Hybrid address spaces: A methodology for implementing scalable high-level programming models on non-coherent many-core architectures

This paper introduces hybrid address spaces as a fundamental design methodology for implementing scalable runtime systems on many-core architectures without hardware support for cache coherence. We use hybrid address spaces for an implementation of MapReduce, a programming model for large-scale data processing, and the implementation of a remote memory access (RMA) model. Both implementations are available on the Intel SCC and are portable to similar architectures. We present the design and implementation of HyMR, a MapReduce runtime system whereby different stages and the synchronization operations between them alternate between a distributed memory address space and a shared memory address space, to improve performance and scalability. We compare HyMR to a reference implementation and we find that HyMR improves performance by a factor of 1.71× over a set of representative MapReduce benchmarks. We also compare HyMR with Phoenix++, a state-of-art implementation for systems with hardware-managed cache coherence in terms of scalability and sustained to peak data processing bandwidth, where HyMR demon- strates improvements of a factor of 3.1× and 3.2× respectively. We further evaluate our hybrid remote memory access (HyRMA) programming model and assess its performance to be superior of that of message passing.

Rapid design of discrete orthonormal wavelet transforms using silicon IP components

A rapid design methodology for orthonormal wavelet transform cores has been developed. This methodology is based on a generic, scaleable architecture utilising time-interleaved coefficients for the wavelet transform filters. The architecture has been captured in VHDL and parameterised in terms of wavelet family, wavelet type, data word length and coefficient word length. The control circuit is embedded within the cores and allows them to be cascaded without any interface glue logic for any desired level of decomposition. Case studies for stand alone and cascaded silicon cores for single and multi-stage wavelet analysis respectively are reported. The design time to produce silicon layout of a wavelet based system has been reduced to typically less than a day. The cores are comparable in area and performance to handcrafted designs. The designs are portable across a range of foundries and are also applicable to FPGA and PLD implementations.

A New Analysis of Mars "Special Regions": Findings of the Second MEPAG Special Regions Science Analysis Group (SR-SAG2)

A committee of the Mars Exploration Program Analysis Group (MEPAG) has reviewed and updated the description of Special Regions on Mars as places where terrestrial organisms might replicate (per the COSPAR Planetary Protection Policy). This review and update was conducted by an international team (SR-SAG2) drawn from both the biological science and Mars exploration communities, focused on understanding when and where Special Regions could occur. The study applied recently available data about martian environments and about terrestrial organisms, building on a previous analysis of Mars Special Regions (2006) undertaken by a similar team. Since then, a new body of highly relevant information has been generated from the Mars Reconnaissance Orbiter (launched in 2005) and Phoenix (2007) and data from Mars Express and the twin Mars Exploration Rovers (all 2003). Results have also been gleaned from the Mars Science Laboratory (launched in 2011). In addition to Mars data, there is a considerable body of new data regarding the known environmental limits to life on Earth—including the potential for terrestrial microbial life to survive and replicate under martian environmental conditions. The SR-SAG2 analysis has included an examination of new Mars models relevant to natural environmental variation in water activity and temperature; a review and reconsideration of the current parameters used to define Special Regions; and updated maps and descriptions of the martian environments recommended for treatment as “Uncertain” or “Special” as natural features or those potentially formed by the influence of future landed spacecraft. Significant changes in our knowledge of the capabilities of terrestrial organisms and the existence of possibly habitable martian environments have led to a new appreciation of where Mars Special Regions may be identified and protected. The SR-SAG also considered the impact of Special Regions on potential future human missions to Mars, both as locations of potential resources and as places that should not be inadvertently contaminated by human activity. Key Words: Martian environments—Mars astrobiology—Extreme environment microbiology—Planetary protection—Exploration resources. Astrobiology 14, 887–968.

