XMDS2: Fast, scalable simulation of coupled stochastic partial differential equations

XMDS2 is a cross-platform, GPL-licensed, open source package for numerically integrating initial value problems that range from a single ordinary differential equation up to systems of coupled stochastic partial differential equations. The equations are described in a high-level XML-based script, and the package generates low-level optionally parallelised C++ code for the efficient solution of those equations. It combines the advantages of high-level simulations, namely fast and low-error development, with the speed, portability and scalability of hand-written code. XMDS2 is a complete redesign of the XMDS package, and features support for a much wider problem space while also producing faster code.Comment: 9 pages, 5 figure

Different forms of the bovine PrP gene have five or six copies of a short, G-C-rich element within the protein-coding exon

Current models of the virus-like agents of scrapie and bovine spongiform encephalopathy (BSE) have to take into account that structural changes in a host-encoded protein (PrP protein) exhibit an effect on the time course of these diseases and the survival time of any man or animal exposed to these pathogens. We report here the sequence of different forms of the bovine PrP gene which contain either five or six copies of a short, G-C-rich element which encodes the octapeptide Pro-His-Gly-Gly-Gly-Trp-Gly-Gln or its longer variants Pro-Gln/His-Gly-Gly-Gly-Gly-Trp-Gly-Gln. Out of 12 cattle, we found eight animals homozygous for genes with six copies of the Gly-rich peptide (6:6), while four were heterozygous (6:5). Two confirmed cases of BSE occurred in (6: 6) homozygous animals. Bovine spongiform encephalopathy (BSE) is a transmissible disease (Fraser et al., 1988; Dawson et al., 1990; Barlow & Middleton, 1990) which produces neuropathological lesions in cattle similar to those seen in ovine scrapie (Wells et al., 1987) and the rare human dementias Creutzfeldt-Jakob disease (CJD) and Gerstmann-Str/iussler syndrome (GSS) (Beck & Daniel, 1987). A cellular membrane protein (PrP) has a key role in the transmission and development of these diseases. This protein accumulates in the brain and other tissues during the protracted time course of these diseases and, in a disease-specific, protease-resistant isoform (SAF-PrP), has been purified by subcellular fractionation of scrapie

Multimode quantum limits to the linewidth of an atom laser

The linewidth of an atom laser can be limited by excitation of higher energy modes in the source Bose-Einstein condensate, energy shifts in that condensate due to the atomic interactions, or phase diffusion of the lasing mode due to those interactions. The first two are effects that can be described with a semiclassical model, and have been studied in detail for both pumped and unpumped atom lasers. The third is a purely quantum statistical effect, and has been studied only in zero dimensional models. We examine an unpumped atom laser in one dimension using a quantum field theory using stochastic methods based on the truncated Wigner approach. This allows spatial and statistical effects to be examined simultaneously, and the linewidth limit for unpumped atom lasers is quantified in various limits.Comment: 8 Figure

Multi-decadal financial assessment of groundwater services for low-income households in rural Kenya

Sustainable financing of groundwater-based drinking water supplies in rural Africa poses one of the biggest obstacles to the global Sustainable Development Goal of safely managed water for all by 2030. Hand-pumped groundwater is the chief mode of supplying safe drinking water to rural populations in Africa, yet around one in three systems is non-functional in part due to a failure of users to pay the costs of ongoing operation and maintenance. Yet there is little empirical evidence about what factors determine rural communities’ capacity to collect revenue from users, and the implications this has for the operational sustainability of services and the water source choices of users. We present findings from a unique study that assesses community-based financing of groundwater services in Kwale (Kenya), the location for one of the first ever large-scale programmes involving handpump-equipped boreholes in rural Africa. The study draws on longitudinal financial records kept by 100 water user groups over three decades, coupled with hydrogeological, community, and household-level data collected from over 500 waterpoints and 3,000 households. We find that among those communities collecting fees on a monthly basis, around one in four households fails to pay in the long-run. Multivariable regression analysis reveals that waterpoints that (i) are situated close to households, (ii) draw on groundwater with a pH above 6.5, (iii) produce palatable water, and (iv) support productive water use activities have significantly higher levels of payment compliance. Payment levels are also strongly related to rainfall patterns, suggestive of complex and dynamic decisions about water source preferences. Those communities charging water users on a pay-as-you-fetch volumetric basis generate the highest levels of revenue, and this translates into significantly shorter breakdown durations. Yet this revenue collection approach is also associated with a higher proportion of households using unsafe water sources, a pattern that occurs across all wealth strata. We conclude that this points to a tension between groundwater service goals of financial sustainability and inclusive access, a conundrum that must be addressed if safe water for all is to become a reality in rural Africa

