Frontal Injuries of the Skull

Results of injuries to the frontal parts of the skull are often serious but treatable by prompt surgery. Various types of fractures are common. Most dangerous is the possibility of infection in the interior cavities of the skull. X-ray study of such injuries is practically mandatory. Failure to give prompt and proper treatment often results in serious complications later. Any injury to the frontal parts of the skull should be viewed by attorneys as serious, with strong probability of future complications except perhaps when prompt medical attention of highly modern character has forestalled some of the possible complications

Collisional and Electromagnetic Physics in Gyrokinetic Models

One of the most challenging problems facing plasma physicists today involves themodeling of plasma turbulence and transport in magnetic confinement experiments.The most successful model to this end so far is the reduced gyrokinetic model. Such amodel cannot be solved analytically, but can be used to simulate the plasma behaviorand transport with the help of present-day supercomputers. This has lead to the developmentof many different codes which simulate the plasma using the gyrokinetic modelin various ways. These models have achieved a large amount of success in describingthe core of the plasma for conventional tokamak devices. However, numerous difficultieshave been encountered when applying these models to more extreme parameterregimes, such as the edge and scrape-off layer of the tokamak, and high plasma devices,such as spherical tokamaks. The development and application of the gyrokineticmodel (specifically with the gyrokinetic code, GENE) to these more extreme parameterranges shall be the focus of this thesis.One of the main accomplishments during this thesis project is the development ofa more advanced collision operator suitable for studying the low temperature plasmaedge. The previous collision operator implemented in the code was found to artificiallycreate free energy at high collisionality, leading to numerical instabilities when oneattempted to model the plasma edge. This made such an analysis infeasible. Thenewly implemented collision operator conserves particles, momentum, and energy tomachine precision, and is guaranteed to dissipate free energy, even in a nonisothermalscenario. Additional finite Larmor radius correction terms have also been implementedin the local code, and the global code version of the collision operator has been adaptedfor use with an advanced block-structured grid scheme, allowing for more affordablecollisional simulations.The GENE code, along with the newly implemented collision operator developedin this thesis, has been applied to study plasma turbulence and transport in the edge(tor = 0:9) of an L-mode magnetic confinement discharge of ASDEX Upgrade. Ithas been found that the primary microinstabilities at that radial position are electrondrift waves destabilized by collisions and electromagnetic effects. At low toroidal modenumbers, ion temperature gradient driven modes and microtearing modes also seem toexist. In nonlinear simulations with the nominal experimental parameters, the simulatedelectron heat flux was four times higher than the experimental reconstruction,and the simulated ion heat flux was twice as high. However, both the ion and electronsimulated heat flux could be brought into agreement with experimental values by loweringthe input logarithmic electron temperature gradient by 40%. It was also foundthat the cross-phases between the electrostatic potential and the moments agreed wellfor the part of the binormal spectrum where the dominant transport occurred, and wasfairly poor at larger scales where minimal transport occurred.Finally, a new scheme for evaluating the electromagnetic fields has been developedto address the instabilities occurring in nonlinear local and global gyrokinetic simulationsat high plasma . This new scheme is based on evaluating the electromagneticinduction explicitly, and constructing the gyrokinetic equation based on the original distribution,rather than the modified distribution which implicitly takes into account theinduction. This new scheme removes the artificial instability occurring in global simulations,enabling the study of high scenarios with GENE. The new electromagneticscheme can also be generalized to a full-f implementation, however, it would requireupdating the field matrix every time-step to avoid the cancellation problem. The newscheme (including the parallel nonlinearity) does not remove the local instability, suggestingthat that instability (caused by magnetic field perturbations shorting out zonalflows) is part of the physics of the local model

High Gene Flow Due to Pelagic Larval Dispersal Among South Pacific Archipelagos in Two Amphidromous Gastropods (Neritomorpha: Neritidae)

The freshwater stream fauna of tropical oceanic islands is dominated by amphidromous species, whose larvae are transported to the ocean and develop in the plankton before recruiting back to freshwater habitat as juveniles. Because stream habitat is relatively scarce and unstable on oceanic islands, this life history would seem to favor either the retention of larvae to their natal streams, or the ability to delay metamorphosis until new habitat is encountered. To distinguish between these hypotheses, we used population genetic methods to estimate larval dispersal among five South Pacific archipelagos in two amphidromous species of Neritid gastropod (Neritina canalis and Neripteron dilatatus). Sequence data from mitochondrial COI revealed that neither species is genetically structured throughout the Western Pacific, suggesting that their larvae have a pelagic larval duration of at least eight weeks, longer than many marine species. Additionally, the two species have recently colonized isolated Central Pacific archipelagos in three independent events. Since colonization, there has been little to no gene flow between the Western and Central Pacific archipelagos in Neritina canalis, and high levels of gene flow across the same region in Neripteron dilatatus. Both species show departures from neutrality and recent dates for colonization of the Central Pacific archipelagos consistent with frequent extinction and recolonization of stream populations in this area. Similar results from other amphidromous species suggest that unstable freshwater habitats promote long-distance dispersal capabilities

