Milling plant and soil material in plastic tubes over-estimates carbon and under-estimates nitrogen concentrations

Milling of plant and soil material in plastic tubes, such as microcentrifuge tubes, over-estimates carbon (C) and under-estimates nitrogen (N) concentrations due to the introduction of polypropylene into milled samples, as identified using Fourier-transform infra-red spectroscopy.

This study compares C and N concentrations of roots and soil milled in microcentrifuge tubes versus stainless steel containers, demonstrating that a longer milling time, greater milling intensity, smaller sample size and inclusion of abrasive sample material all increase polypropylene contamination from plastic tubes leading to overestimation of C concentrations by up to 8 % (0.08 g g(-1)).

Erroneous estimations of C and N, and other analytes, must be assumed after milling in plastic tubes and milling methods should be adapted to minimise such error.

Biotransformation of 2,4,6-trinitrotoluene (TNT) by ectomycorrhizal basidiomycetes

The ability of four ectomycorrhizal basidiomycetes to biotransform 2,4,6-trinitrotoluene (TNT) in axenic culture was tested. All species were capable of TNT biotransformation to a greater or lesser extent. When biotransformation was expressed on a biomass basis 4 out of the 5 isolates tested were equally efficient at transforming TNT. The factors regulating TNT biotransformation were investigated in detail for one fungus, Suillus variegatus. When the fungus was grown under nitrogen limiting conditions the rate of biotransformation decreased relative to nitrogen sufficient conditions, but no decrease was observed under short term carbon starvation. Extracellular enzymes of S. variegatus could transform TNT, but transformation was greater in intact cells. The mycelial cell wall fraction did not degrade TNT. The TNT concentration that caused 50% reduction in biomass (EC₅₀) for S. variegatus was within the range observed for other basidiomycete fungi being between 2-10 μg mL^-1. The potential use of ectomycorrhizal basidiomycetes as in-situ bioremediation agents for TNT contaminated soils is discussed.

Herd-level bovine tuberculosis risk factors: assessing the role of low-level badger population disturbance

Bovine TB (bTB) is endemic in Irish cattle and has eluded eradication despite considerable expenditure, amid debate over the relative roles of badgers and cattle in disease transmission. Using a comprehensive dataset from Northern Ireland (>10,000 km²; 29,513 cattle herds), we investigated interactions between host populations in one of the first large-scale risk factor analyses for new herd breakdowns to combine data on both species. Cattle risk factors (movements, international imports, bTB history, neighbours with bTB) were more strongly associated with herd risk than area-level measures of badger social group density, habitat suitability or persecution (sett disturbance). Highest risks were in areas of high badger social group density and high rates of persecution, potentially representing both responsive persecution of badgers in high cattle risk areas and effects of persecution on cattle bTB risk through badger social group disruption. Average badger persecution was associated with reduced cattle bTB risk (compared with high persecution areas), so persecution may contribute towards sustaining bTB hotspots; findings with important implications for existing and planned disease control programmes.

Meta-analysis of prostate cancer gene expression data identifies a novel discriminatory signature enriched for glycosylating enzymes

BACKGROUND: Tumorigenesis is characterised by changes in transcriptional control. Extensive transcript expression data have been acquired over the last decade and used to classify prostate cancers. Prostate cancer is, however, a heterogeneous multifocal cancer and this poses challenges in identifying robust transcript biomarkers.

METHODS: In this study, we have undertaken a meta-analysis of publicly available transcriptomic data spanning datasets and technologies from the last decade and encompassing laser capture microdissected and macrodissected sample sets.

RESULTS: We identified a 33 gene signature that can discriminate between benign tissue controls and localised prostate cancers irrespective of detection platform or dissection status. These genes were significantly overexpressed in localised prostate cancer versus benign tissue in at least three datasets within the Oncomine Compendium of Expression Array Data. In addition, they were also overexpressed in a recent exon-array dataset as well a prostate cancer RNA-seq dataset generated as part of the The Cancer Genomics Atlas (TCGA) initiative. Biologically, glycosylation was the single enriched process associated with this 33 gene signature, encompassing four glycosylating enzymes. We went on to evaluate the performance of this signature against three individual markers of prostate cancer, v-ets avian erythroblastosis virus E26 oncogene homolog (ERG) expression, prostate specific antigen (PSA) expression and androgen receptor (AR) expression in an additional independent dataset. Our signature had greater discriminatory power than these markers both for localised cancer and metastatic disease relative to benign tissue, or in the case of metastasis, also localised prostate cancer.

