scholarly journals IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring

GigaScience ◽  
2020 ◽  
Vol 9 (10) ◽  
Author(s):  
Katrina L Kalantar ◽  
Tiago Carvalho ◽  
Charles F A de Bourcy ◽  
Boris Dimitrov ◽  
Greg Dingle ◽  
...  
Keyword(s):  
Data Analysis ◽  
Open Source ◽  
Web Application ◽  
Pathogen Detection ◽  
A Priori ◽  
Virus Detection ◽  
Data Interpretation ◽  
Nasopharyngeal Swab ◽  
Microbial Composition ◽  
Detection And Identification

Abstract Background Metagenomic next-generation sequencing (mNGS) has enabled the rapid, unbiased detection and identification of microbes without pathogen-specific reagents, culturing, or a priori knowledge of the microbial landscape. mNGS data analysis requires a series of computationally intensive processing steps to accurately determine the microbial composition of a sample. Existing mNGS data analysis tools typically require bioinformatics expertise and access to local server-class hardware resources. For many research laboratories, this presents an obstacle, especially in resource-limited environments. Findings We present IDseq, an open source cloud-based metagenomics pipeline and service for global pathogen detection and monitoring (https://idseq.net). The IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes an assembly-based alignment pipeline, which results in the assignment of reads and contigs to taxonomic categories. The taxonomic relative abundances are reported and visualized in an easy-to-use web application to facilitate data interpretation and hypothesis generation. Furthermore, IDseq supports environmental background model generation and automatic internal spike-in control recognition, providing statistics that are critical for data interpretation. IDseq was designed with the specific intent of detecting novel pathogens. Here, we benchmark novel virus detection capability using both synthetically evolved viral sequences and real-world samples, including IDseq analysis of a nasopharyngeal swab sample acquired and processed locally in Cambodia from a tourist from Wuhan, China, infected with the recently emergent SARS-CoV-2. Conclusion The IDseq Portal reduces the barrier to entry for mNGS data analysis and enables bench scientists, clinicians, and bioinformaticians to gain insight from mNGS datasets for both known and novel pathogens.

scholarly journals IDseq – An Open Source Cloud-based Pipeline and Analysis Service for Metagenomic Pathogen Detection and Monitoring

2020 ◽  
Author(s):  
Katrina L. Kalantar ◽  
Tiago Carvalho ◽  
Charles F.A. de Bourcy ◽  
Boris Dimitrov ◽  
Greg Dingle ◽  
...  
Keyword(s):  
Data Analysis ◽  
Open Source ◽  
Web Application ◽  
Pathogen Detection ◽  
A Priori ◽  
Virus Detection ◽  
Data Interpretation ◽  
Nasopharyngeal Swab ◽  
Microbial Composition ◽  
Detection And Identification

ABSTRACTBackgroundMetagenomic next generation sequencing (mNGS) has enabled the rapid, unbiased detection and identification of microbes without pathogen-specific reagents, culturing, or a priori knowledge of the microbial landscape. mNGS data analysis requires a series of computationally intensive processing steps to accurately determine the microbial composition of a sample. Existing mNGS data analysis tools typically require bioinformatics expertise and access to local server-class hardware resources. For many research laboratories, this presents an obstacle, especially in resource limited environments.FindingsWe present IDseq, an open source cloud-based metagenomics pipeline and service for global pathogen detection and monitoring (https://idseq.net). The IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes an assembly-based alignment pipeline which results in the assignment of reads and contigs to taxonomic categories. The taxonomic relative abundances are reported and visualized in an easy-to-use web application to facilitate data interpretation and hypothesis generation. Furthermore, IDseq supports environmental background model generation and automatic internal spike-in control recognition, providing statistics which are critical for data interpretation. IDseq was designed with the specific intent of detecting novel pathogens. Here, we benchmark novel virus detection capability using both synthetically evolved viral sequences, and real-world samples, including IDseq analysis of a nasopharyngeal swab sample acquired and processed locally in Cambodia from a tourist from Wuhan, China, infected with the recently emergent SARS-CoV-2.ConclusionThe IDseq Portal reduces the barrier to entry for mNGS data analysis and enables bench scientists, clinicians, and bioinformaticians to gain insight from mNGS datasets for both known and novel pathogens.

scholarly journals A priori estimations of geometric parameters of an anomalous object in modeling the soil structure using RES3DINV software

2020 ◽  
Vol 30 (4) ◽  
pp. 696-710
Author(s):  
O.M. Nemtsova ◽  
T.M. Bannikova ◽  
V.M. Nemtsov
Keyword(s):  
Data Analysis ◽  
A Priori ◽  
Data Interpretation ◽  
Geometric Parameters ◽  
Inversion Method ◽  
A Priori Information ◽  
Input Parameters ◽  
Uniqueness Of The Solution ◽  
Ill Posed ◽  
Priori Information

