"The prospects for Nextgen surveillance of pathogens: A view from a Public Health Lab" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology in October 2014 by William Wolfgang, PhD from Wadsworth Center NYSDOH.
Forensics: Human Identity Testing in the Applied Genetics GroupNathan Olson
"Forensics: Human Identity Testing in the Applied Genetics Group" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Peter Vallone, PhD from NIST.
Metrology for Identity and Other Nominal PropertiesNathan Olson
"Metrology for Identity and Other Nominal Properties" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by David Duewer, PhD from NIST.
Scale Computing & the Time-Starved Administrator’s Guide to Simplifying the S...actualtechmedia
This document discusses how increasing demands on IT administrators are leading to greater complexity in server rooms. It argues that datacenter simplification through technologies like hyperconvergence can help overworked administrators. Hyperconvergence uses commodity hardware and virtualization combined with smart software to simplify storage, networking, availability and management. This allows administrators to do more with less resources and meet rising expectations. The document provides examples of how hyperconvergence has helped large companies and can also benefit mid-sized companies by reducing complexity, costs, hardware requirements and support needs.
Scrum Framework: Manage Anything Efficiently and AccuratelyAmir Syafrudin
Note: This presentation is an update of my previous uploaded presentation found here: http://www.slideshare.net/AmirSyafrudin/scrum-methodology-managing-project-efficiently-and-accurately
This is a presentation material used to introduce Scrum Framework in the Directorate General of Taxes, Ministry of Finance, Republic of Indonesia.
This document outlines various UK employment laws. It discusses health and safety laws requiring safe equipment and assessment of risks. Equal opportunities laws prohibit workplace discrimination based on attributes like age, gender, and race. Employment equality regulations ban unreasonable age discrimination and set minimum retirement, part-time work, and youth wage rates. Employers liability insurance protects employers from injuries to employees. Employee rights laws mandate fair wages, holidays, and various types of leave. Finally, trade unions are defined as organized worker associations that protect rights and interests through actions like strikes.
Forensics: Human Identity Testing in the Applied Genetics GroupNathan Olson
"Forensics: Human Identity Testing in the Applied Genetics Group" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Peter Vallone, PhD from NIST.
Metrology for Identity and Other Nominal PropertiesNathan Olson
"Metrology for Identity and Other Nominal Properties" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by David Duewer, PhD from NIST.
Scale Computing & the Time-Starved Administrator’s Guide to Simplifying the S...actualtechmedia
This document discusses how increasing demands on IT administrators are leading to greater complexity in server rooms. It argues that datacenter simplification through technologies like hyperconvergence can help overworked administrators. Hyperconvergence uses commodity hardware and virtualization combined with smart software to simplify storage, networking, availability and management. This allows administrators to do more with less resources and meet rising expectations. The document provides examples of how hyperconvergence has helped large companies and can also benefit mid-sized companies by reducing complexity, costs, hardware requirements and support needs.
Scrum Framework: Manage Anything Efficiently and AccuratelyAmir Syafrudin
Note: This presentation is an update of my previous uploaded presentation found here: http://www.slideshare.net/AmirSyafrudin/scrum-methodology-managing-project-efficiently-and-accurately
This is a presentation material used to introduce Scrum Framework in the Directorate General of Taxes, Ministry of Finance, Republic of Indonesia.
This document outlines various UK employment laws. It discusses health and safety laws requiring safe equipment and assessment of risks. Equal opportunities laws prohibit workplace discrimination based on attributes like age, gender, and race. Employment equality regulations ban unreasonable age discrimination and set minimum retirement, part-time work, and youth wage rates. Employers liability insurance protects employers from injuries to employees. Employee rights laws mandate fair wages, holidays, and various types of leave. Finally, trade unions are defined as organized worker associations that protect rights and interests through actions like strikes.
Este documento presenta el plan de cuentas de la Academia Naval de Guayaquil para su proyecto de microempresas. Describe la estructura de cuentas del activo, pasivo, patrimonio, gastos e ingresos de la organización, dividiendo cada sección en subcuentas específicas como caja, bancos, cuentas por cobrar, propiedad planta y equipo, cuentas por pagar, capital social, resultados acumulados, costos y gastos operacionales, ingresos por matrículas e ingresos no operacionales.
