Extracting kinetic information from literature with KineticRE

To better understand the dynamic behavior of metabolic networks in a wide variety of conditions, the field of Systems Biology has increased its interest in the use of kinetic models. The different databases, available these days, do not contain enough data regarding this topic. Given that a significant part of the relevant information for the development of such models is still wide spread in the literature, it becomes essential to develop specific and powerful text mining tools to collect these data. In this context, this work has as main objective the development of a text mining tool to extract, from scientific literature, kinetic parameters, their respective values and their relations with enzymes and metabolites. The approach proposed integrates the development of a novel plug-in over the text mining framework @Note2. In the end, the pipeline developed was validated with a case study on Kluyveromyces lactis, spanning the analysis and results of 20 full text documents.

Integrating data from heterogeneous DNA microarray platforms

DNA microarrays are one of the most used technologies for gene expression measurement. However, there are several distinct microarray platforms, from different manufacturers, each with its own measurement protocol, resulting in data that can hardly be compared or directly integrated. Data integration from multiple sources aims to improve the assertiveness of statistical tests, reducing the data dimensionality problem. The integration of heterogeneous DNA microarray platforms comprehends a set of tasks that range from the re-annotation of the features used on gene expression, to data normalization and batch effect elimination. In this work, a complete methodology for gene expression data integration and application is proposed, which comprehends a transcript-based re-annotation process and several methods for batch effect attenuation. The integrated data will be used to select the best feature set and learning algorithm for a brain tumor classification case study. The integration will consider data from heterogeneous Agilent and Affymetrix platforms, collected from public gene expression databases, such as The Cancer Genome Atlas and Gene Expression Omnibus.

Reconstructing transcriptional regulatory networks using data integration and text mining

Transcriptional Regulatory Networks (TRNs) are powerful tool for representing several interactions that occur within a cell. Recent studies have provided information to help researchers in the tasks of building and understanding these networks. One of the major sources of information to build TRNs is biomedical literature. However, due to the rapidly increasing number of scientific papers, it is quite difficult to analyse the large amount of papers that have been published about this subject. This fact has heightened the importance of Biomedical Text Mining approaches in this task. Also, owing to the lack of adequate standards, as the number of databases increases, several inconsistencies concerning gene and protein names and identifiers are common. In this work, we developed an integrated approach for the reconstruction of TRNs that retrieve the relevant information from important biological databases and insert it into a unique repository, named KREN. Also, we applied text mining techniques over this integrated repository to build TRNs. However, was necessary to create a dictionary of names and synonyms associated with these entities and also develop an approach that retrieves all the abstracts from the related scientific papers stored on PubMed, in order to create a corpora of data about genes. Furthermore, these tasks were integrated into @Note, a software system that allows to use some methods from the Biomedical Text Mining field, including an algorithms for Named Entity Recognition (NER), extraction of all relevant terms from publication abstracts, extraction relationships between biological entities (genes, proteins and transcription factors). And finally, extended this tool to allow the reconstruction Transcriptional Regulatory Networks through using scientific literature.

Peúga terapêutica com capacidade de electroestimulação a partir de elétrodos fibrosos para auxílio terapêutico de lesões nos membros inferiores

Pedido de patente provisório nº 20151000053763, data de pedido 18 março 2015, em parceria com a Empresa Barcelcom, S. A..

Biological markers in noninvasive brain stimulation trials in major depressive disorder: a systematic review

Objectives: The therapeutic effects of transcranial magnetic stimulation (TMS) and transcranial direct current stimulation in patients with major depression have shown promising results; however, there is a lack of mechanistic studies using biological markers (BMs) as an outcome. Therefore, our aim was to review noninvasive brain stimulation trials in depression using BMs. Methods: The following databases were used for our systematic review: MEDLINE, Web of Science, Cochrane, and SCIELO. We examined articles published before November 2012 that used TMS and transcranial direct current stimulation as an intervention for depression and had BM as an outcome measure. The search was limited to human studies written in English. Results: Of 1234 potential articles, 52 articles were included. Only studies using TMS were found. Biological markers included immune and endocrine serum markers, neuroimaging techniques, and electrophysiological outcomes. In 12 articles (21.4%), end point BM measurements were not significantly associated with clinical outcomes. All studies reached significant results in the main clinical rating scales. Biological marker outcomes were used as predictors of response, to understand mechanisms of TMS, and as a surrogate of safety. Conclusions: Functional magnetic resonance imaging, single-photon emission computed tomography, positron emission tomography, magnetic resonance spectroscopy, cortical excitability, and brain-derived neurotrophic factor consistently showed positive results. Brain-derived neurotrophic factor was the best predictor of patients’ likeliness to respond. These initial results are promising; however, all studies investigating BMs are small, used heterogeneous samples, and did not take into account confounders such as age, sex, or family history. Based on our findings, we recommend further studies to validate BMs in noninvasive brain stimulation trials in MDD.

