scholarly journals DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Malik Alawi ◽  
Lia Burkhardt ◽  
Daniela Indenbirken ◽  
Kerstin Reumann ◽  
Maximilian Christopeit ◽  
...  
Keyword(s):  
Open Source ◽  
Clinical Samples ◽  
Pathogenic Microorganisms ◽  
Bioinformatics Tool ◽  
Sample Group ◽  
Viral Genomes ◽  
Multiple Virus ◽  
Diagnostic Samples ◽  
Virus Strains

AbstractWe describe DAMIAN, an open source bioinformatics tool designed for the identification of pathogenic microorganisms in diagnostic samples. By using authentic clinical samples and comparing our results to those from established analysis pipelines as well as conventional diagnostics, we demonstrate that DAMIAN rapidly identifies pathogens in different diagnostic entities, and accurately classifies viral agents down to the strain level. We furthermore show that DAMIAN is able to assemble full-length viral genomes even in samples co-infected with multiple virus strains, an ability which is of considerable advantage for the investigation of outbreak scenarios. While DAMIAN, similar to other pipelines, analyzes single samples to perform classification of sequences according to their likely taxonomic origin, it also includes a tool for cohort-based analysis. This tool uses cross-sample comparisons to identify sequence signatures that are frequently present in a sample group of interest (e.g., a disease-associated cohort), but occur less frequently in control cohorts. As this approach does not require homology searches in databases, it principally allows the identification of not only known, but also completely novel pathogens. Using samples from a meningitis outbreak, we demonstrate the feasibility of this approach in identifying enterovirus as the causative agent.

Epidemic Modeling of Multiple Virus Strains: A Case Study of SARS-CoV-2 B.1.1.7 In Moscow

2021 ◽  
Author(s):  
Boris Tseytlin ◽  
Ilya Makarov
Keyword(s):  
High Risk ◽  
Open Source ◽  
Virus Strain ◽  
New Wave ◽  
Epidemic Modeling ◽  
Multiple Virus ◽  
The City ◽  
Virus Strains ◽  
Epidemiological Parameters

Abstract During a long-running pandemic a pathogen can mutate, producing new strains with different epidemiological parameters. Existing approaches to epidemic modeling only consider one virus strain. We have developed a modified Susceptible-Exposed-Infected-Recovered model to simulate multiple virus strains within the same population. As a case study, we investigate the potential effects of SARS-CoV-2 strain B.1.1.7 on the city of Moscow. Our analysis indicates a high risk of a new wave of infections in September-October 2021 with up to 35 000 daily infections at peak. We open-source our code and data.

scholarly journals A Targeted Metagenomics Approach to Study the Diversity of Norovirus GII in Shellfish Implicated in Outbreaks

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 978
Author(s):  
Marion Desdouits ◽  
Candice Wacrenier ◽  
Joanna Ollivier ◽  
Julien Schaeffer ◽  
Françoise S. Le Guyader
Keyword(s):  
Deep Sequencing ◽  
Sanger Sequencing ◽  
Phylogenetic Analyses ◽  
Clinical Samples ◽  
Low Concentrations ◽  
Viral Genes ◽  
Multiple Virus ◽  
Fresh Products ◽  
Norovirus Gii ◽  
Virus Strains

Human noroviruses (NoV) cause epidemics of acute gastroenteritis (AGE) worldwide and can be transmitted through consumption of contaminated foods. Fresh products such as shellfish can be contaminated by human sewage during production, which results in the presence of multiple virus strains, at very low concentrations. Here, we tested a targeted metagenomics approach by deep-sequencing PCR amplicons of the capsid (VP1) and polymerase (RdRp) viral genes, on a set of artificial samples and on shellfish samples associated to AGE outbreaks, to evaluate its advantages and limitations in the identification of strains from the NoV genogroup (G) II. Using artificial samples, the method allowed the sequencing of most strains, but not all, and displayed variability between replicates especially with lower viral concentrations. Using shellfish samples, targeted metagenomics was compared to Sanger-sequencing of cloned amplicons and was able to identify a higher diversity of NoV GII and GIV strains. It allowed phylogenetic analyses of VP1 sequences and the identification, in most samples, of GII.17[P17] strains, also identified in related clinical samples. Despite several limitations, combining RdRp- and VP1-targeted metagenomics is a sensitive approach allowing the study NoV diversity in low-contaminated foods and the identification of NoV strains implicated in outbreaks.

scholarly journals PoreAnalyzer—An Open-Source Framework for the Analysis and Classification of Defects in Additive Manufacturing

