Timing of progression from Chlamydia trachomatis infection to pelvic inflammatory disease: a mathematical modelling study

Background Pelvic inflammatory disease (PID) results from the ascending spread of microorganisms from the vagina and endocervix to the upper genital tract. PID can lead to infertility, ectopic pregnancy and chronic pelvic pain. The timing of development of PID after the sexually transmitted bacterial infection Chlamydia trachomatis (chlamydia) might affect the impact of screening interventions, but is currently unknown. This study investigates three hypothetical processes for the timing of progression: at the start, at the end, or throughout the duration of chlamydia infection. Methods We develop a compartmental model that describes the trial structure of a published randomised controlled trial (RCT) and allows each of the three processes to be examined using the same model structure. The RCT estimated the effect of a single chlamydia screening test on the cumulative incidence of PID up to one year later. The fraction of chlamydia infected women who progress to PID is obtained for each hypothetical process by the maximum likelihood method using the results of the RCT. Results The predicted cumulative incidence of PID cases from all causes after one year depends on the fraction of chlamydia infected women that progresses to PID and on the type of progression. Progression at a constant rate from a chlamydia infection to PID or at the end of the infection was compatible with the findings of the RCT. The corresponding estimated fraction of chlamydia infected women that develops PID is 10% (95% confidence interval 7-13%) in both processes. Conclusions The findings of this study suggest that clinical PID can occur throughout the course of a chlamydia infection, which will leave a window of opportunity for screening to prevent PID.

The Intersection of Economics and Politics in a Small OPEC Country: the Case of Ecuador, 1990 - March 2014

Today, crude oil remains a vital resource all around the world. This non-renewable resource powers countries worldwide. Besides serving as an energy source, crude oil is also the most important component for different world economies, especially in developing countries. Ecuador, a small member of the OPEC oil cartel, presents a case where its economy is oil dependent. A great percentage of the country¿s GDP and government¿s budget comes from oil revenues. Ecuador has always been a primary exporter of raw materials. In the last centuries, the country experienced three important economic booms: cacao, bananas, and, ultimately, crude oil. In this sense, the country has not been able to fully industrialize and begin to export manufactured goods, i.e., Ecuador suffers from the Dutch disease. The latter has deterred Ecuador from achieving broad-based economic development. Given crude oil¿s importance for the Ecuadorian economy, the government has always tried to influence the oil industry in search of profits and benefits. Therefore, this thesis, explores the question: how and to what extent have political interventions affected the oil industry in Ecuador from 1990 until March 2014? In general, this thesis establishes an economic history context during the last twenty-four years, attempting to research how political interventions have shaped Ecuador¿s oil industry and economy. In the analysis, it covers a period where political instability prevailed, until Rafael Correa became president. The thesis examines Ecuador¿s participation in OPEC, trying to find explanations as to why the country voluntarily left the organization in 1992, only to rejoin in 2007 when Correa rose to power. During the ¿Revolución Ciudadana¿ period, the thesis researches reforms to the Law of Hydrocarbons, variations in the relations with other nations, the controversy surrounding the Yasuní-ITT oil block, and the ¿Refinería del Pacífico¿ construction. The thesis is an Industrial Organization detailed case study that analyzes, updates, and evaluates the intersection of economics and politics in Ecuador¿s crude oil industry during the last 24 years. In this sense I have consulted past theses, newspaper articles, books, and other published data about the petroleum industry, both from a global and Ecuadorian perspective. In addition to published sources, I was able to interview sociologists, public figures, history and economics academics, and other experts, accessing unique unpublished data about Ecuador¿s oil industry. I made an effort to collect information that shows the private and public side of the industry, i.e., from government-related and independent sources. I attempted to remain as objective as possible to make conclusions about the appropriate Industrial Organization policy for Ecuador¿s oil industry, addressing the issue from an economic, social, political, and environmental point of view. I found how Ecuador¿s political instability caused public policy to fail, molding the conduct and market structure of the crude oil industry. Throughout history, developed nations have benefited from low oil prices, but things shifted since oil prices began to rise, which is more beneficial for the developing nations that actually possess and produce the raw material. Nevertheless, Ecuador, a victim of the Dutch disease due to its heavy reliance on crude oil as a primary product, has not achieved broad-based development.

