scholarly journals Fast Klebsiella pneumoniae typing for outbreak reconstruction: an highly discriminatory HRM protocol on wzi capsular gene developed using EasyPrimer tool

2019 ◽  
Author(s):  
Matteo Perini ◽  
Aurora Piazza ◽  
Simona Panelli ◽  
Domenico Di Carlo ◽  
Marta Corbella ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Cost Saving ◽  
Large Scale ◽  
Graphical Representation ◽  
Primer Design ◽  
Bacterial Typing ◽  
Gene Alignment ◽  
Surveillance Programs ◽  
Primer Sets ◽  
User Friendly

ABSTRACTIn this work we present EasyPrimer, a user-friendly online tool developed to assist pan-PCR and High Resolution Melting (HRM) primer design. The tool finds the most suitable regions for primer design in a gene alignment and returns a clear graphical representation of their positions on the gene. EasyPrimer is particularly useful in difficult contexts, e.g. on gene alignments of hundreds of sequences and/or on highly variable genes. HRM analysis is an emerging method for fast and cost saving bacterial typing and an HRM scheme of six primer sets on five Multi-Locus Sequence Type (MLST) genes is already available for Klebsiella pneumoniae. We validated the tool designing a scheme of two HRM primer sets on the hypervariable gene wzi of Klebsiella pneumoniae and compared the two schemes. The wzi scheme resulted to have a discriminatory power comparable to the HRM MLST scheme, using only one third of primer sets. Then we successfully used the wzi HRM primer scheme to reconstruct a Klebsiella pneumoniae nosocomial outbreak in few hours. The use of hypervariable genes reduces the number of HRM primer sets required for bacterial typing allowing to perform cost saving, large-scale surveillance programs.

scholarly journals DOGMA: a web server for proteome and transcriptome quality assessment

2019 ◽  
Vol 47 (W1) ◽  
pp. W507-W510 ◽  
Author(s):  
Carsten Kemena ◽  
Elias Dohmen ◽  
Erich Bornberg-Bauer
Keyword(s):  
Next Generation Sequencing ◽  
Quality Assessment ◽  
Large Scale ◽  
Graphical Representation ◽  
Web Server ◽  
Crucial Step ◽  
Core Set ◽  
Core Sets ◽  
User Friendly ◽  
Generation Sequencing

Abstract Even in the era of next generation sequencing, in which bioinformatics tools abound, annotating transcriptomes and proteomes remains a challenge. This can have major implications for the reliability of studies based on these datasets. Therefore, quality assessment represents a crucial step prior to downstream analyses on novel transcriptomes and proteomes. DOGMA allows such a quality assessment to be carried out. The data of interest are evaluated based on a comparison with a core set of conserved protein domains and domain arrangements. Depending on the studied species, DOGMA offers precomputed core sets for different phylogenetic clades. We now developed a web server for the DOGMA software, offering a user-friendly, simple to use interface. Additionally, the server provides a graphical representation of the analysis results and their placement in comparison to publicly available data. The server is freely available under https://domainworld-services.uni-muenster.de/dogma/. Additionally, for large scale analyses the software can be downloaded free of charge from https://domainworld.uni-muenster.de.

scholarly journals MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Matteo Perini ◽  
Gherard Batisti Biffignandi ◽  
Domenico Di Carlo ◽  
Ajay Ratan Pasala ◽  
Aurora Piazza ◽  
...  
Keyword(s):  
High Resolution ◽  
Real Time ◽  
Large Scale ◽  
High Resolution Melting ◽  
Control Strategies ◽  
Rapid Identification ◽  
Clustering Methods ◽  
Molecular Biology Technique ◽  
Surveillance Programs ◽  
User Friendly

