scholarly journals INSaFLU-TELE-Vir: an open web-based bioinformatics suite for influenza and SARS-CoV-2 genome-based surveillance

2021 ◽  
Vol 4 ◽  
Author(s):  
Miguel Pinheiro ◽  
Ricardo Pais ◽  
Joana Isidro ◽  
Miguel Pinto ◽  
Carlijn Bogaardt ◽  
...  
Keyword(s):  
Mutation Detection ◽  
World Health ◽  
Quality Analysis ◽  
Web Based ◽  
Virus Surveillance ◽  
Coverage Analysis ◽  
Minor Variant ◽  
Variant Detection ◽  
Health Organization ◽  
Ngs Data

A new era of virus surveillance is emerging based on the real-time monitoring of virus evolution at whole-genome scale (World Health Organization 2021). Although national and international health authorities have strongly recommended this technological transition, especially for influenza and SARS-CoV-2 (World Health Organization 2021, Revez et al. 2017), the implementation of genomic surveillance can be particularly challenging due to the lack of bioinformatics infrastructures and/or expertise to process and interpret next-generation sequencing (NGS) data (Oakeson et al. 2017). We developed and implemented INSaFLU-TELE-Vir platform (https://insaflu.insa.pt/) (Borges et al. 2018), which is an influenza- and SARS-CoV-2-oriented bioinformatics free web-based suite that handles primary NGS data (reads) towards the automatic generation of the main “genetic requests'' for effective and timely laboratory surveillance. By handling NGS data collected from any amplicon-based schema (making it applicable for other pathogens), INSaFLU-TELE-Vir enables any laboratory to perform multi-step and intensive bioinformatics analyses in a user-oriented manner without requiring advanced training. INSaFLU-TELE-Vir handles NGS data collected from distinct sequencing technologies (Illumina, Ion Torrent and Oxford Nanopore Technologies), with the possibility of constructing comparative analyses using different technologies. It gives access to user-restricted sample databases and project management, being a transparent and flexible tool specifically designed to automatically update project outputs as more samples are uploaded. Data integration is thus cumulative and scalable, fitting the need for both routine surveillance and outbreak investigation activities. The bioinformatics pipeline consists of six core steps: read quality analysis and improvement, human betacoronaviruses (including SARS-CoV-2 Pango lineages) and influenza type/subtype classification, mutation detection and consensus generation, coverage analysis, alignment/phylogeny, intra-host minor variant detection (and automatic detection of putative mixed infections). read quality analysis and improvement, human betacoronaviruses (including SARS-CoV-2 Pango lineages) and influenza type/subtype classification, mutation detection and consensus generation, coverage analysis, alignment/phylogeny, intra-host minor variant detection (and automatic detection of putative mixed infections). The multiple outputs are provided in nomenclature-stable and standardized formats that can be visualized and explored in situ or through multiple compatible downstream applications for fine-tuned data analysis. Novel features are being implemented into the INSaFLU-TELE-Vir bioinformatics toolkit as part of the OHEJP TELE-Vir (https://onehealthejp.eu/jrp-tele-vir/) project, including rapid detection of selected genotype-phenotype associations, and enhanced geotemporal data visualization. All the code is available in github (https://github.com/INSaFLU) with the possibility of a local docker installation (https://github.com/INSaFLU/docker). A detailed documentation and tutorial is also available (https://insaflu.readthedocs.io/en/latest/). In summary, INSaFLU supplies public health laboratories and researchers with an open and user-friendly framework, potentiating a strengthened and timely multi-country genome-based virus surveillance.

