A sentence classification framework to identify geometric errors in radiation therapy from relevant literature

The objective of systematic reviews is to address a research question by summarizing relevant studies following a detailed, comprehensive, and transparent plan and search protocol to reduce bias. Systematic reviews are very useful in the biomedical and healthcare domain; however, the data extraction phase of the systematic review process necessitates substantive expertise and is labour-intensive and time-consuming. The aim of this work is to partially automate the process of building systematic radiotherapy treatment literature reviews by summarizing the required data elements of geometric errors of radiotherapy from relevant literature using machine learning and natural language processing (NLP) approaches. A framework is developed in this study that initially builds a training corpus by extracting sentences containing different types of geometric errors of radiotherapy from relevant publications. The publications are retrieved from PubMed following a given set of rules defined by a domain expert. Subsequently, the method develops a training corpus by extracting relevant sentences using a sentence similarity measure. A support vector machine (SVM) classifier is then trained on this training corpus to extract the sentences from new publications which contain relevant geometric errors. To demonstrate the proposed approach, we have used 60 publications containing geometric errors in radiotherapy to automatically extract the sentences stating the mean and standard deviation of different types of errors between planned and executed radiotherapy. The experimental results show that the recall and precision of the proposed framework are, respectively, 97% and 72%. The results clearly show that the framework is able to extract almost all sentences containing required data of geometric errors

A parallel volume of fluid-Lagrangian Parcel Tracking coupling procedure for diesel spray modelling

A parallel computing Eulerian/Lagrangian multi-scale coupling procedure for diesel spray simulation is presented. Early breakup of the diesel jet is captured by using a compressible Volume of Fluid (VOF) method. In regions where the phase interface can no longer be sufficiently resolved, separated and small scale liquid structures are described by a Lagrangian Parcel Tracking (LPT) approach, in conjunction with secondary breakup modelling and a turbulence stochastic dispersion model. The coupling of these two descriptions utilises a Region Coupling Method and an efficiently parallelised droplet identification and extraction procedure. This approach enables run-time VOF-LPT field coupling and filters small-scale liquid structures that are suitable candidates for Eulerian-liquid-structure/Lagrangian droplet conversion, preserving their position, mass and momentum. The coupling procedure is initially applied to model the atomisation of a simple liquid jet and the results are compared with that of a statistical coupling approach to demonstrate the performance of the developed coupling procedure. Its application is then extended to simulate a real diesel spray from a nozzle with a sharp entrance. Coupling in-nozzle phenomena such as flow separation, flow detachment and turbulence to the primary and secondary spray atomisation, provides a tool for the prediction of complex spray dynamics

Analysis of diesel spray dynamics using a compressible Eulerian/VOF/LES model and microscopic shadowgraphy

This paper presents numerical and experimental analysis of diesel engine spray dynamics in the region very close to the nozzle exit. Diesel fuel is injected through a single solid cone injector with sharp-edged nozzle inlet. Numerical investigations are conducted in an Eulerian framework by applying a Volume of Fluid interface capturing technique integrated with Large-Eddy Simulation turbulence modelling. Cavitation is modelled, by allowing liquid fuel to flash to gas at the fuel vapor pressure. The computational domain and settings mimic the experimental injector internal geometry and experimental operating conditions. In-nozzle disturbances are qualitatively well modelled by implementing the no-slip condition at the injector walls as well as cavitation and compressibility effects for each phase. A mesh dependency study is conducted with four different grid resolutions. Data are presented around the start of penetration (SOP) and up to the time when shock waves at the gas-liquid interface are well developed, the quasi-steady stage of injection. At SOP, an umbrella-shaped leading edge is captured in both the numerical and experimental studies however only the experimental images demonstrated a semi-transparent cloud of air-fuel mixture at the leading edge. A previously undescribed toroidal starting vortex near the nozzle exit is captured experimentally and numerically. Development of cavitation, down to the end of nozzle hole leads to the detachment of liquid from the nozzle hole walls and subsequently the diminution of boundary layer effects and thus reduced in-nozzle turbulence, and increased liquid jet velocity

Two-microphone spatial filtering provides speech reception benefits for cochlear implant users in difficult acoustic environments

This article introduces and provides an assessment of a spatial-filtering algorithm based on two closely-spaced (∼1 cm) microphones in a behind-the-ear shell. The evaluated spatial-filtering algorithm used fast (∼10 ms) temporal-spectral analysis to determine the location of incoming sounds and to enhance sounds arriving from straight ahead of the listener. Speech reception thresholds (SRTs) were measured for eight cochlear implant (CI) users using consonant and vowel materials under three processing conditions: An omni-directional response, a dipole-directional response, and the spatial-filtering algorithm. The background noise condition used three simultaneous time-reversed speech signals as interferers located at 90°, 180°, and 270°. Results indicated that the spatial-filtering algorithm can provide speech reception benefits of 5.8 to 10.7 dB SRT compared to an omni-directional response in a reverberant room with multiple noise sources. Given the observed SRT benefits, coupled with an efficient design, the proposed algorithm is promising as a CI noise-reduction solution.National Institutes of Health (U.S.) (Grant R01 DC 000117)National Institutes of Health (U.S.) (Grant R01 DC DC7152)National Institutes of Health (U.S.) (Grant 2R44DC010524-02

