601 research outputs found
INTEGRATING AUTOMATED IMAGING AND A NOVEL IDENTIFICATION TECHNIQUE TO ESTIMATE MORTALITY AND IDENTIFY FACTORS THAT INFLUENCE THE VERTICAL DISTRIBUTION OF CRASSOSTREA VIRGINICA LARVAE
Understanding the population dynamics and complete life cycle of bivalves is important for effectively manage them. Most of the literature and research to date has focused on juvenile and adult bivalves, much less is known about larvae. The larval stage of the bivalve life cycle has been difficult to study due to the lack of a rapid automated approach for identifying species. However, a new technique, called ShellBi, has emerged that utilizes color patterns on the larval shell under polarized light to identify bivalve larvae. The objective of this chapter was to review the scientific basis for ShellBi and to apply it to bivalve larvae in Choptank River with the goal of distinguishing C. virginica from seven other species that spawn at the same time. A digital camera and polarized light microscope were used to capture images of the shells of bivalve larvae under standard and cross-polarized light. Images of C. virginica were distinguishable from other species based on these patterns, especially at later stages of development. These images could serve as a visual guide to identify C. virginica collected from the Choptank River and other tributaries with similar species in Chesapeake Bay
Efficient operator method for modeling mode mixing in misaligned optical cavities
The transverse field structure and diffraction loss of the resonant modes of Fabry-Pérot optical cavities are acutely sensitive to the alignment and shape of the mirror substrates. We develop extensions to the mode-mixing method applicable to arbitrary mirror shapes, which both facilitate fast calculation of the modes of cavities with transversely misaligned mirrors and enable the determination and transformation of the geometric properties of these modes. We show how these methods extend previous capabilities by including the practically motivated case of transverse mirror misalignment, presenting the ability to study the rich and complex structure of the resonant modes
Estimating connectivity of hard clam (Mercenaria mercenaria) and eastern oyster (Crassostrea virginica) larvae in Barnegat Bay
© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Goodwin, J. D., Munroe, D. M., Defne, Z., Ganju, N. K., & Vasslides, J. Estimating connectivity of hard clam (Mercenaria mercenaria) and eastern oyster (Crassostrea virginica) larvae in Barnegat Bay. Journal of Marine Science and Engineering, 7(6), (2019): 167, doi:10.3390/jmse7060167.Many marine organisms have a well-known adult sessile stage. Unfortunately, our lack of knowledge regarding their larval transient stage hinders our understanding of their basic ecology and connectivity. Larvae can have swimming behavior that influences their transport within the marine environment. Understanding the larval stage provides insight into population connectivity that can help strategically identify areas for restoration. Current techniques for understanding the larval stage include modeling that combines particle attributes (e.g., larval behavior) with physical processes of water movement to contribute to our understanding of connectivity trends. This study builds on those methods by using a previously developed retention clock matrix (RCM) to illustrate time dependent connectivity of two species of shellfish between areas and over a range of larval durations. The RCM was previously used on physical parameters but we expand the concept by applying it to biology. A new metric, difference RCM (DRCM), is introduced to quantify changes in connectivity under different scenarios. Broad spatial trends were similar for all behavior types with a general south to north progression of particles. The DRCMs illustrate differences between neutral particles and those with behavior in northern regions where stratification was higher, indicating that larval behavior influenced transport. Based on these findings, particle behavior led to small differences (north to south movement) in transport patterns in areas with higher salinity gradients (the northern part of the system) compared to neutral particles. Overall, the dominant direction for particle movement was from south to north, which at times was enhanced by winds from the south. Clam and oyster restoration in the southern portion of Barnegat Bay could serve as a larval supply for populations in the north. These model results show that coupled hydrodynamic and particle tracking models have implications for fisheries management and restoration activities.This work is supported by the Barnegat Bay Partnership EPA grants CE98212311, CE98212312.
