Phonon transport in large scale carbon-based disordered materials: Implementation of an efficient order-N and real-space Kubo methodology

We have developed an efficient order-N real-space Kubo approach for the calculation of the phonon conductivity which outperforms state-of-the-art alternative implementations based on the Green's function formalism. The method treats efficiently the time-dependent propagation of phonon wave packets in real space, and this dynamics is related to the calculation of the thermal conductance. Without loss of generality, we validate the accuracy of the method by comparing the calculated phonon mean free paths in disordered carbon nanotubes (isotope impurities) with other approaches, and further illustrate its upscalability by exploring the thermal conductance features in large width edge-disordered graphene nanoribbons (up to ~20 nm), which is out of the reach of more conventional techniques. We show that edge-disorder is the most important scattering mechanism for phonons in graphene nanoribbons with realistic sizes and thermal conductance can be reduced by a factor of ~10.Comment: Accepted for publication in Physical Review B - Rapid Communication

Spike sorting for large, dense electrode arrays

Developments in microfabrication technology have enabled the production of neural electrode arrays with hundreds of closely spaced recording sites, and electrodes with thousands of sites are under development. These probes in principle allow the simultaneous recording of very large numbers of neurons. However, use of this technology requires the development of techniques for decoding the spike times of the recorded neurons from the raw data captured from the probes. Here we present a set of tools to solve this problem, implemented in a suite of practical, user-friendly, open-source software. We validate these methods on data from the cortex, hippocampus and thalamus of rat, mouse, macaque and marmoset, demonstrating error rates as low as 5%

Latest results show urgent need to address child restraint use.

Road traffic crashes are the leading cause of morbidity and mortality in children in South Africa (SA), and are preventable through implementing a systems approach to address the causes. Proper education, child passenger legislation and enforcement of the law are priority actions. It is well known that properly employed seatbelts and child restraints reduce the risk of serious injury and death to children. However, despite campaigns such as ‘Arrive Alive’ to increase the use of child restraints, a 2008 observational study conducted by Red Cross War Memorial Children’s Hospital (RCWMH) in Cape Town, SA, found that a majority of adults and children entering the hospital gates did not use such restraints. It is possible that this was because there was no appropriate child restraint law

Spatially Resolved On-Chip Picosecond Pulse Detection Using Graphene

We present an on-chip time domain terahertz (TD-THz) system in which picosecond pulses are generated in low-temperature-grown gallium arsenide (LT-GaAs) and detected in graphene. The detected pulses were found to vary in amplitude, full width at half maximum (FWHM), and DC offset when sampled optically at different locations along a 50-μm-long graphene photoconductive (PC) detector. The results demonstrate the importance of detection location and switch design in graphene-based on-chip PC detectors

Sperm death and dumping in Drosophila

Mating with more than one male is the norm for females of many species. In addition to generating competition between the ejaculates of different males, multiple mating may allow females to bias sperm use. In Drosophila melanogaster, the last male to inseminate a female sires approximately 80% of subsequent progeny. Both sperm displacement, where resident sperm are removed from storage by the incoming ejaculate of the copulating male, and sperm incapacitation, where incoming seminal fluids supposedly interfere with resident sperm, have been implicated in this pattern of sperm use. But the idea of incapacitation is problematic because there are no known mechanisms by which an individual could damage rival sperm and not their own. Females also influence the process of sperm use, but exactly how is unclear. Here we show that seminal fluids do not kill rival sperm and that any 'incapacitation' is probably due to sperm ageing during sperm storage. We also show that females release stored sperm from the reproductive tract (sperm dumping) after copulation with a second male and that this requires neither incoming sperm nor seminal fluids. Instead, males may cause stored sperm to be dumped or females may differentially eject sperm from the previous mating

Coagulated Mineral Adsorbents for Dye Removal, and Their Process Intensification Using an Agitated Tubular Reactor (ATR)

