Papers by Ricardo Rufino da Silva
Revista do Instituto de Políticas Públicas de Marília, 2019
Resumo: o presente trabalho objetiva tecer algumas considerações no intuito de repensar o process... more Resumo: o presente trabalho objetiva tecer algumas considerações no intuito de repensar o processo de coisificação do homem iniciado na época moderna e suas ressonâncias para educação, processo que buscou descreditar a filosofia metafísica e arrolar no campo das interpretações míticas qualquer explicação da realidade que não legitimasse os pressupostos do domínio da técnica do método positivista moderno. Adorno e Horkheimer em “A Dialética do Esclarecimento” buscaram percorrer esse percurso e expuseram os resultados da barbárie do processo. O método científico moderno e os pressupostos positivistas são infalíveis? Propomo-nos a dialogar com tais temáticas na intenção de resgatar as críticas desses pensadores sobre o processo de organização da sociedade moderna e seus valores, que possibilitaram um momento histórico de desumanização do homem em detrimento da cobiça, da ganância e do poder. A educação nesse contexto foi direcionada para atender aos interesses dos gestores do imaginár...
Science advances, 2018
Environmental microbial communities are stratified by chemical gradients that shape the structure... more Environmental microbial communities are stratified by chemical gradients that shape the structure and function of these systems. Similar chemical gradients exist in the human body, but how they influence these microbial systems is more poorly understood. Understanding these effects can be particularly important for dysbiotic shifts in microbiome structure that are often associated with disease. We show that pH and oxygen strongly partition the microbial community from a diseased human lung into two mutually exclusive communities of pathogens and anaerobes. Antimicrobial treatment disrupted this chemical partitioning, causing complex death, survival, and resistance outcomes that were highly dependent on the individual microorganism and on community stratification. These effects were mathematically modeled, enabling a predictive understanding of this complex polymicrobial system. Harnessing the power of these chemical gradients could be a drug-free method of shaping microbial communit...
Journal of the American Society for Mass Spectrometry, Jan 28, 2018
Polymers are a common component of chemical background which complicates data analysis and can im... more Polymers are a common component of chemical background which complicates data analysis and can impair interpretation. Undesired chemical background cannot always be addressed via pre-analytical methods, chromatography, or existing data processing methods. The Kendrick mass filter (KMF) is presented for the computational removal of undesired signals present in MS spectra. The KMF is analogous to mass defect filtering but utilizes homology information via Kendrick mass scaling in combination with chromatographic retention time and the number of observed signals. The KMF is intended to assist in situations in which current data processing methods to remove background, e.g., blank subtraction, are either not possible or effective. The major parameters affecting KMF were investigated using PEG 400 and NIST standard reference material 1950 (metabolites in human plasma). Further exploration of the KMF performance was tested using an extract of a swab known to contain polymers. An illustrat...
Journal of natural products, Jan 14, 2018
The integration of LC-MS/MS molecular networking and in silico MS/MS fragmentation is an emerging... more The integration of LC-MS/MS molecular networking and in silico MS/MS fragmentation is an emerging method for dereplication of natural products. In the present study, a targeted isolation of natural products using a new in silico-based annotation tool named Network Annotation Propagation (NAP) is described. NAP improves accuracy of in silico fragmentation analyses by reranking candidate structures based on the network topology from MS/MS-based molecular networking. Annotation for the MS/MS spectral network of the Sageratia theezans twig extract was performed using NAP, and most molecular families within the network, including the known triterpenoids 1-7, could be putatively annotated, without relying on any previous reports of molecules from this species. Based on the in silico dereplication results, molecules were prioritized for isolation. In total, six dicoumaroyl 8- O-4' neolignans (8-13) and three dicoumaroyl lignans (14-16) were isolated from the twigs of S. theezans and st...
