Establishing an EGFR mutation screening service for non-small cell lung cancer - sample quality criteria and candidate histological predictors.

INTRODUCTION: EGFR screening requires good quality tissue, sensitivity and turn-around time (TAT). We report our experience of routine screening, describing sample type, TAT, specimen quality (cellularity and DNA yield), histopathological description, mutation result and clinical outcome. METHODS: Non-small cell lung cancer (NSCLC) sections were screened for EGFR mutations (M+) in exons 18-21. Clinical, pathological and screening outcome data were collected for year 1 of testing. Screening outcome alone was collected for year 2. RESULTS: In year 1, 152 samples were tested, most (72%) were diagnostic. TAT was 4.9 days (95%confidence interval (CI)=4.5-5.5). EGFR-M+ prevalence was 11% and higher (20%) among never-smoking women with adenocarcinomas (ADCs), but 30% of mutations occurred in current/ex-smoking men. EGFR-M+ tumours were non-mucinous ADCs and 100% thyroid transcription factor (TTF1+). No mutations were detected in poorly differentiated NSCLC-not otherwise specified (NOS). There was a trend for improved overall survival (OS) among EGFR-M+ versus EGFR-M- patients (median OS=78 versus 17 months). In year 1, test failure rate was 19%, and associated with scant cellularity and low DNA concentrations. However 75% of samples with poor cellularity but representative of tumour were informative and mutation prevalence was 9%. In year 2, 755 samples were tested; mutation prevalence was 13% and test failure only 5.4%. Although samples with low DNA concentration (2.2 ng/μL), the mutation rate was 9.2%. CONCLUSION: Routine epidermal growth factor receptor (EGFR) screening using diagnostic samples is fast and feasible even on samples with poor cellularity and DNA content. Mutations tend to occur in better-differentiated non-mucinous TTF1+ ADCs. Whether these histological criteria may be useful to select patients for EGFR testing merits further investigation.

Vitamin D binding protein isoforms as candidate predictors of disease extension in childhood arthritis

Introduction: Juvenile idiopathic arthritis (JIA) comprises a poorly understood group of chronic autoimmune diseases with variable clinical outcomes. We investigated whether the synovial fluid (SF) proteome could distinguish a subset of patients in whom disease extends to affect a large number of joints.

Methods: SF samples from 57 patients were obtained around time of initial diagnosis of JIA, labeled with Cy dyes and separated by two-dimensional electrophoresis. Multivariate analyses were used to isolate a panel of proteins which distinguish patient subgroups. Proteins were identified using MALDI-TOF mass spectrometry with expression verified by immunochemical methods. Protein glycosylation status was confirmed by hydrophilic interaction liquid chromatography.

Results: A truncated isoform of vitamin D binding protein (VDBP) is present at significantly reduced levels in the SF of oligoarticular patients at risk of disease extension, relative to other subgroups (p < 0.05). Furthermore, sialylated forms of immunopurified synovial VDBP were significantly reduced in extended oligoarticular patients (p < 0.005).

Conclusion: Reduced conversion of VDBP to a macrophage activation factor may be used to stratify patients to determine risk of disease extension in JIA patients.

Glycosylation of Vitamin D Binding Protein Reduced in Juvenile Idiopathic Arthritis Patients At Risk of Disease Extension.

