Faster algorithms for 1-mappability of a sequence

In the k-mappability problem, we are given a string x of length n and integers m and k, and we are asked to count, for each length-m factor y of x, the number of other factors of length m of x that are at Hamming distance at most k from y. We focus here on the version of the problem where k = 1. The fastest known algorithm for k = 1 requires time O(mn log n/ log log n) and space O(n). We present two algorithms that require worst-case time O(mn) and O(n log^2 n), respectively, and space O(n), thus greatly improving the state of the art. Moreover, we present an algorithm that requires average-case time and space O(n) for integer alphabets if m = {\Omega}(log n/ log {\sigma}), where {\sigma} is the alphabet size

Long-term follow-up of myopic choroidal neovascularization treated with ranibizumab

PURPOSE: To evaluate the long-term safety and efficacy of intravitreal ranibizumab in the treatment of myopic choroidal neovascularization (CNV). METHODS: Three-year retrospective, nonrandomized, interventional case series. Forty eyes of 39 patients with myopic CNV were included; 15 with previous photodynamic therapy, and 25 naïve eyes. Best-corrected visual acuity (BCVA) changes, central foveal thickness (CFT), and number of treatments were assessed, from baseline to month 36. RESULTS: Mean visual acuity improved from 55.4 Early Treatment Diabetic Retinopathy Study (ETDRS) letters at baseline to 59.7 letters at 12 months (p = 0.07), 61.8 letters at 24 months (p = 0.008) and 63.4 letters at 36 months (p = 0.039). Twenty-five percent of the patients gained ≥15 letters (3 lines) at 12 months, 30% at 24 months and 35% at 36 months. There was a mean reduction of 80 μm in CFT (p < 0.001). A mean of 4.1 injections were performed in the first year, 2.4 in the second year and 1.1 in the third year. Fifty-three percent of the eyes had no need for treatment during the third year of follow-up. CONCLUSIONS: Intravitreal ranibizumab seems to be an effective and safe therapeutic procedure to treat CNV in highly myopic eyes, with a high proportion of patients gaining or stabilizing BCVA at a 3-year follow-up.info:eu-repo/semantics/publishedVersio

Três rearranjos diferentes, três fenótipos diferentes :Estudo Familiar Cromossoma 14

Introdução – Cromossomas derivativos são o resultado de rearranjos estruturais que tanto podem ocorrer num só, como entre dois ou mais cromossomas. Estes rearranjos dão origem a cromossomas estruturalmente anormais, podendo resultar um fenótipo normal ou mais ou menos grave, dependendo do tipo de anomalia encontrada. Materiais e métodos – Caso índex: homem de 55 anos, referenciado para estudos de citogenética clássica (cariótipo com bandas GTG de alta resolução) e molecular (MLPA – kits P036 e P070 e FISH com sonda subtelomérica especifica para o cromossoma 14) por apresentar um quadro clínico de atraso mental. Posteriormente realizaram-se estudos citogenéticos a uma irmã com atraso cognitivo e baixa estatura, e a mais quatro familiares com fenótipos normais. Resultados – O cariótipo do caso índex revelou a existência de uma anomalia cromossómica estrutural desequilibrada num dos cromossomas 14, sugerindo uma deleção da banda 14q32, e uma duplicação do braço curto localizada na parte terminal do braço longo. Nos estudos de citogenética molecular, a técnica de MLPA identificou uma deleção da região subtelomérica no braço longo do cromossoma 14, em ambos os kits e, posteriormente, a técnica de FISH comprovou essa deleção. Após estudos familiares, concluiu-se que dois dos irmãos apresentavam anomalias cromossómicas distintas do caso índex, envolvendo igualmente o cromossoma 14. Apesar de não ser possível efetuar o cariótipo à mãe (falecida), presume-se que estas alterações tenham tido origem numa anomalia cromossómica materna, uma vez que o pai deste indivíduo apresentava um cariótipo normal. Conclusões – Os autores apresentam os resultados citogenéticos dos vários indivíduos estudados, e realçam a raridade da existência de três rearranjos diferentes (um deles aparentemente equilibrado e dois desequilibrados), envolvendo o cromossoma 14, encontrados numa mesma família

Identification of a cytokine network sustaining neutrophil and Th17 activation in untreated early rheumatoid arthritis

© 2010 Cascão et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Introduction: Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease characterized by sustained synovitis. Recently, several studies have proposed neutrophils and Th17 cells as key players in the onset and perpetuation of this disease. The main goal of this work was to determine whether cytokines driving neutrophil and Th17 activation are dysregulated in very early rheumatoid arthritis patients with less than 6 weeks of disease duration and before treatment (VERA). Methods: Cytokines related to neutrophil and Th17 activation were quantified in the serum of VERA and established RA patients and compared with other very early arthritis (VEA) and healthy controls. Synovial fluid (SF) from RA and osteoarthritis (OA) patients was also analyzed. Results: VERA patients had increased serum levels of cytokines promoting Th17 polarization (IL-1b and IL-6), as well as IL-8 and Th17-derived cytokines (IL-17A and IL-22) known to induce neutrophil-mediated inflammation. In established RA this pattern is more evident within the SF. Early treatment with methotrexate or corticosteroids led to clinical improvement but without an impact on the cytokine pattern. Conclusions: VERA patients already display increased levels of cytokines related with Th17 polarization and neutrophil recruitment and activation, a dysregulation also found in SF of established RA. 0 Thus, our data suggest that a cytokine-milieu favoring Th17 and neutrophil activity is an early event in RA pathogenesis.This work was supported by a grant from Sociedade Portuguesa de Reumatologia/Schering-Plough 2005. RAM and RC were funded by Fundação para a Ciência e a Tecnologia (FCT) SFRH/BD/30247/2006 and SFRH/BD/40513/2007, respectively. MMS-C was funded by Marie Curie Intra-European Fellowship PERG-2008-239422 and a EULAR Young Investigator Award

