Population ecology of the littoral fringe gastropod Littorina planaxis in Northern California

Life history patterns of individual organisms are the result of natural selection and should be correlated with particular physical and biological characteristics of habitats in which they live. The littoral fringe is known to be the most severe physical habitat in the intertidal zone, and it is expected that organisms in it should have population characteristics associated with selective response to physical adversity rather than biological interaction. Ecological studies of populations of Littorina planaxis were made in the Dillon Beach and Bodega Head areas. The study localities differed principally in extent of wave exposure rather than geographical location

Triggers and maintenance of multiple shifts in the state of a natural community

Ecological communities can undergo sudden and dramatic shifts between alternative persistent community states. Both ecological prediction and natural resource management rely on understanding the mechanisms that trigger such shifts and maintain each state. Differentiating between potential mechanisms is difficult, however, because shifts are often recognized only in hindsight and many occur on such large spatial scales that manipulative experiments to test their causes are difficult or impossible. Here we use an approach that focuses first on identifying changes in environmental factors that could have triggered a given state change, and second on examining whether these changes were sustained (and thus potentially maintained the new state) or transitory (explaining the shift but not its persistence). We use this approach to evaluate a community shift in which a benthic marine species of filter feeding sea cucumber (Pachythyone rubra) suddenly came to dominate subtidal rocky reefs that had previously supported high abundances of macroalgae, persisted for more than a decade, then abruptly declined. We found that a sustained period without large wave events coincided with the shift to sea cucumber dominance, but that the sea cucumbers persisted even after the end of this low wave period, indicating that different mechanisms maintained the new community. Additionally, the period of sea cucumber dominance occurred when their predators were rare, and increases in the abundance of these predators coincided with the end of sea cucumber dominance. These results underscore the complex nature of regime shifts and illustrate that focusing separately on the causes and maintenance of state change can be a productive first step for analyzing these shifts in a range of systems

A Novel Method for Polarization Squeezing with Photonic Crystal Fibers

Photonic Crystal Fibers can be tailored to increase the effective Kerr nonlinearity, while producing smaller amounts of excess noise compared to standard silicon fibers. Using these features of Photonic Crystal Fibers we create polarization squeezed states with increased purity compared to standard fiber squeezing experiments. Explicit we produce squeezed states in counter propagating pulses along the same fiber axis to achieve near identical dispersion properties. This enables the production of polarization squeezing through interference in a polarization type Sagnac interferometer. We observe Stokes parameter squeezing of -3.9 +/- 0.3dB and anti-squeezing of 16.2 +/- 0.3dB.Comment: 7 pages, 5 figure

Sublethal toxicant effects with dynamic energy budget theory: application to mussel outplants

We investigate the effectiveness of a sublethal toxic effect model embedded in Dynamic Energy Budget (DEB) theory for the analysis of field data. We analyze the performance of two species of mussels, Mytilus galloprovincialis and M. californianus, near a diffuser discharging produced water in the Southern California Bight, California. Produced water is a byproduct of oil production consisting of fossil water together with compounds added during the extraction process, and generally contains highly elevated levels of pollutants relative to sea water. Produced water negatively affects the production of somatic and reproductive biomass in both mussel species; we show that these negative effects can be quantified with our DEB-based modeling framework through the estimation of toxic effect scaling parameters. Our analyses reveal that the toxic impact of produced water on growth and reproduction of M. californianus is substantially higher than for M. galloprovincialis. Projections of the expected lifetime production of gonad biomass indicate that the environmental impact of produced water can be as large as 100%, whereas short-term assessment without the use of DEB theory projects a maximum effect of only 30%

Use of an automated, integrated laboratory environment to enable predictive modeling approaches for identifying critical process parameters and controlling key quality attributes

An essential part of ensuring a high quality medicine is being able to reliably control Critical Quality Attributes (CQA’s). In the cell culture process, bioreactor conditions, feeds, cell state are some of the many variables that affect CQA’s. Out of this very large set of possible variables, the small subset of these (i.e., critical process parameters, or CPP’s) that have a large effect on the CQA’s must be identified and understood such that those CPP’s can be controlled to ensure quality product. Here, we demonstrate the use of predictive modeling techniques to supplement experimental bioreactor studies when defining critical process parameters (CPP’s) and generating process control strategies. Using predictive models to relate culture process conditions to CQA’s has the benefit of enabling both: 1) using model predictions to supplement experimental data when determining critical process parameters (CPP’s) and the resulting control strategy, and 2) active control of CQA’s based on model forecasts to achieve finer control of CQA’s. In order to support this predictive forecasting approach for bioreactor process definition and control, Bend Research has developed a new bioreactor laboratory environment that allows us to run the right experiments, take the right data, and determine which measurements are actually important in determining CQA’s, and to generate model predictions based on those data sets. Here we demonstrate the application of this new laboratory paradigm in practice, using galactosylation, an important product quality attribute, as the “CQA” of interest. We show how through using automated, perfusion-type systems identification experiments, combined with automated data-generation and reduction tools, we can generate a prediction of the effect of galactose feeding on product qualit

Research priorities in cardiovascular imaging.

