Comparing reverse complementary genomic words based on their distance distributions and frequencies

In this work we study reverse complementary genomic word pairs in the human DNA, by comparing both the distance distribution and the frequency of a word to those of its reverse complement. Several measures of dissimilarity between distance distributions are considered, and it is found that the peak dissimilarity works best in this setting. We report the existence of reverse complementary word pairs with very dissimilar distance distributions, as well as word pairs with very similar distance distributions even when both distributions are irregular and contain strong peaks. The association between distribution dissimilarity and frequency discrepancy is explored also, and it is speculated that symmetric pairs combining low and high values of each measure may uncover features of interest. Taken together, our results suggest that some asymmetries in the human genome go far beyond Chargaff's rules. This study uses both the complete human genome and its repeat-masked version.Comment: Post-print of a paper accepted to publication in "Interdisciplinary Sciences: Computational Life Sciences" (ISSN: 1913-2751, ESSN: 1867-1462

Dissimilar Symmetric Word Pairs in the Human Genome

In this work we explore the dissimilarity between symmetric word pairs, by comparing the inter-word distance distribution of a word to that of its reversed complement. We propose a new measure of dissimilarity between such distributions. Since symmetric pairs with different patterns could point to evolutionary features, we search for the pairs with the most dissimilar behaviour. We focus our study on the complete human genome and its repeat-masked version.Comment: Submitted 13-Feb-2017; accepted, after a minor revision, 17-Mar-2017; 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2017, Porto, Portugal, 21-23 June, 201

Directional outlyingness applied to distances between genomic words

The detection of outlier curves/images is crucial in many areas, such as environmental, meteorological, medical, or economic contexts. In the functional framework, outlying observations are not only those that contain atypically high or low values, but also curves that present a different shape or pattern from the rest of the curves in the sample. In this short paper, we mention some recent methods for outlier detection in functional data and apply a recently proposed measure, the directional outlyingness, and the functional outlier map to detect words with outlying distance distribution in the human genome.publishe

Imaging of human differentiated 3D neural aggregates using light sheet fluorescence microscopy

The development of three dimensional (3D) cell cultures represents a big step for the better understanding of cell behavior and disease in a more natural like environment, providing not only single but multiple cell type interactions in a complex 3D matrix, highly resembling physiological conditions. Light sheet fluorescence microscopy (LSFM) is becoming an excellent tool for fast imaging of such 3D biological structures. We demonstrate the potential of this technique for the imaging of human differentiated 3D neural aggregates in fixed and live samples, namely calcium imaging and cell death processes, showing the power of imaging modality compared with traditional microscopy. The combination of light sheet microscopy and 3D neural cultures will open the door to more challenging experiments involving drug testing at large scale as well as a better understanding of relevant biological processes in a more realistic environment.FCT grants: (SFRH/BD/80717/2011, EXPL/BBB-IMG/0363/2013, PTDC/EBB-BIO/119243/2010, PTDC/EBB-BIO/112786/2009, SFRH/BD/52202/2013, SFRH/BD/78308/2011)

Integrating human stem cell expansion and neuronal differentiation in bioreactors

<p>Abstract</p> <p>Background</p> <p>Human stem cells are cellular resources with outstanding potential for cell therapy. However, for the fulfillment of this application, major challenges remain to be met. Of paramount importance is the development of robust systems for <it>in vitro </it>stem cell expansion and differentiation. In this work, we successfully developed an efficient scalable bioprocess for the fast production of human neurons.</p> <p>Results</p> <p>The expansion of undifferentiated human embryonal carcinoma stem cells (NTera2/cl.D1 cell line) as 3D-aggregates was firstly optimized in spinner vessel. The media exchange operation mode with an inoculum concentration of 4 × 10⁵cell/mL was the most efficient strategy tested, with a 4.6-fold increase in cell concentration achieved in 5 days. These results were validated in a bioreactor where similar profile and metabolic performance were obtained. Furthermore, characterization of the expanded population by immunofluorescence microscopy and flow cytometry showed that NT2 cells maintained their stem cell characteristics along the bioreactor culture time.</p> <p>Finally, the neuronal differentiation step was integrated in the bioreactor process, by addition of retinoic acid when cells were in the middle of the exponential phase. Neurosphere composition was monitored and neuronal differentiation efficiency evaluated along the culture time. The results show that, for bioreactor cultures, we were able to increase significantly the neuronal differentiation efficiency by 10-fold while reducing drastically, by 30%, the time required for the differentiation process.</p> <p>Conclusion</p> <p>The culture systems developed herein are robust and represent one-step-forward towards the development of integrated bioprocesses, bridging stem cell expansion and differentiation in fully controlled bioreactors.</p