Background/Purpose:Juvenile idiopathic arthritis (JIA) comprises a poorly understood group of chronic, childhood onset, autoimmune diseases with variable clinical outcomes. We investigated whether profiling of the synovial fluid (SF) proteome by a fluorescent dye based, two-dimensional gel (DIGE) approach could distinguish the subset of patients in whom inflammation extends to affect a large number of joints, early in the disease process. The post-translational modifications to candidate protein markers were verified by a novel deglycosylation strategy.Methods:SF samples from 57 patients were obtained around time of initial diagnosis of JIA. At 1 year from inclusion patients were categorized according to ILAR criteria as oligoarticular arthritis (n=26), extended oligoarticular (n=8) and polyarticular disease (n=18). SF samples were labeled with Cy dyes and separated by two-dimensional electrophoresis. Multivariate analyses were used to isolate a panel of proteins which distinguish patient subgroups. Proteins were identified using MALDI-TOF mass spectrometry with vitamin D binding protein (VDBP) expression and siaylation further verified by immunohistochemistry, ELISA test and immunoprecipitation. Candidate biomarkers were compared to conventional inflammation measure C-reactive protein (CRP). Sialic acid residues were enzymatically cleaved from immunopurified SF VDBP, enriched by hydrophilic interaction liquid chromatography (HILIC) and analysed by mass spectrometry.Results:Hierarchical clustering based on the expression levels of a set of 23 proteins segregated the extended-to-be oligoarticular from the oligoarticular patients. A cleaved isoform of VDBP, spot 873, is present at significantly reduced levels in the SF of oligoarticular patients at risk of disease extension, relative to other subgroups (p<0.05). Conversely total levels of vitamin D binding protein are elevated in plasma and ROC curves indicate an improved diagnostic sensitivity to detect patients at risk of disease extension, over both spot 873 and CRP levels. Sialysed forms of intact immunopurified VDBP were more prevalent in persistent oligoarticular patient synovial fluids.Conclusion:The data indicate that a subset of the synovial fluid proteome may be used to stratify patients to determine risk of disease extension. Reduced conversion of VDBP to a macrophage activation factor may represent a novel pathway contributing to increased risk of disease extension in JIA patients.

A Planetary Nebula around Nova V458 Vulpeculae Undergoing Flash Ionization

Nova V458 Vul erupted on 2007 August 8 and reached a visual magnitude of 8.1 a few days later. Ha images obtained 6 weeks before the outburst as part of the IPHAS Galactic plane survey reveal an 18th magnitude progenitor surrounded by an extended nebula. Subsequent images and spectroscopy of the nebula reveal an inner nebular knot increasing rapidly in brightness due to flash ionization by the nova event. We derive a distance of 13 kpc based on light travel time considerations, which is supported by two other distance estimation methods. The nebula has an ionized mass of 0.2 Msolar and a low expansion velocity: this rules it out as ejecta from a previous nova eruption, and is consistent with it being a ~14,000 year old planetary nebula, probably the product of a prior common envelope (CE) phase of evolution of the binary system. The large derived distance means that the mass of the erupting WD component of the binary is high. We identify two possible evolutionary scenarios, in at least one of which the system is massive enough to produce a Type Ia supernova upon merging.

Effectiveness of filters in reducing consolidation time in routine laboratory testing

The research reported here is based on the standard laboratory experiments routinely performed in order to measure various geotechnical parameters. These experiments require consolidation of fine-grained samples in triaxial or stress path apparatus. The time required for the consolidation is dependent on the permeability of the soil and the length of the drainage path. The consolidation time is often of the order of several weeks in large clay-dominated samples. Long testing periods can be problematic, as they can delay decisions on design and construction methods. Acceleration of the consolidation process would require a reduction in effective drainage length and this is usually achieved by placing filter drains around the sample. The purpose of the research reported in this paper is to assess if these filter drains work effectively and, if not, to determine what modifications to the filter drains are needed. The findings have shown that use of a double filter reduces the consolidation time several fold.

