A Comparison of Parallel Graph Processing Implementations

The rapidly growing number of large network analysis problems has led to the emergence of many parallel and distributed graph processing systems---one survey in 2014 identified over 80. Since then, the landscape has evolved; some packages have become inactive while more are being developed. Determining the best approach for a given problem is infeasible for most developers. To enable easy, rigorous, and repeatable comparison of the capabilities of such systems, we present an approach and associated software for analyzing the performance and scalability of parallel, open-source graph libraries. We demonstrate our approach on five graph processing packages: GraphMat, the Graph500, the Graph Algorithm Platform Benchmark Suite, GraphBIG, and PowerGraph using synthetic and real-world datasets. We examine previously overlooked aspects of parallel graph processing performance such as phases of execution and energy usage for three algorithms: breadth first search, single source shortest paths, and PageRank and compare our results to Graphalytics.Comment: 10 pages, 10 figures, Submitted to EuroPar 2017 and rejected. Revised and submitted to IEEE Cluster 201

Imaging Carrier Inhomogeneities in Ambipolar Tellurene Field Effect Transistors

Developing van der Waals (vdW) homojunction devices requires materials with narrow bandgaps and simultaneously high hole and electron mobilities for bipolar transport, as well as methods to image and study spatial variations in carrier type and associated conductivity with nanometer spatial resolution. Here we demonstrate the general capability of near-field scanning microwave microscopy (SMM) to image and study the local carrier type and associated conductivity in operando by studying ambiploar field effect transistors (FETs) of the 1D vdW material tellurium in 2D form. To quantitatively understand electronic variations across the device, we produce nanometer resolved maps of the local carrier equivalence backgate voltage. We show that the global device conductivity minimum determined from transport measurements does not arise from uniform carrier neutrality, but rather from the continued coexistence of p-type regions at the device edge and n-type regions in the interior of our micron-scale devices. This work both underscores and addresses the need to image and understand spatial variations in the electronic properties of nanoscale devices.Comment: 15 pages, 4 figure

Firm finances, weather derivatives and geography

This paper considers some intellectual, practical and political dimensions of collaboration between human and physical geographers exploring how firms are using relatively new financial products – weather derivatives – to displace any costs of weather-related uncertainty and risk. The paper defines weather derivatives and indicates how they differ from weather insurance products before considering the geo-political, cultural and economic context for their creation. The paper concludes by reflecting on the challenges of research collaboration across the human–physical geography divide and suggests that while such initiatives may be undermined by a range of institutional and intellectual factors, conversations between physical and human geographers remain and are likely to become increasingly pertinent. The creation of a market in weather derivatives raises a host of urgent political and regulatory questions and the confluence of natural and social knowledges, co-existing within and through the geography academy, provides a constructive and creative basis from which to engage with this new market and wider discourses of uneven economic development and climate change

FGF4 retrogene on CFA12 is responsible for chondrodystrophy and intervertebral disc disease in dogs.

Chondrodystrophy in dogs is defined by dysplastic, shortened long bones and premature degeneration and calcification of intervertebral discs. Independent genome-wide association analyses for skeletal dysplasia (short limbs) within a single breed (PBonferroni = 0.01) and intervertebral disc disease (IVDD) across breeds (PBonferroni = 4.0 × 10-10) both identified a significant association to the same region on CFA12. Whole genome sequencing identified a highly expressed FGF4 retrogene within this shared region. The FGF4 retrogene segregated with limb length and had an odds ratio of 51.23 (95% CI = 46.69, 56.20) for IVDD. Long bone length in dogs is a unique example of multiple disease-causing retrocopies of the same parental gene in a mammalian species. FGF signaling abnormalities have been associated with skeletal dysplasia in humans, and our findings present opportunities for both selective elimination of a medically and financially devastating disease in dogs and further understanding of the ever-growing complexity of retrogene biology

Scoping studies to establish the capability and utility of a real-time bioaerosol sensor to characterise emissions from environmental sources

