A Genetic Algorithm for UAV Routing Integrated with a Parallel Swarm Simulation

This research investigation addresses the problem of routing and simulating swarms of UAVs. Sorties are modeled as instantiations of the NP-Complete Vehicle Routing Problem, and this work uses genetic algorithms (GAs) to provide a fast and robust algorithm for a priori and dynamic routing applications. Swarms of UAVs are modeled based on extensions of Reynolds\u27 swarm research and are simulated on a Beowulf cluster as a parallel computing application using the Synchronous Environment for Emulation and Discrete Event Simulation (SPEEDES). In a test suite, standard measures such as benchmark problems, best published results, and parallel metrics are used as performance measures. The GA consistently provides efficient and effective results for a variety of VRP benchmarks. Analysis of the solution quality over time verifies that the GA exponentially improves solution quality and is robust to changing search landscapes - making it an ideal tool for employment in UAV routing applications. Parallel computing metrics calculated from the results of a PDES show that consistent speedup (almost linear in many cases) can be obtained using SPEEDES as the communication library for this UAV routing application. Results from the routing application and parallel simulation are synthesized to produce a more advanced model for routing UAVs

Alternative Splicing and Polyadenylation Contribute to the Generation of hERG1 C-terminal Isoforms

The human ether-a-go-go-related gene 1 (hERG1) encodes the pore-forming subunit of the rapidly activating delayed rectifier potassium channel. Several hERG1 isoforms with different N- and C-terminal ends have been identified. The hERG1a, hERG1b, and hERG1-3.1 isoforms contain the full-length C terminus, whereas the hERG1USOisoforms, hERG1aUSO and hERG1bUSO, lack most of the C-terminal domain and contain a unique C-terminal end. The mechanisms underlying the generation of hERG1USOisoforms are not understood. We show that hERG1 isoforms with different C-terminal ends are generated by alternative splicing and polyadenylation of hERG1 pre-mRNA. We identified an intrinsically weak, noncanonical poly(A) signal, AGUAAA, within intron 9 of hERG1 that modulates the expression of hERG1a and hERG1aUSO. Replacing AGUAAA with the strong, canonical poly(A) signal AAUAAA resulted in the predominant production of hERG1aUSO and a marked decrease in hERG1 current. In contrast, eliminating the intron 9 poly(A) signal or increasing the strength of 5′ splice site led to the predominant production of hERG1a and a significant increase in hERG1 current. We found significant variation in the relative abundance of hERG1 C-terminal isoforms in different human tissues. Taken together, these findings suggest that post-transcriptional regulation of hERG1 pre-mRNA may represent a novel mechanism to modulate the expression and function of hERG1 channels

Stable cycling in quasi-linkage equilibrium:fluctuating dynamics under gene conversion and selection

Genetic systems with multiple loci can have complex dynamics. For example, mean fitness need not always increase and stable cycling is possible. Here, we study the dynamics of a genetic system inspired by the molecular biology of recognition-dependent double strand breaks and repair as it happens in recombination hotspots. The model shows slow-fast dynamics in which the system converges to the quasi-linkage equilibrium (QLE) manifold. On this manifold, sustained cycling is possible as the dynamics approach a heteroclinic cycle, in which allele frequencies alternate between near extinction and near fixation. We find a closed-form approximation for the QLE manifold and use it to simplify the model. For the simplified model, we can analytically calculate the stability of the heteroclinic cycle. In the discrete-time model the cycle is always stable; in a continuous-time approximation, the cycle is always unstable. This demonstrates that complex dynamics are possible under quasi-linkage equilibrium.Comment: 35 pages, 6 figure

Calcium alginate microencapsulation of ovarian follicles impacts FSH delivery and follicle morphology

