Univariate Bayesian nonparametric binary regression with application in environmental management

In environmental management, we often have to deal with binary response variables whose outcome dictates the course of action. This paper introduces a nonparametric Bayesian binary regression model with a single predictor variable that is more flexible than the commonly used logistic or probit models. Due to the Bayesian feature, the model can be easily used to combine observed data with our knowledge of the subject to produce site-specific results. By using three examples, this paper shows the potential application of the model in the environmental management, and its advantages in terms of flexibility in model specification, robustness to outliers, and realistic interpretation of data.     

Particle capture in the crown of the ciliary suspension feeding polychaete Sabella penicillus: videotape recordings and interpretations

An experimental setup was designed for in situ videotape recording of the particle capture process in the crown of the polychaete Sabella penicillus. Intact individuals of S. penicillus (collected in the Gullmornfjord, Sweden in 1992) were exposed to either 6 m Latex spheres or Rhodomonas sp. flagellate cells (6 m). The capture of the added particles was recorded on video. From frameby-frame analyses particle velocities were estimated and the shape of the three-dimensional particle paths was inferred. The mean velocity of particles approaching the crown was estimated to be ca. 1 mm s^-1, increasing to ca. 1.7 mm s^-1 in the interpinnule channel. At the moment of capture the particles were seen to follow a curved, near circular path close to the tips of the latero-frontal cilia. The transport velocities on the frontal side of the pinnules and filaments were estimated to be up to 0.15 and 0.5 mm s^-1, respectively. Counting captured particles relative to particles arriving within the area of the pinnules gave a rough, direct estimate of nearly 100% retention rate when the polychaete was feeding undisturbed. Together with results from clearance measurements in the literature this implies that the worm is able to capture particles down to 3 m entering the interpinnule channel almost 100% effectively. In view of the 80-m wide interpinnule channel and 40-m spacing between the tips of the latero-frontal cilia on both sides of the channel, this result cannot be explained by mechanisms based solely on direct mechanical contact between cilia and particles but must involve fluid mechanical mechanisms. The present work is the experimental basis for ongoing numerical simulations of the particle motion in the interpinnule channel.     

Analysis of binary data via a centered spatial-temporal autologistic regression model

A centered spatial-temporal autologistic model is developed for analyzing spatial-temporal binary data observed on a lattice over time. We propose expectation-maximization pseudolikelihood and Monte Carlo expectation-maximization likelihood as well as consider Bayesian inference to obtain the estimates of model parameters. Further, we compare the statistical efficiency of the three approaches for various sizes of sampling lattices and numbers of sampling time points. Regarding prediction, we use Monte Carlo to obtain predictive distributions at future time points and compare the performance of the model with the uncentered spatial-temporal autologistic regression model. The methodology is demonstrated via simulation studies and a real data example concerning southern pine beetle outbreak in North Carolina.     

Estimating growth charts via nonparametric quantile regression: a practical framework with application in ecology

We discuss a practical and effective framework to estimate reference growth charts via regression quantiles. Inequality constraints are used to ensure both monotonicity and non-crossing of the estimated quantile curves and penalized splines are employed to model the nonlinear growth patterns with respect to age. A companion R package is presented and relevant code discussed to favour spreading and application of the proposed methods.     

Experimental tests of suspension feeding in Atlantic reef corals

The ability of 15 species of Atlantic reef corals to act as suspension feeders was demonstrated by their removal of suspended particles from sea water in culture vessels. Mean clearance rates varied from 16.6 to 145.5 ml water cleared/h/cm² of live coral tissue. The lowest rates was found in Porites porites which is primarily a tentacle feeder, and the highest in Diploria clivosa which acts as both a tentacle feeder and suspension feeder. Rates of particle clearance in Agaricia agaricites, which is primarily a suspension feeder, were influenced by current velocity and type of food.     

Particle-size selection by Pseudopolydora paucibranchiata (Polychaeta: Spionidae) in suspension feeding and in deposit feeding: influences of ontogeny and flow speed

Pseudopolydora paucibranchiata Okuda suspension feeds and deposit feeds at the sediment-water interface, where it is exposed to a variety of particles differing in physical characteristics and nutritional value. In flume experiments (conducted in August 1994 and May 1995) with two sizes of either suspended or deposited beads, I measured particle-size selection separately in each feeding mode. The same influences of palp width and of ambient flow speed were observed in each mode. At velocities 0.74 cm s^-1 there were no relationships between palp width and the proportion of gut contents composed of large beads. At velocities 1.8 cm s^-1 worms with narrower palps ingested relatively fewer large beads (and more small beads) than did worms with wider palps. Palp width and body length were linearly related, and results were similar when analyzed with body length as the independent variable. As flow speed increased, selectivity changed in a worm-size-specific manner: worms with a palp width -1. Assuming that in the field (1) particle size is the principle criterion for selection, and (2) the amount of digestible food component in deposited and suspended particles, respectively, is related to particle surface area and volume, I hypothesize that changes in selectivity as velocity rises can cause juveniles to experience a decreasing profitability of suspension feeding and a simultaneously increasing profitability of deposit feeding. Juveniles could maintain a diet of high food value despite flow variations by adjusting the proportion of time they spend suspension feeding relative to deposit feeding.     

Feeding and cleaning mechanisms in the suspension feeding bivalve Mytilus edulis

Feeding and pseudofeces formation were studied in intact Mytilus edulis clearing suspensions of graphite particles, and the processes were compared with activities observed in mussels with a severed adductor muscle. Most particulate material in the stomach was present in the suspended state. Ingestion of particles in suspension could take place concurrently with the production of pseudofeces. Severing of the adductor muscle resulted in profuse secretion of mucus that gradually subsided to a constant low level. Addition of graphite particles at concentrations that did not cause mucus secretion in the intact mussels strongly stimulated secretion in the operated mussels, resulting in the accumulation of highly viscid, mucusparticle aggregates. These aggregates were mechanically stable, in contrast to the fragile pseudofeces. It is indicated that normal feeding depends upon hydromechanical mechanisms that produce highly concentrated suspensions of particles for ingestion, and that mucociliary mechanisms serve to clean the gills and other organs of the mantle cavity for excess particulate material. It is further indicated that intact mussels secrete mucus only in the amounts needed to consolidate excess particulate material, and that lesions affect the normal balance between particles in suspension and mucus secretion by enhancing the sensitivity of the mechanisms that control mucus secretion.     

Method for comparing the capture efficiency of benthic sampling devices

Traditional comparisons between the capture efficiency of sampling devices have generally looked at the absolute differences between devices. We recommend that the signal-to-noise ratio be used when comparing the capture efficiency of benthic sampling devices. Using the signal-to-noise ratio rather than the absolute difference has the advantages that the variance is taken into account when determining how important the difference is, the hypothesis and minimum detectable difference can be made identical for all taxa, it is independent of the units used for measurement, and the sample-size calculation is independent of the variance. This new technique is illustrated by comparing the capture efficiency of a 0.05 m² van Veen grab and an airlift suction device, using samples taken from Heron and One Tree lagoons, Australia.     

Effects of current speed on filtration during suspension feeding in Oligometra serripinna (Echinodermata: Crinoidea)

Suspension feeding by the crinod Oligometra serripinna was studied at Lizard Island, Australia, in 1986. Video recordings were made of 90-m particles interacting with the filter of the crinoid in a laboratory flow chamber. A complete census of particles was possible because both the capture event and the filter area could be defined unequivocally. Also, because O. serripinna is a passive suspension feeder, a census of partcles could be made at different ambient current speeds without interference due to active pumping by the crinoid. Experiments were run at seven current speeds from 0.9 to 13.3 cm s^-1. Particles approaching the filter: (1) were captured, (2) passed through the filter without triggering a capture event, (3) passed through the filter after escaping from an unsuccessful capture event, or (4) were deflected around the filter. With increasing current speed, the proportion of deflections declined and the proportion of particles passing through rose: these results could be partially explained by the progressive widening of the spaces within the filter due to distortion of filter parts by the current. The proportion of captures (normalized to approaches) was comparatively low at 0.9 cm s^-1, rose to a relatively constant maximum from 1.7 to 6.4 cm s^-1, and then declined progressively at 9.5 and 13.3 cm s^-1. These proportions were translated into capture rates for whole crinoids by taking into consideration both the encounters with particles and the reduction of filter area by distortion of body parts at higher speeds. When plotted against current speed, capture rate peaked at 6.4 cm s^-1, which was close to the mean current speed that we measured on the reef in the microhabitat of O. serripinna.     

A simple and cheap apparatus for the controlled feeding of suspension feeders

A simple and cheap device, which allows a controlled and continuous food supply of suspension feeding animals in long term experiments, has been developed and is described.     