We extend our deep thanks to anonymous reviewers and Lisa Lucas who provided thoughtful input that improved
the manuscript. We thank Matthew Kozak and Ian Mitchell for technical advice and Elizabeth North for LTRANS
guidance. Joe Caracapa and Jennifer Gius provided help running remote simulations. COAST model source code
is available at https://code.usgs.gov/coawstmodel/COAWST [50]. The hydrodynamic model outoput is available
at: http://geoport.whoi.edu/thredds/catalog/clay/usgs/users/zdefne/GRL/catalog.html [21] and particle tracking
model outputs are available from the corresponding author upon request
Mode mixing and losses in misaligned microcavities
We present a study on the optical losses of Fabry-P\'erot cavities subject to
realistic transverse mirror misalignment. We consider mirrors of the two most
prevalent surface forms: idealised spherical depressions, and Gaussian profiles
generated by laser ablation. We first describe the mode mixing phenomena seen
in the spherical mirror case and compare to the frequently-used clipping model,
observing close agreement in the predicted diffraction loss, but with the
addition of protective mode mixing at transverse degeneracies. We then discuss
the Gaussian mirror case, detailing how the varying surface curvature across
the mirror leads to complex variations in round trip loss and mode profile. In
light of the severe mode distortion and strongly elevated loss predicted for
many cavity lengths and transverse alignments when using Gaussian mirrors, we
suggest that the consequences of mirror surface profile are carefully
considered when designing cavity experiments.Comment: 16 pages, 12 figure
Efficient operator method for modelling mode mixing in misaligned optical cavities
The transverse field structure and diffraction loss of the resonant modes of
Fabry-P\'erot optical cavities are acutely sensitive to the alignment and shape
of the mirror substrates. We develop extensions to the `mode mixing' method
applicable to arbitrary mirror shapes, which both facilitate fast calculation
of the modes of cavities with transversely misaligned mirrors and enable the
determination and transformation of the geometric properties of these modes. We
show how these methods extend previous capabilities by including the
practically-motivated case of transverse mirror misalignment, unveiling rich
and complex structure of the resonant modes.Comment: 17 pages, 7 figure
Optimisation of Scalable Ion-Cavity Interfaces for Quantum Photonic Networks
In the design optimisation of ion-cavity interfaces for quantum networking
applications, difficulties occur due to the many competing figures of merit and
highly interdependent design constraints, many of which present `soft-limits',
amenable to improvement at the cost of engineering time. In this work we
present a systematic approach to this problem which offers a means to identify
efficient and robust operating regimes, and to elucidate the trade-offs
involved in the design process, allowing engineering efforts to be focused on
the most sensitive and critical parameters. We show that in many relevant cases
it is possible to approximately separate the geometric aspects of the
cooperativity from those associated with the atomic system and the mirror
surfaces themselves, greatly simplifying the optimisation procedure. Although
our approach to optimisation can be applied to most operating regimes, here we
consider cavities suitable for typical ion trapping experiments, and with
substantial transverse misalignment of the mirrors. We find that cavities with
mirror misalignments of many micrometres can still offer very high photon
extraction efficiencies, offering an appealing route to the scalable production
of ion-cavity interfaces for large scale quantum networks
Molecular Distributions in Gene Regulatory Dynamics
We show how one may analytically compute the stationary density of the
distribution of molecular constituents in populations of cells in the presence
of noise arising from either bursting transcription or translation, or noise in
degradation rates arising from low numbers of molecules. We have compared our
results with an analysis of the same model systems (either inducible or
repressible operons) in the absence of any stochastic effects, and shown the
correspondence between behaviour in the deterministic system and the stochastic
analogs. We have identified key dimensionless parameters that control the
appearance of one or two steady states in the deterministic case, or unimodal
and bimodal densities in the stochastic systems, and detailed the analytic
requirements for the occurrence of different behaviours. This approach
provides, in some situations, an alternative to computationally intensive
stochastic simulations. Our results indicate that, within the context of the
simple models we have examined, bursting and degradation noise cannot be
distinguished analytically when present alone.Comment: 14 pages, 12 figures. Conferences: "2010 Annual Meeting of The
Society of Mathematical Biology", Rio de Janeiro (Brazil), 24-29/07/2010.