The document describes the editing process of a photo for an Oxfam advertisement. It involves adjusting brightness, contrast, color balance, vibrance, adding text with effects, and placing the Oxfam logo. The edits are aimed at making the model, clothing details, and Oxfam label stand out against the background. This includes adjustments to levels, hue and saturation, posterizing, adding bevel, emboss and stroke to the text. The final edited image meets the creator's vision for the Oxfam advert.
The document defines key terms related to digital communication and collaboration technologies. It explains email methods like web-based mail, POP3, and IMAP and defines blogs, online chat, social bookmarking, URLs, streaming media, VoIP, wikis, HTML, and web feeds. It also briefly outlines social networking on the internet and the World Wide Web.
This document defines and explains several common online terminology:
- Email allows sending messages over the internet to other email accounts instantly. Anyone with an email address can email others including businesses and government agencies.
- A personal website can be used as an online voice to share ideas, customize features, and inspire others as an online diary.
- Online chat provides real-time text message transmission between users over the internet.
- A URL is the address of a specific website or internet file, using slashes to denote directories without spaces or certain characters.
- VoIP allows talking to others long-distance and internationally without phone charges by sending voice digitally over the internet using IP instead of analog phone lines.
- Social
Este documento presenta el plan de cuentas de la Academia Naval de Guayaquil para su proyecto de microempresas. Describe la estructura de cuentas del activo, pasivo, patrimonio, gastos e ingresos de la organización, dividiendo cada sección en subcuentas específicas como caja, bancos, cuentas por cobrar, propiedad planta y equipo, cuentas por pagar, capital social, resultados acumulados, costos y gastos operacionales, ingresos por matrículas, pensiones, ventas y otros ing
The document discusses several drugs used to treat respiratory conditions. It describes how the respiratory system works and then examines specific drugs including: antitussives which suppress coughing; Hycodan, a narcotic cough medicine containing hydrocodone and homatropine; Ventolin (albuterol), a bronchodilator used to treat asthma; Flonase (fluticasone), a steroid nasal spray used for allergies; and inhaled corticosteroids which reduce asthma symptoms and prevent attacks. It emphasizes that proper hand hygiene is important to prevent the spread of infections.
Presentation on material selection and characterization of microbial genomic reference materials being developed at the National Institute of Standards and Technology, USA.
The document describes a reference database of genome sequences for Streptococcus species. It lists 26 Streptococcus genome assemblies from NCBI, including assemblies for S. massiliensis, S. intermedius, S. constellatus, S. anginosus, and some unnamed Streptococcus species. This database can be used as a reference for comparing new Streptococcus genome sequences and identifying species.
This document discusses NIST's work in developing genomic reference materials and methods to evaluate microbial genomics measurements. It describes three projects: 1) assessing genomic purity by detecting low levels of contaminants using sequencing and classification, 2) evaluating SNP calling methods using reference materials and replicates to establish confidence, and 3) developing characterized genomic reference materials for public health pathogens. The overall aim is to build an infrastructure to support genome-based characterization of microbial samples.
The prospects for Nextgen surveillance of pathogens: A view from a Public Hea...nist-spin
"The prospects for Nextgen surveillance of pathogens: A view from a Public Health Lab" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by National Institute for Standards and Technology in October 2014 by William Wolfgang, PhD from Wadsworth Center NYSDOH.
The document provides statistics on Jubilee Health Insurance Limited's business processing unit for the period of January 24th to 28th, 2022. Key metrics include accepting 56% of applications received, debiting 62% of corporate schemes for January, and completing 76% of addition/deletion instructions. A few schemes and policies remain outstanding from previous months. The unit aims to continue improving processing times and reducing pending work.
Este documento presenta el plan de cuentas de la Academia Naval de Guayaquil para su proyecto de microempresas. Describe la estructura de cuentas del activo, pasivo, patrimonio, gastos e ingresos de la organización, dividiendo cada sección en subcuentas específicas como caja, bancos, cuentas por cobrar, propiedad planta y equipo, cuentas por pagar, capital social, resultados acumulados, costos y gastos operacionales, ingresos por matrículas e ingresos no operacionales.
