Modelling transmission and control of Mycobacterium avium subspecies paratuberculosis within Irish dairy herds with compact spring calving

Paratuberculosis is a chronic bacterial infection of the intestine in cattle caused by Mycobacterium avium subspecies paratuberculosis (Map). To better understand Map transmission in Irish dairy herds, we adapted the French stochastic individual-based epidemiological simulation model to account for seasonal herd demographics. We investigated the probability of Map persistence over time, the within-herd prevalence over time, and the relative importance of transmission pathways, and assessed the relative effectiveness of test-and-cull control strategies. We investigated the impact on model outputs of calf separation from cows (calves grazed on pasture adjacent to cows vs. were completely separated from cows) and test-and-cull. Test-and-cull scenarios consisted of highly test-positive cows culled within 13 or 4 weeks after detection, and calf born to highly test-positive cows kept vs removed. We simulated a typical Irish dairy herd with on average 82 lactating cows, 112 animals in total. Each scenario was iterated 1000 times to adjust variation caused by stochasticity. Map was introduced in the fully naive herd through the purchase of a moderately infectious primiparous cow. Infection was considered to persist when at least one infected animal remained in the herd or when Map was present in the environment. The probability of Map persistence 15 years after introduction ranged between 32.2-42.7 % when calves and cows had contact on pasture, and between 18.9-29.4 % when calves and cows were separated on pasture. The most effective control strategy was to cull highly test-positive cows within four weeks of detection (absolute 10 % lower persistence compared to scenarios without control). Removing the offspring of highly test-positive dams did not affect either Map persistence or within-herd prevalence of Map. Mean prevalence 15 years after Map introduction was highest (63.5 %) when calves and cows had contact on pasture. Mean prevalence was 15 % lower (absolute decrease) when cows were culled within 13 weeks of a high test-positive result, and 28 % lower when culled within 4 weeks. Around calving, the infection rate was high, with calves being infected in utero or via the general indoor environment (most important transmission routes). For the remainder of the year, the incidence rate was relatively low with most calves being infected on pasture when in contact with cows. Testing and culling was an effective control strategy when it was used prior to the calving period to minimize the number of highly infectious cows present when calves were born

Herbig-Haro flows in B335

We have observed optical (Halpha and [SII]) and near-IR (S(1) line of H2) deep fields and taken optical spectra using the 2.56m NOT, as well as a near-UV deep field (U band) using the 3.58m NTT. In addition we present new SPITZER (IRAC and MIPS) mid-IR observations. We use previous Halpha and S(1) observations taken 15 and 9 years earlier to make proper motion maps. We then investigate the shock physics by matching our spectra with planar shock models. We discover six new HH objects in B335. From proper motions we find an optically bright, roughly E-W oriented group with high space velocities (200-280 km/s) and a near-IR bright, slower group (15-75 km/s) moving to the ESE. We also find a system of at least 15 H2 knots in the western lobe. This (WNW) counterflow suggests the possibility of a binary outflow source, giving rise to two outflow axes with slightly different orientations. We find that the E-W flow is symmetrical with evidence for two outbursts. We make the first detection of [OI] 6300/63 in HH119 B and Hbeta in HH119 A and B and find their extinctions to be AV~1.4 and 4.4, respectively. HH119 A is found to expand much faster than expected from linear expansion with distance from the outflow source. Using planar shock models we find shock velocities of ~60 km/s (A) and ~35 km/s (B and C). This agrees with A being of higher excitation than B and C. In our U image we detect three of the HH objects and propose that the emission arise from the [OII] 3728 line and the blue continuum. New SPITZER observations show most of the HH objects at 4.5 micron and a E-W elongated hour-glass shaped structure at the outflow source. Even at 24 micron it is not clear whether most of the light is direct or reflected.Comment: 23 pages, 15 figures, accepted in A&

The chemical composition of metal-poor emission-line galaxies in the Data Release 3 of the Sloan Digital Sky Survey

