Moderated statistical tests for assessing differences in tag abundance

MOTIVATION: Digital gene expression (DGE) technologies measure gene expression by counting sequence tags. They are sensitive technologies for measuring gene expression on a genomic scale, without the need for prior knowledge of the genome sequence. As the cost of sequencing DNA decreases, the number of DGE datasets is expected to grow dramatically. Various tests of differential expression have been proposed for replicated DGE data using binomial, Poisson, negative binomial or pseudo-likelihood (PL) models for the counts, but none of the these are usable when the number of replicates is very small. RESULTS: We develop tests using the negative binomial distribution to model overdispersion relative to the Poisson, and use conditional weighted likelihood to moderate the level of overdispersion across genes. Not only is our strategy applicable even with the smallest number of libraries, but it also proves to be more powerful than previous strategies when more libraries are available. The methodology is equally applicable to other counting technologies, such as proteomic spectral counts. AVAILABILITY: An R package can be accessed from http://bioinf.wehi.edu.au/resources/     

A questionnaire technique for assessing the stress at work

Subjective perception of the stress at work is a phenomenon reflecting the experience-mediated relationship between the sum of objective conditions of work and the sum of individual's traits available to cope with demands of the work environment. This relationship is mirrored in the function of the whole organism and can be described using the formula S = f (E, D), where S = the state of the organism, E = exposure (i.e. the sum of all stressors the organism is exposed to), and D = disposition (i.e. the sum of traits the organism has available to cope with these stressors). Based on these theoretical considerations, a questionnaire has been developed as a tool for assessing the work stress in different groups of occupations. This "Work Stress Assessment" (WSA) questionnaire was used in a group of 4800 female employees from various branches of the printing industry. Of a total of 160 questionnaire items, 98 items were selected and used to assess the workload in these employees, using a 5-point rating scale of evaluation. The responses were processed statistically, separately for 3531 blue-collar and 1269 white-collar respondents. The use of the factor analysis method revealed that the two groups of jobs had 16 factors in common, 3 factors were specific for blue-collar and 2 factors for white-collar jobs. Judged by factor components, the responses of subjects were well structured and the perceived stress at work turned out to well reflect the reality of conditions of work, which confirms the construct validity of this methodical approach based on the subjective perception of occupational stress. High coefficients of consistency (0.959 for blue-collar and 0.946 for white-collar occupations) point to the reliability of this questionnaire technique. Thus, the WSA questionnaire appears to suitably complement the other methodical approaches aimed at assessing the stress at work in different groups of occupations.     

Latent likelihood ratio tests for assessing spatial kernels in epidemic models

One of the most important issues in the critical assessment of spatio-temporal stochastic models for epidemics is the selection of the transmission kernel used to represent the relationship between infectious challenge and spatial separation of infected and susceptible hosts. As the design of control strategies is often based on an assessment of the distance over which transmission can realistically occur and estimation of this distance is very sensitive to the choice of kernel function, it is important that models used to inform control strategies can be scrutinised in the light of observation in order to elicit possible evidence against the selected kernel function. While a range of approaches to model criticism is in existence, the field remains one in which the need for further research is recognised. In this paper, building on earlier contributions by the authors, we introduce a new approach to assessing the validity of spatial kernels—the latent likelihood ratio tests—which use likelihood-based discrepancy variables that can be used to compare the fit of competing models, and compare the capacity of this approach to detect model mis-specification with that of tests based on the use of infection-link residuals. We demonstrate that the new approach can be used to formulate tests with greater power than infection-link residuals to detect kernel mis-specification particularly when the degree of mis-specification is modest. This new tests avoid the use of a fully Bayesian approach which may introduce undesirable complications related to computational complexity and prior sensitivity.

     

Clustering-neural network models for freeway work zone capacity estimation

Two neural network models, called clustering-RBFNN and clustering-BPNN models, are created for estimating the work zone capacity in a freeway work zone as a function of seventeen different factors through judicious integration of the subtractive clustering approach with the radial basis function (RBF) and the backpropagation (BP) neural network models. The clustering-RBFNN model has the attractive characteristics of training stability, accuracy, and quick convergence. The results of validation indicate that the work zone capacity can be estimated by clustering-neural network models in general with an error of less than 10%, even with limited data available to train the models. The clustering-RBFNN model is used to study several main factors affecting work zone capacity. The results of such parametric studies can assist work zone engineers and highway agencies to create effective traffic management plans (TMP) for work zones quantitatively and objectively.     

Sleep disorders and medical work capacity

Excessive daily sleepiness attribute to sleep disturbances can be a problem for occupational physician concerning the work ability to security works, night shift work and vehicle driving. It's difficult to detect those pathologies because the workers don't identify their symptoms as serious diseases or because they mask these symptoms for fear of the loose of their job. We've studied one case of SAS (sleep apnea syndrome) and one case of narcolepsy to demonstrate: 1) the criterions of the occupational forecast; 2) the sometimes serious social and occupational consequences of a medical inaptitude sanction. We insist on the necessity of a good collaboration between general practitioner and occupational physician.     