"First International workshop on Differential and Integral Equations with
Applications in Biology and Medicine", Aegean University, Karlovassi, Samos
island (Greece), 6-10/09/201
A pilot study comparing the metabolic profiles of elite-level athletes from different sporting disciplines
Background: The outstanding performance of an elite athlete might be associated with changes in their blood metabolic profile. The aims of this study were to compare the blood metabolic profiles between moderate- and high-power and endurance elite athletes and to identify the potential metabolic pathways underlying these differences. Methods: Metabolic profiling of serum samples from 191 elite athletes from different sports disciplines (121 high- and 70 moderate-endurance athletes, including 44 high- and 144 moderate-power athletes), who participated in national or international sports events and tested negative for doping abuse at anti-doping laboratories, was performed using non-targeted metabolomics-based mass spectroscopy combined with ultrahigh-performance liquid chromatography. Multivariate analysis was conducted using orthogonal partial least squares discriminant analysis. Differences in metabolic levels between high- and moderate-power and endurance sports were assessed by univariate linear models. Results: Out of 743 analyzed metabolites, gamma-glutamyl amino acids were significantly reduced in both high-power and high-endurance athletes compared to moderate counterparts, indicating active glutathione cycle. High-endurance athletes exhibited significant increases in the levels of several sex hormone steroids involved in testosterone and progesterone synthesis, but decreases in diacylglycerols and ecosanoids. High-power athletes had increased levels of phospholipids and xanthine metabolites compared to moderate-power counterparts. Conclusions: This pilot data provides evidence that high-power and high-endurance athletes exhibit a distinct metabolic profile that reflects steroid biosynthesis, fatty acid metabolism, oxidative stress, and energy-related metabolites. Replication studies are warranted to confirm differences in the metabolic profiles associated with athletes’ elite performance in independent data sets, aiming ultimately for deeper understanding of the underlying biochemical processes that could be utilized as biomarkers with potential therapeutic implications
Synchronous beta rhythms of frontoparietal networks support only behaviorally relevant representations
Categorization has been associated with distributed networks of the primate brain, including the prefrontal cortex (PFC) and posterior parietal cortex (PPC). Although category-selective spiking in PFC and PPC has been established, the frequency-dependent dynamic interactions of frontoparietal networks are largely unexplored. We trained monkeys to perform a delayed-match-to-spatial-category task while recording spikes and local field potentials from the PFC and PPC with multiple electrodes. We found category-selective beta- and delta-band synchrony between and within the areas. However, in addition to the categories, delta synchrony and spiking activity also reflected irrelevant stimulus dimensions. By contrast, beta synchrony only conveyed information about the task-relevant categories. Further, category-selective PFC neurons were synchronized with PPC beta oscillations, while neurons that carried irrelevant information were not. These results suggest that long-range beta-band synchrony could act as a filter that only supports neural representations of the variables relevant to the task at hand.National Institute of Mental Health (U.S.) (4R01MH065252)Prop. 63 the Mental Health Services ActUniversity of California, Davis. Behavioral Health Center of Excellenc
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Cigarette Smoke Toxins Deposited on Surfaces: Implications for Human Health
Cigarette smoking remains a significant health threat for smokers and nonsmokers alike. Secondhand smoke (SHS) is intrinsically more toxic than directly inhaled smoke. Recently, a new threat has been discovered – Thirdhand smoke (THS) – the accumulation of SHS on surfaces that ages with time, becoming progressively more toxic. THS is a potential health threat to children, spouses of smokers and workers in environments where smoking is or has been allowed. The goal of this study is to investigate the effects of THS on liver, lung, skin healing, and behavior, using an animal model exposed to THS under conditions that mimic exposure of humans. THS-exposed mice show alterations in multiple organ systems and excrete levels of NNAL (a tobacco-specific carcinogen biomarker) similar to those found in children exposed to SHS (and consequently to THS). In liver, THS leads to increased lipid levels and non-alcoholic fatty liver disease, a precursor to cirrhosis and cancer and a potential contributor to cardiovascular disease. In lung, THS stimulates excess collagen production and high levels of inflammatory cytokines, suggesting propensity for fibrosis with implications for inflammation-induced diseases such as chronic obstructive pulmonary disease and asthma. In wounded skin, healing in THS-exposed mice has many characteristics of the poor healing of surgical incisions observed in human smokers. Lastly, behavioral tests show that THS-exposed mice become hyperactive. The latter data, combined with emerging associated behavioral problems in children exposed to SHS/THS, suggest that, with prolonged exposure, they may be at significant risk for developing more severe neurological disorders. These results provide a basis for studies on the toxic effects of THS in humans and inform potential regulatory policies to prevent involuntary exposure to THS
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