For the dose profiles the agreement is within 1% or 1 mm in all phantoms for all energies and depths. The comparison of the dose distribution calculated using either GEANT4 or MMC in the patient also shows an agreement of within 1% or 1 mm. The efficiency of MMC is up to 200 times higher than for GEANT4. The very good level of agreement in the dose comparisons demonstrate that the newly developed MMC transport results in very accurate and efficient dose calculations for proton beams.

Assessing the Validity of Brain Glucose Concentration Measurement Using Microdialysis

Brain functions, such as learning, orchestrating locomotion, memory recall, and processing information, all require glucose as a source of energy. During these functions, the glucose concentration decreases as the glucose is being consumed by brain cells. By measuring this drop in concentration, it is possible to determine which parts of the brain are used during specific functions and consequently, how much energy the brain requires to complete the function. One way to measure in vivo brain glucose levels is with a microdialysis probe. The drawback of this analytical procedure, as with many steadystate fluid flow systems, is that the probe fluid will not reach equilibrium with the brain fluid. Therefore, brain concentration is inferred by taking samples at multiple inlet glucose concentrations and finding a point of convergence. The goal of this thesis is to create a three-dimensional, time-dependent, finite element representation of the brainprobe system in COMSOL 4.2 that describes the diffusion and convection of glucose. Once validated with experimental results, this model can then be used to test parameters that experiments cannot access. When simulations were run using published values for physical constants (i.e. diffusivities, density and viscosity), the resulting glucose model concentrations were within the error of the experimental data. This verifies that the model is an accurate representation of the physical system. In addition to accurately describing the experimental brain-probe system, the model I created is able to show the validity of zero-net-flux for a given experiment. A useful discovery is that the slope of the zero-net-flux line is dependent on perfusate flow rate and diffusion coefficients, but it is independent of brain glucose concentrations. The model was simplified with the realization that the perfusate is at thermal equilibrium with the brain throughout the active region of the probe. This allowed for the assumption that all model parameters are temperature independent. The time to steady-state for the probe is approximately one minute. However, the signal degrades in the exit tubing due to Taylor dispersion, on the order of two minutes for two meters of tubing. Given an analytical instrument requiring a five μL aliquot, the smallest brain process measurable for this system is 13 minutes.

Secondary Collisions Revisited: Real-World Crash Characteristics and Relationship to Crash Test Criteria

Previous research conducted in the late 1980’s suggested that vehicle impacts following an initial barrier collision increase severe occupant injury risk. Now over twenty-five years old, the data used in the previous research is no longer representative of the currently installed barriers or US vehicle fleet. The purpose of this study is to provide a present-day assessment of secondary collisions and to determine if full-scale barrier crash testing criteria provide an indication of secondary collision risk for real-world barrier crashes. The analysis included 1,383 (596,331 weighted) real-world barrier midsection impacts selected from thirteen years (1997-2009) of in-depth crash data available through the National Automotive Sampling System (NASS) / Crashworthiness Data System (CDS). For each suitable case, the scene diagram and available scene photographs were used to determine roadside and barrier specific variables not available in NASS/CDS. Binary logistic regression models were developed for second event occurrence and resulting driver injury. Barrier lateral stiffness, post-impact vehicle trajectory, vehicle type, and pre-impact tracking conditions were found to be statistically significant contributors toward secondary event occurrence. The presence of a second event was found to increase the likelihood of a serious driver injury by a factor of seven compared to cases with no second event present. Twenty-four full-scale crash test reports were obtained for common non-proprietary US barriers, and the risk of secondary collisions was determined using recommended evaluation criteria from NCHRP Report 350. It was found that the NCHRP Report 350 exit angle criterion alone was not sufficient to predict second collision occurrence for real-world barrier crashes.

