Profile Detection Through Source Code Static Analysis

The present article reflects the progress of an ongoing master\u27s dissertation on language engineering. The main goal of the work here described, is to infer a programmer\u27s profile through the analysis of his source code. After such analysis the programmer shall be placed on a scale that characterizes him on his language abilities. There are several potential applications for such profiling, namely, the evaluation of a programmer\u27s skills and proficiency on a given language or the continuous evaluation of a student\u27s progress on a programming course. Throughout the course of this project and as a proof of concept, a tool that allows the automatic profiling of a Java programmer is under development. This tool is also introduced in the paper and its preliminary outcomes are discussed

Program analysis for Clustering Programmers' Profile

Each programmer has his own way of programming but some criteria can be applied when analysing code: there are a set of best practices that can be checked, or ''not so common'' instructions that are mainly used by experts that can be found. Considering that all programs that are going to be compared are correct, it's possible to infer the experience level of the programmer or the proficiency level of the solution. The approach presented in this paper has as main goal to compare sets of solutions to the same problem and infer the programmers profile. This can be used to evaluate the programmer skills, the proficiency on a given language or evaluate programming students. A tool to automatically profiling Java programmers called PP (Programmer Profiler) is presented in this paper as a proof of concept.This work has been supported by COMPETE: POCI-01-0145-FEDER-007043 and FCT - Fundacao para a Ciencia e Tecnologia within the Project Scope: UID/CEC/00319/2013

Bacteriophages have potential to control foaming caused by Rhodococcus erythropolis in WWTP

Activated-sludge is the most widely used biological process to remove pollutants from wastewater worldwide, mainly due to its economic advantages. Bacteria sum up around 95 % of the total microbial community of the activated-sludge, being responsible for most of the water depuration. Filamentous bacteria are normal components of these artificial ecosystems but their excessive growth leads to potential problems, mainly on the sludge settling (filamentous bulking) or on the formation of scums (filamentous foaming), dramatically reducing the efficiency of the wastewater treatment plants (WWTP). Rhodococcus erythropolis is a gram-positive filamentous bacterium previously identified as one of the sources of foams in activated-sludge. The present work aimed at isolating and characterizing phages infecting R. erythropolis, using sewage water and mixed liquor from an urban WWTP as phage source. Two phages were isolated (one from mixed liquor and the other from sewage) and further characterized genetically and biologically. The TEM analysis revealed that both phages belong to the siphovirus morphotype but with different sizes. The one step growth curve, carried at 28 °C in LB medium, revealed that the Rhodococcus phage isolated from mixed liquor and the one isolated from sewage have significant differences with latent periods of 110 min and 35 min, respectively, and burst sizes of 5 PFU/infected and 106 PFU/infected cell, respectively. Both phages were stable between 4 and 28 °C and between pH values from 7 to 10, which suggests good stability in the WWTP environment. Moreover, phages were able to maintain a R. erytropolis suspension at low levels for up to 30 h post-infection, using MOIs of 0.1, 0.5, and 1. Infection with the mixed liquor phage, maintained the bacterial reduction for 48 h in all MOIs tested. These results demonstrate the potential of using phages to control the problem of bacterial foaming in WWTP.info:eu-repo/semantics/publishedVersio

Novas perspetivas sobre o papel e as aplicações dos bacteriófagos de Helicobacter pylori

