Anomaly detection on streamed data

We introduce powerful but simple methodology for identifying anomalous observations against a corpus of `normal' observations. All data are observed through a vector-valued feature map. Our approach depends on the choice of corpus and that feature map but is invariant to affine transformations of the map and has no other external dependencies, such as choices of metric; we call it conformance. Applying this method to (signatures) of time series and other types of streamed data we provide an effective methodology of broad applicability for identifying anomalous complex multimodal sequential data. We demonstrate the applicability and effectiveness of our method by evaluating it against multiple data sets. Based on quantifying performance using the receiver operating characteristic (ROC) area under the curve (AUC), our method yields an AUC score of 98.9\% for the PenDigits data set; in a subsequent experiment involving marine vessel traffic data our approach yields an AUC score of 89.1\%. Based on comparison involving univariate time series from the UEA \& UCR time series repository with performance quantified using balanced accuracy and assuming an optimal operating point, our approach outperforms a state-of-the-art shapelet method for 19 out of 28 data sets

A Comparative Analysis of STM Approaches to Reduction Operations in Irregular Applications

As a recently consolidated paradigm for optimistic concurrency in modern multicore architectures, Transactional Memory (TM) can help to the exploitation of parallelism in irregular applications when data dependence information is not available up to run- time. This paper presents and discusses how to leverage TM to exploit parallelism in an important class of irregular applications, the class that exhibits irregular reduction patterns. In order to test and compare our techniques with other solutions, they were implemented in a software TM system called ReduxSTM, that acts as a proof of concept. Basically, ReduxSTM combines two major ideas: a sequential-equivalent ordering of transaction commits that assures the correct result, and an extension of the underlying TM privatization mechanism to reduce unnecessary overhead due to reduction memory updates as well as unnecesary aborts and rollbacks. A comparative study of STM solutions, including ReduxSTM, and other more classical approaches to the parallelization of reduction operations is presented in terms of time, memory and overhead.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Functional inhibition of deep brain non-visual opsins facilitates acute long day induction of reproductive recrudescence in male Japanese quail :Deep brain photoreceptors in birds

For nearly a century, we have known that brain photoreceptors regulate avian seasonal biology. Two photopigments, vertebrate ancient opsin (VA) and neuropsin (OPN5), provide possible molecular substrates for these photoreceptor pathways. VA fulfills many criteria for providing light input to the reproductive response, but a functional link has yet to be demonstrated. This study examined the role of VA and OPN5 in the avian photoperiodic response of Japanese quail (Coturnix japonica). Non-breeding male quail were housed under short days (6L:18D) and received an intracerebroventricular infusion of adeno-associated viral vectors with shRNAi that selectively inhibited either VA or OPN5. An empty viral vector acted as a control. Quail were then photostimulated (16L:8D) to stimulate gonadal growth. Two long days significantly increased pituitary thyrotrophin-stimulating hormone β-subunit (TSHβ) and luteinizing hormone β-subunit (LHβ) mRNA of VA shRNAi treated quail compared to controls. Furthermore, at one week there was a significant increase, compared to controls, in both hypothalamic gonadotrophin releasing hormone-I (GnRH-I) mRNA and paired testicular mass in VA shRNAi birds. Opn5 shRNAi facilitated the photoinduced increase in TSHβ mRNA at 2 days, but no other differences were identified compared to controls. Contrary to our expectations, the silencing of deep brain photoreceptors enhanced the response of the reproductive axis to photostimulation rather than preventing it. In addition, we show that VA opsin plays a dominant role in the light-dependent neuroendocrine control of seasonal reproduction in birds. Together our findings suggest the photoperiodic response involves at least two photoreceptor types and populations working together with VA opsin playing a dominant role

Sleep differences in the UK between 1974 and 2015: Insights from detailed time diaries

