Comprehensive molecular pathology analysis of small bowel adenocarcinoma reveals novel targets with potential for clinical utility

Small bowel accounts for only 0.5% of cancer cases in the US but incidence rates have been rising at 2.4% per year over the past decade. One-third of these are adenocarcinomas but little is known about their molecular pathology and no molecular markers are available for clinical use. Using a retrospective 28 patient matched normal-tumor cohort, next-generation sequencing, gene expression arrays and CpG methylation arrays were used for molecular profiling. Next-generation sequencing identified novel mutations in IDH1, CDH1, KIT, FGFR2, FLT3, NPM1, PTEN, MET, AKT1, RET, NOTCH1 and ERBB4. Array data revealed 17% of CpGs and 5% of RNA transcripts assayed to be differentially methylated and expressed respectively (p < 0.01). Merging gene expression and DNA methylation data revealed CHN2 as consistently hypermethylated and downregulated in this disease (Spearman -0.71, p < 0.001). Mutations in TP53 which were found in more than half of the cohort (15/28) and Kazald1 hypomethylation were both were indicative of poor survival (p = 0.03, HR = 3.2 and p = 0.01, HR = 4.9 respectively). By integrating high-throughput mutational, gene expression and DNA methylation data, this study reveals for the first time the distinct molecular profile of small bowel adenocarcinoma and highlights potential clinically exploitable markers.

Twitter Sentiment Analysis for Security-Related Information Gathering

Analysing public sentiment about future events, such as demonstration or parades, may provide valuable information while estimating the level of disruption and disorder during these events. Social media, such as Twitter or Facebook, provides views and opinions of users related to any public topics. Consequently, sentiment analysis of social media content may be of interest to different public sector organisations, especially in the security and law enforcement sector. In this paper we present a lexicon-based approach to sentiment analysis of Twitter content. The algorithm performs normalisation of the sentiment in an effort to provide intensity of the sentiment rather than positive/negative label. Following this, we evaluate an evidence-based combining function that supports the classification process in cases when positive and negative words co-occur in a tweet. Finally, we illustrate a case study examining the relation between sentiment of twitter posts related to English Defence League and the level of disorder during the EDL related events.

Effect of poly ethylene glycol on the mechanical and thermal properties of bioactive Poly (ε–caprolactone) melt extrudates for pharmaceutical applications

This paper investigates the effects of polyethylene glycol (PEG), on the mechanical and thermal properties of nalidixic acid/ploy ε-caprolactone (NA)/PCL blends prepared by hot melt extrusion. The blends were characterized by tensile and flexural analysis, dynamic mechanical analysis, differential scanning calorimetry, thermogravimetric analysis and X-ray diffraction. Experimental data indicated that the addition of NA caused loss of the tensile strength and toughness of PCL. Thermal analysis of the PCL showed that on addition of the thermally unstable NA, thermal degradation occurred early and was autocatalytic. However, the NA did benefit from the heat shielding provided by the PCL matrix resulting in more thermally stable NA particles. Results show that loading PEG in the PCL had a detrimental effect on the tensile strength and toughness of the blends, reducing them by 20-40%. The partial miscibility of the PCL-PEG system, causes an increase in Tg. While increases in the crystallinity is attributed to the plasticisation effect of PEG and the nucleation effect of NA. The average crystal size increased by 8% upon PEG addition.

Pharmacy students' use and views on over-the-counter (OTC) medicines; a questionnaire study

Introduction
The role of the pharmacist centers on ensuring the safe and effective use of medicines, including over-the-counter (OTC) medicines. It is important to ascertain pharmacy students’ use and opinions on OTC medicines, given that they are the pharmacists of the future and that this market continues to expand. This study aimed to investigate Queen’s University Belfast (QUB) final year pharmacy students’ use and views on OTC medicines. Scarce work has been conducted in this area to date.

Methods
Following ethical approval and a pilot study, all students (n=155) were invited to participate in a self-completed questionnaire (n=20 questions), distributed at a mandatory class. Descriptive statistics and non-parametric tests (Chi-squared and Mann Whitney U-test) were used for data analyses.

