Generic Subsequence Matching Framework: Modularity, Flexibility, Efficiency

Subsequence matching has appeared to be an ideal approach for solving many problems related to the fields of data mining and similarity retrieval. It has been shown that almost any data class (audio, image, biometrics, signals) is or can be represented by some kind of time series or string of symbols, which can be seen as an input for various subsequence matching approaches. The variety of data types, specific tasks and their partial or full solutions is so wide that the choice, implementation and parametrization of a suitable solution for a given task might be complicated and time-consuming; a possibly fruitful combination of fragments from different research areas may not be obvious nor easy to realize. The leading authors of this field also mention the implementation bias that makes difficult a proper comparison of competing approaches. Therefore we present a new generic Subsequence Matching Framework (SMF) that tries to overcome the aforementioned problems by a uniform frame that simplifies and speeds up the design, development and evaluation of subsequence matching related systems. We identify several relatively separate subtasks solved differently over the literature and SMF enables to combine them in straightforward manner achieving new quality and efficiency. This framework can be used in many application domains and its components can be reused effectively. Its strictly modular architecture and openness enables also involvement of efficient solutions from different fields, for instance efficient metric-based indexes. This is an extended version of a paper published on DEXA 2012.Comment: This is an extended version of a paper published on DEXA 201

Piecewise Linear Representation Segmentation as a Multiobjective Optimization Problem

Proceedings of: Forth International Workshop on User-Centric Technologies and applications (CONTEXTS 2010). Valencia, September 7-10, 2010Actual time series exhibit huge amounts of data which require an unaffordable computational load to be processed, leading to approximate representations to aid these processes. Segmentation processes deal with this issue dividing time series into a certain number of segments and approximating those segments with a basic function. Among the most extended segmentation approaches, piecewise linear representation is highlighted due to its simplicity. This work presents an approach based on the formalization of the segmentation process as a multiobjetive optimization problem and the resolution of that problem with an evolutionary algorithm.This work was supported in part by Projects CICYT TIN2008-06742-C02-02/TSI, CICYT TEC2008-06732-C02-02/TEC, CAM CONTEXTS (S2009/TIC-1485) and DPS2008-07029-C02-02.Publicad

Discovering frequent patterns on agrometeorological data with TrieMotif

The “food safety” issue has concerned governments from several countries. The accurate monitoring of agriculture have become important specially due to climate change impacts. In this context, the development of new technologies for monitoring are crucial. Finding previously unknown patterns that frequently occur on time series, known as motifs, is a core task to mine the collected data. In this work we present a method that allows a fast and accurate time series motif discovery. From the experiments we can see that our approach is able to efficiently find motifs even when the size of the time series goes longer. We also evaluated our method using real data time series extracted from remote sensing images regarding sugarcane crops. Our proposed method was able to find relevant patterns, as sugarcane cycles and other land covers inside the same area, which are really useful for data analysis.FAPESPCNPqCAPESSticAmsudInternational Conference on Enterprise Information Systems - ICEIS (16. 2014 Lisbon

Activity Predicts Male Reproductive Success in a Polygynous Lizard

Activity patterns and social interactions play a key role in determining reproductive success, although this is poorly understood for species that lack overt social behaviour. We used genetic paternity analysis to quantify both multiple paternity and the relative roles of activity and social behaviour in determining reproductive success in a nondescript Australian lizard. During the breeding season we intensively followed and recorded the behaviour of a group of seven males and 13 females in a naturalistic outdoor enclosure to examine the relative roles of body size, activity and social interactions in determining male fertilization success. We found multiple paternity in 42% of clutches. No single behaviour was a significant predictor of male fertilization success in isolation, but male-female association, interactions and courtship explained 41% of the variation in male fertilization success. Males with the highest number of offspring sired invested heavily in interacting with females but spent very little time in interactions with males. These same males also sired offspring from more clutches. When taken collectively, an index of overall male activity, including locomotion and all social interactions, significantly explained 81% of the variation in the total number of offspring sired and 90% of the variation in the number of clutches in which males sired offspring. We suggest that the most successful male strategy is a form of endurance rivalry in which active mate searching and interactions with females have the greatest fitness benefits.This work was supported by grants from the Australian Research Council to JSK

