scholarly journals The Effect of Simulated Field Storage Conditions on the Accuracy of Rapid User-Friendly Blood Pathogen Detection Kits

2012 ◽  
Vol 177 (5) ◽  
pp. 583-588 ◽  
Author(s):  
Diane R. Bienek ◽  
David G. Charlton
Keyword(s):  
Pathogen Detection ◽  
Storage Conditions ◽  
Simulated Field ◽  
User Friendly

Clin-mNGS: Automated Pipeline for Pathogen Detection from Clinical Metagenomic Data

2020 ◽  
Vol 15 ◽  
Author(s):  
Akshatha Prasanna ◽  
Vidya Niranjan
Keyword(s):  
Antimicrobial Resistance ◽  
High Performance ◽  
Pathogen Detection ◽  
Bacterial Species ◽  
Workflow Management ◽  
Metagenomic Data ◽  
Antimicrobial Resistance Genes ◽  
Culture Independent ◽  
Automated Pipeline ◽  
User Friendly

Background: Since bacteria are the earliest known organisms, there has been significant interest in their variety and biology, most certainly concerning human health. Recent advances in Metagenomics sequencing (mNGS), a culture-independent sequencing technology have facilitated an accelerated development in clinical microbiology and our understanding of pathogens. Objective: For the implementation of mNGS in routine clinical practice to become feasible, a practical and scalable strategy for the study of mNGS data is essential. This study presents a robust automated pipeline to analyze clinical metagenomic data for pathogen identification and classification. Method: The proposed Clin-mNGS pipeline is an integrated, open-source, scalable, reproducible, and user-friendly framework scripted using the Snakemake workflow management software. The implementation avoids the hassle of manual installation and configuration of the multiple command-line tools and dependencies. The approach directly screens pathogens from clinical raw reads and generates consolidated reports for each sample. Results: The pipeline is demonstrated using publicly available data and is tested on a desktop Linux system and a High-performance cluster. The study compares variability in results from different tools and versions. The versions of the tools are made user modifiable. The pipeline results in quality check, filtered reads, host subtraction, assembled contigs, assembly metrics, relative abundances of bacterial species, antimicrobial resistance genes, plasmid finding, and virulence factors identification. The results obtained from the pipeline are evaluated based on sensitivity and positive predictive value. Conclusion: Clin-mNGS is an automated Snakemake pipeline validated for the analysis of microbial clinical metagenomics reads to perform taxonomic classification and antimicrobial resistance prediction.

scholarly journals From Cheese-Making to Consumption: Exploring the Microbial Safety of Cheeses through Predictive Microbiology Models

Foods ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 355
Author(s):  
Arícia Possas ◽  
Olga María Bonilla-Luque ◽  
Antonio Valero
Keyword(s):  
Production Process ◽  
Physicochemical Characteristics ◽  
Storage Conditions ◽  
Starter Cultures ◽  
Predictive Microbiology ◽  
Factors Affecting ◽  
Modeling Approaches ◽  
Modelling Studies ◽  
Foodborne Outbreaks ◽  
User Friendly

Cheeses are traditional products widely consumed throughout the world that have been frequently implicated in foodborne outbreaks. Predictive microbiology models are relevant tools to estimate microbial behavior in these products. The objective of this study was to conduct a review on the available modeling approaches developed in cheeses, and to identify the main microbial targets of concern and the factors affecting microbial behavior in these products. Listeria monocytogenes has been identified as the main hazard evaluated in modelling studies. The pH, aw, lactic acid concentration and temperature have been the main factors contemplated as independent variables in models. Other aspects such as the use of raw or pasteurized milk, starter cultures, and factors inherent to the contaminating pathogen have also been evaluated. In general, depending on the production process, storage conditions, and physicochemical characteristics, microorganisms can grow or die-off in cheeses. The classical two-step modeling has been the most common approach performed to develop predictive models. Other modeling approaches, including microbial interaction, growth boundary, response surface methodology, and neural networks, have also been performed. Validated models have been integrated into user-friendly software tools to be used to obtain estimates of microbial behavior in a quick and easy manner. Future studies should investigate the fate of other target bacterial pathogens, such as spore-forming bacteria, and the dynamic character of the production process of cheeses, among other aspects. The information compiled in this study helps to deepen the knowledge on the predictive microbiology field in the context of cheese production and storage.