Consequences of depleted SERCA2-gated calcium stores in the skin

Sarco(endo)plasmic reticulum Ca2+-ATPase isoform 2 (SERCA2) pumps belong to the family of Ca2+-ATPases responsible for the maintenance of calcium in the endoplasmic reticulum. In epidermal keratinocytes, SERCA2-controlled calcium stores are involved in cell cycle exit and onset of terminal differentiation. Hence, their dysfunction was thought to provoke impaired keratinocyte cohesion and hampered terminal differentiation. Here, we assessed cultured keratinocytes and skin biopsies from a canine family with an inherited skin blistering disorder. Cells from lesional and phenotypically normal areas of one of these dogs revealed affected calcium homeostasis due to depleted SERCA2-gated stores. In phenotypically normal patient cells, this defect compromised upregulation of p21(WAF1) and delayed the exit from the cell cycle. Despite this abnormality it failed to impede the terminal differentiation process in the long term but instead coincided with enhanced apoptosis and appearance of chronic wounds, suggestive of secondary mutations. Collectively, these findings provide the first survey on phenotypic consequences of depleted SERCA-gated stores for epidermal homeostasis that explain how depleted SERCA2 calcium stores provoke focal lesions rather than generalized dermatoses, a phenotype highly reminiscent of the human genodermatosis Darier disease.

Biologically relevant sex differences for fitness-related parameters in active octogenarians

The number of elderly people is growing in western populations, but only few maximal performance data exist for people >75 years, in particular for European octogenarians. This study was performed to characterize maximal performance of 55 independently living subjects (32 women, 81.1 +/- 3.4 years; 23 men, 81.7 +/- 2.9 years) with a focus on sex differences. Maximal performance was determined in a ramp test to exhaustion on a bicycle ergometer with ergospirometry, electrocardiogram and blood lactate measurements. Maximal isometric extension strength of the legs (MEL) was measured on a force platform in a seated position. Body composition was quantified by X-ray absorptiometry. In >25% of the subjects, serious cardiac abnormalities were detected during the ramp test with men more frequently being affected than women. Maximal oxygen consumption and power output were 18.2 +/- 3.2 versus 25.9 +/- 5.9 ml min(-1) kg(-1) and 66 +/- 12 versus 138 +/- 40 W for women versus men, with a significant sex difference for both parameters. Men outperformed women for MEL with 19.0 +/- 3.8 versus 13.6 +/- 3.3 N kg(-1). Concomitantly, we found a higher proportion of whole body fat in women (32.1 +/- 6.2%) compared to men (20.5 +/- 4.4%). Our study extends previously available maximal performance data for endurance and strength to independently living European octogenarians. As all sex-related differences were still apparent after normalization to lean body mass, it is concluded that it is essential to differentiate between female and male subjects when considering maximal performance parameters in the oldest segment of our population.

Statistical evaluation of alternative models of human evolution

An appropriate model of recent human evolution is not only important to understand our own history, but it is necessary to disentangle the effects of demography and selection on genome diversity. Although most genetic data support the view that our species originated recently in Africa, it is still unclear if it completely replaced former members of the Homo genus, or if some interbreeding occurred during its range expansion. Several scenarios of modern human evolution have been proposed on the basis of molecular and paleontological data, but their likelihood has never been statistically assessed. Using DNA data from 50 nuclear loci sequenced in African, Asian and Native American samples, we show here by extensive simulations that a simple African replacement model with exponential growth has a higher probability (78%) as compared with alternative multiregional evolution or assimilation scenarios. A Bayesian analysis of the data under this best supported model points to an origin of our species approximately 141 thousand years ago (Kya), an exit out-of-Africa approximately 51 Kya, and a recent colonization of the Americas approximately 10.5 Kya. We also find that the African replacement model explains not only the shallow ancestry of mtDNA or Y-chromosomes but also the occurrence of deep lineages at some autosomal loci, which has been formerly interpreted as a sign of interbreeding with Homo erectus.

