Marginalizing the likelihood function for modeled gravitational wave searches

Matched filtering is a commonly used technique in gravitational wave searches for signals from compact binary systems and from rapidly rotating neutron stars. A common issue in these searches is dealing with four extrinsic parameters which do not affect the phase evolution of the system: the overall amplitude, initial phase, and two angles determining the overall orientation of the system. The F-statistic maximizes the likelihood function analytically over these parameters, while the B-statistic marginalizes over them. The B-statistic, while potentially more powerful and capable of incorporating astrophysical priors, is not as widely used because of the computational difficulty of performing the marginalization. In this paper we address this difficulty and show how the marginalization can be done analytically by combining the four parameters into a set of complex amplitudes. The results of this paper are applicable to both transient non-precessing binary coalescence events, and to long lived signals from rapidly rotating neutron stars.Comment: 26 page

Middleware and Services for Dynamic Adaptive Neural Network Arrays

Dynamic Adaptive Neural Network Arrays (DANNAs) are neuromorphic systems that exhibit spiking behaviors and can be designed using evolutionary optimization. Array elements are rapidly reconfigurable and can function as either neurons or synapses with programmable interconnections and parameters. Visualization applications can examine DANNA element connections, parameters, and functionality, and evolutionary optimization applications can utilize DANNA to speedup neural network simulations. To facilitate interactions with DANNAs from these applications, we have developed a language-agnostic application programming interface (API) that abstracts away low-level communication details with a DANNA and provides a high-level interface for reprogramming and controlling a DANNA. The library has also been designed in modules in order to adapt to future changes in the design of DANNA, including changes to the DANNA element design, DANNA communication protocol, and connection. In addition to communicating with DANNAs, it is also beneficial for applications to store networks with known functionality. Hence, a Representational State Transfer (REST) API with a MongoDB database back-end has been developed to encourage the collection and exploration of networks

New Coordinates for the Amplitude Parameter Space of Continuous Gravitational Waves

The parameter space for continuous gravitational waves (GWs) can be divided into amplitude parameters (signal amplitude, inclination and polarization angles describing the orientation of the source, and an initial phase) and phase-evolution parameters. The division is useful in part because the Jaranowski-Krolak-Schutz (JKS) coordinates on the four-dimensional amplitude parameter space allow the GW signal to be written as a linear combination of four template waveforms with the JKS coordinates as coefficients. We define a new set of coordinates on the amplitude parameter space, with the same properties, which is more closely connected to the physical amplitude parameters. These naturally divide into two pairs of Cartesian-like coordinates on two-dimensional subspaces, one corresponding to left- and the other to right-circular polarization. We thus refer to these as CPF (circular polarization factored) coordinates. The corresponding two sets of polar coordinates (known as CPF-polar) can be related in a simple way to the physical parameters. We illustrate some simplifying applications for these various coordinate systems, such as: a calculation of Jacobians between various coordinate systems; an illustration of the signal coordinate singularities associated with left- and right-circular polarization, which correspond to the origins of the two two-dimensional subspaces; and an elucidation of the form of the log-likelihood ratio between hypotheses of Gaussian noise with and without a continuous GW signal. These are used to illustrate some of the prospects for approximate evaluation of a Bayesian detection statistic defined by marginalization over the physical parameter space. Additionally, in the presence of simplifying assumptions about the observing geometry, we are able to explicitly evaluate the integral for the Bayesian detection statistic, and compare it to the approximate results.Comment: REVTeX, 18 pages, 8 image files included in 7 figure

Towards the graviton from spinfoams: higher order corrections in the 3d toy model

We consider the recent calculation gr-qc/0508124 of the graviton propagator in the spinfoam formalism. Within the 3d toy model introduced in gr-qc/0512102, we test how the spinfoam formalism can be used to construct the perturbative expansion of graviton amplitudes. Although the 3d graviton is a pure gauge, one can choose to work in a gauge where it is not zero and thus reproduce the structure of the 4d perturbative calculations. We compute explicitly the next to leading and next to next to leading orders, corresponding to one-loop and two-loop corrections. We show that while the first arises entirely from the expansion of the Regge action around the flat background, the latter receives contributions from the microscopic, non Regge-like, quantum geometry. Surprisingly, this new contribution reduces the magnitude of the next to next to leading order. It thus appears that the spinfoam formalism is likely to substantially modify the conventional perturbative expansion at higher orders. This result supports the interest in this approach. We then address a number of open issues in the rest of the paper. First, we discuss the boundary state ansatz, which is a key ingredient in the whole construction. We propose a way to enhance the ansatz in order to make the edge lengths and dihedral angles conjugate variables in a mathematically well-defined way. Second, we show that the leading order is stable against different choices of the face weights of the spinfoam model; the next to leading order, on the other hand, is changed in a simple way, and we show that the topological face weight minimizes it. Finally, we extend the leading order result to the case of a regular, but not equilateral, tetrahedron.Comment: 24 pages, many figure

