608 research outputs found
Computational approaches to standard-compliant biofilm data for reliable analysis and integration
The study of microorganism consortia, also known as biofilms, is associated to a number of applications in biotechnology, ecotechnology and clinical domains. Nowadays, biofilm studies are heterogeneous and data-intensive, encompassing different levels of analysis. Computational modelling of biofilm studies has become thus a requirement to make sense of these vast and ever-expanding biofilm data volumes.
The rationale of the present work is a machine-readable format for representing biofilm studies and supporting biofilm data interchange and data integration. This format is supported by the Biofilm Science Ontology (BSO), the first ontology on biofilms information. The ontology is decomposed into a number of areas of interest, namely: the Experimental Procedure Ontology (EPO) which describes biofilm experimental procedures; the Colony Morphology Ontology (CMO) which characterises morphologically microorganism colonies; and other modules concerning biofilm phenotype, antimicrobial susceptibility and virulence traits. The overall objective behind BSO is to develop semantic resources to capture, represent and share data on biofilms and related experiments in a regularized fashion manner. Furthermore, the present work also introduces a framework in assistance of biofilm data interchange and analysis â BiofOmics (http://biofomics.org) â and a public repository on colony morphology signatures â MorphoCol (http://stardust.deb.uminho.pt/morphocol).The authors thank, among others, Rosario Oliveira, Maria Joao Vieira, Idalina Machado, Nuno Cerca, Mariana Henriques, Pilar Teixeira, Douglas Monteiro, Melissa Negri, Susana Lopes, Carina Almeida, Alexandrina Rodrigues, Tom Coenye, Paul Stoodley and Helder Lopes, for submitting their data and participating in the aforementioned standardisation initiatives. The financial support from the Institute of Biotechnology and Bioengineering Center of Biological Engineering (IBB-CEB), the Fundacao para a Ciencia e Tecnologia (FCT) and European Community fund FEDER (Program COMPETE), projects PTDC/SAU-ESA/646091/2006/ and FCOMP-01-0124-FEDER-007480, and the PhD grant of Ana Margarida Sousa (SFRH/BD/31065/2006) are also gratefully acknowledged
Minimum information about a biofilm experiment (MIABiE) : standards for reporting experiments and data on sessile microbial communities living at interfaces
The minimum information about a biofilm experiment (MIABiE) initiative has arisen from the need to find an adequate and scientifically sound way to control the quality of the documentation accompanying the public deposition of biofilm-related data, particularly those obtained using high-throughput devices and techniques. Thereby, the MIABiE consortium has initiated the identification and organization of a set of modules containing the minimum information that needs to be reported to guarantee the interpretability and independent verification of experimental results and their integration with knowledge coming from other fields. MIABiE does not intend to propose specific standards on how biofilms experiments should be performed, because it is acknowledged that specific research questions require specific conditions which may deviate from any standardization. Instead, MIABiE presents guidelines about the data to be recorded and published in order for the procedure and results to be easily and unequivocally interpreted and reproduced. Overall, MIABiE opens up the discussion about a number of particular areas of interest and attempts to achieve a broad consensus about which biofilm data and metadata should be reported in scientific journals in a systematic, rigorous and understandable manner.The authors would like to thank Thomas Bjarnsholt and Adyary Fallarero for a critical revision of the manuscript. This work was supported by IBB-CEB; Fundacao para a Ciencia e Tecnologia (FCT); the European Community fund FEDER, through Program COMPETE, in the ambit of the FCT Project PTDC/SAU-SAP/113196/2009/FCOMP-01-0124-FEDER-0 16012; the European Union Seventh Framework Programme [FP7/REGPOT-2012-2013.1] under Grant Agreement No. 316265, BIOCAPS; the Agrupamento INBIOMED from DXPCTSUG-FEDER unha maneira de facer Europa (2012/273). T. C. would like to thank FWO Vlaanderen and the Interuniversity Attraction Poles Programme initiated by the Belgian Science Policy Office for funding
BEW: Bioinformatics workbench for analysis of biofilms experimental data
Biofilms research has evolved considerably in the last decade and is now generating large volumes of heterogeneous data. MIABiE, the international initiative on Biofilms, is devising guidelines for data interchange, and some databases provide access to biofilms experiments. However, the field is lacking appropriate bioinformatics tools in support of increasing operational and analytical needs. This paper presents a flexible and extensible open-source workbench for the operation and analysis of biofilms experiments, as follows: (i) the creation of customised experiments, (ii) the collection of various analytical results, following community standardisation guidelines and (iii) on-demand reporting and statistical evaluation
Marshall Space Flight Center Research and Technology Report 2019
Today, our calling to explore is greater than ever before, and here at Marshall Space Flight Centerwe make human deep space exploration possible. A key goal for Artemis is demonstrating and perfecting capabilities on the Moon for technologies needed for humans to get to Mars. This years report features 10 of the Agencys 16 Technology Areas, and I am proud of Marshalls role in creating solutions for so many of these daunting technical challenges. Many of these projects will lead to sustainable in-space architecture for human space exploration that will allow us to travel to the Moon, on to Mars, and beyond. Others are developing new scientific instruments capable of providing an unprecedented glimpse into our universe. NASA has led the charge in space exploration for more than six decades, and through the Artemis program we will help build on our work in low Earth orbit and pave the way to the Moon and Mars. At Marshall, we leverage the skills and interest of the international community to conduct scientific research, develop and demonstrate technology, and train international crews to operate further from Earth for longer periods of time than ever before first at the lunar surface, then on to our next giant leap, human exploration of Mars. While each project in this report seeks to advance new technology and challenge conventions, it is important to recognize the diversity of activities and people supporting our mission. This report not only showcases the Centers capabilities and our partnerships, it also highlights the progress our people have achieved in the past year. These scientists, researchers and innovators are why Marshall and NASA will continue to be a leader in innovation, exploration, and discovery for years to come
A prospect of current microbial diagnosis methods
An accurate identification and characterization of pathogens is crucial in disease management. The appropriateness and
effectiveness of the microbial diagnosis method influence the choice of the antimicrobial agent to be used in the treatment
of infection. Traditionally, bacterial diagnosis is based on conventional and culturing-dependent approaches, such as
culture and counting methods, generally coupled to morphological and physiological characterization. Currently, rapid
technological advances in bacterial identification methods are occurring providing a bewildering wide range of techniques
to detect, identify and differentiate bacteria. Molecular methods, such as ELISA and PCR, had introduced great
improvements in bacterial identification as they contributed to speed up the analysis and the reduction of handling.