A Teaching Database for Diagnosis of Hematologic Neoplasms Using Immunophenotyping by Flow Cytometry

2008 ◽  
Vol 132 (5) ◽  
pp. 829-837
Author(s):  
Andy N. D. Nguyen ◽  
Jitakshi De ◽  
Jacqueline Nguyen ◽  
Anthony Padula ◽  
Zhenhong Qu
Keyword(s):  
Flow Cytometry ◽  
World Health ◽  
Hematologic Neoplasms ◽  
Web Based ◽  
Mathematical Algorithm ◽  
Medical Centers ◽  
Flow Cytometric ◽  
Public Resource ◽  
Immunologic Marker ◽  
Health Organization

Abstract Context.—In the diagnosis of lymphomas and leukemias, flow cytometry has been considered an essential addition to morphology and immunohistochemistry. The interpretation of immunophenotyping results by flow cytometry involves pattern recognition of different hematologic neoplasms that may have similar immunologic marker profiles. An important factor that creates difficulty in the interpretation process is the lack of consistency in marker expression for a particular neoplasm. For this reason, a definitive diagnostic pattern is usually not available for each specific neoplasm. Consequently, there is a need for decision support tools to assist pathology trainees in learning flow cytometric diagnosis of leukemia and lymphoma. Objective.—Development of a Web-enabled relational database integrated with decision-making tools for teaching flow cytometric diagnosis of hematologic neoplasms. Design.—This database has a knowledge base containing patterns of 44 markers for 37 hematologic neoplasms. We have obtained immunophenotyping data published in the scientific literature and incorporated them into a mathematical algorithm that is integrated to the database for differential diagnostic purposes. The algorithm takes into account the incidence of positive and negative expression of each marker for each disorder. Results.—Validation of this algorithm was performed using 92 clinical cases accumulated from 2 different medical centers. The database also incorporates the latest World Health Organization classification for hematologic neoplasms. Conclusions.—The algorithm developed in this database shows significant improvement in diagnostic accuracy over our previous database prototype. This Web-based database is proposed to be a useful public resource for teaching pathology trainees flow cytometric diagnosis.

Web-Based Machine Learning Application for Heart Disease Prediction

2022 ◽  
pp. 383-393
Author(s):  
Lokesh M. Giripunje ◽  
Tejas Prashant Sonar ◽  
Rohit Shivaji Mali ◽  
Jayant C. Modhave ◽  
Mahesh B. Gaikwad
Keyword(s):  
Machine Learning ◽  
Heart Disease ◽  
Random Forest ◽  
Web Application ◽  
Machine Learning Algorithms ◽  
World Health ◽  
Web Based ◽  
The World ◽  
Comprehensive Survey ◽  
Health Organization

Risk because of heart disease is increasing throughout the world. According to the World Health Organization report, the number of deaths because of heart disease is drastically increasing as compared to other diseases. Multiple factors are responsible for causing heart-related issues. Many approaches were suggested for prediction of heart disease, but none of them were satisfactory in clinical terms. Heart disease therapies and operations available are so costly, and following treatment, heart disease is also costly. This chapter provides a comprehensive survey of existing machine learning algorithms and presents comparison in terms of accuracy, and the authors have found that the random forest classifier is the most accurate model; hence, they are using random forest for further processes. Deployment of machine learning model using web application was done with the help of flask, HTML, GitHub, and Heroku servers. Webpages take input attributes from the users and gives the output regarding the patient heart condition with accuracy of having coronary heart disease in the next 10 years.

scholarly journals Exposure assessment of treated greywater reused for irrigation

2021 ◽  
Author(s):  
Siraporn Potivichayanon ◽  
Nalin Sittitoon ◽  
Björn Vinnerås
Keyword(s):  
Exposure Assessment ◽  
Tap Water ◽  
Hazard Quotient ◽  
Total Coliform ◽  
Leafy Vegetables ◽  
World Health ◽  
Quality Analysis ◽  
Metal Exposure ◽  
Health Organization ◽  
Almost All

Abstract The aim of study was to assess the risk of exposure of treated greywater reused for irrigation. It consisted of untreated and treated greywater quality analysis and heavy metal exposure assessment. After treatment with a local conventional stabilization pond, parameters such as BOD, COD, Zn, and Pb dropped to 35.63, 9.95, 0.011, and 0.001 mg/L, respectively. Total coliform and fecal coliform were decreased to 23,417 and 5,666 MPN/100 mL, respectively. These results showed almost all detected contaminants in treated greywater were minimized and did not exceed Thailand's standard and World Health Organization guidelines. After that, treated greywater was reused for irrigation. There were three vegetable plots: treated greywater, tap water with fertilizer, and tap water. There were seven edible plants, four leafy and three fruiting vegetables, cultivated in each plot. Zn, Pb, Cd, Cu, and Hg were detected depending on kind of plant; for example, the maximum concentration was found in leafy vegetables. However, the concentrations of contaminants did not exceed the Codex standard for contaminants and toxins in foods and Thailand's standard. Risk characterization showed no risk with a hazard quotient far less than 1. Therefore, treated greywater reuse could be considered to promote sustainable water management in community.

