Guidelines and considerations for conducting experiments using tissue microarrays

Tissue microarrays (TMAs) represent a powerful method for undertaking large-scale tissue-based biomarker studies. While TMAs offer several advantages, there are a number of issues specific to their use which need to be considered when employing this method. Given the investment in TMA-based research, guidance on design and execution of experiments will be of benefit and should help researchers new to TMA-based studies to avoid known pitfalls. Furthermore, a consensus on quality standards for TMA-based experiments should improve the robustness and reproducibility of studies, thereby increasing the likelihood of identifying clinically useful biomarkers. In order to address these issues, the National Cancer Research Institute Biomarker and Imaging Clinical Studies Group organized a 1-day TMA workshop held in Nottingham in May 2012. The document herein summarizes the conclusions from the workshop. It includes guidance and considerations on all aspects of TMA-based research, including the pre-analytical stages of experimental design, the analytical stages of data acquisition, and the postanalytical stages of data analysis. A checklist is presented which can be used both for planning a TMA experiment and interpreting the results of such an experiment. For studies of cancer biomarkers, this checklist could be used as a supplement to the REMARK guidelines.

Effectiveness of granular columns in containing settlement

Laboratory-based research studies and full-scale evaluations of the behaviour of ground improved with granular columns are ample regarding bearing capacity, but limited in respect to the settlement response. This paper presents a laboratory model study that considers the settlement performance of isolated pad footings bearing on reinforced sand deposits under the influence of a fluctuating groundwater table. This is a particularly onerous condition for loose sand deposits in coastal areas which may undergo significant collapse settlement over time. Loose and dense experimental sand beds were constructed and the performance of rigid footings under a maintained load and bearing on sand incorporating different column configurations were monitored under cycling of the water table over a period of 28 days, with one filling/empting cycle every 18 h. It was found that settlement, while greatly reduced compared with unreinforced footings, was ongoing and typically occurred at a much greater rate for loose sand than dense sand. Also, settlement rates were slightly higher for fully penetrating than partially penetrating columns and also for footings reinforced by a column group rather than a single column. This was attributed to the migration of sand grains into the larger column voids.

Statistically-constrained shallow text marking:Techniques, evaluation paradigm and results

We present three natural language marking strategies based on fast and reliable shallow parsing techniques, and on widely available lexical resources: lexical substitution, adjective conjunction swaps, and relativiser switching. We test these techniques on a random sample of the British National Corpus. Individual candidate marks are checked for goodness of structural and semantic fit, using both lexical resources, and the web as a corpus. A representative sample of marks is given to 25 human judges to evaluate for acceptability and preservation of meaning. This establishes a correlation between corpus based felicity measures and perceived quality, and makes qualified predictions. Grammatical acceptability correlates with our automatic measure strongly (Pearson's r = 0.795, p = 0.001), allowing us to account for about two thirds of variability in human judgements. A moderate but statistically insignificant (Pearson's r = 0.422, p = 0.356) correlation is found with judgements of meaning preservation, indicating that the contextual window of five content words used for our automatic measure may need to be extended. © 2007 SPIE-IS&T.

Spatial statistics to estimate peat thickness using airborne radiometric data

Soil carbon stores are a major component of the annual returns required by EU governments to the Intergovernmental Panel on Climate Change. Peat has a high proportion of soil carbon due to the relatively high carbon density of peat and organic-rich soils. For this reason it has become increasingly important to measure and model soil carbon stores and changes in peat stocks to facilitate the management of carbon changes over time. The approach investigated in this research evaluates the use of airborne geophysical (radiometric) data to estimate peat thickness using the attenuation of bedrock geology radioactivity by superficial peat cover. Remotely sensed radiometric data are validated with ground peat depth measurements combined with non-invasive geophysical surveys. Two field-based case studies exemplify and validate the results. Variography and kriging are used to predict peat thickness from point measurements of peat depth and airborne radiometric data and provide an estimate of uncertainty in the predictions. Cokriging, by assessing the degree of spatial correlation between recent remote sensed geophysical monitoring and previous peat depth models, is used to examine changes in peat stocks over time. The significance of the coregionalisation is that the spatial cross correlation between the remote and ground based data can be used to update the model of peat depth. The result is that by integrating remotely sensed data with ground geophysics, the need is reduced for extensive ground-based monitoring and invasive peat depth measurements. The overall goal is to provide robust estimates of peat thickness to improve estimates of carbon stocks. The implications from the research have a broader significance that promotes a reduction in the need for damaging onsite peat thickness measurement and an increase in the use of remote sensed data for carbon stock estimations.

