Running the Titan_Illumina_PE Workflow on Terra.bio v1

2021 ◽  
Author(s):  
Jill V Hagey ◽  
Kevin Libuit ◽  
Frank J Ambrosio ◽  
Technical Outreach and Assistance for States Team
Keyword(s):  
Public Health ◽  
Technical Assistance ◽  
File Format ◽  
Technical Documentation ◽  
Video Instruction ◽  
The Public ◽  
Viral Genomics ◽  
Genomic Characterization ◽  
Primer Sequence

The Titan_Illumina_PE workflow is a part of the Public Health Viral Genomics Titan series for SARS-CoV-2 genomic characterization. Titan_Illumina_PE was written specifically to process Illumina paired-end (PE) read data. Input reads are assumed to be the product of sequencing tiled PCR-amplicons designed for the SARS-CoV-2 genome. The most common read data analyzed by the Titan_Illumina_PE workflow are generated with the ARTIC V3 protocol. However, alternative primer schemes such as the QIAseq Primer Panel are also suitable for this workflow. The primer sequence coordinates of the PCR scheme utilized must be provided in BED format along with the raw Illumina read data. Upon initiating a Titan_Illumina_PE job, the input primer scheme coordinates and raw paired-end Illumina read data provided for each sample will be processed to perform consensus genome assembly, infer the quality of both raw read data and the generated consensus genome, and assign lineage or clade designations as outlined in the Titan_Illumina_PE data workflow diagram below. Additional technical documentation for the Titan_Illumina_PE workflow is available at: https://public-health-viral-genomics-theiagen.readthedocs.io/en/latest/titan_workflows.html#titan-workflows-for-genomic-characterization Required input data for Titan Illumina PE: Illumina paired-end read data (forward and reverse FASTQ files per sample) Primer sequence coordinates of the PCR scheme utilized in BED file format Video Instruction: Theiagen Genomics: Titan Genomic Characterization https://www.youtube.com/watch?v=zP9I1r6TNrw Theiagen Genomics: Titan Outputs QC https://www.youtube.com/watch?v=Amb-8M71umw For technical assistance please contact us at: [email protected]

Running the Titan_ClearLabs Workflow on Terra.bio v1

2021 ◽  
Author(s):  
Frank J Ambrosio ◽  
Jill V Hagey ◽  
Kevin Libuit ◽  
Technical Outreach and Assistance for States Team
Keyword(s):  
Public Health ◽  
Technical Assistance ◽  
Amplicon Sequencing ◽  
Technical Documentation ◽  
Video Instruction ◽  
The Public ◽  
Viral Genomics ◽  
Genomic Characterization ◽  
Primer Sequence

The Titan_ClearLabs workflow is a part of the Public Health Viral Genomics Titan series for SARS-CoV-2 genomic characterization. Titan_CleanLabs was written to process Clear Labs read data for SARS-CoV-2 ARTIC V3 amplicon sequencing. Upon initiating a Titan_ClearLabs run, input read data provided for each sample will be processed to perform consensus genome assembly, infer the quality of both raw read data and the generated consensus genome, and assign lineage or clade designations as outlined in the Titan_ClearLabs data workflow below. Additional technical documentation for the Titan_ClearLabs workflow is available at: https://public-health-viral-genomics-theiagen.readthedocs.io/en/latest/titan_workflows.html#titan-clearlabs Required input data for Titan_ClearLabs: Cear Labs FASTQ read files (single FASTQ file per sample) Primer sequence coordinates of the PCR scheme utilized in BED file format Video Instruction: Theiagen Genomics: Titan Genomic Characterization https://www.youtube.com/watch?v=zP9I1r6TNrw Theiagen Genomics: Titan Outputs QC https://www.youtube.com/watch?v=Amb-8M71umw For technical assistance, please contact us at: [email protected]

Running the Titan_ONT Workflow on Terra.bio v1

2021 ◽  
Author(s):  
Francis J J. Ambrosio ◽  
Jill V Hagey ◽  
Kevin Libuit ◽  
Technical Outreach and Assistance for States Team
Keyword(s):  
Public Health ◽  
Technical Assistance ◽  
Technical Documentation ◽  
The Public ◽  
Viral Genomics ◽  
Oxford Nanopore ◽  
Genomic Characterization ◽  
Data Files ◽  
Primer Sequence