As infeções por Helicobacter pylori são caracterizadas por uma elevada incidência global, constituindo uma ameaça significativa à saúde pública. Os tratamentos atuais envolvem a administração de antibióticos e inibidores da bomba de protões. No entanto, esta abordagem terapêutica apresenta uma eficácia limitada, principalmente devido ao aumento da resistência aos antibióticos em todo o mundo. Este cenário salienta a necessidade urgente de desenvolver terapias alternativas eficazes. Os bacteriófagos, ou fagos surgem como uma opção promissora para o controlo de infeções por H. pylori, com vários estudos a demonstrar a sua eficácia em outras espécies patogénicas e resistentes a antibióticos. Contudo, até à data, apenas profagos de H. pylori, caracterizados como DNA viral integrado no cromossoma da bactéria, foram descritos, sendo que as informações sobre as suas características são ainda limitadas. Para colmatar este facto, o objetivo deste estudo foi isolar e caracterizar a nível biológico e genético novos fagos de H. pylori de modo a expandir o conhecimento atual sobre o seu papel em potenciais aplicações terapêuticas. Para atingir este objetivo, foi desenvolvido um novo método baseado em PCR para rastrear 74 estirpes clínicas de H. pylori por forma a identificar genes de profagos. A análise dos genomas de 14 estirpes revelou in silico a presença de 12 profagos intactos. Uma análise filogenética demonstrou ainda que estes profagos, bem como todos os fagos de H. pylori reportados até à data, apesar de terem origens diferentes, estão estreitamente relacionados ao nível filogenético. Com base nesta análise inicial, as estirpes positivas para genes de profagos foram sujeitas a tratamentos com Mitomicina C e radiação UV para induzir a libertação de profagos. Como resultado, foram isolados dois novos fagos, HPy1R e HPy2R, ambos com estabilidade relativa num intervalo de pH de 3 a 11 e 37 °C, sugerindo a sua adaptação ao ambiente gástrico humano. Importa referir que não foram detetados genes de resistência a antibióticos nos seus genomas e, embora tenham apresentado um espectro lítico de hospedeiros limitado, ambos os fagos reduziram efetivamente o número de células bacterianas na estirpe hospedeira, quando utilizadas diferentes multiplicidades de infeção (MOIs). Adicionalmente, o tratamento com o fago HPy2R demonstrou uma eficácia significativa, melhorando a viabilidade celular e reduzindo a expressão de interleucina (IL)-8 numa linha celular humana infetada com H. pylori. De modo geral, os nossos resultados representam um avanço significativo na identificação, isolamento e caracterização de novos fagos de H. pylori, fornecendo informações cruciais sobre a sua estabilidade e potencial terapêutico. Estes resultados abrem novas perspetivas para o desenvolvimento de tratamentos alternativos para infeções por H. pylori, especialmente no contexto de resistência aos antibióticos.info:eu-repo/semantics/publishedVersio

Comparison of bioinformatics tools to predict the presence of prophages in Helicobacter pylori genomes

Bacterio(phages) are specific viruses for bacteria, being their natural enemies. When the genome of a phage is integrated into the host bacterial genome, it is named prophage. These are a latent form of phages, in which the viral genes can increase the virulence and/or fitness characteristics of the host. This life cycle - lysogenic - does not cause the bacterial cell to rupture. Prophages have already been identified in most pathogenic bacteria, providing them better chances of survival. In the case of Helicobacter pylori, a human gastric pathogen that causes, among others, chronic gastritis, peptic ulcers, and adenocarcinoma, the presence of important prophage genes in their genomes has already been identified. In our work, a total of 109 complete genomes of human isolates of H. pylori and plasmids, deposited in NCBI archives, between November 5, 2015, and February 21, 2020, and 19 complete genomes of Portuguese clinical isolates, were screened, regarding the presence of prophages. For that, two of the most widely used web servers for identifying putative prophages in bacterial genomes were used: Phaster and Prophage Hunter. With the use of Phaster, 78 prophage sequences were identified, 6 of which were intact (7.7 %). Regarding Prophage Hunter, 199 prophages were identified, in a total of 17 active (8.5 %). The differences observed in the number of prophages identified by each tool is probably due to variances in the identification methods that each tool uses, as already reported. However, the intact sequences identified in Phaster were also predicted, in the same strains, in Prophage Hunter. These results suggest a high probability of these strains having inducible sequences of prophages in their genomes. The use of web servers for the rapid identification and annotation of prophage sequences in bacterial genomes and plasmids has been growing, helping to direct laboratory experiments more easily. In this work, we observed some differences in the results between the two tools used, concluding that new prophage prediction tools using Machine-Learning are required to predict more accurately this important viral sequences.info:eu-repo/semantics/publishedVersio

Helicobacter pylori prophages: screening, detection, induction and potential therapeutic use

