Space-time modelling of emerging infectious diseases: Assessing leptospirosis risk in Sri Lanka

In this research, models were developed to analyze leptospirosis incidence in Sri Lanka and its relation to rainfall. Before any leptospirosis risk models were developed, rainfall data were evaluated from an agro-ecological monitoring network for producing maps of total monthly rainfall in Sri Lanka. Four spatial interpolation techniques were compared: inverse distance weighting, thin-plate splines, ordinary kriging, and Bayesian kriging. Error metrics were used to validate interpolations against independent data. Satellite data were used to assess the spatial pattern of rainfall. Results indicated that Bayesian kriging and splines performed best in low and high rainfall, respectively. Rainfall maps generated from the agro-ecological network were found to have accuracies consistent with previous studies in Sri Lanka. These rainfall data were then used as the primary predictor in a family of time series leptospirosis forecasting models at varying spatial scales across Sri Lanka. Several modelling scenarios were evaluated using proper scoring rules and numerous other metrics to assess model fit and calibration. A negative binomial integer-valued autoregressive conditional heteroscedasticity (INGARCH) model that included current and previous rainfall covariates, as well as regression on previous cases of leptospirosis at a local and seasonal time scale was selected as the best performing model. It was found that rainfall did not have a significant correlation with leptospirosis incidence in Sri Lanka, but the family of INGARCH models developed was able to forecast leptospirosis incidence and effectively provide early warning for leptospirosis outbreaks at the district level across Sri Lanka

Doppler-beaming in the Kepler light curve of LHS 6343 A

Context. Kepler observations revealed a brown dwarf eclipsing the M-type star LHS 6343 A with a period of 12.71 days. In addition, an out-of-eclipse light modulation with the same period and a relative semi-amplitude of 2 x 10^-4 was observed showing an almost constant phase lag to the eclipses produced by the brown dwarf. In a previous work, we concluded that this was due to the light modulation induced by photospheric active regions in LHS 6343 A. Aims. In the present work, we prove that most of the out-of-eclipse light modulation is caused by the Doppler-beaming induced by the orbital motion of the primary star. Methods. We introduce a model of the Doppler-beaming for an eccentric orbit and also considered the ellipsoidal effect. The data were fitted using a Bayesian approach implemented through a Monte Carlo Markov chain method. Model residuals were analysed by searching for periodicities using a Lomb-Scargle periodogram. Results. For the first seven quarters of Kepler observations and the orbit previously derived from the radial velocity measurements, we show that the light modulation of the system outside eclipses is dominated by the Doppler-beaming effect. A period search performed on the residuals shows a significant periodicity of 42.5 +- 3.2 days with a false-alarm probability of 5 x 10^-4, probably associated with the rotational modulation of the primary component.Comment: 6 pages, 7 figure

Optimal design of a series of cstr's performing reversible reactions catalyzed by soluble enzymes: a theoretical study

The condition for the minimum overall reactor volume of a given number of CSTR's in series is theoretically determined for a reversible, single reactant-single product (Uni-Uni) enzyme catalyzed reaction. The reactor network is assumed to operate in steady-state, isothermal conditions with a single phase and a constant activity of biocatalyst. The method is based on a mathematical analysis of the discrete substrate concentration profile along the CSTR's assuming complete micromixing. The algebraic equations describing the critical loci are obtained for the general case, the mathematical proof that these equations define a minimum is presented, and an exact solution arising from an asymptotic situation is found. An approximate analytical method of optimization based on the aforementioned critical behavior is reported and its validity and usefulness discussed. The formula introduced can be used in more general situations as tools for getting the approximate range where the optimal overall volume of the series of CSTR's lies. Hence, the reasoning developed is important for the preliminary CSTR design and relevant in the initial steps of the more involved methods of numerical optimization. Finally, the enzymatic conversion of fumarate to L-malate is examined as a model system in order to assess the usefulness and applicability of the analysis developed

A search for starlight reflected from HD 75289 b

We have used a doppler tomographic analysis to conduct a deep search for the starlight reflected from the planetary companion to HD 75289. In 4 nights on VLT2/UVES in January 2003, we obtained 684 high resolution echelle spectra with a total integration time of 26 hours. We establish an upper limit on the planet's geometric albedo p < 0.12 (to the 99.9% significance level) at the most probable orbital inclination i ~ 60 degrees, assuming a grey albedo, a Venus-like phase function and a planetary radius R_p = 1.6 R_Jup. We are able to rule out some combinations of the predicted planetary radius and atmospheric albedo models with high, reflective cloud decks.Comment: 5 pages, 5 figures, MNRAS accepted 12 Oct 200

