This paper presents new biostatistical methods for the analysis of microbiome data based on a fully parametric approach using all the data. The Dirichlet-multinomial distribution allows the analyst to calculate power and sample sizes for experimental design, perform tests of hypotheses (e.g., compare microbiomes across groups), and to estimate parameters describing microbiome properties. The use of a fully parametric model for these data has the benefit over alternative non-parametric approaches such as bootstrapping and permutation testing, in that this model is able to retain more information contained in the data. This paper details the statistical approaches for several tests of hypothesis and power/sample size calculations, and applies them for illustration to taxonomic abundance distribution and rank abundance distribution data using HMP Jumpstart data on 24 subjects for saliva, subgingival, and supragingival samples. Software for running these analyses is available.

Strength is a critical factor in the health and job performance of police officers. Using a retrospective longitudinal design, the purpose of this study was to identify differences in strength scores from initial recruitment to in-service tests and to compare gender differences. Strength changes were also compared in low- to high-strength groups. Strength scores included bench press, bench press/lean weight, and bench press/weight. Body weight, percent body fat, and bench press scores were retrieved for the 1990-1995 recruit classes and were paired to most recent scores on 2006 in-service fitness record. Sample included 327 police officers: 30 females and 297 males. Mean age at initial recruitment was 24.6 years and for in-service was 37.1 years. Average time between tests was 12.5 years. Over this period bench press and bench press/lean weight significantly increased for both gender groups (p

Catchment and riparian degradation has resulted in declining ecosystem health of streams worldwide. With restoration a priority in many regions, there is an increasing interest in the scale at which land use influences stream ecosystem health. Our goal was to use a substantial data set collected as part of a monitoring program (the Southeast Queensland, Australia, Ecological Health Monitoring Program data set, collected at 116 sites over six years) to identify the spatial scale of land use, or the combination of spatial scales, that most strongly influences overall ecosystem health. In addition, we aimed to determine whether the most influential scale differed for different aspects of ecosystem health. We used linear-mixed models and a Bayesian model-averaging approach to generate models for the overall aggregated ecosystem health score and for each of the five component indicators (fish, macroinvertebrates, water quality, nutrients, and ecosystem processes) that make up the score. Dense forest close to the survey site, mid-dense forest in the hydrologically active near-stream areas of the catchment, urbanization in the riparian buffer, and tree cover at the reach scale were all significant in explaining ecosystem health, suggesting an overriding influence of forest cover, particularly close to the stream. Season and antecedent rainfall were also important explanatory variables, with some land-use variables showing significant seasonal interactions. There were also differential influences of land use for each of the component indicators. Our approach is useful given that restoring general ecosystem health is the focus of many stream restoration projects; it allowed us to predict the scale and catchment position of restoration that would result in the greatest improvement of ecosystem health in the regions streams and rivers. The models we generated suggested that good ecosystem health can be maintained in catchments where 80% of hydrologically active areas in close proximity to the stream have mid-dense forest cover and moderate health can be obtained with 60% cover.

In this study, relationships between flow variation across multiple temporal scales and the distribution and abundance of three fish species, western rainbowfish Melanotaenia australis, sooty grunter Hephaestus fuliginosus and barramundi Lates calcarifer were examined at eight sampling reaches in the Daly River, Northern Territory, Australia. Discharge was highly seasonal during the study period of 2006-2010 with a distinct wet-dry discharge pattern. Significant catchment-wide correlations were identified between species abundance and hydrologic variables across several scales describing the magnitude and variability of flow. A Bayesian hierarchical model which accounted for >80% of variation in abundances for all species and age classes (i.e. juvenile and adult), identified the extent to which the influence of short-term flow variation was dependent upon the historical flow regime. There were distinct ontogenetic differences in these relationships for H. fuliginosus, with variability of recent flows having a negative effect on juveniles which was stronger at locations with higher historical mean daily flow. Lates calcarifer also displayed ontogenetic differences in relationships to flow variation with adults showing a positive association with increase in recent flows and juveniles showing a negative one. The effect of increased magnitude of wet-season flows on M. australis was negative in locations with lower historical mean daily flow but positive in locations with higher historical mean daily flow. The results highlighted how interactions between multiple scales of flow variability influence the abundance of fish species according to their life-history requirements.

Background Previous diffusion tensor imaging (DTI) studies have consistently shown that subjects with cocaine use disorder (CocUD) had altered white matter microstructure in the corpus callosum. It is believed that these alterations are due to preexisting factors, chronic cocaine use, or both. However, there is no published longitudinal DTI study on human cocaine users yet which could shed light on the relationship between cocaine use and DTI findings. Methods This study used a longitudinal design and DTI to test if the white matter microstructure shows quicker alteration in CocUD subjects than controls. DTI data were acquired from eleven CocUD subjects who participated a treatment study and eleven non-drug-using controls at baseline (Scan 1) and after ten weeks (Scan 2). The baseline fractional anisotropy (FA), a general measure of white matter microstucture, and the change in FA (ΔFA, equals Scan 1 FA minus Scan 2 FA) were both compared between groups. Results The two groups did not show a difference in FA at baseline. The CocUD subjects had significantly greater ΔFA than the controls in the left splenium of the corpus callosum. In CocUD subjects, greater ΔFA in this region was associated with shorter lifetime cocaine use and greater number of positive cocaine urine samples collected during the treatment. Conclusion The finding in the left splenium is consistent with previous animal studies and provide indirect evidence about the effects of chronic cocaine use on white matter alterations. The subject sample size is small, therefore the results should be treated as preliminary.