2021 ◽  
Vol 11 (13) ◽  
pp. 6086
Author(s):  
Nils Ellendt ◽  
Fabian Fabricius ◽  
Anastasiya Toenjes
Keyword(s):  
Additive Manufacturing ◽  
Open Source ◽  
Total Porosity ◽  
Shape Accuracy ◽  
Process Maps ◽  
Defect Type ◽  
Open Source Framework ◽  
New Material ◽  
High Cooling Rates

Additive manufacturing processes offer high geometric flexibility and allow the use of new alloy concepts due to high cooling rates. For each new material, parameter studies have to be performed to find process parameters that minimize microstructural defects such as pores or cracks. In this paper, we present a system developed in Python for accelerated image analysis of optical microscopy images. Batch processing can be used to quickly analyze large image sets with respect to pore size distribution, defect type, contribution of defect type to total porosity, and shape accuracy of printed samples. The open-source software is independent of the microscope used and is freely available for use. This framework allows us to perform such an analysis on a circular area with a diameter of 5 mm within 10 s, allowing detailed process maps to be obtained for new materials within minutes after preparation.

scholarly journals Pseudomonas aeruginosa and Staphylococcus aureus virulence factors as biomarkers of infection

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Artur J. Sabat ◽  
Daniele Pantano ◽  
Viktoria Akkerboom ◽  
Erik Bathoorn ◽  
Alexander W. Friedrich
Keyword(s):  
Staphylococcus Aureus ◽  
Pseudomonas Aeruginosa ◽  
Bacterial Infections ◽  
Clinical Status ◽  
Clinical Samples ◽  
Pathogenic Microorganisms ◽  
Bacterial Identification ◽  
Accurate Identification ◽  
Culture Independent ◽  
And Staphylococcus Aureus

Abstract The gold standard for the diagnosis of bacterial infections in clinical samples is based on culture tests that are time-consuming and labor-intense. For these reasons, an extraordinary effort has been made to identify biomarkers as the tools for sensitive, rapid and accurate identification of pathogenic microorganisms. Moreover, biomarkers have been tested to distinguish colonization from infection, monitor disease progression, determine the clinical status of patients or predict clinical outcomes. This mini-review describes Pseudomonas aeruginosa and Staphylococcus aureus biomarkers, which contribute to pathogenesis and have been used in culture-independent bacterial identification directly from patient samples.

scholarly journals Scalable, Micro-Neutralization Assay for Qualitative Assessment of SARS-CoV-2 (COVID-19) Virus-Neutralizing Antibodies in Human Clinical Samples

2021 ◽  
Author(s):  
Richard S. Bennett ◽  
Elena N. Postnikova ◽  
Janie Liang ◽  
Robin Gross ◽  
Steven Mazur ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Imaging System ◽  
Neutralization Assay ◽  
Qualitative Assessment ◽  
Clinical Samples ◽  
Therapeutic Approaches ◽  
Serum Samples ◽  
Specific Test ◽  
Multiple Virus ◽  
Infected Cells

AbstractAs the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic was expanding, it was clear that effective testing for the presence of neutralizing antibodies in the blood of convalescent patients would be critical for development of plasma-based therapeutic approaches. To address the need for a high-quality neutralization assay against SARS-CoV-2, a previously established fluorescence reduction neutralization assay (FRNA) against Middle East respiratory syndrome coronavirus (MERS-CoV) was modified and optimized. The SARS-CoV-2 FRNA provides a quantitative assessment of a large number of infected cells through use of a high-content imaging system. Because of this approach, and the fact that it does not involve subjective interpretation, this assay is more efficient and more accurate than other neutralization assays. In addition, the ability to set robust acceptance criteria for individual plates and specific test wells provided further rigor to this assay. Such agile adaptability avails use with multiple virus variants. By February 2021, the SARS-CoV-2 FRNA had been used to screen over 5,000 samples, including acute and convalescent plasma or serum samples and therapeutic antibody treatments, for SARS-CoV-2 neutralizing titers.

scholarly journals PredicTF: a tool to predict bacterial transcription factors in complex microbial communities

2021 ◽  
Author(s):  
Lummy Maria Oliveira Monteiro ◽  
Joao Saraiva ◽  
Rodolfo Brizola Toscan ◽  
Peter F Stadler ◽  
Rafael Silva-Rocha ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Microbial Communities ◽  
Open Source ◽  
Genetic Information ◽  
Environmental Isolate ◽  
Ammonium Oxidation ◽  
Cellular Gene ◽  
Bacterial Transcription

AbstractTranscription Factors (TFs) are proteins that control the flow of genetic information by regulating cellular gene expression. Here we describe PredicTF, a first platform supporting the prediction and classification of novel bacterial TF in complex microbial communities. We evaluated PredicTF using a two-step approach. First, we tested PredictTF’s ability to predict TFs for the genome of an environmental isolate. In the second evaluation step, PredicTF was used to predict TFs in a metagenome and 11 metatranscriptomes recovered from a community performing anaerobic ammonium oxidation (anammox) in a bioreactor. PredicTF is open source pipeline available at https://github.com/mdsufz/PredicTF.

