Movements, Growth, and Mortality of Chesapeake Bay Summer Flounder Based on Multiple Tagging Technologies

The research projects presented in this dissertation used multiple tagging technologies to examine the movements, growth, and mortality rates of summer flounder tagged and released in Chesapeake Bay. In the first two chapters, I used acoustic, archival, and conventional tags to examine the behavior of summer flounder on different spatial scales. Investigating the movement behavior of individuals on different scales is an important step towards understanding how large-scale distributions of a population are established. Based on the observed behaviors of summer flounder, I hypothesize that the movements of these fish are primarily related to foraging behavior while they are resident in Chesapeake Bay. In the third chapter, I use growth models to investigate hypotheses regarding recreational angler noncompliance with minimum size regulations in Virginia. Angler noncompliance with management regulations can severely degrade the ability of fishery managers to prevent overexploitation of fish populations. Using a growth model fit to recreational angler mark-recapture data, I demonstrate that recreational anglers in Virginia responded to changes in summer flounder management regulations, but considerable levels of noncompliance were detected in years when management agencies drastically increased the minimum size regulations. In the final chapter, I attempt to estimate natural and fishing mortality rates of summer flounder using conventional mark-recapture data collected by an angler tagging program. These mortality rates were estimated using a Barker model, which is a generalization of the Cormack-Jolly-Seber tagging model. Results from this study indicated that sublegal summer flounder experience different emigration or mortality processes than do larger fish. Furthermore, handling and tagging mortality rates of summer flounder were much larger than the recreational discard mortality rate currently used in the stock assessment, implying that the recreational discard mortality rate should be reexamined. The research presented in this dissertation provides information that could be used by management agencies to further understand the behavior of summer flounder, and how to most effectively manage this population

Measurements and Predictions of the Noise from Three-Stream Jets

An experimental and numerical investigation of the noise produced by high-subsonic and supersonic three-stream jets was conducted. The exhaust system consisted of externally-mixed-convergent nozzles and an external plug. Bypass- and tertiary-to-core area ratios between 1.0 and 2.5, and 0.4 and 1.0, respectively, were studied. Axisymmetric and offset tertiary nozzles were investigated for heated and unheated conditions. For axisymmetric configurations, the addition of the third stream was found to reduce peak- and high-frequency acoustic levels in the peak-jet-noise direction, with greater reductions at the lower bypass-to-core area ratios. For the offset configurations, an offset duct was found to decrease acoustic levels on the thick side of the tertiary nozzle relative to those produced by the simulated two-stream jet with up to 8 dB mid-frequency noise reduction at large angles to the jet inlet axis. Noise reduction in the peak-jet-noise direction was greater for supersonic core speeds than for subsonic core speeds. The addition of a tertiary nozzle insert used to divert the third-stream jet to one side of the nozzle system provided no noise reduction. Noise predictions are presented for selected cases using a method based on an acoustic analogy with mean flow interaction effects accounted for using a Green's function, computed in terms of its coupled azimuthal modes for the offset cases, and a source model previously used for round and rectangular jets. Comparisons of the prediction results with data show that the noise model predicts the observed increase in low-frequency noise with the introduction of a third, axisymmetric stream, but not the high-frequency reduction. For an offset third stream, the model predicts the observed trend of decreased sound levels on the thick side of the jet compared with the thin side, but the predicted azimuthal variations are much less than those seen in the data. Also, the shift of the spectral peak to lower frequencies with increasing polar angle is over-predicted. For an offset third stream with a heated core, it is shown that including the enthalpy-flux source terms in the acoustic analogy model improves predictions compared with those obtained using only the momentum flux