Abstract Background The rapid identification of pathogen clones is pivotal for effective epidemiological control strategies in hospital settings. High Resolution Melting (HRM) is a molecular biology technique suitable for fast and inexpensive pathogen typing protocols. Unfortunately, the mathematical/informatics skills required to analyse HRM data for pathogen typing likely limit the application of this promising technique in hospital settings. Results MeltingPlot is the first tool specifically designed for epidemiological investigations using HRM data, easing the application of HRM typing to large real-time surveillance and rapid outbreak reconstructions. MeltingPlot implements a graph-based algorithm designed to discriminate pathogen clones on the basis of HRM data, producing portable typing results. The tool also merges typing information with isolates and patients metadata to create graphical and tabular outputs useful in epidemiological investigations and it runs in a few seconds even with hundreds of isolates. Availability: https://skynet.unimi.it/index.php/tools/meltingplot/. Conclusions The analysis and result interpretation of HRM typing protocols can be not trivial and this likely limited its application in hospital settings. MeltingPlot is a web tool designed to help the user to reconstruct epidemiological events by combining HRM-based clustering methods and the isolate/patient metadata. The tool can be used for the implementation of HRM based real time large scale surveillance programs in hospital settings.

Microcomputer Simulations of Presidential Elections

1983 ◽  
Vol 38 ◽  
pp. 20-20
Author(s):  
Robert S. Ross
Keyword(s):  
Social Sciences ◽  
Large Scale ◽  
Role Playing ◽  
Science Students ◽  
Instructional Programs ◽  
Santa Barbara ◽  
Large Scale Systems ◽  
The Social ◽  
User Friendly ◽  
Machine Interaction

Simulations have been an important adjunct to instructional programs for some time. These have ranged from games, or role playing exercises, such as SIMSOC or Internation Simulation, to student-machine interaction, such as the inter-school simulation run out of University of California, Santa Barbara in the early 70's, to the all machine activities found in some of the early SETUPS. Having social science students use the mainframe computer, however, always posed problems: it definitely was not user-friendly and most instructors had little if any training or interest in the use of large scale systems.The wide-spread use of the micro computer is not only revolutionizing areas traditionally relying upon the computer, but is going to have an impact on the social sciences as well.

scholarly journals fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy

2017 ◽  
Vol 33 (13) ◽  
pp. 2020-2028 ◽  
Author(s):  
Oliver Hilsenbeck ◽  
Michael Schwarzfischer ◽  
Dirk Loeffler ◽  
Sotiris Dimopoulos ◽  
Simon Hastreiter ◽  
...  
Keyword(s):  
Large Scale ◽  
Cell Segmentation ◽  
User Friendly

Cross-contamination in molecular laboratories: A challenge to COVID-19 testing in Bangladesh

2021 ◽  
Vol 2 (5) ◽  
Author(s):  
Mohammad Jahidur Rahman Khan ◽  
◽  
Selim Reza ◽  
Farzana Mim ◽  
Md Abdullah Rumman ◽  
...  
Keyword(s):  
Public Health ◽  
Large Scale ◽  
Diagnostic Testing ◽  
Diagnostic Errors ◽  
Laboratory Diagnosis ◽  
Cross Contamination ◽  
Rt Pcr ◽  
Public Health Response ◽  
Surveillance Programs ◽  
The Government

Rapid and accurate laboratory diagnosis of SARS-CoV-2 infection is crucial for the management of COVID-19 patients and control of the spread of the virus. At the start of the COVID-19 pandemic, Bangladesh had only one government molecular laboratory where real-time RT-PCR will be performed to diagnose SARS-CoV-2 infection. With the increasing number of suspected cases requiring confirmation diagnostic testing, there was a requirement to quickly expand capacity for large-scale testing. The government of Bangladesh established over 100 molecular laboratories within one year to test COVID-19. To fulfil the requirement for expanded testing, the government was compelled to recruit laboratory employees with inadequate experience, technical knowledge, and skills in molecular assays, particularly in processing specimens, interpreting results, recognizing errors, and troubleshooting. As a result, the risk of diagnostic errors, such as cross-contamination, is increased, as is that the risk of false-positive results, which might risk the patient’s health and undermine the efficacy of public health policies, public health response, surveillance programs, and restrictive measures aimed toward containing the outbreak. This review article aims to explain different sources of crosscontamination in the COVID-19 RT-PCR laboratories and the way to forestall them in efficient and practical ways.