However, it has been demonstrated that heterogeneous microbial communities are the main cause of several human
infections. This genetic and phenotypic heterogeneity is crucial to microorganisms achieving adaptation to human host,
and it might reflect distinct pathogenicity potential. The aforementioned molecular methods and new emergent methods,
such as MALDI-TOF MS, have still limitations in full identification and differentiation of microbial heterogeneity.
Therefore, a new generation of diagnosis methods able to detect and characterize microbial heterogeneity should be
developed. Microbial infections are like dynamic systems and it is essential that diagnosis methods and technologies
rapidly evolve to detect and measure changes occurring at individual and population level. This new kind of methods will
allow a relevant shift about infection development understanding, as well about microbial mechanisms of resistance to
antibiotics and human defences and persistence ability in human host that culminate in better medical decisions about
antimicrobial therapy
11th International Conference on Predictive Modelling in Food: book of abstracts
It is our great pleasure to welcome you in Bragança, Portugal, for the 11th International Conference of Predictive Modelling in Food (ICPMF11). Since 1992, ten ICPMF editions have taken place, providing a forum for the exchange of ideas, identification of research needs and novel approaches for the advancement of predictive modelling towards ensuring safety and quality of foods.
Bragança is a typically-Portuguese old town (Romanic origin dates back to the 10th century), located by the Natural Park of Montesinho â one of the wildest forest zones of Europe â and the Douro Valley â the third oldest protected wine region in the world; and surrounded by traditional villages of a distinctive rustic beauty. Bragança houses several traditional industries producing a myriad of local foods, such as cheese, fermented meats, wine, chestnuts and honey, which provide substantial economic sustainability to the region.
ICPMF11 reunites food researchers, stakeholders, risk assessors and users of predictive models to present recent developments and trends in modelling approaches for food quality, safety and sustainability. We succeeded to gather a significant number of delegates from over the world to participate in a comprehensive scientific programme that includes keynote lectures, oral communications and posters, allocated in sessions focusing on:
. Advances in predictive microbiology modelling
. Predictive modelling in innovative food processing and preservation technologies
. Advances in microbial dynamics and interactions
. Advances in software and database tools
. Meta-analysis protocols and applications
. Advances in risk assessment methods and integration of omics techniques
. Advances in predictive modelling in food quality and safety
. Predictive mycology
. Individual cell and whole-cell modelling
Apart from those, ICPMF11 features for the first time a special session dedicated to âInnovative approaches for ensuring safety of traditional foodsâ and the Round Table: âAssuring the Safety of Traditional Foods: A Scientific Contribution to Protecting our Cultural Heritageâ. We, as food researchers based in a Mediterranean mountain region, are aware that the production of traditional foods plays a key role in the development of rural regions, since the agricultural commodities used as raw materials are generally produced locally, allowing and stimulating local commercialisation, thus contributing to a sustainable environment, and employment in rural populations. It was inspiring for us to have received many submissions from both developed and developing countries on the valorisation of traditional foods through the application of up-to-date modelling research.
Besides that, one morning workshop and three afternoon tutorials were programmed during the day before the scientific programme. The workshop âHow to benefit from the Risk Assessment Modelling and Knowledge Integration Platform (RAKIP)â was organised by Matthias Filter. The parallel tutorials âTowards an integrated predictive software map: Practical examples of use of predictive microbiology software tools for food safety and qualityâ; âAdvanced methods in predictive microbiologyâ and âTopics in quantitative microbial risk assessment using Râ were organised by Fernando PĂ©rez-RodrĂguez, Pablo FernĂĄndez, Alberto Garre and Mariem Ellouze; by Lihan Huang, Cheng-An Hwang and Vasco Cadavez; and by Patrick Njage and Ana Sofia Ribeiro Duarte, respectively. We thank these organisers for their proposals.
Abstracts, reviewed by the ICPMF11 Scientific Committee, are published in the present Book of Abstracts while peer-reviewed original research articles will be invited to be published in ICPMF11 Special Issues in the International Journal of Food Microbiology and Microbial Risk Analysis. To stimulate the participation of postgraduate students and young researchers, two kinds of awards were arranged: the Young Researcher Best Oral Presentation prizes, sponsored by Elsevier; and the Developing Scientist Best Poster prizes, sponsored by the International Committee on Food Microbiology and Hygiene (ICFMH) of the International Union of Microbiological Societies (IUMS). For the first time, this ICPMF edition gives out two awards for the Senior Researcher Best Oral Presentation, sponsored by the open-access journal Foods â MDPI.
In addition to the scientific programme, we prepared an exciting social programme for delegates to appreciate the rich culture, gastronomy and traditions of Bragança, w includes welcome reception, live music, tasting of regional food and a gala dinner in the Castle of Bragança.
We look forward to lively discussions, and hope that this meeting will give you the opportunity to strengthen friendship and cooperation, and build new contacts for future research endeavours.info:eu-repo/semantics/publishedVersio
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