Children with cerebral palsy: severity and trends over time

Increasingly, more very-low-birthweight infants in the developed world are now expected to survive the neonatal period than was previously the case. There are concerns that there may be a related increase in the number of infants developing severe sensorimotor impairments. Pooled data from five registers contributing to the UK Network of Cerebral Palsy Registers, Surveys and Databases were used to identify patterns of motor impairment in relation to additional impairments and to birthweight, and to assess whether prevalence of cerebral palsy (CP) by birthweight and by severity of motor impairment had changed over time. Low-birthweight infants are at greater risk of developing CP than larger-birthweight babies. The CP rate amongst children with birthweights <2500 g was significantly higher at 16 per 1000 livebirths [95% confidence interval (CI) 14.9, 16.2] than 1.2 per 1000 livebirths [95% CI 11, 1.2] for normal-birthweight children. Despite being at greater risk of developing CP, smaller-birthweight babies are proportionately less likely to develop the most severe forms of motor impairment. Of those born weighing ≥2500 g, 23% compared with 15% weighing <1000 g (P < 0.001) were in the most severely motor impaired group. Severe motor impairment is associated with higher levels of additional impairments. CP rates for each motor impairment group in the 1990s were similar to those in the late 1970s. Rates of CP among infants born below normal birthweight are high but have decreased over time. The CP rate for infants weighing 1000–1499 g at birth decreased from around 180 per 1000 livebirths in 1979 to around 50 per 1000 livebirths from the early 1990s onwards.

Habitat utilization by juvenile hawksbill turtles (Eretmochelys imbricata, Linnaeus, 1766) around a shallow water coral reef

Contemporary studies of sea turtle diving behaviour are generally based upon sophisticated techniques such as the attachment of time depth recorders. However, if the risks of misinterpretation are to be minimized, it is essential that electronic data are analysed in the light of first-hand observations. To this aim, we set out to make observations of juvenile hawksbill turtles (Eretmochelys imbricata , Linnaeus, 1766) foraging and resting in a shallow water coral reef habitat around the granitic Seychelles (4degrees'S, 55degrees'E). Data were collected from six study sites characterized by a shallow reef plateau (

WASP-23b: a transiting hot Jupiter around a K dwarf and its Rossiter-McLaughlin effect

We report the discovery of a new transiting planet in the southern hemisphere. It was found by the WASP-south transit survey and confirmed photometrically and spectroscopically by the 1.2 m Swiss Euler telescope, LCOGT 2m Faulkes South Telescope, the 60 cm TRAPPIST telescope, and the ESO 3.6 m telescope. The orbital period of the planet is 2.94 days. We find that it is a gas giant with a mass of 0.88 ± 0.10 MJ and an estimated radius of 0.96 ± 0.05 RJ. We obtained spectra during transit with the HARPS spectrograph and detect the Rossiter-McLaughlin effect despite its small amplitude. Because of the low signal-to-noise ratio of the effect and a small impact parameter, we cannot place a strong constraint on the projected spin-orbit angle. We find two conflicting values for the stellar rotation. We find, via spectral line broadening, that v sin I = 2.2 ± 0.3 km s-1, while applying another method, based on the activity level using the index log R'_HK, gives an equatorial rotation velocity of only v = 1.35 ± 0.20 km s-1. Using these as priors in our analysis, the planet might be either misaligned or aligned. This result raises doubts about the use of such priors. There is evidence of neither eccentricity nor any radial velocity drift with time. Using WASP-South photometric observations confirmed with LCOGT Faulkes South Telescope, the 60 cm TRAPPIST telescope, the CORALIE spectrograph and the camera from the Swiss 1.2 m Euler Telescope placed at La Silla, Chile, as well as with the HARPS spectrograph, mounted on the ESO 3.6 m, also at La Silla, under proposal 084.C-0185. The data is publicly available at the CDS Strasbourg and on demand to the main author.RV data is only available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/531/A24Appendix is available in electronic form at http://www.aanda.org

A robotic apparatus that dictates torque fields around joints without affecting inherent joint dynamics