We have re-evaluated empirical expressions for the abundance determination of N, O, Ne, S, Cl, Ar and Fe taking into account the latest atomic data and constructing an appropriate grid of photoionization models with state-of-the art model atmospheres. Using these expressions we have derived heavy element abundances in the $\sim$ 310 emission-line galaxies from the Data Release 3 of the Sloan Digital Sky Survey (SDSS)with an observed Hbeta flux F(Hbeta)> 1E-14 erg s^{-1} cm^{-2} and for which the [O III] 4363 emission line was detected at least at a 2sigma level, allowing abundance determination by direct methods. The oxygen abundance 12 + log O/H of the SDSS galaxies lies in the range from ~ 7.1 (Zsun/30) to 8.5 (0.7 Zsun). The SDSS sample is merged with a sample of 109 blue compact dwarf (BCD) galaxies with high quality spectra, which contains extremely low-metallicity objects. We use the merged sample to study the abundance patterns of low-metallicity emission-line galaxies. We find that extremely metal-poor galaxies (12 + log O/H < 7.6, i.e. Z < Zsun/12) are rare in the SDSS sample. The alpha element-to-oxygen abundance ratios do not show any significant trends with oxygen abundance, in agreement with previous studies, except for a slight increase of Ne/O with increasing metallicity, which we interpret as due to a moderate depletion of O onto grains in the most metal-rich galaxies. The Fe/O abundance ratio is smaller than the solar value, by up to 1 dex at the high metallicity end. (abridged)Comment: 17 pages, 12 figures. Accepted for publication in the Astronomy and Astrophysic

ARL3 mutations cause Joubert syndrome by disrupting ciliary protein composition

Joubert syndrome (JBTS) is a genetically heterogeneous autosomal recessive neurodevelopmental ciliopathy. We investigated further the underlying genetic etiology of Joubert syndrome by studying two unrelated families in whom JBTS was not associated with pathogenic variants in known JBTSrelated genes. Combined autozygosity mapping of both families highlighted a candidate locus on chromosome 10 (chr10: 101569997-109106128 (hg 19)), and exome sequencing revealed two missense variants in ARL3 within the candidate locus. The encoded protein, ADP Ribosylation Factor-Like GTPase 3, ARL3, is a small GTP-binding protein that is involved in directing lipid-modified proteins into the cilium in a GTP-dependent manner. Both missense variants replace the highly conserved Arg149 residue, which we show to be necessary for the interaction with its guanine nucleotide exchange factor ARL13B, such that the mutant protein is associated with reduced INPP5E and NPHP3 localisation in cilia. We propose that ARL3 provides a potential hub in the network of encoded ciliopathy genes, whereby perturbation of ARL3 results in the mislocalisation of multiple ciliary proteins due to abnormal displacement of lipidated protein cargo

A re-appraisal of the reliability of the 20 m multi-stage shuttle run test

This is the author's PDF version of an article published in European journal of applied physiology in 2007. The original publication is available at www.springerlink.co

Breakfast glycaemic index and exercise: combined effects on adolescents' cognition

The aim of the present study was to examine the combined effects of breakfast glycaemic index (GI) and a mid-morning bout of exercise on adolescents’ cognitive function. Participants were randomly allocated to a high or low GI breakfast group in a mixed research design, where each participant completed two experimental trials (exercise and resting). Forty-two adolescents (12.4±0.5 years old), undertook a bout of exercise (ten repeats of level one of the multi-stage fitness test; exercise trial) or continued to rest (resting trial) following consumption of either a high or low GI breakfast. A battery of cognitive function tests (visual search test, Stroop test and Sternberg paradigm) was completed 30 min before and 45 min following the exercise. Average heart rate during exercise was 170±15 beats.min-1. On the complex level of the Stroop test, response times improved across the morning following the low GI breakfast on both the exercise and resting trials, though the improvement was greatest on the exercise trial. However, response times only improved on the resting trial following the high GI breakfast (p = 0.012). On the 5 letter level of the Sternberg paradigm, response times improved across the morning following the low GI breakfast (regardless of exercise) and only on the exercise trial following the high GI breakfast (p = 0.019). The findings of the present study suggest that the combined effects of breakfast GI and exercise in adolescents depend upon the component of cognitive function examined. A low GI breakfast and mid-morning bout of exercise were individually beneficial for response times on the Sternberg paradigm, whereas they conferred additional benefits for response times on the Stroop test

Quantum-mechanical calculation of Stark widths of Ne VII n=3, Δn=0\Delta n=0 transitions

The Stark widths of the Ne VII 2s3s-2s3p singlet and triplet lines are calculated in the impact approximation using quantum-mechanical Convergent Close-Coupling and Coulomb-Born-Exchange approximations. It is shown that the contribution from inelastic collisions to the line widths exceeds the elastic width contribution by about an order of magnitude. Comparison with the line widths measured in a hot dense plasma of a gas-liner pinch indicates a significant difference which may be naturally explained by non-thermal Doppler effects from persistent implosion velocities or turbulence developed during the pinch implosion. Contributions to the line width from different partial waves and types of interactions are discussed as well.Comment: 8 pages, 3 figures; accepted by Phys. Rev.

