A stochastic SICA epidemic model for HIV transmission

We propose a stochastic SICA epidemic model for HIV transmission, described by stochastic ordinary differential equations, and discuss its perturbation by environmental white noise. Existence and uniqueness of the global positive solution to the stochastic HIV system is proven, and conditions under which extinction and persistence in mean hold, are given. The theoretical results are illustrated via numerical simulations.Comment: This is a preprint of a paper whose final and definite form is with 'Applied Mathematics Letters', ISSN 0893-9659. Submitted 22/Jan/2018; Revised 03/May/2018; Accepted for publication 03/May/201

Open Charm and Beauty at Ultrarelativistic Heavy Ion Colliders

Important goals of RHIC and LHC experiments with ion beams include the creation and study of new forms of matter, such as the Quark Gluon Plasma. Heavy quark production and attenuation will provide unique tomographic probes of that matter. We predict the suppression pattern of open charm and beauty in $Au+Au$ collisions at RHIC and LHC energies based on the DGLV formalism of radiative energy loss. A cancelation between effects due to the $\sqrt{s}$ energy dependence of the high $p_T$ slope and heavy quark energy loss is predicted to lead to surprising similarity of heavy quark suppression at RHIC and LHC.Comment: 4 pages, 6 *.eps files combined into 4 figure

Practical quantum realization of the ampere from the electron charge

One major change of the future revision of the International System of Units (SI) is a new definition of the ampere based on the elementary charge \emph{e}. Replacing the former definition based on Amp\`ere's force law will allow one to fully benefit from quantum physics to realize the ampere. However, a quantum realization of the ampere from \emph{e}, accurate to within $10^{-8}$ in relative value and fulfilling traceability needs, is still missing despite many efforts have been spent for the development of single-electron tunneling devices. Starting again with Ohm's law, applied here in a quantum circuit combining the quantum Hall resistance and Josephson voltage standards with a superconducting cryogenic amplifier, we report on a practical and universal programmable quantum current generator. We demonstrate that currents generated in the milliampere range are quantized in terms of $ef_\mathrm{J}$ ($f_\mathrm{J}$ is the Josephson frequency) with a measurement uncertainty of $10^{-8}$. This new quantum current source, able to deliver such accurate currents down to the microampere range, can greatly improve the current measurement traceability, as demonstrated with the calibrations of digital ammeters. Beyond, it opens the way to further developments in metrology and in fundamental physics, such as a quantum multimeter or new accurate comparisons to single electron pumps.Comment: 15 pages, 4 figure

Clonal st131-h22 escherichia coli strains from a healthy pig and a human urinary tract infection carry highly similar resistance and virulence plasmids

© 2019 The Authors. The interplay between food production animals, humans and the environment with respect to the transmission of drugresistant pathogens is widely debated and poorly understood. Pandemic uropathogenic Escherichia coli ST131-H30Rx, with conserved fluoroquinolone and cephalosporin resistance, are not frequently identified in animals. However, the phylogenetic precursor lineage ST131-H22 in animals and associated meat products is being reported with increasing frequency. Here we characterized two highly related ST131-H22 strains, one from a healthy pig and the other from a human infection (in 2007 and 2009, respectively). We used both long and short genome sequencing and compared them to ST131-H22 genome sequences available in public repositories. Even within the context of H22 strains, the two strains in question were highly related, separated by only 20 core SNPs. Furthermore, they were closely related to a faecal strain isolated in 2010 from a geographically distinct, healthy human in New South Wales, Australia. The porcine and hospital strains carried highly similar HI2-ST3 multidrug resistant plasmids with differences in the hospital strain arising due to IS-mediated insertions and rearrangements. Near identical ColV plasmids were also present in both strains, further supporting their shared evolutionary history. This work highlights the importance of adopting a One Health approach to genomic surveillance to gain insights into pathogen evolution and spread

Magnetic and electric contributions to the energy loss in a dynamical QCD medium

The computation of radiative energy loss in a finite size QCD medium with dynamical constituents is a key ingredient for obtaining reliable predictions for jet quenching in ultra-relativistic heavy ion collisions. It was previously shown that energy loss in dynamical QCD medium is significantly higher compared to static QCD medium. To understand this difference, we here analyze magnetic and electric contributions to energy loss in dynamical QCD medium. We find that the significantly higher energy loss in the dynamical case is entirely due to appearance of magnetic contribution in the dynamical medium. While for asymptotically high energies, the energy loss in static and dynamical medium approach the same value, we find that the physical origin of the energy loss in these two cases is different.Comment: 6 pages, 4 figure