Educational interventions in neurology:A comprehensive systematic review

A fear of neurology and neural sciences (neurophobia) may have clinical consequences. There is therefore a need to formulate an evidence-based approach to neurology education. A comprehensive systematic review of educational interventions in neurology was performed. BEI, Cochrane Library, Dialog Datastar, EBSCO Biomedical, EBSCO Psychology & Behavioral Sciences, EMBASE, ERIC, First Search, MDConsult, Medline, Proquest Medical Library and Web of Knowledge databases were searched for all published studies assessing interventions in neurology education among undergraduate students, junior medical doctors and residents up to and including July 2012. Two independent literature searches were performed for relevant studies, which were then classified for level of evidence using the Centre of Evidence-based Medicine criteria and four levels of Kirkpatrick educational outcomes. One systematic review, 16 randomized controlled trials (RCTs), nine non-randomized cohort/follow-up studies, 33 case series or historically controlled studies and three mechanism-based reasoning studies were identified. Educational interventions showed favourable evaluation or assessment outcomes in 15 of 16 (94%) RCTs. Very few studies measured subsequent clinical behaviour (two studies) and patient outcomes (one study). There is very little high quality evidence of demonstrably effective neurology education. However, RCTs are emerging, albeit without meeting comprehensive educational criteria. An improving evidence base in the quality of neurology education will be important to reduce neurophobia. © 2013 EFNS.

The Effectiveness of Weight Management Interventions in Breastfeeding Women—A Systematic Review and Critical Evaluation

Background: The postpartum period is a vulnerable time for excess weight retention, particularly for the increasing number of women who are overweight at the start of their pregnancy and subsequently find it difficult to lose additional weight gained during pregnancy. Although postpartum weight management interventions play an important role in breaking this potentially vicious cycle of weight gain, the effectiveness of such interventions in breastfeeding women remains unclear. Our aim was to systematically review the literature about the effectiveness of weight management interventions in breastfeeding women.

Methods: Seven electronic databases were searched for eligible papers. Intervention studies included were carried out exclusively in breastfeeding mothers, ≤2 years postpartum and with a body mass index greater than 18.5 kg/m2, with an outcome measure of change in weight and/or body composition.

Results: Six studies met the selection criteria, and were stratified according to the type of intervention and outcome measures. Despite considerable heterogeneity among studies, the dietary-based intervention studies appeared to be the most efficacious in promoting weight loss; however, few studies were tailored toward the needs of breastfeeding women.

Conclusions: Weight management interventions which include an energy-restricted diet may play a key role in successful postpartum weight loss for breastfeeding mothers.

Thermolabile methylenetetrahydrofolate reductase (C677T):frequency in the Irish population

BACKGROUND: The genetic variation which underlies the thermolability and low enzyme activity of 5,10-methylenetetrahydrofolate reductase (MTHFR; C677T) has been extensively studied in many populations, including the Irish population.

AIM: To describe the examination of the C677T substitution in two new control samples drawn from the Irish population.

METHODS: A collection of 487 serum samples was obtained through the blood transfusion services of both the Republic of Ireland and Northern Ireland and a further 115 samples from volunteers.

RESULTS: In both samples, the frequency of the thermolabile/low enzyme activity allele (T) was higher than that previously reported for the Irish population.

CONCLUSION: This finding thus supports the need for a greater use of internal control/family-based association studies, as opposed to the classic case control study design, when assessing the contribution of the MTHFR T allele to disease processes.

Smoking and All-cause Mortality in Older Adults: Results From the CHANCES Consortium

INTRODUCTION: Smoking is known to be a major cause of death among middle-aged adults, but evidence on its impact and the benefits of smoking cessation among older adults has remained limited. Therefore, we aimed to estimate the influence of smoking and smoking cessation on all-cause mortality in people aged ≥60 years.

METHODS: Relative mortality and mortality rate advancement periods (RAPs) were estimated by Cox proportional hazards models for the population-based prospective cohort studies from Europe and the U.S. (CHANCES [Consortium on Health and Ageing: Network of Cohorts in Europe and the U.S.]), and subsequently pooled by individual participant meta-analysis. Statistical analyses were performed from June 2013 to March 2014.