We discuss the problem of proper use of software packages that implement methods for solving ill-posed problems. Most of the problems of processing experimental data belong to ill-posed problems. When using methods for solving ill-posed problems, there is a problem of non-uniqueness of the solution, which is solved by introducing a priori information. Obtaining a priori information is possible in different ways, but quantitative estimates involve the use of additional methods for data analysis. Obviously, additional methods should not be more complicated and labor intensive than the main data processing method. Using the RES3DINV electrical prospecting data analysis software as an example, the role of a priori information for obtaining reliable results is demonstrated. The RES3DINV software is used to build a soil model from the measured values of resistivity using electrical survey’s methods. When using the inversion method implemented in the software package, it is necessary to set the input parameters describing the geometric dimensions of the anomalous resistance object, which are usually unknown a priori. By model objects we demonstrate how the incorrect setting of input parameters affects the result of data interpretation. We show that the vector analysis method can be used as a way to obtain a priori information. This method allows us to obtain estimates of the geometric parameters of an anomalous object, does not involve high time and resource expenses, and can be used directly at the site of field experimental measurements.

Auto-Metrology on TEM Images of FinFET

2014 ◽  
Author(s):  
Sajal Biring
Keyword(s):  
Data Analysis ◽  
Data Interpretation ◽  
Visual Judgment ◽  
Manual Measurement ◽  
Size And Shape ◽  
Highly Sensitive ◽  
Edge Detecting ◽  
Geometrical Data ◽  
Precision And Accuracy ◽  
Device Size

Abstract The FinFET has been introduced in the last decade to provide better transistor performance as the device size shrinks. The performance of FinFET is highly sensitive to the size and shape of the fin, which needs to be optimized with tighter control. Manual measurement of nano-scale features on TEM images of FinFET is not only a time consuming and tedious task, but also prone to error owing to visual judgment. Here, an auto-metrology approach is presented to extract the measured values with higher precision and accuracy so that the uncertainty in the manual measurement can be minimized. Firstly, a FinFET TEM image is processed through an edge detecting algorithm to reveal the fin profile precisely. Finally, an algorithm is utilized to calculate out the required geometrical data relevant to the FinFET parameters and summarizes them to a table or plots a graph based on the purpose of data interpretation. This auto-metrology approach is expected to be adopted by academia and/or industry for proper data analysis and interpretation with higher precision and efficiency.

scholarly journals ccNetViz: a WebGL-based JavaScript library for visualization of large networks

2020 ◽  
Vol 36 (16) ◽  
pp. 4527-4529
Author(s):  
Ales Saska ◽  
David Tichy ◽  
Robert Moore ◽  
Achilles Rasquinha ◽  
Caner Akdas ◽  
...  
Keyword(s):  
Systems Biology ◽  
Complex Networks ◽  
Open Source ◽  
High Speed ◽  
A Priori ◽  
Supplementary Information ◽  
Network Visualization ◽  
Supplementary Data ◽  
Web Based ◽  
Flow Of Information

Abstract Summary Visualizing a network provides a concise and practical understanding of the information it represents. Open-source web-based libraries help accelerate the creation of biologically based networks and their use. ccNetViz is an open-source, high speed and lightweight JavaScript library for visualization of large and complex networks. It implements customization and analytical features for easy network interpretation. These features include edge and node animations, which illustrate the flow of information through a network as well as node statistics. Properties can be defined a priori or dynamically imported from models and simulations. ccNetViz is thus a network visualization library particularly suited for systems biology. Availability and implementation The ccNetViz library, demos and documentation are freely available at http://helikarlab.github.io/ccNetViz/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tzipi Braun ◽  
Shiraz Halevi ◽  
Rotem Hadar ◽  
Gilate Efroni ◽  
Efrat Glick Saar ◽  
...  
Keyword(s):  
Clinical Microbiology ◽  
Amplicon Sequencing ◽  
Viral Disease ◽  
Nasopharyngeal Swab ◽  
Microbial Composition ◽  
16S Amplicon Sequencing ◽  
The World ◽  
Health And Disease ◽  
Longitudinal Sampling ◽  
Potential Interactions