scholarly journals Your womb, your choice! Making an informed decision regarding the timing of pregnancy following miscarriage

2020 ◽  
Author(s):  
Faizan Shah ◽  
Sohinee Bhattacharya ◽  
Kathleen Lamont ◽  
Heather May Morgan
Keyword(s):  
Patient Information ◽  
World Health ◽  
Online Information ◽  
Reproductive Choice ◽  
Multiple Sources ◽  
Web Based ◽  
Normal Period ◽  
Discussion Threads ◽  
Health Organization ◽  
The Impact

The ideal interpregnancy interval (IPI) following a miscarriage is controversial as the World Health Organization (WHO) advise women to delay pregnancy for at least six months. Subsequent research has found that IPI less than six months is beneficial for both mother and baby. The impact of this guidance on the decision-making process for couples/women in this predicament is unknown. Views of women regarding the optimum IPI following miscarriage were investigated using a thematic framework applied to discussion threads from a popular online forum, Mumsnet (www.mumsnet.com). A systematic search of all online information was also undertaken to identify all relevant patient information regarding conceiving another pregnancy after a miscarriage. The findings from the search were tabulated and analysed in relation to the themes identified from the discussion threads on Mumsnet. Ninety-four discussion threads were included. Women saw no reason to wait if they felt ready. Women posted about their frustrations at the multiple sources of conflicting advice they received, at the lack of professional sympathy and felt that being told to wait before trying to conceive after a miscarriage was outdated advice. However, these findings were not corroborated by the patient information currently available online. All web-based patient information gave consistent advice, to wait for at least one normal period before trying to conceive again after a miscarriage and to try for another pregnancy when they felt physically mentally and emotionally ready. None advised waiting for six months. This study highlights that sometimes despite contradictory clinical advice, women are keen to make their own decisions regarding reproductive choice. These decisions are often empowered by peer support and advice which women trust over inconsistent information received from healthcare professionals. In this case, health information appears to have been updated in response to womens choice rather than the other way around.

Peter Chew Formula for maximum positive rate based on Covid19 mutant (Preprint)

2021 ◽  
Author(s):  
Peter Chew
Keyword(s):  
World Health Organization ◽  
Mutation Detection ◽  
Transmission Rate ◽  
World Health ◽  
Policy Makers ◽  
High Infection ◽  
Positive Rate ◽  
Health Organization ◽  
Different Levels ◽  
Specific Country

BACKGROUND A higher positive rate indicates that a country has more undetected covid-19 carriers. Every country needs to increase their testing to minimize the positive rate. By increasing the covid-19 test to detect more undetected covid-19 carriers and isolate them to prevent them from infecting others, thereby reducing the number of undetected covid-19 carriers in the country. Since the new covid-19 mutants usually have a higher transmission rate, the maximum positive rate must be lower to ensure that the undetected virus covid-19 carriers are low and the country is controlled OBJECTIVE Since different countries have different covid-19 mutants, different covid-19 mutants have different levels of transmission. Therefore, each country must have a specific maximum positive rate based on its country’s covid-19 mutant. So, a general formula must be created to determine the maximum positive rate for each country based on its country’s covid-19 mutant. METHODS According to criteria published by World Health Organization (WHO) in May 2020, a positive rate of less than 5% covid-19 test is one indicator that the epidemic is under control in a country and the maximum positive rate is inversely proportional to the transmission rate of the covid-19 mutant. By using inversely proportional method, we get P_max= = x/(〖20 (T〗_mutant)) , where P_max=Maximum Positive rate, T_mutant= Transmission mutation covid-19 and x = transmission rate mutant as of may 2020. RESULTS By using the Peter Chew formula to calculate the maximum positive rate of Covid-19 mutants, P_max = x/(〖20 (T〗_mutant)) , each country can calculate a more specific country maximum positive rate, based on Covid -19 Mutation detection in their country. In addition, if a country finds a new highly infectious covid-19 mutant. The World Health Organization (WHO) recommends that a covid-19 positive rate of less than 5% is not suitable for the mentioned country. For example, if a new highly infectious Covid-19 mutant is detected in some countries, it is 10 times more infectious than the Beta variant. By using Peter Chew’s formula to calculate the maximum positive rate of Covid-19 mutants, we can calculate the maximum positive rate for that particular country, which is 0.5%. CONCLUSIONS By using Peter Chew’s formula, the maximum positive rate in each country is determined based on the covid-19 mutants in each country. In addition to providing a suitable maximum positive rate for each country, it can also prevent "policy makers" in certain countries from continuing to use the wrong maximum positive rate for new mutants because they have not updated the latest information, resulting in countries continuing to maintain a high infection rate.

