A Continuum Description of Vibrated Sand

The motion of a thin layer of granular material on a plate undergoing sinusoidal vibrations is considered. We develop equations of motion for the local thickness and the horizontal velocity of the layer. The driving comes from the violent impact of the grains on the plate. A linear stability theory reveals that the waves are excited non-resonantly, in contrast to the usual Faraday waves in liquids. Together with the experimentally observed continuum scaling, the model suggests a close connection between the neutral curve and the dispersion relation of the waves, which agrees quite well with experiments. For strong hysteresis we find localized oscillon solutions.Comment: paper has been considerably extended (11 instead of 6 pages; 6 instead of 4 figures) much better agreement with experiment. obtain now oscillons in 1 dimensio

Analysis of 14 BAC sequences from the Aedes aegypti genome: a benchmark for genome annotation and assembly

In order to provide a set of manually curated and annotated sequences from the Aedes aegypti genome, mapped BAC clones encompassing 1.57 Mb were sequenced, assembled and manually annotated using computational gene-finding, EST matches as well as comparative protein homology

Square patterns in Rayleigh-Benard convection with rotation about a vertical axis

We present experimental results for Rayleigh-Benard convection with rotation about a vertical axis at dimensionless rotation rates in the range 0 to 250 and upto 20% above the onset. Critical Rayleigh numbers and wavenumbers agree with predictions of linear stability analysis. For rotation rates greater than 70 and close to onset, the patterns are cellular with local four-fold coordination and differ from the theoretically expected Kuppers-Lortz unstable state. Stable as well as intermittent defect-free square lattices exist over certain parameter ranges. Over other ranges defects dynamically disrupt the lattice but cellular flow and local four-fold coordination is maintained.Comment: ReVTeX, 4 pages, 7 eps figures include

The use of biomedicine, complementary and alternative medicine, and ethnomedicine for the treatment of epilepsy among people of South Asian origin in the UK

Studies have shown that a significant proportion of people with epilepsy use complementary and alternative medicine (CAM). CAM use is known to vary between different ethnic groups and cultural contexts; however, little attention has been devoted to inter-ethnic differences within the UK population. We studied the use of biomedicine, complementary and alternative medicine, and ethnomedicine in a sample of people with epilepsy of South Asian origin living in the north of England. Interviews were conducted with 30 people of South Asian origin and 16 carers drawn from a sampling frame of patients over 18 years old with epilepsy, compiled from epilepsy registers and hospital databases. All interviews were tape-recorded, translated if required and transcribed. A framework approach was adopted to analyse the data. All those interviewed were taking conventional anti-epileptic drugs. Most had also sought help from traditional South Asian practitioners, but only two people had tried conventional CAM. Decisions to consult a traditional healer were taken by families rather than by individuals with epilepsy. Those who made the decision to consult a traditional healer were usually older family members and their motivations and perceptions of safety and efficacy often differed from those of the recipients of the treatment. No-one had discussed the use of traditional therapies with their doctor. The patterns observed in the UK mirrored those reported among people with epilepsy in India and Pakistan. The health care-seeking behaviour of study participants, although mainly confined within the ethnomedicine sector, shared much in common with that of people who use global CAM. The appeal of traditional therapies lay in their religious and moral legitimacy within the South Asian community, especially to the older generation who were disproportionately influential in the determination of treatment choices. As a second generation made up of people of Pakistani origin born in the UK reach the age when they are the influential decision makers in their families, resort to traditional therapies may decline. People had long experience of navigating plural systems of health care and avoided potential conflict by maintaining strict separation between different sectors. Health care practitioners need to approach these issues with sensitivity and to regard traditional healers as potential allies, rather than competitors or quacks

Are Seyfert Narrow Line Regions Powered by Radio Jets?

