scholarly journals SARS-CoV2 quantification using RT-dPCR: a faster and safer alternative to assist viral genomic copies assessment using RT-qPCR

2020 ◽  
Author(s):  
Paula Rodrigues de Almeida ◽  
Meriane Demoliner ◽  
Ana Karolina Antunes Eisen ◽  
Fágner Henrique Heldt ◽  
Alana Witt Hansen ◽  
...  
Keyword(s):  
Confidence Intervals ◽  
Virus Isolation ◽  
High Accuracy ◽  
Serial Dilution ◽  
Coding Region ◽  
Safe Method ◽  
Rna Extract ◽  
Serial Dilutions

AbstractIn this study, serial dilutions of SARS-CoV 2 RNA extract were tested using RT-dPCR using three different primer-probe assays aiming SARS-CoV 2 nucleocapsid coding region. Narrower confidence intervals, indicating high quantification precision were obtained in 100 and 1000-fold serial dilution and RT-dPCR results were equivalent between different assays in the same dilution. High accuracy of this test allowed conclusions regarding the ability of this technique to evaluate precisely the amount of genomic copies present in a sample. We believe that this fast and safe method can assist other researchers in titration of SARS-CoV2 controls used in RT-qPCR without the need of virus isolation.

scholarly journals Use of Average Mutual Information and Derived Measures to Find Coding Regions

Entropy ◽  
2021 ◽  
Vol 23 (10) ◽  
pp. 1324
Author(s):  
Garin Newcomb ◽  
Khalid Sayood
Keyword(s):  
Mutual Information ◽  
Genome Annotation ◽  
High Accuracy ◽  
Gene Identification ◽  
Coding Region ◽  
Average Mutual Information ◽  
Protein Coding ◽  
Noncoding Sequences ◽  
Coding Regions ◽  
Genomic Regions

One of the important steps in the annotation of genomes is the identification of regions in the genome which code for proteins. One of the tools used by most annotation approaches is the use of signals extracted from genomic regions that can be used to identify whether the region is a protein coding region. Motivated by the fact that these regions are information bearing structures we propose signals based on measures motivated by the average mutual information for use in this task. We show that these signals can be used to identify coding and noncoding sequences with high accuracy. We also show that these signals are robust across species, phyla, and kingdom and can, therefore, be used in species agnostic genome annotation algorithms for identifying protein coding regions. These in turn could be used for gene identification.

Serial Dilution Simulation Lab

2010 ◽  
Vol 72 (5) ◽  
pp. 305-307 ◽  
Author(s):  
Cynthia Keler ◽  
Tabitha Balutis ◽  
Kim Bergen ◽  
Bryanna Laudenslager ◽  
Deanna Rubino
Keyword(s):  
Serial Dilution ◽  
Bacterial Cultures ◽  
Serial Dilutions

Serial dilution is often a difficult concept for students to understand. In this short dry lab exercise, students perform serial dilutions using seed beads. This exercise helps students gain skill at performing dilutions without using reagents, bacterial cultures, or viral cultures, while being able to visualize the process.

scholarly journals Legionella antimicrobial sensitivity testing: comparison of microbroth dilution with BCYE and LASARUS solid media

2020 ◽  
Author(s):  
Edward Portal ◽  
Kirsty Sands ◽  
Artjoms Portnojs ◽  
Victoria J Chalker ◽  
Owen B Spiller
Keyword(s):  
Legionella Pneumophila ◽  
Solid Medium ◽  
Bacterial Species ◽  
Serial Dilution ◽  
Sensitivity Testing ◽  
Antimicrobial Sensitivity ◽  
Solid Media ◽  
Agar Dilution ◽  
Microbroth Dilution ◽  
Serial Dilutions