scholarly journals The Microbe Directory: An annotated, searchable inventory of microbes’ characteristics

2018 ◽  
Vol 2 ◽  
pp. 3 ◽  
Author(s):  
Heba Shaaban ◽  
David A. Westfall ◽  
Rawhi Mohammad ◽  
David Danko ◽  
Daniela Bezdan ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Large Scale ◽  
Research Effort ◽  
Gram Stain ◽  
Web Interface ◽  
Ongoing Effort ◽  
Student Researchers ◽  
User Friendly ◽  
Optimal Ph ◽  
Online Web

The Microbe Directory is a collective research effort to profile and annotate more than 7,500 unique microbial species from the MetaPhlAn2 database that includes bacteria, archaea, viruses, fungi, and protozoa. By collecting and summarizing data on various microbes’ characteristics, the project comprises a database that can be used downstream of large-scale metagenomic taxonomic analyses, allowing one to interpret and explore their taxonomic classifications to have a deeper understanding of the microbial ecosystem they are studying. Such characteristics include, but are not limited to: optimal pH, optimal temperature, Gram stain, biofilm-formation, spore-formation, antimicrobial resistance, and COGEM class risk rating. The database has been manually curated by trained student-researchers from Weill Cornell Medicine and CUNY—Hunter College, and its analysis remains an ongoing effort with open-source capabilities so others can contribute. Available in SQL, JSON, and CSV (i.e. Excel) formats, the Microbe Directory can be queried for the aforementioned parameters by a microorganism’s taxonomy. In addition to the raw database, The Microbe Directory has an online counterpart (https://microbe.directory/) that provides a user-friendly interface for storage, retrieval, and analysis into which other microbial database projects could be incorporated. The Microbe Directory was primarily designed to serve as a resource for researchers conducting metagenomic analyses, but its online web interface should also prove useful to any individual who wishes to learn more about any particular microbe.

scholarly journals SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis

2020 ◽  
Author(s):  
Stevenn Volant ◽  
Pierre Lechat ◽  
Perrine Woringer ◽  
Laurence Motreff ◽  
Christophe Malabat ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Data Processing ◽  
Web Application ◽  
Graphical Representation ◽  
Statistical Modelling ◽  
Metagenomic Data ◽  
Sequencing Data ◽  
Microbiome Research ◽  
Interactive Visualizations ◽  
User Friendly

Abstract BackgroundComparing the composition of microbial communities among groups of interest (e.g., patients vs healthy individuals) is a central aspect in microbiome research. It typically involves sequencing, data processing, statistical analysis and graphical representation of the detected signatures. Such an analysis is normally obtained by using a set of different applications that require specific expertise for installation, data processing and in some case, programming skills. ResultsHere, we present SHAMAN, an interactive web application we developed in order to facilitate the use of (i) a bioinformatic workflow for metataxonomic analysis, (ii) a reliable statistical modelling and (iii) to provide among the largest panels of interactive visualizations as compared to the other options that are currently available. SHAMAN is specifically designed for non-expert users who may benefit from using an integrated version of the different analytic steps underlying a proper metagenomic analysis. The application is freely accessible at http://shaman.pasteur.fr/, and may also work as a standalone application with a Docker container (aghozlane/shaman), conda and R. The source code is written in R and is available at https://github.com/aghozlane/shaman. Using two datasets (a mock community sequencing and published 16S rRNA metagenomic data), we illustrate the strengths of SHAMAN in quickly performing a complete metataxonomic analysis. ConclusionsWe aim with SHAMAN to provide the scientific community with a platform that simplifies reproducible quantitative analysis of metagenomic data.

