Block Coordinate Descent for Sparse NMF

Nonnegative matrix factorization (NMF) has become a ubiquitous tool for data analysis. An important variant is the sparse NMF problem which arises when we explicitly require the learnt features to be sparse. A natural measure of sparsity is the L$_0$ norm, however its optimization is NP-hard. Mixed norms, such as L$_1$/L$_2$ measure, have been shown to model sparsity robustly, based on intuitive attributes that such measures need to satisfy. This is in contrast to computationally cheaper alternatives such as the plain L$_1$ norm. However, present algorithms designed for optimizing the mixed norm L$_1$/L$_2$ are slow and other formulations for sparse NMF have been proposed such as those based on L$_1$ and L$_0$ norms. Our proposed algorithm allows us to solve the mixed norm sparsity constraints while not sacrificing computation time. We present experimental evidence on real-world datasets that shows our new algorithm performs an order of magnitude faster compared to the current state-of-the-art solvers optimizing the mixed norm and is suitable for large-scale datasets

Understanding the Impact of Technology: Learner and School Level Factors

The first part of this report focuses on the factors impacting on learner performance in national tests at primary and secondary level. This was the central research question of this research. The second section focuses on teacher and learner perceptions of their own responses to learning and the learning environment. This was centred on, but not confined to, their school. The institutional structures record the level of development of the schools sampled here and investigate the use of two key technologies – interactive whiteboards and learning platform

A peculiar galaxy appears at redshift 11: properties of a moderate redshift interloper

Laporte et al. (2011) reported a very high redshift galaxy candidate: a lensed J-band dropout (A2667-J1). J1 has a photometric redshift of z=9.6-12, the probability density function for which permits no low or intermediate z solution. We here report new spectroscopic observations of this galaxy with VLT/XShooter, which show clear [OIII]5007AA, Ly-alpha, H-alpha, and H-beta emission and place the galaxy firmly at z=2.082. The oxygen lines contribute only ~25% to the H-band flux, and do not significantly affect the dropout selection of J1. After correcting the broadband fluxes for line emission, we identify two roughly equally plausible natures for A2667-J1: either it is young heavily reddened starburst, or a maximally old system with a very pronounced 4000AA break, upon which a minor secondary burst of star formation is superimposed. Fits show that to make a 3 sigma detection of this object in the B-band (V-band), imaging of depth AB=30.2 (29.5) would be required - despite the relatively bright NIR magnitude, we would need optical data of equivalent depth to the Hubble Ultra Deep Field to rule out the mid-z solution on purely photometric grounds. Assuming that this stellar population can be scaled to the NIR magnitudes of recent HST/WFC3 IR-selected galaxies, we conclude that infeasibly deep optical data AB~32 would be required for the same level of security. There is a population of galaxies at z~2 with continuum colours alone that mimic those of our z=7-12 candidates.Comment: Accepted by Monthly Notices. 5 pages, 2 figure

Vehicle Communication Within Networks - Investigation and Analysis Approach: A Case Study

Today, vehicles are an important source of digital evidence in criminal investigations. Modern day cars store a wealth of digital information, including recent destinations, favorite locations, routes, and personal data, such as call logs, contact lists, SMS messages, pictures, and videos. Moreover, the growth of in-vehicle sensors and event data recorders, which continually provide feedback to automobile manufacturers and third-parties, provide tremendous potential for forensics examiners. Recently, the field of vehicle forensics research has caught the attention of both digital forensics investigators and academics. To date, most relevant research have conventionally focused on digital traces of multimedia and GPS systems found in vehicles. However, today vehicles are manufactured with a vast array of communication options, including Wi-Fi, Bluetooth and NFC (Near Field Communication). Up until recently, these options were reserved only for the more expensive automotive models; nonetheless these capabilities are now available for just about all vehicle models. However, these vehicle communications and their corresponding networks have not been explored in detail as they relate to traditional digital investigations. Consequently, this paper focuses on the communications produced by modern vehicles and identifies relevant and important artefacts. Furthermore, as a case study, we examine types of data that can be captured, and methods used to extract artefacts from this data

Functional plasticity of antibacterial EndoU toxins.