The document describes the editing process of a photo for an Oxfam advertisement. It involves adjusting brightness, contrast, color balance, vibrance, adding text with effects, and placing the Oxfam logo. The edits are aimed at making the model, clothing details, and Oxfam label stand out against the background. This includes adjustments to levels, hue and saturation, posterizing, adding bevel, emboss and stroke to the text. The final edited image meets the creator's vision for the Oxfam advert.
The document defines key terms related to digital communication and collaboration technologies. It explains email methods like web-based mail, POP3, and IMAP and defines blogs, online chat, social bookmarking, URLs, streaming media, VoIP, wikis, HTML, and web feeds. It also briefly outlines social networking on the internet and the World Wide Web.
This document defines and explains several common online terminology:
- Email allows sending messages over the internet to other email accounts instantly. Anyone with an email address can email others including businesses and government agencies.
- A personal website can be used as an online voice to share ideas, customize features, and inspire others as an online diary.
- Online chat provides real-time text message transmission between users over the internet.
- A URL is the address of a specific website or internet file, using slashes to denote directories without spaces or certain characters.
- VoIP allows talking to others long-distance and internationally without phone charges by sending voice digitally over the internet using IP instead of analog phone lines.
- Social
Este documento presenta el plan de cuentas de la Academia Naval de Guayaquil para su proyecto de microempresas. Describe la estructura de cuentas del activo, pasivo, patrimonio, gastos e ingresos de la organización, dividiendo cada sección en subcuentas específicas como caja, bancos, cuentas por cobrar, propiedad planta y equipo, cuentas por pagar, capital social, resultados acumulados, costos y gastos operacionales, ingresos por matrículas, pensiones, ventas y otros ing
The document discusses several drugs used to treat respiratory conditions. It describes how the respiratory system works and then examines specific drugs including: antitussives which suppress coughing; Hycodan, a narcotic cough medicine containing hydrocodone and homatropine; Ventolin (albuterol), a bronchodilator used to treat asthma; Flonase (fluticasone), a steroid nasal spray used for allergies; and inhaled corticosteroids which reduce asthma symptoms and prevent attacks. It emphasizes that proper hand hygiene is important to prevent the spread of infections.
Presentation on material selection and characterization of microbial genomic reference materials being developed at the National Institute of Standards and Technology, USA.
The document describes a reference database of genome sequences for Streptococcus species. It lists 26 Streptococcus genome assemblies from NCBI, including assemblies for S. massiliensis, S. intermedius, S. constellatus, S. anginosus, and some unnamed Streptococcus species. This database can be used as a reference for comparing new Streptococcus genome sequences and identifying species.
This document discusses NIST's work in developing genomic reference materials and methods to evaluate microbial genomics measurements. It describes three projects: 1) assessing genomic purity by detecting low levels of contaminants using sequencing and classification, 2) evaluating SNP calling methods using reference materials and replicates to establish confidence, and 3) developing characterized genomic reference materials for public health pathogens. The overall aim is to build an infrastructure to support genome-based characterization of microbial samples.
The prospects for Nextgen surveillance of pathogens: A view from a Public Hea...nist-spin
"The prospects for Nextgen surveillance of pathogens: A view from a Public Health Lab" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by National Institute for Standards and Technology in October 2014 by William Wolfgang, PhD from Wadsworth Center NYSDOH.
The document provides statistics on Jubilee Health Insurance Limited's business processing unit for the period of January 24th to 28th, 2022. Key metrics include accepting 56% of applications received, debiting 62% of corporate schemes for January, and completing 76% of addition/deletion instructions. A few schemes and policies remain outstanding from previous months. The unit aims to continue improving processing times and reducing pending work.
The document discusses the need for and development of reference materials for quality control of next-generation sequencing for clinical oncology applications. It describes AcroMetrix's Oncology Hotspot Control, which contains over 550 common cancer-related variants across multiple genes at low frequencies to serve as a control. The control has been performance tested at over 30 external sites across various sequencing platforms.
