Is it time for standards and a common data exchange format for digital image analysis?

Digital image analysis is at a crossroads. While the technology has made great strides over the past few decades, there is an urgent need for image analysis to inform the next wave of large scale tissue biomarker discovery studies in cancer. Drawing parallels from the growth of next generation sequencing, this presentation will consider the case for a common language or standard format for storing and communicating digital image analysis data. In this context, image analysis data comprises more than simply an image with markups and attached key-value pair metrics. The desire to objectively benchmark competing platforms or a push for data to be deposited to public repositories much like genomics data may drive the need for a standard that also encompasses granular, cell-by-cell data.

Metagenomic characterisation of the viral community of lough neagh, the largest freshwater lake in Ireland

Lough Neagh is the largest and the most economically important lake in Ireland. It is also one of the most nutrient rich amongst the world's major lakes. In this study, 16S rRNA analysis of total metagenomic DNA from the water column of Lough Neagh has revealed a high proportion of Cyanobacteria and low levels of Actinobacteria, Acidobacteria, Chloroflexi, and Firmicutes. The planktonic virome of Lough Neagh has been sequenced and 2,298,791 2×300 bp Illumina reads analysed. Comparison with previously characterised lakes demonstrates that the Lough Neagh viral community has the highest level of sequence diversity. Only about 15% of reads had homologs in the RefSeq database and tailed bacteriophages (Caudovirales) were identified as a major grouping. Within the Caudovirales, the Podoviridae and Siphoviridae were the two most dominant families (34.3% and 32.8% of the reads with sequence homology to the RefSeq database), while ssDNA bacteriophages constituted less than 1% of the virome. Putative cyanophages were found to be abundant. 66,450 viral contigs were assembled with the largest one being 58,805 bp; its existence, and that of another 34,467 bp contig, in the water column was confirmed. Analysis of the contigs confirmed the high abundance of cyanophages in the water column.

Contribution of biomass combustion to air pollutant emissions

In Portugal, it was estimated that around 1.95 Mton/year of wood is used in residential wood burning for heating and cooking. Additionally, in the last decades, burnt forest area has also been increasing. These combustions result in high levels of toxic air pollutants and a large perturbation of atmospheric chemistry, interfere with climate and have adverse effects on health. Accurate quantification of the amounts of trace gases and particulate matter emitted from residential wood burning, agriculture and garden waste burning and forest fires on a regional and global basis is essential for various purposes, including: the investigation of several atmospheric processes, the reporting of greenhouse gas emissions, and quantification of the air pollution sources that affect human health at regional scales. In Southern Europe, data on detailed emission factors from biomass burning are rather inexistent. Emission inventories and source apportionment, photochemical and climate change models use default values obtained for US and Northern Europe biofuels. Thus, it is desirable to use more specific locally available data. The objective of this study is to characterise and quantify the contribution of biomass combustion sources to atmospheric trace gases and aerosol concentrations more representative of the national reality. Laboratory (residential wood combustion) and field (agriculture/garden waste burning and experimental wildland fires) sampling experiments were carried out. In the laboratory, after the selection of the most representative wood species and combustion equipment in Portugal, a sampling program to determine gaseous and particulate matter emission rates was set up, including organic and inorganic aerosol composition. In the field, the smoke plumes from agriculture/garden waste and experimental wildland fires were sampled. The results of this study show that the combustion equipment and biofuel type used have an important role in the emission levels and composition. Significant differences between the use of traditional combustion equipment versus modern equipments were also observed. These differences are due to higher combustion efficiency of modern equipment, reflecting the smallest amount of particulate matter, organic carbon and carbon monoxide released. With regard to experimental wildland fires in shrub dominated areas, it was observed that the largest organic fraction in the samples studied was mainly composed by vegetation pyrolysis products. The major organic components in the smoke samples were pyrolysates of vegetation cuticles, mainly comprising steradienes and sterol derivatives, carbohydrates from the breakdown of cellulose, aliphatic lipids from vegetation waxes and methoxyphenols from the lignin thermal degradation. Despite being a banned practice in our country, agriculture/garden waste burning is actually quite common. To assess the particulate matter composition, the smoke from three different agriculture/garden residues have been sampled into 3 different size fractions (PM2.5, PM2.5-10 and PM>10). Despite distribution patterns of organic compounds in particulate matter varied among residues, the amounts of phenolics (polyphenol and guaiacyl derivatives) and organic acids were always predominant over other organic compounds in the organosoluble fraction of smoke. Among biomarkers, levoglucosan, β-sitosterol and phytol were detected in appreciable amounts in the smoke of all agriculture/garden residues. In addition, inositol may be considered as an eventual tracer for the smoke from potato haulm burning. It was shown that the prevailing ambient conditions (such as high humidity in the atmosphere) likely contributed to atmospheric processes (e.g. coagulation and hygroscopic growth), which influenced the particle size characteristics of the smoke tracers, shifting their distribution to larger diameters. An assessment of household biomass consumption was also made through a national scale survey. The information obtained with the survey combined with the databases on emission factors from the laboratory and field tests allowed us to estimate the pollutant amounts emitted in each Portuguese district. In addition to a likely contribution to the improvement of emission inventories, emission factors obtained for tracer compounds in this study can be applied in receptor models to assess the contribution of biomass burning to the levels of atmospheric aerosols and their constituents obtained in monitoring campaigns in Mediterranean Europe.