Results
The response rate was 99.4% (154/155). The majority (153/155) reported using OTC medicines; the key consideration during personal product selection was effectiveness. Most [96.1% (147/153)] were in agreement that safety was the over-riding concern during OTC consultations. While 96.1% (149/155) considered that using an evidence-based approach improved the quality of patient care, 68.0% (104/153) would be prepared to sell a product that lacks evidence of effectiveness, provided it would not cause harm.

Conclusions
The importance of evidence of effectiveness was acknowledged, yet many students in this study were prepared to recommend unproven products. Further strategies are required at QUB to ensure this routine consideration alongside safety in practice.

Vitamin D3 suppresses morphological evolution of the cribriform cancerous phenotype

Development of cribriform morphology (CM) heralds malignant change in human colon but lack of mechanistic understanding hampers preventive therapy. This study investigated CM pathobiology in three-dimensional (3D) Caco-2 culture models of colorectal glandular architecture, assessed translational relevance and tested effects of 1,25(OH)2D3, the active form of vitamin D. CM evolution was driven by oncogenic perturbation of the apical polarity (AP) complex comprising PTEN, CDC42 and PRKCZ (phosphatase and tensin homolog, cell division cycle 42 and protein kinase C zeta). Suppression of AP genes initiated a spatiotemporal cascade of mitotic spindle misorientation, apical membrane misalignment and aberrant epithelial configuration. Collectively, these events promoted “Swiss cheese-like” cribriform morphology (CM) comprising multiple abnormal “back to back” lumens surrounded by atypical stratified epithelium, in 3D colorectal gland models. Intestinal cancer driven purely by PTEN-deficiency in transgenic mice developed CM and in human CRC, CM associated with PTEN and PRKCZ readouts. Treatment of PTEN-deficient 3D cultures with 1,25(OH)2D3 upregulated PTEN, rapidly activated CDC42 and PRKCZ, corrected mitotic spindle alignment and suppressed CM development. Conversely, mutationally-activated KRAS blocked 1,25(OH)2D3 rescue of glandular architecture. We conclude that 1,25(OH)2D3 upregulates AP signalling to reverse CM in a KRAS wild type (wt), clinically predictive CRC model system. Vitamin D could be developed as therapy to suppress inception or progression of a subset of colorectal tumors.

Intentionality, morality, and the incest taboo in Madagascar

In a recent article (Astuti & Bloch, 2015), cognitive anthropologists Rita Astuti and Maurice Bloch claim that the Malagasy are ambivalent as to whether considerations of intentionality are relevant to moral judgments concerning incest and its presumed catastrophic consequences: when making moral judgments about those who commit incest, the Malagasy take into account whether the incest is intentional or not, but, when making moral judgments relating to incest’s catastrophic consequences, they do not take intentionality into account. Astuti & Bloch explain the irrelevance of intentionality in terms of incest entailing such a fundamental attack on the transcendental social order that the Malagasy become dumbfounded and leave aside considerations of intentionality. Finally, they claim that a similar dumbfound reaction is what is involved in the moral dumbfounding concerning incest that social psychologist Jonathan Haidt has found in the US. In this article, we argue that (i) Astuti & Bloch are unclear about many aspects of their claims (in particular, about the moral judgments at stake), (ii) they do not provide sufficient evidence that considerations of intentionality are deemed irrelevant to moral judgments relating to incest’s presumed catastrophic consequences (and hence for the claim that the Malagasy are ambivalent), (iii) their hypothesis that conceiving of incest as an attack on the transcendental social renders considerations of intentionality irrelevant lacks coherence, and (iv) the extension of their explanatory account to the moral dumfounding of American students in Haidt’s well-known scenario of intentional incest is unwarranted.