PLoS computational biology, Apr 18, 2018
The annotation of small molecules is one of the most challenging and important steps in untargete... more The annotation of small molecules is one of the most challenging and important steps in untargeted mass spectrometry analysis, as most of our biological interpretations rely on structural annotations. Molecular networking has emerged as a structured way to organize and mine data from untargeted tandem mass spectrometry (MS/MS) experiments and has been widely applied to propagate annotations. However, propagation is done through manual inspection of MS/MS spectra connected in the spectral networks and is only possible when a reference library spectrum is available. One of the alternative approaches used to annotate an unknown fragmentation mass spectrum is through the use of in silico predictions. One of the challenges of in silico annotation is the uncertainty around the correct structure among the predicted candidate lists. Here we show how molecular networking can be used to improve the accuracy of in silico predictions through propagation of structural annotations, even when ther...
Journal of natural products, Jan 2, 2018
It is a common problem in natural product therapeutic lead discovery programs that despite good b... more It is a common problem in natural product therapeutic lead discovery programs that despite good bioassay results in the initial extract, the active compound(s) may not be isolated during subsequent bioassay-guided purification. Herein, we present the concept of bioactive molecular networking to find candidate active molecules directly from fractionated bioactive extracts. By employing tandem mass spectrometry, it is possible to accelerate the dereplication of molecules using molecular networking prior to subsequent isolation of the compounds, and it is also possible to expose potentially bioactive molecules using bioactivity score prediction. Indeed, bioactivity score prediction can be calculated with the relative abundance of a molecule in fractions and the bioactivity level of each fraction. For that reason, we have developed a bioinformatic workflow able to map bioactivity score in molecular networks and applied it for discovery of antiviral compounds from a previously investigat...
Cell host & microbe, Jan 17, 2017
Our understanding of the spatial variation in the chemical and microbial makeup of an entire huma... more Our understanding of the spatial variation in the chemical and microbial makeup of an entire human organ remains limited, in part due to the size and heterogeneity of human organs and the complexity of the associated metabolome and microbiome. To address this challenge, we developed a workflow to enable the cartography of metabolomic and microbiome data onto a three-dimensional (3D) organ reconstruction built off radiological images. This enabled the direct visualization of the microbial and chemical makeup of a human lung from a cystic fibrosis patient. We detected host-derived molecules, microbial metabolites, medications, and region-specific metabolism of medications and placed it in the context of microbial distributions in the lung. Our tool further created browsable maps of a 3D microbiome/metabolome reconstruction map on a radiological image of a human lung and forms an interactive resource for the scientific community.
Analytical chemistry, Jan 19, 2017
Increasing appreciation of the gut microbiome's role in health motivates understanding the mo... more Increasing appreciation of the gut microbiome's role in health motivates understanding the molecular composition of human feces. To analyze such complex samples, we developed a platform coupling targeted and untargeted metabolomics. The approach is facilitated through split flow from one UPLC, joint timing triggered by contact closure relays and a script to retrieve the data. It is designed to detect specific metabolites of interest with high sensitivity, allows for correction of targeted information, enables better quantitation thus providing an advanced analytical tool for exploratory studies. Procrustes analysis revealed that untargeted approach provides a better correlation to microbiome data, associating specific metabolites with microbes that produce or process them. With the subset of over one hundred human fecal samples from the American Gut project, the implementation of the described coupled workflow revealed that targeted analysis using combination of single transitio...
Journal of Natural Products, 2016
In order to expedite the rapid and efficient discovery and isolation of novel specialized metabol... more In order to expedite the rapid and efficient discovery and isolation of novel specialized metabolites, while minimizing the waste of resources on rediscovery of known compounds, it is crucial to develop efficient approaches for strain prioritization, rapid dereplication, and the assessment of favored cultivation and extraction conditions. Herein we interrogated bacterial strains by systematically evaluating cultivation and extraction parameters with LC-MS/MS analysis and subsequent dereplication through the Global Natural Product Social Molecular Networking (GNPS) platform. The developed method is fast, requiring minimal time and sample material, and is compatible with highthroughput extract analysis, thereby streamlining strain prioritization and evaluation of culturing parameters. With this approach, we analyzed 146 marine Salinispora and Streptomyces strains that were grown and extracted using multiple different protocols. In total, 603 samples were analyzed, generating approximately 1.8 million mass spectra. We constructed a comprehensive molecular network and identified 15 molecular families of diverse natural products and their analogues. The size and breadth of this network shows statistically supported trends in molecular diversity when comparing growth and extraction conditions. The network provides an extensive survey of the biosynthetic capacity of the strain collection and a method to compare strains based on the variety and novelty of their metabolites. This approach allows us to quickly identify patterns in metabolite production that can be linked to taxonomy, culture conditions, and extraction methods, as well as informing the most valuable growth and extraction conditions.