We argue that the narrow line regions of Seyfert galaxies are powered by the transport of energy and momentum by the radio-emitting jets and consequently that the ratio of the radio power to jet energy flux is much smaller than is usually assumed for radio galaxies. This can be partially attributed to the smaller ages ($\sim 10^6 yrs$) of Seyferts compared to radio galaxies but one also requires that either the magnetic energy density is more than an order of magnitude below the equipartition value, or more likely, that the internal energy densities of Seyfert jets are dominated by thermal plasma. If Seyfert jets are initially dominated by relativistic plasma, then an analysis of the data on jets in five Seyfert galaxies shows that all but one of these would have mildly relativistic jet velocities near 100 pc in order to power the respective narrow-line regions. However, observations of jet-cloud interactions in the NLR provide additional information on jet velocities and composition via the momentum budget. Our analysis of a jet-cloud interaction in NGC 1068, implies a shocked jet pressure much larger than the minimum pressure of the radio knot, a velocity $\sim 0.06 c$ and a jet temperature $\sim 10^9 K$ implying mildly relativistic electrons but thermal protons. The jet mass flux at this point $\sim 0.5 M_\odot yr^{-1}$, is an order of magnitude higher than the mass accretion rate into the black hole, strongly indicating entrainment. The initial jet mass flux $\sim 0.02 M_\odot yr^{-1}$, comparable to the mass accretion rate and is consistent with the densities inferred for accretion disc coronae from high energy observations, together with an initially mildly relativistic velocity and an initial jet radius of order 10 gravitational radii.Comment: LaTeX2e, uses astrobib.sty, 4 postscript figures; submitted to Ap

A Machine Learning Approach for Using the Postmortem Skin Microbiome to Estimate the Postmortem Interval

Research on the human microbiome, the microbiota that live in, on, and around the human person, has revolutionized our understanding of the complex interactions between microbial life and human health and disease. The microbiome may also provide a valuable tool in forensic death investigations by helping to reveal the postmortem interval (PMI) of a decedent that is discovered after an unknown amount of time since death. Current methods of estimating PMI for cadavers discovered in uncontrolled, unstudied environments have substantial limitations, some of which may be overcome through the use of microbial indicators. In this project, we sampled the microbiomes of decomposing human cadavers, focusing on the skin microbiota found in the nasal and ear canals. We then developed several models of statistical regression to establish an algorithm for predicting the PMI of microbial samples. We found that the complete data set, rather than a curated list of indicator species, was preferred for training the regressor. We further found that genus and family, rather than species, are the most informative taxonomic levels. Finally, we developed a k-nearest- neighbor regressor, tuned with the entire data set from all nasal and ear samples, that predicts the PMI of unknown samples with an average error of ±55 accumulated degree days (ADD). This study outlines a machine learning approach for the use of necrobiome data in the prediction of the PMI and thereby provides a successful proof-of- concept that skin microbiota is a promising tool in forensic death investigations

Colectomy is a risk factor for venous thromboembolism in ulcerative colitis

AIM: To compare venous thromboembolism (VTE) in hospitalized ulcerative colitis (UC) patients who respond to medical management to patients requiring colectomy.METHODS: Population-based surveillance from 1997 to 2009 was used to identify all adults admitted to hospital for a flare of UC and those patients who underwent colectomy. All medical charts were reviewed to confirm the diagnosis and extract clinically relevant information. UC patients were stratified by: (1) responsive to inpatient medical therapy (n = 382); (2) medically refractory requiring emergent colectomy (n = 309); and (3) elective colectomy (n = 329). The primary outcome was the development of VTE during hospitalization or within 6 mo of discharge. Heparin prophylaxis to prevent VTE was assessed. Logistic regression analysis determined the effect of disease course (i.e., responsive to medical therapy, medically refractory, and elective colectomy) on VTE after adjusting for confounders including age, sex, smoking, disease activity, comorbidities, extent of disease, and IBD medications (i.e., corticosteroids, mesalamine, azathioprine, and infliximab). Point estimates were presented as odds ratios (OR) with 95%CI.RESULTS: The prevalence of VTE among patients with UC who responded to medical therapy was 1.3% and only 16% of these patients received heparin prophylaxis. In contrast, VTE was higher among patients who underwent an emergent (8.7%) and elective (4.9%) colectomy, despite greater than 90% of patients receiving postoperative heparin prophylaxis. The most common site of VTE was intra-abdominal (45.8%) followed by lower extremity (19.6%). VTE was diagnosed after discharge from hospital in 16.7% of cases. Elective (adjusted OR = 3.69; 95%CI: 1.30-10.44) and emergent colectomy (adjusted OR = 5.28; 95%CI: 1.93-14.45) were significant risk factors for VTE as compared to medically responsive UC patients. Furthermore, the odds of a VTE significantly increased across time (adjusted OR = 1.10; 95%CI: 1.01-1.20). Age, sex, comorbidities, disease extent, disease activity, smoking, corticosteroids, mesalamine, azathioprine, and infliximab were not independently associated with the development of VTE.CONCLUSION: VTE was associated with colectomy, particularly, among UC patients who failed medical management. VTE prophylaxis may not be sufficient to prevent VTE in patients undergoing colectom

Widespread detection of highly pathogenic H5 influenza viruses in wild birds from the Pacific Flyway of the United States