Regulating Emissions of Greenhouse Gases Under Section 202(a) of the Clean Air Act

The authors consider whether the Environmental Protection Agency's denial of the petition to regulate emissions of greenhouse gases from motor vehicles under Section 202(a) of the Clean Air Act was reasonable in light of the global nature of greenhouse gas emissions and the likely superiority of other methods for combating greenhouse gases.Environment, Health and Safety, Regulatory Reform, Other Topics

Whole Genome Phylogenetic Tree Reconstruction Using Colored de Bruijn Graphs

We present kleuren, a novel assembly-free method to reconstruct phylogenetic trees using the Colored de Bruijn Graph. kleuren works by constructing the Colored de Bruijn Graph and then traversing it, finding bubble structures in the graph that provide phylogenetic signal. The bubbles are then aligned and concatenated to form a supermatrix, from which a phylogenetic tree is inferred. We introduce the algorithms that kleuren uses to accomplish this task, and show its performance on reconstructing the phylogenetic tree of 12 Drosophila species. kleuren reconstructed the established phylogenetic tree accurately, and is a viable tool for phylogenetic tree reconstruction using whole genome sequences. Software package available at: https://github.com/Colelyman/kleurenComment: 6 pages, 3 figures, accepted at BIBE 2017. Minor modifications to the text due to reviewer feedback and fixed typo

Contrasting Demographic History and Phylogeographic Patterns in Two Indo-Pacific Gastropods

Marine species with ranges that span the Indo-Australian Archipelago (IAA) exhibit a range of phylogeographic patterns, most of which are interpreted in the context of vicariance between Indian and Pacific Ocean populations during Pliocene and Pleistocene low sea level stands. However, patterns often vary among ecologically similar taxa, sometimes even within genera. This study compares phylogeographic patterns in two species of highly dispersive Neritid gastropod, Nerita albicilla and Nerita plicata, with nearly sympatric ranges that span the Indo-Pacific. Mitochondrial COI sequences from \u3e 1000 individuals from 97 sites reveal similar phylogenies in both species (two divergent clades differing by 3.2% and 2.3%, for N. albicilla and N. plicata respectively). However, despite ecological similarity and congeneric status, the two species exhibit phylogeographic discordance, with N. albicilla maintaining reciprocal monophyly of Indian and Pacific Ocean populations, while N. plicata is panmictic between oceans, but displays a genetic cline in the Central Pacific. Although this difference might be explained by qualitatively different demographic histories, parameter estimates from three coalescent models indicate that both species have high levels of gene flow between demes (2Ne m \u3e 75), and share a common history of population expansion that is likely associated with cyclical flooding of continental shelves and island lagoons following low sea level stands. Results indicate that ecologically similar co-distributed species may respond very differently to shared environmental processes, suggesting that relatively minor differences in traits such as pelagic larval duration or microhabitat association may profoundly impact phylogeographic structure

Comparative Phylogeography of Two Seastars and Their Ectosymbionts Within the Coral Triangle

Repeated exposure and flooding of the Sunda and Sahul shelves during Pleistocene sea level fluctuations is thought to have contributed to the isolation and diversification of sea basin populations within the Coral Triangle. This hypothesis has been tested in numerous phylogeographic studies, recovering an assortment of genetic patterns that the authors have generally attributed to differences in larval dispersal capability or adult habitat specificity. This study compares phylogeographic patterns from mitochondrial COI sequences among two co-distributed seastars that differ in their adult habitat and dispersal ability, and two seastar ectosymbionts that differ in their degree of host specificity. Of these, only the seastar Linckia laevigata displayed a classic pattern of Indian-Pacific divergence, but with only moderate genetic structure (ΦCT = 0.067). In contrast, the seastar Protoreaster nodosus exhibited strong structure (ΦCT = 0.23) between Teluk Cenderawasih and the remainder of Indonesia, a 12 pattern of regional structure that was echoed in L. laevigata (ΦCT = 0.03) as well as its obligate gastropod parasite Thyca crystallina (ΦCT = 0.04). The generalist commensal shrimp, Periclimenes soror showed little genetic structuring across the Coral Triangle. Despite species-specific phylogeographic patterns, all four species showed departures from neutrality that are consistent with massive range expansions onto the continental shelves as sea levels rose, and date within the Pleistocene epoch. Our results suggest that habitat differences may affect the manner in which species responded to Pleistocene sea level fluctuations, shaping contemporary patterns of genetic structure and diversity