A comparison of endoscopy versus pathology sizing of colorectal adenomas and potential implications for surveillance colonoscopy

Background and AimsTo compare endoscopy and pathology sizing in a large population-based series of colorectal adenomas and to evaluate the implications for patient stratification into surveillance colonoscopy.MethodsEndoscopy and pathology sizes available from intact adenomas removed at colonoscopies performed as part of the Northern Ireland Bowel Cancer Screening Programme, from 2010 to 2015, were included in this study. Chi-squared tests were applied to compare size categories in relation to clinicopathological parameters and colonoscopy surveillance strata according to current American Gastroenterology Association and British Society of Gastroenterology guidelines.ResultsA total of 2521 adenomas from 1467 individuals were included. There was a trend toward larger endoscopy than pathology sizing in 4 of the 5 study centers, but overall sizing concordance was good. Significantly greater clustering with sizing to the nearest 5 mm was evident in endoscopy versus pathology sizing (30% vs 19%, p<0.001), which may result in lower accuracy. Applying a 10-mm cut-off relevant to guidelines on risk stratification, 7.3% of all adenomas and 28.3% of those 8 to 12 mm in size had discordant endoscopy and pathology size categorization. Depending upon which guidelines are applied, 4.8% to 9.1% of individuals had differing risk stratification for surveillance recommendations, with the use of pathology sizing resulting in marginally fewer recommended surveillance colonoscopies.ConclusionsChoice of pathology or endoscopy approaches to determine adenoma size will potentially influence surveillance colonoscopy follow-up in 4.8% to 9.1% of individuals. Pathology sizing appears more accurate than endoscopy sizing, and preferential use of pathology size would result in a small, but clinically important, decreased burden on surveillance colonoscopy demand. Careful endoscopy sizing is required for adenomas removed piecemeal.

Challenging the cancer molecular stratification dogma: Intratumoral heterogeneity undermines consensus molecular subtypes and potential diagnostic value in colorectal cancer

Purpose:
A number of independent gene expression profiling studies have identified transcriptional subtypes in colorectal cancer (CRC) with potential diagnostic utility, culminating in publication of a CRC Consensus Molecular Subtype classification. The worst prognostic subtype has been defined by genes associated with stem-like biology. Recently, it has been shown that the majority of genes associated with this poor prognostic group are stromal-derived. We investigated the potential for tumor misclassification into multiple diagnostic subgroups based on tumoral region sampled.

Experimental Design:
We performed multi-region tissue RNA extraction/transcriptomic analysis using Colorectal Specific Arrays on invasive front, central tumor and lymph node regions selected from tissue samples from 25 CRC patients.

Results:
We identified a consensus 30 gene list which represents the intratumoral heterogeneity within a cohort of primary CRC tumors. Using a series of online datasets, we showed that this gene list displays prognostic potential (HR=2.914 (CI 0.9286-9.162) in stage II/III CRC patients, but in addition we demonstrated that these genes are stromal derived, challenging the assumption that poor prognosis tumors with stem-like biology have undergone a widespread Epithelial Mesenchymal Transition (EMT). Most importantly, we showed that patients can be simultaneously classified into multiple diagnostically relevant subgroups based purely on the tumoral region analysed.

Conclusions:
Gene expression profiles derived from the non-malignant stromal region can influence assignment of CRC transcriptional subtypes, questioning the current molecular classification dogma and highlighting the need to consider pathology sampling region and degree of stromal infiltration when employing transcription-based classifiers to underpin clinical decision-making in CRC.

Immune-derived PD-L1 gene expression defines a subgroup of stage II/III colorectal cancer patients with favorable prognosis that may be harmed by adjuvant chemotherapy

A recent phase 2 study of metastatic colorectal carcinoma (CRC) patients showed that mismatch repair gene status was predictive of clinical response to PD-1-targeting immune checkpoint blockade. Further examination revealed strong correlation between PD-L1 protein expression and microsatellite instability (MSI) in stage IV CRC, suggesting that the amount of PD-L1 protein expression could identify late stage patients who may benefit from immunotherapy. To assess whether the clinical associations between PD-L1 gene expression and MSI identified in metastatic CRC are also present in stage II/III CRC, we used in silico analysis to elucidate the cell types expressing the PD-L1 gene. We found a significant association of PD-L1 gene expression with MSI in early stage CRC (P < 0.001) and show that unlike in non-CRC tumors, PD-L1 is derived predominantly from the immune infiltrate. We demonstrate that PD-L1 gene expression has positive prognostic value in the adjuvant disease setting (PD-L1low v PD-L1high HR = 9.09; CI, 2.11-39.10). PD-L1 gene expression had predictive value, as patients with high PD-L1 expression appear to be harmed by standard-of-care treatment (HR = 4.95; CI,1.10-22.35). Building on the promising results from the metastatic CRC PD-1-targeting trial, we provide compelling evidence that PD-L1high/MSI/immunehigh stage II/III CRC patients should not receive standard chemotherapy. This conclusion supports the rationale to clinically evaluate this patient subgroup for PD-1 blockade treatment.

