De novo Assembly and Analysis of the Northern Leopard Frog Rana pipiens Transcriptome

The northern leopard frog Rana (Lithobates) pipiens is an important animal model, being used extensively in cancer, neurology, physiology, and biomechanical studies. R. pipiens is a native North American frog whose range extends from northern Canada to southwest United States, but over the past few decades its populations have declined significantly and is now considered uncommon in large portions of the United States and Canada. To aid in the study and conservation of R. pipiens, this paper describes the first R. pipiens transcriptome. The R. pipiens transcriptome was annotated using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Eukaryotic Orthologous Groups (KOG). Differential expression analysis revealed universal and tissue specific genes, and endocrine-related genes were identified. Transcriptome assemblies and other sequence data are available for download

The relationship between IGM Lyman-alpha opacity and galaxy density near the end of reionization

Observed scatter in the Lyman-alpha opacity of quasar sightlines at $z<6$ has motivated measurements of the correlation between Ly$\alpha$ opacity and galaxy density, as models that predict this scatter make strong and sometimes opposite predictions for how they should be related. Our previous work associated two highly opaque Ly$\alpha$ troughs at $z\sim5.7$ with a deficit of Lyman-$\alpha$ emitting galaxies (LAEs). In this work, we survey two of the most highly transmissive lines of sight at this redshift, towards the $z=6.02$ quasar SDSS J1306+0356 and the $z=6.17$ quasar PSO J359-06. We find that both fields are underdense in LAEs within 10 $h^{-1}$ Mpc of the quasar sightline, somewhat less extensive than underdensities associated with Ly$\alpha$ troughs. We combine our observations with three additional fields from the literature, and find that while fields with extreme opacities are generally underdense, moderate opacities span a wider density range. The results at high opacities are consistent with models that invoke UV background fluctuations and/or late reionization to explain the observed scatter in IGM Ly$\alpha$ opacities. There is tension at low opacities, however, as the models tend to associate lower IGM Ly$\alpha$ opacities with higher densities. Although the number of fields surveyed is still small, the low-opacity results may support a scenario in which the ionizing background in low-density regions increases more rapidly than some models suggest after becoming ionized. Elevated gas temperatures from recent reionization may also be making these regions more transparent.Comment: 20 pages, 17 figures. Accepted to Ap

Exome analysis of rare and common variants within the NOD signaling pathway

Pediatric inflammatory bowel disease (pIBD) is a chronic heterogeneous disorder. This study looks at the burden of common and rare coding mutations within 41 genes comprising the NOD signaling pathway in pIBD patients. 136 pIBD and 106 control samples underwent whole-exome sequencing. We compared the burden of common, rare and private mutation between these two groups using the SKAT-O test. An independent replication cohort of 33 cases and 111 controls was used to validate significant findings. We observed variation in 40 of 41 genes comprising the NOD signaling pathway. Four genes were significantly associated with disease in the discovery cohort (BIRC2 p = 0.004, NFKB1 p =  0.005, NOD2 p = 0.029 and SUGT1 p = 0.047). Statistical significance was replicated for BIRC2 (p = 0.041) and NOD2 (p = 0.045) in an independent validation cohort. A gene based test on the combined discovery and replication cohort confirmed association for BIRC2 (p = 0.030). We successfully applied burden of mutation testing that jointly assesses common and rare variants, identifying two previously implicated genes (NFKB1 and NOD2) and confirmed a possible role in disease risk in a previously unreported gene (BIRC2). The identification of this novel gene provides a wider role for the inhibitor of apoptosis gene family in IBD pathogenesis

Estimating Bacterial diversity in scirtothrips dorsalis (thysanoptera: thripidae) Via Next generation sequencing

The last 2 decades have produced a better understanding of insect-microbial associations and yielded some important opportunities for insect control. However, most of our knowledge comes from model systems. Thrips (Thysanoptera: Thripidae) have been understudied despite their global importance as invasive species, plant pests and disease vectors. Using a culture and primer independent next-generation sequencing and metagenomics pipeline, we surveyed the bacteria of the globally important pest, Scirtothrips dorsalis Hood. The most abundant bacterial phyla identified were Actinobacteria and Proteobacteria and the most abundant genera were Propionibacterium, Stenotrophomonas, and Pseudomonas. A total of 189 genera of bacteria were identified. The absence of any vertically transferred symbiont taxa commonly found in insects is consistent with other studies suggesting that thrips primarilly acquire resident microbes from their environment. This does not preclude a possible beneficial/intimate association between S. dorsalis and the dominant taxa identified and future work should determine the nature of these associations