A Case Study of OpenMP applied to Map/Reduce-style Computations

As data analytics are growing in importance they are also quickly becoming one of the dominant application domains that require parallel processing. This paper investigates the applicability of OpenMP, the dominant shared-memory parallel programming model in high-performance computing, to the domain of data analytics. We contrast the performance and programmability of key data analytics benchmarks against Phoenix++, a state-of-the-art shared memory map/reduce programming system. Our study shows that OpenMP outperforms the Phoenix++ system by a large margin for several benchmarks. In other cases, however, the programming model is lacking support for this application domain.

Multi-wavelength observations of Proxima Centauri

Aims: We report simultaneous observations of the nearby flare star Proxima Centauri with VLT/UVES and XMM-Newton over three nights in March 2009. Our optical and X-ray observations cover the star's quiescent state, as well as its flaring activity and allow us to probe the stellar atmospheric conditions from the photosphere into the chromosphere, and then the corona during its different activity stages. Methods: Using the X-ray data, we investigate variations in coronal densities and abundances and infer loop properties for an intermediate-sized flare. The optical data are used to investigate the magnetic field and its possible variability, to construct an emission line list for the chromosphere, and use certain emission lines to construct physical models of Proxima Centauri's chromosphere. Results: We report the discovery of a weak optical forbidden Fe xiii line at 3388 Å during the more active states of Proxima Centauri. For the intermediate flare, we find two secondary flare events that may originate in neighbouring loops, and discuss the line asymmetries observed during this flare in H i, He i, and Ca ii lines. The high time-resolution in the Hα line highlights strong temporal variations in the observed line asymmetries, which re-appear during a secondary flare event. We also present theoretical modelling with the stellar atmosphere code PHOENIX to construct flaring chromospheric models. Based on observations collected at the European Southern Observatory, Paranal, Chile, 082.D-0953A and on observations obtained with XMM-Newton, an ESA science mission with instruments and contributions directly funded by ESA Member states and NASA.Full Table 6 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/534/A133

Fast Rule Mining over Multi-dimensional Windows

Association rule mining is an indispensable tool for discovering
insights from large databases and data warehouses.
The data in a warehouse being multi-dimensional, it is often
useful to mine rules over subsets of data defined by selections
over the dimensions. Such interactive rule mining
over multi-dimensional query windows is difficult since rule
mining is computationally expensive. Current methods using
pre-computation of frequent itemsets require counting
of some itemsets by revisiting the transaction database at
query time, which is very expensive. We develop a method
(RMW) that identifies the minimal set of itemsets to compute
and store for each cell, so that rule mining over any
query window may be performed without going back to the
transaction database. We give formal proofs that the set of
itemsets chosen by RMW is sufficient to answer any query
and also prove that it is the optimal set to be computed
for 1 dimensional queries. We demonstrate through an extensive
empirical evaluation that RMW achieves extremely
fast query response time compared to existing methods, with
only moderate overhead in pre-computation and storage

A novel inhibitor of channel activating proteases: Putting the CAP on ENaC

Background: Excessive activation of epithelial sodium channels (ENaC) contributes to CF lung pathophysiology due to the resultant dehydration of the airway surface liquid (ASL) and impaired mucociliary clearance. Regulated proteolysis of the endogenous α and γ subunits of ENaC by apical membrane-bound Channel Activating Proteases (CAPs) is a fundamental regulatory mechanism for channel activity. In the CF lung a stark imbalance between the levels of CAPs and their natural inhibitors drives the activation of normally inactive ENaC. On this basis inhibition of CAPs-ENaC signalling represents a potential therapeutic intervention. To this end we have developed a novel cell impermeable active-site directed compound (QUB-TL1) designed to inactivate key trypsin-like CAPs highly relevant in this regard. Objectives & Methods: Utilize differentiated non-CF and CF human airway epithelial cells to assess the impact of QUB-TL1 on a range of parameters including surface CAP activities, ENaC subunit processing/channel activity, ASL height and mucociliary clearance. Results: Treatment of airway epithelial cells with QUB-TL1 results in the significant downregulation of key endogenous CAP activities found to be excessively active at the surface of CF cultures. QUB-TL1-mediated CAP inhibition subsequently causes the internalisation of a pool of processed (active) ENaCγ prominent at the apical surface of CF cultures which correlates with a decline in channel activity. This downregulation of ENaC activity results in an increase in ASL height and improved mucociliary clearance in CF cells. We further find QUB-TL1 uniquely inhibits the ENaC activating enzyme furin, which is in contrast to the alternate trypsin-like CAP inhibitors camostat mesylate and aprotinin. QUB-TL1-mediated furin inhibition correlates with a reduction in neutrophil elastase-induced ENaC activation. Moreover we find QUB-TL1 treatment protects CF cultures from Pseudomonas aeruginosa exotoxin A-induced cytotoxicity. Pseudomonas aeruginosa exotoxin A is a major toxic product activated by furin and positively associated with mortality. Conclusion: The novel inhibitor (QUB-TL1) dampens CAPs-ENaC signalling which improves hydration status mucociliary clearance in CF airway epithelial cell cultures. Moreover this compound provides additional benefit by preventing Pseudomonas aeruginosa exotoxin A-induced cytotoxicity.

