RCCZ4: A Reference Metric Approach to Z4

The hyperbolic formulations of numerical relativity due to Baumgarte, Shapiro, Shibata & Nakamura (BSSN) and Nagy Ortiz & Reula (NOR), among others, achieve stability through the effective embedding of general relativity within the larger Z4 system. In doing so, various elliptic constraints are promoted to dynamical degrees of freedom, permitting the advection of constraint violating modes. Here we demonstrate that it is possible to achieve equivalent performance through a modification of fully covariant and conformal Z4 (FCCZ4) wherein constraint violations are coupled to a reference metric completely independently of the physical metric. We show that this approach works in the presence of black holes and holds up robustly in a variety of spherically symmetric simulations including the critical collapse of a scalar field. We then demonstrate that our formulation is strongly hyperbolic through the use of a pseudodifferential first order reduction and compare its hyperbolicity properties to those of FCCZ4 and generalized BSSN (GBSSN). Our present approach makes use of a static Lorentzian reference metric and does not appear to provide significant advantages over FCCZ4. However, we speculate that dynamical specification of the reference metric may provide a means of exerting greater control over constraint violations than what is provided by current BSSN-type formulations.Comment: 19 pages, 18 figure

RNA interference by mixtures of siRNAs prepared using custom oligonucleotide arrays

RNA interference (RNAi) is a process in which double-strand RNA (dsRNA) directs the specific degradation of a corresponding target mRNA. The mediators of this process are small dsRNAs, of ∼21 bp in length, called small interfering RNAs (siRNAs). siRNAs, which can be prepared in vitro in a number of ways and then transfected into cells, can direct the degradation of corresponding mRNAs inside these cells. Hence, siRNAs represent a powerful tool for studying gene functions, as well as having the potential of being highly specific pharmaceutical agents. Some limitations in using this technology exist because the preparation of siRNA in vitro and screening for siRNAs efficient in RNAi can be expensive and time-consuming processes. Here, we demonstrate that custom oligonucleotide arrays can be efficiently used for the preparation of defined mixtures of siRNAs for the silencing of exogenous and endogenous genes. The method is fast, inexpensive, does not require siRNA optimization and has a number of advantages over methods utilizing enzymatic preparation of siRNAs by digestion of longer dsRNAs, as well as methods based on chemical synthesis of individual siRNAs or their DNA templates

Non-equilibrium Ionization States Within Galactic Outflows: Explaining Their O VI and N V Column Densities

We present a suite of one-dimensional spherically-symmetric hydrodynamic simulations that study the atomic ionization structure of galactic outflows. We track the ionization state of the outflowing gas with a non-equilibrium atomic chemistry network that includes photoionization, photo-heating, and ion-by-ion cooling. Each simulation describes a steady-state outflow that is defined by its mass and energy input rates, sonic radius, metallicity, and UV flux from both the host galaxy and meta-galactic background. We find that for a large range of parameter choices, the ionization state of the material departs strongly from what it would be in photo-ionization equilibrium, in conflict with what is commonly assumed in the analysis of observations. In addition, nearly all the models reproduce the low N V to O VI column density ratios and the relatively high O VI column densities that are observed.Comment: 16 pages, 11 figures, accepted to ApJ. Comments welcom

Discovery of IPv6 router interface addresses via heuristic methods

With the assignment of the last available blocks of public IPv4 addresses from Internet Assigned Numbers Authority, there is continued pressure for widespread IPv6 adoption. Because the IPv6 address space is orders of magnitude larger than the IPv4 address space, researchers need new methods and techniques to accurately measure and characterize growth in IPv6. This thesis focuses on IPv6 router infrastructure and examines the possibility of using heuristic methods in order to discover IPv6 router interfaces. We consider two heuristic techniques in an attempt to improve upon current state-of-the-art IPv6 router infrastructure discovery methods. The first heuristic examines the ability to generate candidate IPv6 addresses by finding the most common lower 64 bit patterns among IPv6 router interface address observed in historical probing data. The second heuristic generates candidate IPv6 addresses by assuming that an IPv6 address seen in historical probing data is one end of a point-to-point link, and uses the corresponding end’s IPv6 address. Using a distributed active topology measurement system, we test these heuristic methods on the IPv6 Internet. We find that our first heuristic is successful in discovering a non-trivial number of new router interfaces, while the second heuristic is more efficient.http://archive.org/details/discoveryofipvro1094547265Lieutenant, United States NavyApproved for public release; distribution is unlimited

