Neural network approach for question generation using the Revised Bloom's Taxonomy

Questioning is a fundamental part of the learning process. As new content arises and learning it becomes vital to the modern society, question generation becomes a necessary job that requires time and resources to be performed effectively. In this document, we propose a Seq2Seq approach that generates a variety of questions that are relevant to the contexts where they are asked. In order to ensure that the generated questions are diverse, relevant, and valuable to learning situations and environments, we use the Revised Bloom’s Taxonomy (RBT), a learning taxonomy that is oriented to learning objectives and can be used to separate questions based on their required cognitive level. However, neural network models require large collections of data to be trained, and datasets addressing RBT are small and scarce. To address this gap, we designed a question classifier that can be used to label current and future datasets using the guidelines provided by RBT. We employed this classifier to create a labeled dataset, which was then used as training data for our proposed Seq2Seq model. In addition, to cover the different taxonomy levels, we create six different fine-tuned models aimed specifically to each one of RBT cognitive levels. Results show that our approach is promising, guaranteeing a variety of questions for all levels of the taxonomy, surpassing the baseline when measured by BLEU-1, and deemed overall well-written, relevant and understandable, by human evaluators.Questionar é uma parte fundamental do processo de aprendizagem. À medida que novos conteúdos surgem e se torna vital a sua compreensão para a sociedade moderna, a geração de questões torna-se uma necessidade que, quando feita manualmente, requer tempo e recursos para ser eficaz. Neste documento introduzimos uma abordagem Sequence-To-Sequence (Seq2Seq) que consiste na geração de uma variedade de questões relevantes para os contextos nas quais são colocadas. De forma a garantir que as questões geradas são diversas, relevantes e de valor acrescentado para situações de aprendizagem, utilizámos a Taxonomia de Bloom Revista (TBR), uma taxomia de aprendizagem que é orientada aos objetivos da aprendizagem e pode ser utilizada para separar questões com base no seu nível cognitivo. Contudo, os modelos de redes neuronais precisam de grandes conjuntos de dados para o seu treino e os datasets atuais orientados à TBR são pequenos e escassos. Para colmatar esta falha, desenhámos um classificador de questões a ser usado para categorizar atuais e futuros datasets tendo em conta as orientações da taxonomia. Utilizámos este classificador para criar um dataset posteriormente utilizado para treinar o modelo Seq2Seq proposto. Adicionalmente, para cobrir os diferentes níveis da taxonomia, criámos seis modelos fine-tuned específicamente para cada um dos níveis cognitivos da TBR. Os resultados mostram que a nossa abordagem é promissora, garantindo variedade de questões para todos os níveis da taxonomia, ultrapassado a baseline quando avaliada usando BLEU-1, e considerada por avaliadores humanos, de forma geral, como uma abordagem que produz questões bem escritas, relevantes e compreensíveis

One millennium of historical freshwater fish occurrence data for Portuguese rivers and streams

The insights that historical evidence of human presence and man-made documents provide are unique. For example, using historical data may be critical to adequately understand the ecological requirements of species. However, historical information about freshwater species distribution remains largely a knowledge gap. In this Data Descriptor, we present the Portuguese Historical Fish Database (PHish–DB), a compilation of 2214 records (557 at the basin scale, 184 at the sub-basin scale and 1473 at the segment scale) resulting from a survey of 194 historical documents. The database was developed using a three-scale approach that maximises the inclusion of information by allowing different degrees of spatial acuity. PHish database contains records of 25 taxonomical groups and covers a time span of one millennium, from the 11th until the 20th century. This database has already proven useful for two scientific studies, and PHish further use will contribute to correctly assess the full range of conditions tolerated by species, by establishing adequate benchmark conditions, and/or to improve existing knowledge of the species distribution limits.info:eu-repo/semantics/publishedVersio

Tetrabenazine versus deutetrabenazine for Huntington's disease : twins or distant cousins?

© 2017 The Authors. Movement Disorders Clinical Practice published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.Background: Tetrabenazine is the only US Food and Drug Administration‐approved drug for Huntington's disease, and deutetrabenazine was recently tested against placebo. A switching‐trial from tetrabenazine to deutetrabenazine is underway, but no head‐to‐head, blinded, randomized controlled trial is planned. Using meta‐analytical methodology, the authors compared these molecules. Methods: RCTs comparing tetrabenazine or deutetrabenazine with placebo in Huntington's disease were searched. The authors assessed the Cochrane risk‐of‐bias tool, calculated indirect treatment comparisons, and applied the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) framework. Results: The evidence network for this report comprised 1 tetrabenazine trial and 1 deutetrabenazine trial, both against placebo. Risk of bias was moderate in both. Participants in the tetrabenazine and deutetrabenazine trials did not differ significantly on motor scores or adverse events. Depression and somnolence scales significantly favored deutetrabenazine. Conclusion: There is low‐quality evidence that tetrabenazine and deutetrabenazine do not differ in efficacy or safety. It is important to note that these results are likely to remain the only head‐to‐head comparison between these 2 compounds in Huntington's disease.info:eu-repo/semantics/publishedVersio

