Full Open Population Capture-Recapture Models with Individual Covariates

Traditional analyses of capture-recapture data are based on likelihood functions that explicitly integrate out all missing data. We use a complete data likelihood (CDL) to show how a wide range of capture-recapture models can be easily fitted using readily available software JAGS/BUGS even when there are individual-specific time-varying covariates. The models we describe extend those that condition on first capture to include abundance parameters, or parameters related to abundance, such as population size, birth rates or lifetime. The use of a CDL means that any missing data, including uncertain individual covariates, can be included in models without the need for customized likelihood functions. This approach also facilitates modeling processes of demographic interest rather than the complexities caused by non-ignorable missing data. We illustrate using two examples, (i) open population modeling in the presence of a censored time-varying individual covariate in a full robust-design, and (ii) full open population multi-state modeling in the presence of a partially observed categorical variable

Extending the Latent Multinomial Model with Complex Error Processes and Dynamic Markov Bases

The latent multinomial model (LMM) model of Link et al. (2010) provided a general framework for modelling mark-recapture data with potential errors in identification. Key to this approach was a Markov chain Monte Carlo (MCMC) scheme for sampling possible configurations of the counts true capture histories that could have generated the observed data. This MCMC algorithm used vectors from a basis for the kernel of the linear map between the true and observed counts to move between the possible configurations of the true data. Schofield and Bonner (2015) showed that a strict basis was sufficient for some models of the errors, including the model presented by Link et al. (2010), but a larger set called a Markov basis may be required for more complex models. We address two further challenges with this approach: 1) that models with more complex error mechanisms do not fit easily within the LMM and 2) that the Markov basis can be difficult or impossible to compute for even moderate sized studies. We address these issues by extending the LMM to separately model the capture/demographic process and the error process and by developing a new MCMC sampling scheme using dynamic Markov bases. Our work is motivated by a study of Queen snakes (Regina septemvittata) in Kentucky, USA, and we use simulation to compare the use of PIT tags, with perfect identification, and brands, which are prone to error, when estimating survival rates

The early life microbiota protects neonatal mice from pathological small intestinal epithelial cell shedding

The early life gut microbiota plays a crucial role in regulating and maintaining the intestinal barrier, with disturbances in these communities linked to dysregulated renewal and replenishment of intestinal epithelial cells. Here we sought to determine pathological cell shedding outcomes throughout the postnatal developmental period, and which host and microbial factors mediate these responses. Surprisingly, neonatal mice (Day 14 and 21) were highly refractory to induction of cell shedding after intraperitoneal administration of liposaccharide (LPS), with Day 29 mice showing strong pathological responses, more similar to those observed in adult mice. These differential responses were not linked to defects in the cellular mechanisms and pathways known to regulate cell shedding responses. When we profiled microbiota and metabolites, we observed significant alterations. Neonatal mice had high relative abundances of Streptococcus, Escherichia, and Enterococcus and increased primary bile acids. In contrast, older mice were dominated by Candidatus Arthromitus, Alistipes, and Lachnoclostridium, and had increased concentrations of SCFAs and methyamines. Antibiotic treatment of neonates restored LPS-induced small intestinal cell shedding, whereas adult fecal microbiota transplant alone had no effect. Our findings further support the importance of the early life window for microbiota-epithelial interactions in the presence of inflammatory stimuli and highlights areas for further investigation

De novo resistance to arg10-teixobactin occurs slowly and is costly

ABSTRACT Bacterial pathogens are rapidly evolving resistance to all clinically available antibiotics. One part of the solution to this complex issue is to better understand the resistance mechanisms to new and existing antibiotics. Here, we focus on two antibiotics. Teixobactin is a recently discovered promising antibiotic that is claimed to “kill pathogens without detectable resistance” (L. L. Ling, T. Schneider, A. J. Peoples, A. L. Spoering, et al., Nature 517:455– 459, 2015, https://doi.org/10.1038/nature14098). Moenomycin A has been extensively used in animal husbandry for over 50 years with no meaningful antibiotic resistance arising. However, the nature, mechanisms, and consequences of the evolution of resistance to these “resistance-proof” compounds have not been investigated. Through a fusion of experimental evolution, whole-genome sequencing, and structural biology, we show that Staphylococcus aureus can develop significant resistance to both antibiotics in clinically meaningful timescales. The magnitude of evolved resistance to Arg10-teixobactin is 300-fold less than to moenomycin A over 45 days, these are 2,500-fold and 8-fold less than evolved resistance to rifampicin (control), respectively. We have identified a core suite of key mutations, which correlate with the evolution of resistance, that are in genes involved in cell wall modulation, lipid synthesis, and energy metabolism. We show the evolution of resistance to these antimicrobials translates into significant cross-resistance against other clinically relevant antibiotics for moenomycin A but not Arg10-teixobactin. Lastly, we show that resistance is rapidly lost in the absence of antibiotic selection, especially for Arg10-teixobactin. These findings indicate that teixobactin is worth pursuing for clinical applications and provide evidence to inform strategies for future compound development and clinical managemen