Monte Carlo simulation of a dynamic MLC: implementation and applications

PURPOSE: Study of behavior and influence of a multileaf collimator (MLC) on dose calculation, verification, and portal energy spectra in the case of intensity-modulated fields obtained with a step-and-shoot or a dynamic technique. METHODS: The 80-leaf MLC for the Varian Clinac 2300 C/D was implemented in a previously developed Monte Carlo (MC) based multiple source model (MSM) for a 6 MV photon beam. Using this model and the MC program GEANT, dose distributions, energy fluence maps and energy spectra at different portal planes were calculated for three different MLC applications. RESULTS: The comparison of MC-calculated dose distributions in the phantom and portal plane, with those measured with films showed an agreement within 3% and 1.5 mm for all cases studied. The deviations mainly occur in the extremes of the intensity modulation. The MC method allows to investigate, among other aspects, dose components, energy fluence maps, tongue-and-groove effects and energy spectra at portal planes. CONCLUSION: The MSM together with the implementation of the MLC is appropriate for a number of investigations in intensity-modulated radiation therapy (IMRT).

Structural capacity of steel tubular cast-in-place piling

Steel tubular cast-in-place pilings are used throughout the country for many different project types. These piles are a closed-end pipe with varying wall thicknesses and outer diameters, that are driven to depth and then the core is filled with concrete. These piles are typically used for smaller bridges, or secondary structures. Mostly the piling is designed based on a resistance based method which is a function of the soil properties of which the pile is driven through, however there is a structural capacity of these members that is considered to be the upper bound on the loading of the member. This structural capacity is given by the AASHTO LRFD (2010), with two methods. These two methods are based on a composite or non-composite section. Many state agencies and corporations use the non-composite equation because it is requires much less computation and is known to be conservative. However with the trends of the time, more and more structural elements are being investigated to determine ways to better understand the mechanics of the members, which could lead to more efficient and safer designs. In this project, a set of these piling are investigated. The way the cross section reacts to several different loading conditions, along with a more detailed observation of the material properties is considered as part of this research. The evaluation consisted of testing stub sections of pile with varying sizes (10-¾”, 12-¾”), wall thicknesses (0.375”, 0.5”), and testing methods (whole compression, composite compression, push through, core sampling). These stub sections were chosen as they would represent a similar bracing length to many different soils. In addition, a finite element model was developed using ANSYS to predict the strains from the testing of the pile cross sections. This model was able to simulate the strains from most of the loading conditions and sizes that were tested. The bond between the steel shell and the concrete core, along with the concrete strength through the depth of the cross section were some of the material properties of these sections that were investigated.

Genetic association studies under the population stratification, family pedigree and application to genome-wide association studies

