Using Dung to Estimate Gorilla Density: Modeling Dung Production Rate

There is an urgent need for information on western gorilla population sizes and distribution to improve present and plan future conservation actions. Researchers traditionally have estimated gorilla densities on the basis of nest counts despite demonstrated variation in nest production and decay rates. The variation may lead to large biases in estimates of gorilla abundance. We investigated the use of an alternate index of gorilla abundance, via defecation data collected from habituated gorillas at Bai Hokou, Central African Republic. Our sample of 274/370 defecation events/dung piles produced a production rate of ca. 5 dung piles/d: comparable to previous estimates based on much smaller sample sizes. Heuristic models that failed to account for imperfect dung pile detection produced a lower defecation rate estimate than that of a maximum likelihood model that explicitly modeled detection probability. Generalized linear modeling (GLM) showed that dung pile production rate was strongly linked to rainfall, suggesting that failure to correct for seasonal variation in dung pile production rates could lead to substantial biases in gorilla abundance estimates. In our study, failing to distinguish between the number of defecation events and the number of dung piles produced would lead to a ca. 31% overestimate of true gorilla numbers. The use of dung as an index of gorilla abundance shows potential, but more fieldwork and modeling on seasonal variation in dung production rates is required.     

Quantification of Pathologic Air Trapping in Lung Transplant Patients Using CT Density Mapping: Comparison with Other CT Air Trapping Measures

To determine whether density mapping (DM) is more accurate for detection and quantification of pathologic air trapping (pAT) in patients after lung transplantation compared to other CT air trapping measures. One-hundred forty-seven lung and heart-lung transplant recipients underwent CT-examinations at functional residual capacity (FRC) and total lung capacity (TLC) and PFT six months after lung transplantation. Quantification of air trapping was performed with the threshold-based method in expiration (EXP), density mapping (DM) and the expiratory to inspiratory ratio of the mean lung density (E/I-ratio MLD). A non-rigid registration of inspiration-expiration CT-data with a following voxel-to-voxel mapping was carried out for DM. Systematic variation of attenuation ranges was performed for EXP and DM and correlated with the ratio of residual volume to total lung capacity (RV/TLC) by Spearman rank correlation test. AT was considered pathologic if RV/TLC was above the 95^th percentile of the predicted upper limit of normal values. Receiver operating characteristic (ROC) analysis was performed. The optimal attenuation range for the EXP method was from -790 HU to -950 HU (EXP_{-790 to -950HU} ) (r = 0.524, p<0.001) to detect air trapping. Within the segmented lung parenchyma, AT was best defined as voxel difference less than 80 HU between expiration and registered inspiration using the DM method. DM correlated best with RV/TLC (r = 0.663, p<0.001). DM and E/I-ratio MLD showed a larger AUC (0.78; 95% CI 0.69–0.86; 0.76, 95% CI 0.67–0.85) than EXP _{-790 HU to -950 HU} (0.71, 95% CI 0.63–0.78). DM and E/I-ratio MLD showed better correlation with RV/TLC and are more suited quantitative CT-methods to detect pAT in lung transplant patients than the EXP_{-790HU to -950HU}.     

Modelling the Species Distribution of Flat-Headed Cats (Prionailurus planiceps), an Endangered South-East Asian Small Felid

Background

The flat-headed cat (Prionailurus planiceps) is one of the world''s least known, highly threatened felids with a distribution restricted to tropical lowland rainforests in Peninsular Thailand/Malaysia, Borneo and Sumatra. Throughout its geographic range large-scale anthropogenic transformation processes, including the pollution of fresh-water river systems and landscape fragmentation, raise concerns regarding its conservation status. Despite an increasing number of camera-trapping field surveys for carnivores in South-East Asia during the past two decades, few of these studies recorded the flat-headed cat.

