The JCMT Gould Belt Survey: the effect of molecular contamination in SCUBA-2 observations of Orion A

Thermal emission from cold dust grains in giant molecular clouds can be used to probe the physical properties, such as density, temperature and emissivity in star-forming regions. We present the SCUBA-2 shared-risk observations at 450 $\mu$m and 850 $\mu$m of the Orion A molecular cloud complex taken at the James Clerk Maxwell Telescope (JCMT). Previous studies showed that molecular emission lines can contribute significantly to the measured fluxes in those continuum bands. We use the HARP $^{12}$CO J=3-2 integrated intensity map for Orion A in order to evaluate the molecular line contamination and its effects on the SCUBA-2 maps. With the corrected fluxes, we have obtained a new spectral index $\alpha$ map for the thermal emission of dust in the well-known integral-shaped filament. Furthermore, we compare a sample of 33 sources, selected over the Orion A molecular cloud complex for their high $^{12}$CO J=3-2 line contamination, to 27 previously identified clumps in OMC-4. This allows us to quantify the effect of line contamination on the ratio of 850 $\mu$m to 450 $\mu$m flux densities and how it modifies the deduced spectral index of emissivity $\beta$ for the dust grains. We also show that at least one Spitzer-identified protostellar core in OMC-5 has a $^{12}$CO J=3-2 contamination level of 16 %. Furthermore, we find the strongest contamination level (44 %) towards a young star with disk near OMC-2. This work is part of the JCMT Gould Belt Legacy Survey.Comment: 13 pages, 6 figures, Accepted for publication in Monthly Notices of the Royal Astronomical Society (MNRAS

Lepton Acceleration in Pulsar Wind Nebulae

Pulsar Wind Nebulae (PWNe) act as calorimeters for the relativistic pair winds emanating from within the pulsar light cylinder. Their radiative dissipation in various wavebands is significantly different from that of their pulsar central engines: the broadband spectra of PWNe possess characteristics distinct from those of pulsars, thereby demanding a site of lepton acceleration remote from the pulsar magnetosphere. A principal candidate for this locale is the pulsar wind termination shock, a putatively highly-oblique, ultra-relativistic MHD discontinuity. This paper summarizes key characteristics of relativistic shock acceleration germane to PWNe, using predominantly Monte Carlo simulation techniques that compare well with semi-analytic solutions of the diffusion-convection equation. The array of potential spectral indices for the pair distribution function is explored, defining how these depend critically on the parameters of the turbulent plasma in the shock environs. Injection efficiencies into the acceleration process are also addressed. Informative constraints on the frequency of particle scattering and the level of field turbulence are identified using the multiwavelength observations of selected PWNe. These suggest that the termination shock can be comfortably invoked as a principal injector of energetic leptons into PWNe without resorting to unrealistic properties for the shock layer turbulence or MHD structure.Comment: 19 pages, 5 figures, invited review to appear in Proc. of the inaugural ICREA Workshop on "The High-Energy Emission from Pulsars and their Systems" (2010), eds. N. Rea and D. Torres, (Springer Astrophysics and Space Science series

Protocol for a 1-year prospective, longitudinal cohort study of patients undergoing Roux-en-Y gastric bypass and sleeve gastrectomy: the BARI-LIFESTYLE observational study

INTRODUCTION: Roux-en-Y gastric bypass and sleeve gastrectomy are the two most common bariatric surgery performed in the UK that result in comparable weight loss and remission of obesity-associated comorbidities. However, there is a paucity of studies examining the impact of these procedures on body composition, physical activity levels, sedentary behaviour, physical function and strength, dietary intake, health-related quality of life and costs. METHODS AND ANALYSIS: The BARI-LIFESTYLE observational study is a 1-year prospective, longitudinal cohort study within a real-world routine clinical care setting aiming to recruit 100 patients with severe obesity undergoing either primary Roux-en-Y gastric bypass or sleeve gastrectomy from two bariatric centres in London, UK. Participants will be followed up four times during the study period; presurgery baseline (T0) and at 3 (T1), 6 (T2) and 12 months (T3) postsurgery. In addition to the standard follow-up investigations, assessments including dual-energy X-ray absorptiometry scan, bioelectric impedance analysis, 6 min walk test, sit-to-stand test and handgrip test will be undertaken together with completion of questionnaires. Physical activity levels and sedentary behaviour will be assessed using accelerometer, and dietary intake will be recorded using a 3-day food diary. Outcome measures will include body weight, body fat mass, lean muscle mass, bone mineral density, physical activity levels, sedentary behaviour, physical function and strength, dietary intake, health-related quality of life, remission of comorbidities, healthcare resource utilisation and costs. ETHICS AND DISSEMINATION: This study has been reviewed and given a favourable ethical opinion by London-Dulwich Research Ethics Committee (17/LO/0950). The results will be presented to stakeholder groups locally, nationally and internationally and published in peer-reviewed medical journals. The lay-person summary of the findings will be published on the Centre for Obesity Research, University College London website (http://www.ucl.ac.uk/obesity)