The Titan_ONT workflow is a part of the Public Health Viral Genomics Titan series for SARS-CoV-2 genomic characterization. Titan_ONT was written specifically to process basecalled and demultiplexed Oxford Nanopore Technology (ONT) read data. Input reads are assumed to be the product of sequencing ARTIC V3 tiled PCR-amplicons designed for the SARS-CoV-2 genome. Upon initiating a Titan_ONT run, input read data provided for each sample will be processed to perform consensus genome assembly, infer the quality of both raw read data and the generated consensus genome, and assign lineage or clade designations as outlined in the Titan_ONT data workflow diagram below. Additional technical documentation for the Titan_ONT workflow is available at: https://public-health-viral-genomics-theiagen.readthedocs.io/en/latest/titan_workflows.html#titan-workflows-for-genomic-characterization Required input data for Titan_ONT: Basecalled and demultiplexed ONT read data files (single FASTQ file per sample) Primer sequence coordinates of the PCR scheme utilized in BED file format Titan_ONT has not been written to process FAST5 files Video Instruction: Theiagen Genomics: Titan Genomic Characterization https://www.youtube.com/watch?v=zP9I1r6TNrw Theiagen Genomics: Titan Outputs QC https://www.youtube.com/watch?v=Amb-8M71umw For technical assistance please contact us at: [email protected]

Assessing the quality of public health in the Russian Federation and Israel: Main problems and solutions

2020 ◽  
Vol 19 (4) ◽  
pp. 618-632
Author(s):  
A.S. Panchenko
Keyword(s):  
Public Health ◽  
Russian Federation ◽  
Population Based ◽  
The Public ◽  
Disability Adjusted Life ◽  
Problems And Solutions ◽  
The Russian Federation ◽  
Disability Adjusted Life Year ◽  
Practical Recommendations

Subject. The article addresses the public health in the Russian Federation and Israel. Objectives. The focus is on researching the state of public health in Russia and Israel, using the Global Burden of Disease (GBD) project methodology, identifying problem areas and searching for possible ways to improve the quality of health of the Russian population based on the experience of Israel. Methods. The study draws on the ideology of the GBD project, which is based on the Disability-Adjusted Life-Year (DALY) metric. Results. The paper reveals the main causes of DALY losses and important risk factors for cancer for Russia and Israel. The findings show that the total DALY losses for Russia exceed Israeli values. The same is true for cancer diseases. Conclusions. Activities in Israel aimed at improving the quality of public health, the effectiveness of which has been proven, can serve as practical recommendations for Russia. The method of analysis, using the ideology of the GBD project, can be used as a tool for quantitative and comparative assessment of the public health.

scholarly journals Evaluation of Education for Public Health: A Practical Foundation for Solidarity

2019 ◽  
Vol 29 (Supplement_4) ◽  
Author(s):  
M Perkiö ◽  
R Harrison ◽  
M Grivna ◽  
D Tao ◽  
C Evashwich
Keyword(s):  
Public Health ◽  
Health Education ◽  
Health Workforce ◽  
Health Professionals ◽  
Public Health Education ◽  
Public Health Workforce ◽  
Rigorous Evaluation ◽  
The Public ◽  
Public Health Professionals

Abstract Education is a key to creating solidary among the professionals who advance public health’s interdisciplinary mission. Our assumption is that if all those who work in public health shared core knowledge and the skills for interdisciplinary interaction, collaboration across disciplines, venues, and countries would be facilitated. Evaluation of education is an essential element of pedagogy to ensure quality and consistency across boundaries, as articulated by the UNESCO education standards. Our study examined the evaluation studies done by programs that educate public health professionals. We searched the peer reviewed literature published in English between 2000-2017 pertaining to the education of the public health workforce at a degree-granting level. The 2442 articles found covered ten health professions disciplines and had lead authors representing all continents. Only 86 articles focused on evaluation. The majority of the papers examined either a single course, a discipline-specific curriculum or a teaching method. No consistent methodologies could be discerned. Methods ranged from sophisticated regression analyses and trends tracked over time to descriptions of focus groups and interviews of small samples. We found that evaluations were primarily discipline-specific, lacked rigorous methodology in many instances, and that relatively few examined competencies or career expectations. The public health workforce enjoys a diversity of disciplines but must be able to come together to share diverse knowledge and skills. Evaluation is critical to achieving a workforce that is well trained in the competencies pertinent to collaboration. This study informs the pedagogical challenges that must be confronted going forward, starting with a commitment to shared core competencies and to consistent and rigorous evaluation of the education related to training public health professionals. Key messages Rigorous evaluation is not sufficiently used to enhance the quality of public health education. More frequent use of rigorous evaluation in public health education would enhance the quality of public health workforce, and enable cross-disciplinary and international collaboration for solidarity.