This dissertation has three separate parts: the first part deals with the general pedigree association testing incorporating continuous covariates; the second part deals with the association tests under population stratification using the conditional likelihood tests; the third part deals with the genome-wide association studies based on the real rheumatoid arthritis (RA) disease data sets from Genetic Analysis Workshop 16 (GAW16) problem 1. Many statistical tests are developed to test the linkage and association using either case-control status or phenotype covariates for family data structure, separately. Those univariate analyses might not use all the information coming from the family members in practical studies. On the other hand, the human complex disease do not have a clear inheritance pattern, there might exist the gene interactions or act independently. In part I, the new proposed approach MPDT is focused on how to use both the case control information as well as the phenotype covariates. This approach can be applied to detect multiple marker effects. Based on the two existing popular statistics in family studies for case-control and quantitative traits respectively, the new approach could be used in the simple family structure data set as well as general pedigree structure. The combined statistics are calculated using the two statistics; A permutation procedure is applied for assessing the p-value with adjustment from the Bonferroni for the multiple markers. We use simulation studies to evaluate the type I error rates and the powers of the proposed approach. Our results show that the combined test using both case-control information and phenotype covariates not only has the correct type I error rates but also is more powerful than the other existing methods. For multiple marker interactions, our proposed method is also very powerful. Selective genotyping is an economical strategy in detecting and mapping quantitative trait loci in the genetic dissection of complex disease. When the samples arise from different ethnic groups or an admixture population, all the existing selective genotyping methods may result in spurious association due to different ancestry distributions. The problem can be more serious when the sample size is large, a general requirement to obtain sufficient power to detect modest genetic effects for most complex traits. In part II, I describe a useful strategy in selective genotyping while population stratification is present. Our procedure used a principal component based approach to eliminate any effect of population stratification. The paper evaluates the performance of our procedure using both simulated data from an early study data sets and also the HapMap data sets in a variety of population admixture models generated from empirical data. There are one binary trait and two continuous traits in the rheumatoid arthritis dataset of Problem 1 in the Genetic Analysis Workshop 16 (GAW16): RA status, AntiCCP and IgM. To allow multiple traits, we suggest a set of SNP-level F statistics by the concept of multiple-correlation to measure the genetic association between multiple trait values and SNP-specific genotypic scores and obtain their null distributions. Hereby, we perform 6 genome-wide association analyses using the novel one- and two-stage approaches which are based on single, double and triple traits. Incorporating all these 6 analyses, we successfully validate the SNPs which have been identified to be responsible for rheumatoid arthritis in the literature and detect more disease susceptibility SNPs for follow-up studies in the future. Except for chromosome 13 and 18, each of the others is found to harbour susceptible genetic regions for rheumatoid arthritis or related diseases, i.e., lupus erythematosus. This topic is discussed in part III.

Ascorbic acid for amelioration of reperfusion injury in a lung autotransplantation model in sheep

BACKGROUND: Reperfusion injury is the leading cause of early graft dysfunction after lung transplantation. Activation of neutrophilic granulocytes with generation of free oxygen radicals appears to play a key role in this process. The efficacy of ascorbic acid as an antioxidant in the amelioration of reperfusion injury after lung transplantation has not been studied yet. METHODS: An in situ autotransplantation model in sheep is presented. The left lung was flushed (Euro-Collins solution) and reperfused; after 2 hours of cold storage, the right hilus was then clamped (group R [reference], n = 6). Group AA animals (n = 6) were treated with 1 g/kg ascorbic acid before reperfusion. Controls (group C, n = 6) underwent hilar preparation and instrumentation only. RESULTS: In group R, arterio-alveolar oxygen difference (AaDO2) and pulmonary vascular resistance (PVR) were significantly elevated after reperfusion. Five of 6 animals developed frank alveolar edema. All biochemical parameters showed significant PMN activation. In group AA, AaDO2, PVR, work of breathing, and the level of PMN activation were significantly lower. CONCLUSIONS: The experimental model reproduces all aspects of lung reperfusion injury reliably. Ascorbic acid was able to weaken reperfusion injury in this experimental setup.

Individual patient data meta-analysis of diagnostic and prognostic studies in obstetrics, gynaecology and reproductive medicine