Morphine in acute coronary syndrome : systematic review and meta-analysis

© Author(s) (or their employer(s)) 2019. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.Objective: Morphine is frequently used in acute coronary syndrome (ACS) due to its analgesic effect, it being recommended in the main cardiology guidelines in Europe and the USA. However, controversy exists regarding its routine use due to potential safety concerns. We conducted a systematic review of randomised-controlled trials (RCTs) and observational studies to synthesise the available evidence. Design: Systematic review and meta-analysis. Data sources: CENTRAL, MEDLINE, EMBASE and trial registries. Eligibility criteria for selecting studies: We included RCTs and observational studies evaluating the impact of morphine in cardiovascular outcomes or platelet reactivity measures. Data extraction and synthesis: Data were screened, extracted and appraised by two independent reviewers. The data were pooled results using a random-effects model. Outcomes included in-hospital mortality, major adverse cardiovascular events (MACE), platelet reactivity (using VerifyNow) and bleeding, reported as relative risk (RR) with 95%CI. We assessed the confidence in the evidence using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) framework. We followed the Metaanalysis Of Observational Studies in Epidemiology and Preferred Reporting Items for Systematic Reviews and MetaAnalyses guidelines. Results: Five RCTs and 12 observational studies were included, enrolling 69 993 participants. Pooled results showed an increased risk of in-hospital mortality (RR 1.45 [95% CI 1.10 to 1.91], low GRADE confidence), MACE (RR 1.21, 95%CI 1.02 to 1.45) and an increased platelet reactivity at 1 and 2 hours (59.37 platelet reactivity units [PRU], 95%CI 36.04 to 82.71; 68.28 PRU, 95%CI 37.01 to 99.55, high GRADE confidence) associated with morphine. We found no significant difference in the risk of bleeding. We found no differences in subgroup analyses based on study design and ACS subtype. Conclusions: Morphine was associated with an increased risk of in-hospital mortality and MACE but the high risk of bias leads to low result confidence. There is high confidence that morphine decreases the antiplatelet effect of P2Y12 inhibitors.UID/BIM/50005/2019, project funded by Fundação para a Ciência e a Tecnologia (FCT)/ Ministério da Ciência, Tecnologia e Ensino Superior (MCTES) through Fundos do Orçamento de Estado.info:eu-repo/semantics/publishedVersio

Experimental Models as Refined Translational Tools for Breast Cancer Research

Breast cancer is one of the most common cancers worldwide, which makes it a very impactful malignancy in the society. Breast cancers can be classified through different systems based on the main tumor features and gene, protein, and cell receptors expression, which will determine the most advisable therapeutic course and expected outcomes. Multiple therapeutic options have already been proposed and implemented for breast cancer treatment. Nonetheless, their use and efficacy still greatly depend on the tumor classification, and treatments are commonly associated with invasiveness, pain, discomfort, severe side effects, and poor specificity. This has demanded an investment in the research of the mechanisms behind the disease progression, evolution, and associated risk factors, and on novel diagnostic and therapeutic techniques. However, advances in the understanding and assessment of breast cancer are dependent on the ability to mimic the properties and microenvironment of tumors in vivo, which can be achieved through experimentation on animal models. This review covers an overview of the main animal models used in breast cancer research, namely in vitro models, in vivo models, in silico models, and other models. For each model, the main characteristics, advantages, and challenges associated to their use are highlighted.This work was supported by Fundação para a Ciência e Tecnologia (FCT), Portugal under the Project Reference UID/DTP/04138/2019 and UIDB/00313/2020. T.F.-G. was supported by FCT, Portugal under the Reference SFRH/BD/147306/2019.info:eu-repo/semantics/publishedVersio