This manuscript describes how motor behaviour researchers who are not at the same time expert roboticists may implement an experimental apparatus, which has the ability to dictate torque fields around a single joint on one limb or single joints on multiple limbs without otherwise interfering with the inherent dynamics of those joints. Such an apparatus expands the exploratory potential of the researcher wherever experimental distinction of factors may necessitate independent control of torque fields around multiple limbs, or the shaping of torque fields of a given joint independently of its plane of motion, or its directional phase within that plane. The apparatus utilizes torque motors. The challenge with torque motors is that they impose added inertia on limbs and thus attenuate joint dynamics. We eliminated this attenuation by establishing an accurate mathematical model of the robotic device using the Box-Jenkins method, and cancelling out its dynamics by employing the inverse of the model as a compensating controller. A direct measure of the remnant inertial torque as experienced by the hand during a 50 s period of wrist oscillations that increased gradually in frequency from 1.0 to 3.8 Hz confirmed that the removal of the inertial effect of the motor was effectively complete.

Real-time GPU color-based segmentation of football players

In this paper, we propose a multi-camera application capable of processing high resolution images and extracting features based on colors patterns over graphic processing units (GPU). The goal is to work in real time under the uncontrolled environment of a sport event like a football match. Since football players are composed for diverse and complex color patterns, a Gaussian Mixture Models (GMM) is applied as segmentation paradigm, in order to analyze sport live images and video. Optimization techniques have also been applied over the C++ implementation using profiling tools focused on high performance. Time consuming tasks were implemented over NVIDIA's CUDA platform, and later restructured and enhanced, speeding up the whole process significantly. Our resulting code is around 4-11 times faster on a low cost GPU than a highly optimized C++ version on a central processing unit (CPU) over the same data. Real time has been obtained processing until 64 frames per second. An important conclusion derived from our study is the scalability of the application to the number of cores on the GPU. © 2011 Springer-Verlag.

Influence of the Pacific Decadal Oscillation, El Niño-Southern Oscillation and solar forcing on climate and primary productivity changes in the northeast Pacific

Evidence of 11-year Schwabe solar sunspot cycles, El Niño-Southern Oscillation (ENSO) and the Pacific Decadal Oscillation (PDO) were detected in an annual record of diatomaceous laminated sediments from anoxic Effingham Inlet, Vancouver Island, British Columbia. Radiometric dating and counting of annual varves dates the sediments from AD 1947-1993. Intact sediment slabs were X-rayed for sediment structure (lamina thickness and composition based on gray-scale), and subsamples were examined for diatom abundances and for grain size. Wavelet analysis reveals the presence of ~2-3, ~4.5, ~7 and ~9-12-year cycles in the diatom record and an w11e13 year record in the sedimentary varve thickness record. These cycle lengths suggest that both ENSO and the sunspot cycle had an influence on primary productivity and sedimentation patterns. Sediment grain size could not be correlated to the sunspot cycle although a peak in the grain size data centered around the mid-1970s may be related to the 1976-1977 Pacific climate shift, which occurred when the PDO index shifted from negative (cool conditions) to positive (warm conditions). Additional evidence of the PDO regime shift is found in wavelet and cross-wavelet results for Skeletonema costatum, a weakly silicified variant of S. costatum, annual precipitation and April to June precipitation. Higher spring (April/May) values of the North Pacific High pressure index during sunspot minima suggest that during this time, increased cloud cover and concomitant suppression of the Aleutian Low (AL) pressure system led to strengthened coastal upwelling and enhanced diatom production earlier in the year. These results suggest that the 11-year solar cycle, amplified by cloud cover and upwelling changes, as well as ENSO, exert significant influence on marine primary productivity in the northeast Pacific. The expression of these cyclic phenomena in the sedimentary record were in turn modulated by the phase of PDO, as indicated by the change in period of ENSO and suppression of the solar signal in the record after the 1976-1977 regime shift. © 2013 Elsevier Ltd and INQUA. All rights reserved.