The first magnetic maps of a pre-main sequence binary star system - HD 155555

We present the first maps of the surface magnetic fields of a pre-main sequence binary system. Spectropolarimetric observations of the young, 18 Myr, HD 155555 (V824 Ara, G5IV + K0IV) system were obtained at the Anglo-Australian Telescope in 2004 and 2007. Both datasets are analysed using a new binary Zeeman Doppler imaging (ZDI) code. This allows us to simultaneously model the contribution of each component to the observed circularly polarised spectra. Stellar brightness maps are also produced for HD 155555 and compared to previous Doppler images. Our radial magnetic maps reveal a complex surface magnetic topology with mixed polarities at all latitudes. We find rings of azimuthal field on both stars, most of which are found to be non-axisymmetric with the stellar rotational axis. We also examine the field strength and the relative fraction of magnetic energy stored in the radial and azimuthal field components at both epochs. A marked weakening of the field strength of the secondary star is observed between the 2004 and 2007 epochs. This is accompanied by an apparent shift in the location of magnetic energy from the azimuthal to radial field. We suggest that this could be indicative of a magnetic activity cycle. We use the radial magnetic maps to extrapolate the coronal field (by assuming a potential field) for each star individually - at present ignoring any possible interaction. The secondary star is found to exhibit an extreme tilt (~75 deg) of its large scale magnetic field to that of its rotation axis for both epochs. The field complexity that is apparent in the surface maps persists out to a significant fraction of the binary separation. Any interaction between the fields of the two stars is therefore likely to be complex also. Modelling this would require a full binary field extrapolation.Comment: 17 pages, 12 figures, accepted for publication in MNRA

Magnetic fields and accretion flows on the classical T Tauri star V2129 Oph

From observations collected with the ESPaDOnS spectropolarimeter, we report the discovery of magnetic fields at the surface of the mildly accreting classical T Tauri star V2129 Oph. Zeeman signatures are detected, both in photospheric lines and in the emission lines formed at the base of the accretion funnels linking the disc to the protostar, and monitored over the whole rotation cycle of V2129 Oph. We observe that rotational modulation dominates the temporal variations of both unpolarized and circularly polarized line profiles. We reconstruct the large-scale magnetic topology at the surface of V2129 Oph from both sets of Zeeman signatures simultaneously. We find it to be rather complex, with a dominant octupolar component and a weak dipole of strengths 1.2 and 0.35 kG, respectively, both slightly tilted with respect to the rotation axis. The large-scale field is anchored in a pair of 2-kG unipolar radial field spots located at high latitudes and coinciding with cool dark polar spots at photospheric level. This large-scale field geometry is unusually complex compared to those of non-accreting cool active subgiants with moderate rotation rates. As an illustration, we provide a first attempt at modelling the magnetospheric topology and accretion funnels of V2129 Oph using field extrapolation. We find that the magnetosphere of V2129 Oph must extend to about 7R* to ensure that the footpoints of accretion funnels coincide with the high-latitude accretion spots on the stellar surface. It suggests that the stellar magnetic field succeeds in coupling to the accretion disc as far out as the corotation radius, and could possibly explain the slow rotation of V2129 Oph. The magnetospheric geometry we derive produces X-ray coronal fluxes typical of those observed in cTTSs.Comment: MNRAS, in press (18 pages, 17 figures

Planets and Stellar Activity: Hide and Seek in the CoRoT-7 system

Since the discovery of the transiting super-Earth CoRoT-7b, several investigations have yielded different results for the number and masses of planets present in the system, mainly owing to the star's high level of activity. We re-observed CoRoT-7 in January 2012 with both HARPS and CoRoT, so that we now have the benefit of simultaneous radial-velocity and photometric data. This allows us to use the off-transit variations in the star's light curve to estimate the radial-velocity variations induced by the suppression of convective blueshift and the flux blocked by starspots. To account for activity-related effects in the radial-velocities which do not have a photometric signature, we also include an additional activity term in the radial-velocity model, which we treat as a Gaussian process with the same covariance properties (and hence the same frequency structure) as the light curve. Our model was incorporated into a Monte Carlo Markov Chain in order to make a precise determination of the orbits of CoRoT-7b and CoRoT-7c. We measure the masses of planets b and c to be 4.73 +/- 0.95 Mearth and 13.56 +/- 1.08 Mearth, respectively. The density of CoRoT-7b is (6.61 +/- 1.72)(Rp/1.58 Rearth)^(-3) g.cm^(-3), which is compatible with a rocky composition. We search for evidence of an additional planet d, identified by previous authors with a period close to 9 days. We are not able to confirm the existence of a planet with this orbital period, which is close to the second harmonic of the stellar rotation at around 7.9 days. Using Bayesian model selection we find that a model with two planets plus activity-induced variations is most favoured.Comment: Accepted 2014 July 2. Received 2014 June 30; in original form 2013 May 30 (17 pages, 9 figures