AbstractThe coronavirus disease 2019 (COVID-19) has rapidly spread around the world, impacting the lives of many individuals. Growing evidence suggests that the nasopharyngeal and respiratory tract microbiome are influenced by various health and disease conditions, including the presence and the severity of different viral disease. To evaluate the potential interactions between Severe Acute Respiratory Syndrome Corona 2 (SARS-CoV-2) and the nasopharyngeal microbiome. Microbial composition of nasopharyngeal swab samples submitted to the clinical microbiology lab for suspected SARS-CoV-2 infections was assessed using 16S amplicon sequencing. The study included a total of 55 nasopharyngeal samples from 33 subjects, with longitudinal sampling available for 12 out of the 33 subjects. 21 of the 33 subjects had at least one positive COVID-19 PCR results as determined by the clinical microbiology lab. Inter-personal variation was the strongest factor explaining > 75% of the microbial variation, irrespective of the SARS-CoV-2 status. No significant effect of SARS-CoV-2 on the nasopharyngeal microbial community was observed using multiple analysis methods. These results indicate that unlike some other viruses, for which an effect on the microbial composition was noted, SARS-CoV-2 does not have a strong effect on the nasopharynx microbial habitants.

scholarly journals QVigourMap: A GIS Open Source Application for the Creation of Canopy Vigour Maps

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 952
Author(s):  
Lia Duarte ◽  
Ana Cláudia Teodoro ◽  
Joaquim J. Sousa ◽  
Luís Pádua
Keyword(s):  
Open Source ◽  
Precision Agriculture ◽  
Vegetation Indices ◽  
Data Interpretation ◽  
Vegetation Monitoring ◽  
Distribution Maps ◽  
Monitoring Process ◽  
Multi Temporal ◽  
The Creation ◽  
The Right

In a precision agriculture context, the amount of geospatial data available can be difficult to interpret in order to understand the crop variability within a given terrain parcel, raising the need for specific tools for data processing and analysis. This is the case for data acquired from Unmanned Aerial Vehicles (UAV), in which the high spatial resolution along with data from several spectral wavelengths makes data interpretation a complex process regarding vegetation monitoring. Vegetation Indices (VIs) are usually computed, helping in the vegetation monitoring process. However, a crop plot is generally composed of several non-crop elements, which can bias the data analysis and interpretation. By discarding non-crop data, it is possible to compute the vigour distribution for a specific crop within the area under analysis. This article presents QVigourMaps, a new open source application developed to generate useful outputs for precision agriculture purposes. The application was developed in the form of a QGIS plugin, allowing the creation of vigour maps, vegetation distribution maps and prescription maps based on the combination of different VIs and height information. Multi-temporal data from a vineyard plot and a maize field were used as case studies in order to demonstrate the potential and effectiveness of the QVigourMaps tool. The presented application can contribute to making the right management decisions by providing indicators of crop variability, and the outcomes can be used in the field to apply site-specific treatments according to the levels of vigour.

scholarly journals Self-Collection of Saliva Specimens as a Suitable Alternative to Nasopharyngeal Swabs for the Diagnosis of SARS-CoV-2 by RT-qPCR

2021 ◽  
Vol 10 (2) ◽  
pp. 299
Author(s):  
Camino Trobajo-Sanmartín ◽  
Marta Adelantado ◽  
Ana Navascués ◽  
María J. Guembe ◽  
Isabel Rodrigo-Rincón ◽  
...  
Keyword(s):  
Chronic Conditions ◽  
Saliva Sample ◽  
Virus Detection ◽  
Kappa Coefficient ◽  
Nasopharyngeal Swab ◽  
Personal Protection ◽  
Personal Protection Equipment ◽  
Suitable Alternative ◽  
Lysis Buffer ◽  
Sensitivity Specificity

A nasopharyngeal swab is a sample used for the diagnosis of SARS-CoV-2 infection. Saliva is a sample easier to obtain and the risk of contagion for the professional is lower. This study aimed to evaluate the utility of saliva for the diagnosis of SARS-CoV-2 infection. This prospective study involved 674 patients with suspected SARS-CoV-2 infection. Paired nasopharyngeal and saliva samples were processed by RT-qPCR. Sensitivity, specificity, and kappa coefficient were used to evaluate the results from both samples. We considered the influence of age, symptoms, chronic conditions, and sample processing with lysis buffer. Of the 674 patients, 636 (94.4%) had valid results from both samples. The virus detection in saliva compared to a nasopharyngeal sample (gold standard) was 51.9% (95% CI: 46.3%–57.4%) and increased to 91.6% (95% CI: 86.7%–96.5%) when the cycle threshold (Ct) was ≤ 30. The specificity of the saliva sample was 99.1% (95% CI: 97.0%–99.8%). The concordance between samples was 75% (κ = 0.50; 95% CI: 0.45–0.56). The Ct values were significantly higher in saliva. In conclusion, saliva sample utility is limited for clinical diagnosis, but could be a useful alternative for the detection of SARS-CoV-2 in massive screening studies, when the availability of trained professionals for sampling or personal protection equipment is limited.

