Sequential Quantitative Trait Locus Mapping in Experimental Crosses

The etiology of complex diseases is heterogeneous. The presence of risk alleles in one or more genetic loci affects the function of a variety of intermediate biological pathways, resulting in the overt expression of disease. Hence, there is an increasing focus on identifying the genetic basis of disease by sytematically studying phenotypic traits pertaining to the underlying biological functions. In this paper we focus on identifying genetic loci linked to quantitative phenotypic traits in experimental crosses. Such genetic mapping methods often use a one stage design by genotyping all the markers of interest on the available subjects. A genome scan based on single locus or multi-locus models is used to identify the putative loci. Since the number of quantitative trait loci (QTLs) is very likely to be small relative to the number of markers genotyped, a one-stage selective genotyping approach is commonly used to reduce the genotyping burden, whereby markers are genotyped solely on individuals with extreme trait values. This approach is powerful in the presence of a single quantitative trait locus (QTL) but may result in substantial loss of information in the presence of multiple QTLs. Here we investigate the efficiency of sequential two stage designs to identify QTLs in experimental populations. Our investigations for backcross and F2 crosses suggest that genotyping all the markers on 60% of the subjects in Stage 1 and genotyping the chromosomes significant at 20% level using additional subjects in Stage 2 and testing using all the subjects provides an efficient approach to identify the QTLs and utilizes only 70% of the genotyping burden relative to a one stage design, regardless of the heritability and genotyping density. Complex traits are a consequence of multiple QTLs conferring main effects as well as epistatic interactions. We propose a two-stage analytic approach where a single-locus genome scan is conducted in Stage 1 to identify promising chromosomes, and interactions are examined using the loci on these chromosomes in Stage 2. We examine settings under which the two-stage analytic approach provides sufficient power to detect the putative QTLs.

Underestimation of Standard Errors in Multi-Site Time Series Studies

Multi-site time series studies of air pollution and mortality and morbidity have figured prominently in the literature as comprehensive approaches for estimating acute effects of air pollution on health. Hierarchical models are generally used to combine site-specific information and estimate pooled air pollution effects taking into account both within-site statistical uncertainty, and across-site heterogeneity. Within a site, characteristics of time series data of air pollution and health (small pollution effects, missing data, highly correlated predictors, non linear confounding etc.) make modelling all sources of uncertainty challenging. One potential consequence is underestimation of the statistical variance of the site-specific effects to be combined. In this paper we investigate the impact of variance underestimation on the pooled relative rate estimate. We focus on two-stage normal-normal hierarchical models and on under- estimation of the statistical variance at the first stage. By mathematical considerations and simulation studies, we found that variance underestimation does not affect the pooled estimate substantially. However, some sensitivity of the pooled estimate to variance underestimation is observed when the number of sites is small and underestimation is severe. These simulation results are applicable to any two-stage normal-normal hierarchical model for combining information of site-specific results, and they can be easily extended to more general hierarchical formulations. We also examined the impact of variance underestimation on the national average relative rate estimate from the National Morbidity Mortality Air Pollution Study and we found that variance underestimation as much as 40% has little effect on the national average.

Delays in childhood immunization in a conflict area: a study from Sierra Leone during civil war

ABSTRACT: BACKGROUND: Sierra Leone has undergone a decade of civil war from 1991 to 2001. From this period few data on immunization coverage are available, and conflict-related delays in immunization according to the Expanded Programme on Immunization (EPI) schedule have not been investigated. We aimed to study delays in childhood immunization in the context of civil war in a Sierra Leonean community. METHODS: We conducted an immunization survey in Kissy Mess-Mess in the Greater Freetown area in 1998/99 using a two-stage sampling method. Based on immunization cards and verbal history we collected data on immunization for tuberculosis, diphtheria, tetanus, pertussis, polio, and measles by age group (0-8/9-11/12-23/24-35 months). We studied differences between age groups and explored temporal associations with war-related hostilities taking place in the community. RESULTS: We included 286 children who received 1690 vaccine doses; card retention was 87%. In 243 children (85%, 95% confidence interval (CI): 80-89%) immunization was up-to-date. In 161 of these children (56%, 95%CI: 50-62%) full age-appropriate immunization was achieved; in 82 (29%, 95%CI: 24-34%) immunization was not appropriate for age. In the remaining 43 children immunization was partial in 37 (13%, 95%CI: 9-17) and absent in 6 (2%, 95%CI: 1-5). Immunization status varied across age groups. In children aged 9-11 months the proportion with age-inappropriate (delayed) immunization was higher than in other age groups suggesting an association with war-related hostilities in the community. CONCLUSION: Only about half of children under three years received full age-appropriate immunization. In children born during a period of increased hostilities, immunization was mostly inappropriate for age, but recommended immunizations were not completely abandoned. Missing or delayed immunization represents an additional threat to the health of children living in conflict areas.