Percutaneous vein occlusion with small intestinal submucosa: an experimental pilot study in Swine and sheep

PURPOSE: The objective of this study was to investigate the feasibility, outcomes, and amount of small intestinal submucosa (SIS) material needed for embolization of jugular vein (JV) in a swine and sheep model. Our hypothesis was that SIS would cause vein occlusion. MATERIALS AND METHODS: The external JVs (EJV) in swine (n = 6) and JVs in sheep (n = 6) were occluded with SIS fan-folded compressed strips. After percutaneous puncture of the peripheral portion of the EJV or JV, a TIPS set was used to exit their lumen centrally through the skin. The SIS strips were delivered into the isolated venous segment with a pull-through technique via a 10-Fr sheath. Follow-up venograms were done immediately after placement and at the time of sacrifice at 1 or 3 months. Gross examinations focused on the EJV or JV and their surrounding structures. Specimens were evaluated by histology. RESULTS: SIS strip(s) placement was successful in all cases, with immediate vein occlusion seen in 23 of 24 veins (95.8%). All EJVs treated with two strips and all JVs treated with three or four strips remained closed on 1- and 3-month follow-up venograms. Two EJVs treated with one strip and one JV treated with two strips were partially patent on venograms at 1 and 3 months. There has been one skin inflammatory reaction. Necropsies revealed excluded EJV or JV segments with SIS incorporation into the vein wall. Histology demonstrated various stages of SIS remodeling with fibrocytes, fibroblasts, endothelial cells, capillaries, and inflammatory cells. CONCLUSION: We conclude that EJV and JV ablation with SIS strips using percutaneous exit catheterization is feasible and effective in animal models. Further exploration of SIS as vein ablation material is recommended.

Aerothermodynamic cycle analysis of a dual-spool, separate-exhaust turbofan engine with an interstage turbine burner

This study focuses on a specific engine, i.e., a dual-spool, separate-flow turbofan engine with an Interstage Turbine Burner (ITB). This conventional turbofan engine has been modified to include a secondary isobaric burner, i.e., ITB, in a transition duct between the high-pressure turbine and the low-pressure turbine. The preliminary design phase for this modified engine starts with the aerothermodynamics cycle analysis is consisting of parametric (i.e., on-design) and performance (i.e., off-design) cycle analyses. In parametric analysis, the modified engine performance parameters are evaluated and compared with baseline engine in terms of design limitation (maximum turbine inlet temperature), flight conditions (such as flight Mach condition, ambient temperature and pressure), and design choices (such as compressor pressure ratio, fan pressure ratio, fan bypass ratio etc.). A turbine cooling model is also included to account for the effect of cooling air on engine performance. The results from the on-design analysis confirmed the advantage of using ITB, i.e., higher specific thrust with small increases in thrust specific fuel consumption, less cooling air, and less NOx production, provided that the main burner exit temperature and ITB exit temperature are properly specified. It is also important to identify the critical ITB temperature, beyond which the ITB is turned off and has no advantage at all. With the encouraging results from parametric cycle analysis, a detailed performance cycle analysis of the identical engine is also conducted for steady-stateengine performance prediction. The results from off-design cycle analysis show that the ITB engine at full throttle setting has enhanced performance over baseline engine. Furthermore, ITB engine operating at partial throttle settings will exhibit higher thrust at lower specific fuel consumption and improved thermal efficiency over the baseline engine. A mission analysis is also presented to predict the fuel consumptions in certain mission phases. Excel macrocode, Visual Basic for Application, and Excel neuron cells are combined to facilitate Excel software to perform these cycle analyses. These user-friendly programs compute and plot the data sequentially without forcing users to open other types of post-processing programs.

Three dimensional finite element simulation of polymer melting and flow in a single-screw extruder : optimization of screw channel geometry

