Accurate, Fast and Scalable Kernel Ridge Regression on Parallel and Distributed Systems

We propose two new methods to address the weak scaling problems of KRR: the Balanced KRR (BKRR) and K-means KRR (KKRR). These methods consider alternative ways to partition the input dataset into p different parts, generating p different models, and then selecting the best model among them. Compared to a conventional implementation, KKRR2 (optimized version of KKRR) improves the weak scaling efficiency from 0.32% to 38% and achieves a 591times speedup for getting the same accuracy by using the same data and the same hardware (1536 processors). BKRR2 (optimized version of BKRR) achieves a higher accuracy than the current fastest method using less training time for a variety of datasets. For the applications requiring only approximate solutions, BKRR2 improves the weak scaling efficiency to 92% and achieves 3505 times speedup (theoretical speedup: 4096 times).Comment: This paper has been accepted by ACM International Conference on Supercomputing (ICS) 201

Microstructural characterization of AISI 431 martensitic stainless steel laser-deposited coatings

High cooling rates during laser cladding of stainless steels may alter the microstructure and phase constitution of the claddings and consequently change their functional properties. In this research, solidification structures and solid state phase transformation products in single and multi layer AISI 431 martensitic stainless steel coatings deposited by laser cladding at different processing speeds are investigated by optical microscopy, Scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), orientation imaging microscopy (OIM), ternary phase diagram, Schaeffler and TTT diagrams. The results of this study show how partitionless solidification and higher solidification rates alter the microstructure and phase constitution of martensitic stainless steel laser deposited coatings. In addition, it is shown that while different cladding speeds have no effect on austenite–martensite orientation relationship in the coatings, increasing the cladding speed has resulted in a reduction of hardness in deposited coatings which is in contrast to the common idea about obtaining higher hardness values at higher cladding speeds.

Inflammasome activation causes dual recruitment of NLRC4 and NLRP3 to the same macromolecular complex.

Pathogen recognition by nucleotide-binding oligomerization domain-like receptor (NLR) results in the formation of a macromolecular protein complex (inflammasome) that drives protective inflammatory responses in the host. It is thought that the number of inflammasome complexes forming in a cell is determined by the number of NLRs being activated, with each NLR initiating its own inflammasome assembly independent of one another; however, we show here that the important foodborne pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) simultaneously activates at least two NLRs, whereas only a single inflammasome complex is formed in a macrophage. Both nucleotide-binding domain and leucine-rich repeat caspase recruitment domain 4 and nucleotide-binding domain and leucine-rich repeat pyrin domain 3 are simultaneously present in the same inflammasome, where both NLRs are required to drive IL-1β processing within the Salmonella-infected cell and to regulate the bacterial burden in mice. Superresolution imaging of Salmonella-infected macrophages revealed a macromolecular complex with an outer ring of apoptosis-associated speck-like protein containing a caspase activation and recruitment domain and an inner ring of NLRs, with active caspase effectors containing the pro-IL-1β substrate localized internal to the ring structure. Our data reveal the spatial localization of different components of the inflammasome and how different members of the NLR family cooperate to drive robust IL-1β processing during Salmonella infection.S.M.M was supported by a Cambridge International Scholarship. T.P.M was supported by a Wellcome Trust Research Career Development Fellowship (WT085090MA). This study was supported by Biotechnology and Biological Sciences Research Council (BBSRC) grants (BB/H003916/1 and BB/K006436/1) and a BBSRC Research Development Fellowship (BB/H021930/1) awarded to C.E.B.http://www.pnas.org/content/early/2014/05/05/1402911111.abstrac

Actin polymerization as a key innate immune effector mechanism to control Salmonella infection.

Salmonellosis is one of the leading causes of food poisoning worldwide. Controlling bacterial burden is essential to surviving infection. Nucleotide-binding oligomerization domain-like receptors (NLRs), such as NLRC4, induce inflammasome effector functions and play a crucial role in controlling Salmonella infection. Inflammasome-dependent production of IL-1β recruits additional immune cells to the site of infection, whereas inflammasome-mediated pyroptosis of macrophages releases bacteria for uptake by neutrophils. Neither of these functions is known to directly kill intracellular salmonellae within macrophages. The mechanism, therefore, governing how inflammasomes mediate intracellular bacterial-killing and clearance in host macrophages remains unknown. Here, we show that actin polymerization is required for NLRC4-dependent regulation of intracellular bacterial burden, inflammasome assembly, pyroptosis, and IL-1β production. NLRC4-induced changes in actin polymerization are physically manifested as increased cellular stiffness, and leads to reduced bacterial uptake, production of antimicrobial molecules, and arrested cellular migration. These processes act in concert to limit bacterial replication in the cell and dissemination in tissues. We show, therefore, a functional link between innate immunity and actin turnover in macrophages that underpins a key host defense mechanism for the control of salmonellosis.Financial support for this work was provided by a Cambridge International Scholarship (to S.M.M.), European Research Council Starting Investigator Grant “LightTouch” 282060 (to J.R.G.), Biotechnology and Biological Sciences Research Council (BBSRC) Grants BB/H003916/1 and BB/K006436/1 and BBSRC Research Development Fellowship BB/ H021930/1 (to C.E.B.)This is the accepted manuscript. The final version is available from PNAS at http://www.pnas.org/content/111/49/17588.abstract

