Comparison of Tukey's T-Method and Scheffé's S-Method for Various Numbers of All Possible Differences of Averages Contrasts Under Violation of Assumptions

Empirical .05 and .01 rates of Type I error were compared for the Tukey and Scheffé multiple comparison techniques. The experimentwise error rate was defined over five sets of the all possible 25 differences of averages contrasts. The robustness of the Tukey and Scheffé statistics was not only related to the type of assumption violation, but also to the sets containing different numbers of contrasts. The Tukey method could be judged as robust a statistic as the Scheffé method.Yeshttps://us.sagepub.com/en-us/nam/manuscript-submission-guideline

Towards Machine Wald

The past century has seen a steady increase in the need of estimating and predicting complex systems and making (possibly critical) decisions with limited information. Although computers have made possible the numerical evaluation of sophisticated statistical models, these models are still designed \emph{by humans} because there is currently no known recipe or algorithm for dividing the design of a statistical model into a sequence of arithmetic operations. Indeed enabling computers to \emph{think} as \emph{humans} have the ability to do when faced with uncertainty is challenging in several major ways: (1) Finding optimal statistical models remains to be formulated as a well posed problem when information on the system of interest is incomplete and comes in the form of a complex combination of sample data, partial knowledge of constitutive relations and a limited description of the distribution of input random variables. (2) The space of admissible scenarios along with the space of relevant information, assumptions, and/or beliefs, tend to be infinite dimensional, whereas calculus on a computer is necessarily discrete and finite. With this purpose, this paper explores the foundations of a rigorous framework for the scientific computation of optimal statistical estimators/models and reviews their connections with Decision Theory, Machine Learning, Bayesian Inference, Stochastic Optimization, Robust Optimization, Optimal Uncertainty Quantification and Information Based Complexity.Comment: 37 page

Human epididymis protein 4 reference limits and natural variation in a Nordic reference population

The objectives of this study are to establish reference limits for human epididymis protein 4, HE4, and investigate factors influencing HE4 levels in healthy subjects. HE4 was measured in 1,591 samples from the Nordic Reference Interval Project Bio-bank and Database biobank, using the manual HE4 EIA (Fujirebio) for 802 samples and the Architect HE4 (Abbott) for 792 samples. Reference limits were calculated using the statistical software R. The influence of donor characteristics such as age, sex, body mass index, smoking habits, and creatinine on HE4 levels was investigated using a multivariate model. The study showed that age is the main determinant of HE4 in healthy subjects, corresponding to 2% higher HE4 levels at 30 years (compared to 20 years), 9% at 40 years, 20% at 50 years, 37% at 60 years, 63% at 70 years, and 101% at 80 years. HE4 levels are 29% higher in smokers than in nonsmokers. In conclusion, HE4 levels in healthy subjects are associated with age and smoking status. Age-dependent reference limits are suggested

Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling

Background: The human pathogen Listeria monocytogenes resides and proliferates within the cytoplasm of epithelial cells. While the virulence factors essentially contributing to this step of the infection cycle are well characterized, the set of listerial genes contributing to intracellular replication remains to be defined on a genome-wide level. Results: A comprehensive library of L. monocytogenes strain EGD knockout mutants was constructed upon insertion-duplication mutagenesis, and 1491 mutants were tested for their phenotypes in rich medium and in a Caco-2 cell culture assay. Following sequencing of the plasmid insertion site, 141 different genes required for invasion of and replication in Caco-2 cells were identified. Ten in-frame deletion mutants were constructed that confirmed the data. The genes with known functions are mainly involved in cellular processes including transport, in the intermediary metabolism of sugars, nucleotides and lipids, and in information pathways such as regulatory functions. No function could be ascribed to 18 genes, and a counterpart of eight genes is missing in the apathogenic species L. innocua. Mice infection studies revealed the in vivo requirement of IspE (Lmo0190) involved in mevalonate synthesis, and of the novel ABC transporter Lmo0135-0137 associated with cysteine transport. Based on the data of this genome-scale screening, an extreme pathway and elementary mode analysis was applied that demonstrates the critical role of glycerol and purine metabolism, of fucose utilization, and of the synthesis of glutathione, aspartate semialdehyde, serine and branched chain amino acids during intracellular replication of L. monocytogenes. Conclusion: The combination of a genetic screening and a modelling approach revealed that a series of transporters help L. monocytogenes to overcome a putative lack of nutrients within cells, and that a high metabolic flexibility contributes to the intracellular replication of this pathogen

Blended Clustering for Health Data Mining

Exploratory data analysis using data mining techniques is becoming more popular for investigating subtle relationships in health data, for which direct data collection trials would not be possible. Health data mining involving clustering for large complex data sets in such cases is often limited by insufficient key indicative variables. When a conventional clustering technique is then applied, the results may be too imprecise, or may be inappropriately clustered according to expectations. This paper suggests an approach which can offer greater range of choice for generating potential clusters of interest, from which a better outcome might in turn be obtained by aggregating the results. An example use case based on health services utilization characterization according to socio-demographic background is discussed and the blended clustering approach being taken for it is described

Genetic Variations and Haplotype Diversity of the UGT1 Gene Cluster in the Chinese Population