Management of Pasture Quality for Sheep on New Zealand Hill Country

The control of pasture quality over spring is central to the achievement of high levels of sheep performance on hill country. Despite this, with the exception of the work of Lambert et al. (2000), little is known about how farmers actually manage pasture quality. The purpose of this research was to describe how a high performing hill country farmer manages pasture quality on their sheep area over spring and from this develop a framework that will assist other farmers improve their pasture management

Microbial Communities in a High Arctic Polar Desert Landscape

The High Arctic is dominated by polar desert habitats whose microbial communities are poorly understood. In this study, we used next generation sequencing to describe the α- and β-diversity of microbial communities in polar desert soils from the Kongsfjorden region of Svalbard. Ten phyla dominated the soils and accounted for 95% of all sequences, with the Proteobacteria, Actinobacteria, and Chloroflexi being the major lineages. In contrast to previous investigations of Arctic soils, relative Acidobacterial abundances were found to be very low as were the Archaea throughout the Kongsfjorden polar desert landscape. Lower Acidobacterial abundances were attributed to characteristic circumneutral soil pHs in this region, which has resulted from the weathering of underlying carbonate bedrock. In addition, we compared previously measured geochemical conditions as possible controls on soil microbial communities. Phosphorus, pH, nitrogen, and calcium levels all significantly correlated with β-diversity, indicating landscape-scale lithological control of available nutrients, which in turn, significantly influenced soil community composition. In addition, soil phosphorus and pH significantly correlated with α-diversity, particularly with the Shannon diversity and Chao 1 richness indices

Kinesin family member 6 (kif6) is necessary for spine development in zebrafish

Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Developmental Dynamics 243 (2014): 1646–1657, doi:10.1002/dvdy.24208.Idiopathic scoliosis is a form of spinal deformity that affects 2–3% of children and results in curvature of the spine without structural defects of the vertebral units. The pathogenesis of idiopathic scoliosis remains poorly understood, in part due to the lack of a relevant animal model. We performed a forward mutagenesis screen in zebrafish to identify new models for idiopathic scoliosis. We isolated a recessive zebrafish mutant, called skolios, which develops isolated spinal curvature that arises independent of vertebral malformations. Using meiotic mapping and whole genome sequencing, we identified a nonsense mutation in kinesin family member 6 (kif6gw326) unique to skolios mutants. Three additional kif6 frameshift alleles (gw327, gw328, gw329) were generated with transcription activator-like effector nucleases (TALENs). Zebrafish homozygous or compound heterozygous for kif6 frameshift mutations developed a scoliosis phenotype indistinguishable from skolios mutants, confirming that skolios is caused by the loss of kif6. Although kif6 may play a role in cilia, no evidence for cilia dysfunction was seen in kif6gw326 mutants. Overall, these findings demonstrate a novel role for kif6 in spinal development and identify a new candidate gene for human idiopathic scoliosis.2015-11-1

Canine Models of Inherited Musculoskeletal and Neurodegenerative Diseases

Mouse models of human disease remain the bread and butter of modern biology and therapeutic discovery. Nonetheless, more often than not mouse models do not reproduce the pathophysiology of the human conditions they are designed to mimic. Naturally occurring large animal models have predominantly been found in companion animals or livestock because of their emotional or economic value to modern society and, unlike mice, often recapitulate the human disease state. In particular, numerous models have been discovered in dogs and have a fundamental role in bridging proof of concept studies in mice to human clinical trials. The present article is a review that highlights current canine models of human diseases, including Alzheimer\u27s disease, degenerative myelopathy, neuronal ceroid lipofuscinosis, globoid cell leukodystrophy, Duchenne muscular dystrophy, mucopolysaccharidosis, and fucosidosis. The goal of the review is to discuss canine and human neurodegenerative pathophysiologic similarities, introduce the animal models, and shed light on the ability of canine models to facilitate current and future treatment trials