Framework for better living with HIV in England

Duration: April 2007 - May 2009 Sigma Research was funded by Terrence Higgins Trust to co-ordinate the development of a framework to address the health, social care, support and information needs of people with diagnosed HIV in England. It has now been published as the Framework for better living with HIV in England. The over-arching goal of the framework is that all people with diagnosed HIV in England "are enabled to have the maximum level of health, well-being, quality of life and social integration". In its explanation of how this should occur the document presents a road map for social care, support and information provision to people with diagnosed HIV in England. By establishing and communicating aims and objectives, the framework should build consensus and provide a means to establish how interventions could be prioritised and coordinated. The key drivers for the framework were clearly articulated ethical principles, agreed by all those who sign up to it, and an inclusive social development / health promotion approach. Sigma Research worked on the framework with a range of other organisations who sent representatives to a Framework Development Group (see below for membership). The framework is evidence-based and seeks to: Promote and protect the rights and well-being of all people with HIV in England. Maximise the capacity of individuals and groups of people with HIV to care for, advocate and represent themselves effectively. Improve and protect access to appropriate information, social support, social care and clinical services. Minimise social, economic, governmental and judicial change detrimental to the health and well being of people with HIV. Alongside the development of the framework, Sigma Research undertook a national needs assessment among people with diagnosed HIV across the UK called What do you need?. These two projects informed and supported each other. Framework Development Group included: African HV Policy Network Black Health Agency George House Trust NAM NAT (National AIDS Trust) Positively Women Terrence Higgins Trus

Evolution of extreme ontogenetic allometric diversity and heterochrony in pythons, a clade of giant and dwarf snakes

Ontogenetic allometry, how species change with size through their lives, and heterochony, a decoupling between shape, size, and age, are major contributors to biological diversity. However, macroevolutionary allometric and heterochronic trends remain poorly understood because previous studies have focused on small groups of closely related species. Here, we focus on testing hypotheses about the evolution of allometry and how allometry and heterochrony drive morphological diversification at the level of an entire species-rich and diverse clade. Pythons are a useful system due to their remarkably diverse and well-adapted phenotypes and extreme size disparity. We collected detailed phenotype data on 40 of the 44 species of python from 1191 specimens. We used a suite of analyses to test for shifts in allometric trajectories that modify morphological diversity. Heterochrony is the main driver of initial divergence within python clades, and shifts in the slopes of allometric trajectories make exploration of novel phenotypes possible later in divergence history. We found that allometric coefficients are highly evolvable and there is an association between ontogenetic allometry and ecology, suggesting that allometry is both labile and adaptive rather than a constraint on possible phenotypes.Damien Esquerré, Emma Sherratt, J. Scott Keog

Homeobox gene TGIF-1 is increased in placental endothelial cells of human fetal growth restriction.

Aberrant placental angiogenesis is associated with fetal growth restriction (FGR). In the mouse, targeted disruption of the homeobox gene, transforming growth β-induced factor (Tgif-1), which is also a transcription factor, causes defective placental vascularisation. Nevertheless, TGIF-1's role in human placental angiogenesis is unclear. We have previously reported increased TGIF-1 expression in human FGR placentae and demonstrated localisation of TGIF-1 protein in placental endothelial cells (ECs). However, its functional role remains to be investigated. In this study, we aimed to specifically compare TGIF-1 mRNA expression in placental ECs isolated from human FGR-affected pregnancies with gestation-matched control pregnancies in two independent cohorts from Australia and Canada, and to identify the functional role of TGIF-1 in placental angiogenesis using the human umbilical vein endothelial cell-derived cell line, SGHEC-7 and primary human umbilical vein ECs. Real-time PCR revealed that TGIF-1 mRNA expression was significantly increased in ECs isolated from FGR-affected placentae compared with that of controls. The functional roles of TGIF-1 were determined in ECs following TGIF-1 siRNA transfection. TGIF-1 inactivation in ECs significantly reduced TGIF-1 at both the mRNA and protein levels, as well as the proliferative and invasive potential, but significantly increased the angiogenic potential. Using angiogenesis PCR screening arrays, we identified ITGAV, NRP-1, ANPGT-1 and ANPGT-2 as novel downstream targets of TGIF-1, following TGIF-1 inactivation in ECs. Collectively, these results show that increased TGIF-1 in FGR may regulate EC function through mediating the expression of angiogenic molecules and contribute to aberrant placental angiogenesis in FGR pregnancies

