Estimating the annual number of breeding attempts from breeding dates using mixture models

Well-established statistical methods exist to estimate variation in a number of key demographic rates from field data, including life-history transition probabilities and reproductive success per attempt. However, our understanding of the processes underlying population change remains incomplete without knowing the number of reproductive attempts individuals make annually; this is a key demographic rate for which we have no satisfactory method of estimating. Using census data to estimate this parameter from requires disaggregating the overlying temporal distributions of first and subsequent breeding attempts. We describe a Bayesian mixture method to estimate the annual number of reproductive attempts from field data to provide a new tool for demographic inference. We validate our method using comprehensive data on individually-marked song sparrows Melospiza melodia , and then apply it to more typical nest record data collected over 45 years on yellowhammers Emberiza citrinella . We illustrate the utility of our method by testing, and rejecting, the hypothesis that declines in UK yellowhammer populations have occurred concurrently with declines in annual breeding frequency.     

Biases in Multicenter Longitudinal PET Standardized Uptake Value Measurements

This study investigates measurement biases in longitudinal positron-emission tomography/computed tomography (PET/CT) studies that are due to instrumentation variability including human error. Improved estimation of variability between patient scans is of particular importance for assessing response to therapy and multicenter trials. We used National Institute of Standards and Technology-traceable calibration methodology for solid germanium-68/gallium-68 (⁶⁸Ge/⁶⁸Ga) sources used as surrogates for fluorine-18 (¹⁸F) in radionuclide activity calibrators. One cross-calibration kit was constructed for both dose calibrators and PET scanners using the same 9-month half-life batch of ⁶⁸Ge/⁶⁸Ga in epoxy. Repeat measurements occurred in a local network of PET imaging sites to assess standardized uptake value (SUV) errors over time for six dose calibrators from two major manufacturers and for six PET/CT scanners from three major manufacturers. Bias in activity measures by dose calibrators ranged from -50% to 9% and was relatively stable over time except at one site that modified settings between measurements. Bias in activity concentration measures by PET scanners ranged from -27% to 13% with a median of 174 days between the six repeat scans (range, 29 to 226 days). Corresponding errors in SUV measurements ranged from -20% to 47%. SUV biases were not stable over time with longitudinal differences for individual scanners ranging from -11% to 59%. Bias in SUV measurements varied over time and between scanner sites. These results suggest that attention should be paid to PET scanner calibration for longitudinal studies and use of dose calibrator and scanner cross-calibration kits could be helpful for quality assurance and control.     

An Isonema-like flagellate (Protozoa: Mastigophora) infection in larval geoduck clams, Panope abrupta

Cultured geoduck clam (Panope abrupta) larvae were naturally infected with an Isonema-like flagellate. Free-swimming larval clams were initially infected by flagellates that penetrated the mantle and proliferated within the coelom. Larvae with heavy infections accumulated on the tank bottoms and ultimately died. The protozoan was identified as an Isonema-like flagellate based primarily on the presence of a distinctive ingestion apparatus composed of a microtubule complex, the presence of large, peripherally oriented mitochondria with sparse cristae, subplasmalemmal microtubules, the lack of a pellicle, short flagella, and pronounced metaboly. This is the first report of an invasive, pathogenic Isonema and the first report of a protozoan disease of a larval bivalve mollusc.     

Root hydrocarbons as potential markers for determining species composition

Grasslands can be a complex mixture of plant species. A method is described to allow the identification of both roots and shoots of five different grass species, thus permitting greater knowledge about whole plant allocation and competition in mixed pastures. The five species were Lolium perenne, Festuca ovina, Festuca rubra, Poa trivialis and Agrostis capillaris. N‐alkanes with odd‐numbers of carbon atoms in the chains predominate in plants and in the five grass species studied, concentrations of alkanes of chain length of C₂₉, C₃₁ and C₃₃ were highest. Average concentrations of C₂₇‐C₃₃ alkanes in shoots and roots were 187 and 11 mg kg ^{? 1}, respectively. This wide range of values required considerable modifications to the method of analysis, including expressing concentrations on an organic matter basis and scaling‐down the procedure. The n‐alkane concentrations in roots are different from those in shoots and therefore values from shoots cannot be used to predict the composition in roots. Using a canonical variate analysis, all five grass species could be separated using concentrations of C₂₆, C₃₁ and C₃₃ values in the roots. The greatest difference occurred between A. capillaris and the others, whereas discrimination was least between the two Festuca species. Defoliation had contrasting effects on the concentration of a few n‐alkanes, but not in the n‐alkanes used to discriminate between grass species. Alkane analysis shows great potential as a method to quantify the species composition of the root biomass beneath mixed pasture species.     

Fluorescence of fungi in superficial and deep fungal infections

Background  

Fluorescence of many fungi is noted when H&E stained sections are examined under a fluorescent microscope. In theory, this phenomenon could aid in the diagnosis of cutaneous and disseminated fungal infections without the delay associated with special stains. Seventy-six cases of superficial and deep fungal infections and 3 cases of protothecosis were studied to determine the clinical usefulness of this technique.     

Lack of evidence for segregation of a single dominant major gene as the cause of the difference in egg weight between two highly inbred lines of chickens

Data on egg weight from experimental crosses with two inbred lines of chickens suggested evidence for segregation of a single dominant major gene. Because the data could not be transformed to satisfy normality and homoscedasticity conditions, the non-parametric test of Elston and the graphical approach used by Stolk et al. were applied. Due to a bad fit of the backcross B2 (P₂×F1) and the F2 groups, both methods reject the hypothesis of a dominant major gene as the the only cause of the differences in egg weight between the six genetic groups involved.     

Bivalve mollusc viruses

Bivalve molluscs can bioaccumulate, in their tissues, well known viruses that infect humans and higher animals. However, since 1969 there have been reports, based largely on ultrastructural studies, that have indicated there are also viruses which infect these molluscs. Lack of bivalve molluscan cell lines has limited the isolation of these viruses, although some viruses isolated in fish cell lines are claimed to be infective for bivalves. Distinctive morphogenesis and characteristics of iridoviruses have been reported in larval and adult oysters in association with infections of epithelial and haemocytic tissues. Herpes viruses have been reported in the American oyster, Pacific oyster, and European flat oyster from three continents. The herpes viral agent in Pacific oysters has been experimentally transmitted and requires temperatures of 25–26°C for a productive infection and clinical disease. Papova-like viruses, picorna-like, and other small virus-like particles have been reported in several bivalve species. A leukemia-like disease of many bivalve species, collectively termed disseminated neoplasias, is of unconfirmed aetiology, but may be related to retroviral infections. Representatives of the Reoviridae and Birnaviridae have been isolated by using fish cell lines. One definitive study concludes that at least one example is not infective for bivalves while other studies claim molluscan infectivity. Phages have been reported in three pathogenic agents infecting bivalves. Advancement in the field of molluscan virology will require increased application of physical isolation methods, refinement of primary cell culture methods, use of molecular diagnostic tools, and the development of continuous molluscan cell lines.