Spectral characterization of families of split graphs

An upper bound for the sum of the squares of the entries of the principal eigenvector corresponding to a vertex subset inducing a k-regular subgraph is introduced and applied to the determination of an upper bound on the order of such induced subgraphs. Furthermore, for some connected graphs we establish a lower bound for the sum of squares of the entries of the principal eigenvector corresponding to the vertices of an independent set. Moreover, a spectral characterization of families of split graphs, involving its index and the entries of the principal eigenvector corresponding to the vertices of the maximum independent set is given. In particular, the complete split graph case is highlighted.

Eliciting Security Requirements and Tracing them to Design: An Integration of Common Criteria, Heuristics, and UMLsec

Building secure systems is difficult for many reasons. This paper deals with two of the main challenges: (i) the lack of security expertise in development teams, and (ii) the inadequacy of existing methodologies to support developers who are not security experts. The security standard ISO 14508 (Common Criteria) together with secure design techniques such as UMLsec can provide the security expertise, knowledge, and guidelines that are needed. However, security expertise and guidelines are not stated explicitly in the Common Criteria. They are rather phrased in security domain terminology and difficult to understand for developers. This means that some general security and secure design expertise are required to fully take advantage of the Common Criteria and UMLsec. In addition, there is the problem of tracing security requirements and objectives into solution design,which is needed for proof of requirements fulfilment. This paper describes a security requirements engineering methodology called SecReq. SecReq combines three techniques: the Common Criteria, the heuristic requirements editorHeRA, andUMLsec. SecReqmakes systematic use of the security engineering knowledge contained in the Common Criteria and UMLsec, as well as security-related heuristics in the HeRA tool. The integrated SecReq method supports early detection of security-related issues (HeRA), their systematic refinement guided by the Common Criteria, and the ability to trace security requirements into UML design models. A feedback loop helps reusing experiencewithin SecReq and turns the approach into an iterative process for the secure system life-cycle, also in the presence of system evolution.

Kids just wanna have fun: Children's experiences of a weight management programme

Objectives: To explore children's accounts of their experiences of the UK‘s largest childhood obesity programme, MEND (Mind, Exercise, Nutrition…Do it!) (See www.mendprogramme.org). Design: Semi-structured interviews were conducted with children who had completed the MEND obesity programme. Interviews were transcribed verbatim and analysed using Interpretative Phenomenological Analysis (IPA). Method Fourteen children spanning diverse areas of London comprised this study (eight male, six female), aged between 11 and 14 years and in secondary school. Participants were interviewed a year after completing one of the London-based MEND obesity programmes. Results: This article focuses on the most common and striking theme to emerge from the original dataset (The complete analysis may be found in L. Watson, Unpublished doctoral thesis): Fun. Subthemes were: ‘going with the flow’; active participation in activities that led to new experiences (‘actually doing it’ – seeing the fun side); the importance of others in the experience of fun (‘you do games in unity’ – ‘it's not as fun on your own’). Conclusion: Children have fun when engaged in interactive and varied activities with opportunity for individual feedback and improvement. When designing childhood obesity programmes, conditions that optimise children's experience of fun should be emphasised over didactic and risk-heavy information pertaining to childhood obesity.

The economic effects of common agricultural policy on Mediterranean montado/dehesa ecosystem

The decoupling of CAP payments leads production decisions and resources allocation to be more dependent on market prices and competitive advantages. The objective of this paper is to assess the effects of CAP trends on the montado/dehesa traditional ecosystem of Mediterranean regions in terms of farm income, land, labour and capital. A positive mathematical supply model disaggregated by the montado agro-forestry production systems of the Alentejo region in southern Portugal is developed. The results show that decoupling payments of CAP have negative economic effects on agricultural activities and resource use. Agricultural income increases with single farm payments but the foreseen increases in prices do not compensate the loss of the Agenda 2000 area payments in terms of competitiveness. These results reinforce the need to promote alternative agricultural and non-agricultural activities and policies in Mediterranean rural European areas and regions. (C) 2011 Society for Policy Modeling. Published by Elsevier Inc. All rights reserved.

Study of the expression of different genes of long-chain polyunsaturated fatty acids (LC-PUFA) metabolism during the early paralarval development of the common octopus (Octopus vulgaris)

Dissertação de mestrado, Aquacultura e Pescas, Faculdade de Ciências e Tecnologias, Universidade do Algarve, 2015

Temporal distribution of the short-beaked common dolphin (Delphinus delphis) in the south of Madeira Island (Portugal) and relationship with oceanographic variables

Dissertação de mestrado, Biologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

Notable differences in gene expression between injured turbot (Scophthalmus maximus) and brill (Scophthalmus rhombus) skin

Dissertação de mestrado, Engenharia Biológica, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

South Carolina/Common Pleas Court Circuits Meeting Benchmark

This is a list of the courts in all the circuits of South Carolina and the percentage of cases disposed of in 365 day or less. None of the courts met the 80% benchmark.

South Carolina/Common Pleas Court Circuits Meeting Benchmark ... as of August 31, 2014

This is a list of the courts in all the circuits of South Carolina and the percentage of cases disposed of in 365 day or less as of August 31, 2014. None of the courts met the 80% benchmark.

Summary of Pending Common Pleas Cases by Circuit/County For Period 7/1/2014 thru 8/31/2014

This report gives a summary of common pleas cases broken down by county and circuit as of August 31, 2014.

Summary of Pending Common Pleas Cases by Circuit/County For Date 6/30/2014

This report gives a summary of common pleas cases broken down by county and circuit as of June 30, 2014.

South Carolina/common pleas court circuits meeting benchmark 80% of Pending Docket 365 Days or Less From Placement on the Trial Docket as of February 28, 2015

This is a list of the courts in all the circuits of South Carolina and the percentage of cases disposed of in 365 day or less. Only three courts met the 80% benchmark.