CONCLUSION: In conclusion, robust transcript biomarkers are present within datasets assembled over many years and cohorts and our study provides both examples and a strategy for refining and comparing datasets to obtain additional markers as more data are generated.

Quiescent and flaring X-ray emission from the nearby M/T dwarf binary SCR 1845-6357

Aims: X-ray emission is an important diagnostics to study magnetic activity in very low mass stars that are presumably fully convective and have an effectively neutral photosphere. Methods: We investigate an XMM-Newton observation of SCR 1845-6357, a nearby, ultracool M 8.5 / T 5.5 dwarf binary. The binary is unresolved in the XMM detectors, but the X-ray emission is very likely from the M 8.5 dwarf. We compare its flaring emission to those of similar very low mass stars and additionally present an XMM observation of the M 8 dwarf VB 10. Results: We detect quasi-quiescent X-ray emission from SCR 1845-6357 at soft X-ray energies in the 0.2-2.0 keV band, as well as a strong flare with a count rate increase of a factor of 30 and a duration of only 10 min. The quasi-quiescent X-ray luminosity of log LX = 26.2 erg/s and the corresponding activity level of log LX/Lbol = -3.8 point to a fairly active star. Coronal temperatures of up to 5 MK and frequent minor variability support this picture. During the flare, which is accompanied by a significant brightening in the near-UV, plasma temperatures of 25-30 MK are observed and an X-ray luminosity of LX = 8 × 1027 erg/s is reached. Conclusions: The source SCR 1845-6357 is a nearby, very low mass star that emits X-rays at detectable levels in quasi-quiescence, implying the existence of a corona. The high activity level, coronal temperatures and the observed large flare point to a rather active star, despite its estimated age of a few Gyr.

Comparison of optimal designs of steel portal frames including topological asymmetry considering rolled, fabricated and tapered sections

A structural design optimisation has been carried out to allow for asymmetry and fully tapered portal frames. The additional weight of an asymmetric structural shape was found to be on average 5–13% with additional photovoltaic (PV) loading having a negligible effect on the optimum design. It was also shown that fabricated and tapered frames achieved an average percentage weight reduction of 9% and 11%, respectively, as compared to comparable hot-rolled steel frames. When the deflection limits recommended by the Steel Construction Institute were used, frames were shown to be deflection controlled with industrial limits yielding up to 40% saving.

Illness perceptions and coping in physical health conditions: A meta-analysis

Objective: There is a considerable body of research linking elements of Leventhal’s Common Sense Model (CSM) to emotional well-being/distress outcomes among people with physical illness. The present study aims to consolidate this literature and examine the evidence for the role of coping strategies within this literature.
Methods: A systematic review was conducted where the outcomes of interest were: depression, anxiety and quality of life. A total of 1050 articles were identified and 31 articles were considered eligible to be included in the review.
Results: Across a range of illnesses, perceptions of consequences of the illness and emotional representations were consistently the illness perceptions with the strongest relationship with the outcomes. Coping variables tend to be stronger predictors of outcomes than the illness perception variables. The evidence for the mediating effect of coping was inconsistent.
Conclusions: Illness perceptions and coping have an important role to play in the explanation of distress outcomes across a range of physical health conditions. However, some clarity about the theoretical position of coping in relation to illness perceptions, and further longitudinal work is needed if we are to apply this information to the design of interventions for the improvement of psychological health among people with physical health conditions.

Modelação do crescimento de Sardina pilchardus (Walbaum, 1792) em duas zonas (oceanograficamente distintas) da costa portuguesa

Dissertação mest., Biologia Marinha, Universidade do Algarve, 2009

Vindicating Analyticity: Critical notice of Truth in Virtue of Meaning, by Gillian Russell

European Community's Seventh Framework Programme FP7/2007-2013 under grant agreement no. 238128

