Modeling Molecular-Line Emission from Circumstellar Disks

Molecular lines hold valuable information on the physical and chemical composition of disks around young stars, the likely progenitors of planetary systems. This invited contribution discusses techniques to calculate the molecular emission (and absorption) line spectrum based on models for the physical and chemical structure of protoplanetary disks. Four examples of recent research illutrate these techniques in practice: matching resolved molecular-line emission from the disk around LkCa15 with theoertical models for the chemistry; evaluating the two-dimensional transfer of ultraviolet radiation into the disk, and the effect on the HCN/CN ratio; far-infrared CO line emission from a superheated disk surface layer; and inward motions in the disk around L1489 IRS.Comment: 6 pages, no figures. To appear in "The Dense Interstellar Medium in Galaxies", Procs. Fourth Cologne-Bonn-Zermatt-Symposiu

Reproductive performance in sows in relation to Japanese Encephalitis Virus seropositivity in an endemic area

Japanese Encephalitis Virus (JEV) is considered an important reproductive pathogen in pigs. Most studies of the reproductive impact of JEV have been conducted in areas where the disease occurs in seasonal epidemics. In this study, the associations between seropositivity for JEV, measured with an IgG ELISA, and the number of piglets born alive and stillborn were investigated in a tropical area endemic for JEV in Vietnam. Sixty percent of sows from four farms in the Mekong delta of Vietnam were seropositive to JEV and the Odds Ratio for a sow being infected was highest (6.4) in sows above 3.5 years (95% confidence interval 2.2–18.3). There was an association between increasing Optical Density (OD) values from the ELISA and the number of stillborn piglets in sows less than 1.5 years, but no effect of seropositivity could be shown when all sows were studied. OD values had an effect (p = 0.04) on the number of piglets born alive in the statistical analysis only when interacting with the effect of the breeds. An increase in mean OD value of the herd was correlated (p < 0.0001) with an increase in the number of piglets born alive. In this study, there was evidence of a negative association between seropositivity for JEV and the reproductive performance only in sows less than 1.5 years in endemic areas. This could be explained by a year-round infection with the virus, which would lead to immunity in many gilts before their first pregnancy. This, in turn, may imply that JEV infection in pigs is of minor importance for the reproductive performance in endemic areas

The Sudden Dominance of blaCTX–M Harbouring Plasmids in Shigella spp. Circulating in Southern Vietnam

Shigellosis is a disease caused by bacteria belonging to Shigella spp. and is a leading cause of bacterial gastrointestinal infections in infants in unindustrialized countries. The Shigellae are dynamic and capable of rapid change when placed under selective pressure in a human population. Extended spectrum beta lactamases (ESBLs) are enzymes capable of degrading cephalosporins (a group of antimicrobial agents) and the genes that encode them are common in pathogenic E. coli and other related organisms in industrialized countries. In southern Vietnam, we have isolated multiple cephalosporin-resistant Shigella that express ESBLs. Furthermore, over two years these strains have replaced strains isolated from patients with shigellosis that cannot express ESBLs. Our work describes the genes responsible for this characteristic and we investigate one of the elements carrying one of these genes. These finding have implications for treatment of shigellosis and support the growing necessity for vaccine development. Our findings also may be pertinent for other countries undergoing a similar economic transition to Vietnam's and the corresponding effect on bacterial populations

Consistent dust and gas models for protoplanetary disks IV. A panchromatic view of protoplanetary disks

Context. Consistent modeling of protoplanetary disks requires the simultaneous solution of both continuum and line radiative transfer, heating and cooling balance between dust and gas and, of course, chemistry. Such models depend on panchromatic observations that can provide a complete description of the physical and chemical properties and energy balance of protoplanetary systems. Along these lines, we present a homogeneous, panchromatic collection of data on a sample of 85 T Tauri and Herbig Ae objects for which data cover a range from X-rays to centimeter wavelengths. Datasets consist of photometric measurements, spectra, along with results from the data analysis such as line fluxes from atomic and molecular transitions. Additional properties resulting from modeling of the sources such as disk mass and shape parameters, dust size, and polycyclic aromatic hydrocarbon (PAH) properties are also provided for completeness. Aim. The purpose of this data collection is to provide a solid base that can enable consistent modeling of the properties of protoplanetary disks. To this end, we performed an unbiased collection of publicly available data that were combined to homogeneous datasets adopting consistent criteria. Targets were selected based on both their properties and the availability of data. Methods. Data from more than 50 different telescopes and facilities were retrieved and combined in homogeneous datasets directly from public data archives or after being extracted from more than 100 published articles. X-ray data for a subset of 56 sources represent an exception as they were reduced from scratch and are presented here for the first time. Results. Compiled datasets, along with a subset of continuum and emission-line models are stored in a dedicated database and distributed through a publicly accessible online system. All datasets contain metadata descriptors that allow us to track them back to their original resources. The graphical user interface of the online system allows the user to visually inspect individual objects but also compare between datasets and models. It also offers to the user the possibility to download any of the stored data and metadata for further processing

