Analyzing Bivariate Survival Data with Interval Sampling and Application to Cancer Epidemiology

In medical follow-up studies, ordered bivariate survival data are frequently encountered when bivariate failure events are used as the outcomes to identify the progression of a disease. In cancer studies interest could be focused on bivariate failure times, for example, time from birth to cancer onset and time from cancer onset to death. This paper considers a sampling scheme where the first failure event (cancer onset) is identified within a calendar time interval, the time of the initiating event (birth) can be retrospectively confirmed, and the occurrence of the second event (death) is observed sub ject to right censoring. To analyze this type of bivariate failure time data, it is important to recognize the presence of bias arising due to interval sampling. In this paper, nonparametric and semiparametric methods are developed to analyze the bivariate survival data with interval sampling under stationary and semi-stationary conditions. Numerical studies demonstrate the proposed estimating approaches perform well with practical sample sizes in different simulated models. We apply the proposed methods to SEER ovarian cancer registry data for illustration of the methods and theory.

Similarities in the Subgingival Microbiota Assessed by a Curet Sampling Method at Sites With Chronic Periodontitis

Background: The goal of this study was to determine whether site-specific differences in the subgingival microbiota could be detected by the checkerboard method in subjects with periodontitis. Methods: Subjects with at least six periodontal pockets with a probing depth (PD) between 5 and 7 mm were enrolled in the study. Subgingival plaque samples were collected with sterile curets by a single-stroke procedure at six selected periodontal sites from 161 subjects (966 subgingival sites). Subgingival bacterial samples were assayed with the checkerboard DNA-DNA hybridization method identifying 37 species. Results: Probing depths of 5, 6, and 7 mm were found at 50% (n = 483), 34% (n = 328), and 16% (n = 155) of sites, respectively. Statistical analysis failed to demonstrate differences in the sum of bacterial counts by tooth type (P = 0.18) or specific location of the sample (P = 0.78). With the exceptions of Campylobacter gracilis (P <0.001) and Actinomyces naeslundii (P <0.001), analysis by general linear model multivariate regression failed to identify subject or sample location factors as explanatory to microbiologic results. A trend of difference in bacterial load by tooth type was found for Prevotella nigrescens (P <0.01). At a cutoff level of >/=1.0 x 10(5), Porphyromonas gingivalis and Tannerella forsythia (previously T. forsythensis) were present at 48.0% to 56.3% and 46.0% to 51.2% of sampled sites, respectively. Conclusions: Given the similarities in the clinical evidence of periodontitis, the presence and levels of 37 species commonly studied in periodontitis are similar, with no differences between molar, premolar, and incisor/cuspid subgingival sites. This may facilitate microbiologic sampling strategies in subjects during periodontal therapy.

Creep and shrinkage behavior of ultra high-performance concrete under compressive loading with varying curing regimes

This Ultra High Performance Concrete research involves observing early-age creep and shrinkage under a compressive load throughout multiple thermal curing regimes. The goal was to mimic the conditions that would be expected of a precast/prestressing plant in the United States, where UHPC beams would be produced quickly to maximize a manufacturing plant’s output. The practice of steam curing green concrete to accelerate compressive strengths for early release of the prestressing tendons was utilized (140°F [60°C], 95% RH, 14 hrs), in addition to the full thermal treatment (195°F [90°C], 95% RH, 48 hrs) while the specimens were under compressive loading. Past experimental studies on creep and shrinkage characteristics of UHPC have only looked at applying a creep load after the thermal treatment had been administered to the specimens, or on ambient cured specimens. However, this research looked at mimicking current U.S. precast/prestressed plant procedures, and thus characterized the creep and shrinkage characteristics of UHPC as it is thermally treated under a compressive load. Michigan Tech has three moveable creep frames to accommodate two loading criteria per frame of 0.2f’ci and 0.6f’ci. Specimens were loaded in the creep frames and moved into a custom built curing chamber at different times, mimicking a precast plant producing several beams throughout the week and applying a thermal cure to all of the beams over the weekend. This thesis presents the effects of creep strain due to the varying curing regimes. An ambient cure regime was used as a baseline for the comparison against the varying thermal curing regimes. In all cases of thermally cured specimens, the compressive creep and shrinkage strains are accelerated to a maximum strain value, and remain consistent after the administration of the thermal cure. An average creep coefficient for specimens subjected to a thermal cure was found to be 1.12 and 0.78 for the high and low load levels, respectively. Precast/pressed plants can expect that simultaneously thermally curing UHPC elements that are produced throughout the week does not impact the post-cure creep coefficient.