scholarly journals Detection of influenza virus in rectal swabs of patients admitted in hospital for febrile illnesses in Thailand

2021 ◽  
Vol 9 ◽  
pp. 205031212198963
Author(s):  
Artit Sangkakam ◽  
Pasin Hemachudha ◽  
Abhinbhen W Saraya ◽  
Benjamard Thaweethee-Sukjai ◽  
Thaniwan Cheun-Arom ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Gastrointestinal Tract ◽  
Hospital Stay ◽  
Rectal Swab ◽  
Average Length ◽  
Gastrointestinal Symptoms ◽  
Virus Detection ◽  
Length Of Hospital Stay ◽  
Nasopharyngeal Swab ◽  
Influenza Virus Detection

Introduction: Influenza virus favours the respiratory tract as its primary site of host entry and replication, and it is transmitted mainly via respiratory secretions. Nasopharyngeal swab is the gold standard specimen type for influenza detection, but several studies have also suggested that the virus replicates in the human gastrointestinal tract. Methods: A retrospective study was conducted on all patients positive for influenza virus and initially recruited as part of the PREDICT project from 2017 to 2018. The objectives of the study were to investigate whether rectal swab could aid in improving influenza detection, and if there was any correlation between gastrointestinal disturbances and severity of infection, using length of hospital stay as an indicator of severity. Results: Of the 51 influenza-positive patients, 12 had detectable influenza virus in their rectal swab. Among these 12 rectal swab positive patients, influenza virus was not detected in the nasopharyngeal swab of three of them. Gastrointestinal symptoms were observed for 28.2% patients with a negative rectal swab negative and 25.0% patients with a positive rectal swab. Average length of hospital stay was 4.2 days for rectal swab positive group and 3.7 days for rectal swab negative group. This difference was not statistically significant (p = 0.288). Conclusions: There is no correlation between influenza virus detection in rectal swab and gastrointestinal disturbances or disease severity, and there is currently insufficient evidence to support replicative ability in the gastrointestinal tract.

scholarly journals Open Plot Project: an open-source toolkit for 3-D structural data analysis

Solid Earth ◽  
2011 ◽  
Vol 2 (1) ◽  
pp. 53-63 ◽  
Author(s):  
S. Tavani ◽  
P. Arbues ◽  
M. Snidero ◽  
N. Carrera ◽  
J. A. Muñoz
Keyword(s):  
Spatial Distribution ◽  
Data Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Source Code ◽  
Structural Data ◽  
Geological Modelling ◽  
Analysis Tools ◽  
Transect Analysis ◽  
Selection Of

Abstract. In this work we present the Open Plot Project, an open-source software for structural data analysis, including a 3-D environment. The software includes many classical functionalities of structural data analysis tools, like stereoplot, contouring, tensorial regression, scatterplots, histograms and transect analysis. In addition, efficient filtering tools are present allowing the selection of data according to their attributes, including spatial distribution and orientation. This first alpha release represents a stand-alone toolkit for structural data analysis. The presence of a 3-D environment with digitalising tools allows the integration of structural data with information extracted from georeferenced images to produce structurally validated dip domains. This, coupled with many import/export facilities, allows easy incorporation of structural analyses in workflows for 3-D geological modelling. Accordingly, Open Plot Project also candidates as a structural add-on for 3-D geological modelling software. The software (for both Windows and Linux O.S.), the User Manual, a set of example movies (complementary to the User Manual), and the source code are provided as Supplement. We intend the publication of the source code to set the foundation for free, public software that, hopefully, the structural geologists' community will use, modify, and implement. The creation of additional public controls/tools is strongly encouraged.

Brief Synopsis: “Instruction Manual for Juvenile Clinical Pathology”

2021 ◽  
pp. 019262332110413
Author(s):  
Anne Provencher ◽  
Paula Katavolos
Keyword(s):  
Data Analysis ◽  
Clinical Pathology ◽  
Data Interpretation ◽  
Physiological Functions ◽  
Instruction Manual ◽  
Test Article ◽  
Accurate Interpretation ◽  
Key Points ◽  
Pathology Data

This symposium synopsis summarizes key points discussed related to clinical pathology data interpretation for reproduction and juvenile toxicology studies. In pregnant and growing animals, several changes in clinical pathology parameters linked to growth/maturation of organ and physiological functions can occur, and understanding these changes is important to enable accurate interpretation of clinical pathology data. A brief overview of the general approach to clinical pathology data analysis according to contemporary practices is provided, followed by a discussion focused specifically on reproductive and juvenile clinical pathology. In this context, the approach to recognize and differentiate changes that may be related to pregnancy and growth as opposed to those that may be related to test article effects is highlighted.

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