Are cognitive interventions for multiple sclerosis effective and feasible?

Purpose: Fifty percent of patients with Multiple Sclerosis (MS) are estimated to have cognitive impairments leading to considerable decline in productivity and quality of life. Cognitive intervention has been considered to complement pharmacological treatments. However, a lack of agreement concerning the efficacy of cognitive interventions in MS still exists. A systematic review and meta-analysis was conducted to assess the effects of cognitive interventions in MS. Methods: To overcome limitations of previous meta-analyses, several databases were searched only for Randomized Clinical Trials (RCTs) with low risk of bias. Results: Five studies (total of 139 participants) met our eligibility criteria. Although good completion and adherence rates were evident, we found no evidence of intervention effects on cognition or mood in post-intervention or follow-up assessments. Conclusions: This is the first meta-analysis assessing the effects of cognitive intervention in MS including only RCTs with comparable conditions. Research regarding efficacy, cost-effectiveness and feasibility is still in its infancy. Caution is advised when interpreting these results due to the small number of RCTs meeting the inclusion criteria. Considering the costs of disease, good completion and adherence rates of this approach, further research is warranted. Recommendations concerning improved research practices in the field are presented as well.

Microscopy- or DNA-based analyses: Which methodology gives a truer picture of stream-dwelling decomposer fungal diversity?

We assessed aquatic hyphomycete diversity in autumn and spring on oak leaves decomposing in five streams along a gradient of eutrophication in the Northwest of Portugal. Diversity was assessed through microscopy-based (identification by spore morphology) and DNA-based techniques (Denaturing Gradient Gel Electrophoresis and 454 pyrosequencing). Pyrosequencing revealed five times greater diversity than DGGE. About 21% of all aquatic hyphomycete species were exclusively detected by pyrosequencing and 26% exclusively by spore identification. In some streams, more than half of the recorded species would have remained undetected if we had relied only on spore identification. Nevertheless, in spring aquatic hyphomycete diversity was higher based on spore identification, probably because many species occurring in this season are not yet connected to ITS barcodes in genetic databases. Pyrosequencing was a powerful tool for revealing aquatic hyphomycete diversity on decomposing plant litter in streams and we strongly encourage researchers to continue the effort in barcoding fungal species.

Sistema de apoio à decisão clínica: quality of life system

Dissertação de mestrado integrado em Engenharia e Gestão de Sistemas de Informação

Effects of bariatric surgery on the central nervous system and eating behavior in humans: a systematic review on the neuroimaging studies

INTRODUCTION: Neuroimaging studies suggest that obese people might show hyperactivity of brain areas regarding reward processing, and hypoactivity of brain areas concerning cognitive control, when exposed to food cues. Although the effects of bariatric surgery on the central nervous system and eating behavior are well known, few studies have used neuroimage techniques with the aim of investigating the central effects of bariatric surgery in humans. OBJECTIVES: This paper systematically and critically reviews studies using functional neuroimaging to investigate changes on the patterns of activation of central areas related to the regulation of eating behavior after bariatric surgery. METHOD: A search on the databases Medline, Web of Science, Lilacs and Science Direct on Line, was conducted in February 2013, using the keywords "Neuroimaging", "Positron-Emission Tomography", "Magnetic Resonance Imaging", "Gastric Bypass", "Gastroplasty", "Jejunoileal Bypass", "Bariatric Surgery". RESULTS: Seven manuscripts were included; the great majority studied the central effects of Roux en Y gastric bypass, using positron emission tomography or functional magnetic resonance. CONCLUSIONS: Bariatric surgery might normalize the activity of central areas concerned with reward and incentive salience processing, as the nucleus accumbens and mesencephalic tegmental ventral area, as well as circuitries processing behavioral inhibition, as the dorsolateral prefrontal cortex.

Development of an intelligent earthwork optimization system

Tese de Doutoramento em Engenharia Civil.