The JCMT Gould Belt Survey: the effect of molecular contamination in SCUBA-2 observations of Orion A

JOURThis is the final version of the article. It was first published by Oxford Journals for the Royal Astronomical Society via http://dx.doi.org/ 10.1093/mnras/stv3009Thermal emission from cold dust grains in giant molecular clouds can be used to probe the physical properties, such as density, temperature and emissivity in star-forming regions. We present the Submillimetre Common-User Bolometer Array (SCUBA-2) shared-risk observations at 450 and 850 μm of the Orion A molecular cloud complex taken at the James Clerk Maxwell Telescope (JCMT). Previous studies showed that molecular emission lines can contribute significantly to the measured fluxes in those continuum bands. We use the Heterodyne Array Receiver Programme 12CO J = 3-2 integrated intensity map for Orion A in order to evaluate the molecular line contamination and its effects on the SCUBA-2 maps. With the corrected fluxes, we have obtained a new spectral index α map for the thermal emission of dust in the well-known integral-shaped filament. Furthermore, we compare a sample of 33 sources, selected over the Orion A molecular cloud complex for their high 12CO J = 3-2 line contamination, to 27 previously identified clumps in OMC 4. This allows us to quantify the effect of line contamination on the ratio of 850-450 μm flux densities and how it modifies the deduced spectral index of emissivity β for the dust grains. We also show that at least one Spitzer-identified protostellar core in OMC 5 has a 12CO J = 3-2 contamination level of 16 per cent. Furthermore, we find the strongest contamination level (44 per cent) towards a young star with disc near OMC 2. This work is part of the JCMT Gould Belt Legacy Survey

Evolution of reproductive development in the volvocine algae

The evolution of multicellularity, the separation of germline cells from sterile somatic cells, and the generation of a male–female dichotomy are certainly among the greatest innovations of eukaryotes. Remarkably, phylogenetic analysis suggests that the shift from simple to complex, differentiated multicellularity was not a unique progression in the evolution of life, but in fact a quite frequent event. The spheroidal green alga Volvox and its close relatives, the volvocine algae, span the full range of organizational complexity, from unicellular and colonial genera to multicellular genera with a full germ–soma division of labor and male–female dichotomy; thus, these algae are ideal model organisms for addressing fundamental issues related to the transition to multicellularity and for discovering universal rules that characterize this transition. Of all living species, Volvox carteri represents the simplest version of an immortal germline producing specialized somatic cells. This cellular specialization involved the emergence of mortality and the production of the first dead ancestors in the evolution of this lineage. Volvocine algae therefore exemplify the evolution of cellular cooperation from cellular autonomy. They also serve as a prime example of the evolution of complex traits by a few successive, small steps. Thus, we learn from volvocine algae that the evolutionary transition to complex, multicellular life is probably much easier to achieve than is commonly believed

Mathematical and Statistical Techniques for Systems Medicine: The Wnt Signaling Pathway as a Case Study

The last decade has seen an explosion in models that describe phenomena in systems medicine. Such models are especially useful for studying signaling pathways, such as the Wnt pathway. In this chapter we use the Wnt pathway to showcase current mathematical and statistical techniques that enable modelers to gain insight into (models of) gene regulation, and generate testable predictions. We introduce a range of modeling frameworks, but focus on ordinary differential equation (ODE) models since they remain the most widely used approach in systems biology and medicine and continue to offer great potential. We present methods for the analysis of a single model, comprising applications of standard dynamical systems approaches such as nondimensionalization, steady state, asymptotic and sensitivity analysis, and more recent statistical and algebraic approaches to compare models with data. We present parameter estimation and model comparison techniques, focusing on Bayesian analysis and coplanarity via algebraic geometry. Our intention is that this (non exhaustive) review may serve as a useful starting point for the analysis of models in systems medicine.Comment: Submitted to 'Systems Medicine' as a book chapte

Glutathione S-transferase 8-8 expression is lower in alcohol-preferring than in alcohol-nonpreferring rats

OBJECTIVE: A primary focus of alcohol research is to provide novel targets for alcohol treatment by identifying genes that predispose individuals to drink alcohol. Animal models of alcoholism developed by selective breeding are invaluable tools to elucidate both the genetic nature and the underlying biological mechanisms that contribute to alcohol dependence. These selected lines (high alcohol preferring and low alcohol preferring) display phenotypic and genetic differences that can be studied to further our understanding of alcohol preference and related genetic traits. By combining molecular techniques, genetic and physiological factors that underlie the cause of alcoholism can be identified. METHODS: Total gene expression analysis was used to identify genes that are differentially expressed in specific brain regions between alcohol-naive, inbred alcohol-preferring (iP) and -nonpreferring (iNP) rats. Quantitative reverse transcriptase-polymerase chain reaction, in situ hybridization, Western blot, and sequence analysis were used to further characterize rat glutathione S-transferase 8-8 (rGST 8-8). RESULTS: Lower expression of rGST 8-8 mRNA was observed in discrete brain regions of iP compared with iNP animals, and these expression differences were confirmed. To determine additional expression patterns of rGST 8-8, we used in situ hybridization. Rat GST 8-8 was highly expressed in hippocampus, the choroid plexus of the dorsal third ventricle and the lateral ventricle, and ependymal cells along the dorsal third ventricle and the third ventricle. Western blot analysis showed that rGST 8-8 protein levels were lower in the hippocampus and the amygdala of iP compared with iNP. A silent single-nucleotide polymorphism in the coding region and three single-nucleotide polymorphisms in the 3'-UTR were identified in the rGST 8-8 cDNA. CONCLUSION: There is regional variation of rGST 8-8 expression in the brain, at both the mRNA and protein level, and the iP strain has lower innate rGST 8-8 levels than the iNP strain in discrete brain regions

