Leishmania donovani populations in Eastern Sudan: temporal structuring and a link between human and canine transmission.

BACKGROUND: Visceral leishmaniasis (VL), caused by the members of the Leishmania donovani complex, has been responsible for devastating VL epidemics in the Sudan. Multilocus microsatellite and sequence typing studies can provide valuable insights into the molecular epidemiology of leishmaniasis, when applied at local scales. Here we present population genetic data for a large panel of strains and clones collected in endemic Sudan between 1993 and 2001. METHODS: Genetic diversity was evaluated at fourteen microsatellite markers and eleven nuclear sequence loci across 124 strains and clones. RESULTS: Microsatellite data defined six genetic subpopulations with which the nuclear sequence data were broadly congruent. Pairwise estimates of FST (microsatellite) and KST (sequence) indicated small but significant shifts among the allelic repertoires of circulating strains year on year. Furthermore, we noted the co-occurrence of human and canine L. donovani strains in three of the six clusters defined. Finally, we identified widespread deficit in heterozygosity in all four years tested but strong deviation from inter-locus linkage equilibrium in two years. CONCLUSIONS: Significant genetic diversity is present among L. donovani in Sudan, and minor population structuring between years is characteristic of entrenched, endemic disease transmission. Seasonality in vector abundance and transmission may, to an extent, explain the shallow temporal clines in allelic frequency that we observed. Genetically similar canine and human strains highlight the role of dogs as important local reservoirs of visceral leishmaniasis

Relationships between Larval and Juvenile Abundance of Winter-Spawned Fishes in North Carolina, USA

We analyzed the relationships between the larval and juvenile abundances of selected estuarine-dependent fishes that spawn during the winter in continental shelf waters of the U.S. Atlantic coast. Six species were included in the analysis based on their ecological and economic importance and relative abundance in available surveys: spot Leiostomus xanthurus, pinfish Lagodon rhomboides, southern flounder Paralichthys lethostigma, summer flounder Paralichthys dentatus, Atlantic croaker Micropogonias undulatus, and Atlantic menhaden Brevoortia tyrannus. Cross-correlation analysis was used to examine the relationships between the larval and juvenile abundances within species. Tests of synchrony across species were used to find similarities in recruitment dynamics for species with similar winter shelf-spawning life-history strategies. Positive correlations were found between the larval and juvenile abundances for three of the six selected species (spot, pinfish, and southern flounder). These three species have similar geographic ranges that primarily lie south of Cape Hatteras. There were no significant correlations between the larval and juvenile abundances for the other three species (summer flounder, Atlantic croaker, and Atlantic menhaden); we suggest several factors that could account for the lack of a relationship. Synchrony was found among the three southern species within both the larval and juvenile abundance time series. These results provide support for using larval ingress measures as indices of abundance for these and other species with similar geographic ranges and winter shelf-spawning life-history strategies

temporal structuring and a link between human and canine transmission

Background Visceral leishmaniasis (VL), caused by the members of the Leishmania donovani complex, has been responsible for devastating VL epidemics in the Sudan. Multilocus microsatellite and sequence typing studies can provide valuable insights into the molecular epidemiology of leishmaniasis, when applied at local scales. Here we present population genetic data for a large panel of strains and clones collected in endemic Sudan between 1993 and 2001. Methods Genetic diversity was evaluated at fourteen microsatellite markers and eleven nuclear sequence loci across 124 strains and clones. Results Microsatellite data defined six genetic subpopulations with which the nuclear sequence data were broadly congruent. Pairwise estimates of FST (microsatellite) and KST (sequence) indicated small but significant shifts among the allelic repertoires of circulating strains year on year. Furthermore, we noted the co-occurrence of human and canine L. donovani strains in three of the six clusters defined. Finally, we identified widespread deficit in heterozygosity in all four years tested but strong deviation from inter-locus linkage equilibrium in two years. Conclusions Significant genetic diversity is present among L. donovani in Sudan, and minor population structuring between years is characteristic of entrenched, endemic disease transmission. Seasonality in vector abundance and transmission may, to an extent, explain the shallow temporal clines in allelic frequency that we observed. Genetically similar canine and human strains highlight the role of dogs as important local reservoirs of visceral leishmaniasis