BACKGROUND: In clinical practice a diagnosis is based on a combination of clinical history, physical examination and additional diagnostic tests. At present, studies on diagnostic research often report the accuracy of tests without taking into account the information already known from history and examination. Due to this lack of information, together with variations in design and quality of studies, conventional meta-analyses based on these studies will not show the accuracy of the tests in real practice. By using individual patient data (IPD) to perform meta-analyses, the accuracy of tests can be assessed in relation to other patient characteristics and allows the development or evaluation of diagnostic algorithms for individual patients. In this study we will examine these potential benefits in four clinical diagnostic problems in the field of gynaecology, obstetrics and reproductive medicine. METHODS/DESIGN: Based on earlier systematic reviews for each of the four clinical problems, studies are considered for inclusion. The first authors of the included studies will be invited to participate and share their original data. After assessment of validity and completeness the acquired datasets are merged. Based on these data, a series of analyses will be performed, including a systematic comparison of the results of the IPD meta-analysis with those of a conventional meta-analysis, development of multivariable models for clinical history alone and for the combination of history, physical examination and relevant diagnostic tests and development of clinical prediction rules for the individual patients. These will be made accessible for clinicians. DISCUSSION: The use of IPD meta-analysis will allow evaluating accuracy of diagnostic tests in relation to other relevant information. Ultimately, this could increase the efficiency of the diagnostic work-up, e.g. by reducing the need for invasive tests and/or improving the accuracy of the diagnostic workup. This study will assess whether these benefits of IPD meta-analysis over conventional meta-analysis can be exploited and will provide a framework for future IPD meta-analyses in diagnostic and prognostic research.

Admission blood glucose is an independent predictive factor for hospital mortality in polytraumatised patients

PURPOSE: The goal of this study was to analyse a possible association of admission blood glucose with hospital mortality of polytraumatised patients and to develop an outcome prediction model for this patient group. METHODS: The outcome of adult polytraumatised patients admitted to the University Hospital of Berne, Switzerland, between 2002 and 2004 with an ISS > or = 17, and more than one severely injured organ system was retrospectively analysed. RESULTS: The inclusion criteria were met by 555 patients, of which 108 (19.5%) died. Hyperglycaemia proved to be an independent predictor for hospital mortality (P < 0.0001), following multiple regression analysis. After inclusion of admission blood glucose, the calculated mortality prediction model performed better than currently described models (P < 0.0001, AUC 0.924). CONCLUSION: In this retrospective, single-centre study in polytraumatised patients, admission blood glucose proved to be an independent predictor of hospital mortality following regression analysis controlling for age, gender, injury severity and other laboratory parameters. A reliable admission blood glucose-based mortality prediction model for polytraumatised patients could be established. This observation may be helpful in improving the precision of future outcome prediction models for polytraumatised patients. These observations warrant further prospective evaluation.

Making epothilones fluoresce: design, synthesis, and biological characterization of a fluorescent N12-aza-epothilone (azathilone)

A green fluorescent 12-aza-epothilone (azathilone) derivative has been prepared through the attachment of the 4-nitro-2,1,3-benzoxadiazole (NBD) fluorophore to the 12-nitrogen atom of the azamacrolide core structure. While less potent than natural epothilones or different N12-acylated azathilone derivatives, NBD-azathilone (3) promotes tubulin assembly, inhibits cancer cell proliferation in vitro and arrests the cell cycle at the G2/M transition. Most significantly, the binding of 3 to cellular microtubules (MTs) could be directly visualized by confocal fluorescence microscopy. Based on competition binding experiments with laulimalide-stabilized MTs in vitro, the N12-Boc substituted azathilone 1, Epo A, and NBD-azathilone (3) all interact with the same tubulin-binding site. Computational studies provided a structural model of the complexes between beta-tubulin and 1 or 3, respectively, in which the NBD moiety of 3 or the BOC moiety of 1 directly and specifically contribute to MT binding. Collectively, these data demonstrate that the cellular effects of 3 and, by inference, also of other azathilones are the result of their interactions with the cellular MT network.

Model Driven Architecture (MDA): Integration and Model Reuse for Open Source eLearning Platforms

Open Source (OS) community offers numerous eLearning platforms of both types: Learning Management Systems (LMS) and Learning Content Systems (LCS). General purpose OS intermediaries such as SourceForge, ObjectWeb, Apache or specialized intermediaries like CampusSource reduce the cost to locate such eLearning platforms. Still, it is impossible to directly compare the functionalities of those OS software products without performing detailed testing on each product. Some articles available from eLearning Wikipedia show comparisons between eLearning platforms which can help, but at the end they barely serve as documentation which are becoming out of date quickly [1]. The absence of integration activities between OS eLearning platforms - which are sometimes quite similar in terms of functionalities and implementation technologies - is sometimes critical since most of the OS projects possess small financial and human resources. This paper shows a possible solution for these barriers of OS eLearning platforms. We propose the Model Driven Architecture (MDA) concept to capture functionalities and to identify similarities between available OS eLearning platforms. This contribution evolved from a fruitful discussion at the 2nd CampusSource Developer Conference at the University of Muenster (27th August 2004).