Clinical mastitis in ewes; bacteriology, epidemiology and clinical features

<p>Abstract</p> <p>Background</p> <p>Clinical mastitis is an important disease in sheep. The objective of this work was to identify causal bacteria and study certain epidemiological and clinical features of clinical mastitis in ewes kept for meat and wool production.</p> <p>Methods</p> <p>The study included 509 ewes with clinical mastitis from 353 flocks located in 14 of the 19 counties in Norway. Clinical examination and collection of udder secretions were carried out by veterinarians. Pulsed-field gel electrophoresis (PFGE) was performed on 92 <it>Staphylococcus aureus </it>isolates from 64 ewes.</p> <p>Results and conclusion</p> <p><it>S. aureus </it>was recovered from 65.3% of 547 clinically affected mammary glands, coagulase-negative staphylococci from 2.9%, enterobacteria, mainly <it>Escherichia coli</it>, from 7.3%, <it>Streptococcus </it>spp. from 4.6%, <it>Mannheimia haemolytica </it>from 1.8% and various other bacteria from 4.9%, while no bacteria were cultured from 13.2% of the samples. Forty percent of the ewes with unilateral clinical <it>S. aureus </it>mastitis also had a subclinical <it>S. aureus </it>infection in the other mammary gland. Twenty-four of 28 (86%) pairs of <it>S. aureus </it>isolates obtained from clinically and subclinically affected mammary glands of the same ewe were indistinguishable by PFGE. The number of identical pairs was significantly greater than expected, based on the distribution of different <it>S. aureus </it>types within the flocks. One-third of the cases occurred during the first week after lambing, while a second peak was observed in the third week of lactation. Gangrene was present in 8.8% of the clinically affected glands; <it>S. aureus </it>was recovered from 72.9%, <it>Clostridium perfringens </it>from 6.3% and <it>E. coli </it>from 6.3% of the secretions from such glands. This study shows that <it>S. aureus </it>predominates as a cause of clinical ovine mastitis in Norway, also in very severe cases. Results also indicate that <it>S. aureus </it>is frequently spread between udder halves of infected ewes.</p

Learning informally to use the 'full version' of teaching games for understanding

This paper examines an experienced teacher’s employment of the teaching games for understanding (TGfU) model in a UK secondary school. The study sought to investigate how the teacher delivered TGfU and those factors that influenced his informal learning of this instructional model. Occupational socialisation was utilised to determine the factors that influenced his use of TGfU. Qualitative data were collected from interviews, lesson observations and documentary evidence. Inductive data analysis indicated the teacher delivered the ‘full version’ of the model largely congruent with the creators’ intentions. The traditional approach to games teaching seen in his childhood and partially learned in higher education were ‘washed out’ by the influence of teaching colleagues and the development of a student-centred approach to teaching games. This study indicates it is possible to overcome traditional approaches to games teaching and informally learn to use TGfU successfully given conducive circumstances and sufficient time

An Upstream Open Reading Frame Controls Translation of var2csa, a Gene Implicated in Placental Malaria

Malaria, caused by the parasite Plasmodium falciparum, is responsible for substantial morbidity, mortality and economic losses in tropical regions of the world. Pregnant women are exceptionally vulnerable to severe consequences of the infection, due to the specific adhesion of parasite-infected erythrocytes in the placenta. This adhesion is mediated by a unique variant of PfEMP1, a parasite encoded, hyper-variable antigen placed on the surface of infected cells. This variant, called VAR2CSA, binds to chondroitin sulfate A on syncytiotrophoblasts in the intervillous space of placentas. VAR2CSA appears to only be expressed in the presence of a placenta, suggesting that its expression is actively repressed in men, children or non-pregnant women; however, the mechanism of repression is not understood. Using cultured parasite lines and reporter gene constructs, we show that the gene encoding VAR2CSA contains a small upstream open reading frame that acts to repress translation of the resulting mRNA, revealing a novel form of gene regulation in malaria parasites. The mechanism underlying this translational repression is reversible, allowing high levels of protein translation upon selection, thus potentially enabling parasites to upregulate expression of this variant antigen in the presence of the appropriate host tissue