The Pandora software development kit for pattern recognition

The development of automated solutions to pattern recognition problems is important in many areas of scientific research and human endeavour. This paper describes the implementation of the Pandora Software Development Kit, which aids the process of designing, implementing and running pattern recognition algorithms. The Pandora Application Programming Interfaces ensure simple specification of the building-blocks defining a pattern recognition problem. The logic required to solve the problem is implemented in algorithms. The algorithms request operations to create or modify data structures and the operations are performed by the Pandora framework. This design promotes an approach using many decoupled algorithms, each addressing specific topologies. Details of algorithms addressing two pattern recognition problems in High Energy Physics are presented: reconstruction of events at a high-energy e+e- linear collider and reconstruction of cosmic ray or neutrino events in a liquid argon time projection chamber.This work was funded in part by the UK Science and Technology Facilities Council and by the European Union under the Advanced European Infrastructures for Detectors and Accelerators (AIDA) project.This is the final version of the article. It first appeared from Springer via http://dx.doi.org/10.1140/epjc/s10052-015-3659-

Effects of Expression of Streptococcus pneumoniae PspC on the Ability of Streptococcus mitis to Evade Complement-Mediated Immunity

Streptococcus pneumoniae and Streptococcus mitis are genetically closely related and both frequently colonise the naso-oropharynx, yet S. pneumoniae is a common cause of invasive infections whereas S. mitis is only weakly pathogenic. We hypothesise that sensitivity to innate immunity may underlie these differences in virulence phenotype. We compared the sensitivity of S. pneumoniae and S. mitis strains to complement-mediated immunity, demonstrating S. mitis strains were susceptible to complement-mediated opsonophagocytosis. S. pneumoniae resistance to complement is partially dependent on binding of the complement regulator Factor H by the surface protein PspC. However, S. mitis was unable to bind factor H. The S. pneumoniae TIGR4 strain pspC was expressed in the S. mitis SK142 strain to create a S. mitis pspC+ strain. Immunoblots demonstrated the S. mitis pspC+ strain expressed PspC, and flow cytometry confirmed this resulted in Factor H binding to S. mitis, reduced susceptibility to complement and improved survival in whole human blood compared to the wild-type S. mitis strain. However, in mouse models the S. mitis pspC+ strain remained unable to establish persistent infection. Unlike S. pneumoniae strains, culture in serum or blood did not support increased CFU of the S. mitis strains. These results suggest S. mitis is highly sensitive to opsonisation with complement partially due to an inability to bind Factor H, but even when complement sensitivity was reduced by expression of pspC, poor growth in physiological fluid limited the virulence of S. mitis in mice

Patients achieving sustained deep remission, deep remission or sustained remission of rheumatoid arthritis are more likely than other responders to maintain remission or low disease activity after dose reduction or withdrawal of etanercept

Background Biologic disease-modifying antirheumatic drugs (bDMARDs) are important options for managing rheumatoid arthritis (RA). Once patients achieve disease control, clinicians may consider dose reduction or withdrawal of the bDMARD. Results from published studies indicate that some patients will maintain remission; however, others will flare. We analyzed data from three etanercept down-titration studies in patients with RA to determine what extent of remission provides the greatest predictability of maintaining remission following dose reduction or discontinuation. Methods Patients with moderate to severe RA from the PRESERVE, PRIZE, and Treat-to-Target (T2T) randomized controlled trials were included. We determined the proportion of patients achieving remission with etanercept at the last time point in the induction period, and sustained remission (last two time points), according to the Disease Activity Score 28-joints (DAS28), the American College of Rheumatology (ACR)/European League Against Rheumatism (EULAR) Boolean criteria, and the clinical disease activity index (CDAI). We also calculated the proportion achieving DAS28 deep remission (DAS28 ≤ 1.98), sustained deep remission (last two time points), and low disease activity (LDA), and LDA according to the CDAI. Then, we evaluated whether they maintained remission or LDA following etanercept dose reduction or withdrawal. Results Patients achieving sustained and/or deep remission were more likely than patients achieving remission or LDA to maintain remission/LDA after etanercept dose reduction or withdrawal. In PRESERVE, the proportions of patients with DAS28 sustained deep remission, deep remission, sustained remission, remission, and LDA who maintained remission following etanercept dose reduction were 81%, 67%, 58%, 56%, and 36%, respectively, P < 0.001 for trend. In PRESERVE, this trend was significant when etanercept was discontinued and when ACR/EULAR Boolean and CDAI remission criteria were used. Although some sample sizes were small, the PRIZE and T2T studies also demonstrated response trends according to ACR/EULAR Boolean and CDAI remission criteria, and T2T demonstrated response trends according to DAS28. Conclusions These results suggest that patients achieving disease control according to a stringent definition, such as sustained ACR/EULAR Boolean or CDAI remission, or a new definition of sustained deep remission by DAS28, have a higher probability of remaining in remission or LDA following etanercept dose reduction or withdrawal

