Two‐stage orthogonality based estimation for semiparametric varying‐coefficient models and its applications in analyzing AIDS data

Semiparametric smoothing methods are usually used to model longitudinal data, and the interest is to improve efficiency for regression coefficients. This paper is concerned with the estimation in semiparametric varying‐coefficient models (SVCMs) for longitudinal data. By the orthogonal projection method, local linear technique, quasi‐score estimation, and quasi‐maximum likelihood estimation, we propose a two‐stage orthogonality‐based method to estimate parameter vector, coefficient function vector, and covariance function. The developed procedures can be implemented separately and the resulting estimators do not affect each other. Under some mild conditions, asymptotic properties of the resulting estimators are established explicitly. In particular, the asymptotic behavior of the estimator of coefficient function vector at the boundaries is examined. Further, the finite sample performance of the proposed procedures is assessed by Monte Carlo simulation experiments. Finally, the proposed methodology is illustrated with an analysis of an acquired immune deficiency syndrome (AIDS) dataset.     

Methods matter: Different biodiversity survey methodologies identify contrasting biodiversity patterns in a human modified rainforest — A case study with amphibians

Understanding how well tropical forest biodiversity can recover following habitat change is often difficult due to conflicting assessments arising from different studies. One often overlooked potentially confounding factor that may influence assessments of biodiversity response to habitat change, is the possibility that different survey methodologies, targeting the same indicator taxon, may identify different patterns and so lead to different conclusions. Here we investigated whether two different but commonly used survey methodologies used to assess amphibian communities, pitfall trapping and nocturnal transects, indicate the same or different responses of amphibian biodiversity to historic human induced habitat change. We did so in a regenerating rainforest study site located in one of the world’s most biodiverse and important conservation areas: the Manu Biosphere Reserve. We show that the two survey methodologies tested identified contrasting biodiversity patterns in a human modified rainforest. Nocturnal transect surveys indicated biodiversity differences between forest with different human disturbance histories, whereas pitfall trap surveys suggested no differences between forest disturbance types, except for community composition. This pattern was true for species richness, diversity, overall abundance and community evenness and structure. For some fine scale metrics, such as species specific responses and abundances of family groups, both methods detected differences between disturbance types. However, the direction of differences was inconsistent between methods. We highlight that for assessments of rainforest recovery following disturbance, survey methods do matter and that different biodiversity survey methods can identify contrasting patterns in response to different types of historic disturbance. Our results contribute to a growing body of evidence that arboreal species might be more sensitive indicators than terrestrial communities.     

Return migration of Atlantic salmon in the River Tana: the role of environmental factors

Multi-sea-winter Atlantic salmon (75–115 cm fork length L _F, 2–4-winter fish) were radio-tagged in the Tanafjord (700 N), Norway, in 1992–1993, and 130 fish entered the large subarctic River Tana (Teno). They entered the fresh water at any time of the tidal cycle but more so during the high and ebbing tides. No diel rhythm was detected in river entry under polar day conditions. There were no differences in the change of flow between days when salmon moved and when they did not, but during active migration increasing discharge was associated with increased swimming activity of salmon, especially later in the summer. Increasing air temperature was also associated with enhanced migration activity. Low river flow was associated with increasing delay in salmon passing the first riffle area of the river, 35 km from the sea.     

Inter-relationships between standing crop, biodiversity and trait attributes of hydrophytic vegetation in artificial waterways

1. The extensive British canal system potentially provides a favourable habitat for aquatic plants and, because of its uniformity, it is ideal for studying relationships between disturbance intensity (largely from boat traffic) and communities of aquatic macrophytes. 2. The standing crop and species composition of aquatic plants were measured in summer at 396 sites distributed randomly over the canal network. We also quantified the number of rare species and ‘attribute groups’ (groups of species sharing similar suites of biological traits). These data were analysed in relation to standing crop, assumed to indicate a disturbance gradient. 3. Consistent with unimodal models and the Intermediate Disturbance Hypothesis, maximum hydrophyte species richness occurred at an intermediate biomass (50–200 g DWm^?2). This corresponded to a low frequency of low magnitude disturbance (light boat traffic) on navigable sections, or occasional high magnitude disturbance (the post‐interventionist phase) on sections currently unnavigable and subject to active vegetation management. The frequency of rare species was also the greatest under these conditions, reflecting the availability of regeneration niches. 4. Sorting of species into attribute groups revealed that the overall relationship between species richness and standing crop comprised of closely overlapping unimodal responses of nine attribute groups, superimposed on a core vegetation of Potamogeton pectinatus, together with greater representation of filamentous algae, lemnids and elodeids with increasing standing crop (i.e. assumed low disturbance). High species richness was associated with the overlap of functionally different groups of species, rather than with disturbance‐mediated coexistence of functionally similar plants. 5. The analysis of a matrix of sites and the representation of plant traits weighted by the biomass of species that displayed them, in relation to different aspects of disturbance, highlighted a shift from traits associated with resilience (turions, unanchored floating or submerged leaves, low body flexibility, budding, small body size), or competitiveness (entire leaves, low reproductive output, high biomass density, large body size) at high standing crop, through to attributes more associated with resistance to disturbance (rhizomes, tubers, streamlining of foliage, low biomass density) at low standing crop. 6. Comparison with a stochastic null model of change in species number along a constrained gradient, after correction for variation in sampling effort, indicated that sites towards the tails of the gradient (excluding those with extremely low biomass) supported more species than might be expected from chance alone, while the most species‐rich sites in mid‐gradient generally supported many fewer species than expected. 7. We suggest that a disturbance regime that maintains intermediate standing crops would be appropriate for the conservation of species‐rich aquatic vegetation. Precise definition of this regime, under a range of circumstances, requires the study of temporal change at representative sites.     

Furocoumarins from Angelica pachycarpa

A novel furocoumarin isolated from unripe fruits of Angelica pachycarpa has been characterized as (+)-tert- O-methylbyakangelicin. (+)-tert-O-Methyloxypeucedanin hydrate, neobyakangelicol, (±)-byakangelicol, (+)-byakangelicin, phellopterin, isoimperatorin, oxypeucedanin, oxypeucedanin hydrate, pangeline and umbelliprenin were also identified along with (±)-byakangelicin monoacetate, which proved to be an artifact.     

Scale‐dependent strategies for coexistence of mesocarnivores in human‐dominated landscapes

Identifying factors influencing the distribution of and interactions within carnivore communities is important for understanding how they are affected by human activities. Species differ in their ability to adapt to humans depending on their degree of specialization in habitat use and feeding habits. This results in asymmetric changes in the ecology of co‐occurring species that can influence their interactions. We investigated whether human infrastructures and free‐ranging domestic dogs (a species typically associated with humans) influenced the co‐occurrence and habitat use of mesocarnivores in a landscape of high human population density in Maharashtra, India. We used 40 camera trap locations during 233 trapping nights and used Bayesian co‐occurrence occupancy models to investigate the habitat use and coexistence of species at different spatial scales. Additionally, we investigated their temporal overlap in space use. Indian foxes altered their habitat use both spatially and temporally in order to avoid free‐ranging domestic dogs and other larger competitors. The use of human infrastructure by jackals and jungle cats was limited by the presence of dogs. Our results illustrate how habitat use of smaller carnivore species changes both spatially and temporally in order to avoid larger competitors. We also show that the presence of species associated with humans mediates the influence of human infrastructures on the habitat use of mesocarnivores. We highlight the importance of acknowledging the potential impact of urbanization not only on single species, but also on the interactions within the community.