Bursaphelenchus xylophilus : opportunities in comparative genomics and molecular host–parasite interactions

Most Bursaphelenchus species are fungal feeding nematodes that colonize dead or dying trees. However, Bursaphelenchus xylophilus , the pine wood nematode, is also a pathogen of trees and is the causal agent of pine wilt disease. B. xylophilus is native to North America and here it causes little damage to trees. Where it is introduced to new regions it causes huge damage. The most severely affected areas are found in the Far East but more recently B. xylophilus has been introduced into Portugal and the potential for damage here is also high. As incidence and severity of pine wilt disease are linked to temperature we suggest that climate change is likely to exacerbate the problems caused by B. xylophilus and, in addition, will extend (northwards in Europe) the range in which pine wilt disease can occur. Here we review what is currently known about the interactions of B. xylophilus with its hosts, including recent developments in our understanding of the molecular biology of pathogenicity in the nematode. We also examine the potential developments that could be made by more widespread use of genomics tools to understand interactions between B. xylophilus , bacterial pathogens that have been implicated in disease and host trees.

Histórias em Intercompreensão: a voz dos autores

Este relatório foi elaborado no âmbito do lote 7 (Inserção Curricular da Intercompreensão) do projeto MIRIADI. Trata-se de um lote cujo objetivo é desenvolver processos de integração curricular da Intercompreensão (IC) à distância em grupos plurilingues, a partir de trabalhos experimentais levados a cabo no terreno e realizados numa lógica de investigação-ação, tendo em vista compreender as “condições de exequibilidade” desta abordagem didática nos curricula de aprendizagem de línguas e de formação. Procura-se, em particular, identificar empiricamente permeabilidades e resistências dos contextos e dos atores educativos face à IC como conceito prático com relevância profissional, bem como vantagens e limites do ponto de vista da aprendizagem linguística que possam justificar o seu valor educativo. A Intercompreensão tem vindo, nas últimas décadas, a percorrer um percurso de destaque em Didática de Línguas (sobretudo Estrangeiras) na Europa e fora dela, em particular no âmbito das atuais abordagens plurais, ocupando um lugar de visibilidade nos discursos e práticas de investigação e formação desta disciplina e contribuindo para a tonalidade da sua voz mais propriamente politico-ideológica (Alarcão, Andrade, Araújo e Sá, Melo-Pfeifer & Santos, 2009). Contudo, a presença do conceito nos espaços concretos de educação em línguas (tais como escolas, liceus, universidades e outras instituições) é extremamente débil, limitando-se a algumas experiências pontuais, sob o impulso (e mesmo a condução), na maior parte dos casos, dos investigadores e tendo como finalidade principal a produção de conhecimento didático (Degache & Tavares, 2011). Assim, pouco se sabe ainda do que pode ser efetivamente o contributo da IC para o projeto educativo das instituições, e muito menos do modo como o conceito pode ser integrado em práticas curriculares continuadas e sistemáticas de educação em línguas, sabendo-se que estas mesmas práticas são reguladas por múltiplas instâncias, internas e externas, objetivas e subjetivas, que atuam a vários níveis (macro, meso, micro) e que não podem deixar de ser consideradas. O lote 7 de Miriadi propõe abordar estas questões, relativas à integração curricular da IC, a partir de uma outra lógica epistemológica, uma lógica que não busca propostas desenhadas a partir dos resultados da investigação e orientadas para a transferência do conhecimento, ou seja, que não reflete uma perspetiva aplicacionista do saber didático. Ao invés, o trabalho realizado por este lote entende o currículo como uma construção dinâmica que se (re)define e se (re)negocia em função dos contextos específicos em que ocorre, atribuindo-lhe por conseguinte uma natureza contingente, situada, intersubjetiva e local. Nesta perspetiva sócio-construtivista, em que o currículo é uma co-construção que ocorre entre sujeitos precisos nas suas ações educativas quotidianas, a integração curricular da IC produz-se no âmbito destas ações, ou, dito de outra forma, através de práticas situadas nas especificidades e possibilidades que oferecem os contextos concretos, em particular os sujeitos que deles fazem parte. Esta perspetiva de trabalho do lote 7 parece-nos ser a mais coerente com o posicionamento teórico relativamente à IC enquanto conceito didático do projeto MIRIADI. Com efeito, está amplamente estudado que a IC tem vindo a ser tratada segundo diferentes pontos de vista, de acordo com as escolas epistemológicas e as proveniências e ancoragens disciplinares dos seus autores (para uma revisão recente, ver Araújo e Sá, 2013; Olliver, 2013). No âmbito do percurso específico de investigação/formação/intervenção do grupo e-Gala (www.e-gala.eu), no seio do qual emergiu MIRIADI, em particular das suas mais disseminadas realizações – as plataformas Galanet (www.galanet.eu) e Galapro (www-galapro.eu/sessions) -, a IC é abordada numa perspetiva socio-construtivista do saber e da relação comunicativa. Dito de outra forma, MIRIADI define a IC como um processo e uma prática interacional que ocorre entre sujeitos, atores sociais que vivem em diferentes línguas e que se implicam coletivamente num quadro dialógico “où le grand enjeu devient la construction d’un territoire de parole partagé” (Araújo e Sá, Degache & Spita, 2010: 26). Esta aceção interacionista (e plurilingue e intercultural) é complementada pelo recurso a meios de comunicação tecnológicos. Definido o enquadramento conceptual e metodológico do lote7, importa agora explicitar como se desenvolveu o trabalho ao longo dos seus 36 meses de execução. O lote organizou-se em 3 grandes etapas, que envolveram toda a equipa: Etapa 1. Identificação e caracterização de contextos de ensino e formação linguística suscetíveis de poderem beneficiar de uma integração curricular da IC (plurilingue e à distância) (os resultados desta etapa encontram-se na Prestation 7.1. do projeto, referida na nota anterior). Etapa 2. Planificação e desenvolvimento de múltiplas e diversificadas iniciativas de divulgação da IC nesses mesmos contextos, destinadas à comunidade educativa na generalidade (públicos, professores/formadores, órgãos de gestão, funcionários, etc.), tendo em vista a sua familiarização com a IC enquanto conceito didático e prática de educação em línguas, de modo a criar condições (e aberturas) para a sua integração curricular; uma atenção especial foi dada à formação dos agentes educativos. Etapa 3. Planificação, experimentação e avaliação, numa lógica de investigação-ação e em rede (aproveitando-se as potencialidades das plataformas Galapro e Galanet), de propostas de integração curricular da IC; pretendia-se, em especial, com estas propostas, identificar contributos da IC para a qualidade dos projetos educativos dos contextos de integração caracterizados (na etapa 1), mas também constrangimentos, fragilidades, obstáculos e resistências, numa abordagem crítica do conceito que fosse sensível às propriedades dos espaços-alvo de educação em línguas. Neste sentido, foram recolhidos, analisados e discutidos, em função das suas características contextuais (definidas na etapa 1), dados empíricos de natureza diversa (produções dos alunos, transcrições de excertos de aulas, testemunhos espontâneos de alunos e professores, respostas a questionários, entre outros). Este Rapport é um produto da Etapa 3. Trata-se de um documento multimédia, que pretende dar acesso sistematizado e crítico aos discursos e vozes de sujeitos reais que experienciaram propostas didáticas concretas de IC elaboradas durante esta etapa do lote. Mais concretamente, este relatório oferece 6 narrativas de estudos de caso (3 em contexto de ensino secundário e outros 3 no ensino superior), realizados em vários países (Brasil, França, Itália Portugal e República da Maurícia), contendo uma descrição detalhada das situações educativas experimentadas e uma análise dos dados recolhidos, com apresentação dos recursos e materiais utilizados e testemunhos dos sujeitos concretos (professores e alunos). Incluem-se igualmente os instrumentos de recolha de dados e alguns exemplos dos mesmos. Cada narrativa obedece a uma mesma estrutura discursiva, de forma a mais facilmente poderem ser comparáveis, permitindo a extração de conclusões transversais aos vários estudos: introdução; descrição do contexto de intervenção; descrição da intervenção (objetivos, atividades, com acesso aos recursos utilizados, e avaliação); resultados obtidos; conclusões e implicações A secção final, “Témoignages”, apresenta-se sob a forma de um conjunto de vídeos e podcasts, identificados de acordo com a instituição parceira do projeto que os recolheu e organizados segundo três critérios: • as línguas dos locutores (espanhol, francês, italiano e português); • os contextos de formação onde decorreram as experiências de IC (ensino secundário e ensino universitário); • o tipo de intervenientes nas experiências de IC (alunos ou professores). Assume-se mais uma vez, neste Rapport, as dinâmicas de trabalho plurilingue da equipa Miriadi, cuja rentabilidade para a produção do conhecimento didático foi analisada e evidenciada no âmbito de projetos anteriores (ver Melo-Pfeifer, 2014) e se encontra ilustrada, numa outra linguagem, nos nossos postais (disponíveis no Facebook). Assim, com exceção desta introdução, que foi traduzida para francês (ver acima), o documento encontra-se nas línguas de trabalho dos membros da equipa que o redigiram.