Automated classification of self-grooming in mice using open-source software

2017 ◽  
Vol 289 ◽  
pp. 48-56 ◽  
Author(s):  
Bastijn J.G. van den Boom ◽  
Pavlina Pavlidi ◽  
Casper J.H. Wolf ◽  
Adriana H. Mooij ◽  
Ingo Willuhn
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Automated Classification

scholarly journals <i>dh2loop</i> 1.0: an open-source Python library for automated processing and classification of geological logs

2021 ◽  
Vol 14 (11) ◽  
pp. 6711-6740
Author(s):  
Ranee Joshi ◽  
Kavitha Madaiah ◽  
Mark Jessell ◽  
Mark Lindsay ◽  
Guillaume Pirot
Keyword(s):  
Open Source ◽  
Mineral Exploration ◽  
String Matching ◽  
Drill Hole ◽  
Geological Survey ◽  
Database Structure ◽  
Automated Processing ◽  
Study Case ◽  
Textual Form

Abstract. A huge amount of legacy drilling data is available in geological survey but cannot be used directly as they are compiled and recorded in an unstructured textual form and using different formats depending on the database structure, company, logging geologist, investigation method, investigated materials and/or drilling campaign. They are subjective and plagued by uncertainty as they are likely to have been conducted by tens to hundreds of geologists, all of whom would have their own personal biases. dh2loop (https://github.com/Loop3D/dh2loop, last access: 30 September 2021​​​​​​​) is an open-source Python library for extracting and standardizing geologic drill hole data and exporting them into readily importable interval tables (collar, survey, lithology). In this contribution, we extract, process and classify lithological logs from the Geological Survey of Western Australia (GSWA) Mineral Exploration Reports (WAMEX) database in the Yalgoo–Singleton greenstone belt (YSGB) region. The contribution also addresses the subjective nature and variability of the nomenclature of lithological descriptions within and across different drilling campaigns by using thesauri and fuzzy string matching. For this study case, 86 % of the extracted lithology data is successfully matched to lithologies in the thesauri. Since this process can be tedious, we attempted to test the string matching with the comments, which resulted in a matching rate of 16 % (7870 successfully matched records out of 47 823 records). The standardized lithological data are then classified into multi-level groupings that can be used to systematically upscale and downscale drill hole data inputs for multiscale 3D geological modelling. dh2loop formats legacy data bridging the gap between utilization and maximization of legacy drill hole data and drill hole analysis functionalities available in existing Python libraries (lasio, welly, striplog).

Open-source deep learning models for acoustic detection and classification of orcas

2021 ◽  
Vol 150 (4) ◽  
pp. A286-A286
Author(s):  
Sadman Sakib ◽  
Steven Bergner ◽  
Dave Campbell ◽  
Mike Dowd ◽  
Fabio Frazao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Open Source ◽  
Acoustic Detection ◽  
Learning Models

How the FLOSS Research Community Uses Email Archives

2012 ◽  
Vol 4 (1) ◽  
pp. 37-59 ◽  
Author(s):  
Megan Squire
Keyword(s):  
Software Engineering ◽  
Open Source ◽  
Open Source Software ◽  
Development Process ◽  
Relevant Literature ◽  
Research Community ◽  
Email Message ◽  
Object Of Study ◽  
Broad Overview

Artifacts of the software development process, such as source code or emails between developers, are a frequent object of study in empirical software engineering literature. One of the hallmarks of free, libre, and open source software (FLOSS) projects is that the artifacts of the development process are publicly-accessible and therefore easily collected and studied. Thus, there is a long history in the FLOSS research community of using these artifacts to gain understanding about the phenomenon of open source software, which could then be compared to studies of software engineering more generally. This paper looks specifically at how the FLOSS research community has used email artifacts from free and open source projects. It provides a classification of the relevant literature using a publicly-available online repository of papers about FLOSS development using email. The outcome of this paper is to provide a broad overview for the software engineering and FLOSS research communities of how other researchers have used FLOSS email message artifacts in their work.

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