Psychometric properties of assessment instruments for autism spectrum disorder: a systematic review of Brazilian studies

Objective To systematically review the scientific literature on the psychometric properties of international instruments for the assessment of autism spectrum disorder (ASD) in the Brazilian population. Methods A search of bibliographic references was conducted in six electronic databases: PsycINFO, PubMed, IndexPsi, Lilacs, Capes (theses and dissertations) and SciELO. The studies were selected by two independent researchers. Results The procedure identified 11 studies of the Brazilian population that encompassed six ASD assessment tools. Given the information provided, the adaptation of the M-CHAT, a screening instrument, was the best conducted. All steps of the adaptation process were described and the changes made to the final version of the instrument were presented, which was not addressed in other studies. In terms of reliability, all of the instruments that assessed internal consistency showed adequate values. In addition, the ADI-R and the CARS adaptations also satisfactorily contemplated inter-rater reliability and test-retest indices, respectively. Finally, all studies aiming to validate instruments showed evidence of validity and sensitivity, and specificity values above 0.90 were observed in the ASQ, ADI-R and ABC. Conclusion Considering both the psychometric aspects and the copyright information, the screening instrument that currently appears to be best indicated for clinical and research use is the M-CHAT. It was also noticed that there are still no specific ASD diagnostic tools available for use in Brazil. This lack of diagnostic instruments consists in a critical situation for the improvement of clinical practice and the development of research in this area.

Cognitive-behavioral therapy for anxiety disorders in children and adolescents: a systematic review of follow-up studies

Objective To conduct a systematic review about the long-term response to cognitive-behavioral therapy (CBT) for anxiety disorders (ADs) in children and adolescents. Methods The PubMed and ISI Web of Science databases were consulted. Search in the databases was performed in November 2012 and included cohort studies after CBT for ADs in children and adolescents with a follow-up period over 12 months. Results A total of 10 papers met the inclusion criteria. The follow-up period ranged from 12 months to 13 years and the results generally showed maintenance of the short-term benefits with CBT. However, the studies presented limitations, especially regarding methods, such as lack of a control group and losses to follow-up. Conclusion The long-term benefits of CBT were identified, however it would be interesting to conduct other studies with more frequent assessment periods, in order to minimize losses to follow-up, in addition to evaluating children and adolescents in the various stages of their development.

Virtual reality in assessment and treatment of schizophrenia: a systematic review

Objective To conduct a systematic review about the use of virtual reality (VR) for evaluation, treatment and/or rehabilitation of patients with schizophrenia, focused on: areas, fields and objectives; methodological issues; features of the VR used; viability and efficiency of this resource. Methods Searches were performed about schizophrenia and virtual reality in PsycINFO, Academic Search Complete, MEDLINE Complete, CINAHL with Full Text, Web of Science and Business Source Premier databases, using the following keywords: [“schizophrenia”] AND [“virtual reality” OR “serious game”] AND [“treatment” OR “therapy” OR “rehabilitation”]. The search was carried out between November 2013 and June 2014 without using any search limiters. Results A total of 101 papers were identified, and after the application of exclusion criteria, 33 papers remained. The studies analysed focused on the use of VR for the evaluation of cognitive, social, perceptual and sensory skills, and the vast majority were experimental studies, with virtual reality specifically created for them. All the reviewed papers point towards a reliable and safe use of VR for evaluating and treating cognitive and social deficits in patients with schizophrenia, with different results in terms of generalisation, motivation, assertiveness and task participation rate. Some problems were highlighted, such as its high cost and a constant need for software maintenance. Conclusion The studies show that using the virtual reality may streamline traditional evaluation/rehabilitation programmes, allowing to enhance the results achieved, both in the cognitive and in the social field, helping for the legitimisation of this population’s psycho-social inclusion.

Minilaparoscopy and sentinel lymph node in uterine cancer

CRSLS MIS Case Reports from SLS.org.

Concepts and objects of awareness in Alzheimer’s disease: an updated systematic review

ABSTRACT Objectives To compare and discuss the objects of awareness in Alzheimer’s disease (AD): awareness of cognitive deficits, of functional activities, of social-emotional functioning and behavioral impairment. Methods A search in the PsycINFo, Pilots, PubMed/Medline and ISI electronic databases according to Prisma methodology was performed. We included studies about awareness in people with AD published between 2010 and 2015, with the combination of keywords: “Alzheimer AND awareness of deficits”, “Alzheimer AND anosognosia”, “Alzheimer AND insight”, “dementia AND awareness of deficits”, “dementia AND anosognosia”, “dementia AND insight”. The articles were categorized according to the specific object of awareness. Results Seven hundred and ten records were identified and, after application of the exclusion criteria, 191 studies were retrieved for potential use. After excluding the duplicates, 46 studies were included. Most studies assessed the cognitive domain of awareness, followed by the functional, social-emotional, and behavioral impairment domains. Memory deficits were not sufficient to explain impaired awareness in AD. Longitudinal studies did not find discrepancies between patients and caregivers’ reports, indicating that awareness is not related to cognition. Conflicting findings were observed, including the relation between awareness, mood, severity of disease, and personal characteristics. Conclusions The studies show lack of conceptual consensus and significant methodological differences. The inclusion of samples without differentiation of dementia etiology is associated to symptomatic differences, which affect awareness domains. Awareness in AD is a complex and multidimensional construct. Different objects elicit different levels of awareness.