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

Documentation of a fully integrated epidemiological-demographic-macroeconomic model of Malaria: The case of Ghana

We develop a novel and fully integrated epidemiological-demographic-macroeconomic EDM-malaria simulation model framework for modelling of P. falciparum malaria transmission in Ghana. Our model framework represents a milestone, as the first fully integrated EDM model framework for any type of infectious disease. The complex specification and integration of regional epidemiological-demographic models within a malaria-focussed macroeconomic Computable General Equilibrium model is fully described and documented, and ideas are outlined for future applications to investigate the interplay between macroeconomic and health disease burdens, to measure the health and economic impacts of economic growth and malaria interventions, and to study the importance (or lack thereof) of the general omission of proper epidemiological underpinnings and integration of economic incentive feedback effects in the existing literature on macroeconomic assessment of infectious disease

CE17015

In the southwest of Ireland and the Celtic Sea (ICES Divisions VIIaS, g & j), herring are an important commercial species to the pelagic and polyvalent fleet. For a period in the 1970s and1980s, larval surveys were conducted for herring in this area. However, since 1989, acoustic surveys have been carried out, and currently are the only tuning indices available for this stock. In the Celtic Sea and VIIj, herring acoustic surveys have been carried out since 1989. Since 2004 the survey has been fixed in October and carried out onboard the RV Celtic Explorer. The geographical confines of the annual 21 day survey have been modified in recent years to include areas to the south of the main winter spawning grounds in an effort to identify the whereabouts of winter spawning fish before the annual inshore spawning migration. Spatial resolution of acoustic transects has been increased over the entire south coast survey area. The acoustic component of the survey has been further complemented since 2004 by detailed hydrographic, marine mammal and seabird surveys

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

Dairy Ingredients in Chocolate

End of Project ReportThe main objective was to assess and control the contribution of various ingredient components to chocolate behaviour and to optimise ingredients for specific chocolate applications. A key aim, therefore, was to understand the role of composition and particle structure and to produce spray dried powders with a functionality in chocolate as close as possible to roller dried powders. By demonstrating how the powder properties affect chocolate, it should be possible to control the functional properties of the powders to meet any powder or chocolate specification. Novel powder compositions indicated by this work should also be useful to chocolate makers. The ability to make chocolate under test conditions and to assess the role of milk powders or other ingredients has been put in place for the first time in Ireland. Previous knowledge of milk seasonality and of powder technology has provided a basis for understanding variations in milk powder functionality in chocolate. Spray dried powders with mean free fat values of 50 to 94%, particle sizes of 30 to 65 mm and vacuole volumes of 0.0 to 3.9 ml/100g were produced from milks of varying composition but under the same processing conditions. Advances were made in analysing powder structure through microscopy, particle size and occluded air measurement. Valuable new information has been generated on the changes in free fat, solid fat content, particle size and occluded air in powders. Explanations were provided for the first time for the complex effects of these properties on chocolate viscosity and yield value. This information will also make a positive contribution to other projects in the milk powder area. Good contacts have been established with multinational manufacturers and with producers of milk powder for chocolate.Department of Agriculture, Food and the Marin

Blood feeding patterns of mosquitoes: random or structured?

<p>Abstract</p> <p>Background</p> <p>The foraging behavior of blood-sucking arthropods is the defining biological event shaping the transmission cycle of vector-borne parasites. It is also a phenomenon that pertains to the realm of community ecology, since blood-feeding patterns of vectors can occur across a community of vertebrate hosts. Although great advances in knowledge of the genetic basis for blood-feeding choices have been reported for selected vector species, little is known about the role of community composition of vertebrate hosts in determining such patterns.</p> <p>Methods & Results</p> <p>Here, we present an analysis of feeding patterns of vectors across a variety of locations, looking at foraging patterns of communities of mosquitoes, across communities of hosts primarily comprised of mammals and birds. Using null models of species co-occurrence, which do not require ancillary information about host abundance, we found that blood-feeding patterns were aggregated in studies from multiple sites, but random in studies from a single site. This combination of results supports the idea that mosquito species in a community may rely primarily on host availability in a given landscape, and that contacts with specific hosts will be influenced more by the presence/absence of hosts than by innate mosquito choices. This observation stresses the importance of blood-feeding plasticity as a key trait explaining the emergence of many zoonotic mosquito transmitted diseases.</p> <p>Discussion</p> <p>From an epidemiological perspective our observations support the idea that phenomena promoting synchronization of vectors and hosts can promote the emergence of vector-borne zoonotic diseases, as suggested by observations on the linkages between deforestation and the emergence of several human diseases.</p