scholarly journals Increasing the public health potential of basic research and the scientist satisfaction. An international survey of bioscientists

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 56 ◽  
Author(s):  
Giorgio Scita ◽  
Carmen Sorrentino ◽  
Andrea Boggio ◽  
David Hemenway ◽  
Andrea Ballabeni
Keyword(s):  
Public Health ◽  
Diagnostic Method ◽  
Intrinsic Value ◽  
Basic Research ◽  
Previous Survey ◽  
The Public ◽  
Quality Of Work ◽  
Survey Results

Basic scientific research generates knowledge that has intrinsic value which is independent of future applications. Basic research may also lead to practical benefits, such as a new drug or diagnostic method.  Building on our previous study of basic biomedical and biological researchers at Harvard, we present findings from a new survey of similar scientists from three countries.  This survey asked about the scientists’ motivations, goals and perspectives along with their attitudes concerning  policies designed to increase both the practical (i.e. public health) benefits of basic research as well as their own personal satisfaction. Close to 900 basic investigators responded to the survey; results corroborate the main findings from the previous survey of Harvard scientists.  In addition, we find that most bioscientists disfavor present policies that require a discussion of the public health potential of their proposals in grants but generally favor softer policies aimed at increasing the quality of work and the potential practical benefits of basic research. In particular, bioscientists are generally supportive of those policies entailing the organization of more meetings between scientists and the general public, the organization of more academic discussion about the role of scientists in the society, and the implementation of a “basic bibliography” for each new approved drug.

The Reality of Accessibility in the Public Health Systems

2013 ◽  
pp. 691-719
Author(s):  
Guillermo López Cala ◽  
Yolanda María de la Fuente Robles ◽  
Rosa María Fernández Alcalá
Keyword(s):  
Public Health ◽  
Quality Of Life ◽  
Empirical Study ◽  
Health Centers ◽  
The Public ◽  
Basic Health ◽  
Important Concept ◽  
Use Of Technology ◽  
Information And Communication

This chapter deals with accessibility, a relevant and important concept for every citizen in the improvement of their quality of life in any environment or daily situation. Specifically, an empirical study about accessibility in the public health centers of a Basic Health Area (BHA) of Jaén is carried out. From this study, accessibility deficiencies in health buildings are revealed, and explicit proposals are provided with the aim of improving accessibility in different scopes such as information and communications. The improvement plans based on the use of Technology, Information, and Communication (TIC) tools help sensory disabled users that attend to the Health Center.

scholarly journals Probiotics and constipation: mechanisms of action, evidence for effectiveness and utilisation by patients and healthcare professionals

2019 ◽  
Vol 79 (1) ◽  
pp. 147-157 ◽  
Author(s):  
Eirini Dimidi ◽  
S. Mark Scott ◽  
Kevin Whelan
Keyword(s):  
Public Health ◽  
Chronic Constipation ◽  
Healthcare Professionals ◽  
Mechanisms Of Action ◽  
Current Evidence ◽  
Present Evidence ◽  
The Public ◽  
Considerable Impact ◽  
Public Health Strategies