Single-screw extrusion is one of the widely used processing methods in plastics industry, which was the third largest manufacturing industry in the United States in 2007 [5]. In order to optimize the single-screw extrusion process, tremendous efforts have been devoted for development of accurate models in the last fifty years, especially for polymer melting in screw extruders. This has led to a good qualitative understanding of the melting process; however, quantitative predictions of melting from various models often have a large error in comparison to the experimental data. Thus, even nowadays, process parameters and the geometry of the extruder channel for the single-screw extrusion are determined by trial and error. Since new polymers are developed frequently, finding the optimum parameters to extrude these polymers by trial and error is costly and time consuming. In order to reduce the time and experimental work required for optimizing the process parameters and the geometry of the extruder channel for a given polymer, the main goal of this research was to perform a coordinated experimental and numerical investigation of melting in screw extrusion. In this work, a full three-dimensional finite element simulation of the two-phase flow in the melting and metering zones of a single-screw extruder was performed by solving the conservation equations for mass, momentum, and energy. The only attempt for such a three-dimensional simulation of melting in screw extruder was more than twenty years back. However, that work had only a limited success because of the capability of computers and mathematical algorithms available at that time. The dramatic improvement of computational power and mathematical knowledge now make it possible to run full 3-D simulations of two-phase flow in single-screw extruders on a desktop PC. In order to verify the numerical predictions from the full 3-D simulations of two-phase flow in single-screw extruders, a detailed experimental study was performed. This experimental study included Maddock screw-freezing experiments, Screw Simulator experiments and material characterization experiments. Maddock screw-freezing experiments were performed in order to visualize the melting profile along the single-screw extruder channel with different screw geometry configurations. These melting profiles were compared with the simulation results. Screw Simulator experiments were performed to collect the shear stress and melting flux data for various polymers. Cone and plate viscometer experiments were performed to obtain the shear viscosity data which is needed in the simulations. An optimization code was developed to optimize two screw geometry parameters, namely, screw lead (pitch) and depth in the metering section of a single-screw extruder, such that the output rate of the extruder was maximized without exceeding the maximum temperature value specified at the exit of the extruder. This optimization code used a mesh partitioning technique in order to obtain the flow domain. The simulations in this flow domain was performed using the code developed to simulate the two-phase flow in single-screw extruders.

Automated optimization of polymer extrusion dies using finite element analysis

An extrusion die is used to continuously produce parts with a constant cross section; such as sheets, pipes, tire components and more complex shapes such as window seals. The die is fed by a screw extruder when polymers are used. The extruder melts, mixes and pressures the material by the rotation of either a single or double screw. The polymer can then be continuously forced through the die producing a long part in the shape of the die outlet. The extruded section is then cut to the desired length. Generally, the primary target of a well designed die is to produce a uniform outlet velocity without excessively raising the pressure required to extrude the polymer through the die. Other properties such as temperature uniformity and residence time are also important but are not directly considered in this work. Designing dies for optimal outlet velocity variation using simple analytical equations are feasible for basic die geometries or simple channels. Due to the complexity of die geometry and of polymer material properties design of complex dies by analytical methods is difficult. For complex dies iterative methods must be used to optimize dies. An automated iterative method is desired for die optimization. To automate the design and optimization of an extrusion die two issues must be dealt with. The first is how to generate a new mesh for each iteration. In this work, this is approached by modifying a Parasolid file that describes a CAD part. This file is then used in a commercial meshing software. Skewing the initial mesh to produce a new geometry was also employed as a second option. The second issue is an optimization problem with the presence of noise stemming from variations in the mesh and cumulative truncation errors. In this work a simplex method and a modified trust region method were employed for automated optimization of die geometries. For the trust region a discreet derivative and a BFGS Hessian approximation were used. To deal with the noise in the function the trust region method was modified to automatically adjust the discreet derivative step size and the trust region based on changes in noise and function contour. Generally uniformity of velocity at exit of the extrusion die can be improved by increasing resistance across the die but this is limited by the pressure capabilities of the extruder. In optimization, a penalty factor that increases exponentially from the pressure limit is applied. This penalty can be applied in two different ways; the first only to the designs which exceed the pressure limit, the second to both designs above and below the pressure limit. Both of these methods were tested and compared in this work.