Utilisation of a novel ProteaseTag™ activity immunoassay for the specific measurement of neutrophil elastase in BAL from children with cystic fibrosis

Introduction: Neutrophil elastase (NE) is a serine protease implicated in the pathogenesis of several respiratory diseases including cystic fibrosis (CF). The presence of free NE in BAL is a predictor of subsequent bronchiectasis in children with CF (Sly et al, 2013, NEJM 368: 1963-1970). Furthermore, children with higher levels of sputum NE activity (NEa) tend to experience a more rapid decline in FEV1 over time even after adjusting for age, gender and baseline FEV1 (Sagel et al, 2012, AJRCCM 186: 857-865). Its detection and quantification in biological samples is however confounded by a lack of robust methodologies. Standard assays using chromogenic or fluorogenic substrates are not specific when added to complex samples containing multiple proteolytic and hydrolytic enzymes. ELISA systems measure total protein levels which can be a mixture of latent, active and protease-inhibitor complexes. We have therefore developed a novel assay (ProteaseTag™ Active NE Immunoassay), which couples an activity dependent NE-Tag with a specific antibody step, resulting in an assay which is both selective and specific for NEa. Aims: To clinically validate ProteaseTag™ Active NE for the detection of free NEa in BAL from children with CF. Methods: A total of 95 paediatric BAL samples [CF (n=76; 44M, 32F) non-CF (n=19; 12M, 7F)] collected through the Study of Host Immunity and Early Lung Disease in CF (SHIELD CF) were analysed for NEa using ProteaseTag™ Active NE (ProAxsis Ltd) and a fluorogenic substrate-based assay utilising Suc-AAPV-AMC (Sigma). IL-8 was measured by ELISA (R&D Systems). Results were analysed to show comparisons in free NEa between CF and non-CF samples alongside correlations with a range of clinical parameters. Results: NEa measured by ProteaseTag™ Active NE correlated significantly with age (r=0.3, p=0.01) and highly significantly with both IL-8 (r=0.4, p=<0.0001) and the absolute neutrophil count (ANC) (r=0.4, p=<0.0001). These correlations were not observed when NEa was measured by the substrate assay even though a significant correlation was found between the two assays (r=0.8, p<0.0001). A trend towards significance was found between NEa in the CF and non-CF groups when measured by ProteaseTag™ Active NE (p=0.07). Highly significant differences were found with the other inflammatory parameters between the 2 groups (IL-8: p=0.0002 and ANC: p=0.006). Conclusion: NEa as a primary efficacy endpoint in clinical trials or as a marker of inflammation within the clinic has been hampered by the lack of a robust and simple to use assay. ProteaseTag™ Active NE has been shown to be a specific and superior tool in the measurement of NEa in paediatric CF BAL samples (supporting data from previous studies using adult CF expectorated samples). The technology is currently being transferred to a lateral flow device for use at Point of Care. Acknowledgements: This work was supported by the National Children’s Research Centre, Dublin (SHIELD CF) and grants from the Medical Research Council and Cystic Fibrosis Foundation Therapeutics.