Helicobacter pylori is a microaerophilic bacterium that chronically infects the human gastric mucosa. Infections caused by this pathogen are difficult to treat, mainly due to the increased resistance of this species to conventional antibiotics. Therefore, it is important to develop antibiotic alternative or complementary approaches to tackle H. pylori infections. Bacterio(phages) have proven to be efficient antibacterial agents, however it is very difficult to isolate strictly lytic phages infecting H. pylori. Nevertheless, this bacterial species presents prophages in their genomes and although strictly lytic phages have been consensually preferred for phage therapy purposes, temperate prophages holds a great but an exploited potential. In the present work, we developed a new PCR-based screening method to detect the presence of prophages genes in a set of H. pylori Portuguese clinical strains. The genomes of selected strains were then sequenced using a combined Illumina platform and MinION nanopore-based sequencing strategy. Prophages content was then analysed using the PHASTER tool. After sequencing analysis, UV light was used to induce phages, from which one was further characterized in terms of morphology, host range, stability on an in vitro gastric model, genome analysis and efficacy against a H. pylori culture. The complementarity between Illumina and Nanopore results, allowed us to identify a total of 10 intact, 7 questionable and 47 incomplete prophages on the 14 sequenced strains. One predicted intact prophage was induced successfully, and presents a genome length of 31 162 bp with 37.1 % G+C content. Interestingly, this new podovirus infects five H. pylori strains, and in the gastric in vitro model only a small loss of phage titer was observed in the gastric phase, suggesting that this phage could be adapted to the stomach environment. Farther, this phage demonstrated to be capable of maintaining the H. pylori population at low levels for up to 24 h post-infection with MOIs of 0.01, 0.1 and 1. Overall, a new PCR screening method was developed to detect prophages on H. pylori and positive correlations with sequencing results were observed. Moreover, this new isolated phage seems to have therapeutic potential to treat H. pylori gastric infections.This work was supported by the Portuguese Foundation for Science and Technology – Fundação para a Ciência e Tecnologia (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit, and Project PTDC/SAU-PUB/29182/2017 [POCI-01-0145-FEDER-029182]. Rute Ferreira is recipient of a FCT PhD grant with the reference SFRH/BD/146496/2019info:eu-repo/semantics/publishedVersio

Screening and in silico characterization of prophages in Helicobacter pylori genomes

Temperate bacterio(phages) play an important role on the evolution of pathogenic bacteria. Nevertheless, information on their role in Helicobacter pylori (an important gastric pathogen bacterium) is scarce. The present study developed a workflow for the identification of prophages in Portuguese H. pylori clinical strains, proposing the use of a new PCR-based screening method. The genome of strains with different PCR profiles were then sequenced. In the fourteen genomes analysed, nine intact prophages were identified by PHASTER. These prophages were annotated by analogy with other identified phages, where seven contained the integrase gene, corroborating the results obtained in the PCR screening, with only one exception. Still, in PCR screening, the holin gene was identified in 75 % of the strains containing intact phages, but BLASTp homologies only recognized this gene in one of the prophages. Fifty-six percent are podovirus, while in 44 % it was not possible to assign any family, according to the VirFam tool. Using the Resistance Gene Identifier of CARD it was identified the Acinetobacter mutant Lpx gene conferring resistance to colistin in two intact prophages. The BLASTp search identified a putative ABC binding cassette transporter in one of the intact prophages. On the bacterial genomes, 71 % have the CRISPR-Cas system classified as evidence level 1 by CRISPRCasFinder, which typically indicate potentially invalid CRISPR arrays. The use of an initial PCR screening method increased the identification of intact prophage-containing strains from 20 % to 57 %. Furthermore, the few virulence factors identified in prophages, and the possible inactivity of CRISPR-Cas in the bacterial genomes, allow the choice of strains for the isolation of phages for future studies. Overall, our results represent a significant contribution to the knowledge of prophages in H. pylori, and provide valuable insights into their potential use in phage therapy.info:eu-repo/semantics/publishedVersio

Characterization and genomic analysis of a new phage infecting Helicobacter pylori