CE18010

The WESPAS survey program is the consolidation of two existing survey programs carried out by FEAS, the Malin Shelf herring acoustic survey and the boarfish acoustic survey. The Malin Shelf herring acoustic survey has been carried out annually since 2008 and reports on the annual abundance of summer feeding aggregations of herring to the west of Scotland and to the north and west of Ireland from 54°N to 58°30’N. The boarfish survey was conducted from 2011 using a chartered fishing vessel and reported the abundance of spawning aggregations of boarfish from 47°N to 57°N. In 2016 both surveys were combined and since then have been carried out onboard the RV Celtic Explorer over a 42 day period providing synoptic coverage of shelf waters from 47°N northwards to 58°30’N. Age stratified relative stock abundance estimates of boarfish, herring and horse mackerel within the survey area were calculated using acoustic data and biological data from trawl sampling. Stock estimates of boarfish and horse mackerel were submitted to the ICES assessment Working Group for Widely Distributed Stocks (WGWIDE) meeting in August 2018. Herring estimates are submitted to the Herring Assessment Working Group (HAWG) meeting in March every year. Survey performance will be reviewed at the ICES Planning Group meeting for International Pelagic Surveys (WGIPS) meeting in January 2019

In praise of Prais-Winsten: An evaluation of methods used to account for autocorrelation in interrupted time series

Interrupted time series are increasingly being used to assess the population impact of public health interventions. These data are usually correlated over time (auto correlated) and this must be accounted for in the analysis. Typically, this is done using either the Prais-Winsten method, the Newey-West method, or autoregressive-moving-average (ARMA) modeling. In this paper, we illustrate these methods via a study of pneumococcal vaccine introduction and explore their performance under 20 simulated autocorrelation scenarios with sample sizes ranging between 20 and 300. We show that in terms of mean square error, the Prais-Winsten and ARMA methods perform best, while in terms of coverage the Prais-Winsten method generally performs better than other methods. All three methods are unbiased. As well as having good statistical properties, the Prais-Winsten method is attractive because it is decision-free and produces a single measure of autocorrelation that can be compared between studies and used to guide sample size calculations. We would therefore encourage analysts to consider using this simple method to analyze interrupted time series

Comparison of isocaloric very low carbohydrate/high saturated fat and high carbohydrate/low saturated fat diets on body composition and cardiovascular risk

BACKGROUND: It is speculated that high saturated fat very low carbohydrate diets (VLCARB) have adverse effects on cardiovascular risk but evidence for this in controlled studies is lacking. The objective of this study was to compare, under isocaloric conditions, the effects of a VLCARB to 2 low saturated fat high carbohydrate diets on body composition and cardiovascular risk. METHODS: Eighty three subjects, 48 ± 8 y, total cholesterol 5.9 ± 1.0 mmol/L, BMI 33 ± 3 kg/m(2 )were randomly allocated to one of 3 isocaloric weight loss diets (6 MJ) for 8 weeks and on the same diets in energy balance for 4 weeks: Very Low Fat (VLF) (CHO:Fat:Protein; %SF = 70:10:20; 3%), High Unsaturated Fat (HUF) = (50:30:20; 6%), VLCARB (4:61:35; 20%) RESULTS: Percent fat mass loss was not different between diets VLCARB -4.5 ± 0.5, VLF-4.0 ± 0.5, HUF -4.4 ± 0.6 kg). Lean mass loss was 32-31% on VLCARB and VLF compared to HUF (21%) (P < 0.05). LDL-C increased significantly only on VLCARB by 7% (p < 0.001 compared with the other diets) but apoB was unchanged on this diet and HDL-C increased relative to the other 2 diets. Triacylglycerol was lowered by 0.73 ± 0.12 mmol/L on VLCARB compared to -0.15 ± 0.07 mmol/L on HUF and -0.06 ± 0.13 mmol/L on VLF (P < 0.001). Plasma homocysteine increased 6.6% only on VLCARB (P = 0.026). VLCARB lowered fasting insulin 33% compared to a 19% fall on HUF and no change on VLF (P < 0.001). The VLCARB meal also provoked significantly lower post prandial glucose and insulin responses than the VLF and HUF meals. All diets decreased fasting glucose, blood pressure and CRP (P < 0.05). CONCLUSION: Isocaloric VLCARB results in similar fat loss than diets low in saturated fat, but are more effective in improving triacylglycerols, HDL-C, fasting and post prandial glucose and insulin concentrations. VLCARB may be useful in the short-term management of subjects with insulin resistance and hypertriacylglycerolemia