Cheetahs, Acinonyx jubatus, balance turn capacity with pace when chasing prey

Predator–prey interactions are fundamental in the evolution and structure of ecological communities. Our understanding, however, of the strategies used in pursuit and evasion remains limited. Here, we report on the hunting dynamics of the world's fastest land animal, the cheetah, Acinonyx jubatus. Using miniaturized data loggers, we recorded fine-scale movement, speed and acceleration of free-ranging cheetahs to measure how hunting dynamics relate to chasing different sized prey. Cheetahs attained hunting speeds of up to 18.94 m s-1 and accelerated up to 7.5 m s-2 with greatest angular velocities achieved during the terminal phase of the hunt. The interplay between forward and lateral acceleration during chases showed that the total forces involved in speed changes and turning were approximately constant over time but varied with prey type. Thus, rather than a simple maximum speed chase, cheetahs first accelerate to decrease the distance to their prey, before reducing speed 5–8 s from the end of the hunt, so as to facilitate rapid turns to match prey escape tactics, varying the precise strategy according to prey species. Predator and prey thus pit a fine balance of speed against manoeuvring capability in a race for survival.

ALMA hints at the presence of two companions in the disk around HD 100546

HD 100546 is a well-studied Herbig Be star-disk system that likely hosts a close-in companion with compelling observational evidence for an embedded protoplanet at 68 AU. We present ALMA observations of the HD 100546 disk which resolve, for the first time, the gas and dust structure at (sub)mm wavelengths. The CO emission (at 345.795 GHz) originates from an extensive molecular disk (390 AU in radius) whereas the continuum emission is more compact (230 AU in radius) suggesting radial drift of the mm-sized grains. The CO emission is similar in extent to scattered light images indicating well-mixed gas and um-sized grains in the disk atmosphere. Assuming an azimuthally-symmetric disk, the continuum visibilities at long baselines (> 100 klambda) are reproduced by a compact ring with a width of 21 AU centered at 26 AU. An outer component is required to fit the short baselines: assuming a flat brightness distribution, the best-fit model is a ring with a width of 75 AU centered at 190 AU. The influence of a companion and protoplanet on the dust evolution is investigated. The companion at 10 AU facilitates the accumulation of mm-sized grains within a compact ring, ~20-30 AU, by ~10 Myr. The injection of a protoplanet at 1 Myr hastens the ring formation (~1.2 Myr) and also triggers the development of an outer ring (~100-200 AU). These observations provide additional evidence for the presence of a close-in companion and hint at dynamical clearing by a protoplanet at 68 AU.

City visioning and the turn to community:The case of Derry/Londonderry

In the 1980s, urban re-imaging and place marketing were vital elements in the strategies of post-industrial cities aiming to redefine their role, make themselves more competitive and attract global investment and tourists. By the early 1990s, the questionable effects of trickle-down economics on deprived housing estates and the rediscovery of the 'community' as a social partner shifted both the substance and process of vision exercises. This paper examines the experience of building an input into a city vision that aimed to address social and ethno-religious segregation in Derry/Londonderry. Designing a consensus statement for a city that cannot agree its name, was wrecked by bloody violence and has its hinterland fractured by a contested international border, is a difficult and delicate process. The city had a population of 105 800 people in 1998, but is divided by the river Foyle between the mainly Catholic Cityside (to the north and west) and the mainly Protestant Waterside (to the south and east). The analysis connects with the literature on urban policy that emphasises the importance of argumentation and democratic debate in strategic planning and local regeneration (Forester, 1989; Healey, 1996). The paper concludes by arguing that strategies for 'listening' would help to shape a vision that could mobilise community interests around some common urban regional issues and help to promote social and ethno-religious polarisation as mainstream policy concerns.

The Effect of the Secret Ballot on Party System Fragmentation: A Test of Three Competing Arguments

Few studies have examined the impact that the adoption of the secret ballot had on party system fragmentation outside the United States. This article tests arguments maintaining that the adoption of the secret ballot had a negative, positive or nil effect on party system fragmentation. Using time-series cross-sectional data from
several countries adopting the secret ballot around the turn of the twentieth century, the results demonstrate that the adoption of the secret ballot did not hinder – though did not favour, either – the development of multiparty systems.