Planetary Science Virtual Observatory architecture

In the framework of the Europlanet-RI program, a prototype of Virtual Observatory dedicated to Planetary Science was defined. Most of the activity was dedicated to the elaboration of standards to retrieve and visualize data in this field, and to provide light procedures to teams who wish to contribute with on-line data services. The architecture of this VO system and selected solutions are presented here, together with existing demonstrators

Improving the molecular diagnosis of Chlamydia psittaci and Chlamydia abortus infection with a species-specific duplex real-time PCR.

Chlamydia psittaci and Chlamydia abortus are closely related intracellular bacteria exhibiting different tissue tropism that may cause severe but distinct infection in humans. C. psittaci causes psittacosis, a respiratory zoonotic infection transmitted by birds. C. abortus is an abortigenic agent in small ruminants, which can also colonize the human placenta and lead to foetal death and miscarriage. Infections caused by C. psittaci and C. abortus are underestimated mainly due to diagnosis difficulties resulting from their strict intracellular growth. We developed a duplex real-time PCR to detect and distinguish these two bacteria in clinical samples. The first PCR (PCR1) targeted a sequence of the 16S-23S rRNA operon allowing the detection of both C. psittaci and C. abortus. The second PCR (PCR2) targeted the coding DNA sequence CPSIT_0607 unique to C. psittaci. The two PCRs showed 100 % detection for ≥ 10 DNA copies per reaction (1000 copies ml- 1). Using a set of 120 samples, including bacterial reference strains, clinical specimens and infected cell culture material, we monitored 100 % sensitivity and 100 % specificity for the detection of C. psittaci and C. abortus for PCR1. When PCR1 was positive, PCR2 could discriminate C. psittaci from C. abortus with a positive predictive value of 100 % and a negative predictive value of 88 %. In conclusion, this new duplex PCR represents a low-cost and time-saving method with high-throughput potential, expected to improve the routine diagnosis of psittacosis and pregnancy complication in large-scale screening programs and also during outbreaks

The EPN-TAP protocol for the Planetary Science Virtual Observatory

A Data Access Protocol has been set up to search and retrieve Planetary Science data in general. This protocol will allow the user to select a subset of data from an archive in a standard way, based on the IVOA Table Access Protocol (TAP). The TAP mechanism is completed by an underlying Data Model and reference dictionaries. This paper describes the principle of the EPN- TAP protocol and interfaces, underlines the choices that have been made, and discusses possible evolutions.Comment: 21 pages. Submitted to Astronomy & Computing, S.I. Virtual Observator

On discretization in time in simulations of particulate flows

We propose a time discretization scheme for a class of ordinary differential equations arising in simulations of fluid/particle flows. The scheme is intended to work robustly in the lubrication regime when the distance between two particles immersed in the fluid or between a particle and the wall tends to zero. The idea consists in introducing a small threshold for the particle-wall distance below which the real trajectory of the particle is replaced by an approximated one where the distance is kept equal to the threshold value. The error of this approximation is estimated both theoretically and by numerical experiments. Our time marching scheme can be easily incorporated into a full simulation method where the velocity of the fluid is obtained by a numerical solution to Stokes or Navier-Stokes equations. We also provide a derivation of the asymptotic expansion for the lubrication force (used in our numerical experiments) acting on a disk immersed in a Newtonian fluid and approaching the wall. The method of this derivation is new and can be easily adapted to other cases

CN and OH emissions in the 67P/Churyumov-Gerasimenko coma with Rosetta/VIRTIS-M spectrometer

Observations with the visible channel of the Visible and InfraRed Thermal Imaging Spectrometer (VIRTIS) on board Rosetta taken when the spacecraft was at a distance of 80-140 km from 67P/Churyumov-Gerasimenko (67P/C-G) allowed the detection of daughter gaseous species in its inner coma. The detection of the violet doublet emission of CN at 388.3 nm has occurred during the coma monitoring campaign in November-December 2015, when the instrument has operated with long integration times (50 s) necessary to boost the instrumental SNR and detect these faint emissions. Other features, like the C3 and C2 signatures around 420-480 nm, might possibly be visible in few cases but with a very low intensity. For this reason, we concentrate our analysis in the spectral region from 250 to 450 nm, where the detector sensitivity allows the positive detection of the above mentioned CN violet line at 388.3 nm, and the OH doublet emission at 309 nm. The CN emission at 388.3 nm is observed on both the day and night sides of 67P/C-G with a higher intensity on the dayside. In addition, at a preliminary analysis, the hydroxyl doublet emission intensity seems to be comparable to the violet CN line. The same emissions were also identified in spectra acquired using ground-based facilities, when the comet had just passed the perihelion (Fitzsimmons et al., 2016). These gaseous species emissions appear well contrasted with respect to the dust broad continuum, preferentially observed on the dayside. Distribution and variability of the OH and CN band intensities will be discussed with respect to observation parameters