Measurements and Predictions of the Noise from Three-Stream Jets

An experimental and numerical investigation of the noise produced by high-subsonic and supersonic three-stream jets was conducted. The exhaust system consisted of externally-mixed-convergent nozzles and an external plug. Bypass- and tertiary- to-core area ratios between 1.0 and 2.5, and 0.4 and 1.0, respectively, were studied. Axisymmetric and offset tertiary nozzles were investigated for heated and unheated conditions. For axisymmetric configurations, the addition of the third stream was found to reduce peak- and high-frequency acoustic levels in the peak-jet-noise direction, with greater reductions at the lower bypass-to-core area ratios. For the offset configurations, an offset duct was found to decrease acoustic levels on the thick side of the tertiary nozzle relative to those produced by the simulated two-stream jet with up to 8 dB mid-frequency noise reduction at large angles to the jet inlet axis. Noise reduction in the peak-jet-noise direction was greater for supersonic core speeds than for subsonic core speeds. The addition of a tertiary nozzle insert used to divert the third-stream jet to one side of the nozzle system provided no noise reduction. Noise predictions are presented for selected cases using a method based on an acoustic analogy with mean flow interaction effects accounted for using a Green's function, computed in terms of its coupled azimuthal modes for the offset cases, and a source model previously used for round and rectangular jets. Comparisons of the prediction results with data show that the noise model predicts the observed increase in low-frequency noise with the introduction of a third, axisymmetric stream, but not the high-frequency reduction. For an offset third stream, the model predicts the observed trend of decreased sound levels on the thick side of the jet compared with the thin side, but the predicted azimuthal variations are much less than those seen in the data. Also, the shift of the spectral peak to lower frequencies with increasing polar angle is over-predicted. For an offset third stream with a heated core, it is shown that including the enthalpy-flux source terms in the acoustic analogy model improves predictions compared with those obtained using only the momentum- flux

Cervical and breast cancer screening uptake among women with serious mental illness: a data linkage study

Background Breast and cancer screening uptake has been found to be lower among women with serious mental illness (SMI). This study aims to corroborate these findings in the UK and to identify variation in screening uptake by illness/treatment factors, and primary care consultation frequency. Methods Linked population-based primary and secondary care data from the London borough of Lambeth (UK) were used to compare breast and cervical screening receipt among linked eligible SMI patients (n = 625 and n = 1393), to those without SMI known only to primary care (n = 106,554 and n = 25,385) using logistic regression models adjusted first for socio-demographic factors and second, additionally for primary care consultation frequency. Results Eligible SMI patients were less likely to have received breast (adjusted odds ratio (OR) 0.69, 95 % confidence interval (CI), 0.57 - 0.84, p < 0.001) or cervical screening (adjusted OR 0.72, CI: 0.60 - 0.85, p < 0.001). Schizophrenia diagnosis, depot injectable antipsychotic prescription, and illness severity and risk were associated with the lowest odds of uptake of breast (adjusted ORs 0.46 to 0.59, all p < 0.001) and cervical screening (adjusted ORs 0.48 - 0.65, all p < 0.001). Adjustments for consultation frequency further reduced effect sizes for all subgroups of SMI patient, in particular for cervical screening. Conclusions Women with SMI are less likely to receive breast and cervical cancer screening than comparable women without SMI. Higher primary care consultation rates among SMI patients is likely a mediating factor between SMI status and uptake, particularly for cervical screening - a service organised in primary care. To tackle health disparities linked to SMI, efforts at increasing screening uptake are key and should be targeted at women with other markers of illness severity or risk, beyond SMI status alone

Quantifying ERK activity in response to inhibition of the BRAFV600E-MEK-ERK cascade using mathematical modelling