It is often stated that sleep deprivation is on the rise, with work suggested as a main cause. However, the evidence for increasing sleep deprivation comes from surveys using habitual sleep questions. An alternative source of information regarding sleep behaviour is time‐use studies. This paper investigates changes in sleep time in the UK using the two British time‐use studies that allow measuring “time in bed not asleep” separately from “actual sleep time”. Based upon the studies presented here, people in the UK sleep today 43 min more than they did in the 1970s because they go to bed earlier (~30 min) and they wake up later (~15 min). The change in sleep duration is driven by night sleep and it is homogeneously distributed across the week. The former results apply to men and women alike, and to individuals of all ages and employment status, including employed individuals, the presumed major victims of the sleep deprivation epidemic and the 24/7 society. In fact, employed individuals have experienced a reduction in short sleeping of almost 4 percentage points, from 14.9% to 11.0%. There has also been a reduction of 15 percentage points in the amount of conflict between workers work time and their sleep time, as measured by the proportion of workers that do some work within their “ideal sleep window” (as defined by their own chronotype)

Acid pH activation of the PmrA/PmrB two-component regulatory system of Salmonella enterica

Acid pH often triggers changes in gene expression. However, little is known about the identity of the gene products that sense fluctuations in extracytoplasmic pH. The Gram-negative pathogen Salmonella enterica serovar Typhimurium experiences a number of acidic environments both inside and outside animal hosts. Growth in mild acid (pH 5.8) promotes transcription of genes activated by the response regulator PmrA, but the signalling pathway(s) that mediates this response has thus far remained unexplored. Here we report that this activation requires both PmrA's cognate sensor kinase PmrB, which had been previously shown to respond to Fe(3+) and Al(3+), and PmrA's post-translational activator PmrD. Substitution of a conserved histidine or of either one of four conserved glutamic acid residues in the periplasmic domain of PmrB severely decreased or abolished the mild acid-promoted transcription of PmrA-activated genes. The PmrA/PmrB system controls lipopolysaccharide modifications mediating resistance to the antibiotic polymyxin B. Wild-type Salmonella grown at pH 5.8 were > 100 000-fold more resistant to polymyxin B than organisms grown at pH 7.7. Our results suggest that protonation of the PmrB periplasmic histidine and/or of the glutamic acid residues activate the PmrA protein, and that mild acid promotes cellular changes resulting in polymyxin B resistance

A Survey of Ocean Simulation and Rendering Techniques in Computer Graphics

This paper presents a survey of ocean simulation and rendering methods in computer graphics. To model and animate the ocean's surface, these methods mainly rely on two main approaches: on the one hand, those which approximate ocean dynamics with parametric, spectral or hybrid models and use empirical laws from oceanographic research. We will see that this type of methods essentially allows the simulation of ocean scenes in the deep water domain, without breaking waves. On the other hand, physically-based methods use Navier-Stokes Equations (NSE) to represent breaking waves and more generally ocean surface near the shore. We also describe ocean rendering methods in computer graphics, with a special interest in the simulation of phenomena such as foam and spray, and light's interaction with the ocean surface

Molecular processes underlying synergistic linuron mineralization in a triple-species bacterial consortium biofilm revealed by differential transcriptomics

The proteobacteria Variovorax sp. WDL1, Comamonas testosteroni WDL7, and Hyphomicrobium sulfonivorans WDL6 compose a triple-species consortium that synergistically degrades and grows on the phenylurea herbicide linuron. To acquire a better insight into the interactions between the consortium members and the underlying molecular mechanisms, we compared the transcriptomes of the key biodegrading strains WDL7 and WDL1 grown as biofilms in either isolation or consortium conditions by differential RNAseq analysis. Differentially expressed pathways and cellular systems were inferred using the network-based algorithm PheNetic. Coculturing affected mainly metabolism in WDL1. Significantly enhanced expression of hylA encoding linuron hydrolase was observed. Moreover, differential expression of several pathways involved in carbohydrate, amino acid, nitrogen, and sulfur metabolism was observed indicating that WDL1 gains carbon and energy from linuron indirectly by consuming excretion products from WDL7 and/or WDL6. Moreover, in consortium conditions, WDL1 showed a pronounced stress response and overexpression of cell to cell interaction systems such as quorum sensing, contact-dependent inhibition, and Type VI secretion. Since the latter two systems can mediate interference competition, it prompts the question if synergistic linuron degradation is the result of true adaptive cooperation or rather a facultative interaction between bacteria that coincidentally occupy complementary metabolic niches