scholarly journals Controlling critical mistag-associated false discoveries in metagenetic data

2022 ◽  
Author(s):  
Rodney T Richardson
Keyword(s):  
Latin Square ◽  
Cost Effective ◽  
Environmental Research ◽  
Strongly Correlated ◽  
Straightforward Method ◽  
Cost Effective Approach ◽  
And Control ◽  
False Discoveries ◽  
Binomial Process ◽  
Index Combination

Metagenetic methods are commonplace within ecological and environmental research. One concern with these methods is the phenomenon of critical mistagging, where sequences from one sample are erroneously inferred to have originated from another sample due to errors in the attachment, PCR replication or sequencing of sample-specific dual-index tags. For studies using PCR-based library preparation on large sample sizes, the most cost-effective approach to limiting mistag-associated false detections involves using an unsaturated Latin square dual-indexing design. This allows researchers to estimate mistagging rates during sequencing but the statistical procedures for filtering out detections using this mistag rate have received little attention. We propose a straightforward method to limit mistag-associated false discoveries during metabarcoding applications. We analyzed two Illumina metabarcoding datasets produced using unsaturated Latin square designs to explore the distribution of mistagged sequences across dual-index combinations on a per taxon basis. We tested these data for conformity to the assumptions that 1) mistagging follows a binomial distribution [i.e., X ~ B(n, p)] where p, the probability of a sequence being mistagged, varies minimally across taxa and 2) mistags are distributed uniformly across dual-index combinations. We provide R functions that estimate the 95th percentile of expected mistags per dual-index combination for each taxon under these assumptions. We show that mistagging rates were consistent across taxa within the datasets analyzed and that modelling mistagging as a binomial process with uniform distribution across dual-index combinations enabled robust control of mistag-associated false discoveries. We propose that this method of taxon-specific filtering of detections based on the maximum mistags expected per dual-index combination should be broadly accepted during metagenetic analysis, provided that experimental and control sequence abundances per taxon are strongly correlated. When this assumption is violated, data may be better fit by assuming that the distribution of mistags across combinations follows Poisson characteristics [i.e., X ~ Pois(𝜆)], with 𝜆 empirically estimated from the abundance distribution of mistags among control samples. We provide a second R function for this case, though we have yet to observe such a dataset. Both functions and demonstrations associated with this work are freely available at https://github.com/RTRichar/ModellingCriticalMistags.

scholarly journals A simple and cost-effective approach for technical validation of next generation methylation sequencing data

2019 ◽  
Author(s):  
Ali Javadmanesh ◽  
Afsaneh Mojtabanezhad Shariatpanahi ◽  
Ehsan Shams Davodly ◽  
Marjan Azghandi ◽  
Maryam Yassi ◽  
...  
Keyword(s):  
Dna Methylation ◽  
High Resolution ◽  
High Resolution Melting ◽  
Cost Effective ◽  
Next Generation ◽  
Sequencing Data ◽  
Cost Effective Approach ◽  
Technical Validation ◽  
R Programming ◽  
And Control

Abstract Background DNA methylation is a fundamental epigenetic process that, in most cases, modulates genetic expression levels. Changes in DNA methylation, either hypo- or hypermethylation, have a key role in many biological processes and several human diseases such as cancer. In the current study, we offered an approach to validate the next generation methylation sequencing data.Methods Genomic DNA was extracted from target and control samples (6 in each group), followed by bisulfite conversion. Next generation methylation sequencing and methylation sensitive high-resolution melting assay were carried out. The primers for methylation sequencing validation were designed by R programming language.Results In the current study, two groups, case and control, were discriminated based on methylation sequencing results and the real time PCR-based results were in accordance with the next generation methylation sequencing.Discussion Methylation sensitive high-resolution melting validation assay is a simple and cost-effective method, which confirmed next generation methylation sequencing results.

scholarly journals Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Fiona Allum ◽  
◽  
Xiaojian Shao ◽  
Frédéric Guénard ◽  
Marie-Michelle Simon ◽  
...  
Keyword(s):  
Large Scale ◽  
Hdl Cholesterol ◽  
Cost Effective ◽  
Strongly Correlated ◽  
Genome Wide ◽  
Cost Effective Approach ◽  
Genome Bisulfite Sequencing ◽  
Comparable Accuracy ◽  
Capture Sequencing