The aim of this study was to understand the efficacy of widely available minerals as dual-function adsorbers and weighter materials, for the removal of toxic azo-type textile dyes when combined with coprecipitation processes. Specifically, the adsorption of an anionic direct dye was measured on various mineral types with and without the secondary coagulation of iron hydroxide (‘FeOOH’) in both a bench-scale stirred tank, as well as an innovative agitated tubular reactor (ATR). Talc, calcite and modified bentonite were all able to remove 90–95% of the dye at 100 and 200 ppm concentrations, where the kinetics were fitted to a pseudo second-order rate model and adsorption was rapid (99% of the dye was achieved for all the coagulated systems, where additionally, they produced significantly enhanced settling rates and bed compression. The greatest settling rate (9 mm min−1) and solids content increase (450% w/w) were observed for the calcium carbonate system, which also displayed the most homogenous distribution. This system was selected for scale-up and benchmarking in the ATR. Dye removal and sediment dispersion in the ATR were enhanced with respect to the bench scale tests, although lower settling rates were observed due to the relatively high shear rate of the agitator. Overall, results highlight the applicability of these cost-effective minerals as both dye adsorbers and sludge separation modifiers to accelerate settling and compression in textile water treatment. Additionally, the work indicates the suitability of the ATR as a flexible, modular alternative to traditional stirred tank reactors

A realistic assessment of methods for extracting gene/protein interactions from free text

Background: The automated extraction of gene and/or protein interactions from the literature is one of the most important targets of biomedical text mining research. In this paper we present a realistic evaluation of gene/protein interaction mining relevant to potential non-specialist users. Hence we have specifically avoided methods that are complex to install or require reimplementation, and we coupled our chosen extraction methods with a state-of-the-art biomedical named entity tagger. Results: Our results show: that performance across different evaluation corpora is extremely variable; that the use of tagged (as opposed to gold standard) gene and protein names has a significant impact on performance, with a drop in F-score of over 20 percentage points being commonplace; and that a simple keyword-based benchmark algorithm when coupled with a named entity tagger outperforms two of the tools most widely used to extract gene/protein interactions. Conclusion: In terms of availability, ease of use and performance, the potential non-specialist user community interested in automatically extracting gene and/or protein interactions from free text is poorly served by current tools and systems. The public release of extraction tools that are easy to install and use, and that achieve state-of-art levels of performance should be treated as a high priority by the biomedical text mining community

Micro-Electro-Mechanical-Systems (MEMS) and Fluid Flows

The micromachining technology that emerged in the late 1980s can provide micron-sized sensors and actuators. These micro transducers are able to be integrated with signal conditioning and processing circuitry to form micro-electro-mechanical-systems (MEMS) that can perform real-time distributed control. This capability opens up a new territory for flow control research. On the other hand, surface effects dominate the fluid flowing through these miniature mechanical devices because of the large surface-to-volume ratio in micron-scale configurations. We need to reexamine the surface forces in the momentum equation. Owing to their smallness, gas flows experience large Knudsen numbers, and therefore boundary conditions need to be modified. Besides being an enabling technology, MEMS also provide many challenges for fundamental flow-science research

Risk Factors for Norovirus, Sapporo-like Virus, and Group A Rotavirus Gastroenteritis

Viral pathogens are the most common causes of gastroenteritis in the community. To identify modes of transmission and opportunities for prevention, a case-control study was conducted and risk factors for gastroenteritis attributable to norovirus (NV), Sapporo-like virus (SLV), and rotavirus were studied. For NV gastroenteritis, having a household member with gastroenteritis, contact with a person with gastroenteritis outside the household, and poor food-handling hygiene were associated with illness (population attributable risk fractions [PAR] of 17%, 56%, and 47%, respectively). For SLV gastroenteritis, contact with a person with gastroenteritis outside the household was associated with a higher risk (PAR 60%). For rotavirus gastroenteritis, contact with a person with gastroenteritis outside the household and food-handling hygiene were associated with a higher risk (PAR 86% and 46%, respectively). Transmission of these viral pathogens occurs primarily from person to person. However, for NV gastroenteritis, foodborne transmission seems to play an important role