scholarly journals Surveillance of Mosquitoes for Zika Virus in Westchester County, New York

2017 ◽  
Author(s):  
Randolph Earl Schilke
Keyword(s):  
New York ◽  
Aedes Albopictus ◽  
Zika Virus ◽  
New York State ◽  
World Health ◽  
Department Of Health ◽  
Virus Surveillance ◽  
Local Vector ◽  
Westchester County ◽  
Health Organization

In 2015 in Brazil, Zika virus showed features of geographic expansion and potentially increased virulence. In 2016, New York State issued emergency regulations after the World Health Organization declared Zika virus a Public Health Emergency of International Concern. In this study, mosquito surveillance was conducted in Westchester County, New York, to identify Zika virus and other arboviruses. Twenty trap sites were used for surveillance of Aedes albopictus mosquitoes, the Zika virus vector. The Westchester County Department of Health performed testing for Zika, West Nile, Eastern equine encephalitis, and other flaviviruses on 369 batches comprising 8,891 mosquitoes. Aedes albopictus mosquitoes were identified in Nassau, Rockland, Suffolk, Westchester, and New York City. Despite the increased capacity for specimen analysis, Zika virus was not detected. This study provides the first evidence of appropriate Zika virus surveillance. However, the results do not allow determination of the potential mechanism of local vector-to-human transmission of Zika virus among Aedes albopictus mosquitoes. This study adds to the evidence regarding the distribution, emergence, and trapping capabilities of potential Zika virus vectors.

scholarly journals A Miniaturized Microbe-Silicon-Chip Based on Bioluminescent Engineered Escherichia coli for the Evaluation of Water Quality and Safety

2021 ◽  
Vol 18 (14) ◽  
pp. 7580
Author(s):  
Emanuele Luigi Sciuto ◽  
Domenico Corso ◽  
Sebania Libertino ◽  
Jan Roelof van der Meer ◽  
Giuseppina Faro ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Water Quality ◽  
Inorganic Mercury ◽  
Heavy Metal Accumulation ◽  
World Health ◽  
Quality Analysis ◽  
Sensing Element ◽  
Silicon Photomultiplier ◽  
Engineered Escherichia Coli ◽  
Health Organization

Conventional high throughput methods assaying the chemical state of water and the risk of heavy metal accumulation share common constraints of long and expensive analytical procedures and dedicated laboratories due to the typical bulky instrumentation. To overcome these limitations, a miniaturized optical system for the detection and quantification of inorganic mercury (Hg2+) in water was developed. Combining the bioactivity of a light-emitting mercury-specific engineered Escherichia coli—used as sensing element—with the optical performance of small size and inexpensive Silicon Photomultiplier (SiPM)—used as detector—the system is able to detect mercury in low volumes of water down to the concentration of 1 µg L−1, which is the tolerance value indicated by the World Health Organization (WHO), providing a highly sensitive and miniaturized tool for in situ water quality analysis.

scholarly journals Impacts on dietary habits and health of Indian population during COVID-19 lockdown