Detectability vs. time and costs in pooled DNA extraction of cutaneous swabs: a study on the amphibian chytrid fungi

2019 ◽  
Vol 40 (1) ◽  
pp. 29-39 ◽  
Author(s):  
Joana Sabino-Pinto ◽  
E. Tobias Krause ◽  
Molly C. Bletz ◽  
An Martel ◽  
Frank Pasmans ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Pathogen Detection ◽  
Batrachochytrium Dendrobatidis ◽  
Quantitative Polymerase Chain Reaction ◽  
Large Fraction ◽  
Work Load ◽  
Detection Sensitivity ◽  
Pooled Dna ◽  
Reaction Volumes ◽  
User Friendly

Abstract Epidemiology relies on understanding the distribution of pathogens which often can be detected through DNA-based techniques, such as quantitative Polymerase Chain Reaction (qPCR). Typically, the DNA of each individual sample is separately extracted and undergoes qPCR analysis. However, when performing field surveys and long-term monitoring, a large fraction of the samples is generally expected to be negative, especially in geographical areas still considered free of the pathogen. If pathogen detection within a population – rather than determining its individual prevalence – is the focus, work load and monetary costs can be reduced by pooling samples for DNA extraction. We test and refine a user-friendly technique where skin swabs can be pooled during DNA extraction to detect the amphibian chytrid fungi, Batrachochytrium dendrobatidis and B. salamandrivorans (Bsal). We extracted pools with different numbers of samples (from one to four swabs), without increasing reaction volumes, and each pool had one sample inoculated with a predetermined zoospore amount. Pool size did not reduce the ability to detect the two fungi, except if inoculated with extremely low zoospore amounts (one zoospore). We confirm that pooled DNA extraction of cutaneous swabs can substantially reduce processing time and costs without minimizing detection sensitivity. This is of relevance especially for the new emerging pathogen Bsal, for which pooled DNA extraction had so far not been tested and massive monitoring efforts in putatively unaffected regions are underway.

scholarly journals Home Administration of CVD 103-HgR: A Live Attenuated Oral Cholera Vaccine

2021 ◽  
Vol 104 (4) ◽  
pp. 1232-1240
Author(s):  
R. Paul Duffin ◽  
Michael Delbuono ◽  
Lawrence Chew ◽  
James Johnstone ◽  
Volker Niedan ◽  
...  
Keyword(s):  
Vaccine Development ◽  
Oral Vaccine ◽  
Storage Conditions ◽  
Hot Water ◽  
World Health ◽  
Self Administration ◽  
Health Agencies ◽  
Oral Cholera Vaccine ◽  
The Stability ◽  
User Friendly

ABSTRACTVaccination is a well-established means for prevention and spread of disease in people traveling abroad. Although vaccines to diseases such as cholera are recommended by world health agencies, they are seldom required even when traveling to endemic regions. Consequences of noncompliance can affect traveler’s health and spread diseases to new regions, as occurred in Haiti in 2010 when United Nations peacekeepers from Nepal, where a cholera outbreak was underway, introduced the disease to the region. Steps to increase vaccine recommendation compliance should therefore be an integral part of vaccine development. PXVX0200 contains Center for Vaccine Development 103-HgR live, attenuated recombinant Vibrio cholerae vaccine strain, and is indicated for single-dose immunization against the bacteria that causes cholera. It is supplied as one buffer and one active component packet to be mixed into water and ingested. Administration instructions are designed to be “user friendly” with flexibility for self-administration, thus promoting compliance. Studies to support self-administration were conducted to cover stability of the vaccine outside of normal storage conditions, potency in case of misadministration, and disposal procedures to minimize environmental impact. The principal findings showed that the stability of vaccine was maintained under conditions allowing for transport times and temperature conditions as well as when misadministration errors were made. Finally, the vaccine was effectively neutralized with hot water and soap to prevent bacterial environmental contamination in the event of an accidental spill. The conclusion is that PXVX0200 oral vaccine is stable, easy to formulate and dispose of, and is amenable to self-administration.

