Effect of detection heterogeneity in occupancy‐detection models: an experimental test of time‐to‐first‐detection methods

Imperfect detection can bias estimates of site occupancy in ecological surveys but can be corrected by estimating detection probability. Time‐to‐first‐detection (TTD) occupancy models have been proposed as a cost–effective survey method that allows detection probability to be estimated from single site visits. Nevertheless, few studies have validated the performance of occupancy‐detection models by creating a situation where occupancy is known, and model outputs can be compared with the truth. We tested the performance of TTD occupancy models in the face of detection heterogeneity using an experiment based on standard survey methods to monitor koala Phascolarctos cinereus populations in Australia. Known numbers of koala faecal pellets were placed under trees, and observers, uninformed as to which trees had pellets under them, carried out a TTD survey. We fitted five TTD occupancy models to the survey data, each making different assumptions about detectability, to evaluate how well each estimated the true occupancy status. Relative to the truth, all five models produced strongly biased estimates, overestimating detection probability and underestimating the number of occupied trees. Despite this, goodness‐of‐fit tests indicated that some models fitted the data well, with no evidence of model misfit. Hence, TTD occupancy models that appear to perform well with respect to the available data may be performing poorly. The reason for poor model performance was unaccounted for heterogeneity in detection probability, which is known to bias occupancy‐detection models. This poses a problem because unaccounted for heterogeneity could not be detected using goodness‐of‐fit tests and was only revealed because we knew the experimentally determined outcome. A challenge for occupancy‐detection models is to find ways to identify and mitigate the impacts of unobserved heterogeneity, which could unknowingly bias many models.     

Many‐to‐one form‐to‐function mapping weakens parallel morphological evolution

Evolutionary ecologists aim to explain and predict evolutionary change under different selective regimes. Theory suggests that such evolutionary prediction should be more difficult for biomechanical systems in which different trait combinations generate the same functional output: “many‐to‐one mapping.” Many‐to‐one mapping of phenotype to function enables multiple morphological solutions to meet the same adaptive challenges. Therefore, many‐to‐one mapping should undermine parallel morphological evolution, and hence evolutionary predictability, even when selection pressures are shared among populations. Studying 16 replicate pairs of lake‐ and stream‐adapted threespine stickleback (Gasterosteus aculeatus), we quantified three parts of the teleost feeding apparatus and used biomechanical models to calculate their expected functional outputs. The three feeding structures differed in their form‐to‐function relationship from one‐to‐one (lower jaw lever ratio) to increasingly many‐to‐one (buccal suction index, opercular 4‐bar linkage). We tested for (1) weaker linear correlations between phenotype and calculated function, and (2) less parallel evolution across lake‐stream pairs, in the many‐to‐one systems relative to the one‐to‐one system. We confirm both predictions, thus supporting the theoretical expectation that increasing many‐to‐one mapping undermines parallel evolution. Therefore, sole consideration of morphological variation within and among populations might not serve as a proxy for functional variation when multiple adaptive trait combinations exist.     

On Estimating the Relationship between Longitudinal Measurements and Time‐to‐Event Data Using a Simple Two‐Stage Procedure

Summary Ye, Lin, and Taylor (2008, Biometrics 64 , 1238–1246) proposed a joint model for longitudinal measurements and time‐to‐event data in which the longitudinal measurements are modeled with a semiparametric mixed model to allow for the complex patterns in longitudinal biomarker data. They proposed a two‐stage regression calibration approach that is simpler to implement than a joint modeling approach. In the first stage of their approach, the mixed model is fit without regard to the time‐to‐event data. In the second stage, the posterior expectation of an individual's random effects from the mixed‐model are included as covariates in a Cox model. Although Ye et al. (2008) acknowledged that their regression calibration approach may cause a bias due to the problem of informative dropout and measurement error, they argued that the bias is small relative to alternative methods. In this article, we show that this bias may be substantial. We show how to alleviate much of this bias with an alternative regression calibration approach that can be applied for both discrete and continuous time‐to‐event data. Through simulations, the proposed approach is shown to have substantially less bias than the regression calibration approach proposed by Ye et al. (2008) . In agreement with the methodology proposed by Ye et al. (2008) , an advantage of our proposed approach over joint modeling is that it can be implemented with standard statistical software and does not require complex estimation techniques.     