Diabetes Mellitus - Estudo de AEQ dos Parâmetros Glicose e HbA1c (2008-2012)

Segundo o Internacional Diabetes Federation (IDF) (2012), a Diabetes atinge 371 milhões de pessoas em todo o mundo, correspondendo a 8,3% da população mundial. Estima-se que em cerca de 50% dessas pessoas a diabetes ainda não foi diagnosticada. Em 2012 morreram devido à diabetes 4,8 milhões de pessoas, sendo que metade tinha idade inferior a 60 anos. Segundo a IDF, Portugal posiciona-se entre os países europeus com maior taxa de prevalência de diabetes. A prevalência de diabéticos em Portugal em 2011, numa população entre os 20 e 79 anos foi de 12.7%, sendo que 7,2% diziam respeito a prevalência de diabetes diagnosticada e 5,5% a diabetes não diagnosticada. Em 2009, a percentagem de diabéticos em Portugal rondava os 11,7% e em 2010 os 12,4%. Dado a incidência a nível mundial da Diabetes Mellitus, torna-se de elevada importância avaliar toda a sua envolvência e estudar bem quais os critérios a ter em consideração. Propusemo-nos estudar os parâmetros bioquímicos relacionados com esta patologia - Glicose e Hemoglobina Glicada A1c (HbA1c), recorrendo à análise dos resultados dos últimos cinco anos (2008-2012) dos ensaios interlaboratoriais e metodologias utilizadas do Programa Nacional de Avaliação Externa da Qualidade, do Instituto Nacional de Saúde Doutor Ricardo Jorge (PNAEQ-INSA), Lisboa, Portugal

Evaluating the impact of sprouting conditions on the glucosinolate content of Brassica oleracea sprouts

The glucosinolates content of brassica plants is a distinctive characteristic, representing a healthy advan- tage as many of these compounds are associated to antioxidant and anti-carcinogenic properties. Brassica sprouts are still an underutilized source of these bioactive compounds. In this work, four varieties of bras- sica sprouts (red cabbage, broccoli, Galega kale and Penca cabbage), including two local varieties from the North of Portugal, were grown to evaluate the glucosinolate profile and myrosinase activity during the sprouting. Also the influence of light/darkness exposure during sprouting on the glucosinolate content was assessed. Glucosinolate content and myrosinase activity of the sprouts was evaluated by HPLC meth- ods. All sprouts revealed a higher content of aliphatic glucosinolates than of indole glucosinolates, con- trary to the profile described for most of brassica mature plants. Galega kale sprouts had the highest glucosinolate content, mainly sinigrin and glucoiberin, which are recognized for their beneficial health effects. Penca cabbage sprouts were particularly richer in glucoraphanin, who was also one of the major compounds in broccoli sprouts. Red cabbage showed a higher content of progoitrin. Regarding myrosi- nase activity, Galega kale sprouts showed the highest values, revealing that the use of light/dark cycles and a sprouting phase of 7?9 days could be beneficial to preserve the glucosinolate content of this variety.B514-8F2F-A1FB | Ana ValeN/

Immunocompetent human 3D brain cell cultures to advance ATMP development

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Delayed epistaxis secondary to intracavernous pseudoaneurysm of internal carotid artery

Post-traumatic pseudoaneurysm of the internal carotid artery is a very rare but potentially fatal cause of epistaxis. Early diagnosis is essential for an adequate management of this entity. The authors present a case of pseudoaneurysm of the internal carotid artery that developed massive epistaxis six months after skull base trauma.Pseudoaneurisma traumático da artéria carótida interna é uma causa rara de epistaxe, porém potencialmente fatal. O diagnóstico precoce é essencial para um adequado manejo da patologia. Os autores relatam um caso de pseudoaneurisma da carótida interna que se apresentou como epistaxe maciça após seis meses de trauma craniano prévio.Hospital do Servidor Público do Estado de São Paulo Serviço de Otorrinolaringologia/Cabeça e PescoçoUniversidade Federal de São Paulo (UNIFESP) Escola Paulista de MedicinaUNIFESP, EPMSciEL