The Pandora multi-algorithm approach to automated pattern recognition in LAr TPC detectors

The development and operation of Liquid Argon Time Projection Chambers (LAr TPCs) for neutrino physics has created a need for new approaches to pattern recognition, in order to fully exploit the superb imaging capabilities offered by this technology. The Pandora Software Development Kit provides functionality to aid the process of designing, implementing and running pattern recognition algorithms. It promotes the use of a multi-algorithm approach to pattern recognition: individual algorithms each address a specific task in a particular topology; a series of many tens of algorithms then carefully builds-up a picture of the event. The input to the Pandora pattern recognition is a list of 2D Hits. The output from the chain of over 70 algorithms is a hierarchy of reconstructed 3D Particles, each with an identified particle type, vertex and direction

Are lay people good at recognising the symptoms of schizophrenia?

©2013 Erritty, Wydell. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.This article has been made available through the Brunel Open Access Publishing Fund.Aim: The aim of this study was to explore the general public’s perception of schizophrenia symptoms and the need to seekhelp for symptoms. The recognition (or ‘labelling’) of schizophrenia symptoms, help-seeking behaviours and public awareness of schizophrenia have been suggested as potentially important factors relating to untreated psychosis. Method: Participants were asked to rate to what extent they believe vignettes describing classic symptoms (positive and negative) of schizophrenia indicate mental illness. They were also asked if the individuals depicted in the vignettes required help or treatment and asked to suggest what kind of help or treatment. Results: Only three positive symptoms (i.e., Hallucinatory behaviour, Unusual thought content and Suspiciousness) of schizophrenia were reasonably well perceived (above 70%) as indicating mental illness more than the other positive or negative symptoms. Even when the participants recognised that the symptoms indicated mental illness, not everyone recommended professional help. Conclusion: There may be a need to improve public awareness of schizophrenia and psychosis symptoms, particularly regarding an awareness of the importance of early intervention for psychosis

Observation of contemporaneous optical radiation from a gamma-ray burst

The origin of gamma-ray bursts (GRBs) has been enigmatic since their discovery. The situation improved dramatically in 1997, when the rapid availability of precise coordinates for the bursts allowed the detection of faint optical and radio afterglows - optical spectra thus obtained have demonstrated conclusively that the bursts occur at cosmological distances. But, despite efforts by several groups, optical detection has not hitherto been achieved during the brief duration of a burst. Here we report the detection of bright optical emission from GRB990123 while the burst was still in progress. Our observations begin 22 seconds after the onset of the burst and show an increase in brightness by a factor of 14 during the first 25 seconds; the brightness then declines by a factor of 100, at which point (700 seconds after the burst onset) it falls below our detection threshold. The redshift of this burst, approximately 1.6, implies a peak optical luminosity of 5 times 10^{49} erg per second. Optical emission from gamma-ray bursts has been generally thought to take place at the shock fronts generated by interaction of the primary energy source with the surrounding medium, where the gamma-rays might also be produced. The lack of a significant change in the gamma-ray light curve when the optical emission develops suggests that the gamma-rays are not produced at the shock front, but closer to the site of the original explosion.Comment: 10 pages, 2 figures. Accepted for publication in Nature. For additional information see http://www.umich.edu/~rotse

Exploring How Eruption Source Parameters Affect Volcanic Radiative Forcing Using Statistical Emulation

The radiative forcing caused by a volcanic eruption is dependent on several eruption source parameters such as the mass of sulfur dioxide (SO2) emitted, the eruption column height, and the eruption latitude. General circulation models with prognostic aerosol and chemistry schemes can be used to investigate how each parameter influences the volcanic forcing. However, the range of multidimensional parameter space that can be explored is restricted because such simulations are computationally expensive. Here we use statistical emulation to explore the radiative impact of eruptions over a wide covarying range of SO2 emission magnitudes, injection heights, and eruption latitudes based on only 30 simulations. We use the emulators to build response surfaces to visualize and predict the sulfate aerosol e-folding decay time, the stratospheric aerosol optical depth, and net radiative forcing of thousands of different eruptions. We find that the volcanic stratospheric aerosol optical depth and net radiative forcing are primarily determined by the mass of SO2 emitted, but eruption latitude is the most important parameter in determining the sulfate aerosol e-folding decay time. The response surfaces reveal joint effects of the eruption source parameters in influencing the net radiative forcing, such as a stronger influence of injection height for tropical eruptions than high-latitude eruptions. We also demonstrate how the emulated response surfaces can be used to find all combinations of eruption source parameters that produce a particular volcanic response, often revealing multiple solutions