so much work, so many lost opportunities

Mainoli, B., Machado, T., Duarte, G. S., Prada, L., Gonçalves, N., Ferreira, J. J., & Costa, J. (2021). Analysis of clinical and methodological characteristics of early COVID-19 treatment clinical trials: so much work, so many lost opportunities. BMC Medical Research Methodology, 21(1), 1-10. [42]. https://doi.org/10.1186/s12874-021-01233-wBackground: The COVID-19 pandemic continues to rage on, and clinical research has been promoted worldwide. We aimed to assess the clinical and methodological characteristics of treatment clinical trials that have been set forth as an early response to the COVID-19 pandemic. Methods: First, we reviewed all registered clinical trials on COVID-19. The World Health Organization International Trials Registry Platform and national trial registries were searched for COVID-19 trials through April 19th, 2020. For each record, independent researchers extracted interventions, participants, and methodological characteristics. Second, on September 14th, 2020 we evaluated the recruitment status and availability of the results of COVID-19 treatment trials previously identified. Results: In April 2020, a total of 580 trials evaluating COVID-19 treatment were registered. Reporting quality was poor (core participant information was missing in 24.1 to 92.7%). Between 54.0 and 93.8% of the trials did not plan to include older people or those with a higher baseline risk. Most studies were randomised (67.9%), single-centre (58.3%), non-industry-funded (81.1%), to be conducted in China (47.6%), with a median duration of 184 days and a median sample size of 100 participants. Core endpoints (mortality, clinical status, and hospitalization length) were planned to be assessed in 5.2 to 13.1% of the trials. Five months later, 66 trials (11.4%) were reported as “Completed”, and only 46 (7.9%) had public results available. One hundred forty-four of 580 trials (24.8%) either had the status “Not yet recruiting” or “Suspended”, and 18 (3.1%) trials were prematurely stopped (“Terminated” or “Withdrawn”) The number of completed trials and trials with results are much lower than anticipated, considering the planned follow-up. Conclusions: Our results raise concerns about the success of the initial global research effort on COVID-19 treatment. The clinical and methodological characteristics of early COVID-19 treatment trials limit their capability to produce clear answers to critical questions in the shortest possible time.publishersversionpublishe

Placebo response in chronic peripheral neuropathic pain trials: systematic review and meta-analysis

Objective: To estimate the magnitude of the placebo and nocebo responses in chronic peripheral neuropathic pain (CNP) and explore possible associations with trial characteristics. // Methods: We searched CENTRAL, MEDLINE, and Embase for randomized controlled trials (RCTs) from inception to May 2020. We included placebo-controlled RCTs of ≥8 weeks investigating first-line pharmacological interventions for CNP. Primary endpoints were the placebo response, the proportion of patients receiving placebo with pain intensity reduction (PIR) ≥30% from baseline, and the nocebo response, the proportion of patients receiving placebo experiencing adverse events (AEs). Screening, data extraction, and bias assessment (with the Cochrane risk of bias tool) were conducted by independent reviewers. We pooled data using a random-effects model. // Results: We included 50 trials, with a combined 5,693 participants allocated to placebo, conducted between 1998 and 2020. Overall, 38% of patients receiving placebo reported PIR≥30% (95% CI 34 to 42, I2=86%); 23% reported PIR≥50% (95% CI 20 to 26; I2=81%). 50% of patients receiving placebo reported AEs (95% CI 0.43 to 0.58; I2=97%); 2% reported serious AEs (95% CI 2 to 3; I2=58%). In patients receiving active interventions, the placebo response accounts for 75% of the treatment effect on PIR≥30%, and the nocebo response accounts for 75% of the AEs. Interpreted inversely, only 25% of responses and 25% of adverse events can be attributed to the intervention. Publication year positively correlated with PIR≥30% and negatively correlated with AEs. Female sex negatively correlated with AEs. // Conclusions: The placebo and nocebo responses in parallel-designed RCTs in CNP are substantial and should be considered in trial interpretation and in the design of future trials

Four cases of cell cannibalism in highly malignant feline and canine tumors

Four cases of tumors in which cell internalization was frequently visualized are reported: one feline mammary carcinoma, one feline cutaneous squamous cell carcinoma, one canine pulmonary squamous cell carcinoma and one canine pleural mesothelioma. Cell internalization was observed by cytology in two of these cases (the feline mammary tumour and the pleural effusion in the canine mesothelioma) and by histopathology in all but the canine mesothelioma. Immunohistochemical staining for pancytokeratin was positive for both internalized and host cells, while E-cadherin expression was frequently absent, although internalized cells occasionally stained positive. This cell-to-cell interaction seems to be associated with tumors displaying a strong epithelial-mesenchymal transitional phenotype, in which cancer cells become engulfed by other cancer cells. Such event could be regarded as an important hallmark of very high malignancy.This work was supported by ‘Fundação para a Ciência e Tecnologia’ through the Project PEst-OE/AGR/U10276/2014 and through PhD fellowship SFRH/BD/70720/2010