Array CGH analysis and developmental delay: A diagnostic tool for neurologists

Developmental delay occurs in 1-3% of the population, with unknown etiology in approximately 50% of cases. Initial genetic work up for developmental delay previously included chromosome analysis and subtelomeric FISH (fluorescent in situ hybridization). Array Comparative Genomic Hybridization (aCGH) has emerged as a tool to detect genetic copy number changes and uniparental disomy and is the most sensitive test in providing etiological diagnosis in developmental delay. aCGH allows for the provision of prognosis and recurrence risks, improves access to resources, helps limit further investigations and may alter medical management in many cases. aCGH has led to the delineation of novel genetic syndromes associated with developmental delay. An illustrative case of a 31-year-old man with long standing global developmental delay and recently diagnosed 4q21 deletion syndrome with a deletion of 20.8 Mb genomic interval is provided. aCGH is now recommended as a first line test in children and adults with undiagnosed developmental delay and congenital anomalies

Oscillating red giants in the CoRoT exo-field: Asteroseismic mass and radius determination

Context. Observations and analysis of solar-type oscillations in red-giant stars is an emerging aspect of asteroseismic analysis with a number of open questions yet to be explored. Although stochastic oscillations have previously been detected in red giants from both radial velocity and photometric measurements, those data were either too short or had sampling that was not complete enough to perform a detailed data analysis of the variability. The quality and quantity of photometric data as provided by the CoRoT satellite is necessary to provide a breakthrough in observing p-mode oscillations in red giants. We have analyzed continuous photometric time-series of about 11 400 relatively faint stars obtained in the exofield of CoRoT during the first 150 days long-run campaign from May to October 2007. We find several hundred stars showing a clear power excess in a frequency and amplitude range expected for red-giant pulsators. In this paper we present first results on a sub-sample of these stars. Aims. Knowing reliable fundamental parameters like mass and radius is essential for detailed asteroseismic studies of red-giant stars. As the CoRoT exofield targets are relatively faint (11-16 mag) there are no (or only weak) constraints on the star's location in the H-R diagram. We therefore aim to extract information about such fundamental parameters solely from the available time series. Methods. We model the convective background noise and the power excess hump due to pulsation with a global model fit and deduce reliable estimates for the stellar mass and radius from scaling relations for the frequency of maximum oscillation power and the characteristic frequency separation.Comment: 10 pages, 7 figures, accepted for publication in A&

A coordinated optical and X-ray spectroscopic campaign on HD179949: searching for planet-induced chromospheric and coronal activity

HD179949 is an F8V star, orbited by a close-in giant planet with a period of ~3 days. Previous studies suggested that the planet enhances the magnetic activity of the parent star, producing a chromospheric hot spot which rotates in phase with the planet orbit. However, this phenomenon is intermittent since it was observed in several but not all seasons. A long-term monitoring of the magnetic activity of HD179949 is required to study the amplitude and time scales of star-planet interactions. In 2009 we performed a simultaneous optical and X-ray spectroscopic campaign to monitor the magnetic activity of HD179949 during ~5 orbital periods and ~2 stellar rotations. We analyzed the CaII H&K lines as a proxy for chromospheric activity, and we studied the X-ray emission in search of flux modulations and to determine basic properties of the coronal plasma. A detailed analysis of the flux in the cores of the CaII H&K lines and a similar study of the X-ray photometry shows evidence of source variability, including one flare. The analysis of the the time series of chromospheric data indicates a modulation with a ~11 days period, compatible with the stellar rotation period at high latitudes. Instead, the X-ray light curve suggests a signal with a period of ~4 days, consistent with the presence of two active regions on opposite hemispheres. The observed variability can be explained, most likely, as due to rotational modulation and to intrinsic evolution of chromospheric and coronal activity. There is no clear signature related to the orbital motion of the planet, but the possibility that just a fraction of the chromospheric and coronal variability is modulated with the orbital period of the planet, or the stellar-planet beat period, cannot be excluded. We conclude that any effect due to the presence of the planet is difficult to disentangle