The aim of this narrative review is to assess and present evidence on the mechanisms of action of probiotics in constipation, their effectiveness and their utilisation by patients and healthcare professionals. Chronic constipation is a common bothersome disorder that has a considerable impact on patients' quality of life. Probiotics have been increasingly investigated for their effectiveness in various disorders, including chronic constipation. Probiotics may affect gut motility and constipation through their impact on the gut microbiota and fermentation, the central and enteric nervous system and the immune system. However, evidence for the effectiveness of probiotics in the management of constipation remains varied, with some strains demonstrating improvements, while others show no effect. Despite the uncertainty in evidence and the fact that the majority of healthcare professionals do not recommend probiotics for constipation, an increased prevalence of probiotic use by people with constipation has been shown. Therefore, there is a need for public health strategies to inform the public about where strong evidence of probiotic effectiveness exist, and where evidence is still weak. Education of healthcare professionals on the increased utilisation of probiotics for constipation by the public and on current evidence for the effectiveness of specific strains is also required.

scholarly journals Pain neuroscience education and physical exercise for patients with chronic spinal pain in primary healthcare: a randomised trial protocol

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Miguel A. Galán-Martín ◽  
Federico Montero-Cuadrado ◽  
Enrique Lluch-Girbes ◽  
M. Carmen Coca-López ◽  
Agustín Mayo-Iscar ◽  
...  
Keyword(s):  
Public Health ◽  
Quality Of Life ◽  
Primary Care ◽  
Chronic Pain ◽  
Clinical Practice ◽  
Physical Exercise ◽  
Public Health System ◽  
The Public ◽  
Neuroscience Education

Abstract Background Chronic musculoskeletal pain affects more than 20% of the population, and the prevalence is increasing, causing suffering, loss of quality of life, disability, and an enormous expenditure on healthcare resources. The most common location for chronic pain is the spine. Many of the treatments used are mainly passive (pharmacological and invasive) and poor outcomes. The treatments currently applied in the public health system do not comply with the recommendations of the main clinical practice guidelines, which suggest the use of educational measures and physical exercise as the first-line treatment. A protocol based on active coping strategies is described, which will be evaluated through a clinical trial and which could facilitate the transfer of the recommendations of the clinical practice guidelines to a primary care setting. Methods Randomised and multicentre clinical trials, which will be carried out in 10 Primary Care centres. The trial will compare the effect of a Pain Neuroscience Education program (six sessions, 10 h) and group physical exercise (18 sessions program carried out in six weeks, 18 h), with usual care physiotherapy treatment. Group physical exercise incorporates dual tasks, gaming, and reinforcement of contents of the educational program. The aim is to assess the effect of the intervention on quality of life, as well as on pain, disability, catastrophism, kinesiophobia, central sensitisation, and drug use. The outcome variables will be measured at the beginning of the intervention, after the intervention (week 11), at six months, and a year. Discussion Therapeutic interventions based on active coping strategies are essential for the treatment of chronic pain and the sustainability of the Public Health System. Demonstrating whether group interventions have an effect size is essential for optimising resources in such a prevalent problem. Trial registration NCT03654235 “Retrospectively registered” 31 August 2018.

scholarly journals An outbreak of food poisoning caused by Salmonella typhi-murium, phage-type 12, probably spread by infected meat

1963 ◽  
Vol 61 (4) ◽  
pp. 419-424 ◽  
Author(s):  
R. W. S. Harvey ◽  
T. H. Price ◽  
W. Bate ◽  
D. R. Allen
Keyword(s):  
Public Health ◽  
Technical Assistance ◽  
Phage Type ◽  
Food Poisoning ◽  
Salmonella Typhi ◽  
Phage Typing ◽  
Public Health Laboratory ◽  
Reference Laboratory ◽  
The Public ◽  
Infected Meat

An outbreak of food poisoning caused by Salmonella typhi-murium, phage-type 12, in which 122 persons were infected, is described.Isolation of the same organism from the drains of two large abattoirs, from pig faeces at one abattoir, and from the floor drains of fifteen out of fifty-four butchers' shops and bakehouses examined, together with records showing that this organism had been recently isolated from pigs and cattle in the neighbourhood, suggested that meat was the vehicle of infection.We are indebted to Dr E. S. Anderson and the staff of the Central Enteric Reference Laboratory and Bureau, Colindale, for phage-typing the cultures of S. typhi-murium.We should like to thank Prof. Scott Thomson for his encouragement and advice in the preparation of this paper and Mr J. Morgan and Mr B. M. Jones of the Public Health Laboratory, Cardiff, for their technical assistance.

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