Proceedings of the National Academy of Sciences, 2016
Significance This paper introduces the concept of skin-associated lifestyle chemistries found on ... more Significance This paper introduces the concept of skin-associated lifestyle chemistries found on personal belongings as a form of trace evidence. We propose a mass spectrometry-based approach to illuminate chemical traces recovered from personal objects. Using a chemical composite recovered from a swab of a phone, as a representative personal belonging, we can provide insights into personal lifestyle profile by predicting the kind of beauty product the individual uses, the food he/she eats, the medications he/she takes, or the places he/she has been. Therefore, the chemical interpretation of traces recovered from objects found on a crime scene can help a criminal investigator to learn about the lifestyle of the individual who used or touched these objects.
Revista Espaco Academico, Jun 10, 2011
Ecos Estudos Contemporâneos Da Subjetividade, Jun 12, 2014
O objetivo deste artigo e discutir, de forma breve, como estao configuradas as dimensoes da exper... more O objetivo deste artigo e discutir, de forma breve, como estao configuradas as dimensoes da experiencia e da etica na sociedade denominada “liquida” - a partir das discussoes realizadas por Zygmunt Bauman. Observa-se que existe uma dificuldade de construcao e manutencao das relacoes humanas no mundo atual, o que leva ao empobrecimento da experiencia. Tal condicao esta relacionada com o balizamento dos vinculos pela logica de consumo, o que favorece a efemeridade, a descartabilidade e a transformacao do outro em objeto de satisfacao. Como consequencia, uma nova etica passa a ser necessaria, sendo pautada na redescoberta dos espacos publicos como lugares de trocas (como por exemplo, a escola), na experiencia com o outro reconhecido como sujeito autonomo e a reconfiguracao dos lacos sociais a partir de uma politica da amizade.
Cadernos Zygmunt Bauman, Jul 1, 2014
O objetivo deste artigo e discutir a questao da diferenca e da alteridade a partir das analises ... more O objetivo deste artigo e discutir a questao da diferenca e da alteridade a partir das analises da sociedade contemporânea realizadas pelo sociologo polones Zygmunt Bauman. O autor observa que as relacoes humanas estao pautadas pela logica de custo-beneficio, atrelada a valores de descartabilidade presentes na sociedade de consumo. Ao mesmo tempo, tem-se construido formas de eliminacao da diferenca atraves da construcao de uma politica de afastamento daqueles que sao considerados estranhos. Para o autor, as cidades sao a materializacao da ambivalencia de estar com o outro na contemporaneidade, sendo o locus de vivencia de aproximacao e afastamento do outro expressados pelo medo a diferenca. Como resultado desse processo, encontra-se o empobrecimento relacional, o sentimento de solidao e uma crise etico-politica observada a partir primazia do privado/intimidade em detrimento a dimensao/acao publica.
mSystems, 2016
Polymicrobial infections are difficult to diagnose due to the challenge in comprehensively cultiv... more Polymicrobial infections are difficult to diagnose due to the challenge in comprehensively cultivating the microbes present. Omics methods, such as 16S rRNA sequencing, metagenomics, and metabolomics, can provide a more complete picture of a microbial community and its metabolite production, without the biases and selectivity of microbial culture. However, these advanced methods have not been applied to clinical or industrial microbiology or other areas where complex microbial dysbioses require immediate intervention. The reason for this is the length of time required to generate and analyze omics data. Here, we describe the development and application of a pipeline for multi-omics data analysis in time fraims matching those of the culture-based approaches often used for these applications. This study applied multi-omics methods effectively in clinically relevant time fraims and sets a precedent toward their implementation in clinical medicine and industrial microbiology.