AIM: A modified Delphi approach was used to develop consensus opinion among British Society for Cardiac Imaging/British Society of Cardiac CT (BSCI/BSCCT) members in order to prioritise research questions in cardiovascular imaging. METHODS: All members of the BSCI/BSCCT were invited to submit research questions that they considered to be of the highest clinical and/or academic priority in the field of cardiovascular imaging (phase 1). Subsequently a steering committee removed duplicate questions and combined questions of a similar theme by consensus agreement where appropriate. BSCI/BSCCT members were invited to rank the resulting research questions in two further iterative rounds (phases 2 and 3) to determine a final list of high-priority research questions. RESULTS: A total of 111 research questions were submitted in phase 1 by 30 BSCI/BSCCT members. While there was a broad range of topics, from determining the optimal features/markers of the vulnerable plaque to investigating how cardiac imaging can best be used to maximise clinical outcomes and economic costs, multimodality imaging-related (n=44, 40%) questions dominated the categories and coronary artery imaging (n=40, 36%) was the most common topic. Over two iterative rounds of prioritisation of these research questions, the original 111 were reduced to 75 questions in round 2, and 25 in round 3. From these 25 a final Top 10 list was distilled by consensus grouping. CONCLUSION: This study has identified and ranked the top research priorities in cardiovascular imaging, as identified by the BSCI/BSCCT membership. This is a first step towards identifying the cardiovascular imaging research priorities within the UK and may assist researchers and funding bodies alike in setting priorities

Long-term anaesthesia of broiler chickens

Objective To provide stable anaesthesia of long duration in broiler chickens in order to perform a terminal caecal ligated loop procedure. Study design Prospective experimental study. Animals Seven clinically healthy broiler chickens (Gallus domesticus) aged 27–36 days, weighing 884–2000 g. Methods Anaesthesia was induced and maintained with isoflurane in oxygen. All birds underwent intermittent positive pressure ventilation for the duration. End-tidal carbon dioxide, peripheral haemoglobin oxygen saturation, heart rate and oesophageal temperature were monitored continuously. All birds received intraosseous fluids. Butorphanol (2 mg kg–1) was administered intramuscularly at 2 hourly intervals. Euthanasia by parenteral pentobarbitone was performed at the end of procedure. Results Stable anaesthesia was maintained in four chickens for durations ranging from 435 to 510 minutes. One bird died and one was euthanized after 130 and 330 minutes, respectively, owing to surgical complications and another died from anaesthetic complication after 285 minutes. Conclusions and clinical relevance Long-term, stable anaesthesia is possible in clinically healthy chickens, provided complications such as hypothermia and hypoventilation are addressed and vital signs are carefully monitored. There are no known previous reports describing monitored, controlled anaesthesia of this duration in chickens

PocketMatch: A new algorithm to compare binding sites in protein structures

Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental
requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of
the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison.

Results: Here we present a new algorithm PocketMatch for comparison of binding sites in a frame invariant
manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites. A comprehensive sensitivity analysis and an extensive validation of the algorithm have been carried out. Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unless
combined with chemical nature of amino acids.

Conclusions: A new algorithm has been developed to compare binding sites in accurate, efficient and
high-throughput manner. Though the representation used is conceptually simplistic, we demonstrate that along
with the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. Novel methodology has also been presented for validating the algorithm for accuracy and sensitivity with respect to geometry and chemical nature of the site. The method is also fast and takes about 1/250th second for one comparison on a single processor. A parallel version on BlueGene has also been implemented

Coral Reef Monitoring by Scuba Divers Using Underwater Photogrammetry and Geodetic Surveying

Underwater photogrammetry is increasingly being used by marine ecologists because of its ability to produce accurate, spatially detailed, non-destructive measurements of benthic communities, coupled with affordability and ease of use. However, independent quality control, rigorous imaging system set-up, optimal geometry design and a strict modeling of the imaging process are essential to achieving a high degree of measurable accuracy and resolution. If a proper photogrammetric approach that enables the formal description of the propagation of measurement error and modeling uncertainties is not undertaken, statements regarding the statistical significance of the results are limited. In this paper, we tackle these critical topics, based on the experience gained in the Moorea Island Digital Ecosystem Avatar (IDEA) project, where we have developed a rigorous underwater photogrammetric pipeline for coral reef monitoring and change detection. Here, we discuss the need for a permanent, underwater geodetic network, which serves to define a temporally stable reference datum and a check for the time series of photogrammetrically derived three-dimensional (3D) models of the reef structure. We present a methodology to evaluate the suitability of several underwater camera systems for photogrammetric and multi-temporal monitoring purposes and stress the importance of camera network geometry to minimize the deformations of photogrammetrically derived 3D reef models. Finally, we incorporate the measurement and modeling uncertainties of the full photogrammetric process into a simple and flexible framework for detecting statistically significant changes among a time series of models