RESULTS: A total of 489,056 participants aged ≥60 years at baseline from 22 population-based cohort studies were included. Overall, 99,298 deaths were recorded. Current smokers had 2-fold and former smokers had 1.3-fold increased mortality compared with never smokers. These increases in mortality translated to RAPs of 6.4 (95% CI=4.8, 7.9) and 2.4 (95% CI=1.5, 3.4) years, respectively. A clear positive dose-response relationship was observed between number of currently smoked cigarettes and mortality. For former smokers, excess mortality and RAPs decreased with time since cessation, with RAPs of 3.9 (95% CI=3.0, 4.7), 2.7 (95% CI=1.8, 3.6), and 0.7 (95% CI=0.2, 1.1) for those who had quit <10, 10 to 19, and ≥20 years ago, respectively.

CONCLUSIONS: Smoking remains as a strong risk factor for premature mortality in older individuals and cessation remains beneficial even at advanced ages. Efforts to support smoking abstinence at all ages should be a public health priority.

Participating in a fruit and vegetable intervention trial improves longer term fruit and vegetable consumption and barriers to fruit and vegetable consumption: a follow-up of the ADIT study

BACKGROUND: Fruit and vegetable (FV) based intervention studies can be effective in increasing short term FV consumption. However, the longer term efficacy of such interventions is still unclear. The aim of the current study was to examine the maintenance of change in FV consumption 18-months after cessation of a FV intervention and to examine the effect of participating in a FV intervention on barriers to FV consumption.

METHODS: A follow-up of a randomised controlled FV trial in 83 older adults (habitually consuming ≤2 portions/day) was conducted. At baseline, participants were assigned to continue consuming ≤2 portions FV/day or consume ≥5 portions FV/day for 16-weeks. We assessed FV intake and barriers to FV consumption at baseline, end of intervention and 18-months post-intervention.

RESULTS: At 18-months, mean FV intakes in both groups were greater than baseline. The 5 portions/day group continued to show greater increases in FV consumption at 18-months than the 2 portions/day group (p < 0.01). At 18-months, both groups reported greater liking (p < 0.01) and ease in consuming FV (p = 0.001) while difficulties with consuming FV decreased (p < 0.001). The 2 portions/day group reported greater awareness of FV recommendations at 18-months (p < 0.001).

CONCLUSIONS: Participating in a FV intervention can lead to longer-term positive changes in FV consumption regardless of original group allocation.

TRIAL REGISTRATION: Clinical Trials.gov NCT00858728 .

Generating a Word-Emotion Lexicon from #Emotional Tweets

Research in emotion analysis of text suggest that emotion lexicon based features are superior to corpus based n-gram features. However the static nature of the general purpose emotion lexicons make them less suited to social media analysis, where the need to adopt to changes in vocabulary usage and context is crucial. In this paper we propose a set of methods to extract a word-emotion lexicon automatically from an emotion labelled corpus of tweets. Our results confirm that the features derived from these lexicons outperform the standard Bag-of-words features when applied to an emotion classification task. Furthermore, a comparative analysis with both manually crafted lexicons and a state-of-the-art lexicon generated using Point-Wise Mutual Information, show that the lexicons generated from the proposed methods lead to significantly better classi- fication performance.

Music therapy for end-of-life care: an updated systematic review

Background: Music therapy during palliative and end-of-life care is well established and positive benefits for patients have been reported.
Aim: Assess the effectiveness of music therapy versus standard care alone or standard care in combination with other therapies for improving psychological, physiological and social outcomes among adult patients in any palliative care setting.
Data sources: In order to update an existing Cochrane systematic review, we searched MEDLINE, CINAHL, EMBASE, PsycINFO, CENTRAL, ClinicalTrials.gov register, and Current Controlled Trials register to identify randomised or quasi-randomised controlled trails published between 2009 and April 2015. Nine electronic music therapy journals were searched from 2009 until April 2015, along with reference lists and contact was made with key experts in music therapy. Only studies published in English were eligible for inclusion. Two reviewers independently screened titles, abstracts, assessed relevant studies for eligibility, extracted data and judged risk of bias for included studies. Disagreements were resolved through discussion with a third reviewer. Data were synthesised in Revman using the random effects model. Heterogeneity was assessed using l2.
Results: Three studies were included in the review. Findings suggest music therapy may be effective for helping to reduce pain in palliative care patients (standard mean deviation (SMD) = -0.42, 95% CI -0.68 to -0.17, P = 0.001).
Conclusions: Available evidence did not support the use of music therapy to improve overall quality-of-life in palliative care. While this review suggests music therapy may be effective for reducing pain, this is based on studies with a high risk of bias. Further high quality research is required.