Performance of dental implants after staged sinus floor elevation procedures: 5-year results of a prospective study in partially edentulous patients

OBJECTIVES: The aim of this prospective study was to evaluate the 5-year performance and success rate of titanium screw-type implants with the titanium plasma spray (TPS) or the sand-blasted, large grit, acid-etched (SLA) surface inserted in a two-stage sinus floor elevation (SFE) procedure in the posterior maxilla. MATERIAL AND METHODS: A total of 59 delayed SFEs were performed in 56 patients between January 1997 and December 2001, using a composite graft with autogenous bone chips combined with deproteinized bovine bone mineral (DBBM) or synthetic porous beta-tricalcium phosphate (beta-TCP). After a healing period averaging 7.75 months, 111 dental implants were inserted. After an additional 8-14-week healing period, all implants were functionally loaded with cemented crowns or fixed partial dentures. The patients were recalled at 12 and 60 months for clinical and radiographic examination. RESULTS: One patient developed an acute infection in the right maxillary sinus after SFE and did not undergo implant therapy. Two of the 111 inserted implants had to be removed because of a developing atypical facial pain, and 11 implants were lost to follow-up and were considered drop-outs. The remaining 98 implants showed favorable clinical and radiographic findings at the 5-year examination. The peri-implant soft tissues were stable over time; the mean probing depths and mean attachment levels did not change during the follow-up period. The measurement of the bone crest levels (DIB values) indicated stability as well. Based on strict success criteria, all 98 implants were considered successfully integrated, resulting in a 5-year success rate of 98% (for TPS implants 89%, for SLA implants 100%). CONCLUSION: This prospective study assessing the performance of dental implants inserted after SFE demonstrated that titanium implants can achieve and maintain successful tissue integration with high predictability for at least 5 years of follow-up in carefully selected patients.

Afghanistan connection : heroin production, distribution, and consumption

Heroin prices are a reflection of supply and demand, and similar to any other market, profits motivate participation. The intent of this research is to examine the change in Afghan opium production due to political conflict affecting Europe’s heroin market and government policies. If the Taliban remain in power, or a new Afghan government is formed, the changes will affect the heroin market in Europe to a certain degree. In the heroin market, the degree of change is dependent on many socioeconomic forces such as law enforcement, corruption, and proximity to Afghanistan. An econometric model that examines the degree of these socioeconomic effects has not been applied to the heroin trade in Afghanistan before. This research uses a two-stage least squares econometric model to reveal the supply and demand of heroin in 36 different countries from the Middle East to Western Europe in 2008. An application of the two-stage least squares model to the heroin market in Europe will attempt to predict the socioeconomic consequences of Afghanistan opium production.

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.

STATISTICAL METHODS FOR RARE AND COMMON VARIANT ASSOCIATION STUDIES

Complex human diseases are a major challenge for biological research. The goal of my research is to develop effective methods for biostatistics in order to create more opportunities for the prevention and cure of human diseases. This dissertation proposes statistical technologies that have the ability of being adapted to sequencing data in family-based designs, and that account for joint effects as well as gene-gene and gene-environment interactions in the GWA studies. The framework includes statistical methods for rare and common variant association studies. Although next-generation DNA sequencing technologies have made rare variant association studies feasible, the development of powerful statistical methods for rare variant association studies is still underway. Chapter 2 demonstrates two adaptive weighting methods for rare variant association studies based on family data for quantitative traits. The results show that both proposed methods are robust to population stratification, robust to the direction and magnitude of the effects of causal variants, and more powerful than the methods using weights suggested by Madsen and Browning [2009]. In Chapter 3, I extended the previously proposed test for Testing the effect of an Optimally Weighted combination of variants (TOW) [Sha et al., 2012] for unrelated individuals to TOW &ndash F, TOW for Family &ndash based design. Simulation results show that TOW &ndash F can control for population stratification in wide range of population structures including spatially structured populations, is robust to the directions of effect of causal variants, and is relatively robust to percentage of neutral variants. In GWA studies, this dissertation consists of a two &ndash locus joint effect analysis and a two-stage approach accounting for gene &ndash gene and gene &ndash environment interaction. Chapter 4 proposes a novel two &ndash stage approach, which is promising to identify joint effects, especially for monotonic models. The proposed approach outperforms a single &ndash marker method and a regular two &ndash stage analysis based on the two &ndash locus genotypic test. In Chapter 5, I proposed a gene &ndash based two &ndash stage approach to identify gene &ndash gene and gene &ndash environment interactions in GWA studies which can include rare variants. The two &ndash stage approach is applied to the GAW 17 dataset to identify the interaction between KDR gene and smoking status.