Protocol-directed sedation versus non-protocol-directed sedation to reduce duration of mechanical ventilation in mechanically ventilated intensive care patients

Background The sedation needs of critically ill patients have been recognized as a core component of critical care and meeting these is vital to assist recovery and ensure humane treatment. There is growing evidence to suggest that sedation requirements are not always optimally managed. Sub-optimal sedation incorporates both under- and over-sedation and has been linked to both short-term (e.g. length of stay) and long-term (e.g. psychological recovery) outcomes. Various strategies have been proposed to improve sedation management and address aspects of assessment as well as delivery of sedation. Objectives To assess the effects of protocol-directed sedation management on the duration of mechanical ventilation and other relevant patient outcomes in mechanically ventilated intensive care unit (ICU) patients. We looked at various outcomes and examined the role of bias in order to examine the level of evidence for this intervention. Search methods We searched the Cochrane Central Register of Controlled trials (CENTRAL) (2013; Issue 11), MEDLINE (OvidSP) (1990 to November 2013), EMBASE (OvidSP) (1990 to November 2013), CINAHL (BIREME host) (1990 to November 2013), Database of Abstracts of Reviews of Effects (DARE) (1990 to November 2013), LILACS (1990 to November 2013), Current Controlled Trials and US National Institutes of Health Clinical Research Studies (1990 to November 2013), and reference lists of articles. We re-ran the search in October 2014. We will deal with any studies of interest when we update the review. Selection criteria We included randomized controlled trials (RCTs) conducted in adult ICUs comparing management with and without protocol-directed sedation. Data collection and analysis Two authors screened the titles and abstracts and then the full-text reports identified from our electronic search. We assessed seven domains of potential risk of bias for the included studies. We examined the clinical, methodological and statistical heterogeneity and used the random-effects model for meta-analysis where we considered it appropriate. We calculated the mean difference (MD) for duration of mechanical ventilation and risk ratio (RR) for mortality across studies, with 95% confidence intervals (CI). Main results We identified two eligible studies with 633 participants. Both included studies compared the use of protocol-directed sedation, specifically protocols delivered by nurses, with usual care. We rated the risk of selection bias due to random sequence generation low for one study and unclear for one study. The risk of selection bias related to allocation concealment was low for both studies. We also assessed detection and attrition bias as low for both studies while we considered performance bias high due to the inability to blind participants and clinicians in both studies. Risk due to other sources of bias, such as potential for contamination between groups and reporting bias, was considered unclear. There was no clear evidence of differences in duration of mechanical ventilation (MD -5.74 hours, 95% CI -62.01 to 50.53, low quality evidence), ICU length of stay (MD -0.62 days, 95% CI -2.97 to 1.73) and hospital length of stay (MD -3.78 days, 95% CI -8.54 to 0.97) between people being managed with protocol-directed sedation versus usual care. Similarly, there was no clear evidence of difference in hospital mortality between the two groups (RR 0.96, 95% CI 0.71 to 1.31, low quality evidence). ICU mortality was only reported in one study preventing pooling of data. There was no clear evidence of difference in the incidence of tracheostomy (RR 0.77, 95% CI 0.31 to 1.89). The studies reported few adverse event outcomes; one study reported self extubation while the other study reported re-intubation; given this difference in outcomes, pooling of data was not possible. There was significant heterogeneity between studies for duration of mechanical ventilation (I2 = 86%, P value = 0.008), ICU length of stay (I2 = 82%, P value = 0.02) and incidence of tracheostomy (I2 = 76%, P value = 0.04), with one study finding a reduction in duration of mechanical ventilation and incidence of tracheostomy and the other study finding no difference. Authors' conclusions There is currently insufficient evidence to evaluate the effectiveness of protocol-directed sedation. Results from the two RCTs were conflicting, resulting in the quality of the body of evidence as a whole being assessed as low. Further studies, taking into account contextual and clinician characteristics in different ICU environments, are necessary to inform future practice. Methodological strategies to reduce the risk of bias need to be considered in future studies