Simulationsgestützte Entwicklung eines Lenkkonzeptes für Routenzüge

Schleppzüge haben für den innerbetrieblichen Materialtransport in den letzten Jahren stark an Bedeutung gewonnen. Wichtige Eigenschaften sind die Manövrierbarkeit und die Spurtreue, da sie maßgeblich den Flächenbedarf bestimmen. In diesem Beitrag wird das Nachlaufverhalten von Schleppzügen, die sich durch ihr Fahrwerks- und Lenkkonzept unterscheiden, untersucht sowie eine neue Lenkkinematik vorgestellt. Um die Spurtreue der verschiedenen Konzepte objektiv vergleichen zu können, werden zunächst Fahrmanöver und ein Gütekriterium definiert, so dass die Abweichungen von der Spurtreue quantitativ beschrieben und verglichen werden können. Mit einem in diesem Beitrag vorgestellten analytischen Modell können bereits für die stationäre Kreisfahrt wichtige Aus-sagen über die Spurabweichungen getroffen werden. Zu-sätzlich werden Simulationen durchgeführt, die eine tiefere physikalische Modellierung und die Untersuchung komple-xerer Fahrmanöver erlauben. Außerdem wird dargestellt, dass auch die Art des Fahrmanövers Einfluss auf die Spurabweichung hat. Fahrwerks- und Lenkkonzepte, die bei stationärer Kreisfahrt ein sehr gutes Nachlaufverhalten aufweisen und bisher als spurtreu bezeichnet wurden, zeigen beim Ein- oder Ausfahren aus der Kurve zum Teil erhebliche Spurabweichungen. Mit diesen Erkenntnissen wird ein neues Lenkkonzept vorgestellt, das sich insbesondere durch einen sehr einfachen Aufbau sowie eine hohe Spurtreue auszeichnet.

Reanalysis-driven climate simulation over CORDEX North America domain using the Canadian Regional Climate Model, version 5: model performance evaluation

The performance of reanalysis-driven Canadian Regional Climate Model, version 5 (CRCM5) in reproducing the present climate over the North American COordinated Regional climate Downscaling EXperiment domain for the 1989–2008 period has been assessed in comparison with several observation-based datasets. The model reproduces satisfactorily the near-surface temperature and precipitation characteristics over most part of North America. Coastal and mountainous zones remain problematic: a cold bias (2–6 °C) prevails over Rocky Mountains in summertime and all year-round over Mexico; winter precipitation in mountainous coastal regions is overestimated. The precipitation patterns related to the North American Monsoon are well reproduced, except on its northern limit. The spatial and temporal structure of the Great Plains Low-Level Jet is well reproduced by the model; however, the night-time precipitation maximum in the jet area is underestimated. The performance of CRCM5 was assessed against earlier CRCM versions and other RCMs. CRCM5 is shown to have been substantially improved compared to CRCM3 and CRCM4 in terms of seasonal mean statistics, and to be comparable to other modern RCMs.

Ankle joint pressure changes in a pes cavovarus model: supramalleolar valgus osteotomy versus lateralizing calcaneal osteotomy