Pathomx:an interactive workflow-based tool for the analysis of metabolomic data

BACKGROUND: Metabolomics is a systems approach to the analysis of cellular processes through small-molecule metabolite profiling. Standardisation of sample handling and acquisition approaches has contributed to reproducibility. However, the development of robust methods for the analysis of metabolomic data is a work-in-progress. The tools that do exist are often not well integrated, requiring manual data handling and custom scripting on a case-by-case basis. Furthermore, existing tools often require experience with programming environments such as MATLAB® or R to use, limiting accessibility. Here we present Pathomx, a workflow-based tool for the processing, analysis and visualisation of metabolomic and associated data in an intuitive and extensible environment. RESULTS: The core application provides a workflow editor, IPython kernel and a HumanCyc™-derived database of metabolites, proteins and genes. Toolkits provide reusable tools that may be linked together to create complex workflows. Pathomx is released with a base set of plugins for the import, processing and visualisation of data. The IPython backend provides integration with existing platforms including MATLAB® and R, allowing data to be seamlessly transferred. Pathomx is supplied with a series of demonstration workflows and datasets. To demonstrate the use of the software we here present an analysis of 1D and 2D (1)H NMR metabolomic data from a model system of mammalian cell growth under hypoxic conditions. CONCLUSIONS: Pathomx is a useful addition to the analysis toolbox. The intuitive interface lowers the barrier to entry for non-experts, while scriptable tools and integration with existing tools supports complex analysis. We welcome contributions from the community. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-014-0396-9) contains supplementary material, which is available to authorized users

The LMC eclipsing binary HV 2274 revisited

We reanalyse the UV/optical spectrum and optical broad-band data of the eclipsing binary HV 2274 in the LMC, and derive its distance following the method given by Guinan et al. (1998a,b) of fitting theoretical spectra to the stars' UV/optical spectrum plus optical photometry. We describe the method in detail, pointing out the various assumptions that have to be made; moreover, we discuss the systematic effects of using different sets of model atmospheres and different sets of optical photometric data. It turns out that different selections of the photometric data, the set of model atmospheres and the constraints on the value of the ratio of selective to total extinction in the $V$-band, result in a 25% range in distances (although some of these models have a large ${\chi}^2$). For our best choice of these quantities the derived value for the reddening to HV 2274 is E(B-V) = 0.103 $\pm$ 0.007, and the de-reddened distance modulus is DM = 18.46 $\pm$ 0.06; the DM to the center of the LMC is found to be 18.42 $\pm$ 0.07. This is significantly larger than the DM of 18.30 $\pm$ 0.07 derived by Guinan et al. (1998a).Comment: Accepted by: Astronomy and Astrophysic

Constraints on Randall-Sundrum model from top-antitop production at the LHC

We study the top pair production cross section at the LHC in the context of Randall-Sundrum model including the Kaluza-Klein (KK) excited gravitons. It is shown that the recent measurement of the cross section of this process at the LHC restricts the parameter space in Randall-Sundrum (RS) model considerably. We show that the coupling parameter ($\frac{k}{\bar{M}_{pl}}$) is excluded by this measurement from 0.03 to 0.22 depending on the mass of first KK excited graviton ($m_1$). We also study the effect of KK excitations on the spin correlation of the top pairs. It is shown that the spin asymmetry in $t\bar{t}$ events is sensitive to the RS model parameters with a reasonable choice of model parameters.Comment: 17 pages, 6 figure

The ecological and cultural importance of a species at risk of extinction, Pacific lamprey

The cultural and ecological values of Pacific lamprey (Lampetra tridentata) have not been understood by Euro-Americans and thus their great decline has almost gone unnoticed except by Native Americans, who elevated the issue and initiated research to restore its populations, at least in the Columbia Basin. They regard Pacific lamprey as a highly valued resource and as a result ksuyas (lamprey) has become one of their cultural icons. Ksuyas are harvested to this day as a subsistence food by various tribes along the Pacific coast and are highly regarded for their cultural value. Interestingly, our review suggests that the Pacific lamprey plays an important role in the food web, may have acted as a buffer for salmon from predators, and may have been an important source of marine nutrients to oligotrophic watersheds. This is very different from the Euro- American perception that lampreys are pests. We suggest that cultural biases affected management policies

