Sistema centralizado de monitorização de logs orientado a microsserviços

Recentemente os sistemas baseados em microsserviços têm demonstrado uma forte adesão no mundo organizacional. Inclusivamente empresas como a Netflix, Amazon e o The Guardian estão a adotar este estilo arquitetural como forma de evoluir as suas aplicações. Se bem que existem vantagens associadas ao uso de microsserviços no desenvolvimento de um sistema (maior modularidade e escalabilidade, melhor separação de responsabilidades, entre outros), existem também fatores que afetam negativamente o dito sistema. Um desses pontos negativos remete para o tempo despendido a diagnosticar problemas ou anomalias no sistema. Assim sendo, a presente dissertação foca-se no desenvolvimento de uma solução centralizada de monitorização de logs que visa diminuir o consumo de tempo e a taxa de erro humano que existe quando se efetua a depuração de sistemas baseados em microsserviços. De maneira a atingir este objetivo, analisaram-se soluções semelhantes à pretendida nesta dissertação e projetos anteriormente elaborados de modo a se obter um ponto de referência aquando da definição dos requisitos da solução. Apresentam-se diferentes arquiteturas passíveis de se aplicar à solução e finalmente após uma escolha devidamente fundamentada da arquitetura, detalha-se o processo de implementação da mesma tirando proveito de tecnologias open-source pertencentes à ELK stack. Por último, avalia-se os atributos de qualidade da solução tais como a eficiência, usabilidade e funcionalidade da mesma. Conclui-se que a solução final responde de um modo satisfatório aos requisitos estabelecidos, que incluem não só mas também as funções de alertas automáticos e de visualização de informação do sistema monitorizado.Recently microservices based systems have shown strong adoption in the enterprise world. Even companies like Netflix, Amazon and The Guardian are now deploying this architectural style as a way to evolve their applications. While there are advantages associated with the use of microservices in the development of a system (greater modularity and scalability, better separation of responsibilities, among others), there are also factors that negatively affect the system. One of these negative points refers to the time spent in order to diagnose problems or anomalies in the system. Therefore, this dissertation focuses on developing a centralized log monitoring solution that aims to decrease the time consumption and human error rate that exists when debugging microservices-based systems. To achieve this goal, solutions similar to the one intended in this dissertation and previously developed projects were analyzed in order to obtain a reference point when defining the solution’s requirements. Different architectures that can be applied to the solution are portrayed and finally after a well-founded choice of architecture, the process of its implementation is detailed while taking advantage of open-source technologies belonging to the ELK stack. Lastly, the quality attributes of the solution are evaluated, such as efficiency, usability and functionality. It was concluded that the final solution satisfactorily meets the established requirements, which include not only but also the functions of automatic alerts and the visualization of information from the monitored system

Machine learning and materials modelling interpretation of in vivo toxicological response to TiO2 nanoparticles library (UV and non-UV exposure)

Assessing the risks of nanomaterials/nanoparticles (NMs/NPs) under various environmental conditions requires a more systematic approach, including the comparison of effects across many NMs with identified different but related characters/descriptors. Hence, there is an urgent need to provide coherent (eco)toxicological datasets containing comprehensive toxicity information relating to a diverse spectra of NPs characters. These datasets are test benches for developing holistic methodologies with broader applicability. In the present study we assessed the effects of a custom design Fe-doped TiO2 NPs library, using the soil invertebrate Enchytraeus crypticus (Oligochaeta), via a 5-day pulse via aqueous exposure followed by a 21-days recovery period in soil (survival, reproduction assessment). Obviously, when testing TiO2, realistic conditions should include UV exposure. The 11 Fe-TiO2 library contains NPs of size range between 5-27 nm with varying þ (enabling the photoactivation of TiO2 at energy wavelengths in the visible-light range). The NPs were each described by 122 descriptors, being a mixture of measured and atomistic model descriptors. The data were explored using single and univariate statistical methods, combined with machine learning and multiscale modelling techniques. An iterative pruning process was adopted for identifying automatically the most significant descriptors. TiO2 NPs toxicity decreased when combined with UV. Notably, the short-term water exposure induced lasting biological responses even after longer-term recovery in clean exposure. The correspondence with Fe-content correlated with the band-gap hence the reduction of UV oxidative stress. The inclusion of both measured and modelled materials data benefitted the explanation of the results, when combined with machine learning

Compostagem e hidrólise alcalina da casca de coco seco usada como cama de ovinos.