Expansion Dating: Calibrating Molecular Clocks in Marine Species from Expansions onto the Sunda Shelf Following the Last Glacial Maximum

The rate of change in DNA is an important parameter for understanding molecular evolution and hence for inferences drawn from studies of phylogeography and phylogenetics. Most rate calibrations for mitochondrial coding regions in marine species have been made from divergence dating for fossils and vicariant events older than 1-2 My and are typically 0.5-2% per lineage per million years. Recently, calibrations made with ancient DNA (aDNA) from younger dates have yielded faster rates, suggesting that estimates of the molecular rate of change depend on the time of calibration, decaying from the instantaneous mutation rate to the phylogenetic substitution rate. aDNA methods for recent calibrations are not available for most marine taxa so instead we use radiometric dates for sea-level rise onto the Sunda Shelf following the Last Glacial Maximum (starting similar to 18,000 years ago), which led to massive population expansions for marine species. Instead of divergence dating, we use a two-epoch coalescent model of logistic population growth preceded by a constant population size to infer a time in mutational units for the beginning of these expansion events. This model compares favorably to simpler coalescent models of constant population size, and exponential or logistic growth, and is far more precise than estimates from the mismatch distribution. Mean rates estimated with this method for mitochondrial coding genes in three invertebrate species are elevated in comparison to older calibration points (2.3-6.6% per lineage per million years), lending additional support to the hypothesis of calibration time dependency for molecular rates

Expansion Dating: Calibrating Molecular Clocks in Marine Species from Expansions onto the Sunda Shelf following the Last Glacial Maximum

The rate of change in DNA is an important parameter for understanding molecular evolution, and hence for inferences drawn from studies of phylogeography and phylogenetics. Most rate calibrations for mitochondrial coding regions in marine species have been made from divergence dating for fossils and vicariant events older than 1-2 million years, and are typically 0.5% - 2% per lineage per million years. Recently, calibrations made with ancient DNA from younger dates have yielded faster rates, suggesting that estimates of the molecular rate of change depend on the time of calibration, decaying from the instantaneous mutation rate to the phylogenetic substitution rate. Ancient DNA methods for recent calibrations are not available for most marine taxa so instead we use radiometric dates for sea-level rise onto the Sunda Shelf following the Last Glacial Maximum (starting ~18,000 years ago), which led to massive population expansions for marine species. Instead of divergence dating, we use a two epoch coalescent model of logistic population growth preceded by a constant population size to infer a time in mutational units for the beginning of these expansion events. This model compares favorably to simpler coalescent models of constant population size, and exponential or logistic growth, and is far more precise than estimates from the mismatch distribution. Mean rates estimated with this method for mitochondrial coding genes in three invertebrate species are elevated in comparison to older calibration points (2.3% - 6.6% per lineage per million years), lending additional support to the hypothesis of calibration time-dependency for molecular rates

Climate oscillations, glacial refugia, and dispersal ability: factors influencing the genetic structure of the least salmonfly, Pteronarcella badia (Plecoptera), in Western North America

Background: Phylogeographic studies of aquatic insects provide valuable insights into mechanisms that shape the genetic structure of communities, yet studies that include broad geographic areas are uncommon for this group. We conducted a broad scale phylogeographic analysis of the least salmonfly Pteronarcella badia (Plecoptera) across western North America. We tested hypotheses related to mode of dispersal and the influence of historic climate oscillations on population genetic structure. In order to generate a larger mitochondrial data set, we used 454 sequencing to reconstruct the complete mitochondrial genome in the early stages of the project. Results: Our analysis revealed high levels of population structure with several deeply divergent clades present across the sample area. Evidence from five mitochondrial genes and one nuclear locus identified a potentially cryptic lineage in the Pacific Northwest. Gene flow estimates and geographic clade distributions suggest that overland flight during the winged adult stage is an important dispersal mechanism for this taxon. We found evidence of multiple glacial refugia across the species distribution and signs of secondary contact within and among major clades. Conclusions: This study provides a basis for future studies of aquatic insect phylogeography at the inter-basin scale in western North America. Our findings add to an understanding of the role of historical climate isolations in shaping assemblages of aquatic insects in this region. We identified several geographic areas that may have historical importance for other aquatic organisms with similar distributions and dispersal strategies as P. badia. This work adds to the ever-growing list of studies that highlight the potential of next-generation DNA sequencing in a phylogenetic context to improve molecular data sets from understudied groups