IMP: Imperial Metagenomics Pipeline for high-throughput sequence data

We have developed an in-house pipeline for the processing and analyses of sequence data generated during Illumina technology-based metagenomic studies of the human gut microbiota. Each component of the pipeline has been selected following comparative analysis of available tools; however, the modular nature of software facilitates replacement of any individual component with an alternative should a better tool become available in due course. The pipeline consists of quality analysis and trimming followed by taxonomic filtering of sequence data allowing reads associated with samples to be binned according to whether they represent human, prokaryotic (bacterial/archaeal), viral, parasite, fungal or plant DNA. Viral, parasite, fungal and plant DNA can be assigned to species level on a presence/absence basis, allowing – for example – identification of dietary intake of plant-based foodstuffs and their derivatives. Prokaryotic DNA is subject to taxonomic and functional analyses, with assignment to taxonomic hierarchies (kingdom, class, order, family, genus, species, strain/subspecies) and abundance determination. After de novo assembly of sequence reads, genes within samples are predicted and used to build a non-redundant catalogue of genes. From this catalogue, per-sample gene abundance can be determined after normalization of data based on gene length. Functional annotation of genes is achieved through mapping of gene clusters against KEGG proteins, and InterProScan. The pipeline is undergoing validation using the human faecal metagenomic data of Qin et al. (2014, Nature 513, 59–64). Outputs from the pipeline allow development of tools for the integration of metagenomic and metabolomic data, moving metagenomic studies beyond determination of gene richness and representation towards microbial-metabolite mapping. There is scope to improve the outputs from viral, parasite, fungal and plant DNA analyses, depending on the depth of sequencing associated with samples. The pipeline can easily be adapted for the analyses of environmental and non-human animal samples, and for use with data generated via non-Illumina sequencing platforms.

Statistical classification of road pavements using near field vehicle rolling noise measurements

Low noise surfaces have been increasingly considered as a viable and cost-effective alternative to acoustical barriers. However, road planners and administrators frequently lack information on the correlation between the type of road surface and the resulting noise emission profile. To address this problem, a method to identify and classify different types of road pavements was developed, whereby near field road noise is analyzed using statistical learning methods. The vehicle rolling sound signal near the tires and close to the road surface was acquired by two microphones in a special arrangement which implements the Close-Proximity method. A set of features, characterizing the properties of the road pavement, was extracted from the corresponding sound profiles. A feature selection method was used to automatically select those that are most relevant in predicting the type of pavement, while reducing the computational cost. A set of different types of road pavement segments were tested and the performance of the classifier was evaluated. Results of pavement classification performed during a road journey are presented on a map, together with geographical data. This procedure leads to a considerable improvement in the quality of road pavement noise data, thereby increasing the accuracy of road traffic noise prediction models.

A Problemática da estratégia no sector das energias renováveis em Portugal

Dissertação apresentada ao Instituto Superior de Contabilidade e Administração do Porto para obtenção do Grau de Mestre em Gestão das Organizações, Ramo de Gestão de Empresas Orientada pelo Professor Doutor Eduardo Manuel Lopes de Sá e Silva

Erros de medicação num serviço de internamento hospitalar : estudo de prevalência

RESUMO - Os erros de medicação (EM) são uma das principais causas de eventos adversos, estimando-se serem as causas não relacionados com procedimentos cirúrgicos mais frequentes. Estes podem ser classificados por erros latentes ou erros ativos. Objetivos Definiram-se como principais objetivos deste estudo, determinar a prevalência de EM ativos num internamento hospitalar evitados e não evitados, nos momentos da prescrição escrita, transcrição, distribuição e administração, bem como a sua relação com algumas variáveis, como o Grupo farmacológico, Via de administração, Especialidade médica do prescritor e Área médica do médico responsável pelo episódio de internamento (MREI). Metodologia O estudo foi do tipo observacional descritivo de abordagem quantitativa, transversal com recrutamento prospetivo. Foi utilizado um instrumento de observação (check-list) para o registo de todos os EM e das variáveis em cada fase. Resultados Foram observadas 513 unidades amostrais com uma prevalência de 98,2% de EM, num total de 1655 erros dos quais 75% foram evitados. Nas variáveis Grupo farmacológico e Área médica do MREI não foram encontradas relações estatísticas relevantes. Obteve-se um OR=1,97 [1,18;3,27] para medicamentos orais quando comparados aos endovenosos nos erros de prescrição (EP) e um OR=7 [2,77;17,71] quando comparados com os endovenosos na transcrição dos Serviços Farmacêuticos (TSF). A anestesiologia apresentou um OR=0,41 [0,27;0,63] nos EP comparativamente às outras especialidades. Do total de EM observaram-se 30% de erros de prescrição (EP), 20% de erros na transcrição do internamento, 36% de erros na TSF, 2% de erros na distribuição e 12% de erros na administração. Os erros mais prevalentes foram a identificação do prescritor ilegível (16%) e a identificação do doente omissa na TSF (16%). Conclusão Apesar da elevada prevalência de EM observados, a maioria dos erros foram corrigidos e não chegaram ao doente. Tendo em conta os EM observados, a utilização de meios informáticos e o aumento da adesão dos enfermeiros ao procedimento de identificação dos doentes poderão permitir a redução do número de EM em cerca de 80%, reduzindo também a probabilidade de ocorrência de eventos adversos relacionados com os erros ativos na utilização de medicamentos.