lncRNA requirements for mouse acute myeloid leukemia and normal differentiation

A substantial fraction of the genome is transcribed in a cell type-specific manner, producing long non-coding RNAs (lncRNAs), rather than protein-coding transcripts. Here we systematically characterize transcriptional dynamics during hematopoiesis and in hematological malignancies. Our analysis of annotated and de novo assembled lncRNAs showed many are regulated during differentiation and mis-regulated in disease. We assessed lncRNA function via an in vivo RNAi screen in a model of acute myeloid leukemia. This identified several lncRNAs essential for leukemia maintenance, and found that a number act by promoting leukemia stem cell signatures. Leukemia blasts show a myeloid differentiation phenotype when these lncRNAs were depleted, and our data indicates that this effect is mediated via effects on the c-MYC oncogene. Bone marrow reconstitutions showed that a lncRNA expressed across all progenitors was required for the myeloid lineage, whereas the other leukemia-induced lncRNAs were dispensable in the normal setting

Successful treatment of tracheal stenosis by rigid bronchoscopy and topical mitomycin C: a case report

Tracheal stenosis is a known complication of prolonged intubation. It is difficult to treat and traditional surgical approach is associated with significant risk and complications. Recurrent stenosis due to granulation tissue necessitates repeated procedures. We describe a case of short web-like tracheal stenosis (concentric membranous stenosis less than 1 cm in length without associated cartilage damage) managed by a minimally invasive thoracic endoscopic approach. Topical application of Mitomycin C, a potent fibroblast inhibitor reduces granulation tissue formation and prevents recurrence

Viral Findings in Adult Hematological Patients with Neutropenia

BACKGROUND: Until recently, viral infections in patients with hematological malignancies were concerns primarily in allogeneic hematopoietic stem cell transplant (HSCT) recipients. During the last years, changed treatment regimens for non-transplanted patients with hematological malignancies have had potential to increase the incidence of viral infections in this group. In this study, we have prospectively investigated the prevalence of a broad range of respiratory viruses in nasopharyngeal aspirate (NPA) as well as viruses that commonly reactivate after allogeneic HSCT. METHODOLOGY/PRINCIPAL FINDINGS: Patients with hematological malignancies and therapy induced neutropenia (n = 159) were screened regarding a broad range of common respiratory viruses in the nasopharynx and for viruses commonly detected in severely immunosuppressed patients in peripheral blood. Quantitative PCR was used for detection of viruses. A viral pathogen was detected in 35% of the patients. The detection rate was rather similar in blood (22%) and NPA (18%) with polyoma BK virus and rhinovirus as dominating pathogens in blood and NPA, respectively. Patients with chronic lymphocytic leukemia (CLL) (p<0.01) and patients with fever (p<0.001) were overrepresented in the virus-positive group. Furthermore, viral findings in NPA were associated with upper respiratory symptoms (URTS) (p<0.0001). CONCLUSIONS/SIGNIFICANCE: Both respiratory viral infections and low titers of viruses in blood from patients with neutropenia were common. Patients with CLL and patients with fever were independently associated to these infections, and viral findings in NPA were associated to URTS indicating active infection. These findings motivate further studies on viruses' impact on this patient category and their potential role as causative agents of fever during neutropenia

Mycobacterium tuberculosis nucleoid-associated DNA-binding protein H-NS binds with high-affinity to the Holliday junction and inhibits strand exchange promoted by RecA protein

A number of studies have shown that the structure and composition of bacterial nucleoid influences many a processes related to DNA metabolism. The nucleoid-associated proteins modulate not only the DNA conformation but also regulate the DNA metabolic processes such as replication, recombination, repair and transcription. Understanding of how these processes occur in the context of Mycobacterium tuberculosis nucleoid is of considerable medical importance because the nucleoid structure may be constantly remodeled in response to environmental signals and/or growth conditions. Many studies have concluded that Escherichia coli H-NS binds to DNA in a sequence-independent manner, with a preference for A-/T-rich tracts in curved DNA; however, recent studies have identified the existence of medium- and low-affinity binding sites in the vicinity of the curved DNA. Here, we show that the M. tuberculosis H-NS protein binds in a more structure-specific manner to DNA replication and repair intermediates, but displays lower affinity for double-stranded DNA with relatively higher GC content. Notably, M. tuberculosis H-NS was able to bind Holliday junction (HJ), the central recombination intermediate, with substantially higher affinity and inhibited the three-strand exchange promoted by its cognate RecA. Likewise, E. coli H-NS was able to bind the HJ and suppress DNA strand exchange promoted by E. coli RecA, although much less efficiently compared to M. tuberculosis H-NS. Our results provide new insights into a previously unrecognized function of H-NS protein, with implications for blocking the genome integration of horizontally transferred genes by homologous and/or homeologous recombination