Methodology/Principal Findings

In this study, we designed a predictive species distribution model using the Maximum Entropy (MaxEnt) algorithm to reassess the potential current distribution and conservation status of the flat-headed cat. Eighty-eight independent species occurrence records were gathered from field surveys, literature records, and museum collections. These current and historical records were analysed in relation to bioclimatic variables (WorldClim), altitude (SRTM) and minimum distance to larger water resources (Digital Chart of the World). Distance to water was identified as the key predictor for the occurrence of flat-headed cats (>50% explanation). In addition, we used different land cover maps (GLC2000, GlobCover and SarVision LLC for Borneo), information on protected areas and regional human population density data to extract suitable habitats from the potential distribution predicted by the MaxEnt model. Between 54% and 68% of suitable habitat has already been converted to unsuitable land cover types (e.g. croplands, plantations), and only between 10% and 20% of suitable land cover is categorised as fully protected according to the IUCN criteria. The remaining habitats are highly fragmented and only a few larger forest patches remain.

Conclusion/Significance

Based on our findings, we recommend that future conservation efforts for the flat-headed cat should focus on the identified remaining key localities and be implemented through a continuous dialogue between local stakeholders, conservationists and scientists to ensure its long-term survival. The flat-headed cat can serve as a flagship species for the protection of several other endangered species associated with the threatened tropical lowland forests and surface fresh-water sources in this region.     

利用次序统计量估计种群的平均寿命

本文讨论威布尔分布Ｗ（α,λ）中次序统计量的分布;建立了用次序统计量对威布尔分布进行参数估计,进而估计种群平均寿命和方差的方法,该方法可广泛用于可靠性统计产品平均寿命和方差的估计。     

Using dragonflies to monitor and prioritize lotic systems: a South African perspective

The ever-worsening condition of streams due to local, regional, and global demands on water has resulted in the development of increasingly streamlined, rapid assessment methods using macroinvertebrates. Biotic indices in particular are versatile and robust, although not always easy to use. For example, the family-level South African Scoring System is an effective water quality measure, but is time-consuming and requires high-level expert training. The index could be used alongside the species-level Dragonfly Biotic Index (DBI), originally developed for monitoring habitat integrity, with which it is significantly and strongly correlated. We review here the relevant biotic indices in stream biomonitoring and their advantages and disadvantages, and present a new extension of the DBI, the Habitat Condition Scale (HCS). The HCS enables comparison and ranking of sites in terms of their habitat condition. Indeed, the DBI is a very flexible index, having been used in site selection and prioritization for conservation, as well as the measurement of habitat recovery. The theoretical framework behind the index demonstrates the potential of the index to track biotic changes due to climate change. The index could also be easily adapted for use in other biogeographical regions, given that species distributions, threat levels and sensitivities are well-known, and that there is an adequate number of endemic species. However, like all benthic macroinvertebrate indices, the DBI cannot always identify exactly which in-water impacts have an effect and to what extent. The real power of the DBI lies in being able to quantify community response to known physical changes on the riverscape and across the region.     

Using Sex Pheromone and a Multi-Scale Approach to Predict the Distribution of a Rare Saproxylic Beetle

The European red click beetle, Elater ferrugineus L., is associated with wood mould in old hollow deciduous trees. As a result of severe habitat fragmentation caused by human disturbance, it is threatened throughout its distribution range. A new pheromone-based survey method, which is very efficient in detecting the species, was used in the present study to relate the occurrence of E. ferrugineus to the density of deciduous trees. The latter data were from a recently completed regional survey in SE Sweden recording >120,000 deciduous trees. The occurrence of E. ferrugineus increased with increasing amount of large hollow and large non-hollow trees in the surrounding landscape. Quercus robur (oak) was found to be the most important substrate for E. ferrugineus, whereas two groups of tree species (Carpinus betulus, Fagus sylvatica, Ulmus glabra, vs. Acer platanoides, Aesculus hippocastanum, Fraxinus excelsior, Tilia cordata) were less important but may be a complement to oak in sustaining populations of the beetle. The occurrence of E. ferrugineus was explained by the density of oaks at two different spatial scales, within the circle radii 327 m and 4658 m. In conclusion, priority should be given to oaks in conservation management of E. ferrugineus, and then to the deciduous trees in the genera listed above. Conservation planning at large spatial and temporal scales appears to be essential for long-term persistence of E. ferrugineus. We also show that occurrence models based on strategic sampling might result in pessimistic predictions. This study demonstrates how pheromone-based monitoring make insects excellent tools for sustained feedback to models for landscape conservation management.     

