Genome sequence of enterovirus D68 from St. Louis, Missouri, USA, 2016

Enterovirus D68 (EV-D68) was rarely observed prior to a widespread outbreak in 2014. We observed its reemergence in St. Louis in 2016 and sequenced the EV-D68 genomes from two patient samples. The 2016 viruses in St. Louis differed from those we had sequenced from the 2014 outbreak but were similar to other viruses circulating nationally in 2016

Large water-hammer pressure for column separation in pipelines

Water-hammer pressures in a pipeline due to the collapse of a vapor cavity adjacent to a valve are investigated. A water-hammer event is initiated by the closure of a valve in a simple reservoir-pipeline-valve system. The sequence of events following an instantaneous valve closure leading to the formation and collapse of a vapor cavity and the resultant occurrence of a short-duration pressure pulse are described. Short-duration pressure pulses result from the superposition of the valve-closure water-hammer wave and the wave generated by the collapse of the vapor cavity. The resulting maximum pressure may exceed the Joukowsky pressure generated from the initial valve closure. A series of numerical model analyses exhibiting short-duration pressure pulses are presented. In addition, experimental results supporting the findings of the numerical studies are also presented. Experimental plots of hydraulic grade line versus time exhibit short-duration pressure pulses of different shape and characteristics.Angus R. Simpson and E. Benjamin Wyli

Whole-genome sequencing of Klebsiella pneumoniae isolates to track strain progression in a single patient with recurrent urinary tract infection

Klebsiella pneumoniae is an important uropathogen that increasingly harbors broad-spectrum antibiotic resistance determinants. Evidence suggests that some same-strain recurrences in women with frequent urinary tract infections (UTIs) may emanate from a persistent intravesicular reservoir. Our objective was to analyze K. pneumoniae isolates collected over weeks from multiple body sites of a single patient with recurrent UTI in order to track ordered strain progression across body sites, as has been employed across patients in outbreak settings. Whole-genome sequencing of 26 K. pneumoniae isolates was performed utilizing the Illumina platform. PacBio sequencing was used to create a refined reference genome of the original urinary isolate (TOP52). Sequence variation was evaluated by comparing the 26 isolate sequences to the reference genome sequence. Whole-genome sequencing of the K. pneumoniae isolates from six different body sites of this patient with recurrent UTI demonstrated 100% chromosomal sequence identity of the isolates, with only a small P2 plasmid deletion in a minority of isolates. No single nucleotide variants were detected. The complete absence of single-nucleotide variants from 26 K. pneumoniae isolates from multiple body sites collected over weeks from a patient with recurrent UTI suggests that, unlike in an outbreak situation with strains collected from numerous patients, other methods are necessary to discern strain progression within a single host over a relatively short time frame.</p

Legacy Data, Radiocarbon Dating and Robustness Reasoning

Archaeologists put a premium on pressing “legacy data” into service, given the notoriously selective and destructive nature of their practices of data capture. Legacy data consist of material and records that been assembled over decades, sometimes centuries, often by means and for purposes long since discredited or superseded. The primary strategies by which archaeologists put the data to work for new purposes are, I argue, secondary retrieval, recontextualization, and experimental modelling. I focus here on a particularly telling and complex example of secondary retrieval: the extraction of new data from old by means of radiocarbon dating. This is by no means a straightforward process of retrieving physical samples from legacy data to which 14C techniques can be applied that can, on their own, decisively settle chronological questions. When Libby’s post-war radiocarbon revolution got under way, it was expected to establish an absolute chronology that would render obsolete the local and relative chronologies on which archaeologists had long relied. Transformative though it has been, bringing these tools of physical dating to bear on archaeological problems has been a long, tortuous process, now described as proceeding through two subsequent radiocarbon revolutions. The second was an extended (and on-going) process of calibration by which 14C chronologies were corrected and refined, often against the very lines of evidence they were meant to displace. The most recent, a “pragmatic Bayesian” approach to archaeological dating, is motivated by concern that, no matter how much it is refined, radiocarbon dating cannot on its own resolve the chronological problems that archaeologists address; the challenge, its advocates argue, is to ‘fully integrate archaeological information with 14C dating in order to address archaeologically relevant (and therefore socially relevant) timescales and episodes’ (Manning 2015: 151). This is a genre of “robustness” reasoning that illustrates its epistemic risks as well as its appeal. As recent philosophical debate makes clear (Soler et al. 2012, Soler 2014), it depends on appeals to the convergence of independent lines of evidence that may have more rhetorical than epistemic force and that may be spurious. Drawing on this philosophical literature I identify a set of conditions that must be met if these risks are to be avoided, all of which are an explicit focus of debate in cases of contestation about and reconciliation of chronologies based on legacy data

Fluctuation Induced Instabilities in Front Propagation up a Co-Moving Reaction Gradient in Two Dimensions

We study 2D fronts propagating up a co-moving reaction rate gradient in finite number reaction-diffusion systems. We show that in a 2D rectangular channel, planar solutions to the deterministic mean-field equation are stable with respect to deviations from planarity. We argue that planar fronts in the corresponding stochastic system, on the other hand, are unstable if the channel width exceeds a critical value. Furthermore, the velocity of the stochastic fronts is shown to depend on the channel width in a simple and interesting way, in contrast to fronts in the deterministic MFE. Thus, fluctuations alter the behavior of these fronts in an essential way. These affects are shown to be partially captured by introducing a density cutoff in the reaction rate. Some of the predictions of the cutoff mean-field approach are shown to be in quantitative accord with the stochastic results

Studies in the Diterpenoid Series

Abstract Not Provided

Equine grass sickness : the geochemical connection

A new study uses the British Geological Survey’s geochemical map to investigate whether minerals in the environment are a factor in this predominantly fatal neurodegenerative disease of horse

Electrochemical methods for the dechlorination and detection of chilorinated ethenes

Chlorinated ethenes in the environment are dechlorinated by accepting electrons from electron donors found in nature. Such reductive dechlorination forms the basis of this research into remediation and detection of these compounds in the environment. The reducing abilities of one of the strongest electron donors known, tetraki s(dimethylamino)ethylene (TDAE), were used to abiotically simulate reductive dechlorination. TDAE was found to form an electron donor-acceptor complex with tetrachloroethene, and to very rapidly reduce trichloroethene and cis-dichloroethene via removal of the most positive chlorine. Microbiological studies of bacteria utilising chlorinated ethenes in their metabolic systems established that Vitamin B,2 (cyanocobalamm) is of great importance to the dechlorination process, acting as a cofactor for the organism's dehalogenase enzyme. The dechlorination mechanism involves cobalt (I) as the active transition metal in extremely reducing conditions. A series of analytical experiments were undertaken to establish the reductive capability of cobalt (I), both in a simple cobalt salt and in vitamin 812, under reducing conditions. Molasses was used as a hydrogen source and an electron donor in simulation of the biotic process. Results indicate that Vitamin B12 is more successful at dechlorination than simple cobalt salts, but neither system presents an ideal method for commercial dechlorination based on current experimental process. Remediation of environmental tetra- and trichloroethene contamination would be improved by the development of on-line sensors. Glutathione, an intracellular sulfhydryl tripeptide comprising glutamyl, cysteinyl, and glycinyl, bonds with alkyl halides via the thiol group in its cysteine moeity, and displays characteristic redox behaviour, presenting an ideal prospective system for development of a relevant biosensor. Potentiometric and amperometric studies have been carried out to determine the efficacy of the proposed system; results indicate that response to and selectivity for alkyl halides at environmental concentrations can be achieved