Helicobacter pylori, a significant human gastric pathogen, has been demonstrating increased antibiotic resistance, causing difficulties in infection treatment. It is therefore important to develop alternatives or complementary approaches to antibiotics to tackle H. pylori infections, and (bacterio)phages have proven to be effective antibacterial agents. In this work, prophage isolation was attempted using H. pylori strains and UV radiation. One phage was isolated and further characterized to assess potential phage-inspired therapeutic alternatives to H. pylori infections. HPy1R is a new podovirus prophage with a genome length of 31,162 bp, 37.1% GC, encoding 36 predicted proteins, of which 17 were identified as structural. Phage particles remained stable at 37 °C, from pH 3 to 11, for 24 h in standard assays. Moreover, when submitted to an in vitro gastric digestion model, only a small decrease was observed in the gastric phase, suggesting that it is adapted to the gastric tract environment. Together with its other characteristics, its capability to suppress H. pylori population levels for up to 24 h post-infection at multiplicities of infection of 0.01, 0.1, and 1 suggests that this newly isolated phage is a potential candidate for phage therapy in the absence of strictly lytic phages.This study was supported by the Portuguese Foundation for Science and Technology (FCT), under the scope of the strategic funding of the UIDB/04469/2020 unit, and Project Helicophage PTDC/SAU-PUB/29182/2017 (POCI-01-0145-FEDER-029182). R.F. and R.F.S.G. acknowledge the FCT grants SFRH/BD/146496/2019 and SFRH/BD/140182/2018, respectivelyinfo:eu-repo/semantics/publishedVersio

H. pylori phages: from genome release to hope for use as therapy

The increasing antibiotic-resistant Helicobacter pylori infections worldwide and the ineffectiveness of treatments led the World Health Organization to designate clarithromycin-resistant H. pylori as a high-priority bacterium for antibiotic research and development. (Bacterio)phages, viruses that infect bacteria, showing effectiveness in the treatment of pathogenic bacteria, could be a promising alternative strategy in the fight against H. pylori infections. Material and methods In this work, a collection of 74 Portuguese H. pylori-clinical strains was used to screen for the presence of phage genes, using a new PCR-based method. Selected strains were subsequently sequenced and prophage isolation was attempted using UV radiation. Three phages were isolated, one of which was further characterized genetically and biologically. Results PCR-based detection indicated the presence of target phage sequences in 14 strains, and the induction strategies resulted in the release of a new phage. It presents a genome length of 31,162 bp with a G+C content of 37.1 %. This podovirus showed capability to form phage plaques in five strains, was stable under an in vitro gastric digestion model, and was able to maintain a H. pylori population at low levels for up to 24h post-infection. Conclusion The new PCR screening method proved to be very effective in the selection of strains carrying prophages, resulting in the isolation of a new H. pylori phage. This phage presented very promising characteristics in terms of stability and efficacy, being therefore a small step towards the future use of phage therapy in the fight against H. pylori infections.info:eu-repo/semantics/publishedVersio

Tratamento cirúrgico da otite média secretora na população infantil: uma revisão sistemática

Este artigo tem como objetivo realizar uma revisão sistemática da produção bibliográfica referente a eficácia do tratamento cirúrgico e suas indicações como terapêutica do quadro clínico de otite média com efusão na população pediátrica.  Após formular a frase de pesquisa, foram realizadas buscas na base de dados Medline, sendo utilizados os seguintes descritores: Otitis Media with Effusion, Middle Ear Effusion, Secretory Otitis Media e Serous Otitis Media. Foram incluídos ensaios clínicos e ensaios clínicos randomizados que apresentavam dados que versavam diretamente sobre as intervenções cirúrgicas da otite média com efusão e foram analisados os resultados obtidos nas avaliações. Os resultados indicaram que a inserção de tubos de ventilação combinada com a adenoidectomia resultou em menor recorrência do quadro em comparação com a inserção do tubo de ventilação de forma isolada. Além disso, observou-se que a inserção do tubo de ventilação em crianças com otite média com efusão persistente não apresentou efeito benéfico na qualidade de vida geral, mas evidências indicaram um desfecho positivo na saúde funcional relacionada à dificuldade auditiva nesta população. Por fim, observou-se que nas crianças com fissura palatina que passaram por reparo no palato mole e que permaneceram com o quadro de otite média com efusão, a inserção do tubo de ventilação deve ser considerada. A análise dos estudos destacou a complexidade das decisões clínicas em relação às intervenções cirúrgicas para o quadro descrito, considerando fatores como recorrência, qualidade de vida e características individuais dos pacientes