In-vitro investigation of out-of-field cell survival following the delivery of conformal, intensity-modulated radiation therapy (IMRT) and volumetric modulated arc therapy (VMAT) plans

The aim of this work is to determine the out-of-field survival of cells irradiated with either the primary field or scattered radiation in the presence and absence of intercellular communication following delivery of conformal, IMRT and VMAT treatment plans. Single beam, conformal, IMRT and VMAT plans were created to deliver 3 Gy to half the area of a T80 flask containing either DU-145 or AGO-1522 cells allowing intercellular communication between the in-and out-of-field cell populations. The same plans were delivered to a similar custom made phantom used to hold two T25 culture flasks, one flask in-field and one out-of-field to allow comparison of cell survival responses when intercellular communication is physically inhibited. Plans were created for the delivery of 8 Gy to the more radio-resistant DU-145 cells only in the presence and absence of intercellular communication. Cell survival was determined by clonogenic assay. In both cell lines, the out-of-field survival was not statistically different between delivery techniques for either cell line or dose. There was however, a statistically significant difference between survival out-of-field when intercellular communication was intact (single T80 culture flask) or inhibited (multiple T25 culture flasks) to in-field for all plans. No statistically significant difference was observed in-field with or without cellular communication to out-of-field for all plans. These data demonstrate out-of-field effects as important determinants of cell survival following exposure to modulated irradiation fields when cellular communication between differentially irradiated cell populations is present. This data is further evidence that refinement of existing radiobiological models to include indirect cell killing effects is required.

Profiling excretory/secretory proteins of Trichinella spiralis muscle larvae by two-dimensional gel electrophoresis and mass spectrometry

Infection of mammalian skeletal muscle with the intracellular parasite Trichinella spiralis results in profound alterations in the host cell and a realignment of host cell gene expression. The role of parasite excretory/secretory (E/S) products in mediating these effects is unknown, largely due to the difficulty in identifying and assigning function to individual proteins. In this study, we have used two-dimensional electrophoresis to analyse the profile of muscle larva excreted/secreted proteins and have coupled this to protein identification using MALDI-TOF mass spectrometry. Interpretation of the peptide mass fingerprint data has relied primarily on the interrogation of a custom-made Trichinella EST database and the NemaGene cluster database for T. spiralis. Our results suggest that this proteomic approach is a useful tool to study protein expression in Trichinella spp. and will contribute to the identification of excreted/secreted proteins.

Popular Culture, 1600-1914

A review of changes in language, custom, amusements during Ulster's transition from a rural to an urban industrial society

CO2 uptake by a soil microcosm

Sequestration of CO2 via biological sinks is a matter of great scientific importance due to the potential lowering of atmospheric CO2. In this study, a custom built incubation chamber was used to cultivate a soil microbial community to instigate chemoautotrophy of a temperate soil. Real-time atmospheric CO2 concentrations were monitored and estimations of total CO2 uptake were made. After careful background flux corrections, 4.52 +/- 0.05 g CO2 kg I dry soil was sequestered from the chamber atmosphere over 40 h. Using isotopically labelled (CO2)-C-13 and GCMS-IRMS, labelled fatty acids were identified after only a short incubation, hence confirming CO2 sequestration for soil. The results of this in vivo study provide the ground work for future studies intending to mimic the in situ environment by providing a reliable method for investigating CO2 uptake by soil microorganisms.(C) 2012 Elsevier Ltd. All rights reserved.

NuGO contributions to GenePattern

NuGO, the European Nutrigenomics Organization, utilizes 31 powerful computers for, e.g., data storage and analysis. These so-called black boxes (NBXses) are located at the sites of different partners. NuGO decided to use GenePattern as the preferred genomic analysis tool on each NBX. To handle the custom made Affymetrix NuGO arrays, new NuGO modules are added to GenePattern. These NuGO modules execute the latest Bioconductor version ensuring up-to-date annotations and access to the latest scientific developments. The following GenePattern modules are provided by NuGO: NuGOArrayQualityAnalysis for comprehensive quality control, NuGOExpressionFileCreator for import and normalization of data, LimmaAnalysis for identification of differentially expressed genes, TopGoAnalysis for calculation of GO enrichment, and GetResultForGo for retrieval of information on genes associated with specific GO terms. All together, these NuGO modules allow comprehensive, up-to-date, and user friendly analysis of Affymetrix data. A special feature of the NuGO modules is that for analysis they allow the use of either the standard Affymetrix or the MBNI custom CDF-files, which remap probes based on current knowledge. In both cases a .chip-file is created to enable GSEA analysis. The NuGO GenePattern installations are distributed as binary Ubuntu (.deb) packages via the NuGO repository.