Abstract Most genome-wide methylation studies (EWAS) of multifactorial disease traits use targeted arrays or enrichment methodologies preferentially covering CpG-dense regions, to characterize sufficiently large samples. To overcome this limitation, we present here a new customizable, cost-effective approach, methylC-capture sequencing (MCC-Seq), for sequencing functional methylomes, while simultaneously providing genetic variation information. To illustrate MCC-Seq, we use whole-genome bisulfite sequencing on adipose tissue (AT) samples and public databases to design AT-specific panels. We establish its efficiency for high-density interrogation of methylome variability by systematic comparisons with other approaches and demonstrate its applicability by identifying novel methylation variation within enhancers strongly correlated to plasma triglyceride and HDL-cholesterol, including at CD36. Our more comprehensive AT panel assesses tissue methylation and genotypes in parallel at ∼4 and ∼3 M sites, respectively. Our study demonstrates that MCC-Seq provides comparable accuracy to alternative approaches but enables more efficient cataloguing of functional and disease-relevant epigenetic and genetic variants for large-scale EWAS.

The role of hybrid computers in simulation and control

SIMULATION ◽  
1971 ◽  
Vol 16 (3) ◽  
pp. 112-115 ◽  
Author(s):  
Frank W. Paul
Keyword(s):  
Low Cost ◽  
Cost Effective ◽  
Analog Computer ◽  
Computer Usage ◽  
Cost Effective Approach ◽  
Specialized Technique ◽  
Hybrid Computer ◽  
The Cost ◽  
And Control

This paper discusses the present atzd futtsre of hybrid computation: Has it reached its zenith, or will it continue to develop as a powerful but specialized technique? The minicomputer has made current hybrid systems practical by providing a low-cost digital component. Unless the cost of the analog computer is reduced, the increasing power and decreasing cost of the minicomputer may severely limit future hybrid computer usage by providing an economic all-digital alternative. However, problems with alternative solution techniques indicate that for some important applications the hybrid computer will be the most cost- effective approach.

scholarly journals Study of Factors Influence to Poor Attendance for the Second Diagnostic Visit to the Pen Program of Early Detection of Diabetes and Hypertension in PHCCs in Kirkuk, Iraq

2020 ◽  
Vol 3 (2) ◽  
pp. 218-228
Author(s):  
Suha Tahir ◽  
Suhaila Tahir
Keyword(s):  
Early Detection ◽  
Screening Program ◽  
Cost Effective ◽  
Health District ◽  
Limited Resources ◽  
Preclinical Stage ◽  
Primary Health ◽  
Cost Effective Approach ◽  
And Control

PEN was held in PHCs in Kirkuk city by WHO. To prevent and control the NCD and to provide a cost-effective approach for early detection of D.M and hypertension by recognition the preclinical stage of the disease. With selecting 5 random chosen PHCCs in first primary health district, for the month between (January to end of July) 2018. With using very simple techniques, in very limited resources for PHCs, The results showed the highest percentages of attending the NCD unit was in Tareeq – Baghdad, while the lowest in Tissin, and the females are more than the males. The highest percentage registered for hypertension was in Baglar , while the highest positive screened was in Tissin. For D.M. the highest no. of visitor registered for first and second visit was in Baglar. This gives as a conclusion that there was a defect in screening program regarding the second visit in NCD unit in PHCs.

Scalable Plasmonic Nanolithography: Prototype System Design and Construction

2016 ◽  
Author(s):  
Yuan Wang ◽  
Mohamed E. Saad ◽  
Kang Ni ◽  
Yen Chi Chang ◽  
Cheng-Wei Chen ◽  
...  
Keyword(s):  
High Throughput ◽  
High Speed ◽  
Low Cost ◽  
Cost Effective ◽  
Prototype System ◽  
Cost Effective Approach ◽  
Nanoscale Metrology ◽  
And Control ◽  
Next Generation Lithography ◽  
Plasmonic Nanolithography

Maskless nanolithography is an agile and cost effective approach if their throughputs can be scaled for mass production purposes. Using plasmonic nanolithography (PNL) approach, direct pattern writing was successfully demonstrated with around 20 nm half-pitch at high speed. Here, we report our recent efforts of implementing a high-throughput PNL prototype system with unique metrology and control features, which are designed to use an array of plasmonic lenses to pattern sub-100 nm features on a rotating substrate. Taking the advantage of air bearing surface techniques, the system can expose the wafer pixel by pixel with a speed of ∼10 m/s, much faster than any conventional scanning based lithography system. It is a low-cost, high-throughput maskless approach for the next generation lithography and also for the emerging nanotechnology applications, such as nanoscale metrology and imaging.