Learning Bayesian Networks with Bounded Tree-Width via Guided Search

Bounding the tree-width of a Bayesian network can reduce the chance of overfitting, and allows exact inference to be performed efficiently. Several existing algorithms tackle the problem of learning bounded tree-width Bayesian networks by learning from k-trees as super-structures, but they do not scale to large domains and/or large tree-width. We propose a guided search algorithm to find k-trees with maximum Informative scores, which is a measure of quality for the k-tree in yielding good Bayesian networks. The algorithm achieves close to optimal performance compared to exact solutions in small domains, and can discover better networks than existing approximate methods can in large domains. It also provides an optimal elimination order of variables that guarantees small complexity for later runs of exact inference. Comparisons with well-known approaches in terms of learning and inference accuracy illustrate its capabilities.

Experiencing Youth Justice and Penality

Much of the recent literature on youth justice has focused on administrative aspects of the system and the socio-political contexts that have led to the ‘production’ of the youthful offender as a subject and locus of intervention. This has largely been driven by the extent to which youth justice has been crafted as a distinct penal sphere, evident in its unyoking from universal children’s services (Muncie and Goldson, 2013) and the establishment of separate agencies to administer and govern this ‘system’ (Souhami, 2014). Driven by policy hyperactivity and a plethora of legislation expanding the reach of the system, for much of the 1990s and 2000s increasing numbers of young people were brought under its gaze.

Particular attention has been paid to the impact of neo-liberal governance on the discourses, rationales and philosophies underpinning contemporary youth justice policy and practice. Writing specifically in the English and Welsh context, several authors have identified that the resulting ‘system’ embodies multiple, contradictory and competing discourses (Muncie, 2006; Fergusson, 2007; Gray, 2013). Within this ‘melting pot’ Fergusson (2007) notes the disjuncture between policy rhetoric, implementation and lived experience and Phoenix (2015) argues that systems-based analyses, much in favour amongst academics, foreclose a wider consideration of questions of what ‘justice’ actually means.

Recent attention towards the perspectives of practitioners working in this sphere has pointed to greater nuances than broader penal narratives suggest (see: Field, 2007; Briggs, 2013; Gray, 2013; Kelly and Armitage, 2015). Yet similar attention has not been given to experiences of youth justice (for an exception see – Phoenix and Kelly, 2013). However, it is precisely young people’s experiences, which would add significantly to current knowledge and potentially bridge the gap between discussions about penal philosophies, how youth justice policies are framed, how they are enacted and how they are experienced.

This chapter provides an overview of recent developments in the field of youth justice and penality in the United Kingdom. The chapter argues that a theoretical focus on macro-level trends (Hannah-Moffat and Lynch, 2012), alongside a narrowly defined research agenda, have largely excluded young people’s experiences of justice and punishment from contemporary analysis. Drawing on young people experiences of different aspects of youth justice in Northern Ireland and beyond, the chapter illuminates what a close understanding of lived experience can add to knowledge. In particular it demonstrates that the effects of interventions can be different to their aims and intentions; and that re-instating the youth experience can add support to calls for greater attention to wider issues of social justice.

Evaluation of the protective effect of Phlomis purpurea against Phytophthora cinnamomi in Fagaceae and of root metabolites involved

Tese de doutoramento, Ciências Agrárias (Proteção de Plantas), Faculdade de Ciência e Tecnologia, Universidade do Algarve, 2014

Correction of transmitter gain and phase errors at the receiver

This paper explores the benefits of compensating transmitter gain and phase inbalances in the receiver for quadrature communication systems. It is assumed that the gain and phase imbalances are introduced at the transmitter only. A simple non-data aided DSP algorithm is used at the reciever to compensate for the imbalances. Computer simulation has been formed to study a coherent QPSK communication system.

Walls of Indifference: Arizona and the Ecology of Militarization

Thesis (Ph.D.)--University of Washington, 2013