A novel highly pathogenic avian influenza virus belonging to the H5 clade 2.3.4.4 variant viruses was detected in North America in late 2014. Motivated by the identification of these viruses in domestic poultry in Canada, an intensive study was initiated to conduct highly pathogenic avian influenza surveillance in wild birds in the Pacific Flyway of the United States. A total of 4,729 hunter-harvested wild birds were sampled and highly pathogenic avian influenza virus was detected in 1.3% (n = 63). Three H5 clade 2.3.4.4 subtypes were isolated from wild birds, H5N2, H5N8, and H5N1, representing the wholly Eurasian lineage H5N8 and two novel reassortant viruses. Testing of 150 additional wild birds during avian morbidity and mortality investigations in Washington yielded 10 (6.7%) additional highly pathogenic avian influenza isolates (H5N8 = 3 and H5N2 = 7). The geographically widespread detection of these viruses in apparently healthy wild waterfowl suggest that the H5 clade 2.3.4.4 variant viruses may behave similarly in this taxonomic group whereby many waterfowl species are susceptible to infection but do not demonstrate obvious clinical disease. Despite these findings in wild waterfowl, mortality has been documented for some wild bird species and losses in US domestic poultry during the first half of 2015 were unprecedented

Enhanced biodegradation of PAHs in historically contaminated soil by M. gilvum inoculated biochar

The inoculation of rice straw biochar with PAH-degrading Mycobacterium gilvum (1.27 × 1011 ± 1.24 × 1010 cell g−1), and the subsequent amendment of this composite material to PAHs contaminated (677 mg kg−1) coke plant soil, was conducted in order to investigate if would enhance PAHs biodegradation in soils. The microbe-biochar composite showed superior degradation capacity for phenanthrene, fluoranthene and pyrene. Phenanthrene loss in the microbe-biochar composite, free cell alone and biochar alone treatments was, respectively, 62.6 ± 3.2%, 47.3 ± 4.1% and non-significant (P > 0.05); whereas for fluoranthene loss it was 52.1 ± 2.3%; non-significant (P > 0.05) and non-significant (P > 0.05); and for pyrene loss it was 62.1 ± 0.9%; 19.7 ± 6.5% and 13.5 ± 2.8%. It was hypothesized that the improved remediation was underpinned by i) biochar enhanced mass transfer of PAHs from the soil to the carbonaceous biochar “sink”, and ii) the subsequent degradation of the PAHs by the immobilized M. gilvum. To test this mechanism, a surfactant (Brij 30; 20 mg g−1 soil), was added to impede PAHs mass transfer to biochar and sorption. The surfactant increased solution phase PAH concentrations and significantly (P < 0.05) reduced PAH degradation in the biochar immobilized M. gilvum treatments; indicating the enhanced degradation occurred between the immobilized M. gilvum and biochar sorbed PAHs

Canadian Association of Gastroenterology Clinical Practice Guideline for the Medical Management of Pediatric Luminal Crohn's Disease

Background & Aims: We aim to provide guidance for medical treatment of luminal Crohn's disease in children. Methods: We performed a systematic search of publication databases to identify studies of medical management of pediatric Crohn's disease. Quality of evidence and strength of recommendations were rated according to the GRADE (Grading of Recommendation Assessment, Development, and Evaluation) approach. We developed statements through an iterative online platform and then finalized and voted on them. Results: The consensus includes 25 statements focused on medical treatment options. Consensus was not reached, and no recommendations were made, for 14 additional statements, largely due to lack of evidence. The group suggested corticosteroid therapies (including budesonide for mild to moderate disease). The group suggested exclusive enteral nutrition for induction therapy and biologic tumor necrosis factor antagonists for induction and maintenance therapy at diagnosis or at early stages of severe disease, and for patients failed by steroid and immunosuppressant induction therapies. The group recommended against the use of oral 5-aminosalicylate for induction or maintenance therapy in patients with moderate disease, and recommended against thiopurines for induction therapy, corticosteroids for maintenance therapy, and cannabis in any role. The group was unable to clearly define the role of concomitant immunosuppressants during initiation therapy with a biologic agent, although thiopurine combinations are not recommended for male patients. No consensus was reached on the role of aminosalicylates in treatment of patients with mild disease, antibiotics or vedolizumab for induction or maintenance therapy, or methotrexate for induction therapy. Patients in clinical remission who are receiving immunomodulators should be assessed for mucosal healing within 1 year of treatment initiation. Conclusions: Evidence-based medical treatment of Crohn's disease in children is recommended, with thorough ongoing assessments to define treatment success