Growth by insertion: The family of bacterial DDxP proteins

We have identified a variety of proteins in species of the Legionella, Aeromonas, Pseudomonas, Vibrio, Nitrosomonas, Nitrosospira, Variovorax, Halomonas, and Rhizobia genera, which feature repetitive modules of different length and composition, invariably ending at the COOH side with Asp–Asp–x–Pro (DDxP) motifs. DDxP proteins range in size from 900 to 6200 aa (amino acids), and contain 1 to 5 different module types, present in one or multiple copies. We hypothesize that DDxP proteins were modeled by the action of specific endonucleases inserting DNA segments into genes encoding DDxP motifs. Target site duplications (TSDs) formed upon repair of staggered ends generated by endonuclease cleavage would explain the DDxP motifs at repeat ends. TSDs acted eventually as targets for the insertion of more modules of the same or different types. Repeat clusters plausibly resulted from amplification of both repeat and flanking TSDs. The proposed growth shown by the insertion model is supported by the identification of homologous proteins lacking repeats in Pseudomonas and Rhizobium. The 85 DDxP repeats identified in this work vary in length, and can be sorted into short (136–215 aa) and long (243–304 aa) types. Conserved Asp–Gly–Asp–Gly–Asp motifs are located 11–19 aa from the terminal DDxP motifs in all repeats, and far upstream in most long repeats

Levetiracetam in patients with epilepsy and chronic liver disease: observations in a case series.

OBJECTIVES: To evaluate levetiracetam (LEV) tolerability in patients with epilepsy and liver disease. METHODS: Fourteen patients with epilepsy and concomitant liver disease were treated with LEV in an open prospective investigation mimicking the daily clinical practice. All patients were stabilized (ie, for at least 1 year) on traditional antiepileptic drugs with complete or partial control of seizures. In the 6-month pre-LEV baseline period, seizure frequency ranged from 3 to 300. Levetiracetam was added on to the basal treatment at a starting daily dose of 250 mg, and the dose was adjusted according to the tolerability and the therapeutic response. Four patients discontinued the drug within the first 3 months because of intolerable side effects. The remaining 10 continued LEV treatment, and the present follow-up is 12 to 38 months. RESULTS: In the last 6 months of observation, none of the patients showed worsening of liver function on the basis of blood chemistry, and in 4 patients, a complete normalization or a trend toward physiological values of transaminase and/or gamma-glutamyltransferase activity was observed. A greater than 50% reduction in seizure frequency occurred in all uncontrolled patients, 2 of whom achieved seizure freedom during LEV treatment. CONCLUSIONS: Based on these observations, LEV seems to be an attractive therapeutic option in epileptic patients with chronic liver diseases

Electrical resistivity tomography investigations in the ufita Valley (southern Italy).

Several Electrical Resistivity Tomography (ERT) surveys have been carried out to study the subsurface structural and sedimentary settings of the upper Ufita River valley, and to evaluate their efficiency to distinguish the geological boundary between shallow Quaternary sedimentary deposits and clayey bedrock characterized by moderate resistivity contrast. Five shallow ERTs were carried out across a morphological scarp running at the foot of the northeastern slope of the valley. This valley shoulder is characterized by a set of triangular facets, that some authors associated to the presence of a SW-dipping normal fault. The geological studies allow us to interpret the shallow ERTs results obtaining a resistivity range for each Quaternary sedimentary deposit. The tomographies showed the geometrical relationships of alluvial and slope deposits, having a maximum thickness of 30-40 m, and the morphology of the bedrock. The resistivity range obtained for each sedimentary body has been used for calibrating the tomographic results of one 3560m-long deep ERT carried out across the deeper part of the intramountain depression with an investigation depth of about 170 m. The deep resistivity result highlighted the complex alluvial setting, characterized by alternating fine grained lacustrine deposits and coarser gravelly fluvial sediments

Pathology and molecular analysis of ' Hapalotrema mistroides ' (Digenea: Spirorchiidae) infecting a Mediterranean loggerhead turtle ' Caretta caretta '

Turtle blood flukes belonging to the family Spirorchiidae (Digenea) represent a major threat for sea turtle health and are considered the most important parasitic cause of turtle stranding and mortality worldwide. Despite the large diversity of spirorchiid species found globally, there are only 2 records for free-ranging Mediterranean sea turtles that date back to the late 1800s involving just Hapalotrema mistroides Monticelli, 1896. This study describes the first fatal confirmed case of spirorchiidiasis in a free-ranging Mediterranean loggerhead turtle Caretta caretta (Linnaeus) and, owing to the complexities of taxonomic identification of these parasites, provides the first molecular characterization and phylogenetic analysis of H. mistroides from the Mediterranean Sea. The loggerhead turtle showed cachexia and digestive disorders associated with severe damage to the pancreas and intestinal ganglia, caused by deposition of Hapalotrema eggs forming granulomas. Massive Hapalotrema egg emboli in several tissues and organs and encephalitis were the most probable contributions to the death of the turtle. The congruence between the phylogenetic analysis of both the ITS2 and 28S rDNA resolved the Italian and USA H. mistroides as the same species, confirming the parasite identification. The case here described clearly indicates that the blood flukes should be considered in the differential diagnosis of Mediterranean sea turtle diseases

A Cross-correlation method to search for gravitational wave bursts with AURIGA and Virgo