A novel dual excitation wavelength based bioaerosol sensor with multiple fluorescence bands called Spectral Intensity Bioaerosol Sensor (SIBS) has been assessed across five contrasting outdoor environments. The mean concentrations of total and fluorescent particles across the sites were highly variable being the highest at the agricultural farm (2.6 cm−3 and 0.48 cm−3, respectively) and the composting site (2.32 cm−3 and 0.46 cm−3, respectively) and the lowest at the dairy farm (1.03 cm−3 and 0.24 cm−3, respectively) and the sewage treatment works (1.03 cm−3 and 0.25 cm−3, respectively). In contrast, the number-weighted fluorescent fraction was lowest at the agricultural site (0.18) in comparison to the other sites indicating high variability in nature and magnitude of emissions from environmental sources. The fluorescence emissions data demonstrated that the spectra at different sites were multimodal with intensity differences largely at wavelengths located in secondary emission peaks for λex 280 and λex 370. This finding suggests differences in the molecular composition of emissions at these sites which can help to identify distinct fluorescence signature of different environmental sources. Overall this study demonstrated that SIBS provides additional spectral information compared to existing instruments and capability to resolve spectrally integrated signals from relevant biological fluorophores could improve selectivity and thus enhance discrimination and classification strategies for real-time characterisation of bioaerosols from environmental sources. However, detailed lab-based measurements in conjunction with real-world studies and improved numerical methods are required to optimise and validate these highly resolved spectral signatures with respect to the diverse atmospherically relevant biological fluorophores

A Subfield Lattice Attack on Overstretched NTRU Assumptions:Cryptanalysis of Some FHE and Graded Encoding Schemes

International audienc

The N-terminus of Stag1 is required to repress the 2C program by maintaining rRNA expression and nucleolar integrity

Our understanding of how STAG proteins contribute to cell identity and disease have largely been studied from the perspective of chromosome topology and protein-coding gene expression. Here, we show that STAG1 is the dominant paralog in mouse embryonic stem cells (mESCs) and is required for pluripotency. mESCs express a wide diversity of naturally occurring Stag1 isoforms, resulting in complex regulation of both the levels of STAG paralogs and the proportion of their unique terminal ends. Skewing the balance of these isoforms impacts cell identity. We define a novel role for STAG1, in particular its N-terminus, in regulating repeat expression, nucleolar integrity, and repression of the two-cell (2C) state to maintain mESC identity. Our results move beyond protein-coding gene regulation via chromatin loops to new roles for STAG1 in nucleolar structure and function, and offer fresh perspectives on how STAG proteins, known to be cancer targets, contribute to cell identity and disease

Rapid quantification of the malaria biomarker hemozoin by improved biocatalytically initiated precipitation atom transfer radical polymerizations

The fight against tropical diseases such as malaria requires the development of innovative biosensing techniques. Diagnostics must be rapid and robust to ensure prompt case management and to avoid further transmission. The malaria biomarker hemozoin can catalyze atom transfer radical polymerizations (ATRP), which we exploit in a polymerization-amplified biosensing assay for hemozoin based on the precipitation polymerization of N-isopropyl acrylamide (NIPAAm). The reaction conditions are systematically investigated using synthetic hemozoin to gain fundamental understanding of the involved reactions and to greatly reduce the amplification time, while maintaining the sensitivity of the assay. The use of excess ascorbate allows oxygen to be consumed in situ but leads to the formation of reactive oxygen species and to the decomposition of the initiator 2-hydroxyethyl 2-bromoisobutyrate (HEBIB). Addition of sodium dodecyl sulfate (SDS) and pyruvate results in better differentiation between the blank and hemozoin-containing samples. Optimized reaction conditions (including reagents, pH, and temperature) reduce the amplification time from 37 ± 5 min to 3 ± 0.5 min while maintaining a low limit of detection of 1.06 ng mL-1. The short amplification time brings the precipitation polymerization assay a step closer to a point-of-care diagnostic device for malaria. Future efforts will be dedicated to the isolation of hemozoin from clinical sample

Reconstruction of primary vertices at the ATLAS experiment in Run 1 proton–proton collisions at the LHC

This paper presents the method and performance of primary vertex reconstruction in proton–proton collision data recorded by the ATLAS experiment during Run 1 of the LHC. The studies presented focus on data taken during 2012 at a centre-of-mass energy of √s=8 TeV. The performance has been measured as a function of the number of interactions per bunch crossing over a wide range, from one to seventy. The measurement of the position and size of the luminous region and its use as a constraint to improve the primary vertex resolution are discussed. A longitudinal vertex position resolution of about 30μm is achieved for events with high multiplicity of reconstructed tracks. The transverse position resolution is better than 20μm and is dominated by the precision on the size of the luminous region. An analytical model is proposed to describe the primary vertex reconstruction efficiency as a function of the number of interactions per bunch crossing and of the longitudinal size of the luminous region. Agreement between the data and the predictions of this model is better than 3% up to seventy interactions per bunch crossing