BACKGROUND: We have previously shown that suspension culture prevents follicle flattening and maintains three-dimensional follicle architecture better than culture on flat plates. However, many of the follicles cultured in suspension do eventually rupture, as basement membrane integrity is lost and the three-dimensional structure of the follicle is altered. Therefore, the objective of this study is to support three-dimensional follicle architecture during in vitro growth of ovarian follicles through encapsulation in calcium alginate, while maintaining responsiveness to FSH stimulation. METHODS: Preantral follicles (150 – 160 micrometers in diameter) were isolated from the ovaries of juvenile rats and grown in culture tubes or encapsulated in calcium alginate and grown in culture tubes. Previous studies revealed that follicles maintained structural integrity but did not grow as well when encapsulated in calcium alginate. In these studies, we evaluated the effect of calcium alginate on FSH-stimulated follicle growth, survival, and morphology in suspension culture. Follicles were grown under 5 culture conditions: 1) not encapsulated; with FSH in the medium, 2) encapsulated in the absence of FSH, grown in medium without FSH, 3) encapsulated with calcium alginate containing FSH but grown in medium without FSH, 4) encapsulated without FSH but grown in medium containing FSH and 5) encapsulated with calcium alginate containing FSH and in medium containing FSH. To assess growth rates, follicles were cultured for 72 hours and analyzed for follicle size increase and DNA content. Survival analysis for encapsulated and unencapsulated follicles was performed by constructing a Kaplan Meier survival curve of daily observations of intact follicle survival. Three-dimensional architecture was assessed histologically and by analysis of the pattern of connexin 43 expression in the cultured follicles. RESULTS: In the absence of FSH, follicle diameter increased by only 6.4%. When FSH was included in the alginate bead alone or the media alone, the follicle diameter increased by 13.5% and 19.9% respectively. This was greater than follicles cultured in the absence of FSH (p < 0.05), but less than that of the FSH-treated unencapsulated follicles (p < 0.05). However, when follicles were cultured with FSH included in both the media and the bead, a 32.6% increase in follicle diameter was observed, statistically no different than the growth rate of the unencapsulated follicles grown with FSH. CONCLUSION: Microencapsulation supports three-dimensional follicle growth, but may limit access to hormones in the medium resulting in altered development compared to unencapsulated follicles. Inclusion of FSH in the alginate bead restores the follicle growth response to FSH, while also providing a scaffold of support for three-dimensional growth. The application of tissue engineering principles to the problems of follicle culture in vitro may provide advances applicable to fertility preservation in women and endangered species

Sectionality or Why Section Determines Grades: an Exploration of Engineering Core Course Section Grades using a Hierarchical Linear Model and the Multiple-Institution Database for Investigating Engineering Longitudinal Development

Grades, how they are earned, and the institutional impetuses that drive them, are an issue of central importance in the engineering discipline. (1-4) How grades are earned, how different institutions address grades and grade inequities, how instructional practices and policies affect grades, and other grading notions have been studied widely in engineering education. (5-8) The effect of faculty on student grades, while studied, (9) has not been probed as extensively within engineering education using a hierarchical linear model (HLM).One of the great, open questions in engineering education is whether or not the section makes a difference in a student’s grade. In other words, the effect of sectionality on grades to a large extent is unknown. Sectionality combines instructor effects, effects related to time-of-day of instruction, effects related to any tendency for students to coordinate their enrollment, and other effects. Experience and anecdotal evidence suggest that sectionality affects grades, but large-scale empirical studies of this phenomenon do not exist. Due to the inherent structured nature between course sections and students, standard linear regression models do not offer a robust solution to probing longitudinal systems containing multilevel variables. Hierarchical Linear Models (HLMs) provide a robust solution to studying nested or hierarchical systems when compared with standard regression techniques. We constructed a simple HLM to probe inter-section and intra-section variability in grades within the Multiple Institution Database for Investigating Engineering Longitudinal Development (MIDFIELD) by the calculation of intraclass correlation coefficient (ICCs). (10, 11) We then examined grades from three sets of courses endemic to the first year engineering experience: the first chemistry course; the first calculus course; and the first physics course. Our preliminary results indicate that the choice of a HLM to analyze our longitudinal database is correct due to strong variability in grades explained by the high intraclass correlation coefficient (ICC) for most of our MIDFIELD institutions across all three course types analyzed

phyr: Anrpackage for phylogenetic species-distribution modelling in ecological communities