Jet energy measurement with the ATLAS detector in proton-proton collisions at root s=7 TeV

The jet energy scale and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of √s = 7TeV corresponding to an integrated luminosity of 38 pb-1. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0. 4 or R=0. 6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pT≥20 GeV and pseudorapidities {pipe}η{pipe}<4. 5. The jet energy systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams, exploiting the transverse momentum balance between central and forward jets in events with dijet topologies and studying systematic variations in Monte Carlo simulations. The jet energy uncertainty is less than 2. 5 % in the central calorimeter region ({pipe}η{pipe}<0. 8) for jets with 60≤pT<800 GeV, and is maximally 14 % for pT<30 GeV in the most forward region 3. 2≤{pipe}η{pipe}<4. 5. The jet energy is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pT, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pT jets recoiling against a high-pT jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, aiming for an improved jet energy resolution and a reduced flavour dependence of the jet response. The systematic uncertainty of the jet energy determined from a combination of in situ techniques is consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pT jets. Special cases such as event topologies with close-by jets, or selections of samples with an enhanced content of jets originating from light quarks, heavy quarks or gluons are also discussed and the corresponding uncertainties are determined. © 2013 CERN for the benefit of the ATLAS collaboration

Observation of associated near-side and away-side long-range correlations in √sNN=5.02 TeV proton-lead collisions with the ATLAS detector

Two-particle correlations in relative azimuthal angle (Δϕ) and pseudorapidity (Δη) are measured in √sNN=5.02  TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1  μb-1 of data as a function of transverse momentum (pT) and the transverse energy (ΣETPb) summed over 3.1<η<4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2<|Δη|<5) “near-side” (Δϕ∼0) correlation that grows rapidly with increasing ΣETPb. A long-range “away-side” (Δϕ∼π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣETPb, is found to match the near-side correlation in magnitude, shape (in Δη and Δϕ) and ΣETPb dependence. The resultant Δϕ correlation is approximately symmetric about π/2, and is consistent with a dominant cos⁡2Δϕ modulation for all ΣETPb ranges and particle pT

Consistent Dust and Gas Models for Protoplanetary Disks. III. Models for Selected Objects from the FP7 DIANA Project

The European FP7 project DIANA has performed a coherent analysis of a large set of observational data of protoplanetary disks by means of thermo-chemical disk models. The collected data include extinction-corrected stellar UV and X-ray input spectra (as seen by the disk), photometric fluxes, low and high resolution spectra, interferometric data, emission line fluxes, line velocity profiles and line maps, which probe the dust, polycyclic aromatic hydrocarbons (PAHs) and the gas in these objects. We define and apply a standardized modeling procedure to fit these data by state-of-the-art modeling codes (ProDiMo, MCFOST, MCMax), solving continuum and line radiative transfer (RT), disk chemistry, and the heating and cooling balance for both the gas and the dust. 3D diagnostic RT tools (e.g., FLiTs) are eventually used to predict all available observations from the same disk model, the DIANA-standard model. Our aim is to determine the physical parameters of the disks, such as total gas and dust masses, the dust properties, the disk shape, and the chemical structure in these disks. We allow for up to two radial disk zones to obtain our best-fitting models that have about 20 free parameters. This approach is novel and unique in its completeness and level of consistency. It allows us to break some of the degeneracies arising from pure Spectral Energy Distribution (SED) modeling. In this paper, we present the results from pure SED fitting for 27 objects and from the all inclusive DIANA-standard models for 14 objects. Our analysis shows a number of Herbig Ae and T Tauri stars with very cold and massive outer disks which are situated at least partly in the shadow of a tall and gas-rich inner disk. The disk masses derived are often in excess to previously published values, since these disks are partially optically thick even at millimeter wavelength and so cold that they emit less than in the Rayleigh–Jeans limit. We fit most infrared to millimeter emission line fluxes within a factor better than 3, simultaneously with SED, PAH features and radial brightness profiles extracted from images at various wavelengths. However, some line fluxes may deviate by a larger factor, and sometimes we find puzzling data which the models cannot reproduce. Some of these issues are probably caused by foreground cloud absorption or object variability. Our data collection, the fitted physical disk parameters as well as the full model output are available to the community through an online database (http://www.univie.ac.at/diana)