The document discusses Malaysia's intensified case finding (ICF) program for tuberculosis (TB) detection. It provides an overview of the 3 main components of ICF: intensified case finding, isoniazid preventive therapy, and infection control. It emphasizes finding TB cases early through screening high-risk groups like people living with HIV and in institutional settings like prisons. The goal is to reduce TB transmission in communities and improve TB treatment outcomes.
This document provides an overview of acute kidney injury (AKI). It begins with objectives of defining, staging and managing AKI, understanding referral criteria, highlighting less common intrinsic renal pathology, and understanding long term implications. It then outlines topics to be covered including perspectives on AKI, identification and definition, pathogenesis, guidelines, less common causes, dialysis and outcomes. It discusses perceptions of AKI between different specialties. It provides data on AKI incidence, risk factor assessment, investigations, treatment including fluids and renal replacement therapy. It discusses evidence and guidelines around these topics. It highlights long term outcomes of AKI including increased risk of chronic kidney disease and end stage kidney disease. Biomarkers for early detection of AKI
Dr. Paul Yeske - Assessment of The Likelihood of Mycoplasma hyopneumoniae Lat...John Blue
This document summarizes a study assessing the likelihood of lateral transmission of Mycoplasma hyopneumoniae in finishing pig sites. The objectives were to determine the incidence rate of lateral infections and identify risk factors. 100 finishing sites were tested prior to marketing using serology and PCR tests. 6 sites tested positive, a lateral transmission rate of 6%. Vaccination status and herd management practices may have impacted the risk of lateral transmission between sites. The preliminary results provide insight into the rate of Mycoplasma spread between pig groups in finishing facilities.
Dr. Paul Yeske - Assessment of The Likelihood of Mycoplasma hyopneumoniae Lat...John Blue
This document summarizes a study assessing the likelihood of lateral transmission of Mycoplasma hyopneumoniae in finishing pigs. The objectives were to determine the incidence rate of lateral infections in finishing pigs and identify risk factors. 100 finishing sites were tested prior to marketing using serology and PCR tests. 6 sites tested positive, a lateral transmission rate of 6%. Vaccination status and production system were identified as potential risk factors. The preliminary results provide insight into the rate of Mycoplasma transmission between pigs in finishing facilities.
Chuan phat trien cua tre duoi 5 tuoi WHOhangntbk83
This document contains tables of standardized weight measurements for boys and girls under 5 years old according to WHO standards from 2006. The tables list ages in months along the top and left side, with columns showing the average weight as well as weights that are 1, 2, and 3 standard deviations below and above the average.
This document contains tables listing weight standards (in kilograms) for girls under 5 years old according to the WHO 2006 standards. The tables provide weight values from -3 standard deviations to +3 standard deviations in monthly intervals from birth to 60 months.
Risk Assessment for an Earthquake Scenario in Istanbul CityAlireza Babaee
Presentation of project in the course "Tools for Risk Mitigation" for M.Sc. "Civil Engineering for Risk Mitigation" at Politecnico di Milano.
Submitted by:
Maryam Izadifar, Alireza Babaee, Iman Gharraie, Tohid Hejazi
Submitted to:
Professor Scira Menoni
Vulnerability and risk assessment of the Istanbul City for a given earthquake...Maryam Izadifar
Presentation of project in the course "Tools for Risk Mitigation" for M.Sc. "Civil Engineering for Risk Mitigation" at Politecnico di Milano.
Submitted by:
Maryam Izadifar, Alireza Babaee, Iman Gharraie, Tohid Hejazi
Submitted to:
Professor Scira Menoni
This document summarizes a study on identifying the most significant factors causing environmental pollution in Kurdistan.
The study conducted a survey of 30 experts who rated 15 potential factors on their importance. The factors with the highest average ratings were identified as the most significant in causing pollution. These included lack of waste quantification and monitoring, lack of worker skills and technical expertise, and absence of government inspections and enforcement actions.
The study recommends improving regulations and enforcement, promoting recycling, reducing pesticide and fertilizer use, conducting more research on pollution impacts, and developing taxes to incentivize private industry to improve environmental management.