An Activity-Based Nanosensor for Traumatic Brain Injury.

Currently, traumatic brain injury (TBI) is detected by medical imaging; however, medical imaging requires expensive capital equipment, is time- and resource-intensive, and is poor at predicting patient prognosis. To date, direct measurement of elevated protease activity has yet to be utilized to detect TBI. In this work, we engineered an activity-based nanosensor for TBI (TBI-ABN) that responds to increased protease activity initiated after brain injury. We establish that a calcium-sensitive protease, calpain-1, is active in the injured brain hours within injury. We then optimize the molecular weight of a nanoscale polymeric carrier to infiltrate into the injured brain tissue with minimal renal filtration. A calpain-1 substrate that generates a fluorescent signal upon cleavage was attached to this nanoscale polymeric carrier to generate an engineered TBI-ABN. When applied intravenously to a mouse model of TBI, our engineered sensor is observed to locally activate in the injured brain tissue. This TBI-ABN is the first demonstration of a sensor that responds to protease activity to detect TBI

Erratum : Squeezing and entanglement delay using slow light

An inconsistency was found in the equations used to calculate the variance of the quadrature fluctuations of a field propagating through a medium demonstrating electromagnetically induced transparency (EIT). The decoherence term used in our original paper introduces inconsistency under weak probe approximation. In this erratum we give the Bloch equations with the correct dephasing terms. The conclusions of the original paper remain the same. Both entanglement and squeezing can be delayed and preserved using EIT without adding noise when the decoherence rate is small.Comment: 1 page, no figur

Paired atom laser beams created via four-wave mixing

A method to create paired atom laser beams from a metastable helium atom laser via four-wave mixing is demonstrated. Radio frequency outcoupling is used to extract atoms from a Bose Einstein condensate near the center of the condensate and initiate scattering between trapped and untrapped atoms. The unequal strengths of the interactions for different internal states allows an energy-momentum resonance which leads to the creation of pairs of atoms scattered from the zero-velocity condensate. The resulting scattered beams are well separated from the main atom laser in the 2-dimensional transverse atom laser profile. Numerical simulations of the system are in good agreement with the observed atom laser spatial profiles, and indicate that the scattered beams are generated by a four-wave mixing process, suggesting that the beams are correlated.Comment: 5 pages, 3 figure

How severe is antibiotic pharmacokinetic variability in critically ill patients and what can be done about it?

The pharmacokinetics (PK) of antimicrobial agents administered to critically ill patients exhibit marked variability. This variability results from pathophysiological changes that occur in critically ill patients. Changes in volume of distribution, clearance, and tissue penetration all affect the drug concentrations at the site of infection. PK-pharmacodynamic indices (fC(max):MIC; AUC(0-24):MIC; fT(>MIC); fC(min):MIC) for both antimicrobial effect and suppression of emergence of resistance are described for many antimicrobial drugs. Changing the regimen by which antimicrobial drugs are delivered can help overcome the PK variability and optimise target attainment. This will deliver optimised antimicrobial chemotherapy to individual critically ill patients. Delivery of beta-lactams antimicrobial agents by infusions, rather than bolus dosing, is effective at increasing the duration of the dosing interval that the drug concentration is above the MIC. Therapeutic drug monitoring, utilising population PK mathematical models with Bayesian estimation, can also be used to optimise regimens following measurement of plasma drug concentrations. Clinical trials are required to establish if patient outcomes can be improved by implementing these techniques. (C) 2014 Elsevier Inc. All rights reserved