Oxidative balance in birds: an atoms‐to‐organisms‐to‐ecology primer for ornithologists

All air‐breathing organisms must face the challenge of oxidative damage, and understanding how animals cope can lend insight into their ecology. Unlike other vertebrates, birds rely primarily on fats to fuel endurance exercise such as migration, and therefore face a greater potential for damage from the reactive by‐products of their own metabolism. We review the physiological ecology of migrating birds through the lens of oxidation–reduction chemistry, underscoring how oxidative balance in wild birds may affect their dietary choices and use of critical stopover habitats during migration. Recent studies reveal that migratory birds prepare for oxidative challenges either by up‐regulating endogenous antioxidants or by consuming them in their diet, and they repair oxidative damage after long flights, although much remains to be discovered about how birds maintain oxidative balance over the course of migration. We conclude by describing some of the most used and useful measures of antioxidant status and oxidative damage that field ornithologists can include in their tool kit of techniques to probe the oxidative balance of wild birds.     

Bayesian Estimation of the Time‐Varying Sensitivity of a Diagnostic Test with Application to Mother‐to‐Child Transmission of HIV

Summary We present a Bayesian model to estimate the time‐varying sensitivity of a diagnostic assay when the assay is given repeatedly over time, disease status is changing, and the gold standard is only partially observed. The model relies on parametric assumptions for the distribution of the latent time of disease onset and the time‐varying sensitivity. Additionally, we illustrate the incorporation of historical data for constructing prior distributions. We apply the new methods to data collected in a study of mother‐to‐child transmission of HIV and include a covariate for sensitivity to assess whether two different assays have different sensitivity profiles.     

Interfacial Solar‐to‐Heat Conversion for Desalination

Solar desalination is a promising and sustainable solution for water shortages in the future. Interfacial solar‐to‐heat conversion for desalination has attracted increasing attention in the past decades, due to the heat localization induced high thermal efficiency, simple structure, and low cost. In this review, the authors summarize and analyze the critical processes involved in such a solar desalination system, including the thermal conversion and transport, salt dissipation, and vapor manipulation. Mathematical models of heat transfer and salt dissipation are also built for quantitative analysis of systematic performance relative to properties of employed materials and system designs. Recent efforts devoted to improving the overall thermal efficiency, salt rejection, and water yield are then summarized. Based on the analysis and previous results, opportunities for further interfacial solar desalination development are highlighted.     

Many‐to‐one Comparisons in Stratified Designs

Cheung and Holland (1992) extended Dunnett's procedure for comparing all active treatments with a control simultaneously within each of r groups while maintaining the Type I error rate at some designated level α allowing different sample sizes for each of the group‐treatment categories. This paper shows that exact percentage points can be easily calculated with current available statistical software (SAS). This procedure is compared to resampling techniques and a Bonferroni corrected Dunnett‐within‐group procedure by means of a simulation study.     

MAIGO2 is involved in abscisic acid‐mediated response to abiotic stresses and Golgi‐to‐ER retrograde transport

The central role of multisubunit tethering complexes in intracellular trafficking has been established in yeast and mammalian systems. However, little is known about their roles in the stress responses and the early secretory pathway in Arabidopsis. In this study, Maigo2 (MAG2), which is equivalent to the yeast Tip20p and mammalian Rad50‐interacting protein, is found to be required for the responses to salt stress, osmotic stress and abscisic acid in seed germination and vegetative growth, and MAG2‐like (MAG2L) is partially redundant with MAG2 in response to environmental stresses. MAG2 strongly interacts with the central region of ZW10, and both proteins are important as plant endoplasmic reticulum (ER)‐stress regulators. ER morphology and vacuolar protein trafficking are unaffected in the mag2, mag2l and zw10 mutants, and the secretory marker to the apoplast is correctly transported in mag2 plants, which indicate that MAG2 functions as a complex with ZW10, and is potentially involved in Golgi‐to‐ER retrograde trafficking. Therefore, a new role for ER–Golgi membrane trafficking in abiotic‐stress and ER‐stress responses is discovered.     

