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.

Natural killer T cell dysfunction in CD39-null mice protects against concanavalin A-induced hepatitis

Concanavalin A (Con A)-induced injury is an established natural killer T (NKT) cell-mediated model of inflammation that has been used in studies of immune liver disease. Extracellular nucleotides, such as adenosine triphosphate, are released by Con A-stimulated cells and bind to specific purinergic type 2 receptors to modulate immune activation responses. Levels of extracellular nucleotides are in turn closely regulated by ectonucleotidases, such as CD39/NTPDase1. Effects of extracellular nucleotides and CD39 on NKT cell activation and upon hepatic inflammation have been largely unexplored to date. Here, we show that NKT cells express both CD39 and CD73/ecto-5'-nucleotidase and can therefore generate adenosine from extracellular nucleotides, whereas natural killer cells do not express CD73. In vivo, mice null for CD39 are protected from Con A-induced liver injury and show substantively lower serum levels of interleukin-4 and interferon-gamma when compared with matched wild-type mice. Numbers of hepatic NKT cells are significantly decreased in CD39 null mice after Con A administration. Hepatic NKT cells express most P2X and P2Y receptors; exceptions include P2X3 and P2Y11. Heightened levels of apoptosis of CD39 null NKT cells in vivo and in vitro appear to be driven by unimpeded activation of the P2X7 receptor. CONCLUSION: CD39 and CD73 are novel phenotypic markers of NKT cells. Deletion of CD39 modulates nucleotide-mediated cytokine production by, and limits apoptosis of, hepatic NKT cells providing protection against Con A-induced hepatitis. This study illustrates a further role for purinergic signaling in NKT-mediated mechanisms that result in liver immune injury.

Public values and perceptions of industrial heritage in the Keweenaw Peninsula, Michigan

The purpose of this research is to assess public values and perceptions concerning industrial heritage in the Keweenaw by studying visitors at an endangered mining site tour. This research presents and analyzes feedback collected directly from participants in the Cliff Mine (Michigan) archaeological field school public tour surveys in June 2011, gathers semi-structured interview data from survey participants and local experts, and synthesizes and collates both survey and interview data. As those who study heritage site visitors have found, in all outreach there is a necessity for deeper understanding of visitors for the outreach to be effective. An appropriate metric for collecting public values and opinions was created and used at the Cliff Mine archaeological field school public tours. To accomplish research goals, an opinion survey was created to collect demographic information and qualitative feedback from visitors at the Cliff Mine field school. The survey, a pre-tour and post-tour question list, found that all visitors who filled out a survey supported preservation and most were adults over 46 years of age. Most visitors were white-collar professionals, identified as local residents, and found out about the tour through the newspaper. Interview questions were constructed to supplement and expand on the visitor survey results. In addition, local experts involved in Keweenaw heritage were interviewed. All interviewees supported heritage preservation but often had conflicting views when activities such as mineral collecting were factored into the preservation question. By analyzing responses to the survey and interviews, improvements to outreach efforts at the Cliff Mine are recommended. Future research should further explore perceptions of social class and identity, and should seek out stakeholders not contacted through this research, in order to improve outreach and include all community groups.

Effects of Standard Labor-Wear on Swimming and Treading Water

We tested the hypothesis that occupational clothing would impair performance during swimming. The sub questions included: (1) Will the standard work wear of a railway worker or laborer impede swimming ability? (2) Will this clothing impact the individual’s ability to tread water? We addressed the research questions with three hypotheses. Analysis showed statistically significant p-values and all three null hypotheses were rejected in favor of the three research hypotheses, showing strong evidence that standard labor wear had adverse effects on 11.43 meter/12.5 yard swim time, water treading time and rate of perceived exertion (RPE) during water treading. The mean swim time more than doubled when the subjects wore standard labor-wear and their average rate of perceived exertion increased from 11.6 in standard swim wear to 17.1 in standard laborwear. It may be beneficial for those workers who work near water to be exposed to educational programs that allow in-water experiences so they develop an understanding of their abilities in, and respect for, the water.

Heart Rate Effects of Longboard Skateboarding

The longboard skateboard has a longer, and usually wider, deck than the standard skateboard to provide greater support for the rider during the higher speeds attained on this version of the skateboard. Fourteen volunteer subjects participated in downhill and uphill longboarding trials. Heart rates were monitored during both trials, and the downhill and uphill average heart rates were compared with resting heart rates and then compared with accepted intensity recommendations for health and fitness benefits. The study questions were: Does longboarding have an acute effect on heart rates? If so, will longboarding uphill and/or downhill cause heart rate changes to levels recommended to improve cardiorespiratory health and fitness? With these questions as guidance we developed four hypotheses. With beats/minute and average uphill heart rate of 167.8 beats/minute statistical analysis showed statistically significant p values < .0001 and each null hypothesis was rejected in favor of their respective research hypotheses. Based on average age and average resting heart rate, average age-predicted maximum heart rate was 193.2 beats/minute and heart rate reserve was 133.2 beats/minute. The average percentages of heart rate reserve for the downhill section (131.4 beats/minute) and uphill section )(167.8 beats/minute) were 54% and 81% respectively. Downhill heart rates are within moderate intensity levels, 40% to 60% of heart rate reserve, and uphill heart rates are within vigorous intensity levels, greater than 60% of heart rate reserve. These results indicate that longboarding can increase heart rate to suggested levels suggested by the American College of Sports Medicine for improving cardiovascular health and fitness.