Vertebrates require tremendous molecular diversity to defend against numerous small hydrophobic chemicals. UDP-glucuronosyltransferases (UGTs) are a large family of detoxification enzymes that glucuronidate xenobiotics and endobiotics, facilitating their excretion from the body. The UGT1 gene cluster contains a tandem array of variable first exons, each preceded by a specific promoter, and a common set of downstream constant exons, similar to the genomic organization of the protocadherin (Pcdh), immunoglobulin, and T-cell receptor gene clusters. To assist pharmacogenomics studies in Chinese, we sequenced nine first exons, promoter and intronic regions, and five common exons of the UGT1 gene cluster in a population sample of 253 unrelated Chinese individuals. We identified 101 polymorphisms and found 15 novel SNPs. We then computed allele frequencies for each polymorphism and reconstructed their linkage disequilibrium (LD) map. The UGT1 cluster can be divided into five linkage blocks: Block 9 (UGT1A9), Block 9/7/6 (UGT1A9, UGT1A7, and UGT1A6), Block 5 (UGT1A5), Block 4/3 (UGT1A4 and UGT1A3), and Block 3′ UTR. Furthermore, we inferred haplotypes and selected their tagSNPs. Finally, comparing our data with those of three other populations of the HapMap project revealed ethnic specificity of the UGT1 genetic diversity in Chinese. These findings have important implications for future molecular genetic studies of the UGT1 gene cluster as well as for personalized medical therapies in Chinese

Time in a Bottle: The Evolutionary Fate of Species Discrimination in Sibling Drosophila Species

Disadvantageous hybridization favors the evolution of prezygotic isolating behaviors, generating a geographic pattern of interspecific mate discrimination where members of different species drawn from sympatric populations exhibit stronger preference for members of their own species than do individuals drawn from allopatric populations. Geographic shifts in species' boundaries can relax local selection against hybridization; under such scenarios the fate of enhanced species preference is unknown. Lineages established from populations in the region of sympatry that have been maintained as single-species laboratory cultures represent cases where allopatry has been produced experimentally. Using such cultures dating from the 1950s, we assess how Drosophila pseudoobscura and D. persimilis mate preferences respond to relaxed natural selection against hybridization. We found that the propensity to hybridize generally declines with increasing time in experimental allopatry, suggesting that maintaining enhanced preference for conspecifics may be costly. However, our data also suggest a strong role for drift in determining mating preferences once secondary allopatry has been established. Finally, we discuss the interplay between populations in establishing the presence or absence of patterns consistent with reinforcement

The physical and mental health of a large military cohort: baseline functional health status of the Millennium Cohort

<p>Abstract</p> <p>Background:</p> <p>The US military is currently involved in large, lengthy, and complex combat operations around the world. Effective military operations require optimal health of deployed service members, and both mental and physical health can be affected by military operations.</p> <p>Methods:</p> <p>Baseline data were collected from 77,047 US service members during 2001–2003 as part of a large, longitudinal, population-based military health study (the Millennium Cohort Study). The authors calculated unadjusted, adjusted, and weighted means for the Medical Outcomes Study Short Form 36-item Survey for Veterans physical (PCS) and mental component summary (MCS) scores over a variety of demographic and military characteristics at baseline.</p> <p>Results:</p> <p>The unadjusted mean PCS and MCS scores for this study were 53.4 (95% confidence interval: 53.3–53.4) and 52.8 (95% confidence interval: 52.7–52.9). Average PCS and MCS scores were slightly more favorable in this military sample compared to those of the US general population of the same age and sex. Factors independently associated with more favorable health status included male gender, being married, higher educational attainment, higher military rank, and Air Force service. Combat specialists had similar health status compared to other military occupations. Having been deployed to Southwest Asia, Bosnia, or Kosovo between 1998 and 2000 was not associated with diminished health status.</p> <p>Conclusion:</p> <p>The baseline health status of this large population-based military cohort is better than that of the US general population of the same age and sex distribution over the same time period, especially in older age groups. Deployment experiences during the period of 1998–2001 were not associated with decreased health status. These data will serve as a useful reference for other military health studies and for future longitudinal analyses.</p

Flanker performance in female college students with ADHD: a diffusion model analysis

Attention-deficit hyperactivity disorder (ADHD) is characterized by poor adaptation to environmental demands, which leads to various everyday life problems. The present study had four aims: (1) to compare performance in a flanker task in female college students with and without ADHD (N = 39) in a classical analyses of reaction time and error rate and studying the underlying processes using a diffusion model, (2) to compare the amount of focused attention, (3) to explore the adaptation of focused attention, and (4) to relate adaptation to psychological functioning. The study followed a 2-between (group: ADHD vs. control) × 2-within (flanker conflict: incongruent vs. congruent) × 2-within (conflict frequency: 20 vs. 80 %) design. Compared to a control group, the ADHD group displayed prolonged response times accompanied by fewer errors in a flanker task. Results from the diffusion model analyses revealed that the members of the ADHD group showed deficits in non-decisional processes (i.e., higher non-decision time) and leaned more toward accuracy than participants without ADHD (i.e., setting higher boundaries). The ADHD group showed a more focused attention and less adaptation to the task conditions which is related to psychological functioning. Deficient non-decisional processes and poor adaptation are in line with theories of ADHD and presumably typical for the ADHD population, although this has not been shown using a diffusion model. However, we assume that the cautious strategy of trading speed of for accuracy is specific to the subgroup of female college students with ADHD and might be interpreted as a compensation mechanism