A response to Rome: lessons from pre- and post-publication data-sharing in the C. elegans research community

<p>Abstract</p> <p>Background</p> <p>In recent years numerous studies have undertaken to measure the impact of patents, material transfer agreements, data-withholding and commercialization pressures on biomedical researchers. Of particular concern is the theory that such pressures may have negative effects on academic and other upstream researchers. In response to these concerns, commentators in some research communities have called for an increased level of access to, and sharing of, data and research materials. We have been studying how data and materials are shared in the community of researchers who use the nematode <it>Caenorhabditis elegans </it>(<it>C. elegans</it>) as a model organism for biological research. Specifically, we conducted a textual analysis of academic articles referencing <it>C. elegans</it>, reviewed <it>C. elegans </it>repository request lists, scanned patents that reference <it>C. elegans </it>and conducted a broad survey of <it>C. elegans </it>researchers. Of particular importance in our research was the role of the <it>C. elegans </it>Gene Knockout Consortium in the facilitation of sharing in this community.</p> <p>Results</p> <p>Our research suggests that a culture of sharing exists within the <it>C. elegans </it>research community. Furthermore, our research provides insight into how this sharing operates and the role of the culture that underpins it.</p> <p>Conclusions</p> <p>The greater scientific community is likely to benefit from understanding the factors that motivate <it>C. elegans </it>researchers to share. In this sense, our research is a 'response' to calls for a greater amount of sharing in other research communities, such as the mouse community, specifically, the call for increased investment and support of centralized resource sharing infrastructure, grant-based funding of data-sharing, clarity of third party recommendations regarding sharing, third party insistence of post-publication data sharing, a decrease in patenting and restrictive material transfer agreements, and increased attribution and reward.</p

The Antarctic ozone hole during 2014

We review the 2014 Antarctic ozone hole, making use of a variety of ground-based and space-based measurements of ozone and ultra-violet radiation, supplemented by meteorological reanalyses. Although the polar vortex was relatively stable in 2014 and persisted some weeks longer into November than was the case in 2012 or 2013, the vortex temperature was close to the long-term mean in September and October with modest warming events occurring in both months, preventing severe depletion from taking place. Of the seven metrics reported here, all were close to their respective median values of the 1979–2014 record, being ranked between 16th and 21st of the 35 years for which adequate satellite observations exist

The Antarctic ozone hole during 2015 and 2016

We reviewed the 2015 and 2016 Antarctic ozone holes, making use of a variety of ground-based and spacebased measurements of ozone and ultraviolet radiation, supplemented by meteorological reanalyses. The ozone hole of 2015 was one of the most severe on record with respect to maximum area and integrated deficit and was notably longlasting, with many values above previous extremes in October, November and December. In contrast, all assessed metrics for the 2016 ozone hole were at or below their median values for the 37 ozone holes since 1979 for which adequate satellite observations exist. The 2015 ozone hole was influenced both by very cold conditions and enhanced ozone depletion caused by stratospheric aerosol resulting from the April 2015 volcanic eruption of Calbuco (Chile)

The water cycle and regolith-atmosphere interaction at Gale crater, Mars

We perform mesoscale simulations of the water cycle in a region around Gale crater, including the diffusion of water vapour in and out of the regolith, and compare our results with measurements from the REMS instrument on board the Curiosity rover. Simulations are performed at three times of year, and show that diffusion in and out of the regolith and adsorption/desorption needs to be taken into account in order to match the diurnal variation of relative humidity measured by REMS. During the evening and night, local downslope flows transport water vapour down the walls of Gale crater. When including regolith-atmosphere interaction, the amount of vapour reaching the crater floor is reduced (by factors of 2–3 depending on season) due to vapour diffusing into the regolith along the crater walls. The transport of vapour into Gale crater is also affected by the regional katabatic flow over the dichotomy boundary, with the largest flux of vapour into the regolith initially occurring on the northern crater wall, and moving to the southern wall by early morning. Upslope winds during the day transport vapour desorbing and mixing out of the regolith up crater walls, where it can then be transported a few hundred metres into the atmosphere at convergence boundaries. Regolith-atmosphere interaction limits the formation of surface ice by reducing water vapour abundances in the lower atmosphere, though in some seasons ice can still form in the early morning on eastern crater walls. Subsurface ice amounts are small in all seasons, with ice only existing in the upper few millimetres of regolith during the night. The results at Gale crater are representative of the behaviour at other craters in the mesoscale domain