This document summarizes a presentation on fluorescence-guided urologic surgery. The speaker discusses using indocyanine green (ICG) to identify lymph nodes during prostate cancer surgery. It is suggested that ICG-guided lymph node dissection may allow surgeons to stop further lymphadenectomy if frozen sections of fluorescent nodes are negative. Limitations include the potential for missing non-fluorescent nodes. The potential for stopping extended lymphadenectomy in low-risk patients based on ICG guidance is presented. Cytokeratin 19 is also discussed as a marker for detecting micrometastases, with a project underway to evaluate its expression in automated molecular node analysis.
This document provides information about Eastern Screw Co., a manufacturer and supplier of stainless steel fasteners. It summarizes their capabilities including manufacturing a wide range of fastener types in various materials, diameters and lengths. It also details their inventory, locations, services, and machining capabilities.
Dimecres 19 de maig de 2021, de 9.15 a 11h, en el marc de la EU Green Week 2021, la Sub-direcció general de Prevenció i Control de la Contaminació Atmosfèrica del Departament de Territori i Sostenibilitat organitza un seminari web on es presenten les principals novetats de la campanya 2021 i es parla de la correlació COVID-Ozó troposfèric.
The document provides information about the Measles and Rubella surveillance activities conducted at the Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGI) in Lucknow, India. SGPGI serves as a reference laboratory under the World Health Organization's Global Measles Laboratory Network. Key points:
1) SGPGI processes thousands of serum, urine, and throat samples each year for measles and rubella detection using ELISA and PCR techniques.
2) The laboratory achieves high accuracy rates of over 90% on external proficiency testing and maintains timely reporting of results.
3) In addition to diagnostic testing, SGPGI conducts genomic sequencing and analysis to identify circulating measles and rub
Missing Data in Research on Child MaltreatmentBASPCAN
Implications of non-response and loss to follow up and some possible solutions.
James Doidge PhD Candidate, University of South Australia
Prof Leonie Segal, Supervisor, University of South Australia
A. Prof Paul Delfabbro, Supervisor, University of Adelaide
ATP Collaborators
Dr Ben Edwards, AIFS
Prof John Toumbourou, Deakin
Dr Daniel Higgins, AIFS
Ms Suzanne Vassall
20150918 F. Vialard - Prevalence of recurrent pathogenic microdeletion and mi...Roberto Scarafia
This document discusses changes in prenatal screening and diagnosis. It describes a BACs-on-Beads technology called Prenatal BoBs that can detect pathogenic microdeletions and microduplications in pregnancies. A worldwide study of over 9,500 pregnancies found 44 cryptic imbalances not detectable by conventional methods, with an additive detection rate of 1/220. The majority (71.2%) involved the 22q11.2 region. The document discusses the potential role and limitations of Prenatal BoBs compared to chromosomal microarray analysis, and whether screening for 22q11.2 abnormalities should be done using non-invasive prenatal testing.
The daily report provides commodity futures data for various agricultural commodities traded on the NCDEX and MCX exchanges in India. It includes pivot point price levels for different contract months of commodities like chana, guar gum, guar seed, jeera, pepper, soybean and mentha oil. Charts of daily chana and soyaoil price movements are also included. The report disclaims responsibility for any losses from investment decisions based on its analysis.
Similar to The prospects for Nextgen surveillance of pathogens: A view from a Public Health Lab (20)
The debris of the ‘last major merger’ is dynamically youngSérgio Sacani
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
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because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
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Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
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The cost of acquiring information by natural selectionCarl Bergstrom
This is a short talk that I gave at the Banff International Research Station workshop on Modeling and Theory in Population Biology. The idea is to try to understand how the burden of natural selection relates to the amount of information that selection puts into the genome.
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The cost of information acquisition by natural selection
Ryan Seamus McGee, Olivia Kosterlitz, Artem Kaznatcheev, Benjamin Kerr, Carl T. Bergstrom
bioRxiv 2022.07.02.498577; doi: https://doi.org/10.1101/2022.07.02.498577
Authoring a personal GPT for your research and practice: How we created the Q...Leonel Morgado
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
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PPT on Direct Seeded Rice presented at the three-day 'Training and Validation Workshop on Modules of Climate Smart Agriculture (CSA) Technologies in South Asia' workshop on April 22, 2024.