Howard Florey, Alexander Fleming and the fairy tale of penicillin

The document attached has been archived with permission from the editor of the Medical Journal of Australia. An external link to the publisher’s copy is included.The public myth of the discovery of penicillin is an archetypal "quest story" of the type common to every human culture. But the real story of the discovery, testing and refinement of penicillin is a complex tale of accident, serendipity, oversight, conflict, the pressure of war, idiosyncratic personalities and even - the invention of history.Peter D Goldsworthy and Alexander C McFarlan

Collection of Epithelial Cells from Rodent Mammary Gland Via Laser Capture Microdissection Yielding High-Quality RNA Suitable for Microarray Analysis

Laser capture microdissection (LCM) enables collection of cell populations highly enriched for specific cell types that have the potential of yielding critical information about physiological and pathophysiological processes. One use of cells collected by LCM is for gene expression profiling. Samples intended for transcript analyses should be of the highest quality possible. RNA degradation is an ever-present concern in molecular biological assays, and LCM is no exception. This paper identifies issues related to preparation, collection, and processing in a lipid-rich tissue, rodent mammary gland, in which the epithelial to stromal cell ratio is low and the stromal component is primarily adipocytes, a situation that presents numerous technical challenges for high-quality RNA isolation. Our goal was to improve the procedure so that a greater probe set present call rate would be obtained when isolated RNA was evaluated using Affymetrix microarrays. The results showed that the quality of RNA isolated from epithelial cells of both mammary gland and mammary adenocarcinomas was high with a probe set present call rate of 65% and a high signal-to-noise ratio

Gene Expression Analysis of In Vivo Fluorescent Cells

BACKGROUND: The analysis of gene expression for tissue homogenates is of limited value because of the considerable cell heterogeneity in tissues. However, several methods are available to isolate a cell type of interest from a complex tissue, the most reliable one being Laser Microdissection (LMD). Cells may be distinguished by their morphology or by specific antigens, but the obligatory staining often results in RNA degradation. Alternatively, particular cell types can be detected in vivo by expression of fluorescent proteins from cell type-specific promoters. METHODOLOGY/PRINCIPAL FINDINGS: We developed a technique for fixing in vivo fluorescence in brain cells and isolating them by LMD followed by an optimized RNA isolation procedure. RNA isolated from these cells was of equal quality as from unfixed frozen tissue, with clear 28S and 18S rRNA bands of a mass ratio of approximately 2ratio1. We confirmed the specificity of the amplified RNA from the microdissected fluorescent cells as well as its usefulness and reproducibility for microarray hybridization and quantitative real-time PCR (qRT-PCR). CONCLUSIONS/SIGNIFICANCE: Our technique guarantees the isolation of sufficient high quality RNA obtained from specific cell populations of the brain expressing soluble fluorescent marker, which is a critical prerequisite for subsequent gene expression studies by microarray analysis or qRT-PCR

CRF-Like Diuretic Hormone Negatively Affects Both Feeding and Reproduction in the Desert Locust, Schistocerca gregaria

Diuretic hormones (DH) related to the vertebrate Corticotropin Releasing Factor (CRF) have been identified in diverse insect species. In the migratory locust, Locusta migratoria, the CRF-like DH (CRF/DH) is localized in the same neurosecretory cells as the Ovary Maturating Parsin (OMP), a neurohormone that stimulates oocyte growth, vitellogenesis and hemolymph ecdysteroid levels in adult female locusts. In this study, we investigated whether CRF-like DH can influence feeding and reproduction in the desert locust, Schistocerca gregaria. We identified two highly similar S. gregaria CRF-like DH precursor cDNAs, each of which also encodes an OMP isoform. Alignment with other insect CRF-like DH precursors shows relatively high conservation of the CRF/DH sequence while the precursor region corresponding to OMP is not well conserved. Quantitative real-time RT-PCR revealed that the precursor transcripts mainly occur in the central nervous system and their highest expression level was observed in the brain. Injection of locust CRF/DH caused a significantly reduced food intake, while RNAi knockdown stimulated food intake. Therefore, our data indicate that CRF-like DH induces satiety. Furthermore, injection of CRF/DH in adult females retarded oocyte growth and caused lower ecdysteroid titers in hemolymph and ovaries, while RNAi knockdown resulted in opposite effects. The observed effects of CRF/DH may be part of a wider repertoire of neurohormonal activities, constituting an integrating control system that affects food intake and excretion, as well as anabolic processes like oocyte growth and ecdysteroidogenesis, following a meal. Our discussion about the functional relationship between CRF/DH and OMP led to the hypothesis that OMP may possibly act as a monitoring peptide that can elicit negative feedback effects