Redução para piano: três especificidades

Este projeto de investigação foca a análise das diversas problemáticas no domínio da redução para piano suscitadas por linguagens e por obras emblemáticas do repertório musical contemporâneo. O estudo teve como principal objetivo compreender realizar uma redução para piano, tendo como base os estudos que se debruçam sobre questões de orquestração, transcrição, acompanhamento, bem como inúmeros exemplos de reduções existentes. São realizados estudos sobre as diferenças entre redução e transcrição para piano, sobre os critérios de escolha de material musical, sobre a reorquestração da conteúdo nas reduções, sobre a problemática de execução das reduções ao piano, sobre questões de leitura à primeira vista e, finalmente, sobre aspetos de apresentação. O conteúdo de investigação é dividido de acordo com três especificidades das reduções para piano. Como exemplo de cada uma delas foram realizadas novas reduções das seguintes obras: Concerto da Camera col Violoncello Obbligato de Lopes-Graça; Pli selon pli de Boulez e ópera Lady Sarashina de Eötvös. A génese destas obras e os procedimentos necessários à sua redução foram também objeto de estudo nesta dissertação. Todas as reduções foram apresentadas publicamente e preparadas para edição. O estudo aqui realizado pretende contribuir para a melhoria do conhecimento sobre as reduções para piano, procurando definir ou ajudar à compreensão das soluções viáveis pianisticamente e facilmente aplicáveis na prática. This research project focuses on the analysis of various problems in the field of piano reduction that are caused by languages and emblematic works of contemporary repertoire. This work aims to understand how to make a piano reduction and is based on studies that address various issues in orchestration, transcription, accompaniment and numerous examples of existing piano reductions. Studies were made on the difference between piano reduction and transcription, on the selection criteria of musical material, on re-orchestration of content in piano reduction, and on issues related with performance of reduction at the piano, sight-reading and aspects of score presentation. The content of this research is divided into three specifications of piano reductions. For each section an example was done of each of these works: Lopes-Graça´s Concerto da Camera col Violoncello Obbligato; Boulez´s Pli selon pli and Eötvös´s opera Lady Sarashina. The genesis of these works and their related process of reduction was also studied in this dissertation. All reductions were prepared for edition and presentation to the public. This study aims to contribute to the knowledge on piano reduction, seeking for viable pianistic solutions which can be easily applied in practice.

Avanços metodológicos na síntese de novos derivados de flavonas

As estirilflavonas poli-hidroxiladas são compostos heterocíclicos de natureza polifenólica que suscitam interesse devido à atividade biológica que possuem atuando, por exemplo, como antioxidantes. O desenvolvimento de novas rotas de síntese de estirilflavonas constitui um desafio e é neste contexto que se têm efetuado vários estudos sobre a aplicação de reações de acoplamento cruzado catalisadas por paládio, como a reação de Heck, na preparação deste tipo de compostos. Nesta dissertação reporta-se a síntese de (E)-8-estirilflavonas através da reação de Heck de 8-iodoflavonas com derivados de estireno com rendimentos excelentes, descrevendo-se um estudo no qual se optimizaram as condições experimentais desta reação. Adicionalmente, descrevem-se duas tentativas de desmetilação da (E)-8-[2-(4-metoxifenil)vinil]-4’,5,7-trimetoxiflavona. As 8- iodoflavonas foram preparadas com elevada regiosseletividade através da ciclização oxidativa/iodação das (E)-2’-hidroxicalconas correspondentes por aplicação do sistema de reagentes I2/DMSO. A propósito, descreve-se um estudo de ciclização oxidativa/iodação da (E)-2’-hidroxi-4,4’,6’- trimetoxicalcona, no qual se testou a aplicação do sistema de reagentes I2/DMSO na síntese de iodoflavonas em reações one-pot. As (E)-2’- hidroxicalconas foram sintetizadas através da condensação aldólica catalisada por base entre a 2’-hidroxi-4’,6’-dimetoxiacetofenona, previamente preparada, e derivados de benzaldeído. A caraterização estrutural da maioria dos compostos obtidos neste trabalho foi efetuada com base em estudos de espetroscopia de ressonância magnética nuclear (RMN), nomeadamente de 1H e 13C, e, sempre que possível, em estudos bidimensionais de correlação espetroscópica heteronuclear (HSQC e HMBC), bem como em estudos de espetrometria de massa (EM).

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.

A Pesquisa em tradução literária – proposta metodológica

Uma referência ainda hoje obrigatória no âmbito da investigação em tradução é, sem dúvida, a célebre conferência de James S. Holmes “The Name and Nature of Translation Studies”, apresentada no III Congresso Internacional de Linguística Aplicada (Copenhague, 1972) e publicada numa versão revista e ampliada em Translated! (1988), na qual Holmes nos proporciona um esquema teórico sobre o que envolve o estudo científico da Tradução.