Imparted Montana Values and the Election

A Montana Public Radio Commentary from Evan Barrett.

Early loading of nonsubmerged titanium implants with a chemically modified sand-blasted and acid-etched surface: 6-month results of a prospective case series study in the posterior mandible focusing on peri-implant crestal bone changes and implant stability quotient (ISQ) values

PURPOSE: The aim of this prospective case series study was to evaluate the short-term success rates of titanium screw-type implants with a chemically modified sand-blasted and acid-etched (mod SLA) surface after 3 weeks of healing. MATERIAL AND METHODS: A total of 56 implants were inserted in the posterior mandible of 40 partially edentulous patients exhibiting bone densities of class I to III. After a healing period of 3 weeks, all implants were functionally loaded with a screw-retained crown or fixed dental prosthesis. The patients were recalled at weeks 4, 7, 12, and 26 for monitoring and assessment of clinical and radiological parameters, including implant stability quotient (ISQ) measurements. RESULTS: None of the implants failed to integrate. However, two implants were considered "spinners" at day 21 and left unloaded for an extended period. Therefore, 96.4% of the inserted implants were loaded according to the protocol tested. All 56 implants including the "spinners" showed favorable clinical and radiographic findings at the 6-month follow-up examination. The ISQ values increased steadily throughout the follow-up period. At the time of implant placement, the range of ISQ values exhibited a mean of 74.33, and by week 26, a mean value of 83.82 was recorded. Based on strict criteria, all 56 implants were considered successfully integrated, resulting in a 6-month survival and success rate of 100.0%. CONCLUSION: This prospective study using an early-loading protocol after 3 weeks of healing demonstrated that titanium implants with the modified SLA surface can achieve and maintain successful tissue integration over a period of at least 6 months. The ISQ method seems feasible to monitor implant stability during the initial wound-healing period.

Diffusion-weighted imaging of the parotid gland: Influence of the choice of b-values on the apparent diffusion coefficient value

PURPOSE: To determine how the ADC value of parotid glands is influenced by the choice of b-values. MATERIALS AND METHODS: In eight healthy volunteers, diffusion-weighted echo-planar imaging (DW-EPI) was performed on a 1.5 T system, with b-values (in seconds/mm2) of 0, 50, 100, 150, 200, 250, 300, 500, 750, and 1000. ADC values were calculated by two alternative methods (exponential vs. logarithmic fit) from five different sets of b-values: (A) all b-values; (B) b=0, 50, and 100; (C) b=0 and 750; (D) b=0, 500, and 1000; and (E) b=500, 750, and 1000. RESULTS: The mean ADC values for the different settings were (in 10(-3) mm2/second, exponential fit): (A) 0.732+/-0.019, (B) 2.074+/-0.084, (C) 0.947+/-0.020, (D) 0.890+/-0.023, and (E) 0.581+/-0.021. ADC values were significantly (P <0.001) different for all pairwise comparisons of settings (A-E) of b-values, except for A vs. D (P=0.172) and C vs. D (P=0.380). The ADC(B) was significantly higher than ADC(C) or ADC(D), which was significantly higher than ADC(E). ADC values from exponential vs. logarithmic fit (P=0.542), as well as left vs. right parotid gland (P=0.962), were indistinguishable. CONCLUSION: The ADC values calculated from low b-value settings were significantly higher than those calculated from high b-value settings. These results suggest that not only true diffusion but also perfusion and saliva flow may contribute to the ADC.

Datenanalyse. Das Null-Ritual und der Umgang mit Effekten in der Zeitschrift für Sportpsychologie

Ziel dieses Beitrages ist die Analyse der Anwendung empirischer Tests in der deutschsprachigen Sportpsychologie. Die Ergebnisse vergleichbarer Analysen, bspw. in der Psychologie, zeigen, dass zwischen Anforderungen aus Testkonzepten und empirischer Realität Unterschiede existieren, die bislang für die Sportpsychologie nicht beschrieben und bewertet worden sind. Die Jahrgänge 1994–2007 der Zeitschrift für Sportpsychologie (früher psychologie und sport) wurden danach untersucht, ob Forschungsfragen formuliert, welche Stichprobenart gewählt, welches Testkonzept verwendet, welches Signifikanzniveau benutzt und ob statistische Probleme diskutiert wurden. 83 Artikel wurden von zwei unabhängigen Bewertern nach diesen Aspekten kategorisiert. Als Ergebnis ist festzuhalten, dass in der sportpsychologischen Forschung überwiegend eine Mischung aus Fishers Signifikanztesten sowie Neyman-Pearsons-Hypothesentesten zur Anwendung kommt,das sogenannte „Hybrid-Modell” oder „Null-Ritual”. Die Beschreibung der Teststärke ist kaum zu beobachten. Eine zeitliche Analyse der Beiträge zeigt, dass vor allem die Benutzung von Effektgrößen in den letzten Jahren zugenommen hat. Abschließend werden Ansätze zur Verbesserung und der Vereinheitlichung der Anwendung empirischer Tests vorgeschlagen und diskutiert.