High genetic diversity at the extreme range edge: nucleotide variation at nuclear loci in Scots pine (Pinus sylvestris L.) in Scotland

Nucleotide polymorphism at 12 nuclear loci was studied in Scots pine populations across an environmental gradient in Scotland, to evaluate the impacts of demographic history and selection on genetic diversity. At eight loci, diversity patterns were compared between Scottish and continental European populations. At these loci, a similar level of diversity (θsil=~0.01) was found in Scottish vs mainland European populations, contrary to expectations for recent colonization, however, less rapid decay of linkage disequilibrium was observed in the former (ρ=0.0086±0.0009, ρ=0.0245±0.0022, respectively). Scottish populations also showed a deficit of rare nucleotide variants (multi-locus Tajima's D=0.316 vs D=−0.379) and differed significantly from mainland populations in allelic frequency and/or haplotype structure at several loci. Within Scotland, western populations showed slightly reduced nucleotide diversity (πtot=0.0068) compared with those from the south and east (0.0079 and 0.0083, respectively) and about three times higher recombination to diversity ratio (ρ/θ=0.71 vs 0.15 and 0.18, respectively). By comparison with results from coalescent simulations, the observed allelic frequency spectrum in the western populations was compatible with a relatively recent bottleneck (0.00175 × 4Ne generations) that reduced the population to about 2% of the present size. However, heterogeneity in the allelic frequency distribution among geographical regions in Scotland suggests that subsequent admixture of populations with different demographic histories may also have played a role

Ultrasonic Monitoring of Recrystallization Textures in Aluminum

The present paper is an attempt to use ultrasonic velocity measurements to characterize the texture of an aluminum-magnesium alloy (Al 5xxx) and to compare the results with orientation imaging microscopy (OIM) results. The results are characterized in terms of three orientation distribution coefficients (ODC’s), W400, W420, and W440, each of which describes a particular forming anisotropy, and each of which has significant impact on the final products

Dependency-aware Attention Control for Unconstrained Face Recognition with Image Sets

This paper targets the problem of image set-based face verification and identification. Unlike traditional single media (an image or video) setting, we encounter a set of heterogeneous contents containing orderless images and videos. The importance of each image is usually considered either equal or based on their independent quality assessment. How to model the relationship of orderless images within a set remains a challenge. We address this problem by formulating it as a Markov Decision Process (MDP) in the latent space. Specifically, we first present a dependency-aware attention control (DAC) network, which resorts to actor-critic reinforcement learning for sequential attention decision of each image embedding to fully exploit the rich correlation cues among the unordered images. Moreover, we introduce its sample-efficient variant with off-policy experience replay to speed up the learning process. The pose-guided representation scheme can further boost the performance at the extremes of the pose variation.Comment: Fixed the unreadable code in CVF version. arXiv admin note: text overlap with arXiv:1707.00130 by other author

The effect of agitation speed, enzyme loading and substrate concentration on enzymatic hydrolysis of cellulose from brewer’s spent grain

Brewer’s spent grain components (cellulose, hemicellulose and lignin) were fractionated in a two-step chemical pretreatment process using dilute sulfuric acid and sodium hydroxide solutions. The cellulose pulp produced was hydrolyzed with a cellulolytic complex, Celluclast 1.5 L, at 45 ºC to convert the cellulose into glucose. Several conditions were examined: agitation speed (100, 150 and 200 rpm), enzyme loading (5, 25 and 45 FPU/g substrate), and substrate concentration (2, 5 and 8% w/v), according to a 2 3 full factorial design aiming to maximize the glucose yield. The obtained results were interpreted by analysis of variance and response surface methodology. The optimal conditions for enzymatic hydrolysis of brewer’s spent grain were identified as 100 rpm, 45 FPU/g and 2% w/v substrate. Under these conditions, a glucose yield of 93.1% and a cellulose conversion (into glucose and cellobiose) of 99.4% was achieved. The easiness of glucose release from BSG makes this substrate a raw material with great potential to be used in bioconversion processes.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo), Brazil. Novozymes ( FAPESP )Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq