Minimal Forbidden Factors of Circular Words

Minimal forbidden factors are a useful tool for investigating properties of words and languages. Two factorial languages are distinct if and only if they have different (antifactorial) sets of minimal forbidden factors. There exist algorithms for computing the minimal forbidden factors of a word, as well as of a regular factorial language. Conversely, Crochemore et al. [IPL, 1998] gave an algorithm that, given the trie recognizing a finite antifactorial language $M$, computes a DFA recognizing the language whose set of minimal forbidden factors is $M$. In the same paper, they showed that the obtained DFA is minimal if the input trie recognizes the minimal forbidden factors of a single word. We generalize this result to the case of a circular word. We discuss several combinatorial properties of the minimal forbidden factors of a circular word. As a byproduct, we obtain a formal definition of the factor automaton of a circular word. Finally, we investigate the case of minimal forbidden factors of the circular Fibonacci words.Comment: To appear in Theoretical Computer Scienc

Minimal Absent Words in Four Human Genome Assemblies

Minimal absent words have been computed in genomes of organisms from all domains of life. Here, we aim to contribute to the catalogue of human genomic variation by investigating the variation in number and content of minimal absent words within a species, using four human genome assemblies. We compare the reference human genome GRCh37 assembly, the HuRef assembly of the genome of Craig Venter, the NA12878 assembly from cell line GM12878, and the YH assembly of the genome of a Han Chinese individual. We find the variation in number and content of minimal absent words between assemblies more significant for large and very large minimal absent words, where the biases of sequencing and assembly methodologies become more pronounced. Moreover, we find generally greater similarity between the human genome assemblies sequenced with capillary-based technologies (GRCh37 and HuRef) than between the human genome assemblies sequenced with massively parallel technologies (NA12878 and YH). Finally, as expected, we find the overall variation in number and content of minimal absent words within a species to be generally smaller than the variation between species

Origem coronária anómala: da suspeita à revascularizac¸ão cirúrgica

Congenital anomalies of the coronary arteries are uncommon and can present a diagnostic challenge. The authors present the case of a patient with recurrent chest pain during exertion admitted for acute coronary syndrome. Coronary angiography revealed no coronary lesions but showed that the right coronary artery originated from the anterolateral aortic wall, above the sinuses of Valsalva, leading to suspicion of compression by the pulmonary artery, confirmed by CT angiography. The patient underwent surgical revascularization with a good result. The authors highlight the need to consider compression of an anomalous coronary artery by the pulmonary artery in the differential diagnosis of recurrent chest pain on exertion and acute myocardial infarction without significant coronary stenosis

Developmental Defects of Enamel in Primary Teeth and Association with Early Life Course Events: A Study of 6--36 Month old Children in Manyara, Tanzania.

Children with low birth weight show an increased prevalence of developmental defects of enamel in the primary dentition that subsequently may predispose to early childhood caries (ECC).Focusing 6--36 months old, the purpose of this study was to assess the frequency of enamel defects in the primary dentition and identify influences of early life course factors; socio-demographics, birth weight, child's early illness episodes and mothers' perceived size of the child at birth, whilst controlling for more recent life course events in terms of current breastfeeding and oral hygiene. A cross-sectional study was conducted in the high fluoride area of Manyara, northern Tanzania including 1221 child-mother pairs who attended Reproductive and Child Health (RCH) clinics for immunization and/or growth monitoring. After the primary caregivers had completed face to face interviews at the health care facility, children underwent oral clinical examination whereby ECC and developmental defects of enamel were recorded using field criteria. All erupted teeth were examined and the enamel defects were assessed on buccal surfaces according to the modified DDE Index. The prevalence of enamel defects was 33.3%. Diffuse opacities were the most common defects identified (23.1%), followed by hypoplasia (7.6%) and demarcated opacities (5.0%). The most frequently affected teeth were the upper central incisors (29.0% - 30.5%), whereas lower central incisors (4.3% to 4.5%) were least frequently affected. Multiple logistic regression analysis, adjusting for confounding the factors revealed that having normal birth weight (equal or more than 2500 g) associated with lower odds of having enamel hypoplasia [OR 0.22 (95% CI 0.1-0.7)]. No statistically significant association occurred between birth weight and diffuse opacities, demarcated opacities or combined DDE. Children with the history of low birth weight were more likely than their normal birth weight counterparts to present with enamel hypoplasia. In view of the frequent occurrence of enamel defects and the fact that hypoplasia may constitute a risk factor for future ECC, enamel defects should be included as a dental health indicator in epidemiological studies of children in northern Tanzania

SAW: A Method to Identify Splicing Events from RNA-Seq Data Based on Splicing Fingerprints

Splicing event identification is one of the most important issues in the comprehensive analysis of transcription profile. Recent development of next-generation sequencing technology has generated an extensive profile of alternative splicing. However, while many of these splicing events are between exons that are relatively close on genome sequences, reads generated by RNA-Seq are not limited to alternative splicing between close exons but occur in virtually all splicing events. In this work, a novel method, SAW, was proposed for the identification of all splicing events based on short reads from RNA-Seq. It was observed that short reads not in known gene models are actually absent words from known gene sequences. An efficient method to filter and cluster these short reads by fingerprint fragments of splicing events without aligning short reads to genome sequences was developed. Additionally, the possible splicing sites were also determined without alignment against genome sequences. A consensus sequence was then generated for each short read cluster, which was then aligned to the genome sequences. Results demonstrated that this method could identify more than 90% of the known splicing events with a very low false discovery rate, as well as accurately identify, a number of novel splicing events between distant exons