A compostagem a partir do aproveitamento da casca de coco seco (CCS) é dificultada por sua lenta degradação. O objetivo do presente trabalho foi avaliar a aceleração da compostagem da CCS por meio da hidrólise alcalina com cal hidratada e sua utilização prévia como cama de ovinos (Cov). Utilizaram-se 2 % de cal em relação a massa seca de CCS tratada. Após 60 dias como camas de ovinos, a CCS foi enleirada e estabelecidos os tratamentos: Cov de CCS hidrolisada; Cov de CCS não hidrolisada; CCS hidrolisada + sulfato de amônio; CCS não hidrolisada + sulfato de amônio; CCS hidrolisada e CCS não hidrolisada. Amostras foram coletadas aos 31 dias após a colocação dos animais e aos 1, 18, 53, 116 e 172 dias após o enleiramento. Observou-se a necessidade de ajuste do tempo de permanência da CCS no aprisco, o qual poderá ser reduzido. Os compostos apresentaram valores de C, N, relação C/N e CTC dentro dos limites fixados pela legislação vigente. O uso da CCS hidrolisada com cal hidratada como cama de ovinos, reduziu os teores de lignina em 51,87% em relação à CCS não hidrolisada, constituindo uma estratégia adequada para acelerar a compostagem desse resíduo

Enchytraeus albidus Microarray: Enrichment, Design, Annotation and Database (EnchyBASE)

Enchytraeus albidus (Oligochaeta) is an ecologically relevant species used as standard test organisms for risk assessment. Effects of stressors in this species are commonly determined at the population level using reproduction and survival as endpoints. The assessment of transcriptomic responses can be very useful e.g. to understand underlying mechanisms of toxicity with gene expression fingerprinting. In the present paper the following is being addressed: 1) development of suppressive subtractive hybridization (SSH) libraries enriched for differentially expressed genes after metal and pesticide exposures; 2) sequencing and characterization of all generated cDNA inserts; 3) development of a publicly available genomic database on E. albidus. A total of 2100 Expressed Sequence Tags (ESTs) were isolated, sequenced and assembled into 1124 clusters (947 singletons and 177 contigs). From these sequences, 41% matched known proteins in GenBank (BLASTX, e-value≤10-5) and 37% had at least one Gene Ontology (GO) term assigned. In total, 5.5% of the sequences were assigned to a metabolic pathway, based on KEGG. With this new sequencing information, an Agilent custom oligonucleotide microarray was designed, representing a potential tool for transcriptomic studies. EnchyBASE (http://bioinformatics.ua.pt/enchybase/) was developed as a web freely available database containing genomic information on E. albidus and will be further extended in the near future for other enchytraeid species. The database so far includes all ESTs generated for E. albidus from three cDNA libraries. This information can be downloaded and applied in functional genomics and transcription studies

Gene Expression Responses Linked to Reproduction Effect Concentrations (EC10,20,50,90) of Dimethoate, Atrazine and Carbendazim, in Enchytraeus albidus