scholarly journals CrosstalkNet: mining large-scale bipartite co-expression networks to characterize epi-stroma crosstalk

2017 ◽  
Author(s):  
Venkata Manem ◽  
George Adam ◽  
Tina Gruosso ◽  
Mathieu Gigoux ◽  
Nicholas Bertos ◽  
...  
Keyword(s):  
Stromal Cells ◽  
Large Scale ◽  
Network Visualization ◽  
Visualization Tool ◽  
Biological Processes ◽  
Web Based ◽  
Link Type ◽  
A Cell ◽  
Large Scale Networks ◽  
User Friendly

ABSTRACTBackground:Over the last several years, we have witnessed the metamorphosis of network biology from being a mere representation of molecular interactions to models enabling inference of complex biological processes. Networks provide promising tools to elucidate intercellular interactions that contribute to the functioning of key biological pathways in a cell. However, the exploration of these large-scale networks remains a challenge due to their high-dimensionality.Results:CrosstalkNet is a user friendly, web-based network visualization tool to retrieve and mine interactions in large-scale bipartite co-expression networks. In this study, we discuss the use of gene co-expression networks to explore the rewiring of interactions between tumor epithelial and stromal cells. We show how CrosstalkNet can be used to efficiently visualize, mine, and interpret large co-expression networks representing the crosstalk occurring between the tumour and its microenvironment.Conclusion:CrosstalkNet serves as a tool to assist biologists and clinicians in exploring complex, large interaction graphs to obtain insights into the biological processes that govern the tumor epithelial-stromal crosstalk. A comprehensive tutorial along with case studies are provided with the application.Availability:The web-based application is available at the following location: http://epistroma.pmgenomics.ca/app/. The code is open-source and freely available from http://github.com/bhklab/EpiStroma-webapp.Contact:[email protected]

scholarly journals 243 PREGNANCY RATES IN THE FIELD AFTER THE TRANSFER OF BOVINE IVP EMBRYOS VITRIFIED BY THE CRYOLOGIC VITRIFICATION METHOD

2005 ◽  
Vol 17 (2) ◽  
pp. 272 ◽  
Author(s):  
R. Fry ◽  
C. Earl ◽  
K. Fry ◽  
W. Lindemans
Keyword(s):  
Large Scale ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Pregnancy Rates ◽  
Chi Square ◽  
Full Field ◽  
Transfer Programs ◽  
Short Period ◽  
Rectal Palpation ◽  
User Friendly

Although large numbers of IVP embryos can be produced from donor cattle in a short period of time, commercial acceptance of the technology depends on the ability to cryopreserve these embryos and achieve a 50% pregnancy rate in large-scale embryo transfer programs. Many studies have reported low pregnancy rates of about 20% after the transfer of cryopreserved IVP embryos. We have developed the user friendly CryoLogic Vitrification Method (CVM) that vitrifies embryos on a solid surface at −196°C and warms them rapidly in a one-step procedure prior to transfer (Lindemans et al. 2004 Reprod. Fertil. Dev. 16, 174). We present an overview of the pregnancy rates in the field after vitrification of bovine IVP embryos by the CVM. The bos taurus IVP embryos in southern Australia (bT) and the bos indicus-based IVP embryos in northern Australia (bI) were produced by our standard TVR and IVP methodology (Fry et al., 2003 Theriogenology 59, 446). Pregnancy was determined by rectal palpation between Day 40 and Day 90 and differences between treatments were analyzed by chi-square. The development of the CVM has enabled the successful cryopreservation of bovine IVP embryos. In the laboratory the typical survival (90% re-expansion) and development (80% hatching) of IVP embryos post-vitrification is high and, as demonstrated here, the pregnancy rates after transfer are approaching commercially acceptable levels. However, further research is required to identify factors that may influence success under full field conditions, for both the IVP and the vitrification technologies. Table 1. Pregnancy rates for fresh IVP, CVM-vitrified IVP, and traditionally flushed embryos cryopreserved in glycerol

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