scholarly journals Progress and Challenges towards Point-of-Care Diagnostic Development for Dengue

2017 ◽  
Vol 55 (12) ◽  
pp. 3339-3349 ◽  
Author(s):  
Junxiong Pang ◽  
Po Ying Chia ◽  
David C. Lye ◽  
Yee Sin Leo
Keyword(s):  
Point Of Care ◽  
Storage Conditions ◽  
Antibody Detection ◽  
Advantages And Disadvantages ◽  
Public Health Significance ◽  
Clinical Presentations ◽  
Health Significance ◽  
User Friendly ◽  
Point Of Care Tests ◽  
Detection Strategies

ABSTRACTDengue detection strategies involve viral RNA, antigen, and/or antibody detection. Each strategy has its advantages and disadvantages. Optimal, user-friendly, rapid diagnostic tests based on immunochromatographic assays are pragmatic point-of-care tests (POCTs) in regions where dengue is endemic where there are limited laboratory capabilities and optimal storage conditions. Increasingly, there is a greater public health significance for a multiplexing assay that differentiates dengue from Zika or pathogens with similar clinical presentations. Although there have been many assay/platform developments toward POCTs, independent validation and implementation remain very limited. This review highlights the current key progress and challenges toward the development of a dengue POCT.

scholarly journals GenomeGraphR: A user-friendly open-source web application for foodborne pathogen Whole Genome Sequencing data integration, analysis, and visualization.

2018 ◽  
Author(s):  
Moez Sanaa ◽  
Régis Pouillot ◽  
Francisco J Garces-Vega ◽  
Errol Strain ◽  
Jane M Van Doren
Keyword(s):  
Genome Sequencing ◽  
Pathogen Detection ◽  
Foodborne Pathogen ◽  
Whole Genome Sequence ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
High Quality ◽  
User Friendly ◽  
Integration Analysis

Food safety risk assessments and large-scale epidemiological investigations have the potential to provide better and new types of information when whole genome sequence (WGS) data are effectively integrated. Today, the NCBI Pathogen Detection database WGS collections have grown significantly through improvements in technology, coordination, and collaboration, such as the GenomeTrakr and PulseNet networks. However, high-quality genomic data is not often coupled with high-quality epidemiological or food chain metadata. We have created a set of tools for cleaning, curation, integration, analysis and visualization of microbial genome sequencing data. It has been tested using Salmonella enterica and Listeria monocytogenes data sets provided by NCBI Pathogen Detection (160,000 sequenced isolates). GenomeGraphR presents foodborne pathogen WGS data and associated curated metadata in a user-friendly interface that allows a user to query a variety of research questions such as, transmission sources and dynamics, global reach, and persistence of genotypes associated with contamination in the food supply and foodborne illness across time or space. The application is freely available (https://fda-riskmodels.foodrisk.org/genomegraphr/).

scholarly journals A non-enzymatic, isothermal strand displacement and amplification assay for rapid detection of SARS-CoV-2 RNA

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Mohsen Mohammadniaei ◽  
Ming Zhang ◽  
Jon Ashley ◽  
Ulf Bech Christensen ◽  
Lennart Jan Friis-Hansen ◽  
...  
Keyword(s):  
Signal Amplification ◽  
Rapid Detection ◽  
Room Temperature ◽  
Storage Conditions ◽  
Strand Displacement ◽  
Rna Detection ◽  
Reverse Transcription Step ◽  
Amplification Assay ◽  
User Friendly ◽  
And Storage

AbstractThe current nucleic acid signal amplification methods for SARS-CoV-2 RNA detection heavily rely on the functions of biological enzymes which imposes stringent transportation and storage conditions, high cost and global supply shortages. Here, a non-enzymatic whole genome detection method based on a simple isothermal signal amplification approach is developed for rapid detection of SARS-CoV-2 RNA and potentially any types of nucleic acids regardless of their size. The assay, termed non-enzymatic isothermal strand displacement and amplification (NISDA), is able to quantify 10 RNA copies.µL−1. In 164 clinical oropharyngeal RNA samples, NISDA assay is 100 % specific, and it is 96.77% and 100% sensitive when setting up in the laboratory and hospital, respectively. The NISDA assay does not require RNA reverse-transcription step and is fast (<30 min), affordable, highly robust at room temperature (>1 month), isothermal (42 °C) and user-friendly, making it an excellent assay for broad-based testing.

