Imperfect observations in ecological studies

Every ecological data set is the result of sampling the biota at sampling locations. Such samples are rarely a census of the biota at the sampling locations and so will inherently contain biases. It is crucial to account for the bias induced by sampling if valid inference on biodiversity quantities is to be drawn from the observed data. The literature on accounting for sampling effects is large, but most are dedicated to the specific type of inference required, the type of analysis performed and the type of survey undertaken. There is no general and systematic approach to sampling. Here, we explore the unification of modelling approaches to account for sampling. We focus on individuals in ecological communities as the fundamental sampling element, and show that methods for accounting for sampling at the species level can be equated to individual sampling effects. Particular emphasis is given to the case where the probability of observing an individual, when it is present at the site sampled, is less than one. We call these situations ‘imperfect observations’. The proposed framework is easily implemented in standard software packages. We highlight some practical benefits of this formal framework: the ability of predicting the true number of individuals using an expectation that conditions on the observed data, and designing appropriate survey plans accounting forPublisher PDFPeer reviewe

Imperfect observations in ecological studies

© 2016 The Author(s) Every ecological data set is the result of sampling the biota at sampling locations. Such samples are rarely a census of the biota at the sampling locations and so will inherently contain biases. It is crucial to account for the bias induced by sampling if valid inference on biodiversity quantities is to be drawn from the observed data. The literature on accounting for sampling effects is large, but most are dedicated to the specific type of inference required, the type of analysis performed and the type of survey undertaken. There is no general and systematic approach to sampling. Here, we explore the unification of modelling approaches to account for sampling. We focus on individuals in ecological communities as the fundamental sampling element, and show that methods for accounting for sampling at the species level can be equated to individual sampling effects. Particular emphasis is given to the case where the probability of observing an individual, when it is present at the site sampled, is less than one. We call these situations ‘imperfect observations’. The proposed framework is easily implemented in standard software packages. We highlight some practical benefits of this formal framework: the ability of predicting the true number of individuals using an expectation that conditions on the observed data, and designing appropriate survey plans accounting for uncertainty due to sampling. The principles and methods are illustrated with marine survey data from tropical northern Australia

Outcomes of 23-gauge pars plana vitrectomy in combined scleral buckling and vitrectomy for complex rhegmatogenous retinal detachments

Rhegmatogenous retinal detachments associated with proliferative vitreoretinopathy, giant retinal tears, ocular trauma, proliferative diabetic retinopathy, or necrotizing retinitis are considered more complex than those without these factors. The aim of the current review is to address the surgical outcomes and complications of 23-gauge pars plana vitrectomy with scleral buckling (23GPPV/SB) for repair of these complex retinal detachments. This retrospective study involved 54 eyes of 53 patients who underwent 23GPPV/SB between July 2007 and September 2009. Preoperative diagnosis, surgical technique, preoperative and postoperative visual acuities, intraoperative and postoperative complications, and anatomic reattachment rates were examined. Fifty-four eyes of 53 patients were reviewed in this study and indications for surgery varied. Mean logarithm of the minimal angle of resolution (logMAR) pre- and post-operative visual acuities were 1.166 (20/293) and 0.780 (20/120), respectively, which led to a statistically significant improvement in logMAR (P=0.0165). Single operation and final reattachment rates were 87% (47 of 54 eyes) and 100%, respectively. Postoperative complications included choroidal effusion/hemorrhage (14.8%, 8 of 54 eyes) and vitreous hemorrhage (11.1%, 6 of 54 eyes). Other more infrequent complications included hyphema (9.3%, 5 of 54 eyes), hypotony (5.6%, 3 of 54 eyes) and ocular hypertension > 35 mmHg (3.7%, 2 of 54 eyes). A total of 31.5% (17 of 54 eyes) of patients had a complication in the postoperative time period, but 58.8% of these resolved spontaneously without requiring an intervention. 23GPPV/SB may be considered for complex retinal detachment repair with good anatomic reattachment rates, but with relatively high complication rates

Effects of Ignoring Survey Design Information for Data Reuse

Data are currently being used, and reused, in ecological research at an unprecedented rate. To ensure appropriate reuse however, we need to ask the question: "Are aggregated databases currently providing the right information to enable effective and unbiased reuse?" We investigate this question, with a focus on designs that purposefully favor the selection of sampling locations (upweighting the probability of selection of some locations). These designs are common and examples are those designs that have uneven inclusion probabilities or are stratified. We perform a simulation experiment by creating data sets with progressively more uneven inclusion probabilities and examine the resulting estimates of the average number of individuals per unit area (density). The effect of ignoring the survey design can be profound, with biases of up to 250% in density estimates when naive analytical methods are used. This density estimation bias is not reduced by adding more data. Fortunately, the estimation bias can be mitigated by using an appropriate estimator or an appropriate model that incorporates the design information. These are only available however, when essential information about the survey design is available: the sample location selection process (e.g., inclusion probabilities), and/or covariates used in their specification. The results suggest that such information must be stored and served with the data to support meaningful inference and data reuse.Peer reviewe