On the Use of Bone Remodelling Models to Estimate the Density Distribution of Bones. Uniqueness of the Solution

Bone remodelling models are widely used in a phenomenological manner to estimate numerically the distribution of apparent density in bones from the loads they are daily subjected to. These simulations start from an arbitrary initial distribution, usually homogeneous, and the density changes locally until a bone remodelling equilibrium is achieved. The bone response to mechanical stimulus is traditionally formulated with a mathematical relation that considers the existence of a range of stimulus, called dead or lazy zone, for which no net bone mass change occurs. Implementing a relation like that leads to different solutions depending on the starting density. The non-uniqueness of the solution has been shown in this paper using two different bone remodelling models: one isotropic and another anisotropic. It has also been shown that the problem of non-uniqueness is only mitigated by removing the dead zone, but it is not completely solved unless the bone formation and bone resorption rates are limited to certain maximum values.     

Using Environmental DNA to Estimate the Distribution of an Invasive Fish Species in Ponds

Knowledge of the presence of an invasive species is critical to monitoring the sustainability of communities and ecosystems. Environmental DNA (eDNA), DNA fragments that are likely to be bound to organic matters in the water or in shed cells, has been used to monitor the presence of aquatic animals. Using an eDNA-based method, we estimated the presence of the invasive bluegill sunfish, Lepomis macrochirus, in 70 ponds located in seven locales on the Japanese mainland and on surrounding islands. We quantified the concentration of DNA copies in a 1 L water sample using quantitative real-time polymerase chain reaction (qPCR) with a primer/probe set. In addition, we visually observed the bluegill presence in the ponds from the shoreline. We detected bluegill eDNA in all the ponds where bluegills were observed visually and some where bluegills were not observed. Bluegills were also less prevalent on the islands than the mainland, likely owing to limited dispersal and introduction by humans. Our eDNA method simply and rapidly detects the presence of this invasive fish species with less disturbance to the environment during field surveys than traditional methods.     

Simultaneously Capturing Real-time Images in Two Emission Channels Using a Dual Camera Emission Splitting System: Applications to Cell Adhesion

Multi-color immunofluorescence microscopy to detect specific molecules in the cell membrane can be coupled with parallel plate flow chamber assays to investigate mechanisms governing cell adhesion under dynamic flow conditions. For instance, cancer cells labeled with multiple fluorophores can be perfused over a potentially reactive substrate to model mechanisms of cancer metastasis. However, multi-channel single camera systems and color cameras exhibit shortcomings in image acquisition for real-time live cell analysis. To overcome these limitations, we used a dual camera emission splitting system to simultaneously capture real-time image sequences of fluorescently labeled cells in the flow chamber. Dual camera emission splitting systems filter defined wavelength ranges into two monochrome CCD cameras, thereby simultaneously capturing two spatially identical but fluorophore-specific images. Subsequently, psuedocolored one-channel images are combined into a single real-time merged sequence that can reveal multiple target molecules on cells moving rapidly across a region of interest.     