Funding: UK Medical Research Council (Grant Number(s): MR/R017506/1).Background Simultaneous inhibition of multiple components of the BRAF-MEK-ERK cascade (vertical inhibition) has become a standard of care for treating BRAF-mutant melanoma. However, the molecular mechanism of how vertical inhibition synergistically suppresses intracellular ERK activity, and consequently cell proliferation, are yet to be fully elucidated. Methods We develop a mechanistic mathematical model that describes how the mutant BRAF inhibitor, dabrafenib, and the MEK inhibitor, trametinib, affect BRAFV600E-MEK-ERK signalling. The model is based on a system of chemical reactions that describes cascade signalling dynamics. Using mass action kinetics, the chemical reactions are re-expressed as ordinary differential equations that are parameterised by in vitro data and solved numerically to obtain the temporal evolution of cascade component concentrations. Results The model provides a quantitative method to compute how dabrafenib and trametinib can be used in combination to synergistically inhibit ERK activity in BRAFV600E-mutant melanoma cells. The model elucidates molecular mechanisms of vertical inhibition of the BRAFV600E-MEK-ERK cascade and delineates how elevated BRAF concentrations generate drug resistance to dabrafenib and trametinib. The computational simulations further suggest that elevated ATP levels could be a factor in drug resistance to dabrafenib. Conclusions The model can be used to systematically motivate which dabrafenib–trametinib dose combinations, for treating BRAFV600E-mutated melanoma, warrant experimental investigation.Publisher PDFPeer reviewe

Proton therapy for atypical meningiomas

We report clinical outcomes of proton therapy in patients with World Health Organization grade 2 (atypical) meningiomas. Between 2005 and 2013, 22 patients with atypical meningiomas were treated to a median dose of 63 Gy (RBE) using proton therapy, as an adjuvant therapy after surgery (n = 12) or for recurrence or progression of residual tumor (n = 10). Six patients had presumed radiation-induced meningiomas, but none had received prior radiotherapy for their meningioma. The median follow-up time after radiation was 39 months (range 7–104) and all patients remain alive at last follow-up. The 5-year estimate of local control was 71.1 % (95 % CI 49.3–92.9 %). The 5-year estimate of local control was 87.5 % following a radiation dose >60 Gy (RBE), compared to 50.0 % for ≤60 Gy (RBE) (p = 0.038). The 5-year estimate of neuraxis dissemination was 5 % (95 % CI 0–14.6 %) and 6.2 % (95 % CI 0–18.2 %) for metastases outside of the central nervous system. Radiation necrosis was observed in one patient with a history of prior cranial irradiation. Fractionated proton therapy was associated with favorable tumor control rates for grade 2 meningiomas. Prospective studies are needed to define the optimal radiation dose for high-grade meningiomas

Genomic analysis of the protein secretion systems in Clostridium acetobutylicum ATCC 824

AbstractConsistent information about protein secretion in Gram-positive bacteria is essentially restricted to the model organism Bacillus subtilis. Among genome-sequenced clostridia, Clostridium acetobutylicum has been the most extensively studied from a physiological point of view and is the organism for which the largest variety of molecular biology tools have been developed. Following in silico analyses, both secreted proteins and protein secretion systems were identified. The Tat (Twin arginine translocation; TC #2.A.64) pathway and ABC (ATP binding cassette) protein exporters (TC #3.A.1.) could not be identified, but the Sec (secretion) pathway (TC #3.A.5) appears to be used prevalently. Similarly, a flagella export apparatus (FEA; TC #3.A.6.), holins (TC #1.E.), and an ESAT-6/WXG100 (early secreted antigen target of 6 kDa/proteins with a WXG motif of ∼100 residues) secretion system were identified. Here, we report for the first time the identification of a fimbrilin protein exporter (FPE; TC #3.A.14) and a Tad (tight adherence) export apparatus in C. acetobutylicum. This investigation highlights the potential use of this saprophytic bacterium in biotechnological and biomedical applications as well as a model organism for studying protein secretion in pathogenic Gram-positive bacteria

Developing an Onboard Traffic-Aware Flight Optimization Capability for Near-Term Low-Cost Implementation

The concept of Traffic Aware Strategic Aircrew Requests (TASAR) combines Automatic Dependent Surveillance Broadcast (ADS-B) IN and airborne automation to enable user-optimal in-flight trajectory replanning and to increase the likelihood of Air Traffic Control (ATC) approval for the resulting trajectory change request. TASAR is designed as a near-term application to improve flight efficiency or other user-desired attributes of the flight while not impacting and potentially benefiting ATC. Previous work has indicated the potential for significant benefits for each TASAR-equipped aircraft. This paper will discuss the approach to minimizing TASAR's cost for implementation and accelerating readiness for near-term implementation