ASTAXANTHIN PRODUCTION FROM HAEMATOCOCCUS PLUVIALIS UNDER VARIOUS LIGHT INTENSITIES AND CARBON DIOXIDE CONCENTRATIONS

The microalga Haematococcus pluvialis was cultivated in MES-volvox medium at various light intensities and CO2 concentrations. It was found that CO2 concentrations of 10 and 15%, in combination with high irradiance at initial pH =6.7, accelerate astaxanthin accumulation in H. pluvialis cells but obstruct cell growth. The purpose of this research study was to devise a one-stage process consisting of the simultaneous cultivation of H. pluvialis and astaxanthin production using high light intensity and high CO2 concentration. This could be achieved at 200 µE/m2s and 15% CO2 in growth medium at initial pH = 4.3. Compared to the traditional two-stage H. pluvialis cultivation system, this one-step process can save up to 8-9 days of astaxanthin production time. The astaxanthin content in H. pluvialis cells induced with high light intensity only or with a combination of high light intensity and high CO2 concentration had comparable astaxanthin content; 94 and 97 mg/g dry biomass, respectively. However, it was extremely low in nitrate-free medium at high irradiance alone or combined with high CO2 concentration, with an average value of 4 mg/g dry biomass. Cell density was 40% less in cultures under discontinuous illumination compared to continuous illumination. This process could serve as a microalgal CO2 mitigation system after further understanding of the CO2 fixation ability of H. pluvialis has been gained.

Separation of Cadmium from Zinc in the Purification Step of the Leaching Cycle

The purpose of this investigation is to determine the effect of the factors listed previously by conducting a series of tests that will indicate the ex­tent to which the purification is influenced by time, temperature, zinc oust size, zinc dust quantity, iron concentration, two stage precipitation, and aeration.

Displacement of a dental implant into the maxillary sinus: report of an unusual complication when performing staged sinus floor elevation procedures

Grafting of the maxillary sinus in both one- and two-stage protocols has become a highly predictable surgical technique for site development and for the placement of implants to support dentures. However, despite the predictability and high success rates reported for dental implants placed either simultaneously with or after a sinus floor elevation (SFE) procedure, complications have been reported. The aim of the following case report is to present an uncommon complication in a staged SFE procedure: the displacement of a dental implant into the maxillary sinus during insertion. As implant dentistry is becoming more and more popular among practitioners, and ever more demanding procedures for initial site development in jaws with bony deficiencies are being introduced into daily practice, the displacement of dental implants into the maxillary sinus during implant placement may become a more frequent complication. Management of this complication is presented, discussed, and evaluated in light of the current literature.

Ridge augmentation and maxillary sinus grafting with a biphasic calcium phosphate: histologic and histomorphometric observations

OBJECTIVES: This retrospective study reports on histologic and histomorphometric observations performed on human biopsies harvested from sites augmented exclusively by biphasic calcium phosphate [BCP: hydroxyapatite (HA)/ tricalcium phosphate (TCP) 60/40] and healed for a minimum of 6 months. MATERIALS AND METHODS: Five patients benefited from three augmentation regimens (i.e.: one-stage lateral augmentation; two-stage lateral augmentation; and two-stage sinus grafting). In all patients, a degradable collagen membrane served as a cell-occlusive barrier. Core biopsies were obtained from lateral as from crestal aspects 6-10 months after augmentation surgeries. For histologic and histomorphometric evaluations, the non-decalcified tissue processing was performed. RESULTS: The histological examination of 11 biopsies showed graft particles frequently being bridged by the new bone, and a close contact between the graft particles and newly formed bone was seen in all samples. The mean percentages of newly formed bone, soft tissue compartment, and graft material were 38.8% (+/-5.89%), 41.75% (+/-6.08%), and 19.63% (+/-4.85%), respectively. Regarding bone-to-graft contact values, the percentage of bone coverage of graft particles for all biopsies ranged from 27.83% to 80.17%. The mean percentage of bone coverage was 55.39% (+/-13.03%). CONCLUSIONS: Data from the present study demonstrated osteoconductivity scores for the BCP material (HA/TCP 60/40) in patients resembling those previously shown for grafting materials of xenogenic and alloplastic origin.