We present a method to search for transient GWs using a network of detectors with different spectral and directional sensitivities: the interferometer Virgo and the bar detector AURIGA. The data analysis method is based on the measurements of the correlated energy in the network by means of a weighted cross-correlation. To limit the computational load, this coherent analysis step is performed around time-frequency coincident triggers selected by an excess power event trigger generator tuned at low thresholds. The final selection of GW candidates is performed by a combined cut on the correlated energy and on the significance as measured by the event trigger generator. The method has been tested on one day of data of AURIGA and Virgo during September 2005. The outcomes are compared to the results of a stand-alone time-frequency coincidence search. We discuss the advantages and the limits of this approach, in view of a possible future joint search between AURIGA and one interferometric detector.Comment: 11 pages, 6 figures, submitted to CQG special issue for Amaldi 7 Proceeding

The variable finesse locking technique

Virgo is a power recycled Michelson interferometer, with 3 km long Fabry-Perot cavities in the arms. The locking of the interferometer has been obtained with an original lock acquisition technique. The main idea is to lock the instrument away from its working point. Lock is obtained by misaligning the power recycling mirror and detuning the Michelson from the dark fringe. In this way, a good fraction of light escapes through the antisymmetric port and the power build-up inside the recycling cavity is extremely low. The benefit is that all the degrees of freedom are controlled when they are almost decoupled, and the linewidth of the recycling cavity is large. The interferometer is then adiabatically brought on to the dark fringe. This technique is referred to as variable finesse, since the recycling cavity is considered as a variable finesse Fabry-Perot. This technique has been widely tested and allows us to reach the dark fringe in few minutes, in an essentially deterministic way

Virgo calibration and reconstruction of the gravitational wave strain during VSR1

Virgo is a kilometer-length interferometer for gravitational waves detection located near Pisa. Its first science run, VSR1, occured from May to October 2007. The aims of the calibration are to measure the detector sensitivity and to reconstruct the time series of the gravitational wave strain h(t). The absolute length calibration is based on an original non-linear reconstruction of the differential arm length variations in free swinging Michelson configurations. It uses the laser wavelength as length standard. This method is used to calibrate the frequency dependent response of the Virgo mirror actuators and derive the detector in-loop response and sensitivity within ~5%. The principle of the strain reconstruction is highlighted and the h(t) systematic errors are estimated. A photon calibrator is used to check the sign of h(t). The reconstructed h(t) during VSR1 is valid from 10 Hz up to 10 kHz with systematic errors estimated to 6% in amplitude. The phase error is estimated to be 70 mrad below 1.9 kHz and 6 micro-seconds above.Comment: 8 pages, 8 figures, proceedings of Amaldi 8 conference, to be published in Journal of Physics Conference Series (JPCS). Second release: correct typo

Reconstruction of the gravitational wave signal h(t)h(t) during the Virgo science runs and independent validation with a photon calibrator

The Virgo detector is a kilometer-scale interferometer for gravitational wave detection located near Pisa (Italy). About 13 months of data were accumulated during four science runs (VSR1, VSR2, VSR3 and VSR4) between May 2007 and September 2011, with increasing sensitivity. In this paper, the method used to reconstruct, in the range 10 Hz-10 kHz, the gravitational wave strain time series $h(t)$ from the detector signals is described. The standard consistency checks of the reconstruction are discussed and used to estimate the systematic uncertainties of the $h(t)$ signal as a function of frequency. Finally, an independent setup, the photon calibrator, is described and used to validate the reconstructed $h(t)$ signal and the associated uncertainties. The uncertainties of the $h(t)$ time series are estimated to be 8% in amplitude. The uncertainty of the phase of $h(t)$ is 50 mrad at 10 Hz with a frequency dependence following a delay of 8 $\mu$s at high frequency. A bias lower than $4\,\mathrm{\mu s}$ and depending on the sky direction of the GW is also present.Comment: 35 pages, 16 figures. Accepted by CQ

Calibration and sensitivity of the Virgo detector during its second science run

The Virgo detector is a kilometer-length interferometer for gravitational wave detection located near Pisa (Italy). During its second science run (VSR2) in 2009, six months of data were accumulated with a sensitivity close to its design. In this paper, the methods used to determine the parameters for sensitivity estimation and gravitational wave reconstruction are described. The main quantities to be calibrated are the frequency response of the mirror actuation and the sensing of the output power. Focus is also put on their absolute timing. The monitoring of the calibration data as well as the parameter estimation with independent techniques are discussed to provide an estimation of the calibration uncertainties. Finally, the estimation of the Virgo sensitivity in the frequency-domain is described and typical sensitivities measured during VSR2 are shown.Comment: 30 pages, 23 figures, 1 table. Published in Classical and Quantum Gravity (CQG), Corrigendum include

Sensitivity to Gravitational Waves from Compact Binary Coalescences Achieved during LIGO's Fifth and Virgo's First Science Run

We summarize the sensitivity achieved by the LIGO and Virgo gravitational wave detectors for compact binary coalescence (CBC) searches during LIGO's fifth science run and Virgo's first science run. We present noise spectral density curves for each of the four detectors that operated during these science runs which are representative of the typical performance achieved by the detectors for CBC searches. These spectra are intended for release to the public as a summary of detector performance for CBC searches during these science runs.Comment: 12 pages, 5 figure