The wind and the magnetospheric accretion onto the T Tauri star S Coronae Australis at sub-Au resolution

This is the author accepted manuscript. The final version is available from EDP Sciences via the DOI in this record.Aims. To investigate the inner regions of protoplanetary discs, we performed near-infrared interferometric observations of the classical T Tauri binary system S CrA. Methods. We present the first VLTI-GRAVITY high spectral resolution (R - 4000) observations of a classical T Tauri binary, S CrA (composed of S CrAN and S CrAS and separated by -10:04), combining the four 8m telescopes in dual-field mode. Results. Our observations in the near-infrared K-band continuum reveal a disc around each binary component, with similar halfflux radii of about 0.1 au at d - 130 pc, inclinations (i = 28 - 3-and i = 22 - 6-), and position angles (PA = 0- 6- and PA = -2-12-), suggesting that they formed from the fragmentation of a common disc. The S CrAN spectrum shows bright He i and Br line emission exhibiting inverse P Cygni profiles, typically associated with infalling gas. The continuum-compensated Br line visibilities of S CrAN show the presence of a compact Br emitting region whose radius is about -0.06 au, which is twice as big as the truncation radius. This component is mostly tracing a wind. Moreover, a slight radius change between the blue-And red-shifted Br line components is marginally detected. Conclusions. The presence of an inverse P Cygni profile in the He i and Br lines, along with the tentative detection of a slightly larger size of the blue-shifted Br line component, hint at the simultaneous presence of a wind and magnetospheric accretion in S CrA N.Science Foundation IrelandAlexander von Humboldt Foundation Fellowship ProgrammeFrench PNPSLabEx OSUG@202

Molecular epidemiology of Japanese encephalitis in northern Vietnam, 1964?2011: genotype replacement

Background: Japanese encephalitis virus (JEV) is an arthropod-borne virus causing serious public health issues in Asia. JEV consists of five genotypes and recent studies have shown the emergence of JEV genotype I (GI) and its replacement of genotype III (GIII). Using an archival JEV collection, we investigated the molecular evolution of JEV in Vietnam over the last 48 years (1964-2012) in humans, mosquitoes, and pigs, within the global context. Methods: The nine JEV isolates from humans, pigs, and mosquitoes sequenced in this study and 29 sequences available in GenBank were used to analyze the envelope (E) protein of the Vietnamese JEVs. A collection of 225 cerebrospinal fluid specimens from patients with suspected Japanese encephalitis (JE) was also tested and genotyped with real-time RT-PCR. Results: The 38 E genes identified with sequencing and nine Vietnamese JEV strains genotyped with real-time RT-PCR, belonging to two lineages, evolved in accordance with those in the rest of the world. The first GIII strain was detected in humans in Vietnam in 1964, and in mosquitoes in 1979, whereas GI strains were first detected in humans and mosquitoes in 1990 and 1994, respectively. After 2004, GI was the only genotype detected in Vietnam, demonstrating that the GIIII strains had been displaced by GI strains. Five haplotypes were identified in the Vietnamese JEVs, with SKSS predominant. The S123N and S123R substitutions in the E protein were already present in the Vietnamese JEVs. Conclusion: This study describes the long evolutionary history of JEV in Vietnam over 34 years, which correlates well with the global evolution of JEV. The Vietnamese GIII strains have been replaced by GI strains in mosquitoes, pigs, and humans. The predominant haplotypes of the Vietnamese strains support this genotype displacement in Vietnam. Further surveillance is required to confirm the disappearance of the GIII strains in nature and the emergence of new pathogens causing encephalitis in Vietnam, after the long-term use of JEV vaccines in that country

Observation of Associated Near-Side and Away-Side Long-Range Correlations in sqrt[s_{NN}]=5.02 TeV Proton-Lead Collisions with the ATLAS Detector.

Two-particle correlations in relative azimuthal angle (Δϕ) and pseudorapidity (Δη) are measured in sqrt[s_{NN}]=5.02  TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1  μb^{-1} of data as a function of transverse momentum (p_{T}) and the transverse energy (ΣE_{T}^{Pb}) summed over 3.1<η<4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2<|Δη|<5) "near-side" (Δϕ∼0) correlation that grows rapidly with increasing ΣE_{T}^{Pb}. A long-range "away-side" (Δϕ∼π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣE_{T}^{Pb}, is found to match the near-side correlation in magnitude, shape (in Δη and Δϕ) and ΣE_{T}^{Pb} dependence. The resultant Δϕ correlation is approximately symmetric about π/2, and is consistent with a dominant cos⁡2Δϕ modulation for all ΣE_{T}^{Pb} ranges and particle p_{T}