Biases in abundance derivations for metal-rich nebulae

Using ab-initio photoionization models of giant HII regions, we test methods for abundance determinations based on a direct measurement of the electron temperature, now possible even for moderate to high-metallicity objects. We find that, for metallicities larger than solar, the computed abundances deviate systematically from the real ones, generally by larger amounts for more metal-rich HII regions. We discuss the reasons for this, and present diagrams allowing the reader to better understand the various factors coming into play. We briefly discuss less classical methods to derive abundances in metal-rich HII regions. In particular, we comment on the interest of the oxygen and carbon recombination lines. We also show that, contrary to the case of giant HII regions, the physical conditions in bright extragalactic planetary nebulae are such that their chemical composition can be accurately derived even at high metallicities. Thus, extragalactic planetary nebulae are promising potential probes of the metallicity of the interstellar medium in the internal parts of spiral galaxies as well as in metal-rich elliptical galaxies.Comment: 15 pages, 13 figures, Accepted for publication in A&

The chemical composition of the Orion star-forming region: II. Stars, gas, and dust: the abundance discrepancy conundrum

We re-examine the recombination/collisional emission line (RL/CEL) nebular abundance discrepancy problem in the light of recent high-quality abundance determinations in young stars in the Orion star-forming region. We re-evaluate the CEL and RL abundances of several elements in the Orion nebula and estimate the associated uncertainties, taking into account the uncertainties in the ionization correction factors for unseen ions. We estimate the amount of oxygen trapped in dust grains for several scenarios of dust formation. We compare the resulting gas+dust nebular abundances with the stellar abundances of a sample of 13 B-type stars from the Orion star-forming region (Ori\,OB1), analyzed in Papers I and III of this series. We find that the oxygen nebular abundance based on recombination lines agrees much better with the stellar abundances than the one derived from the collisionally excited lines. This result calls for further investigation. If the CEL/RL abundance discrepancy were caused by temperature fluctuations in the nebula, as argued by some authors, the same kind of discrepancy should be seen for the other elements, such as C, N and Ne, which is not what we find in the present study. Another problem is that with the RL abundances, the energy balance of the Orion nebula is not well understood. We make some suggestions concerning the next steps to undertake to solve this problem.Comment: 11 pages, 8 tables, 5 figures (To be published in A&A

A novel homozygous UMOD mutation reveals gene dosage effects on uromodulin processing and urinary excretion

Heterozygous mutations in $\textit{UMOD}$ encoding the urinary protein uromodulin are the most common genetic cause of autosomal dominant tubulointerstitial kidney disease (ADTKD). We describe the exceptional case of a patient from a consanguineous family carrying a novel homozygous $\textit{UMOD}$ mutation (p.C120Y) affecting a conserved cysteine residue within the EGF-like domain III of uromodulin. Comparison of heterozygote and homozygote mutation carriers revealed a gene dosage effect with unprecedented low levels of uromodulin and aberrant uromodulin fragments in the urine of the homozygote proband. Despite an amplified biological effect of the homozygote mutation, the proband did not show a strikingly more severe clinical evolution nor was the near absence of urinary uromodulin associated with urinary tract infections or kidney stones.J.A.S. is supported by the Kidney Research Fund and the Medical Research Council (MR/M012212/1). S.A.R. is a Kidney Research UK Post-Doctoral Fellow. O.D. is supported by grants from the European Community’s Seventh Framework Programme (305608 EURenOmics), the Swiss National Centre of Competence in Research Kidney Control of Homeostasis (NCCR Kidney.CH) programme, the Swiss National Science Foundation (31003A_169850) and the Rare Disease Initiative Zu¨rich (Radiz), a clinical research priority program of the University of Zurich, Switzerland. E.O. is supported by the Fonds National de la Recherche Luxembourg (6903109) and the University Research Priority Programme ‘Integrative Human Physiology, ZIHP’ of the University of Zurich