Model-based approaches are increasingly popular in ecological studies. A good example of this trend is the use of joint species distribution models to ask questions about ecological communities. However, most current applications of model-based methods do not include phylogenies despite the well-known importance of phylogenetic relationships in shaping species distributions and community composition. In part, this is due to a lack of accessible tools allowing ecologists to fit phylogenetic species distribution models easily. To fill this gap, therpackagephyr(pronounced fire) implements a suite of metrics, comparative methods and mixed models that use phylogenies to understand and predict community composition and other ecological and evolutionary phenomena. Thephyrworkhorse functions are implemented in C++ making all calculations and model estimations fast. phyrcan fit a variety of models such as phylogenetic joint-species distribution models, spatiotemporal-phylogenetic autocorrelation models, and phylogenetic trait-based bipartite network models.phyralso estimates phylogenetically independent trait correlations with measurement error to test for adaptive syndromes and performs fast calculations of common alpha and beta phylogenetic diversity metrics. Allphyrmethods are united under Brownian motion or Ornstein-Uhlenbeck models of evolution, and phylogenetic terms are modelled as phylogenetic covariance matrices. The functions and model formula syntax we propose inphyrprovide an easy-to-use collection of tools that we hope will ignite the use of phylogenies to address a variety of ecological questions

PPE – Can you have too much of a good thing?

PresentationSpecifying Personal Protective Equipment (PPE) after a hazard has been identified is a critical aspect of a facility’s ability to protect their workers. In a chemical manufacturing facility, manual operations and maintenance activities have the potential to expose workers to hazardous chemicals and flammable atmospheres. Even though it is generally recognized to be one of the least effective safeguards in the hierarchy of controls, PPE is often the last line of defense, and sometimes the only feasible defense, that isolates workers from potential hazards. As a result, companies may lean toward putting workers in higher levels of PPE to provide additional protection. However, in many cases higher levels of PPE may introduce new hazards associated with limited worker mobility, fatigue, unreliable job performance, or limited egress. Therefore, PPE specification should focus not only on what is necessary to protect the worker, but also what is appropriate for a given job task. In this paper, a risk-based approach to PPE selection, specification, and use will be presented. Discussion will focus on potential hazards that can be inadvertently introduced because of PPE over-specification. Studies related to the impact of PPE on worker performance will be presented to help demonstrate the potential negative impacts of over specifying PPE. Lastly, a case study will be presented where a PPE specification was questioned, and the impact of increasing the PPE specification for a job task was evaluated

Inflammatory Markers Associated With Subclinical Coronary Artery Disease: The Multicenter AIDS Cohort Study.

BackgroundDespite evidence for higher risk of coronary artery disease among HIV+ individuals, the underlying mechanisms are not well understood. We investigated associations of inflammatory markers with subclinical coronary artery disease in 923 participants of the Multicenter AIDS Cohort Study (575 HIV+ and 348 HIV- men) who underwent noncontrast computed tomography scans for coronary artery calcification, the majority (n=692) also undergoing coronary computed tomography angiography.Methods and resultsOutcomes included presence and extent of coronary artery calcification, plus computed tomography angiography analysis of presence, composition, and extent of coronary plaques and severity of coronary stenosis. HIV+ men had significantly higher levels of interleukin-6 (IL-6), intercellular adhesion molecule-1, C-reactive protein, and soluble-tumor necrosis factor-α receptor (sTNFαR) I and II (all P&lt;0.01) and a higher prevalence of noncalcified plaque (63% versus 54%, P=0.02) on computed tomography angiography. Among HIV+ men, for every SD increase in log-interleukin-6 and log&nbsp;intercellular adhesion molecule-1, there was a 30% and 60% increase, respectively, in the prevalence of coronary stenosis ≥50% (all P&lt;0.05). Similarly, sTNFαR I and II in HIV+ participants were associated with an increase in prevalence of coronary stenosis ≥70% (P&lt;0.05). Higher levels of interleukin-6, sTNFαR I, and sTNFαR II were also associated with greater coronary artery calcification score in HIV+ men (P&lt;0.01).ConclusionsHigher inflammatory marker levels are associated with greater prevalence of coronary stenosis in HIV+ men. Our findings underscore the need for further study to elucidate the relationships of inflammatory pathways with coronary artery disease in HIV+ individuals