Amplification and next generation sequencing of near full-length human enteroviruses for identification and characterisation from clinical samples

© 2018, The Author(s). More than 100 different enterovirus (EV) genotypes infect humans and contribute to substantial morbidity. However, current methods for characterisation of full-length genomes are based on Sanger sequencing of short genomic regions, which are labour-intensive and do not enable comprehensive characterisation of viral populations. Here, we describe a simple and sensitive protocol for the amplification and sequencing of near full-length genomes of human EV species using next generation sequencing. EV genomes were amplified from 89% of samples tested, with Ct values ranging between 15.7 and 39.3. These samples included 7 EV-A genotypes (CVA2, 5–7, 10, 16 and EV71), 19 EV-B genotypes (CVA9, CVB1-6, ECHO3, 4, 6, 7, 9, 11, 16, 18, 25, 29, 30, and EV69), 3 EV-C genotypes (CVA19 and PV2, 3) and 1 EV-D genotype (EV70). We characterised 70 EVs from 58 clinical stool samples and eight reference strains, with a minimum of 100X depth. We found evidence of co-infection in four clinical specimens, each containing two distinct EV genotypes (CVB3/ECHO7, CVB3/ECHO18 and ECHO9/30). Characterisation of the complete genome provided conclusive genotyping of EVs, which can be applied to investigate the intra-host virus evolution of EVs, and allows further identification and investigation of EV outbreaks

Crotalus atrox venom preconditioning increases plasma fibrinogen and reduces perioperative hemorrhage in a rat model of surgical brain injury.

Perioperative bleeding is a potentially devastating complication in neurosurgical patients, and plasma fibrinogen concentration has been identified as a potential modifiable risk factor for perioperative bleeding. The aim of this study was to evaluate preconditioning with Crotalus atrox venom (Cv-PC) as potential preventive therapy for reducing perioperative hemorrhage in the rodent model of surgical brain injury (SBI). C. atrox venom contains snake venom metalloproteinases that cleave fibrinogen into fibrin split products without inducing clotting. Separately, fibrinogen split products induce fibrinogen production, thereby elevating plasma fibrinogen levels. Thus, the hypothesis was that preconditioning with C. atrox venom will produce fibrinogen spilt products, thereby upregulating fibrinogen levels, ultimately improving perioperative hemostasis during SBI. We observed that Cv-PC SBI animals had significantly reduced intraoperative hemorrhage and postoperative hematoma volumes compared to those of vehicle preconditioned SBI animals. Cv-PC animals were also found to have higher levels of plasma fibrinogen at the time of surgery, with unchanged prothrombin time. Cv-PC studies with fractions of C. atrox venom suggest that snake venom metalloproteinases are largely responsible for the improved hemostasis by Cv-PC. Our findings indicate that Cv-PC increases plasma fibrinogen levels and may provide a promising therapy for reducing perioperative hemorrhage in elective surgeries

Crystal Field Triplets: A New Route to Non-Fermi Liquid Physics

A model for crystal field triplet ground states on rare earth or actinide ions with dipolar and quadrupolar couplings to conduction electrons is studied for the first time with renormalization group methods. The quadrupolar coupling leads to a new nontrivial, non-Fermi liquid fixed point, which survives in an intermediate valence Anderson model. The calculated magnetic susceptibility displays one parameter scaling, going as $T^{-\alpha}$ ($\alpha \approx 0.4$) at intermediate temperatures, reminiscent of the non-Fermi liquid alloy UCu_{5-x}Pd_x.Comment: 4 pages, 3 figures, REVTe

Itinerancy and Hidden Order in URu2Si2URu_2Si_2

We argue that key characteristics of the enigmatic transition at $T_0= 17.5K$ in $URu_2Si_2$ indicate that the hidden order is a density wave formed within a band of composite quasiparticles, whose detailed structure is determined by local physics. We expand on our proposal (with J.A. Mydosh) of the hidden order as incommnesurate orbital antiferromagnetism and present experimental predictions to test our ideas. We then turn towards a microscopic description of orbital antiferromagnetism, exploring possible particle-hole pairings within the context of a simple one-band model. We end with a discussion of recent high-field and thermal transport experiment, and discuss their implications for the nature of the hidden order.Comment: 18 pages, 7 figures. v2 contains added referenc

Design mining interacting wind turbines

© 2016 by the Massachusetts Institute of Technology. An initial study has recently been presented of surrogate-assisted evolutionary algorithms used to design vertical-axis wind turbines wherein candidate prototypes are evaluated under fan-generated wind conditions after being physically instantiated by a 3D printer. Unlike other approaches, such as computational fluid dynamics simulations, no mathematical formulations were used and no model assumptions weremade. This paper extends that work by exploring alternative surrogate modelling and evolutionary techniques. The accuracy of various modelling algorithms used to estimate the fitness of evaluated individuals from the initial experiments is compared. The effect of temporally windowing surrogate model training samples is explored. A surrogateassisted approach based on an enhanced local search is introduced; and alternative coevolution collaboration schemes are examined

Streptomyces aridus sp. nov., isolated from a high altitude Atacama Desert soil and emended description of Streptomyces noboritoensis Isono et al. 1957.

