Setting an optimal α that minimizes errors in null hypothesis significance tests

Null hypothesis significance testing has been under attack in recent years, partly owing to the arbitrary nature of setting α (the decision-making threshold and probability of Type I error) at a constant value, usually 0.05. If the goal of null hypothesis testing is to present conclusions in which we have the highest possible confidence, then the only logical decision-making threshold is the value that minimizes the probability (or occasionally, cost) of making errors. Setting α to minimize the combination of Type I and Type II error at a critical effect size can easily be accomplished for traditional statistical tests by calculating the α associated with the minimum average of α and β at the critical effect size. This technique also has the flexibility to incorporate prior probabilities of null and alternate hypotheses and/or relative costs of Type I and Type II errors, if known. Using an optimal α results in stronger scientific inferences because it estimates and minimizes both Type I errors and relevant Type II errors for a test. It also results in greater transparency concerning assumptions about relevant effect size(s) and the relative costs of Type I and II errors. By contrast, the use of α = 0.05 results in arbitrary decisions about what effect sizes will likely be considered significant, if real, and results in arbitrary amounts of Type II error for meaningful potential effect sizes. We cannot identify a rationale for continuing to arbitrarily use α = 0.05 for null hypothesis significance tests in any field, when it is possible to determine an optimal α.     

'Changing climate, changing health, changing stories' profile: using an EcoHealth approach to explore impacts of climate change on inuit health

Global climate change and its impact on public health exemplify the challenge of managing complexity and uncertainty in health research. The Canadian North is currently experiencing dramatic shifts in climate, resulting in environmental changes which impact Inuit livelihoods, cultural practices, and health. For researchers investigating potential climate change impacts on Inuit health, it has become clear that comprehensive and meaningful research outcomes depend on taking a systemic and transdisciplinary approach that engages local citizens in project design, data collection, and analysis. While it is increasingly recognised that using approaches that embrace complexity is a necessity in public health, mobilizing such approaches from theory into practice can be challenging. In 2009, the Rigolet Inuit Community Government in Rigolet, Nunatsiavut, Canada partnered with a transdisciplinary team of researchers, health practitioners, and community storytelling facilitators to create the Changing Climate, Changing Health, Changing Stories project, aimed at developing a multi-media participatory, community-run methodological strategy to gather locally appropriate and meaningful data to explore climate-health relationships. The goal of this profile paper is to describe how an EcoHealth approach guided by principles of transdisciplinarity, community participation, and social equity was used to plan and implement this climate-health research project. An overview of the project, including project development, research methods, project outcomes to date, and challenges encountered, is presented. Though introduced in this one case study, the processes, methods, and lessons learned are broadly applicable to researchers and communities interested in implementing EcoHealth approaches in community-based research.     

Effects of release method on the survival,somatic growth,and body condition of headstarted turtles

Headstarting involves ex situ rearing of vulnerable life stages, then releasing individuals into the wild once they are larger and less vulnerable to predation. Sometimes, headstarted animals display underdeveloped behaviors that may lead to an acclimation period of reduced survival and growth after release. Using data from a 6-year headstarting program, we tested whether the early release condition affected survival, body condition, and somatic growth rate in 2 groups of headstarted Blanding's turtles (Emydoidea blandingii) released into Rouge National Urban Park (RNUP) in Toronto, Ontario, Canada. The first group included turtles released directly into the wild (i.e., hard release). The second group included turtles released into an in situ enclosure in which individuals remained for a week without food supplementation before being fully released into the wild (i.e., delayed release). Release condition did not affect survival or growth rate. In the delayed-release group, body condition initially declined rapidly and remained low for up to 1 year after release. Given the lack of wild juveniles in RNUP, we compared body condition of headstarted turtles at various time points since release to similar-sized wild juveniles from 2 other Ontario populations, one from Algonquin Provincial Park (APP) and one near Lake Erie (LE). Body condition of headstarted turtles was similar to those of wild APP turtles regardless of release method, and higher than those of wild LE turtles. Our results indicate that delayed release did not improve post-release outcomes for headstarted turtles in an urban landscape and headstarted turtles sustain similar health metrics as wild turtles.     

Effects of chronic NaHCO3 ingestion during interval training on changes to muscle buffer capacity, metabolism, and short-term endurance performance.

This study determined the effects of altering the H(+) concentration during interval training, by ingesting NaHCO(3) (Alk-T) or a placebo (Pla-T), on changes in muscle buffer capacity (beta m), endurance performance, and muscle metabolites. Pre- and posttraining peak O(2) uptake (V(O2 peak)), lactate threshold (LT), and time to fatigue at 100% pretraining V(O2 peak) intensity were assessed in 16 recreationally active women. Subjects were matched on the LT, were randomly placed into the Alk-T (n = 8) or Pla-T (n = 8) groups, and performed 8 wk (3 days/wk) of six to twelve 2-min cycle intervals at 140-170% of their LT, ingesting NaHCO(3) or a placebo before each training session (work matched between groups). Both groups had improvements in beta m (19 vs. 9%; P < 0.05) and V(O2 peak) (22 vs. 17%; P < 0.05) after the training period, with no differences between groups. There was a significant correlation between pretraining beta m and percent change in beta m (r = -0.70, P < 0.05). There were greater improvements in both the LT (26 vs. 15%; P = 0.05) and time to fatigue (164 vs. 123%; P = 0.05) after Alk-T, compared with Pla-T. There were no changes to pre- or postexercise ATP, phosphocreatine, creatine, and intracellular lactate concentrations, or pH(i) after training. Our findings suggest that training intensity, rather than the accumulation of H(+) during training, may be more important to improvements in beta m. The group ingesting NaHCO(3) before each training session had larger improvements in the LT and endurance performance, possibly because of a reduced metabolic acidosis during training and a greater improvement in muscle oxidative capacity.     

