On Professional Discourse in Folklore: A Response to Oring

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The heterogeneity of the biliary tree

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The Scattering Theory of Oscillator Defects in an Optical Fiber

We examine harmonic oscillator defects coupled to a photon field in the environs of an optical fiber. Using techniques borrowed or extended from the theory of two dimensional quantum fields with boundaries and defects, we are able to compute exactly a number of interesting quantities. We calculate the scattering S-matrices (i.e. the reflection and transmission amplitudes) of the photons off a single defect. We determine using techniques derived from thermodynamic Bethe ansatz (TBA) the thermodynamic potentials of the interacting photon-defect system. And we compute several correlators of physical interest. We find the photon occupancy at finite temperature, the spontaneous emission spectrum from the decay of an excited state, and the correlation functions of the defect degrees of freedom. In an extension of the single defect theory, we find the photonic band structure that arises from a periodic array of harmonic oscillators. In another extension, we examine a continuous array of defects and exactly derive its dispersion relation. With some differences, the spectrum is similar to that found for EM wave propagation in covalent crystals. We then add to this continuum theory isolated defects, so as to obtain a more realistic model of defects embedded in a frequency dependent dielectric medium. We do this both with a single isolated defect and with an array of isolated defects, and so compute how the S-matrices and the band structure change in a dynamic medium.Comment: 32 pages, TeX with harvmac macros, three postscript figure

Tunneling in a cavity

The mechanism of coherent destruction of tunneling found by Grossmann et al. [Phys. Rev. Lett. 67, 516 (1991)] is studied from the viewpoint of quantum optics by considering the photon statistics of a single mode cavity field which is strongly coupled to a two-level tunneling system (TS). As a function of the interaction time between TS and cavity the photon statistics displays the tunneling dynamics. In the semi-classical limit of high photon occupation number $n$, coherent destruction of tunneling is exhibited in a slowing down of an amplitude modulation for certain parameter ratios of the field. The phenomenon is explained as arising from interference between displaced number states in phase space which survives the large $n$ limit due to identical $n^{-1/2}$ scaling between orbit width and displacement.Comment: 4 pages Revtex, 2 PS-figures, appears in The Physical Review

Anaplasma phagocytophilum in White-tailed Deer

We examined the reservoir potential of white-tailed deer for Anaplasma phagocytophilum. Results suggest that white-tailed deer harbor a variant strain not associated with human infection, but contrary to published reports, white-tailed deer are not a reservoir for strains that cause human disease. These results will affect surveillance studies of vector and reservoir populations

Transforming the study of organisms: Phenomic data models and knowledge bases

The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem

Resource-Area-Dependence Analysis: inferring animal resource needs from home-range and mapping data

An animal’s home-range can be expected to encompass the resources it requires for surviving or reproducing. Thus, animals inhabiting a heterogeneous landscape, where resource patches vary in size, shape and distribution, will naturally have home-ranges of varied sizes, so that each home-range encompasses a minimum required amount of a resource. Home-range size can be estimated from telemetry data, and often key resources, or proxies for them such as the areas of important habitat types, can be mapped. We propose a new method, Resource-Area-Dependence Analysis (RADA), which uses a sample of tracked animals and a categorical map to i) infer in which map categories important resources are accessible, ii) within which home range cores they are found, and iii) estimate the mean minimum areas of these map categories required for such resource provision. We provide three examples of applying RADA to datasets of radio-tracked animals from southern England: 15 red squirrels Sciurus vulgaris, 17 gray squirrels S. carolinensis and 114 common buzzards Buteo buteo. The analyses showed that each red squirrel required a mean (95% CL) of 0.48 ha (0.24–-0.97) of pine wood within the outermost home-range, each gray squirrel needed 0.34 ha (0.11–1.12) ha of mature deciduous woodland and 0.035–0.046 ha of wheat, also within the outermost home-range, while each buzzard required 0.54 ha (0.35–0.82) of rough ground close to the home-range center and 14 ha (11–17) of meadow within an intermediate core, with 52% of them also relying on 0.41 ha (0.29–0.59) of suburban land near the home-range center. RADA thus provides a useful tool to infer key animal resource requirements during studies of animal movement and habitat use

FishNet: an online database of zebrafish anatomy

Background: Over the last two decades, zebrafish have been established as a genetically versatile model system for investigating many different aspects of vertebrate developmental biology. With the credentials of zebrafish as a developmental model now well recognized, the emerging new opportunity is the wider application of zebrafish biology to aspects of human disease modelling. This rapidly increasing use of zebrafish as a model for human disease has necessarily generated interest in the anatomy of later developmental phases such as the larval, juvenile, and adult stages, during which many of the key aspects of organ morphogenesis and maturation take place. Anatomical resources and references that encompass these stages are non-existent in zebrafish and there is therefore an urgent need to understand how different organ systems and anatomical structures develop throughout the life of the fish. Results: To overcome this deficit we have utilized the technique of optical projection tomography to produce three-dimensional (3D) models of larval fish. In order to view and display these models we have created FishNet http://www.fishnet.org.au, an interactive reference of zebrafish anatomy spanning the range of zebrafish development from 24 h until adulthood. Conclusion: FishNet contains more than 36 000 images of larval zebrafish, with more than 1 500 of these being annotated. The 3D models can be manipulated on screen or virtually sectioned. This resource represents the first complete embryo to adult atlas for any species in 3D

Quantitative Evidence for the Effects of Multiple Drivers on Continental-Scale Amphibian Declines

Since amphibian declines were first proposed as a global phenomenon over a quarter century ago, the conservation community has made little progress in halting or reversing these trends. The early search for a “smoking gun” was replaced with the expectation that declines are caused by multiple drivers. While field observations and experiments have identified factors leading to increased local extinction risk, evidence for effects of these drivers is lacking at large spatial scales. Here, we use observations of 389 time-series of 83 species and complexes from 61 study areas across North America to test the effects of 4 of the major hypothesized drivers of declines. While we find that local amphibian populations are being lost from metapopulations at an average rate of 3.79% per year, these declines are not related to any particular threat at the continental scale; likewise the effect of each stressor is variable at regional scales. This result - that exposure to threats varies spatially, and populations vary in their response - provides little generality in the development of conservation strategies. Greater emphasis on local solutions to this globally shared phenomenon is needed