Off-center explosions of Chandrasekhar-mass white dwarfs:An explanation of super-bright type la supernovae?

Context. The recent discovery of a very bright type la supernova, SNLS-03D3bb (=SN 2003fg), in the Supernova Legacy Survey (SNLS) has raised the question of whether super-Chandrasekhar-mass white-dwarf stars are needed to explain such bright explosions. Progenitors of this sort could form by mergers of pairs of rather massive white dwarfs. Binary systems of two white dwarfs in close orbit, where their total mass significantly exceeds the Chandrasekhar mass, have not yet been found. Therefore SNLS-03D3bb could establish the first clear case of a double-degenerate progenitor of a (peculiar) type la supernovae. Moreover, if this interpretation is correct, it casts some doubt on the universality of the calibration relations used to make SNe la distance indicators for cosmology. Aims. We aim to evaluate the case for a super-Chandrasekhar-mass progenitor for SNLS-03D3bb in light of previous theoretical work on super-Chandrasekhar-mass explosions. Furthermore, we propose an alternative scenario involving only a Chandrasekhar-mass progenitor. Methods. We present a theoretically motivated critical discussion of the expected observational fingerprints of super-Chandrasekharmass explosions. As an alternative, we describe a simple class of aspherical Chandrasekhar-mass models in which the products of nuclear burning are displaced from the center. We then perform simple radiative transfer calculations to predict synthetic lightcurves for one such off-center explosion model. Results. In important respects, the expected observational consequences of super-Chandrasekhar-mass explosions are not consistent with the observations of SNLS-03D3bb. We demonstrate that the lopsided explosion of a Chandrasekhar-mass white dwarf could provide a better explanation. © ESO 2007.

Initial validation of the Behavioral Indicators of Infant Pain (BIIP)

Accurate pain assessment in preterm infants in the neonatal intensive care unit (NICU) is complex. Infants who are born at early gestational ages (GA), and who have had greater early pain exposure, have dampened facial responses which may lead to under-treatment. Since behavioral and physiological responses to pain in infants are often dissociated, using multidimensional scales which combine these indicators into a single score may limit our ability to determine the effects of interventions on each system. Our aim was to design a unidimensional scale which would combine the relatively most specific, individual, behavioral indicators for assessing acute pain in this population. The Behavioral Indicators of Infant Pain (BIIP) combines sleep/wake states, 5 facial actions and 2 hand actions. Ninety-two infants born between 23 and 32 weeks GA were assessed during 3, 1 min Phases of blood collection. Outcome measures included changes in BIIP and in Neonatal Infant Pain Scale (NIPS) scores coded in real time from continuous bedside video recordings; changes in heart rate (HR) were obtained using custom physiological processing software. Scores on the BIIP changed significantly across Phases of blood collection (p

Bedside application of the Neonatal Facial Coding System in pain assessment of premature neonates

Assessment of infant pain is a pressing concern, especially within the context of neonatal intensive care where infants may be exposed to prolonged and repeated pain during lengthy hospitalization. In the present study the feasibility of carrying out the complete Neonatal Facial Coding System (NFCS) in real time at bedside, specifically reliability, construct and concurrent validity, was evaluated in a tertiary level Neonatal Intensive Care Unit (NICU). Heel lance was used as a model of procedural pain, and observed with n = 40 infants at 32 weeks gestational age. Infant sleep/wake state, NFCS facial activity and specific hand movements were coded during baseline, unwrap, swab, heel lance, squeezing and recovery events. Heart rate was recorded continuously and digitally sampled using a custom designed computer system. Repeated measures analysis of variance (ANOVA) showed statistically significant differences across events for facial activity (P <0.0001) and heart rate (P <0.0001). Planned comparisons showed facial activity unchanged during baseline, swab and unwrap, then increased significantly during heel lance (P <0.0001), increased further during squeezing (P <0.003), then decreased during recovery (P <0.0001). Systematic shifts in sleep/wake state were apparent. Rise in facial activity was consistent with increased heart rate, except that facial activity more closely paralleled initiation of the invasive event. Thus facial display was more specific to tissue damage compared with heart rate. Inter-observer reliability was high. Construct validity of the NFCS at bedside was demonstrated as invasive procedures were distinguished from tactile. While bedside coding of behavior does not permit raters to be blind to events, mechanical recording of heart rate allowed for an independent source of concurrent validation for bedside application of the NFCS scale.

Efficacy of a powered wheelchair simulator for school aged children: A randomised controlled trial.