BACKGROUND: A fixed cavovarus foot deformity can be associated with anteromedial ankle arthrosis due to elevated medial joint contact stresses. Supramalleolar valgus osteotomies (SMOT) and lateralizing calcaneal osteotomies (LCOT) are commonly used to treat symptoms by redistributing joint contact forces. In a cavovarus model, the effects of SMOT and LCOT on the lateralization of the center of force (COF) and reduction of the peak pressure in the ankle joint were compared. METHODS: A previously published cavovarus model with fixed hindfoot varus was simulated in 10 cadaver specimens. Closing wedge supramalleolar valgus osteotomies 3 cm above the ankle joint level (6 and 11 degrees) and lateral sliding calcaneal osteotomies (5 and 10 mm displacement) were analyzed at 300 N axial static load (half body weight). The COF migration and peak pressure decrease in the ankle were recorded using high-resolution TekScan pressure sensors. RESULTS: A significant lateral COF shift was observed for each osteotomy: 2.1 mm for the 6 degrees (P = .014) and 2.3 mm for the 11 degrees SMOT (P = .010). The 5 mm LCOT led to a lateral shift of 2.0 mm (P = .042) and the 10 mm LCOT to a shift of 3.0 mm (P = .006). Comparing the different osteotomies among themselves no significant differences were recorded. No significant anteroposterior COF shift was seen. A significant peak pressure reduction was recorded for each osteotomy: The SMOT led to a reduction of 29% (P = .033) for the 6 degrees and 47% (P = .003) for the 11 degrees osteotomy, and the LCOT to a reduction of 41% (P = .003) for the 5 mm and 49% (P = .002) for the 10 mm osteotomy. Similar to the COF lateralization no significant differences between the osteotomies were seen. CONCLUSION: LCOT and SMOT significantly reduced anteromedial ankle joint contact stresses in this cavovarus model. The unloading effects of both osteotomies were equivalent. More correction did not lead to significantly more lateralization of the COF or more reduction of peak pressure but a trend was seen. CLINICAL RELEVANCE: In patients with fixed cavovarus feet, both SMOT and LCOT provided equally good redistribution of elevated ankle joint contact forces. Increasing the amount of displacement did not seem to equally improve the joint pressures. The site of osteotomy could therefore be chosen on the basis of surgeon's preference, simplicity, or local factors in case of more complex reconstructions.

Thoracic radiotherapy treatment planning with cine PET/CT

Purpose: Respiratory motion causes substantial uncertainty in radiotherapy treatment planning. Four-dimensional computed tomography (4D-CT) is a useful tool to image tumor motion during normal respiration. Treatment margins can be reduced by targeting the motion path of the tumor. The expense and complexity of 4D-CT, however, may be cost-prohibitive at some facilities. We developed an image processing technique to produce images from cine CT that contain significant motion information without 4D-CT. The purpose of this work was to compare cine CT and 4D-CT for the purposes of target delineation and dose calculation, and to explore the role of PET in target delineation of lung cancer. Methods: To determine whether cine CT could substitute 4D-CT for small mobile lung tumors, we compared target volumes delineated by a physician on cine CT and 4D-CT for 27 tumors with intrafractional motion greater than 1 cm. We assessed dose calculation by comparing dose distributions calculated on respiratory-averaged cine CT and respiratory-averaged 4D-CT using the gamma index. A threshold-based PET segmentation model of size, motion, and source-to-background was developed from phantom scans and validated with 24 lung tumors. Finally, feasibility of integrating cine CT and PET for contouring was assessed on a small group of larger tumors. Results: Cine CT to 4D-CT target volume ratios were (1.05±0.14) and (0.97±0.13) for high-contrast and low-contrast tumors respectively which was within intraobserver variation. Dose distributions on cine CT produced good agreement (< 2%/1 mm) with 4D-CT for 71 of 73 patients. The segmentation model fit the phantom data with R2 = 0.96 and produced PET target volumes that matched CT better than 6 published methods (-5.15%). Application of the model to more complex tumors produced mixed results and further research is necessary to adequately integrate PET and cine CT for delineation. Conclusions: Cine CT can be used for target delineation of small mobile lesions with minimal differences to 4D-CT. PET, utilizing the segmentation model, can provide additional contrast. Additional research is required to assess the efficacy of complex tumor delineation with cine CT and PET. Respiratory-averaged cine CT can substitute respiratory-averaged 4D-CT for dose calculation with negligible differences.