A quantitative matrigel assay for assessing repopulating capacity of prostate stem cells

Homeostasis of prostate tissue is maintained by stem cells, although such cells have not been well characterized. Here, we report establishment of such a method using matrigel. Matrigel containing a single-cell suspension from adult prostatic cells was subcutaneously grafted into the flank of nude mice. Prostatic duct-like structures derived from donor tissue were observed in the gel 2 weeks after transplantation. Luminal and basal cells observed in the gel expressed several markers characteristic of prostatic and/or epithelial cells. When a mixture with both EGFP-positive and negative prostate cells was transplanted, prostatic ducts consisted of either EGFP-positive or negative cells and chimeric patterns were rarely observed, suggesting that ducts were reconstituted from a single cell. Stem cell number and function were also evaluated by competition with control cells. Overall this method revealed that cells localized in the proximal portion in prostate ducts had higher reconstitution capacity than those in the distal portion. We conclude that prostate stem/progenitor cells exist and that our method is applicable to analysis of prostate stem cells, epithelial mesenchyme interactions, and prostate cancer stem cells.     

Nutritional status and physical work capacity

The functional consequences of nutritional intake and resulting nutritional status are reviewed in terms of maximal oxygen consumption, physical work capacity, heart rate response to exercise, work productivity, and endurance at submaximal work loads. The results of both acute “laboratory” and chronic “naturally occurring” malnutrition are considered as well as the effects of dietary supplementation and recovery from previously existing undernutrition. Obesity and anemia are also treated as separate but related nutritional entities.     

Batch tests for assessing decolourisation of azo dyes by methanogenic and mixed cultures

Most of the published studies on azo dye colour removal involve anaerobic mixed cultures and there is some interest in the knowledge of how dye reduction occurs, if by facultative, strictly anaerobic or both bacterial trophic groups present in classic anaerobic digestors. This paper describes the behaviour of methanogenic and mixed bacteria cultures on the colour removal in batch systems, of a commercial azo dye, C.I. Acid Orange 7, used in paper and textile industries. The aim of this study is to demonstrate, by analysing dye decolourisation, that it occurs with mixed cultures as well as with strictly anaerobic (methanogenic) cultures. Tests were performed with a range of dye concentrations between 60 and 300 mg l⁻¹. The influence of dye concentration on the carbon source removal and decolourisation processes was studied. The effect of carbon source concentration on colour removal was also analysed for both cultures. The degradation rates in mixed and methanogenic cultures were compared. The consumption of carbon source was monitored by COD analysis and dye degradation by ultraviolet-visible spectrophotometry and thin layer chromatography.     

Validity of the dictionary of occupational titles for assessing upper extremity work demands

Objectives

The Dictionary of Occupational Titles (DOT) is used in vocational rehabilitation to guide decisions about the ability of a person with activity limitations to perform activities at work. The DOT has categorized physical work demands in five categories. The validity of this categorization is unknown. Aim of this study was to investigate whether the DOT could be used validly to guide decisions for patients with injuries to the upper extremities. Four hypotheses were tested.

Methods

A database including 701 healthy workers was used. All subjects filled out the Dutch Musculoskeletal Questionnaire, from which an Upper Extremity Work Demands score (UEWD) was derived. First, relation between the DOT-categories and UEWD-score was analysed using Spearman correlations. Second, variance of the UEWD-score in occupational groups was tested by visually inspecting boxplots and assessing kurtosis of the distribution. Third, it was investigated whether occupations classified in one DOT-category, could significantly differ on UEWD-scores. Fourth, it was investigated whether occupations in different DOT-categories could have similar UEWD-scores using Mann Whitney U-tests (MWU).

Results

Relation between the DOT-categories and the UEWD-score was weak (r_sp = 0.40; p<.01). Overlap between categories was found. Kurtosis exceeded ±1.0 in 3 occupational groups, indicating large variance. UEWD-scores were significantly different within one DOT-category (MWU = 1.500; p<.001). UEWD scores between DOT-categories were not significantly different (MWU = 203.000; p = .49).

Conclusion

All four hypotheses could not be rejected. The DOT appears to be invalid for assessing upper extremity work demands.     

Increased chronic acceleration exposure enhances work capacity

Adult male chickens adapted to 1.75 or 2.5 G from long term centrifugation, were maximally exercised on an animal treadmill at 1 g (Earth's gravity) and compared with the exercise capacities of control chickens raised at 1 g. The increased-G birds had statistically significantly greater exercise capacities than the controls during the first 3 weeks of the study after the initial exercise exposure. Thereafter however for the following two months of the study, there was no difference in either group's exercise capacities. This early increased work capacity was attributed to the increased-G birds improved ability to maximize their muscular strength with neurological adaptation. The increased-G birds lost body mass at a 31% greater rate during exercise than the controls although this difference was not statistically significant. This increased body mass loss was considered to have resulted from increased use of glycogen during exercise.