Purpose: To determine the efficacy of a custom made wheelchair simulation in training children to use a powered wheelchair (PWC). Design: Randomised controlled trial employing the 4C/ID-model of learning. Twenty-eight typically developing children (13M, 15F; mean age 6 years, SD 6 months) were assessed on their operation of a PWC using a functional evaluation rating scale. Participants were randomly assigned to intervention (8x 30minute training sessions using a joystick operated wheelchair simulation) or control conditions (no task), and were re-assessed on their PWC use following the intervention phase. Additional data from the simulation on completion times, errors and total scores were recorded for the intervention group. Results: Analysis of variance showed a main effect of time, with planned comparisons revealing a statistically significant change in PWC use for the intervention (p = 0.022) but not the control condition. Whilst the intervention group showed greater improvement than the controls this did not reach statistical significance. Multiple regression analyses showed that gender was predictive of pre-test (p = 0.005) functional ability. Implications: A simulated wheelchair task appears to be effective in helping children learn to operate a PWC. Greater attention should be given to female learners who underperformed when compared to their male counterparts. This low cost intervention could be easily employed at home to reduce PWC training times in children with motor disorders.

Generic low-latency NoC router architecture for FPGA computing systems

A novel cost-effective and low-latency wormhole router for packet-switched NoC designs, tailored for FPGA, is presented. This has been designed to be scalable at system level to fully exploit the characteristics and constraints of FPGA based systems, rather than custom ASIC technology. A key feature is that it achieves a low packet propagation latency of only two cycles per hop including both router pipeline delay and link traversal delay - a significant enhancement over existing FPGA designs - whilst being very competitive in terms of performance and hardware complexity. It can also be configured in various network topologies including 1-D, 2-D, and 3-D. Detailed design-space exploration has been carried for a range of scaling parameters, with the results of various design trade-offs being presented and discussed. By taking advantage of abundant buildin reconfigurable logic and routing resources, we have been able to create a new scalable on-chip FPGA based router that exhibits high dimensionality and connectivity. The architecture proposed can be easily migrated across many FPGA families to provide flexible, robust and cost-effective NoC solutions suitable for the implementation of high-performance FPGA computing systems. © 2011 IEEE.

Incidence of glaucoma in patients with uveitis

Purpose: To evaluate the incidence of glaucoma and elevation of intraocular pressure (IOP) in patients with inflammatory eye disease. Methods: Retrospective review of medical records of 391 consecutive patients with uveitis attending a uveitis clinic of an academic Department of Ophthalmology from January 1999 to August 2002. Demographic, ocular and systemic variables were recorded. The diagnosis and treatment of uveitis were recorded. Uveitis was classified according to standard anatomic, etiological and clinical criteria. "Glaucoma" was defined as elevated IOP (>21 mm Hg) or glaucomatous optic nerve damage requiring medical and/or surgical anti-glaucoma treatment. Kaplan-Maier analysis and log-rank tests were used to evaluate and compare the incidence of glaucoma. Results: The incidence of glaucoma as defined above at 3 and 12 months after acute uveitis was 7.6%. In patients with chronic uveitis (n = 337), the incidence of glaucoma at 1 and 5 years was 6.5% and 11.1%, respectively. There was no statistically significant difference in the incidence of glaucoma between different types of uveitis, idiopathic versus non-idiopathic, and among anterior, intermediate, posterior and panuveitis. Visual loss occurred more frequently in patients with glaucoma than in patients without glaucoma. Conclusion: In patients with chronic inflammatory eye disease, the presence of glaucoma was associated with an increasing risk of visual loss. The incidence of glaucoma increased with time and was similar among the different types of uveitis.

In vitro o-antigen ligase assay

WaaL is a membrane enzyme that catalyzes the glycosidic bonding of a sugar at the proximal end of the undecaprenyl-diphosphate (Und-PP)-O-antigen with a terminal sugar of the lipid A-core oligosaccharide (OS). This is a critical step in lipopolysaccharide synthesis. We describe here an assay to perform the ligation reaction in vitro utilizing native substrates.

In Vitro UDP-Sugar:Undecaprenyl-Phosphate Sugar-1-Phosphate Transferase Assay and Product Detection by Thin Layer Chromatography

In vitro assays are invaluable for the biochemical characterization of UDP-sugar:undecaprenyl-phosphate sugar-1-phosphate transferases. These assays typically involve the use of a radiolabeled substrate and subsequent extraction of the product, which resides in a lipid environment. Here, we describe the preparation of bacterial membranes containing these enzymes, a standard in vitro transferase assay with solvents containing chloroform and methanol, and two methods to measure product formation: scintillation counting and thin layer chromatography.