Hermitian curve interpolation for CT-data re-sampling

Purpose: Development of an interpolation algorithm for re‐sampling spatially distributed CT‐data with the following features: global and local integral conservation, avoidance of negative interpolation values for positively defined datasets and the ability to control re‐sampling artifacts. Method and Materials: The interpolation can be separated into two steps: first, the discrete CT‐data has to be continuously distributed by an analytic function considering the boundary conditions. Generally, this function is determined by piecewise interpolation. Instead of using linear or high order polynomialinterpolations, which do not fulfill all the above mentioned features, a special form of Hermitian curve interpolation is used to solve the interpolation problem with respect to the required boundary conditions. A single parameter is determined, by which the behavior of the interpolation function is controlled. Second, the interpolated data have to be re‐distributed with respect to the requested grid. Results: The new algorithm was compared with commonly used interpolation functions based on linear and second order polynomial. It is demonstrated that these interpolation functions may over‐ or underestimate the source data by about 10%–20% while the parameter of the new algorithm can be adjusted in order to significantly reduce these interpolation errors. Finally, the performance and accuracy of the algorithm was tested by re‐gridding a series of X‐ray CT‐images. Conclusion: Inaccurate sampling values may occur due to the lack of integral conservation. Re‐sampling algorithms using high order polynomialinterpolation functions may result in significant artifacts of the re‐sampled data. Such artifacts can be avoided by using the new algorithm based on Hermitian curve interpolation

Proteins in silico-modeling and sampling

Proteins are linear chain molecules made out of amino acids. Only when they fold to their native states, they become functional. This dissertation aims to model the solvent (environment) effect and to develop & implement enhanced sampling methods that enable a reliable study of the protein folding problem in silico. We have developed an enhanced solvation model based on the solution to the Poisson-Boltzmann equation in order to describe the solvent effect. Following the quantum mechanical Polarizable Continuum Model (PCM), we decomposed net solvation free energy into three physical terms– Polarization, Dispersion and Cavitation. All the terms were implemented, analyzed and parametrized individually to obtain a high level of accuracy. In order to describe the thermodynamics of proteins, their conformational space needs to be sampled thoroughly. Simulations of proteins are hampered by slow relaxation due to their rugged free-energy landscape, with the barriers between minima being higher than the thermal energy at physiological temperatures. In order to overcome this problem a number of approaches have been proposed of which replica exchange method (REM) is the most popular. In this dissertation we describe a new variant of canonical replica exchange method in the context of molecular dynamic simulation. The advantage of this new method is the easily tunable high acceptance rate for the replica exchange. We call our method Microcanonical Replica Exchange Molecular Dynamic (MREMD). We have described the theoretical frame work, comment on its actual implementation, and its application to Trp-cage mini-protein in implicit solvent. We have been able to correctly predict the folding thermodynamics of this protein using our approach.

MATURE FINE TAILINGS (MFTs): A STUDY OF COMPRESSIVE STRENGTH AND RHEOLOGICAL PROPERTIES OF ATHABASCA OIL SANDS PETROLEUM MINING WASTE APPLIED IN CONCRETE MIXTURES

This study investigates the compressive properties of concrete incorporating Mature Fine Tailings (MFTs) waste stream from a tar sands mining operation. The objectives of this study are to investigate material properties of the MFT material itself, as well as establish general feasibility of the utilization of MFT material in concrete mixtures through empirical data and visual observations. Investigations undertaken in this study consist of moisture content, materials finer than No. 200 sieve, Atterburg Limits as well as visual observations performed on MFT material as obtained. Control concrete mixtures as well as MFT replacement mixture designs (% by wt. of water) were guided by properties of the MFT material that were experimentally established. The experimental design consists of compression testing of 4”-diameter concrete cylinders of a control mixture, 30% MFT, 50% MFT and 70% MFT replacement mixtures with air-entrainer additive, as well as a control mixture and 30% MFT replacement mixture with no air-entrainer. A total of 6 mixtures (2 control mixtures, 4 replacement mixtures) moist-cured in lime water after 24 hours initial curing were tested for ultimate compressive strength at 7 days and 28 days in accordance to ASTM C39. The test results of fresh concrete material show that the addition of air-entrainer to the control mixture increases slump from 4” to 5.5”. However, the use of MFT material in concrete mixtures significantly decreases slump as compared to controls. All MFT replacement mixtures (30%, 50%, and 70%) with air-entrainer present slumps of 1”. 30% MFT with no air-entrainer presents a slump of 1.5”. It was found that 7-day ultimate compressive stress was not a good predictor of 28-day ultimate compressive stress. 28-day results indicate that the use of MFT material in concrete with air-entrainer decreases ultimate compressive stress for 30%, 50% and 70% MFT replacement amounts by 14.2%, 17.3% and 25.1% respectively.