Quel destin pour l'imaginaire épique et le héros guerrier dans l'écriture? Le témoignage de guerre au Québec de 1914 à nos jours

Cette thèse de doctorat, intitulée «Le récit personnel de guerre dans le Canada français/Québec du XXe siècle», est consacrée à l'étude du traitement de l'imaginaire épique et du héros guerrier dans plus d'une trentaine de témoignages de guerre d'expression française de 1914 à nos jours. Elle établit que le discours sur les combats qui s'y formule «retrouve spontanément le ton de l'épopée, langue maternelle du récit militaire héroïque, celle de l'Iliade » (Maurice RIEUNEAU, Guerre et révolution dans le roman français 1919-1939, Klincksieck, «Bibliothèque du XXe siècle», 1974, p. 157). Cette résilience épique et héroïque remarquable vaut pour toutes les époques. Fait à noter: même dans les récits contestataires, la contestation s'énonce en termes épiques, de héros qui poursuit son combat dans l'espace textuel. Voilà qui nuance quelque peu les résultats d'autres analyses, en particulier en Europe, où les spécialistes retiennent du XXe siècle: «Le récit de guerre [...] a périmé les plaisirs de l'épopée [...].» (Jean KAEMPFER, Poétique du récit de guerre, Paris, José Corti, 1998, p. 39). Avec la (post)modernité, l'épopée se réoriente. Dépassant le complexe du perdant qui marque plusieurs générations de francophones et les rend réceptifs aux valeurs de force et de virilité, le discours sort du repli sur soi, de l'isolement, de la solitude agressive pour pactiser avec l'ennemi juré (l'Allemand, le Japonais, mais aussi le Britannique, le Canadien anglais). Bref, l'identité, ébranlée par la différence, s'équilibre dans une démarche d'assainissement de la mémoire. L'affirmation progressive de soi se double d'une ouverture sur l'étranger, celui d'ailleurs et, à plus forte raison, d'ici.

O Tecer da Memória em Narrativas de Antônio Torres e António Lobo Antunes

Tese apresentada e reformulada de acordo com as orientações do Júri (19 de Dezembro de 2012), para cumprimento dos requisitos necessários à obtenção do grau de Doutor em Estudos Portugueses, Especialidade de Literatura Comparatista.

Réplica, Ruptura, Recomeço: A Passagem de Pessoa no Espaço Literário

Tese apresentada para cumprimento dos requisitos necessários à obtenção do grau de Doutor em Estudos Portugueses – Estudos de Literatura (Teoria da Literatura),