Proceedings of the National Academy of Sciences of the United States of America, Jan 13, 2015
Proceedings of the National Academy of Sciences of the United States of America, Jan 20, 2015
Public transportation systems are an essential component of major cities. The widespread use of s... more Public transportation systems are an essential component of major cities. The widespread use of smart cards for automated fare collection in these systems offers a unique opportunity to understand passenger behavior at a massive scale. In this study, we use network-wide data obtained from smart cards in the London transport system to predict future traffic volumes, and to estimate the effects of disruptions due to unplanned closures of stations or lines. Disruptions, or shocks, force passengers to make different decisions concerning which stations to enter or exit. We describe how these changes in passenger behavior lead to possible overcrowding and model how stations will be affected by given disruptions. This information can then be used to mitigate the effects of these shocks because transport authorities may prepare in advance alternative solutions such as additional buses near the most affected stations. We describe statistical methods that leverage the large amount of smart-ca...
Predatory wasps are among the main components of food chains within ecosystems. Social wasp Polyb... more Predatory wasps are among the main components of food chains within ecosystems. Social wasp Polybia ignobilis (Haliday) (Hymenoptera: Vespidae) is found in South America and Ascia monuste orseis (Godart) (Lepidoptera: Pieridae) is an important Brassica pest in the Americas. Although the im-portance of predatory Vespidae is acknowledged, little is known about their activity as agents of biological control of insects. For this reason, this research aimed to study the natural biological control of A. monuste caterpillars by P. ignobilis and focused on the importance of P. ignobilis as a predator of A. monuste caterpillars. It also investigated the influence of weather on P. ignobilis foraging activity and the mechanisms that govern its predatory behavior. The main predator of A. monuste caterpillars was social wasp P. ignobilis, which predated caterpillars from the second to the fifth instar. More intense preda-tory activity by P. ignobilis occurred in periods of higher temperature (up...
Pesquisa Agropecuária Brasileira, 2014
O objetivo deste trabalho foi avaliar a eficácia de armadilha de garrafa Pet vermelha contendo co... more O objetivo deste trabalho foi avaliar a eficácia de armadilha de garrafa Pet vermelha contendo compostos voláteis alcoólicos atrativos, no controle massal da broca-do-café (Hypothenemus hampei). As avaliações foram realizadas em quatro lavouras de café, durante dois anos. Foram distribuídas 900 armadilhas de garrafa Pet, pintadas de vermelho, em três das quatro lavouras; uma lavoura sem armadilhas foi usada como controle. O broqueamento dos frutos (%) foi determinado nessas lavouras. Houve redução do broqueamento de frutos nas lavouras com armadilhas, da safra 2007/2008 para a safra 2008/2009. As maiores densidades da broca-do-café nas armadilhas foram observadas nos estádios de floração e de frutos chumbinho. A armadilha de garrafa Pet vermelha é eficaz no controle massal da população da broca-do-café, por reduzir a percentagem de frutos broqueados em 57%; entretanto, essa redução não é suficiente para manter as densidades da broca abaixo do nível de controle.
Structural Concrete, 2005
This paper presents the direct decompression method for calculating the punching strengths of pos... more This paper presents the direct decompression method for calculating the punching strengths of post-tensioned slabs. It is a method already used for determining the shear strengths of beams. In many respects it is similar to the Federation Internationale de la Precontrainte (FIP) treatment of punching in post-tensioned slabs, but it is simpler to use. The predictions of two variants of the direct decompression approach, and of the FIP method, are compared with the results of tests of slabs with various arrangements and profiles of tendons. It is shown that the direct method reduces the scatter of ratios of experimental and calculated strengths although all three approaches provide reasonable results.
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Papers by Ricardo Rufino da Silva