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.

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.

An in vitro study of the radiobiological effects of flattening filter free radiotherapy treatments

Flattening filter free (FFF) linear accelerators allow for an increase in instantaneous dose-rate of the x-ray pulses by a factor of 2-6 over the conventional flattened output. As a result, radiobiological investigations are being carried out to determine the effect of these higher dose-rates on cell response. The studies reported thus far have presented conflicting results, highlighting the need for further investigation. To determine the radiobiological impact of the increased dose-rates from FFF exposures a Varian Truebeam medical linear accelerator was used to irradiate two human cancer cell lines in vitro, DU-145 prostate and H460 non-small cell lung, with both flattened and FFF 6 MV beams. The fluence profile of the FFF beam was modified using a custom-designed Nylon compensator to produce a similar dose profile to the flattened beam (6X) at the cell surface but at a higher instantaneous dose-rate. For both cell lines there appeared to be no significant change in cell survival. Curve fitting coefficients for DU145 cells irradiated with constant average dose-rates were 6X: alpha = 0.09 +/- 0.03, beta = 0.03 +/- 0.01 and 6FFF: alpha = 0.14 +/- 0.13, beta = 0.03 +/- 0.02 with a significance of p = 0.75. For H460 cells irradiated with the same instantaneous dose-rate but different average dose-rate the fit coefficients were 6FFF (low dose-rate): alpha = 0.21 +/- 0.11, 0.07 +/- 0.02 and 6FFF (high dose-rate): alpha = 0.21 +/- 0.16, 0.07 +/- 0.03, with p = 0.79. The results indicate that collective damage behaviour does not occur at the instantaneous dose-rates investigated here and that the use of either modality should result in the same clinical outcome, however this will require further validation in vivo.

Association Study of 167 Candidate Genes for Schizophrenia Selected by a Multi-Domain Evidence-Based Prioritization Algorithm and Neurodevelopmental Hypothesis

Integrating evidence from multiple domains is useful in prioritizing disease candidate genes for subsequent testing. We ranked all known human genes (n = 3819) under linkage peaks in the Irish Study of High-Density Schizophrenia Families using three different evidence domains: 1) a meta-analysis of microarray gene expression results using the Stanley Brain collection, 2) a schizophrenia protein-protein interaction network, and 3) a systematic literature search. Each gene was assigned a domain-specific p-value and ranked after evaluating the evidence within each domain. For comparison to this
ranking process, a large-scale candidate gene hypothesis was also tested by including genes with Gene Ontology terms related to neurodevelopment. Subsequently, genotypes of 3725 SNPs in 167 genes from a custom Illumina iSelect array were used to evaluate the top ranked vs. hypothesis selected genes. Seventy-three genes were both highly ranked and involved in neurodevelopment (category 1) while 42 and 52 genes were exclusive to neurodevelopment (category 2) or highly ranked (category 3), respectively. The most significant associations were observed in genes PRKG1, PRKCE, and CNTN4 but no individual SNPs were significant after correction for multiple testing. Comparison of the approaches showed an excess of significant tests using the hypothesis-driven neurodevelopment category. Random selection of similar sized genes from two independent genome-wide association studies (GWAS) of schizophrenia showed the excess was unlikely by chance. In a further meta-analysis of three GWAS datasets, four candidate SNPs reached nominal significance. Although gene ranking using integrated sources of prior information did not enrich for significant results in the current experiment, gene selection using an a priori hypothesis (neurodevelopment) was superior to random selection. As such, further development of gene ranking strategies using more carefully selected sources of information is warranted.

AC magnetic heating of superparamagnetic Fe and Co nanoparticles

AC magnetic heating of superparamagnetic Co and Fe nanoparticles for application in hyperthermia was measured to find a size of nanoparticles that would result in an optimal heating for given amplitude and frequency of ac externally applied magnetic field. To measure it, a custom-made power supply connected to a 20-turn insulated copper coil in the shape of a spiral solenoid cooled with water was used. A fiber-optic temperature sensor has been used to measure the temperature with an accuracy of 0.0001 K. The magnetic field with magnitude of 20.6 µT and a frequency of oscillation equal to 348 kHz was generated inside the coil to heat magnetic nanoparticles. The maximum specific power loss or the highest heating rate for Co magnetic nanoparticles was achieved for nanoparticles of 8.2 nm in diameter. The maximum heating rate for coated Fe was found for nanoparticles with diameter of 18.61 nm. © (2013) Trans Tech Publications, Switzerland.

The marginal willingness-to-pay for attributes of a hypothetical HIV vaccine

This paper estimates the marginal willingness-to-pay for attributes of a hypothetical HIV vaccine using discrete choice modeling. We use primary data from 326 respondents from Bangkok and Chiang Mai, Thailand, in 2008–2009, selected using purposive, venue-based sampling across two strata. Participants completed a structured questionnaire and full rank discrete choice modeling task administered using computer-assisted personal interviewing. The choice experiment was used to rank eight hypothetical HIV vaccine scenarios, with each scenario comprising seven attributes (including cost) each of which had two levels. The data were analyzed in two alternative specifications: (1) best-worst; and (2) full-rank, using logit likelihood functions estimated with custom routines in Gauss matrix programming language. In the full-rank specification, all vaccine attributes are significant predictors of probability of vaccine choice. The biomedical attributes of the hypothetical HIV vaccine (efficacy, absence of VISP, absence of side effects, and duration of effect) are the most important attributes for HIV vaccine choice. On average respondents are more than twice as likely to accept a vaccine with 99% efficacy, than a vaccine with 50% efficacy. This translates to a willingness to pay US$383 more for a high efficacy vaccine compared with the low efficacy vaccine. Knowledge of the relative importance of determinants of HIV vaccine acceptability is important to ensure the success of future vaccination programs. Future acceptability studies of hypothetical HIV vaccines should use more finely grained biomedical attributes, and could also improve the external validity of results by including more levels of the cost attribute.

Reconfigurable Architectures for Network Processing

An overview of research on reconfigurable architectures for network processing applications within the Institute of Electronics, Communications and Information Technology (ECIT) is presented. Three key network processing topics, namely node throughput, Quality of Service (QoS) and security are examined where custom reconfigurability allows network nodes to adapt to fluctuating network traffic and customer demands. Various architectural possibilities have been investigated in order to explore the options and tradeoffs available when using reconfigurability for packet/frame processing, packet-scheduling and data encryption/decryption. This research has shown there is no common approach that can be applied. Rather the methodologies used and the cost-benefits for incorporation of reconfigurability depend on each of the functions considered, for example being well suited to encryption/decryption but not packet/frame processing. © 2005 IEEE.