Sampling-Design Effects on Properties of Species-Area Relationships - A Case Study from Estonian Dry Grassland Communities

Despite widespread use of species-area relationships (SARs), dispute remains over the most representative SAR model. Using data of small-scale SARs of Estonian dry grassland communities, we address three questions: (1) Which model describes these SARs best when known artifacts are excluded? (2) How do deviating sampling procedures (marginal instead of central position of the smaller plots in relation to the largest plot; single values instead of average values; randomly located subplots instead of nested subplots) influence the properties of the SARs? (3) Are those effects likely to bias the selection of the best model? Our general dataset consisted of 16 series of nested-plots (1 cm(2)-100 m(2), any-part system), each of which comprised five series of subplots located in the four corners and the centre of the 100-m(2) plot. Data for the three pairs of compared sampling designs were generated from this dataset by subsampling. Five function types (power, quadratic power, logarithmic, Michaelis-Menten, Lomolino) were fitted with non-linear regression. In some of the communities, we found extremely high species densities (including bryophytes and lichens), namely up to eight species in 1 cm(2) and up to 140 species in 100 m(2), which appear to be the highest documented values on these scales. For SARs constructed from nested-plot average-value data, the regular power function generally was the best model, closely followed by the quadratic power function, while the logarithmic and Michaelis-Menten functions performed poorly throughout. However, the relative fit of the latter two models increased significantly relative to the respective best model when the single-value or random-sampling method was applied, however, the power function normally remained far superior. These results confirm the hypothesis that both single-value and random-sampling approaches cause artifacts by increasing stochasticity in the data, which can lead to the selection of inappropriate models.

Compressive strength of interbody cages in the lumbar spine: the effect of cage shape, posterior instrumentation and bone density

One goal of interbody fusion is to increase the height of the degenerated disc space. Interbody cages in particular have been promoted with the claim that they can maintain the disc space better than other methods. There are many factors that can affect the disc height maintenance, including graft or cage design, the quality of the surrounding bone and the presence of supplementary posterior fixation. The present study is an in vitro biomechanical investigation of the compressive behaviour of three different interbody cage designs in a human cadaveric model. The effect of bone density and posterior instrumentation were assessed. Thirty-six lumbar functional spinal units were instrumented with one of three interbody cages: (1) a porous titanium implant with endplate fit (Stratec), (2) a porous, rectangular carbon-fibre implant (Brantigan) and (3) a porous, cylindrical threaded implant (Ray). Posterior instrumentation (USS) was applied to half of the specimens. All specimens were subjected to axial compression displacement until failure. Correlations between both the failure load and the load at 3 mm displacement with the bone density measurements were observed. Neither the cage design nor the presence of posterior instrumentation had a significant effect on the failure load. The loads at 3 mm were slightly less for the Stratec cage, implying lower axial stiffness, but were not different with posterior instrumentation. The large range of observed failure loads overlaps the potential in vivo compressive loads, implying that failure of the bone-implant interface may occur clinically. Preoperative measurements of bone density may be an effective tool to predict settling around interbody cages.

Prediction of total quarter milk somatic cell counts based on foremilk sampling

Determination of somatic cell count (SCC) is used worldwide in dairy practice to describe the hygienic status of the milk and the udder health of cows. When SCC is tested on a quarter level to detect single quarters with high SCC levels of cows for practical reasons, mostly foremilk samples after prestimulation (i.e. cleaning of the udder) are used. However, SCC is usually different in different milk fractions. Therefore, the goal of this study was the investigation of the use of foremilk samples for the estimation of total quarter SCC. A total of 378 milkings in 19 dairy cows were performed with a special milking device to drain quarter milk separately. Foremilk samples were taken after udder stimulation and before cluster attachment. SCC was measured in foremilk samples and in total quarter milk. Total quarter milk SCC could not be predicted precisely from foremilk SCC measurements. At relatively high foremilk SCC levels (>300 x 10(3) cells/ml) foremilk SCC were higher than total quarter milk. At around (50-300) x 10(3) cells/ml foremilk and total quarter SCC did not differ considerably. Most interestingly, if foremilk SCC was lower than 50 x 10(3) cells/ml the total quarter SCC was higher than foremilk SCC. In addition, individual cows showed dramatic variations in foremilk SCC that were not very well related to total quarter milk SCC. In conclusion, foremilk samples are useful to detect high quarter milk SCC to recognize possibly infected quarters, only if precise cell counts are not required. However, foremilk samples can be deceptive if very low cell numbers are to be detected.

Design-based stereology: Planning, volumetry and sampling are crucial steps for a successful study

Quantitative data obtained by means of design-based stereology can add valuable information to studies performed on a diversity of organs, in particular when correlated to functional/physiological and biochemical data. Design-based stereology is based on a sound statistical background and can be used to generate accurate data which are in line with principles of good laboratory practice. In addition, by adjusting the study design an appropriate precision can be achieved to find relevant differences between groups. For the success of the stereological assessment detailed planning is necessary. In this review we focus on common pitfalls encountered during stereological assessment. An exemplary workflow is included, and based on authentic examples, we illustrate a number of sampling principles which can be implemented to obtain properly sampled tissue blocks for various purposes.