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With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...Advanced-Concepts-Team
Presentation in the Science Coffee of the Advanced Concepts Team of the European Space Agency on the 07.06.2024.
Speaker: Diego Blas (IFAE/ICREA)
Title: Gravitational wave detection with orbital motion of Moon and artificial
Abstract:
In this talk I will describe some recent ideas to find gravitational waves from supermassive black holes or of primordial origin by studying their secular effect on the orbital motion of the Moon or satellites that are laser ranged.
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...
The prospects for Nextgen surveillance of pathogens: A view from a Public Health Lab
1. The prospects for Nextgen surveillance of
pathogens: A view from a Public Health Lab
William Wolfgang
Wadsworth Center NYSDOH
NIST Workshop 10/20/14
3. We collaborate with a number of different
groups on Pathogen sequencing projects
• Global Microbial Identifier (GMI) initiative
• CDC: Listeria monocytogenes initiative and AMD initiative
• FDA: GenomeTrakr initiative
• Minnesota and Washington Departments of Health
• And we hope to do more
4. At the Wadsworth we need standards
• As we translate to new technologies we need to know:
• Faster
• Cheaper
• Better
• For this we need to make accurate and meaningful comparisons.
• To do this we need standards.
5. Why use Nextgen for Salmonella typing?
• PFGE has low discriminatory power.
.
Each year
• 1 million cases Salmonella in US.
• 19,000 hospitalizations and 378 deaths.
• The Wadsworth receives about 1,500/yr.
7. Proof of principle study on a Salmonella
Enteritidis outbreak
• Sept. 2010 Connecticut Dept. of Health identifies a Salmonella
outbreak in a long term care facility (LTCF).
• Outbreak was linked to cannoli from a Westchester bakery.
• Both NY and CT cases consumed cannoli’s.
• Isolates had the most common PFGE pattern.
9. Whole genome Cluster Analysis ( WGCA)
can identify an outbreak cluster not detected
88
7.3 SNPs
1106235
1033603
1035184
1127690
1037723
1035183
1036319
+
1031528
1033369
+
1035417
+
1132014
1033213
+
1034599
1034587
+
1035179
1122186
1130508
1030147
1034601
+
1103844
1034213
1033371
+
1035181
1036119
1028670
1121079
1035178
1035182
1029153
1131312
1038792
+
1036979
+
1029949
1039087
1035180
100
100
100
85
88
68
100
100
A
B
LTCF
by PFGE
All isolates are PFGE PATTERN 4
10. Implementing WGCA for SE in real-time.
• Evaluate WGCA compared to PFGE.
• Speed - Faster
• Cost - Cheaper
• More Actionable Clusters – Better
• Develop an in house bioinformatics pipeline.
• Develop communication pipeline to epidemiologists.
• Determine cluster parameters that represent an outbreak from a single
source (assign a probability).
• Use data sets to evaluate evolving informatic methods.
• Become proficient (PT programs).
11. Over the past 12 months
• Sequenced all Salmonella Enteritidis (379 genomes).
• All data at NCBI
• Developed an in House pipeline to analyze the data.
• SNP based phylogenetic trees were constructed in real time.
• 63 phylogenetic clusters were reported to epidemiologists.
• 0 to 5 snps differences
15. Can we develop cluster metrics that give a
probability of linkage to a single source?
• Perform phylogenetic analysis of epidemiologically confirmed
outbreaks.
I. Calculate SNP distance.
II. Examine tree structure.
• Do for many serovars of each species.
• This could be done relatively easily by freezer diving and HiSeq
runs.
• For SE SNP distances appear to be small (0-3 snps)
I. Based on 9 bonafide outbreaks from NY and MN.
16. NY-swgs1311
swgs1065
Large Western NY pattern 5 cluster
• 13 isolates collected over 10
months (0 to 6 snps distance)
• First isolates in fall 2013.
• February 2014, two distinct clades
form.