Bacteria use several different secretion systems to deliver toxic EndoU ribonucleases into neighboring cells. Here, we present the first structure of a prokaryotic EndoU toxin in complex with its cognate immunity protein. The contact-dependent growth inhibition toxin CdiA-CTSTECO31 from Escherichia coli STEC_O31 adopts the eukaryotic EndoU fold and shares greatest structural homology with the nuclease domain of coronavirus Nsp15. The toxin contains a canonical His-His-Lys catalytic triad in the same arrangement as eukaryotic EndoU domains, but lacks the uridylate-specific ribonuclease activity that characterizes the superfamily. Comparative sequence analysis indicates that bacterial EndoU domains segregate into at least three major clades based on structural variations in the N-terminal subdomain. Representative EndoU nucleases from clades I and II degrade tRNA molecules with little specificity. In contrast, CdiA-CTSTECO31 and other clade III toxins are specific anticodon nucleases that cleave tRNAGlu between nucleotides C37 and m2 A38. These findings suggest that the EndoU fold is a versatile scaffold for the evolution of novel substrate specificities. Such functional plasticity may account for the widespread use of EndoU effectors by diverse inter-bacterial toxin delivery systems

Heat-induced and spontaneous expression of Hsp70.1Luciferase transgene copies localized on Xp22 in female bovine cells

<p>Abstract</p> <p>Background</p> <p>Expression of several copies of the heat-inducible <it>Hsp70.1Luciferase </it>(<it>LUC</it>) transgene inserted at a single X chromosome locus of a bull (<it>Bos taurus</it>) was assessed in females after X-chromosome inactivation (XCI). Furthermore, impact of the chromosomal environment on the spontaneous expression of these transgene copies before XCI was studied during early development in embryos obtained after in vitro fertilization (IVF), when the locus was carried by the X chromosome inherited from the bull, and after somatic cell nuclear transfer (SCNT) cloning, when the locus could be carried by the inactive Xi or the active Xa chromosome in a female donor cell, or by the (active) X in a male donor cell.</p> <p>Findings</p> <p>Transgene copies were mapped to bovine Xp22. In XX^{<it>LUC </it>}female fibroblasts, i.e. after random XCI, the proportions of late-replicating inactive and early-replicating active X^{<it>LUC </it>}chromosomes were not biased and the proportion of cells displaying an increase in the level of immunostained luciferase protein after heat-shock induction was similar to that in male fibroblasts. Spontaneous transgene expression occurred at the 8-16-cell stage both in transgenic (female) embryos obtained after IVF and in male and female embryos obtained after SCNT.</p> <p>Conclusions</p> <p>The X^{<it>LUC </it>}chromosome is normally inactivated but at least part of the inactivated X-linked <it>Hsp70.1Luciferase </it>transgene copies remains heat-inducible after random XCI in somatic cells. Before XCI, the profile of the transgenes' spontaneous expression is independent of the epigenetic origin of the X^{<it>LUC </it>}chromosome since it is similar in IVF female, SCNT male and SCNT female embryos.</p

Pushing the Scalability of RDF Engines on IoT Edge Devices

Semantic interoperability for the Internet of Things (IoT) is enabled by standards and technologies from the Semantic Web. As recent research suggests a move towards decentralised IoT architectures, we have investigated the scalability and robustness of RDF (Resource Description Framework)engines that can be embedded throughout the architecture, in particular at edge nodes. RDF processing at the edge facilitates the deployment of semantic integration gateways closer to low-level devices. Our focus is on how to enable scalable and robust RDF engines that can operate on lightweight devices. In this paper, we have first carried out an empirical study of the scalability and behaviour of solutions for RDF data management on standard computing hardware that have been ported to run on lightweight devices at the network edge. The findings of our study shows that these RDF store solutions have several shortcomings on commodity ARM (Advanced RISC Machine) boards that are representative of IoT edge node hardware. Consequently, this has inspired us to introduce a lightweight RDF engine, which comprises an RDF storage and a SPARQL processor for lightweight edge devices, called RDF4Led. RDF4Led follows the RISC-style (Reduce Instruction Set Computer) design philosophy. The design constitutes a flash-aware storage structure, an indexing scheme, an alternative buffer management technique and a low-memory-footprint join algorithm that demonstrates improved scalability and robustness over competing solutions. With a significantly smaller memory footprint, we show that RDF4Led can handle 2 to 5 times more data than popular RDF engines such as Jena TDB (Tuple Database) and RDF4J, while consuming the same amount of memory. In particular, RDF4Led requires 10%–30% memory of its competitors to operate on datasets of up to 50 million triples. On memory-constrained ARM boards, it can perform faster updates and can scale better than Jena TDB and Virtuoso. Furthermore, we demonstrate considerably faster query operations than Jena TDB and RDF4J.BMBF, 01IS18025A, Verbundprojekt BIFOLD-BBDC: Berlin Institute for the Foundations of Learning and DataBMBF, 01IS18037A, Verbundprojekt BIFOLD-BZML: Berlin Institute for the Foundations of Learning and DataEC/H2020/661180/EU/A Scalable and Elastic Platform for Near-Realtime Analytics for The Graph of Everything/SMARTE

