Coincidence and coherent data analysis methods for gravitational wave bursts in a network of interferometric detectors

Network data analysis methods are the only way to properly separate real gravitational wave (GW) transient events from detector noise. They can be divided into two generic classes: the coincidence method and the coherent analysis. The former uses lists of selected events provided by each interferometer belonging to the network and tries to correlate them in time to identify a physical signal. Instead of this binary treatment of detector outputs (signal present or absent), the latter method involves first the merging of the interferometer data and looks for a common pattern, consistent with an assumed GW waveform and a given source location in the sky. The thresholds are only applied later, to validate or not the hypothesis made. As coherent algorithms use a more complete information than coincidence methods, they are expected to provide better detection performances, but at a higher computational cost. An efficient filter must yield a good compromise between a low false alarm rate (hence triggering on data at a manageable rate) and a high detection efficiency. Therefore, the comparison of the two approaches is achieved using so-called Receiving Operating Characteristics (ROC), giving the relationship between the false alarm rate and the detection efficiency for a given method. This paper investigates this question via Monte-Carlo simulations, using the network model developed in a previous article.Comment: Spelling mistake corrected in one author's nam

Comparison of filters for detecting gravitational wave bursts in interferometric detectors

Filters developed in order to detect short bursts of gravitational waves in interferometric detector outputs are compared according to three main points. Conventional Receiver Operating Characteristics (ROC) are first built for all the considered filters and for three typical burst signals. Optimized ROC are shown for a simple pulse signal in order to estimate the best detection efficiency of the filters in the ideal case, while realistic ones obtained with filters working with several ``templates'' show how detection efficiencies can be degraded in a practical implementation. Secondly, estimations of biases and statistical errors on the reconstruction of the time of arrival of pulse-like signals are then given for each filter. Such results are crucial for future coincidence studies between Gravitational Wave detectors but also with neutrino or optical detectors. As most of the filters require a pre-whitening of the detector noise, the sensitivity to a non perfect noise whitening procedure is finally analysed. For this purpose lines of various frequencies and amplitudes are added to a Gaussian white noise and the outputs of the filters are studied in order to monitor the excess of false alarms induced by the lines. The comparison of the performances of the different filters finally show that they are complementary rather than competitive.Comment: 32 pages (14 figures), accepted for publication in Phys. Rev.

Minimax estimation of the Wigner function in quantum homodyne tomography with ideal detectors

We estimate the quantum state of a light beam from results of quantum homodyne measurements performed on identically prepared pulses. The state is represented through the Wigner function, a ``quasi-probability density'' on $\mathbb{R}^{2}$ which may take negative values and must respect intrinsic positivity constraints imposed by quantum physics. The data consists of $n$ i.i.d. observations from a probability density equal to the Radon transform of the Wigner function. We construct an estimator for the Wigner function, and prove that it is minimax efficient for the pointwise risk over a class of infinitely differentiable functions. A similar result was previously derived by Cavalier in the context of positron emission tomography. Our work extends this result to the space of smooth Wigner functions, which is the relevant parameter space for quantum homodyne tomography.Comment: 15 page

Regularization of statistical inverse problems and the Bakushinskii veto

In the deterministic context Bakushinskii's theorem excludes the existence of purely data driven convergent regularization for ill-posed problems. We will prove in the present work that in the statistical setting we can either construct a counter example or develop an equivalent formulation depending on the considered class of probability distributions. Hence, Bakushinskii's theorem does not generalize to the statistical context, although this has often been assumed in the past. To arrive at this conclusion, we will deduce from the classic theory new concepts for a general study of statistical inverse problems and perform a systematic clarification of the key ideas of statistical regularization.Comment: 20 page

Multigene Phylogeny of Choanozoa and the Origin of Animals

Animals are evolutionarily related to fungi and to the predominantly unicellular protozoan phylum Choanozoa, together known as opisthokonts. To establish the sequence of events when animals evolved from unicellular ancestors, and understand those key evolutionary transitions, we need to establish which choanozoans are most closely related to animals and also the evolutionary position of each choanozoan group within the opisthokont phylogenetic tree. Here we focus on Ministeria vibrans, a minute bacteria-eating cell with slender radiating tentacles. Single-gene trees suggested that it is either the closest unicellular relative of animals or else sister to choanoflagellates, traditionally considered likely animal ancestors. Sequencing thousands of Ministeria protein genes now reveals about 14 with domains of key significance for animal cell biology, including several previously unknown from deeply diverging Choanozoa, e.g. domains involved in hedgehog, Notch and tyrosine kinase signaling or cell adhesion (cadherin). Phylogenetic trees using 78 proteins show that Ministeria is not sister to animals or choanoflagellates (themselves sisters to animals), but to Capsaspora, another protozoan with thread-like (filose) tentacles. The Ministeria/Capsaspora clade (new class Filasterea) is sister to animals and choanoflagellates, these three groups forming a novel clade (filozoa) whose ancestor presumably evolved filose tentacles well before they aggregated as a periciliary collar in the choanoflagellate/sponge common ancestor. Our trees show ichthyosporean choanozoans as sisters to filozoa; a fusion between ubiquitin and ribosomal small subunit S30 protein genes unifies all holozoa (filozoa plus Ichthyosporea), being absent in earlier branching eukaryotes. Thus, several successive evolutionary innovations occurred among their unicellular closest relatives prior to the origin of the multicellular body-plan of animals

Biogenesis of the inner membrane complex is dependent on vesicular transport by the alveolate specific GTPase Rab11B