The Optical Spectrum of the Vela Pulsar

Our knowledge of the optical spectra of Isolated Neutron Stars (INSs) is limited by their intrinsic faintness. Among the fourteen optically identified INSs, medium resolution spectra have been obtained only for a handful of objects. No spectrum has been published yet for the Vela pulsar (PSR B0833-45), the third brightest (V=23.6) INS with an optical counterpart. Optical multi-band photometry underlines a flat continuum.In this work we present the first optical spectroscopy observations of the Vela pulsar, performed in the 4000-11000 A spectral range.Our observations have been performed at the ESO VLT using the FORS2 instrument. The spectrum of the Vela pulsar is characterized by a flat power-law (alpha = -0.04 +/- 0.04), which compares well with the values obtained from broad-band photometry. This confirms, once more, that the optical emission of Vela is entirely of magnetospheric origin. The comparison between the optical spectral indeces of rotation-powered INSs does not show evidence for a spectral evolution suggesting that, as in the X-rays, the INS aging does not affect the spectral properties of the magnetospheric emission. At the same time, the optical spectral indeces are found to be nearly always flatter then the X-rays ones, clearly suggesting a general spectral turnover at lower energies.Comment: 7 pages, 8 figures, accepted for publication in A&

Faint NUV/FUV Standards from Swift/UVOT, GALEX and SDSS Photometry

At present, the precision of deep ultraviolet photometry is somewhat limited by the dearth of faint ultraviolet standard stars. In an effort to improve this situation, we present a uniform catalog of eleven new faint (u sim17) ultraviolet standard stars. High-precision photometry of these stars has been taken from the Sloan Digital Sky Survey and Galaxy Evolution Explorer and combined with new data from the Swift Ultraviolet Optical Telescope to provide precise photometric measures extending from the Near Infrared to the Far Ultraviolet. These stars were chosen because they are known to be hot (20,000 < T_eff < 50,000 K) DA white dwarfs with published Sloan spectra that should be photometrically stable. This careful selection allows us to compare the combined photometry and Sloan spectroscopy to models of pure hydrogen atmospheres to both constrain the underlying properties of the white dwarfs and test the ability of white dwarf models to predict the photometric measures. We find that the photometry provides good constraint on white dwarf temperatures, which demonstrates the ability of Swift/UVOT to investigate the properties of hot luminous stars. We further find that the models reproduce the photometric measures in all eleven passbands to within their systematic uncertainties. Within the limits of our photometry, we find the standard stars to be photometrically stable. This success indicates that the models can be used to calibrate additional filters to our standard system, permitting easier comparison of photometry from heterogeneous sources. The largest source of uncertainty in the model fitting is the uncertainty in the foreground reddening curve, a problem that is especially acute in the UV.Comment: Accepted for publication in Astrophysical Journal. 31 pages, 13 figures, electronic tables available from ApJ or on reques

Rationing tests for drug-resistant tuberculosis - who are we prepared to miss?

BACKGROUND: Early identification of patients with drug-resistant tuberculosis (DR-TB) increases the likelihood of treatment success and interrupts transmission. Resource-constrained settings use risk profiling to ration the use of drug susceptibility testing (DST). Nevertheless, no studies have yet quantified how many patients with DR-TB this strategy will miss. METHODS: A total of 1,545 subjects, who presented to Lima health centres with possible TB symptoms, completed a clinic-epidemiological questionnaire and provided sputum samples for TB culture and DST. The proportion of drug resistance in this population was calculated and the data was analysed to demonstrate the effect of rationing tests to patients with multidrug-resistant TB (MDR-TB) risk factors on the number of tests needed and corresponding proportion of missed patients with DR-TB. RESULTS: Overall, 147/1,545 (9.5%) subjects had culture-positive TB, of which 32 (21.8%) had DR-TB (MDR, 13.6%; isoniazid mono-resistant, 7.5%; rifampicin mono-resistant, 0.7%). A total of 553 subjects (35.8%) reported one or more MDR-TB risk factors; of these, 506 (91.5%; 95% CI, 88.9-93.7%) did not have TB, 32/553 (5.8%; 95% CI, 3.4-8.1%) had drug-susceptible TB, and only 15/553 (2.7%; 95% CI, 1.5-4.4%) had DR-TB. Rationing DST to those with an MDR-TB risk factor would have missed more than half of the DR-TB population (17/32, 53.2%; 95% CI, 34.7-70.9). CONCLUSIONS: Rationing DST based on known MDR-TB risk factors misses an unacceptable proportion of patients with drug-resistance in settings with ongoing DR-TB transmission. Investment in diagnostic services to allow universal DST for people with presumptive TB should be a high priority