• Suggests bug has evolved
• Does this cluster represent 1, 2, or
3 sources?
NY-swgs1335
NY-swgs1347
NY-swgs1366
NY-swgs1305
swgs1217
7/05/14 Oneida
5/12/14 Ontario
2/6/14 Onondaga
NY-swgs1387_NEW
NY-swgs1360
6/22/14 Seneca
NY-swgs1339
6/11/14 Oswego
2/22/14 Oneida
2/21/14 Onondaga
12/12/13 Cattaraugus
9/25/13 Niagara
10/15/13 Monroe
swgs1224
2/22/14 Onondaga
NY-swgs1333
swgs1226
swgs1223
swgs1079
swgs1008
swgs1018
NY-swgs1355
7/22/14 Onondaga
6/3/14 Erie
1+snps+
NY-swgs1375_NEW
17. One person
two outbreaks
• GC-35 appears 6/9/14
• PFGE pattern 4
• Isolate from food a handler
• Total of 5 cases through 8/7/14
• GC-40 appears 6/30/14
• PFGE pattern 21
• isolate recovered from the same
food handler
JEGX01.0021++
JEGX01.0004
18. WGCA is better, but is it faster and cheaper?
metric( PFGE( WGCA(
TAT : extraction to
analysis
2 days 6+days+
Cost+ $69+ $294+
Technician+@me+ 8h+ 10h+
Ac@onable+clusters++ 3+nonEendemic+ 63+
19. We have created a two State Network
• Collaborating with Minnesota.
• Currently no informatics in house.
• We pull their sequences off Basespace.
• Run through our pipeline.
20. Tree from Merged
data
• Does pipeline
used to merge
the data affect
tree structure?
• Do sequence
metrics affect
merged tree
structure?
Travel+associated+
21. National Genomic Surveillance Machine
• State labs feed the machine by uploading sequences from isolates
received through surveillance.
• Federal and other support for reagents and equipment.
• NCBI to analyze the products of this machine and reports results to
state and federal agencies.
22. Current FDA Genome Trackr
network
State Health labs
• New York
• Florida
• Arizona
• Washington
• Minnesota
• Virginia
• Maryland
FDA labs
• 9 FDA field labs
• CFSAN - MOD1
• CFSAN - Wiley
• IEH (contracting lab)
International labs
• Mexico
• Ireland
• UK (FERA)
• Columbia
Contributors
• Turkey
• Brazil
• Italy
24. Expected Outcomes for WGS surveillance
• Laboratory
• Improve outbreak cluster detection.
• Clusters will be detected more rapidly and from fewer isolates.
• Epi
• Allow identification of clusters within endemic patterns.
• Solve more clusters.
• Public Health
• More efficient identification and removal of pathogen sources.
25. Challenges exist
• Creating a network.
• Increasing amounts of data.
• Metadata: how much should be public?
• In real time?
• What elements?
• Paying
• As sequencing technology and bioinformatics evolve:
• Need to maintain backward compatibility
• Transitioning:
• What to do first.
• Integration with serology and PFGE typing.
26. Standards I would like to see
• Pipeline quality and reproducibility.
• Tree quality and reproducibility.
• Probability metrics that a cluster is from a single source.
27. Summary
• WGS can improve surveillance activities and outbreak traceback.
• It is practical to develop network.
• We need standards.
28. • Cornell Acknowledgments
Martin Wiedmann
Henk den Bakker
• FDA
Eric Brown
Peter Evans
Marc Allard
Errol Strain
Ruth Timme
• Connecticut DOH
Stacey Kinney
John Fontana
• Minnesota DOH
David Boxrud
Angie Jones
Victoria Lappi
• Washington State DOH
Ailyn Perez-Osorio
Zhen Li
• Wadsworth Center Genomics Core
Matt Shudt
Zhen Zhang
Charles MacGowan
Melissa Leisner
Danielle Loranger
Mike Palumbo
Pascal LaPierre
• Kara Michell
• Wadsworth PulseNet Lab
Dianna Bopp
Deb Baker
Lisa Thompson
• NCBI
Bill Klimke
Martin Shumway