Damage Mechanism Evaluation of Large-Scale Concrete Structures Affected by Alkali-Silica Reaction Using Pattern Recognition

Alkali-silica reaction has caused damage to concrete structures, endangering structural serviceability and integrity. This is of concern in sensitive structures such as nuclear power plants. In this study, acoustic emission (AE) was employed as a structural health monitoring strategy in large-scale, reinforced concrete specimens affected by alkali-silica reaction with differing boundary conditions resembling the common conditions found in nuclear containments. An agglomerative hierarchical algorithm was utilized to classify the AE data based on energy-frequency based features. The AE signals were transferred into the frequency domain and the energies in several frequency bands were calculated and normalized to the total energy of signals. Principle component analysis was used to reduce feature redundancy. Then the selected principal components were considered as features in an input of the pattern recognition algorithm. The sensor located in the center of the confined specimen registered the largest portion of AE energy release, while in the unconfined specimen the energy is distributed more uniformly. This confirms the results of the volumetric strain, which shows that the expansion in the confined specimen is oriented along the thickness of the specimen

Outbreak of West Nile virus causing severe neurological involvement in children, Nuba Mountains, Sudan, 2002.

An atypical outbreak of West Nile virus (WNV) occurred in Ngorban County, South Kordophan, Sudan, from May to August 2002. We investigated the epidemic and conducted a case-control study in the village of Limon. Blood samples were obtained for cases and controls. Patients with obvious sequelae underwent cerebrospinal fluid (CSF) sampling as well. We used enzyme-linked immunosorbent assay (ELISA) and neutralization tests for laboratory diagnosis and identified 31 cases with encephalitis, four of whom died. Median age was 36 months. Bivariate analysis did not reveal any significant association with the risk factors investigated. Laboratory analysis confirmed presence of IgM antibodies caused by WNV in eight of 13 cases, indicative of recent viral infection. The unique aspects of the WNW outbreak in Sudan, i.e. disease occurrence solely among children and the clinical domination of encephalitis, involving severe neurological sequelae, demonstrate the continuing evolution of WNV virulence. The spread of such a virus to other countries or continents cannot be excluded

Modelling high redshift Lyman-alpha Emitters

We present a new model for high redshift Lyman-Alpha Emitters (LAEs) in the cosmological context which takes into account the resonant scattering of Ly-a photons through expanding gas. The GALICS semi-analytic model provides us with the physical properties of a large sample of high redshift galaxies. We implement a gas outflow model for each galaxy based on simple scaling arguments. The coupling with a library of numerical experiments of Ly-a transfer through expanding or static dusty shells of gas allows us to derive the Ly-a escape fractions and profiles. The predicted distribution of Ly-a photons escape fraction shows that galaxies with a low star formation rate have a f_esc of the order of unity, suggesting that, for those objects, Ly-a may be used to trace the star formation rate assuming a given conversion law. In galaxies forming stars intensely, the escape fraction spans the whole range from 0 to 1. The model is able to get a good match to the UV and Ly-a luminosity function (LF) data at 3 < z < 5. We find that we are in good agreement with both the bright Ly-a data and the faint population observed by Rauch et al. (2008) at z=3. Most of the Ly-a profiles of our LAEs are redshifted by the diffusion in the outflow which suppresses IGM absorption. The bulk of the observed Ly-a equivalent width (EW) distribution is recovered by our model, but we fail to obtain the very large values sometimes detected. Predictions for stellar masses and UV LFs of LAEs show a satisfactory agreement with observational estimates. The UV-brightest galaxies are found to show only low Ly-a EWs in our model, as it is reported by many observations of high redshift LAEs. We interpret this effect as the joint consequence of old stellar populations hosted by UV-bright galaxies, and high HI column densities that we predict for these objects, which quench preferentially resonant Ly-a photons via dust extinction.Comment: 17 pages, 12 figures, 3 tables, accepted for publication in MNRA