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Partial likelihood, introduced in Cox (1975, Partial likelihood. Biometrika , 62 (2),269–276), formalizes the construction of the inference function developed in Cox (1972, Regression models and life-tables (with discussion). Journal of the Royal Statistical Society Series B , 34 (2),187–220) and referred there to as a conditional likelihood. Partial likelihood can also be viewed as a version of composite likelihood, a different example of which was studied in Cox, and Reid (2004, A note on pseudolikelihood constructed from marginal densities. Biometrika, 91(3),729–737). In this note, I describe the links between partial and composite likelihood, and the connections to profile, marginal, and conditional likelihood. Somewhat tangentially, two recent applications of the Cox proportional hazards model from the medical literature are briefly discussed, as they highlight the model's ongoing relevance while also raising some more general questions about inference. [ABSTRACT FROM AUTHOR]

Skin bacterial communities can protect amphibians from a fungal pathogen; however, little is known about how these communities are maintained. We used a neutral model of community ecology to identify bacteria that are maintained on salamanders by selection or by dispersal from a bacterial reservoir (soil) and ecological drift. We found that 75% (9/12) of bacteria that were consistent with positive selection,

Beneficial cutaneous bacteria on amphibians can protect against the lethal disease chytridiomycosis, which has devastated many amphibian species and is caused by the fungus Batrachochytrium dendrobatidis. We describe the diversity of bacteria on red-backed salamanders (Plethodon cinereus) in the wild and the stability of these communities through time in captivity using culture-independent Illumina 16S rRNA gene sequencing. After field sampling, salamanders were housed with soil from the field or sterile media. The captive conditions led to different trajectories of bacterial communities. Eight OTUs present on >90% of salamanders in the field, through time, and in both treatments were defined as the core community, suggesting that some bacteria are closely associated with the host and are independent of an environmental reservoir. One of these taxa, a Pseudomonas sp., was previously cultured from amphibians and found to be antifungal. As all host-associated bacteria were found in the soil reservoir, environmental microbes strongly influence host-microbial diversity and likely regulate the core community. Using PICRUSt, an exploratory bioinformatics tool to predict gene functions, we found that core skin bacteria provided similar gene functions to the entire community. We suggest that future experiments focus on testing whether core bacteria on salamander skin contribute to the observed resistance to chytridiomycosis in this species even under hygenic captive conditions. For disease-susceptible hosts, providing an environmental reservoir with defensive bacteria in captive-rearing programs may improve outcomes by increasing bacterial diversity on threatened amphibians or increasing the likelihood that defensive bacteria are available for colonization.

Frances O’Callaghan,1 Olav Muurlink,2,3 Natasha Reid4 1School of Applied Psychology, Griffith Health, Griffith University, Southport, QLD, Australia; 2School of Business and Law, Central Queensland University, Brisbane, QLD, Australia; 3Griffith Institute for Educational Research, Griffith University, Southport, QLD, Australia; 4Child Health Research Centre, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia Abstract: Caffeine (particularly in the form of coffee) is one of the most widely consumed stimulants in the world, with 90% of American adults consuming caffeine-infused beverages almost daily. While there is substantial evidence that caffeine enhances performance, caffeine withdrawal leads to deficits at both the individual (eg, cognitive, emotional, and behavioral processes) and societal (eg, increases in work accidents) level. Scholars for some time have considered that the supposed psychoactive benefits of caffeine may be the result of the mere reversal of deleterious effects of caffeine withdrawal, rather than a net benefit of caffeine ingestion. In this integrative review, we examine evidence illuminating the relationship between caffeine consumption and subsequent quality and quantity of nighttime rest. Secondly, we consider evidence as to whether performance deficits caused by sleep deprivation linked to caffeine can be reversed by caffeine consumption during the subsequent daytime period. Finally, we consider how these two stages can be reconciled in a single model that enables calculation of the net caffeine effect on daytime functioning. The literature highlights a range of positive impacts of caffeine consumption on both physical and cognitive functioning. There are also a number of factors that complicate any conclusions that can be drawn regarding the potential of caffeine to improve performance. Most critically, performance improvements the next day may simply be a result of the reversal of caffeine withdrawal. Animal studies and well-controlled human studies involving high habitual and low habitual users tend to confirm a “net benefit” for caffeine use. Further research, particularly with (necessarily rare) caffeine-naive populations, is required to elucidate the complexities of the relationship between caffeine, sleep, and daytime functioning. However, the convenience of accessing caffeine compared to ensuring adequate restorative sleep means that caffeine has applied advantages that are likely to see its use as a performance “enhancing” substance persist. Keywords: caffeine, daytime functioning, sleep, sleep deprivation

Abstract Novel outbreaks of emerging pathogens require rapid responses to enable successful mitigation. We simulated a 1‐day emergency meeting where experts were engaged to recommend mitigation strategies for a new outbreak of the amphibian fungal pathogen Batrachochytrium salamandrivorans. Despite the inevitable uncertainty, experts suggested and discussed several possible strategies. However, their recommendations were undermined by imperfect initial definitions of the objectives and scope of management. This problem is likely to arise in most real‐world emergency situations. The exercise thus highlighted the importance of clearly defining the context, objectives, and spatial–temporal scale of mitigation decisions. Managers are commonly under pressure to act immediately. However, an iterative process in which experts and managers cooperate to clarify objectives and uncertainties, while collecting more information and devising mitigation strategies, may be slightly more time consuming but ultimately lead to better outcomes.

The author comments on the article "The Anticipated and Actual Impact of Apology Laws: How Much Is an Apology Worth?," by Leah D. B. Carter published within the issue. It discusses the functions of the medical liability system, the lack of correlation between malpractice suits and quality of care, and the consequences of medical error disclosure and apology laws for the healthcare system in general.