The OmpA-like protein Loa22 is essential for leptospiral virulence

Pathogenic mechanisms of Leptospira interrogans, the causal agent of leptospirosis, remain largely unknown. This is mainly due to the lack of tools for genetic manipulations of pathogenic species. In this study, we characterized a mutant obtained by insertion of the transposon Himar1 into a gene encoding a putative lipoprotein, Loa22, which has a predicted OmpA domain based on sequence identity. The resulting mutant did not express Loa22 and was attenuated in virulence in the guinea pig and hamster models of leptospirosis, whereas the genetically complemented strain was restored in Loa22 expression and virulence. Our results show that Loa22 was expressed during host infection and exposed on the cell surface. Loa22 is therefore necessary for virulence of L. interrogans in the animal model and represents, to our knowledge, the first genetically defined virulence factor in Leptospira species.     

Long‐read sequence capture of the haemoglobin gene clusters across codfish species

Combining high‐throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short‐read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long‐read sequencing technology for comparative genomic analyses of the haemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom‐made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100 kb) and MN (~200 kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage‐specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long‐read capture as a versatile approach for comparative genomic studies by generation of a cross‐species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes.     

Road avoidance and its energetic consequences for reptiles

Roads are one of the most widespread human‐caused habitat modifications that can increase wildlife mortality rates and alter behavior. Roads can act as barriers with variable permeability to movement and can increase distances wildlife travel to access habitats. Movement is energetically costly, and avoidance of roads could therefore impact an animal's energy budget. We tested whether reptiles avoid roads or road crossings and explored whether the energetic consequences of road avoidance decreased individual fitness. Using telemetry data from Blanding's turtles (Emydoidea blandingii; 11,658 locations of 286 turtles from 15 sites) and eastern massasaugas (Sistrurus catenatus; 1,868 locations of 49 snakes from 3 sites), we compared frequency of observed road crossings and use of road‐adjacent habitat by reptiles to expected frequencies based on simulated correlated random walks. Turtles and snakes did not avoid habitats near roads, but both species avoided road crossings. Compared with simulations, turtles made fewer crossings of paved roads with low speed limits and more crossings of paved roads with high speed limits. Snakes made fewer crossings of all road types than expected based on simulated paths. Turtles traveled longer daily distances when their home range contained roads, but the predicted energetic cost was negligible: substantially less than the cost of producing one egg. Snakes with roads in their home range did not travel further per day than snakes without roads in their home range. We found that turtles and snakes avoided crossing roads, but road avoidance is unlikely to impact fitness through energetic expenditures. Therefore, mortality from vehicle strikes remains the most significant impact of roads on reptile populations.     

Quantitative assessment of the effects of space allowance, group size and floor characteristics on the lying behaviour of growing-finishing pigs

To obtain quantitative information that can be later used in animal welfare modelling, the relationship between the lying behaviour of growing-finishing pigs (initial body weight (BW) between 19 and 87 kg) and different factors related to the housing conditions, with a potential negative effect on their welfare, was studied by means of a meta-analytical approach. Data from 22 experiments reported in 21 scientific publications were collected. The space allowance, expressed on an allometric basis by means of a k-value (m2/BW0.667), the group size (n) and the floor characteristics (fully and partly slatted v. non-slatted floor), as well as their significant two-way interactions were used as fixed effects, and the experiment was used as a random factor to take into account the interexperiment effect. Further regression analyses were performed on the predicted values of observations in order to improve the adjustment of data. A significant quadratic relationship was established between space allowance (k-value, P < 0.05; squared k-value, P < 0.01) and the percentage of time spent lying. A significant interaction between the k-value and the floor type was also found (P < 0.05), showing that the relationship between space allowance and lying behaviour is affected by the presence or absence of slats. Threshold k-values were obtained using broken-line analyses, being about 0.039 for slatted floors and almost double for non-slatted floors. Compared to other studies, these values suggest that the ability to rest as space availability decreases may be compromised before a reduced performance becomes apparent. Group size did not show a significant effect. Additional information should be added to the model, as further data become available, to adjust the proposed parameters as well as to try to include the effect of other important aspects such as that of ambient temperature.     

A virulence and antimicrobial resistance DNA microarray detects a high frequency of virulence genes in Escherichia coli isolates from Great Lakes recreational waters

Escherichia coli is generally described as a commensal species with occasional pathogenic strains. Due to technological limitations, there is currently little information concerning the prevalence of pathogenic E. coli strains in the environment. For the first time, using a DNA microarray capable of detecting all currently described virulence genes and commonly found antimicrobial resistance genes, a survey of environmental E. coli isolates from recreational waters was carried out. A high proportion (29%) of 308 isolates from a beach site in the Great Lakes carried a pathotype set of virulence-related genes, and 14% carried antimicrobial resistance genes, findings consistent with a potential risk for public health. The results also showed that another 8% of the isolates had unusual virulence gene combinations that would be missed by conventional screening. This new application of a DNA microarray to environmental waters will likely have an important impact on public health, epidemiology, and microbial ecology in the future.