Computational study of internal and external condensing flows and experimental synthesis to investigate their attainability and stability in ground-based and space-based environments

This doctoral thesis presents the computational work and synthesis with experiments for internal (tube and channel geometries) as well as external (flow of a pure vapor over a horizontal plate) condensing flows. The computational work obtains accurate numerical simulations of the full two dimensional governing equations for steady and unsteady condensing flows in gravity/0g environments. This doctoral work investigates flow features, flow regimes, attainability issues, stability issues, and responses to boundary fluctuations for condensing flows in different flow situations. This research finds new features of unsteady solutions of condensing flows; reveals interesting differences in gravity and shear driven situations; and discovers novel boundary condition sensitivities of shear driven internal condensing flows. Synthesis of computational and experimental results presented here for gravity driven in-tube flows lays framework for the future two-phase component analysis in any thermal system. It is shown for both gravity and shear driven internal condensing flows that steady governing equations have unique solutions for given inlet pressure, given inlet vapor mass flow rate, and fixed cooling method for condensing surface. But unsteady equations of shear driven internal condensing flows can yield different “quasi-steady” solutions based on different specifications of exit pressure (equivalently exit mass flow rate) concurrent to the inlet pressure specification. This thesis presents a novel categorization of internal condensing flows based on their sensitivity to concurrently applied boundary (inlet and exit) conditions. The computational investigations of an external shear driven flow of vapor condensing over a horizontal plate show limits of applicability of the analytical solution. Simulations for this external condensing flow discuss its stability issues and throw light on flow regime transitions because of ever-present bottom wall vibrations. It is identified that laminar to turbulent transition for these flows can get affected by ever present bottom wall vibrations. Detailed investigations of dynamic stability analysis of this shear driven external condensing flow result in the introduction of a new variable, which characterizes the ratio of strength of the underlying stabilizing attractor to that of destabilizing vibrations. Besides development of CFD tools and computational algorithms, direct application of research done for this thesis is in effective prediction and design of two-phase components in thermal systems used in different applications. Some of the important internal condensing flow results about sensitivities to boundary fluctuations are also expected to be applicable to flow boiling phenomenon. Novel flow sensitivities discovered through this research, if employed effectively after system level analysis, will result in the development of better control strategies in ground and space based two-phase thermal systems.

Gunshot injuries detected by post-mortem multislice computed tomography (MSCT): a feasibility study

Modern cross-sectional imaging techniques are being increasingly implemented in forensic pathology. These methods may serve as an adjuvant to classic forensic autopsies or even replace them altogether in the future. In order to assess the practicability of such a method, namely post-mortem multislice computed tomography (MSCT) in fatal gunshot injuries, 22 corpses underwent such an examination prior to forensic autopsy. The cardinal questions of the location of entrance and exit wounds, the detection of bullets and bullet fragments in the body, the bullet course, inflicted injuries and cause of death were addressed at MSCT and autopsy. The results of the two techniques revealed that post-mortem MSCT can answer these questions reliably and is therefore a useful tool in the assessment of such injuries.

Biomechanics of meniscal horn attachments

Menisci are anchored to the tibia by means of ligament-like structures called meniscal attachments. Failure material properties of bovine meniscal attachments were obtained. There were no significant differences in the structural properties or ultimate stress between the meniscal attachments (p>0.05). Furthermore, Glycosaminoglycan (GAG) fraction and crimping frequency was obtained for each attachment using histology and differential interference contrast (DIC) respectively. Results showed that the anterior attachment’s insertion had the greatest GAG fraction when compared to the posterior attachment’s insertion. Crimp frequency of the collagen fibrils was homogeneous along the length. Moreover, Scanning Electron Microscopy (SEM) technique was used to reveal the morphology of collagen in human meniscal attachments. Its midsubstance was composed of collagen fascicles running parallel to the longitudinal axis, with a few fibrils running obliquely, and others transversely. There were no differences between attachments for crimping angle or length. Since ligamentous-type tissues are comprised mainly of water, the fluid pressure within meniscal horn attachments was measured using a Fiber Optic Microsensor (FOM). Four cadaveric human joints were subjected to 2BW compressive load (ramp) at 0-, 15-, and 30-degrees of flexion for a minute and then the load was hold for 20 minutes (equilibrium). There were significant differences between 0- and 15- (p1– c5) were obtained. Significant differences were found on the straightened collagen fibers coefficient (c5) between MP and LA attachments (p