BACKGROUND: Molecular mechanisms of response to pesticides are scarce and information on such responses from soil invertebrates is almost inexistent. Enchytraeus albidus (Oligochaeta) is a standard soil ecotoxicology model species for which effects of many pesticides are known on survival, reproduction and avoidance behaviour. With the recent microarray development additional information can be retrieved on the molecular effects. METHODOLOGY/PRINCIPAL FINDINGS: Experiments were performed to investigate the transcription responses of E. albidus when exposed to three pesticides - dimethoate (insecticide), atrazine (herbicide) and carbendazim (fungicide) - in a range of concentrations that inhibited reproduction by 10%, 20%, 50% and 90% (EC(10), EC(20), EC(50) and EC(90), respectively). The goal of this study was to further identify key biological processes affected by each compound and if dose-related. All three pesticides significantly affected biological processes like translation, regulation of the cell cycle or general response to stress. Intracellular signalling and microtubule-based movement were affected by dimethoate and carbendazim whereas atrazine affected lipid and steroid metabolism (also by dimethoate) or carbohydrate metabolism (also by carbendazim). Response to DNA damage/DNA repair was exclusively affected by carbendazim. CONCLUSIONS: Changes in gene expression were significantly altered after 2 days of exposure in a dose-related manner. The mechanisms of response were comparable with the ones for mammals, suggesting across species conserved modes of action. The present results indicate the potential of using gene expression in risk assessment and the advantage as early markers

Purinergic signalling links mechanical breath profile and alveolar mechanics with the pro-inflammatory innate immune response causing ventilation-induced lung injury

Severe pulmonary infection or vigorous cyclic deformation of the alveolar epithelial type I (AT I) cells by mechanical ventilation leads to massive extracellular ATP release. High levels of extracellular ATP saturate the ATP hydrolysis enzymes CD39 and CD73 resulting in persistent high ATP levels despite the conversion to adenosine. Above a certain level, extracellular ATP molecules act as danger-associated molecular patterns (DAMPs) and activate the pro-inflammatory response of the innate immunity through purinergic receptors on the surface of the immune cells. This results in lung tissue inflammation, capillary leakage, interstitial and alveolar oedema and lung injury reducing the production of surfactant by the damaged AT II cells and deactivating the surfactant function by the concomitant extravasated serum proteins through capillary leakage followed by a substantial increase in alveolar surface tension and alveolar collapse. The resulting inhomogeneous ventilation of the lungs is an important mechanism in the development of ventilation-induced lung injury. The high levels of extracellular ATP and the upregulation of ecto-enzymes and soluble enzymes that hydrolyse ATP to adenosine (CD39 and CD73) increase the extracellular adenosine levels that inhibit the innate and adaptive immune responses rendering the host susceptible to infection by invading microorganisms. Moreover, high levels of extracellular adenosine increase the expression, the production and the activation of pro-fibrotic proteins (such as TGF-β, α-SMA, etc.) followed by the establishment of lung fibrosis

Bioaccumulation and Toxicity of Organic Chemicals in Terrestrial Invertebrates

Terrestrial invertebrates are key components in ecosystems, with crucial roles in soil structure, functioning, and ecosystem services. The present chapter covers how terrestrial invertebrates are impacted by organic chemicals, focusing on up-to-date information regarding bioavailability, exposure routes and general concepts on bioaccumulation, toxicity, and existing models. Terrestrial invertebrates are exposed to organic chemicals through different routes, which are dependent on both the organismal traits and nature of exposure, including chemical properties and media characteristics. Bioaccumulation and toxicity data for several groups of organic chemicals are presented and discussed, attempting to cover plant protection products (herbicides, insecticides, fungicides, and molluscicides), veterinary and human pharmaceuticals, polycyclic aromatic compounds, polychlorinated biphenyls, flame retardants, and personal care products. Chemical mixtures are also discussed bearing in mind that chemicals appear simultaneously in the environment. The biomagnification of organic chemicals is considered in light of the consumption of terrestrial invertebrates as novel feed and food sources. This chapter highlights how science has contributed with data from the last 5 years, providing evidence on bioavailability, bioaccumulation, and toxicity derived from exposure to organic chemicals, including insights into the main challenges and shortcomings to extrapolate results to real exposure scenarios

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field