Abstract Objectives There is a lack of international unification for AST methodology for Legionella pneumophila. Current literature contains multiple possible methods and this study compares each of them to determine methodological concordance. Methods Antibiotic susceptibility of 50 L. pneumophila strains was determined using broth microdilution (BMD), serial antimicrobial dilution in traditional buffered charcoal yeast extract (BCYE) agar (as well as comparison with gradient strip overlay on BCYE) and in a novel charcoal-free agar (LASARUS) for rifampicin, azithromycin, levofloxacin and doxycycline. Results The deviation of tested media relative to BMD highlighted the overall similarity of BMD and LASARUS across all antimicrobials tested (within one serial dilution). BCYE agar dilution showed an increased MIC of up to five serial dilutions relative to BMD, while MICs by gradient strip overlay on BCYE were elevated by two to three serial dilutions, with the exception of doxycycline, which was decreased by three serial dilutions relative to MIC values determined by BMD. The MIC range for azithromycin was wider than for other antimicrobials tested and found to be caused by the presence or absence of the lpeAB gene. Conclusions BMD-based antimicrobial susceptibility testing (AST) methodology should be the internationally agreed gold standard for Legionella spp. AST, as is common for other bacterial species. Traditional BCYE gave significantly elevated MIC results and its use should be discontinued for Legionella spp., while MIC determination using LASARUS solid medium gave results concordant (within one serial dilution) with BMD for all antimicrobials tested. To the best of our knowledge, this study is the first to identify the lpeAB gene in UK isolates.

Fuzzification Methods and Prediction Accuracy of Fuzzy Autocorrelation Model

2017 ◽  
Vol 21 (6) ◽  
pp. 1009-1016 ◽  
Author(s):  
Yoshiyuki Yabuuchi ◽  
Keyword(s):  
Time Series ◽  
Confidence Intervals ◽  
Model Prediction ◽  
Prediction Accuracy ◽  
Time Series Data ◽  
High Accuracy ◽  
Fuzzy Time Series ◽  
Ar Model ◽  
Series Data ◽  
High Prediction

The fuzzy autocorrelation model is a fuzzified autoregressive (AR) model. The aim of the fuzzy autocorrelation model is to describe the possible states of the system with high accuracy. This model uses autocorrelation similar to the Box–Jenkins model. The fuzzy autocorrelation model occasionally increases the vagueness. Although the problem can be mitigated using fuzzy confidence intervals instead of fuzzy time-series data, the unnatural estimations do not improve. Subsequently, an alternate method was used to fuzzify the time-series data and mitigate the unnatural estimation problem. This method also improved the model prediction accuracy. This paper focuses on fuzzification method, and discusses the prediction accuracy of the model and fuzzification of the time-series data. The analysis of the Nikkei stock average shows a high prediction accuracy and manageability of a fuzzy autocorrelation model. In this pape, a quartile is employed as an alternate fuzzification method. The model prediction accuracy and estimation behavior are verified through an analysis. Finally, the proposed method was found to be successful in mitigating the problems.

Confidence Intervals for Microbial Density Using Serial Dilutions with MPN Estimates

1996 ◽  
Vol 38 (4) ◽  
pp. 489-505 ◽  
Author(s):  
Wallace E. Garthright ◽  
Robert J. Blodgett
Keyword(s):  
Confidence Intervals ◽  
Microbial Density ◽  
Serial Dilutions

scholarly journals Optimizing production of serially diluted compounds and distribution to multiple targets

2001 ◽  
Vol 23 (6) ◽  
pp. 179-182 ◽  
Author(s):  
Cole O. Harris ◽  
Stephanie L. Schweiker
Keyword(s):  
Robotic System ◽  
Serial Dilution ◽  
Automation System ◽  
Laboratory Automation ◽  
Multiple Target ◽  
Target Compound ◽  
Multiple Targets ◽  
Dilution Assay ◽  
Serial Dilution Assay ◽  
Serial Dilutions

The need for a multiple-target compound selectivity programme led to the establishment of a single robotic system that produces a compound's serial dilution and its distribution to multiple replicate assay plates. A Genesis RSP 150 integrated into a Zymate Laboratory Automation System XP produced the serial dilutions, and the subsequent replicate assay plates were produced quickly and accurately by an efficient use of the carousels and rapid plate. Currently, this process allows for the production of over 200 serial dilution assay plates in a workday.

scholarly journals An Integrated Centrifugal Degassed PDMS-Based Microfluidic Device for Serial Dilution

Micromachines ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 482
Author(s):  
Anyang Wang ◽  
Samaneh Moghadasi Boroujeni ◽  
Philip J. Schneider ◽  
Liam B. Christie ◽  
Kyle A. Mancuso ◽  
...  
Keyword(s):  
Centrifugal Force ◽  
Microfluidic Device ◽  
Quantitative Polymerase Chain Reaction ◽  
Surface Condition ◽  
Hybrid Approach ◽  
Serial Dilution ◽  
Chamber Volume ◽  
Polymerase Chain ◽  
Good Agreement ◽  
Serial Dilutions