Frequency and Clinical Implications of Discordant Creatine Kinase-MB and Troponin Measurements in Acute Coronary Syndromes

OBJECTIVES We sought to evaluate the association between discordant cardiac marker results and in-hospital mortality and treatment patterns in patients with non-ST-segment elevation acute coronary syndromes (NSTE ACS). BACKGROUND Creatine kinase-MB (CK-MB) and cardiac troponins (cTn) are often measured concurrently in patients with NSTE ACS. The significance of discordant CK-MB and cTn results is unknown. METHODS Among 29,357 ACS patients in the CRUSADE initiative who had both CK-MB and cTn measured during the first 36 hours, we examined relationships of four marker combinations (CK-MB-/cTn-, CK-MB+ /cTn-, CK-MB-/cTn+ , and CK-MB+ /cTn+) with mortality and American College of Cardiology/American Heart Association guidelines-recommended acute care. RESULTS The CK-MB and cTn results were discordant in 28% of patients (CK-MB+ /cTn-, 10%; CK-MB-/cTn+ , 18%). In-hospital mortality was 2.7% among CK-MB-/cTn- patients; 3.0%, CK-MB+ /cTn-; 4.5%, CK-MB-/cTn+ ; and 5.9%, CK-MB+ /cTn+ . After adjustment for other presenting risk factors, patients with CK-MB+ /cTn- had a mortality odds ratio (OR) of 1.02 (95% confidence interval [CI] 0.75 to 1.38), those with CK-MB-/ cTn+ had an OR of 1.15 (95% CI 0.86 to 1.54), and those with CK-MB+ /cTn+ had an OR of 1.53 (95% CI 1.18 to 1.98). Despite variable risk, patients with CK-MB+ /cTn- and CK-MB-/cTn+ were treated similarly with early antithrombotic agents and catheter-based interventions. CONCLUSIONS Among patients with NSTE ACS, an elevated troponin level identifies patients at increased acute risk regardless of CK-MB status, but an isolated CK-MB+ status has limited prognostic value. Recognition of these risk differences may contribute to more appropriate early use of antithrombotic therapy and invasive management for all cTn+ patients

Mechanical versus manual chest compression for out-of-hospital cardiac arrest (PARAMEDIC) : a pragmatic, cluster randomised controlled trial

BACKGROUND: Mechanical chest compression devices have the potential to help maintain high-quality cardiopulmonary resuscitation (CPR), but despite their increasing use, little evidence exists for their effectiveness. We aimed to study whether the introduction of LUCAS-2 mechanical CPR into front-line emergency response vehicles would improve survival from out-of-hospital cardiac arrest. METHODS: The pre-hospital randomised assessment of a mechanical compression device in cardiac arrest (PARAMEDIC) trial was a pragmatic, cluster-randomised open-label trial including adults with non-traumatic, out-of-hospital cardiac arrest from four UK Ambulance Services (West Midlands, North East England, Wales, South Central). 91 urban and semi-urban ambulance stations were selected for participation. Clusters were ambulance service vehicles, which were randomly assigned (1:2) to LUCAS-2 or manual CPR. Patients received LUCAS-2 mechanical chest compression or manual chest compressions according to the first trial vehicle to arrive on scene. The primary outcome was survival at 30 days following cardiac arrest and was analysed by intention to treat. Ambulance dispatch staff and those collecting the primary outcome were masked to treatment allocation. Masking of the ambulance staff who delivered the interventions and reported initial response to treatment was not possible. The study is registered with Current Controlled Trials, number ISRCTN08233942. FINDINGS: We enrolled 4471 eligible patients (1652 assigned to the LUCAS-2 group, 2819 assigned to the control group) between April 15, 2010 and June 10, 2013. 985 (60%) patients in the LUCAS-2 group received mechanical chest compression, and 11 (<1%) patients in the control group received LUCAS-2. In the intention-to-treat analysis, 30 day survival was similar in the LUCAS-2 group (104 [6%] of 1652 patients) and in the manual CPR group (193 [7%] of 2819 patients; adjusted odds ratio [OR] 0·86, 95% CI 0·64-1·15). No serious adverse events were noted. Seven clinical adverse events were reported in the LUCAS-2 group (three patients with chest bruising, two with chest lacerations, and two with blood in mouth). 15 device incidents occurred during operational use. No adverse or serious adverse events were reported in the manual group. INTERPRETATION: We noted no evidence of improvement in 30 day survival with LUCAS-2 compared with manual compressions. On the basis of ours and other recent randomised trials, widespread adoption of mechanical CPR devices for routine use does not improve survival