A polyphasic study was undertaken to determine the taxonomic status of a Streptomyces strain which had been isolated from a high altitude Atacama Desert soil and shown to have bioactive properties. The strain, isolate H9(T), was found to have chemotaxonomic, cultural and morphological properties that place it in the genus Streptomyces. 16S rRNA gene sequence analyses showed that the isolate forms a distinct branch at the periphery of a well-delineated subclade in the Streptomyces 16S rRNA gene tree together with the type strains of Streptomyces crystallinus, Streptomyces melanogenes and Streptomyces noboritoensis. Multi-locus sequence analysis (MLSA) based on five house-keeping gene alleles showed that isolate H9(T) is closely related to the latter two type strains and to Streptomyces polyantibioticus NRRL B-24448(T). The isolate was distinguished readily from the type strains of S. melanogenes, S. noboritoensis and S. polyantibioticus using a combination of phenotypic properties. Consequently, the isolate is considered to represent a new species of Streptomyces for which the name Streptomyces aridus sp. nov. is proposed; the type strain is H9(T) (=NCIMB 14965(T)=NRRL B65268(T)). In addition, the MLSA and phenotypic data show that the S. melanogenes and S. noboritoensis type strains belong to a single species, it is proposed that S. melanogenes be recognised as a heterotypic synonym of S. noboritoensis for which an emended description is given. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10482-017-0838-2) contains supplementary material, which is available to authorized users

Methamphetamine Use, Transmission Risk Behavior and Internet Use Among HIV-Infected Patients in Medical Care, San Francisco, 2008

Methamphetamine use is associated with adverse health outcomes and HIV incidence. Few studies have assessed methamphetamine use, sexual behavior and Internet use among HIV-infected patients. Surveys were administered to a sample of HIV-infected patients seeking medical care in a San Francisco county hospital and university-based clinic. In 2008, 35% of homosexual participants, 26% of heterosexual participants and 11% of female participants reported methamphetamine use in the past year. Of participants, 29% reported using the Internet to find sex partners; Internet-users versus non-Internet-users reported a higher median number of sex partners in 6 months (4 vs. 1), were more likely to report unprotected sex (32 vs. 10%), and higher rates of methamphetamine use in the past 12 months (48 vs. 24%). Given the association among methamphetamine use, increased sex partners and Internet use, the Internet may present a new and effective medium for interventions to reduce methamphetamine-associated sexual risk behavior

Anti-Parasitic Compounds from Streptomyces sp. Strains Isolated from Mediterranean Sponges

Actinomycetes are prolific producers of pharmacologically important compounds accounting for about 70% of the naturally derived antibiotics that are currently in clinical use. In this study, we report on the isolation of Streptomyces sp. strains from Mediterranean sponges, on their secondary metabolite production and on their screening for anti-infective activities. Bioassay-guided isolation and purification yielded three previously known compounds namely, cyclic depsipeptide valinomycin, indolocarbazole alkaloid staurosporine and butenolide. This is the first report of the isolation of valinomycin from a marine source. These compounds exhibited novel anti-parasitic activities specifically against Leishmania major (valinomycin IC50 < 0.11 μM; staurosporine IC50 5.30 μM) and Trypanosoma brucei brucei (valinomycin IC50 0.0032 μM; staurosporine IC50 0.022 μM; butenolide IC50 31.77 μM). These results underscore the potential of marine actinomycetes to produce bioactive compounds as well as the re-evaluation of previously known compounds for novel anti-infective activities

The Internet and HIV study: design and methods

BACKGROUND: The Internet provides a new meeting ground, especially for gay men, that did not exist in the early 1990s. Several studies have found increased levels of high risk sexual behaviour and sexually transmissible infections (STI) among gay men who seek sex on the Internet, although the underlying processes are not fully understood. Research funded by the UK Medical Research Council (2002–2004) provided the opportunity to consider whether the Internet represents a new sexual risk environment for gay and bisexual men living in London. METHODS: The objectives of the Internet and HIV study are to: (i) measure the extent to which gay men living in London seek sexual partners on the Internet; (ii) compare the characteristics of London gay men who do and do not seek sex on the Internet; (iii) examine whether sex with Internet-partners is less safe than with other sexual partners; (iv) compare use of the Internet with other venues where men meet sexual partners; (v) establish whether gay men use the Internet to actively seek partners for unprotected anal intercourse; (vi) determine the potential for using the Internet for HIV prevention. These objectives have been explored using quantitative and qualitative research methods in four samples of London gay men recruited and interviewed both online and offline. The four samples were: (i) gay men recruited through Internet chat rooms and profiles; (ii) HIV positive gay men attending an NHS hospital outpatients clinic; (iii) gay men seeking an HIV test in an NHS HIV testing or sexual health clinic; (iv) gay men recruited in the community. RESULTS: Quantitative data were collected by means of confidential, anonymous self-administered questionnaires (n>4000) completed on-line by the Internet sample. Qualitative data were collected by means of one-to-one interviews (n = 128) conducted either face-to-face or on-line. CONCLUSION: The strength of the Internet and HIV study is its methodological plurality, drawing on both qualitative and quantitative research among online and offline samples, as well as taking advantage of recent advances in web survey design. The study's findings will help us better understand the role of the Internet in relation to gay men's sexual practic