The evolution of oscillatory behavior in age-structured species

A major challenge in ecology is to explain why so many species show oscillatory population dynamics and why the oscillations commonly occur with particular periods. The background environment, through noise or seasonality, is one possible driver of these oscillations, as are the components of the trophic web with which the species interacts. However, the oscillation may also be intrinsic, generated by density-dependent effects on the life history. Models of structured single-species systems indicate that a much broader range of oscillatory behavior than that seen in nature is theoretically possible. We test the hypothesis that it is selection that acts to constrain the range of periods. We analyze a nonlinear single-species matrix model with density dependence affecting reproduction and with trade-offs between reproduction and survival. We show that the evolutionarily stable state is oscillatory and has a period roughly twice the time to maturation, in line with observed patterns of periodicity. The robustness of this result to variations in trade-off function and density dependence is tested

Two-Dimensional High-Lift Aerodynamic Optimization Using Neural Networks

The high-lift performance of a multi-element airfoil was optimized by using neural-net predictions that were trained using a computational data set. The numerical data was generated using a two-dimensional, incompressible, Navier-Stokes algorithm with the Spalart-Allmaras turbulence model. Because it is difficult to predict maximum lift for high-lift systems, an empirically-based maximum lift criteria was used in this study to determine both the maximum lift and the angle at which it occurs. The 'pressure difference rule,' which states that the maximum lift condition corresponds to a certain pressure difference between the peak suction pressure and the pressure at the trailing edge of the element, was applied and verified with experimental observations for this configuration. Multiple input, single output networks were trained using the NASA Ames variation of the Levenberg-Marquardt algorithm for each of the aerodynamic coefficients (lift, drag and moment). The artificial neural networks were integrated with a gradient-based optimizer. Using independent numerical simulations and experimental data for this high-lift configuration, it was shown that this design process successfully optimized flap deflection, gap, overlap, and angle of attack to maximize lift. Once the neural nets were trained and integrated with the optimizer, minimal additional computer resources were required to perform optimization runs with different initial conditions and parameters. Applying the neural networks within the high-lift rigging optimization process reduced the amount of computational time and resources by 44% compared with traditional gradient-based optimization procedures for multiple optimization runs

Foot Muscle Energy Reserves in Diabetic Patients Without and With Clinical Peripheral Neuropathy

Objective: To investigate changes in the foot muscle energy reserves in diabetic non-neuropathic and neuropathic patients. Research Design and Methods: We measured the phosphocreatinine (PCr)/inorganic phosphate (Pi) ratio, total $^{31}$P concentration, and the lipid/water ratio in the muscles in the metatarsal head region using MRI spectroscopy in healthy control subjects and non-neuropathic and neuropathic diabetic patients. Results: The PCr/Pi ratio was higher in the control subjects (3.23 $\pm$ 0.43) followed by the non-neuropathic group (2.61 $\pm$ 0.36), whereas it was lowest in the neuropathic group (0.60 $\pm$ 1.02) (P < 0.0001). There were no differences in total $^{31}$P concentration and lipid/water ratio between the control and non-neuropathic groups, but both measurements were different in the neuropathic group (P < 0.0001). Conclusions: Resting foot muscle energy reserves are affected before the development of peripheral diabetic neuropathy and are associated with the endothelial dysfunction and inflammation

Modeling the evolution space of breakage fusion bridge cycles with a stochastic folding process

Breakage-Fusion-Bridge cycles in cancer arise when a broken segment of DNA is duplicated and an end from each copy joined together. This structure then 'unfolds' into a new piece of palindromic DNA. This is one mechanism responsible for the localised amplicons observed in cancer genome data. The process has parallels with paper folding sequences that arise when a piece of paper is folded several times and then unfolded. Here we adapt such methods to study the breakage-fusion-bridge structures in detail. We firstly consider discrete representations of this space with 2-d trees to demonstrate that there are 2^(n(n-1)/2) qualitatively distinct evolutions involving n breakage-fusion-bridge cycles. Secondly we consider the stochastic nature of the fold positions, to determine evolution likelihoods, and also describe how amplicons become localised. Finally we highlight these methods by inferring the evolution of breakage-fusion-bridge cycles with data from primary tissue cancer samples

Workers Without Health Insurance: Who Are They and How Can Policy Reach Them?