We propose an integrated serial dilution generator utilizing centrifugal force with a degassed polydimethylsiloxane (PDMS) microfluidic device. Using gas-soluble PDMS as a centrifugal microfluidic device material, the sample can be dragged in any arbitrary direction using vacuum-driven force, as opposed to in a single direction, without adding further actuation components. The vacuum-driven force allows the device to avoid the formation of air bubbles and exhibit high tolerance in the surface condition. The device was then used for sample metering and sample transferring. In addition, centrifugal force was used for sample loading and sample mixing. In this study, a series of ten-fold serial dilutions ranging from 100 to 10−4 with about 8 μL in each chamber was achieved, while the serial dilution ratio and chamber volume could easily be altered by changing the geometrical designs of the device. As a proof of concept of our hybrid approach with the centrifugal and vacuum-driven forces, ten-fold serial dilutions of a cDNA (complementary DNA) sample were prepared using the device. Then, the diluted samples were collected by fine needles and subject to a quantitative polymerase chain reaction (qPCR), and the results were found to be in good agreement with those for samples prepared by manual pipetting.

A New 1,000 kV Electron Microscope

1967 ◽  
Vol 25 ◽  
pp. 260-261
Author(s):  
M. Nishigaki ◽  
S. Katagiri ◽  
H. Kimura ◽  
B. Tadano
Keyword(s):  
Electron Microscope ◽  
High Voltage ◽  
Basic Research ◽  
Chromatic Aberration ◽  
High Accuracy ◽  
Biological Specimen ◽  
Voltage Electron ◽  
High Voltage Electron Microscope ◽  
High Voltage Electron

The high voltage electron microscope has many advantageous features in comparison with the ordinary electron microscope. They are a higher penetrating efficiency of the electron, low chromatic aberration, high accuracy of the selected area diffraction and so on. Thus, the high voltage electron microscope becomes an indispensable instrument for the metallurgical, polymer and biological specimen studies. The application of the instrument involves today not only basic research but routine survey in the various fields. Particularly for the latter purpose, the performance, maintenance and reliability of the microscope should be same as those of commercial ones. The authors completed a 500 kV electron microscope in 1964 and a 1,000 kV one in 1966 taking these points into consideration. The construction of our 1,000 kV electron microscope is described below.

Types of Stressors on Nonprofessional Against-Suicide and Pro-Suicide Message Boards

Crisis ◽  
2019 ◽  
Vol 40 (4) ◽  
pp. 257-264 ◽  
Author(s):  
Thomas Niederkrotenthaler ◽  
Benedikt Till
Keyword(s):  
Content Analysis ◽  
Interpersonal Problems ◽  
Suicide Method ◽  
Presenting Problems ◽  
Message Boards ◽  
Safe Method ◽  
Different Types ◽  
Psychiatric Problems

Abstract. Background: Little is known about presenting problems of primary posters (i.e., posters opening the thread) and their responders in nonprofessional against-suicide and pro-suicide message boards. Aims: We aimed to compare problems described in suicide message boards between different types of users (primary posters and respondents) and between against-suicide, neutral, and pro-suicide message boards. Method: In all, 1,182 archival threads with 20,499 individual postings from seven nonprofessional suicide message boards supporting an against-suicide, neutral, or pro-suicide attitude were randomly selected. Problems mentioned by primary posters and their respondents were coded with content analysis. Differences between pro-suicide, neutral, and against suicide boards, as well as correlations between primary posters and respondents, were calculated. Results: Interpersonal problems were most frequently mentioned by primary posters in against-suicide threads (40.9%) and less frequently in pro-suicide threads (11.8%; p < .001). In pro-suicide boards, the most frequent stressors were suicide method-related (e.g., how to identify a safe method: 26.2% vs. 2.5% in against-suicide boards, p < .001). Primary posters resembled respondents in terms of presenting problems in pro-suicide boards, but not in against-suicide boards. Limitations: Only self-reported problems were assessed. Conclusion: The results confirm a stronger focus on death than on life among users in pro-suicide message boards, and posters with similar problems meet in pro-suicide boards. The posters appear to clearly emphasize social strains over psychiatric problems compared with some professional settings.

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