A General Solution Framework for Component-Commonality Problems

Component commonality - the use of the same version of a component across multiple products - is being increasingly considered as a promising way to offer high external variety while retaining low internal variety in operations. However, increasing commonality has both positive and negative cost effects, so that optimization approaches are required to identify an optimal commonality level. As components influence to a greater or lesser extent nearly every process step along the supply chain, it is not surprising that a multitude of diverging commonality problems is being investigated in literature, each of which are developing a specific algorithm designed for the respective commonality problem being considered. The paper on hand aims at a general framework which is flexible and efficient enough to be applied to a wide range of commonality problems. Such a procedure based on a two-stage graph approach is presented and tested. Finally, flexibility of the procedure is shown by customizing the framework to account for different types of commonality problems.

Variability in the prevalence of adult ADHD in treatment seeking substance use disorder patients: results from an international multi-center study exploring DSM-IV and DSM-5 criteria

Background: Available studies vary in their estimated prevalence of attention deficit/hyperactivity disor-der (ADHD) in substance use disorder (SUD) patients, ranging from 2 to 83%. A better understanding ofthe possible reasons for this variability and the effect of the change from DSM-IV to DSM-5 is needed.Methods: A two stage international multi-center, cross-sectional study in 10 countries, among patientsform inpatient and outpatient addiction treatment centers for alcohol and/or drug use disorder patients. Atotal of 3558 treatment seeking SUD patients were screened for adult ADHD. A subsample of 1276 subjects,both screen positive and screen negative patients, participated in a structured diagnostic interview. 5AdultsResults: Prevalence of DSM-IV and DSM-5 adult ADHD varied for DSM-IV from 5.4% (CI 95%: 2.4–8.3) forHungary to 31.3% (CI 95%:25.2–37.5) for Norway and for DSM-5 from 7.6% (CI 95%: 4.1–11.1) for Hungary to32.6% (CI 95%: 26.4–38.8) for Norway. Using the same assessment procedures in all countries and centersresulted in substantial reduction of the variability in the prevalence of adult ADHD reported in previousstudies among SUD patients (2–83% → 5.4–31.3%). The remaining variability was partly explained byprimary substance of abuse and by country (Nordic versus non-Nordic countries). Prevalence estimatesfor DSM-5 were slightly higher than for DSM-IV.Conclusions: Given the generally high prevalence of adult ADHD, all treatment seeking SUD patientsshould be screened and, after a confirmed diagnosis, treated for ADHD since the literature indicates poorprognoses of SUD in treatment seeking SUD patients with ADHD.

Proceedings of the Seventh Annual Biochemical Engineering Symposium

This is the seventh in a series of symposia devoted to talks by students on their biochemical engineering research. The first four meetings were held alternately at Kansas State University and the University of Nebraska–Lincoln, with participants from those two schools. The next two took place at Kansas State and then in conjunction with the 8lst American Institute of Chemical Engineers National Meeting in Kansas City, with attendees from Kansas State and Iowa State Universities. This meeting, at Iowa State, was the first to include participation from the University of Missouri–Columbia. Contents"Properties of Soluble and In:anoblized Dextransucrase," Hossein Kaboli and Yah Eric Chen, Iowa State University "Growth of Lipid-Producing Organisms on Formic and Acetic Acid-Containing Waste Waters," Lin-Chang Chiang, University of Missouri–Columbia "Design of an Automated Alkaline Copper Reducing Sugar Assay," Alfred R. Fratzke and James R. Frederick, Iowa State University "Determination of Oxygen Transfer Coefficients in Hydrocarbon Fermentations Using a Material Balance Method," Sarafin N. Sanchez and J. R. Gutierrez, Kansas State University "Oxygen Transfer Characteristics in One Stage and Two Stage Air-Lift Towers," Mark E. Orazem, Kansas State University "A Comparison of Biological Digestibility Tests for Cellulose," Dou-Houng Hwang, University of Missouri–Columbia "Mechanism of Enzymatic Hydrolysis of Cellulose," L. T. Fan, Yong-Hyun Lee, and Liang-Shih Fan, Kansas State University "Purification of Xylan-Hydrolyzing Enzymes," James R. Frederick, Alfred R. Fratzke, and Mary M. Frederick, Iowa State University "Cellulase Production from Bagasse and Pith," A. Ferrer, Y. Alroy, and I. Brito, Kansas State University