Short-term versus long-term changes in the benthic communities of a small coastal lagoon: implications for ecological status assessment

The characteristic high variability and low predictability of coastal lagoons, due to strong changes in marine and freshwater inputs, make these ecosystems an interesting casestudy. The small Melides landlocked coastal lagoon in SW Portugal is a paradigmatic example, with a biological community highly stressed by these phenomena. Benthic macroinvertebrate samples were collected in 1998/99 and 2009 and each year, in different seasons and addressing different environmental conditions influenced by the connection to the sea and rainfall regime. Major spatial and temporal patterns in benthic communities were investigated using some invertebrate attributes (e.g. community composition, density, species richness and diversity). A very low taxonomic species richness and diversity was found in the Melides lagoon and only a much reduced number of species occurred along all sampling periods and in both sampling campaigns. Although the colonization events play a crucial role, the persistence of the observed species was mainly associated to abiotic factors, such as salinity, temperature and dissolved oxygen. Despite the potential reduction in anthropogenic pressure, by the construction of a sewage treatment plant and a reduction of urban occupation, the ecological status did not improve and the high level of natural environmental variably in the lagoon seems to be the dominant stressor influencing benthic invertebrate communitie

LOCUS (LOng Covid–Understanding Symptoms, events and use of services in Portugal): A three-component study protocol

Approximately 10% of patients experience symptoms of Post COVID-19 Condition (PCC) after a SARS-CoV-2 infection. Akin acute COVID-19, PCC may impact a multitude of organs and systems, such as the cardiovascular, respiratory, musculoskeletal, and neurological systems. The frequency and associated risk factors of PCC are still unclear among both community and hospital settings in individuals with a history of COVID-19. The LOCUS study was designed to clarify the PCC's burden and associated risk factors. LOCUS is a multi-component study that encompasses three complementary building blocks. The "Cardiovascular and respiratory events following COVID-19" component is set to estimate the incidence of cardiovascular and respiratory events after COVID-19 in eight Portuguese hospitals via electronic health records consultation. The "Physical and mental symptoms following COVID-19" component aims to address the community prevalence of self-reported PCC symptoms through a questionnaire-based approach. Finally, the "Treating and living with Post COVID-19 Condition" component will employ semi-structured interviews and focus groups to characterise reported experiences of using or working in healthcare and community services for the treatment of PCC symptoms. This multi-component study represents an innovative approach to exploring the health consequences of PCC. Its results are expected to provide a key contribution to the optimisation of healthcare services design.info:eu-repo/semantics/publishedVersio

Capsules from Pathogenic and Non-Pathogenic Cryptococcus spp. Manifest Significant Differences in Structure and Ability to Protect against Phagocytic Cells

Capsule production is common among bacterial species, but relatively rare in eukaryotic microorganisms. Members of the fungal Cryptococcus genus are known to produce capsules, which are major determinants of virulence in the highly pathogenic species Cryptococcus neoformans and Cryptococcus gattii. Although the lack of virulence of many species of the Cryptococcus genus can be explained solely by the lack of mammalian thermotolerance, it is uncertain whether the capsules from these organisms are comparable to those of the pathogenic cryptococci. In this study, we compared the characteristic of the capsule from the non-pathogenic environmental yeast Cryptococcus liquefaciens with that of C. neoformans. Microscopic observations revealed that C. liquefaciens has a capsule visible in India ink preparations that was also efficiently labeled by three antibodies generated to specific C. neoformans capsular antigens. Capsular polysaccharides of C. liquefaciens were incorporated onto the cell surface of acapsular C. neoformans mutant cells. Polysaccharide composition determinations in combination with confocal microscopy revealed that C. liquefaciens capsule consisted of mannose, xylose, glucose, glucuronic acid, galactose and N-acetylglucosamine. Physical chemical analysis of the C. liquefaciens polysaccharides in comparison with C. neoformans samples revealed significant differences in viscosity, elastic properties and macromolecular structure parameters of polysaccharide solutions such as rigidity, effective diameter, zeta potential and molecular mass, which nevertheless appeared to be characteristics of linear polysaccharides that also comprise capsular polysaccharide of C. neoformans. The environmental yeast, however, showed enhanced susceptibility to the antimicrobial activity of the environmental phagocytes, suggesting that the C. liquefaciens capsular components are insufficient in protecting yeast cells against killing by amoeba. These results suggest that capsular structures in pathogenic Cryptococcus species and environmental species share similar features, but also manifest significant difference that could influence their potential to virulence