Apicomplexan parasites belong to a recently recognised group of protozoa referred to as Alveolata. These protists contain membranous sacs (alveoli) beneath the plasma membrane, termed the Inner Membrane Complex (IMC) in the case of Apicomplexa. During parasite replication the IMC is formed de novo within the mother cell in a process described as internal budding. We hypothesized that an alveolate specific factor is involved in the specific transport of vesicles from the Golgi to the IMC and identified the small GTPase Rab11B as an alveolate specific Rab-GTPase that localises to the growing end of the IMC during replication of Toxoplasma gondii. Conditional interference with Rab11B function leads to a profound defect in IMC biogenesis, indicating that Rab11B is required for the transport of Golgi derived vesicles to the nascent IMC of the daughter cell. Curiously, a block in IMC biogenesis did not affect formation of sub-pellicular microtubules, indicating that IMC biogenesis and formation of sub-pellicular microtubules is not mechanistically linked. We propose a model where Rab11B specifically transports vesicles derived from the Golgi to the immature IMC of the growing daughter parasites

An elliptical tiling method to generate a 2-dimensional set of templates for gravitational wave search

Searching for a signal depending on unknown parameters in a noisy background with matched filtering techniques always requires an analysis of the data with several templates in parallel in order to ensure a proper match between the filter and the real waveform. The key feature of such an implementation is the design of the filter bank which must be small to limit the computational cost while keeping the detection efficiency as high as possible. This paper presents a geometrical method which allows one to cover the corresponding physical parameter space by a set of ellipses, each of them being associated to a given template. After the description of the main characteristics of the algorithm, the method is applied in the field of gravitational wave (GW) data analysis, for the search of damped sine signals. Such waveforms are expected to be produced during the de-excitation phase of black holes -- the so-called 'ringdown' signals -- and are also encountered in some numerically computed supernova signals.Comment: Accepted in PR

Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains

Many of the eukaryotic phylogenomic analyses published to date were based on alignments of hundreds to thousands of genes. Frequently, in such analyses, the most realistic evolutionary models currently available are often used to minimize the impact of systematic error. However, controversy remains over whether or not idiosyncratic gene family dynamics (i.e., gene duplications and losses) and incorrect orthology assignments are always appropriately taken into account. In this paper, we present an innovative strategy for overcoming orthology assignment problems. Rather than identifying and eliminating genes with paralogy problems, we have constructed a data set comprised exclusively of conserved single-copy protein domains that, unlike most of the commonly used phylogenomic data sets, should be less confounded by orthology miss-assignments. To evaluate the power of this approach, we performed maximum likelihood and Bayesian analyses to infer the evolutionary relationships within the opisthokonts (which includes Metazoa, Fungi, and related unicellular lineages). We used this approach to test 1) whether Filasterea and Ichthyosporea form a clade, 2) the interrelationships of early-branching metazoans, and 3) the relationships among early-branching fungi. We also assessed the impact of some methods that are known to minimize systematic error, including reducing the distance between the outgroup and ingroup taxa or using the CAT evolutionary model. Overall, our analyses support the Filozoa hypothesis in which Ichthyosporea are the first holozoan lineage to emerge followed by Filasterea, Choanoflagellata, and Metazoa. Blastocladiomycota appears as a lineage separate from Chytridiomycota, although this result is not strongly supported. These results represent independent tests of previous phylogenetic hypotheses, highlighting the importance of sophisticated approaches for orthology assignment in phylogenomic analyses. © The Author 2011. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved

Phylogenomics Reshuffles the Eukaryotic Supergroups

Background. Resolving the phylogenetic relationships between eukaryotes is an ongoing challenge of evolutionary biology. In recent years, the accumulation of molecular data led to a new evolutionary understanding, in which all eukaryotic diversity has been classified into five or six supergroups. Yet, the composition of these large assemblages and their relationships remain controversial. Methodology/Principle Findings. Here, we report the sequencing of expressed sequence tags (ESTs) for two species belonging to the supergroup Rhizaria and present the analysis of a unique dataset combining 29908 amino acid positions and an extensive taxa sampling made of 49 mainly unicellular species representative of all supergroups. Our results show a very robust relationship between Rhizaria and two main clades of the supergroup chromalveolates: stramenopiles and alveolates. We confirm the existence of consistent affinities between assemblages that were thought to belong to different supergroups of eukaryotes, thus not sharing a close evolutionary history. Conclusions. This well supported phylogeny has important consequences for our understanding of the evolutionary history of eukaryotes. In particular, it questions a single red algal origin of the chlorophyll-c containing plastids among the chromalveolates. We propose the abbreviated name ‘SAR’ (Stramenopiles+Alveolates+Rhizaria) to accommodate this new super assemblage of eukaryotes, which comprises the largest diversity of unicellular eukaryotes

Detection of a close supernova gravitational wave burst in a network of interferometers, neutrino and optical detectors

Trying to detect the gravitational wave (GW) signal emitted by a type II supernova is a main challenge for the GW community. Indeed, the corresponding waveform is not accurately modeled as the supernova physics is very complex; in addition, all the existing numerical simulations agree on the weakness of the GW emission, thus restraining the number of sources potentially detectable. Consequently, triggering the GW signal with a confidence level high enough to conclude directly to a detection is very difficult, even with the use of a network of interferometric detectors. On the other hand, one can hope to take benefit from the neutrino and optical emissions associated to the supernova explosion, in order to discover and study GW radiation in an event already detected independently. This article aims at presenting some realistic scenarios for the search of the supernova GW bursts, based on the present knowledge of the emitted signals and on the results of network data analysis simulations. Both the direct search and the confirmation of the supernova event are considered. In addition, some physical studies following the discovery of a supernova GW emission are also mentioned: from the absolute neutrino mass to the supernova physics or the black hole signature, the potential spectrum of discoveries is wide.Comment: Revised version, accepted for publication in Astroparticle Physic