2020 ◽  
Vol 7 (6) ◽  
pp. 38-48
Author(s):  
Ramasamy Rajesh Kumar ◽  
◽  
Saravanakumari Arumugham Dhanaraj ◽  
Rashmi Saini ◽  
Punita Kumari ◽  
...  
Keyword(s):  
World Health Organization ◽  
Indian Population ◽  
Dietary Habits ◽  
Prime Minister ◽  
Age Groups ◽  
Social Behaviors ◽  
World Health ◽  
Web Based ◽  
Health Organization

In late 2019 the outbreak of a novel infectious coronavirus (SARS CoV2) which became globalpandemic and named as Coronavirus disease (CoViD-19) World Health Organization (WHO). On 22March, 2020 the Prime Minister of India announced and 14 hours’ public curfew and from 24 March,2020 announced sudden complete lockdown. The sudden complete lockdown made changes in theliving habits and social behaviors of public. Web based survey was conducted among the Indianpopulation of different age groups to understand the impacts on dietary habits and health during thesudden complete lockdown in India.

scholarly journals Viral Sovereignty or Sequence Etiquette? Asian Science, Open Data, and Knowledge Control in Global Virus Surveillance

2020 ◽  
Vol 14 (3) ◽  
pp. 479-505
Author(s):  
Lyle Fearnley
Keyword(s):  
Global Health ◽  
Sequence Data ◽  
Open Data ◽  
Influenza Viruses ◽  
World Health ◽  
Influenza Surveillance ◽  
Republic Of China ◽  
Virus Surveillance ◽  
Pandemic Flu ◽  
Health Organization

Abstract On several occasions, the People’s Republic of China refused to share influenza viruses isolated on their territory with the World Health Organization pandemic flu surveillance system. Scholars in STS and allied disciplines have described these disputes as examples of growing conflict between global health norms of free exchange and Asian state claims of viral sovereignty. However, the discussion has largely overlooked the fact that laboratories in China freely shared genetic sequence data from isolated viruses, even when they refused to ship physical samples, a fact that complicates the opposition of open data and viral sovereignty with the different material forms of the physical sample and the nucleotide sequence. This article provides a comprehensive comparison of the heterogeneous circulations of influenza virus samples and virus gene sequences in global health influenza surveillance and argues this difference is rooted in the different knowledge-control regimes designed for exchanging samples and sequences. Engaging with debates on the position of Asian science within global scientific circulations, the article suggests that Asian scientists confront a multiplicity of global scientific infrastructures and do not necessarily rely on the authority of nation-state sovereignty to reshape global exchanges.

scholarly journals Hansen’s disease: life quality analysis according to clinical characteristics

2021 ◽  
Vol 14 (10) ◽  
Author(s):  
Letícia Silveira Goulart ◽  
Isabella Alcantara de Oliveira ◽  
Raquel Aparecida Rodrigues Nicacio ◽  
Graziele Ferreira Pinto ◽  
Fernanda Rocha Anjos de Oliveira ◽  
...  
Keyword(s):  
Linear Regression ◽  
Life Quality ◽  
World Health ◽  
Quality Analysis ◽  
Public Health Issue ◽  
High Morbidity ◽  
World Health Organization Quality ◽  
Clinical Variables ◽  
Significant Difference ◽  
Health Organization

Hansen´s disease is an infectious and contagious disease with high morbidity indexes. It is a public health issue with patients´ negative life quality (LQ). Current study determines the life quality-based clinical factors of patients with Hansen´s Disease. Sixty-three patients with Hansen´s Disease participated in the research. They were attended to in a Reference Service Centre. World Health Organization Quality of Life Bref (WHOQOL- BREF) was applied to evaluate their LQ and linear regression was employed to assess the association between clinical variables and WHOQOL-BREF domains. Statistical analysis of mean LQ scores showed a significant difference in the physical domains for variables comorbidity (p= 0.043) and intake of medicines (p=0.007). After multiple linear regression, no other clinical variables under analysis proved to be associated with LQ. Patients with self-reported comorbidity and those who continually use medicine have lower LQ averages within the physical domain. Activities that contribute towards the promotion of integral health assistance and for the improvement of LQ for patients with Hansen´s Disease should be enhanced.

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