Using Fluorescent Proteins to Monitor Glycosome Dynamics in the African Trypanosome

Trypanosoma brucei is a kinetoplastid parasite that causes human African trypanosomiasis (HAT), or sleeping sickness, and a wasting disease, nagana, in cattle¹. The parasite alternates between the bloodstream of the mammalian host and the tsetse fly vector. The composition of many cellular organelles changes in response to these different extracellular conditions^2-5.Glycosomes are highly specialized peroxisomes in which many of the enzymes involved in glycolysis are compartmentalized. Glycosome composition changes in a developmental and environmentally regulated manner^4-11. Currently, the most common techniques used to study glycosome dynamics are electron and fluorescence microscopy; techniques that are expensive, time and labor intensive, and not easily adapted to high throughput analyses.To overcome these limitations, a fluorescent-glycosome reporter system in which enhanced yellow fluorescent protein (eYFP) is fused to a peroxisome targeting sequence (PTS2), which directs the fusion protein to glycosomes¹², has been established. Upon import of the PTS2eYFP fusion protein, glycosomes become fluorescent. Organelle degradation and recycling results in the loss of fluorescence that can be measured by flow cytometry. Large numbers of cells (5,000 cells/sec) can be analyzed in real-time without extensive sample preparation such as fixation and mounting. This method offers a rapid way of detecting changes in organelle composition in response to fluctuating environmental conditions.     

Using Fish Population Metrics to Compare the Effects of Artificial Reef Density

Artificial reefs continue to be added as habitat throughout the world, yet questions remain about how reef design affects fish diversity and abundance. In the present study, the effects of reef density were assessed for fish communities and sizes of economically valuable Lutjanus campechanus 13 km off Port Mansfield, Texas, at a reef composed of more than 4000 concrete culverts. The study spanned from May to June in 2013 and 2014, and sites sampled included natural reefs, bare areas, and varying culvert patch density categories, ranging from 1–190 culverts. Abundances of adults and species evenness of juvenile populations differed between the years. Fish communities did not significantly differ among density categories; however, highest species richness and total abundances were observed at intermediate culvert densities and at natural reefs. Whereas the abundance of L. campechanus did not differ among density categories, mean total lengths of L. campechanus were greatest at the lower density. Our findings suggest that reefs should be deployed with intermediate patch density of 71–120 culverts in a 30-m radius to yield the highest fish abundances.     

Trapping a folding intermediate of the alpha-helix: stabilization of the pi-helix

We report the design, synthesis, and characterization of a short peptide trapped in a pi-helix configuration. This high-energy conformation was nucleated by a preorganized pi-turn, which was obtained by replacing an N-terminal intramolecular main chain i and i + 5 hydrogen bond with a carbon-carbon bond. Our studies highlight the nucleation parameter as a key factor contributing to the relative instability of the pi-helix and allow us to estimate fundamental helix-coil transition parameters for this conformation.     

A Methodological Framework to Estimate the Site Fidelity of Tagged Animals Using Passive Acoustic Telemetry

The rapid expansion of the use of passive acoustic telemetry technologies has facilitated unprecedented opportunities for studying the behavior of marine organisms in their natural environment. This technological advance would greatly benefit from the parallel development of dedicated methodologies accounting for the variety of timescales involved in the remote detection of tagged animals related to instrumental, environmental and behavioral events. In this paper we propose a methodological framework for estimating the site fidelity (“residence times”) of acoustic tagged animals at different timescales, based on the survival analysis of continuous residence times recorded at multiple receivers. Our approach is validated through modeling and applied on two distinct datasets obtained from a small coastal pelagic species (bigeye scad, Selar crumenophthalmus) and a large, offshore pelagic species (yellowfin tuna, Thunnus albacares), which show very distinct spatial scales of behavior. The methodological framework proposed herein allows estimating the most appropriate temporal scale for processing passive acoustic telemetry data depending on the scientific question of interest. Our method provides residence times free of the bias inherent to environmental and instrumental noise that can be used to study the small scale behavior of acoustic tagged animals. At larger timescales, it can effectively identify residence times that encompass the diel behavioral excursions of fish out of the acoustic detection range. This study provides a systematic framework for the analysis of passive acoustic telemetry data that can be employed for the comparative study of different species and study sites. The same methodology can be used each time discrete records of animal detections of any nature are employed for estimating the site fidelity of an animal at different timescales.     

