The CHilean Automatic Supernova sEarch (CHASE)

The CHASE project started in 2007 with the aim of providing young southern supernovae (SNe) to the Carnegie Supernova Project (CSP) and Millennium Center for Supernova Studies (MCSS) follow-up programs. So far CHASE has discovered 33 SNe with an average of more than 2.5 SNe per month in 2008. In addition to the search we are carrying out a follow-up program targeting bright SNe. Our fully automated data reduction allows us to follow the evolution on the light curve in real time, triggering further observations if something potentially interesting is detectedComment: 4 pages, 2 figures, conference proceedin

IN-SYNC. V. Stellar kinematics and dynamics in the Orion A Molecular Cloud

The kinematics and dynamics of young stellar populations enable us to test theories of star formation. With this aim, we continue our analysis of the SDSS-III/APOGEE IN-SYNC survey, a high resolution near infrared spectroscopic survey of young clusters. We focus on the Orion A star-forming region, for which IN-SYNC obtained spectra of $\sim2700$ stars. In Paper IV we used these data to study the young stellar population. Here we study the kinematic properties through radial velocities ($v_r$). The young stellar population remains kinematically associated with the molecular gas, following a $\sim10\:{\rm{km\:s}}^{-1}$ gradient along filament. However, near the center of the region, the $v_r$ distribution is slightly blueshifted and asymmetric; we suggest that this population, which is older, is slightly in foreground. We find evidence for kinematic subclustering, detecting statistically significant groupings of co-located stars with coherent motions. These are mostly in the lower-density regions of the cloud, while the ONC radial velocities are smoothly distributed, consistent with it being an older, more dynamically evolved cluster. The velocity dispersion $\sigma_v$ varies along the filament. The ONC appears virialized, or just slightly supervirial, consistent with an old dynamical age. Here there is also some evidence for on-going expansion, from a $v_r$--extinction correlation. In the southern filament, $\sigma_v$ is $\sim2$--$3$ times larger than virial in the L1641N region, where we infer a superposition along the line of sight of stellar sub-populations, detached from the gas. On the contrary, $\sigma_v$ decreases towards L1641S, where the population is again in agreement with a virial state.Comment: 14 pages, 13 figures, ApJ accepte

Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines

Background: Accurately identifying SNPs from bacterial sequencing data is an essential requirement for using genomics to track transmission and predict important phenotypes such as antimicrobial resistance. However, most previous performance evaluations of SNP calling have been restricted to eukaryotic (human) data. Additionally, bacterial SNP calling requires choosing an appropriate reference genome to align reads to, which, together with the bioinformatic pipeline, affects the accuracy and completeness of a set of SNP calls obtained. This study evaluates the performance of 209 SNP calling pipelines using a combination of simulated data from 254 strains of 10 clinically common bacteria and real data from environmentally-sourced and genomically diverse isolates within the genera Citrobacter, Enterobacter, Escherichia and Klebsiella. Results: We evaluated the performance of 209 SNP calling pipelines, aligning reads to genomes of the same or a divergent strain. Irrespective of pipeline, a principal determinant of reliable SNP calling was reference genome selection. Across multiple taxa, there was a strong inverse relationship between pipeline sensitivity and precision, and the Mash distance (a proxy for average nucleotide divergence) between reads and reference genome. The effect was especially pronounced for diverse, recombinogenic, bacteria such as Escherichia coli, but less dominant for clonal species such as Mycobacterium tuberculosis. Conclusions: The accuracy of SNP calling for a given species is compromised by increasing intra-species diversity. When reads were aligned to the same genome from which they were sequenced, among the highest performing pipelines was Novoalign/GATK. By contrast, when reads were aligned to particularly divergent genomes, the highest-performing pipelines often employed the aligners NextGenMap or SMALT, and/or the variant callers LoFreq, mpileup or Strelka

Code-based Syndromic Surveillance for Influenzalike Illness by International Classification of Diseases, Ninth Revision

ICD-9 codes collected automatically in a syndromic system are sensitive and specific in detecting outbreaks caused by respiratory viruses

IN-SYNC II: Virial Stars from Sub-Virial Cores -- The Velocity Dispersion of Embedded Pre-Main-Sequence Stars in NGC 1333

The initial velocity dispersion of newborn stars is a major unconstrained aspect of star formation theory. Using near-infrared spectra obtained with the APOGEE spectrograph, we show that the velocity dispersion of young (1-2 Myr) stars in NGC 1333 is 0.92+/-0.12 km/s after correcting for measurement uncertainties and the effect of binaries. This velocity dispersion is consistent with the virial velocity of the region and the diffuse gas velocity dispersion, but significantly larger than the velocity dispersion of the dense, star-forming cores, which have a sub-virial velocity dispersion of 0.5 km/s. Since the NGC 1333 cluster is dynamically young and deeply embedded, this measurement provides a strong constraint on the initial velocity dispersion of newly-formed stars. We propose that the difference in velocity dispersion between stars and dense cores may be due to the influence of a 70 micro-Gauss magnetic field acting on the dense cores, or be the signature of a cluster with initial sub-structure undergoing global collapse.Comment: Accepted to ApJ. 23 pages, 9 figures and 3 table

Salmonella enterica ssp. arizonae infection in a 43-year-old Italian man with hypoglobulinemia: a case report and review of the literature

<p>Abstract</p> <p>Introduction</p> <p><it>Salmonella enterica </it>ssp. <it>arizonae </it>is an uncommon human pathogen with serious infections reported in immunocompromised hosts. In Europe, only a few cases have been described. Patients with this infection usually have a history of contact with reptiles or travel abroad. We present a case report of infection in a patient with hypoglobulinemia and a literature review.</p> <p>Case presentation</p> <p>We describe the case of a 43-year-old Caucasian Italian man with hypoglobulinemia who presented to our hospital with sepsis and diarrhea. A stool culture yielded <it>S. enterica </it>ssp. <it>arizonae</it>. Our patient was treated with oral ciprofloxacin and made a full recovery. We also present a review of the cases of <it>S. enterica </it>ssp. <it>arizonae </it>infections previously reported in Europe.</p> <p>Conclusions</p> <p>The majority of infections from <it>S. enterica </it>ssp. <it>arizonae </it>occur in patients who are immunocompromised. Data from the literature suggests that it may be difficult to eradicate the bacteria and thus, prolonged antibiotic courses are often used. It would be advisable for clinicians to investigate for pre-existing immune dysfunction if <it>S. enterica </it>ssp. <it>arizonae </it>is isolated. In Italy, although there have only been a few cases, the likely route of transmission remains unclear and requires further surveillance.</p

Ubiquitin ligase UBR3 regulates cellular levels of the essential DNA repair protein APE1 and is required for genome stability

APE1 (Ref-1) is an essential human protein involved in DNA damage repair and regulation of transcription. Although the cellular functions and biochemical properties of APE1 are well characterized, the mechanism involved in regulation of the cellular levels of this important DNA repair/transcriptional regulation enzyme, remains poorly understood. Using an in vitro ubiquitylation assay, we have now purified the human E3 ubiquitin ligase UBR3 as a major activity that polyubiquitylates APE1 at multiple lysine residues clustered on the N-terminal tail. We further show that a knockout of the Ubr3 gene in mouse embryonic fibroblasts leads to an up-regulation of the cellular levels of APE1 protein and subsequent genomic instability. These data propose an important role for UBR3 in the control of the steady state levels of APE1 and consequently error free DNA repair