Functional analysis of a putative membrane-bound endo-β-1,4-glucanase from Panicum virgatum

Cellulose is the most abundant carbohydrate in the world and is degraded by the synergistic action of multiple enzymes. One large family of enzymes capable of hydrolyzing cellulose is glycoside hydrolase family 9 (GH9), which includes several endoglucanases. Recent research into the molecular biology of plants has revealed certain genes coding for endo-β-1,4-glucanases (EGases). The EGases in plants are primarily functional during cell elongation through wall stress relaxation. GH9 enzymes have been found in insects, bacteria, oomycetes, and fungi. In insects, EGases enable the organism to digest cellulose; in fungi, EGases are suspected to play an important role in obtaining nutrition for the fungi and may be associated with defense mechanisms. In these systems, EGases play an important role in breaking the internal bonds of cellulose resulting in a disruption of the crystalline structure. EGases are able to cleave cellulose at the β-1,4 linkages in the cellulose chain with a net inversion of anomeric configuration. A putative EGase from switchgrass (Panicum virgatum) was isolated from leaf cDNA. This gene of interest was cloned into Escherichia coli via the pET160 expression system. Selection by antibiotic resistance confirmed transformation of E. coli. Protein expression was detected via SDS-PAGE and tested to confirm cellulose lysing. The optimal pH and temperature were determined using 3,5-Dinitrosalycilic acid (DNSA) assay at different pH and temperature settings measuring reduced sugars released. Functionality in plants was determined through a gene rescue experiment using Arabidopsis thaliana mutants known to be deficient in putative EGase homologs. Switchgrass containing an overexpression of the EGase was compared to wildtype switchgrass via histology and microscopy. The confirmation of a functional EGase from switchgrass may aid in the development of switchgrass transformants with an amorphous cellulose structure, thereby reducing the amount of resources required during biofuel refinery

Population structure and local selection yield high genomic variation in Mimulus guttatus

Across western North America, Mimulus guttatus exists as many local populations adapted to site-specific environmental challenges. Gene flow between locally adapted populations will affect genetic diversity both within demes and across the larger metapopulation. Here, we analyse 34 whole-genome sequences from the intensively studied Iron Mountain population (IM) in conjunction with sequences from 22 Mimulus individuals sampled from across western North America. Three striking features of these data address hypotheses about migration and selection in a locally adapted population. First, we find very high levels of intrapopulation polymorphism (synonymous =0.033). Variation outside of genes is likely even higher but difficult to estimate because excessive divergence reduces the efficiency of read mapping. Second, IM exhibits a significantly positive genomewide average for Tajima\u27s D. This indicates allele frequencies are typically more intermediate than expected from neutrality, opposite the pattern observed in many other species. Third, IM exhibits a distinctive haplotype structure with a genomewide excess of positive associations between rarer alleles at linked loci. This suggests an important effect of gene flow from other Mimulus populations, although a residual effect of population founding might also contribute. The combination of multiple analyses, including a novel tree-based analytic method, illustrates how the balance of local selection, limited dispersal and metapopulation dynamics manifests across the genome. The overall genomic pattern of sequence diversity suggests successful gene flow of divergent immigrant genotypes into IM. However, many loci show patterns indicative of local adaptation, particularly at SNPs associated with chromosomal inversions

A new malaria vector in Africa: Predicting the expansion range of Anopheles stephensi and identifying the urban populations at risk

In 2012, an unusual outbreak of urban malaria was reported from Djibouti City in the Horn of Africa and increasingly severe outbreaks have been reported annually ever since. Subsequent investigations discovered the presence of an Asian mosquito species; Anopheles stephensi, a species known to thrive in urban environments. Since that first report, An. stephensi has been identified in Ethiopia and Sudan, and this worrying development has prompted the World Health Organization (WHO) to publish a vector alert calling for active mosquito surveillance in the region. Using an up-to-date database of published locational records for An. stephensi across its full range (Asia, Arabian Peninsula, Horn of Africa) and a set of spatial models that identify the environmental conditions that characterize a species’ preferred habitat, we provide evidence-based maps predicting the possible locations across Africa where An. stephensi could establish if allowed to spread unchecked. Unsurprisingly, due to this species’ close association with man-made habitats, our maps predict a high probability of presence within many urban cities across Africa where our estimates suggest that over 126 million people reside. Our results strongly support the WHO’s call for surveillance and targeted vector control and provide a basis for the prioritization of surveillance