Inhibited Production of iNOS by Murine J774 Macrophages Occurs via a phoP

Background. There are no reported data to explain how Salmonella suppress nitrite ion production in macrophages or whether this phenomenon is unique to typhoidal or non-typhoidal serovars. The aims of this study were, therefore, to investigate these phenomena. Methods. We measured survival of S. typhimurium 14028 and its phoP mutant in murine J774 macrophages, cultured with or without interferon gamma. We compared expression of inducible nitric oxide synthase (iNOS) mRNA and protein, and nitrite ion production and also examined binding of nuclear factor B (NFB) and activator protein 1 (AP-1) to macrophage DNA. Results. S. typhimurium 14028 inhibited binding of NFB and AP-1 to DNA in murine J774. A macrophages via an intact phoP regulon. This correlated with increased survival and reduced iNOS expression. Suppression of NFB activity was ameliorated in macrophages cultured with IFN-γ and this correlated with increased expression of iNOS mRNA and nitrite ion production, although IFN-γ had no effect on AP-1/DNA interaction. We show, that with one exception, suppression of iNOS is unique to typhoidal serovars. Conclusion. S. typhimurium inhibit NFB and AP-1 interaction with macrophage DNA via the PhoP regulon, this reduces nitrite ion production and is principally associated with typhoidal serovars

Impact of high CO2 on the geochemistry of the coralline algae Lithothamnion glaciale

Coralline algae are a significant component of the benthic ecosystem. Their ability to withstand physical stresses in high energy environments relies on their skeletal structure which is composed of high Mg-calcite. High Mg-calcite is, however, the most soluble form of calcium carbonate and therefore potentially vulnerable to the change in carbonate chemistry resulting from the absorption of anthropogenic CO2 by the ocean. We examine the geochemistry of the cold water coralline alga Lithothamnion glaciale grown under predicted future (year 2050) high pCO2 (589 μatm) using Electron microprobe and NanoSIMS analysis. In the natural and control material, higher Mg calcite forms clear concentric bands around the algal cells. As expected, summer growth has a higher Mg content compared to the winter growth. In contrast, under elevated CO2 no banding of Mg is recognisable and overall Mg concentrations are lower. This reduction in Mg in the carbonate undermines the accuracy of the Mg/Ca ratio as proxy for past temperatures in time intervals with significantly different carbonate chemistry. Fundamentally, the loss of Mg in the calcite may reduce elasticity thereby changing the structural properties, which may affect the ability of L. glaciale to efficiently function as a habitat former in the future ocean

Efficacy of CMX001 as a Prophylactic and Presymptomatic Antiviral Agent in New Zealand White Rabbits Infected with Rabbitpox Virus, a Model for Orthopoxvirus Infections of Humans

CMX001, a lipophilic nucleotide analog formed by covalently linking 3-(hexdecyloxy)propan-1-ol to cidofovir (CDV), is being developed as a treatment for smallpox. CMX001 has dramatically increased potency versus CDV against all dsDNA viruses and, in contrast to CDV, is orally available and has shown no evidence of nephrotoxicity in healthy volunteers or severely ill transplant patients to date. Although smallpox has been eliminated from the environment, treatments are urgently being sought due to the risk of smallpox being used as a bioterrorism agent and for monkeypox virus, a zoonotic disease of Africa, and adverse reactions to smallpox virus vaccinations. In the absence of human cases of smallpox, new treatments must be tested for efficacy in animal models. Here we first review and discuss the rabbitpox virus (RPV) infection of New Zealand White rabbits as a model for smallpox to test the efficacy of CMX001 as a prophylactic and early disease antiviral. Our results should also be applicable to monkeypox virus infections and for treatment of adverse reactions to smallpox vaccination

United States Patent Application Publication

A multiple robot control architecture including a plurality of robotic agricultural machines including a first and second robotic agricultural machine. Each robotic agricultural machine including at least one controller configured to implement a plurality of finite state machines Within an individual robot control architecture (IRCA) and a global information module (GIM) communicatively coupled to the IRCA. The GIMs of the first and second robotic agricultural machines being configured to cooperate to cause said first robotic agricultural machine and said second agricultural machine to perform at least one agricultural task