Social and ethical criteria for prioritizing patients: a survey of students and health professionals in Portugal

O estudo quali-quantitativo explora o dilema ético da microalocação dos recursos da saúde. Objetiva identificar e comparar a opinião de dois grupos da sociedade portuguesa - estudantes e profissionais de saúde sobre a importância das características pessoais dos pacientes no momento de os priorizar e se as escolhas se explicam por referenciais bioéticos de caráter utilitaristas ou deontológicos. Os dados foram recolhidos através de um questionário aplicado a uma amostra de 180 estudantes universitários e 60 profissionais de saúde. Os respondentes perante hipotéticos cená- rios de emergência clínica tiveram de escolher de entre dois pacientes (distinguidos por idade, sexo, responsabilidade social, situação económica e laboral, comportamentos lesivos da saúde e registo criminal) quem tratar e justificar a escolha. Foram usados testes estatísticos de associação para comparar as respostas dos dois grupos e análise de conteúdo para categorizar as justificações. Os resultados sugerem a existência de diferenças nas escolhas dos dois grupos, com os profissionais de saúde a revelarem aceitar menos a utilização de critérios sociais em contexto de escassez e coexistência de critérios utilitaristas e deontológicos, com predomínio da eficiência por parte dos profissionais de saúde e da equidade por parte dos estudantesThis qualitative/quantitative study examines the ethical dilemma of microallocation of health resources. It seeks to identify and compare the opinion of two groups in Portuguese society – students and health professionals – on the importance of personal characteristics of patients at the moment of prioritizing them and if the choices can be explained by bioethical references of a utilitarian or deontological nature. Data were collected by means of a questionnaire administered to a sample of 180 students and 60 health professionals. Faced with hypothetical emergency scenarios, the respondents had to choose between two patients (distinguished by: age, gender, social responsibility, economic and employment situation, harmful health behaviors and criminal record), duly selecting who to treat and then justifying their choice. The results suggest the existence of differences in choices between the two groups, with health professionals revealing they are less prepared to accept the use of social criteria in a context of scarce resources and co-existence of utilitarian and deontological criteria, with a predominance of efficiency on the part of health professionals and equity on the part of students.info:eu-repo/semantics/publishedVersio

Minimal Absent Words in Prokaryotic and Eukaryotic Genomes

Minimal absent words have been computed in genomes of organisms from all domains of life. Here, we explore different sets of minimal absent words in the genomes of 22 organisms (one archaeota, thirteen bacteria and eight eukaryotes). We investigate if the mutational biases that may explain the deficit of the shortest absent words in vertebrates are also pervasive in other absent words, namely in minimal absent words, as well as to other organisms. We find that the compositional biases observed for the shortest absent words in vertebrates are not uniform throughout different sets of minimal absent words. We further investigate the hypothesis of the inheritance of minimal absent words through common ancestry from the similarity in dinucleotide relative abundances of different sets of minimal absent words, and find that this inheritance may be exclusive to vertebrates

The Long Life of Birds: The Rat-Pigeon Comparison Revisited

The most studied comparison of aging and maximum lifespan potential (MLSP) among endotherms involves the 7-fold longevity difference between rats (MLSP 5y) and pigeons (MLSP 35y). A widely accepted theory explaining MLSP differences between species is the oxidative stress theory, which purports that reactive oxygen species (ROS) produced during mitochondrial respiration damage bio-molecules and eventually lead to the breakdown of regulatory systems and consequent death. Previous rat-pigeon studies compared only aspects of the oxidative stress theory and most concluded that the lower mitochondrial superoxide production of pigeons compared to rats was responsible for their much greater longevity. This conclusion is based mainly on data from one tissue (the heart) using one mitochondrial substrate (succinate). Studies on heart mitochondria using pyruvate as a mitochondrial substrate gave contradictory results. We believe the conclusion that birds produce less mitochondrial superoxide than mammals is unwarranted

ROBO2 is a stroma suppressor gene in the pancreas and acts via TGF-β signalling.

Whereas genomic aberrations in the SLIT-ROBO pathway are frequent in pancreatic ductal adenocarcinoma (PDAC), their function in the pancreas is unclear. Here we report that in pancreatitis and PDAC mouse models, epithelial Robo2 expression is lost while Robo1 expression becomes most prominent in the stroma. Cell cultures of mice with loss of epithelial Robo2 (Pdx1Cre;Robo2F/F) show increased activation of Robo1+ myofibroblasts and induction of TGF-β and Wnt pathways. During pancreatitis, Pdx1Cre;Robo2F/F mice present enhanced myofibroblast activation, collagen crosslinking, T-cell infiltration and tumorigenic immune markers. The TGF-β inhibitor galunisertib suppresses these effects. In PDAC patients, ROBO2 expression is overall low while ROBO1 is variably expressed in epithelium and high in stroma. ROBO2low;ROBO1high patients present the poorest survival. In conclusion, Robo2 acts non-autonomously as a stroma suppressor gene by restraining myofibroblast activation and T-cell infiltration. ROBO1/2 expression in PDAC patients may guide therapy with TGF-β inhibitors or other stroma /immune modulating agents