Nanostructured p‐n Junctions for Kinetic‐to‐Electrical Energy Conversion

Piezoelectric ZnO nanorods grown on a flexible substrate are combined with the p‐type semiconducting polymer PEDOT:PSS to produce a p‐n junction device that successfully demonstrates kinetic‐to‐electrical energy conversion. Both the voltage and current output of the devices are measured to be in the range of 10 mV and 10 μA cm^?2. Combining these figures for the best device gives a maximum possible power density of 0.4 mW cm^?3. Systematic testing of the devices is performed showing that the voltage output increases linearly with applied stress, and is reduced significantly by illumination with super‐band gap light. This provides strong evidence that the voltage output results from piezoelectric effects in the ZnO. The behavior of the devices is explained by considering the time‐dependent changes in band structure resulting from the straining of a piezoelectric material within a p‐n junction. It is shown that the rate of screening of the depolarisation field determines the power output of a piezoelectric energy harvesting device. This model is consistent with the behavior of a number of previous devices utilising the piezoelectric effect in ZnO.     

Design‐to‐Device Approach Affords Panchromatic Co‐Sensitized Solar Cells

Data‐driven materials discovery has become increasingly important in identifying materials that exhibit specific, desirable properties from a vast chemical search space. Synergic prediction and experimental validation are needed to accelerate scientific advances related to critical societal applications. A design‐to‐device study that uses high‐throughput screens with algorithmic encodings of structure–property relationships is reported to identify new materials with panchromatic optical absorption, whose photovoltaic device applications are then experimentally verified. The data‐mining methods source 9431 dye candidates, which are auto‐generated from the literature using a custom text‐mining tool. These candidates are sifted via a data‐mining workflow that is tailored to identify optimal combinations of organic dyes that have complementary optical absorption properties such that they can harvest all available sunlight when acting as co‐sensitizers for dye‐sensitized solar cells (DSSCs). Six promising dye combinations are shortlisted for device testing, whereupon one dye combination yields co‐sensitized DSSCs with power conversion efficiencies comparable to those of the high‐performance, organometallic dye, N719. These results demonstrate how data‐driven molecular engineering can accelerate materials discovery for panchromatic photovoltaic or other applications.     

Solar‐to‐Hydrogen Energy Conversion Based on Water Splitting

Artificial photosynthesis provides a blueprint to harvest solar energy to sustain the future energy demands. Solar‐driven water splitting, converting solar energy into hydrogen energy, is the prototype of photosynthesis. Various systems have been designed and evaluated to understand the reaction pathways and/or to meet the requirements of potential applications. In solar‐to‐hydrogen conversion, electrocatalytic hydrogen and oxygen evolution reactions are key research areas that are meaningful both theoretically and practically. To utilize hydrogen energy, fuel cell technology has been extensively investigated because of its high efficiency in releasing chemical energy. In this review, general concepts of the photosynthesis in green plants are discussed, different strategies for the light‐driven water splitting proposed in laboratories are introduced, the progress of electrocatalytic hydrogen and oxygen evolution reactions are reviewed, and finally, the reactions in hydrogen fuel cells are briefly discussed. Overall, the mass and energy circulation in the solar‐hydrogen‐electricity circle are delineated. The authors conclude that attention from scientists and engineers of relevant research areas is still highly needed to eliminate the wide disparity between the aspirations and realities of artificial photosynthesis.     

Side chain‐to‐side chain cyclization by click reaction

Cu^I‐catalyzed azide‐alkyne 1,3‐dipolar Huisgen's cycloaddition (CuAAC) is a click reaction that has drawn a lot of attention, in general, and in the field of peptide and protein sciences, in particular. Among several reported applications, the preparation of novel heterodetic cyclopeptides by an intramolecular side chain‐to‐side chain CuAAC, forming a 1,4‐disubstituted[1,2,3]triazolyl‐containing bridge, is of great interest. Herein, we provide a detailed protocol for the syntheses of model heterodetic cyclopeptides as a prototypical intramolecular CuAAC, using as a model a sequence derived from parathyroid hormone‐related protein. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.