The Added Value of Graphical Input and Display for Electron Lens Design

1990 ◽  
Vol 48 (1) ◽  
pp. 190-191
Author(s):  
B. Lencova ◽  
G. Wisselink
Keyword(s):  
Flux Density ◽  
Numerical Data ◽  
Added Value ◽  
Lens Design ◽  
Step Size ◽  
Magnetic Lens ◽  
Flux Lines ◽  
Fine Mesh ◽  
Electron Lens ◽  
User Friendly

Recent progress in computer technology enables the calculation of lens fields and focal properties on commonly available computers such as IBM ATs. If we add to this the use of graphics, we greatly increase the applicability of design programs for electron lenses. Most programs for field computation are based on the finite element method (FEM). They are written in Fortran 77, so that they are easily transferred from PCs to larger machines.The design process has recently been made significantly more user friendly by adding input programs written in Turbo Pascal, which allows a flexible implementation of computer graphics. The input programs have not only menu driven input and modification of numerical data, but also graphics editing of the data. The input programs create files which are subsequently read by the Fortran programs. From the main menu of our magnetic lens design program, further options are chosen by using function keys or numbers. Some options (lens initialization and setting, fine mesh, current densities, etc.) open other menus where computation parameters can be set or numerical data can be entered with the help of a simple line editor. The "draw lens" option enables graphical editing of the mesh - see fig. I. The geometry of the electron lens is specified in terms of coordinates and indices of a coarse quadrilateral mesh. In this mesh, the fine mesh with smoothly changing step size is calculated by an automeshing procedure. The options shown in fig. 1 allow modification of the number of coarse mesh lines, change of coordinates of mesh points or lines, and specification of lens parts. Interactive and graphical modification of the fine mesh can be called from the fine mesh menu. Finally, the lens computation can be called. Our FEM program allows up to 8000 mesh points on an AT computer. Another menu allows the display of computed results stored in output files and graphical display of axial flux density, flux density in magnetic parts, and the flux lines in magnetic lenses - see fig. 2. A series of several lens excitations with user specified or default magnetization curves can be calculated and displayed in one session.

A Review of 21 iPad Applications for Augmentative and Alternative Communication Purposes

2012 ◽  
Vol 21 (2) ◽  
pp. 60-71 ◽  
Author(s):  
Ashley Alliano ◽  
Kimberly Herriger ◽  
Anthony D. Koutsoftas ◽  
Theresa E. Bartolotta
Keyword(s):  
Augmentative And Alternative Communication ◽  
Cost Effective ◽  
Alternative Form ◽  
Alternative Communication ◽  
Text To Speech ◽  
Reference Guide ◽  
Expressive Communication ◽  
Communication Needs ◽  
User Friendly ◽  
Ipad Applications

Abstract Using the iPad tablet for Augmentative and Alternative Communication (AAC) purposes can facilitate many communicative needs, is cost-effective, and is socially acceptable. Many individuals with communication difficulties can use iPad applications (apps) to augment communication, provide an alternative form of communication, or target receptive and expressive language goals. In this paper, we will review a collection of iPad apps that can be used to address a variety of receptive and expressive communication needs. Based on recommendations from Gosnell, Costello, and Shane (2011), we describe the features of 21 apps that can serve as a reference guide for speech-language pathologists. We systematically identified 21 apps that use symbols only, symbols and text-to-speech, and text-to-speech only. We provide descriptions of the purpose of each app, along with the following feature descriptions: speech settings, representation, display, feedback features, rate enhancement, access, motor competencies, and cost. In this review, we describe these apps and how individuals with complex communication needs can use them for a variety of communication purposes and to target a variety of treatment goals. We present information in a user-friendly table format that clinicians can use as a reference guide.

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