Function of lateral cilia in suspension feeding of lophophorates (Brachiopoda,Phoronida, Ectoprocta)

Suspension feeding by the brachiopod Laqueus californianus (Koch), the phoronid Phoronis vancouverensis Pixell, the ectoprocts Bugula sp., Membranipora villosa Hincks, and Schizoporella unicornis (Johnston), and actinotrocha and cyphonautes larvae was observed. Lophophorates retain particles on the upstream side of the band of lateral cilia, even after particles have moved lateral to the frontal surface. This suggests that these animals utilize an induced local reversal of beat of the lateral cilia for concentration and capture of suspended food particles. Retention of particles can cease while the current past the tentacles continues. Movement of particles down the frontal surface of the tentacles of L. californianus and the ectoproct species confirms previous observations that mucus strands are not used in particle capture. Possible functions of latero-frontal cilia or bristles are considered. Distribution of the feeding mechanism among phyla, clearance rates, and the lack of fusion of tentacles in brachiopods are discussed. The impingement mechanism previously suggested for lophophorates cannot account for the movements of particles observed here.     

Modeling the impact of feeding stations on vulture scavenging service efficiency

Vultures, the only vertebrate obligate scavengers, are currently facing a dramatic worldwide decline with over half of vulture species now classified as threatened. To address this widespread decline, the use of feeding stations has been widely advocated in recovery programs. However, providing food that is more predictable in time and space than natural resources could disrupt the ecological scavenging service provided by vultures. In this study, we build a multi-agent system (MAS), which describes the social foraging behavior of Gyps vultures in order to investigate how resource predictability in space and resource management affect scavenging service efficiency. We study the possibility that vultures take into account feeding station location in addition of using local enhancement. Our results show that the efficiency of the scavenging service is heavily affected by the way resources are distributed between feeding stations and natural areas. Nevertheless, it appears possible to minimize a loss in service efficiency by increasing the number of feeding stations while keeping the total amount of resources available constant, thus reducing the predictability of the resources located on the stations. We illustrate our work in the case of European feeding stations that provide supplementary resources in areas where natural ones are scarce. Moreover, we discuss the implications worldwide, in particular in the case of India, where feeding stations for vultures are intended to lure individuals away from potentially harmful natural carrion.     

Higher efficiency and lower environmental impact of membrane separation for carbon dioxide capture in coal power plants

Environmental Chemistry Letters - Global warming may be slowed down by carbon capture and storage systems that allow to sequester carbon dioxide from large fixed point sources such as power plants...     

The structure of the latero-frontal cirri on the gills of certain lamellibranch molluscs and their role in suspension feeding

Photomicroscopy and scanning electron microscopy were used to determine the fine structure of the latero-frontal cirri on the gills of three species of bivalve mollusc: Mytilus edulis Linn., Barnea candida (Linn.), and Petricola pholadiformis Lam. The component cilia are seen to branch off alternately along the length of each cirrus. Each of these free, lateral lengths of the cilia are separated from the next on their side by a mean distance of 0.6 m. They extend to a mean length of 2.7 m in M. edulis, the species described in detail. It is shown that a complete straining mesh can be formed over the gill ostium during normal filtering and the aperture of this mesh correlates well with the previously recorded filtering efficiency for Mytilus.     

Early warnings of unknown nonlinear shifts: a nonparametric approach

Early warning signals (EWS) of regime shifts are challenging in cases where the true natural data-generating process is uncertain. Nonparametric drift-diffusion-jump models address this problem by fitting a general model that can approximate a wide range of data-generating processes. Drift measures the local rate of change. Diffusion measures relatively small shocks that occur at each time step. Jumps are large intermittent shocks. Total variance combines the contributions of diffusion and jumps. Nonparametric methods are well suited to emerging technology for automated, high-frequency sensors. Total variance is the most precisely measured indicator. Jump intensity appears to be a useful EWS. Estimates of the drift are highly uncertain unless long time series with many regime shifts are available. EWS computed from drift estimates (such as autocorrelation coefficients or return rates) have low precision and should be used with caution. Nonetheless, in the current state of knowledge, it is premature to disregard any potential EWS.     