Using Satellite Remote Sensing to Estimate the Colored Dissolved Organic Matter Absorption Coefficient in Lakes

Given the importance of colored dissolved organic matter (CDOM) for the structure and function of lake ecosystems, a method that could estimate the amount of CDOM in lake waters over large geographic areas would be highly desirable. Satellite remote sensing has the potential to resolve this problem. We carried out model simulations to evaluate the suitability of different satellite sensors (Landsat, IKONOS, and the Advanced land Imager [ALI]) to map the amount of CDOM in concentration ranges that occur in boreal lakes of the Nordic countries. The results showed that the 8-bit radiometric resolution of Landsat 7 is not adequate when absorption by CDOM at 420 nm is higher than 3 m⁻¹. On the other hand, the 16-bit radiometric resolution of ALI, a prototype of the next generation of Landsat, is suitable for mapping CDOM in a wider range of concentrations. An ALI image of southern Finland was acquired on 14, July 2002 and in situ measurements were carried out in 15 lakes (18 stations). The results showed that there is a high correlation (R² = 0.84) between the 565 nm/660 nm ALI band ratio and the CDOM absorption coefficient in lakes. Analysis of 245 lakes in the acquired satellite image showed a normal distribution of CDOM concentration among the lakes. However, the size distribution of lakes was highly skewed toward small lakes, resulting in the CDOM concentration per unit lake area being skewed toward high values. We showed that remote sensing enables synoptic monitoring of the CDOM concentration in a large number of lakes and thus enables scaling up to the level of large ecosystems and biomes.     

Using Species Distribution Model to Estimate the Wintering Population Size of the Endangered Scaly-Sided Merganser in China

Scaly-sided Merganser is a globally endangered species restricted to eastern Asia. Estimating its population is difficult and considerable gap exists between populations at its breeding grounds and wintering sites. In this study, we built a species distribution model (SDM) using Maxent with presence-only data to predict the potential wintering habitat for Scaly-sided Merganser in China. Area under the receiver operating characteristic curve (AUC) method suggests high predictive power of the model (training and testing AUC were 0.97 and 0.96 respectively). The most significant environmental variables included annual mean temperature, mean temperature of coldest quarter, minimum temperature of coldest month and precipitation of driest quarter. Suitable conditions for Scaly-sided Merganser are predicted in the middle and lower reaches of the Yangtze River, especially in Jiangxi, Hunan and Hubei Provinces. The predicted suitable habitat embraces 6,984 km of river. Based on survey results from three consecutive winters (2010–2012) and previous studies, we estimated that the entire wintering population of Scaly-sided Merganser in China to be 3,561 ± 478 individuals, which is consistent with estimate in its breeding ground.     

Using the Prevalence of Individual Species of Intestinal Nematode Worms to Estimate the Combined Prevalence of Any Species

Objectives

To assess if a probabilistic model could be used to estimate the combined prevalence of infection with any species of intestinal nematode worm when only the separate prevalence of each species is reported, and to estimate the extent to which simply taking the highest individual species prevalence underestimates the combined prevalence.

Methods

Data were extracted from community surveys that reported both the proportion infected with individual species and the combined proportion infected, for a minimum sample of 100 individuals. The predicted combined proportion infected was calculated based on the assumption that the probability of infection with one species was independent of infection with another species, so the probability of combined infections was multiplicative.

Findings

Thirty-three reports describing 63 data sets from surveys conducted in 20 countries were identified. A strong correlation was found between the observed and predicted combined proportion infected (r = 0.996, P<0.001). When the observed and predicted values were plotted against each other, a small correction of the predicted combined prevalence by dividing by a factor of 1.06 achieved a near perfect correlation between the two sets of values. The difference between the single highest species prevalence and the observed combined prevalence was on average 7% or smaller at a prevalence of ≤40%, but at prevalences of 40–80%, the difference was about 12%.

Conclusions

A simple probabilistic model of combined infection with a small correction factor is proposed as a novel method to estimate the number of individuals that would benefit from mass deworming when data are reported only for separate species.