The relation between media promotions and service volume for a statewide tobacco quitline and a web-based cessation program

<p>Abstract</p> <p>Background</p> <p>This observational study assessed the relation between mass media campaigns and service volume for a statewide tobacco cessation quitline and stand-alone web-based cessation program.</p> <p>Methods</p> <p>Multivariate regression analysis was used to identify how weekly calls to a cessation quitline and weekly registrations to a web-based cessation program are related to levels of broadcast media, media campaigns, and media types, controlling for the impact of external and earned media events.</p> <p>Results</p> <p>There was a positive relation between weekly broadcast targeted rating points and the number of weekly calls to a cessation quitline and the number of weekly registrations to a web-based cessation program. Additionally, print secondhand smoke ads and online cessation ads were positively related to weekly quitline calls. Television and radio cessation ads and radio smoke-free law ads were positively related to web program registration levels. There was a positive relation between the number of web registrations and the number of calls to the cessation quitline, with increases in registrations to the web in 1 week corresponding to increases in calls to the quitline in the subsequent week. Web program registration levels were more highly influenced by earned media and other external events than were quitline call volumes.</p> <p>Conclusion</p> <p>Overall, broadcast advertising had a greater impact on registrations for the web program than calls to the quitline. Furthermore, registrations for the web program influenced calls to the quitline. These two findings suggest the evolving roles of web-based cessation programs and Internet-use practices should be considered when creating cessation programs and media campaigns to promote them. Additionally, because different types of media and campaigns were positively associated with calls to the quitline and web registrations, developing mass media campaigns that offer a variety of messages and communicate through different types of media to motivate tobacco users to seek services appears important to reach tobacco users. Further research is needed to better understand the complexities and opportunities involved in simultaneous promotion of quitline and web-based cessation services.</p

International variation in survival after out-of-hospital cardiac arrest : A validation study of the Utstein template

Introduction: Out-of-hospital cardiac arrest (OHCA) survival varies greatly between communities. The Utstein template was developed and promulgated to improve the comparability of OHCA outcome reports, but it has undergone limited empiric validation. We sought to assess how much of the variation in OHCA survival between emergency medical services (EMS) across the globe is explained by differences in the Utstein factors. We also assessed how accurately the Utstein factors predict OHCA survival. Methods: We performed a retrospective analysis of patient-level prospectively collected data from 12 OHCA registries from 12 countries for the period 1 Jan 2006 through 31 Dec 2011. We used generalized linear mixed models to examine the variation in survival between EMS agencies (n = 232). Results: Twelve registries contributed 86,759 cases. Patient arrest characteristics, EMS treatment and patient outcomes varied across registries. Overall survival to hospital discharge was 10% (range, 6% to 22%). Overall survival with Cerebral Performance Category of 1 or 2 (available for 8/12 registries) was 8%(range, 2% to 20%). The area-under-the-curve for the Utstein model was 0.85 (Wald CI: 0.85-0.85). The Utstein factors explained 51% of the EMS agency variation in OHCA survival. Conclusions: The Utstein factors explained 51%. of the variation in survival to hospital discharge among multiple large geographically separate EMS agencies. This suggests that quality improvement and public health efforts should continue to target modifiable Utstein factors to improve OHCA survival. Further study is required to identify the reasons for the variation that is incompletely understood.Peer reviewe