Offers a detailed picture of the 16 million uninsured working population in the U.S., identifies potential causes and effects, and examines the policy implications and options

Differential impact of a shared nematode parasite on two gamebird hosts: implications for apparent competition

If the deleterious effects of non-specfic parasites are greater on vulnerable host species than on reservoir host species then exclusion of the vulnerable host through apparent competition is more likely. Evidence suggests that such a mechanism occurs in interactions between the ring-necked pheasant (Phasianus colchicus), the grey partridge (Perdix perdix), and their shared caecal nematode Heterakis gallinarum. Modelling of the system predicts that the reduced parasite impact on the pheasant compared to the partridge results in the force of infection transmitted from pheasants to partridges being sufficient to cause partridge exclusion. Since the parasite impacts are currently estimated from correlational work, controlled infections were conducted to experimentally compare the impact of H. gallinarum on the two hosts and verify cause and effect. While challenged partridges showed reduced mass gain, decreased food consumption, and impaired caecal activity, in comparison to controls, the only detectable effect of parasite challenge on the pheasant was impaired caecal activity. The impact ofH. gallinarum on challenged partridges conforms with previous correlational data, supporting the prediction that parasite-mediated apparent competition with the ring-necked pheasant may result in grey partridge exclusion. However, the observed decrease in the caecal activity of challenged pheasants could imply that H. gallinarum may also have an impact on the fecundity and survival of pheasants in the wild, particularly if food is limiting. If this is the case, the associated decrease in the force of infection to which the partridge is exposed may be sufficient to change the model prediction from partridge exclusion to pheasant and partridge coexistence

Postfire Characteristics of Existing and Potential Black-capped Vireo (Vireo Atricapillus) Nesting Habitat on the Wichita Mountains Wildlife Refuge, Oklahoma

Each chapter of this thesis is complete for publication in a specific scientific journal. Chapter I is written in the style of Conservation Biology, and Chapter II is in the style of The Southwestern Naturalist. Additional data and study site maps are included in a 1995 report entitled "Effects of fire on existing and potential nesting habitat of the black-capped vireo (Vireo atricapillus) on the Wichita Mountains Wildlife Refuge". This report can be obtained from either the United States Fish and Wildlife Service, Wichita Mountains Wildlife Refuge, Oklahoma, or the Oklahoma Cooperative Fish and Wildlife Research Unit at Oklahoma State University. I greatly appreciate the guidance of Drs. James H. Shaw, Terrence G. Bidwell, and David M. Leslie, Jr. during my research. The outstanding scholarship of Jim Shaw was an inspiring example for me. I am also grateful to Joe Kimball of the Wichita Mountains Wildlife Refuge for his assistance throughout this project. I thank my parents, Norman and Marion Greenman, for their extreme patience and support during my long college career. Finally, I thank my friend Marcus Koenen for helping in countless ways.Wildlife and Fisheries Ecolog

Synthesis, characterization and biological evaluation of a new photoactive hydrogel against Gram-positive and Gram-negative bacteria

In 2013, the World Health Organization reported that 884 million people lack access to clean potable water. Photodynamic antimicrobial chemotherapy (PACT) is a very promising alternative to conventional antibiotics for the efficient inactivation of pathogenic microorganisms. We report the synthesis, characterization and antibacterial activity of a polyacrylamide-based hydrogel (7), with a new photoactive phenothiazinium compound (6) immobilized on it, to be used as a novel water-sterilizing device. The hydrogel was characterized by IR and scanning electron microscopy and incorporation of the dye confirmed by UV-visible spectroscopy. Antibacterial tests using the recombinant bioluminescent Gram-positive Staphylococcus aureus RN4220 and Gram-negative Escherichia coli DH5α were performed to assess the ability of the hydrogel to inactivate bacterial strains in solution. The hydrogel is characterized by a non-ordered microporous structure and is able to generate reactive oxygen species. The hydrogel is able to inactivate planktonic cells of the S. aureus and E. coli (3.3 log and 2.3 log killing, respectively) after 25 min of irradiation with white light at 14.5 mW cm−2. The contact surface does not influence the kill rates while the killing rate increased by increasing the total amount of the hydrogel (0.27 log drop to 1.65 log drop with 0.5 mg cm−3 to 2.5 mg cm−3 of total amount of dye). The hydrogel was found to be active for four cycles, suggesting the possibility of reuse and it was shown to be active against both Gram-positive and Gram-negative species with no leaching of the active molecule

Hidden breakpoints in genome alignments

During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain and loss occurs in addition to other types of rearrangement, breakpoints of rearrangement can exist that are only detectable by comparison of three or more genomes. An arbitrarily large number of these "hidden" breakpoints can exist among genomes that exhibit no rearrangements in pairwise comparisons. We present an extension of the multichromosomal breakpoint median problem to genomes that have undergone gene gain and loss. We then demonstrate that the median distance among three genomes can be used to calculate a lower bound on the number of hidden breakpoints present. We provide an implementation of this calculation including the median distance, along with some practical improvements on the time complexity of the underlying algorithm. We apply our approach to measure the abundance of hidden breakpoints in simulated data sets under a wide range of evolutionary scenarios. We demonstrate that in simulations the hidden breakpoint counts depend strongly on relative rates of inversion and gene gain/loss. Finally we apply current multiple genome aligners to the simulated genomes, and show that all aligners introduce a high degree of error in hidden breakpoint counts, and that this error grows with evolutionary distance in the simulation. Our results suggest that hidden breakpoint error may be pervasive in genome alignments.Comment: 13 pages, 4 figure