Situational Strategic Awareness Monitoring Surveillance System–Microcomputer and Microcomputer Clustering used for Intelligent, Economical, Scalable, and Deployable Approach for Safeguarding Materials

2020 ◽  
Vol 2020 (3) ◽  
pp. 60408-1-60408-10
Author(s):  
Kenly Maldonado ◽  
Steve Simske
Keyword(s):  
Surveillance System ◽  
Cost Effective ◽  
Government Agencies ◽  
Electronic Systems ◽  
Time Data ◽  
Potential Threat ◽  
Intelligent Surveillance ◽  
World Markets ◽  
Programming Software ◽  
And Control

The principal objective of this research is to create a system that is quickly deployable, scalable, adaptable, and intelligent and provides cost-effective surveillance, both locally and globally. The intelligent surveillance system should be capable of rapid implementation to track (monitor) sensitive materials, i.e., radioactive or weapons stockpiles and person(s) within rooms, buildings, and/or areas in order to predict potential incidents proactively (versus reactively) through intelligence, locally and globally. The system will incorporate a combination of electronic systems that include commercial and modifiable off-the-shelf microcomputers to create a microcomputer cluster which acts as a mini supercomputer which leverages real-time data feed if a potential threat is present. Through programming, software, and intelligence (artificial intelligence, machine learning, and neural networks), the system should be capable of monitoring, tracking, and warning (communicating) the system observer operations (command and control) within a few minutes when sensitive materials are at potential risk for loss. The potential customer is government agencies looking to control sensitive materials and/or items in developing world markets intelligently, economically, and quickly.

Role of Rasayana in Prevention of COVID-19 - A Review

2020 ◽  
Vol 11 (SPL1) ◽  
pp. 716-722
Author(s):  
Sneha Dhakite ◽  
Sadhana Misar Wajpeyi
Keyword(s):  
Immune System ◽  
Respiratory System ◽  
Viral Infections ◽  
Cost Effective ◽  
The Body ◽  
Healthy Life ◽  
Vital Functions ◽  
Healthy Life Style ◽  
And Control

The “Coronavirus disease 19 (COVID-19)” is caused by “Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)”, a newly discovered member of the Coronaviridae family of viruses which is a highly communicable. There is no effective medical treatment till date for Coronavirus disease hence prevention is the best way to keep disease away. Rasayana proved to be highly efficacious and cost effective for the Prevention and Control of viral infections when vaccines and standard therapies are lacking. Rasayana Chikitsa is one of the eight branches of Ashtanga Ayurveda which helps to maintain healthy life style. Rasayana improves immunity and performs many vital functions of human body. Vyadhikshamatva that is immune mechanism of the body is involved in Prevention of the occurrence of a new disease and it also decreases the virulence and progression of an existing disease. In COVID-19 the Respiratory system mainly get affected which is evident from its symptoms like cold, cough and breathlessness. Here the drugs help in enhancing immune system and strengthening functions of Respiratory system can be useful. For this purpose, the Rasayana like Chyavanprasha, Agastya Haritaki, Pippali Rasayana, Guduchi, Yashtimadhu, Haridra, Ashwagandha, Tulsi are used. Rasayana working on Respiratory system are best for Prevention of Coronavirus and boosting immune system. Rasayana Chikitsa can be effective in the Prevention as well as reducing symptoms of COVID-19.

E-Insurance :A Platform For Insurance Penetration In India

2019 ◽  
Vol 118 (6) ◽  
pp. 90-93
Author(s):  
L. Terina Grazy ◽  
Dr.G. Parimalarani
Keyword(s):  
Insurance Industry ◽  
Cost Effective ◽  
Online Marketing ◽  
Insurance Companies ◽  
The Internet ◽  
Insurance Sector ◽  
The People ◽  
Cost Effective Approach ◽  
Time And Energy ◽  
Work Done

E-commerce is a part of Internet Marketing. The arrival of Internet made the world very simple and dynamic in all the areas. Internet is the growing business as a result most of the people are using it in their day to day life. E-commerce is attractive and efficient way for both buyers and sellesr as it reduce cost, time and energy for the buyer. No surprise the insurance sector has become quite active within the internet sphere. Most insurance companies are offering policies to be brought online and also the portals for paying premiums. It actually saves from hassles involved in going to an insurance office and spend hours to get the insurance work done. Insurance has become an important and crucial aspect of life. Online insurance is the best and most cost effective approach of taking the insurance deal. This paper focused on influence of online marketing on the insurance industry in India, usage of internet in India , the internet penetration in India and the online sale of insurance product by the insurance sector.

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