Genomic analysis of multidrug-resistant Escherichia coli ST58 causing urosepsis

© 2018 Sequence type 58 (ST58) phylogroup B1 Escherichia coli have been isolated from a wide variety of mammalian and avian hosts but are not noted for their ability to cause serious disease in humans or animals. Here we determined the genome sequences of two multidrug-resistant E. coli ST58 strains from urine and blood of one patient using a combination of Illumina and Single Molecule, Real-Time (SMRT) sequencing. Both ST58 strains were clonal and were characterised as serotype O8:H25, phylogroup B1 and carried a complex resistance locus/loci (CRL) that featured an atypical class 1 integron with a dfrA5 (trimethoprim resistance) gene cassette followed by only 24 bp of the 3ʹ-CS. CRL that carry this particular integron have been described previously in E. coli from cattle, pigs and humans in Australia. The integron abuts a copy of Tn6029, an IS26-flanked composite transposon encoding blaTEM, sul2 and strAB genes that confer resistance to ampicillin, sulfathiazole and streptomycin, respectively. The CRL resides within a novel Tn2610-like hybrid Tn1721/Tn21 transposon on an IncF, ColV plasmid (pSDJ2009-52F) of 138 553 bp that encodes virulence associated genes implicated in life-threatening extraintestinal pathogenic E. coli (ExPEC) infections. Notably, pSDJ2009-52F shares high sequence identity with pSF-088-1, a plasmid reported in an E. coli ST95 strain from a patient with blood sepsis from a hospital in San Francisco. These data suggest that extraintestinal infections caused by E. coli carrying ColV-like plasmids, irrespective of their phylogroup or ST, may pose a potential threat to human health, particularly to the elderly and immunocompromised

A comparison of three dual drainage models: Shallow Water vs Local Inertial vs Diffusive Wave

This is the author accepted manuscript. The final version is available from IWA Publishing via the DOI in this record.In this study we compared three overland flow models, a full dynamic model (SWE), a local inertial equations model (GWM), and a diffusive wave model (PDWAVE). The three models are coupled with the same full dynamic sewer network model (SIPSON). We adopted the volume exchange between sewer and overland flow models, and the hydraulic head and discharge rates at the linked manholes to evaluate differences between the models. For that purpose we developed a novel methodology based on RGB scale. The test results of a real case study show a close agreement between coupled models in terms of the extents of flooding, depth and volume exchanged, despite highly complex flows and geometries. The diffusive wave model gives slightly higher maximum flood depths and a slower propagation of the flood front when compared to the other two models. The Local inertial model shows to slight extent higher depths downstream as the wave front is slower than the one in the fully dynamic model. Overall, the simplified overland models can produce comparable results to fully dynamic models with less computational costThis research is partially funded by the FCT (Portuguese Foundation for Science and Technology) through the Doctoral Grant SFRH/BD/81869/2011 financed through the POPH/FSE program (Programa Operacional Potencial Humano/Fundo Social Europeu). This study had the support of the Portuguese Foundation for Science and Technology (FCT) Project UID/MAR/04292/2013 and the UK’s Natural Environment Research Council (NERC) Project Susceptibility of catchments to INTense RAinfall and flooding (SINATRA, NE/K008765/1)

Multidrug resistant uropathogenic Escherichia coli ST405 with a novel, composite IS26 transposon in a unique chromosomal location

© 2019 Roy Chowdhury, McKinnon, Liu and Djordjevic. Escherichia coli ST405 is an emerging urosepsis pathogen, noted for carriage of blaCTX-M, blaNDM, and a repertoire of virulence genes comparable with O25b:H4-ST131. Extraintestinal and multidrug resistant E. coli ST405 are poorly studied in Australia. Here we determined the genome sequence of a uropathogenic, multiple drug resistant E. coli ST405 (strain 2009-27) from the mid-stream urine of a hospital patient in Sydney, Australia, using a combination of Illumina and SMRT sequencing. The genome of strain 2009-27 assembled into two unitigs; a chromosome comprising 5,287,472 bp and an IncB/O plasmid, pSDJ2009-27, of 89,176 bp. In silico and phenotypic analyses showed that strain 2009-27 is a serotype O102:H6, phylogroup D ST405 resistant to ampicillin, azithromycin, kanamycin, streptomycin, trimethoprim, and sulphafurazole. The genes encoding resistance to these antibiotics reside within a novel, mobile IS26-flanked transposon, identified here as Tn6242, in the chromosomal gene yjdA. Tn6242 comprises four modules that each carries resistance genes flanked by IS26, including a class 1 integron with dfrA17 and aadA5 gene cassettes, a variant of Tn6029, and mphA. We exploited unique genetic signatures located within Tn6242 to identify strains of ST405 from Danish patients that also carry the transposon in the same chromosomal location. The acquisition of Tn6242 into yjdA in ST405 is significant because it (i) is vertically inheritable; (ii) represents a reservoir of resistance genes that can transpose onto resident/circulating plasmids; and (iii) is a site for the capture of further IS26-associated resistance gene cargo