Effects of prey escape ability,flow speed,and predator feeding mode on zooplankton capture by barnacles

Experimental studies of feeding on zooplankton often involve the use of non-evasive Artemia spp. to represent zooplanktonic prey. Some zooplankton, however, such as copepods, are potentially evasive due to possession of effective predator-avoidance mechanisms such as high-speed escape swimming. In the present study, we compared the efficiencies with which non-evasive (A. salina) and evasive (copepods) zooplankton were captured by a sessile, suspension feeder, the coral-inhabiting barnacle Nobia grandis (Crustacea, Cirripedia). N. grandis specimens and zooplankton used in the present study were collected near Eilat, Israel in 1993. The effect of different flow speeds (from 0 to 14 cm s^-1) on captures of the two preys was also investigated. Additionally, we examined the effect of a flow-induced barnacle behavioral switch from active to passive suspension feeding, on zooplankton capture. Two video cameras were used to make close-up, three dimensional recordings of predator-prey encounters in a computer-controlled flow tank. Frame-by-frame video analysis revealed a highly significant difference (P< 0.001) in the efficiency with which A. salina and copepods were caught (A. salina being much more readily captured than copepods). After an encounter with cirri of feeding barnacles, copepods were usually able to swim out of the barnacles capture zone within one video frame (40 ms), by accelerating from a slow swimming speed (approximately 1.85 cm s^-1) to a mean escape swimming speed of 18.11 cm s^-1 (ca. 360 body lengths s^-1). This was not the case for A. salina nauplii, which usually remained in contact with cirri before being transferred to the mouth and ingested. Thus, experimental studies addressing the methodology of organisms feeding on zooplankton should consider that slow-swimming prey like Artemia sp. nauplii may only represent the non-evasive fraction of natural mesozooplankton assemblages.     

Measuring and decomposing changes in agricultural productivity, nitrogen use efficiency and cumulative exergy efficiency: Application to OECD agriculture

This paper uses an aggregate quantity space to decompose the temporal changes in nitrogen use efficiency and cumulative exergy use efficiency into changes of Moorsteen-Bjurek (MB) Total Factor Productivity (TFP) changes and changes in the aggregate nitrogen and cumulative exergy contents. Changes in productivity can be broken into technical change and changes in various efficiency measures such as technical efficiency, scale efficiency and residual mix efficiency. Changes in the aggregate nitrogen and cumulative exergy contents can be driven by changes in the quality of inputs and outputs and changes in the mixes of inputs and outputs. Also with cumulative exergy content analysis, changes in the efficiency in input production can increase or decrease the cumulative exergy transformity of agricultural production. The empirical study in 30 member countries of the Organisation for Economic Co-operation Development from 1990 to 2003 yielded some important findings. The production technology progressed but there were reductions in technical efficiency, scale efficiency and residual mix efficiency levels. This result suggests that the production frontier had shifted up but there existed lags in the responses of member countries to the technological change. Given TFP growth, improvements in nutrient use efficiency and cumulative exergy use efficiency were counteracted by reductions in the changes of the aggregate nitrogen contents ratio and aggregate cumulative exergy contents ratio. The empirical results also confirmed that different combinations of inputs and outputs as well as the quality of inputs and outputs could have more influence on the growth of nutrient and cumulative exergy use efficiency than factors that had driven productivity change.     

Effects of feeding rate on conversion efficiency and chemical composition of the fish Tilapia mossambica

Average daily rations of 14, 35 or 58 mg Tubifex tubifex worm per gram of the fish Tilapia mossambica Peters represent maintenance, optimum or maximum feeding levels. At these levels, conversion efficiency (K ₁) is 5,9 or 24%. An amount of 65 mg worm/g fish/day, when fed under experimental conditions, is converted with the poorest conversion efficiency (4%). Test individuals fed at 11 to 49 mg worm/g fish/day show a decreasing trend in water content (78.1 to 74.8%), and an increasing trend in fat content (32.1 to 44.2%). Below or above this feeding rate range, water content increases, while fat content decreases. The range of individual variations in fat content is nearly 3 times greater than that of ash and 15 times greater than that of water. Test individuals starved for 60 days lose 2.1 mg dry body weight/g/day. This loss is contributed by calorifically equivalent amounts of fat and protein. The endogenous loss of nitrogen by these individuals averaged 0.18 mg N/g body weight/day.     

中国能源利用效率区域差异基尼系数分析

基尼系数是经济学中对贫富差距量化评价的重要工具.文章从基尼系数的经济学内涵出发,将基尼系数的概念和意义应用于地区能源利用效率分析.以全国各地区的能源消耗分配为例,应用基尼系数法分析了地区总体经济发展水平,地区工业化程度,地区经济重型化程度对能源消费强度分配公平性的影响,并提出了以绿色贡献系数作为判断不公平因子的依据.绘制各影响因素的洛伦茨曲线,计算出中国2006年的能源消耗基尼系数,根据基尼系数和绿色贡献系数对能源消费强度地区差异进行量化分析,最后得出合理的结论.