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Article: The role of genetic sequencing and analysis in the polio eradication programme.

Jorgensen, David / Pons-Salort, Margarita / Shaw, Alexander G / Grassly, Nicholas C

2020 Volume 6, Issue 2, Page(s) veaa040

Abstract: Genetic sequencing of polioviruses detected through clinical and environmental surveillance is used to confirm detection, identify their likely origin, track geographic patterns of spread, and determine the appropriate vaccination response. The critical ... ...

Abstract	Genetic sequencing of polioviruses detected through clinical and environmental surveillance is used to confirm detection, identify their likely origin, track geographic patterns of spread, and determine the appropriate vaccination response. The critical importance of genetic sequencing and analysis to the Global Polio Eradication Initiative has grown with the increasing incidence of vaccine-derived poliovirus (VDPV) infections in Africa specifically (470 reported cases in 2019), and globally, alongside persistent transmission of serotype 1 wild-type poliovirus in Pakistan and Afghanistan (197 reported cases in 2019). Adapting what has been learned about the virus genetics and evolution to address these threats has been a major focus of recent work. Here, we review how phylogenetic and phylogeographic methods have been used to trace the spread of wild-type polioviruses and identify the likely origins of VDPVs. We highlight the analysis methods and sequencing technology currently used and the potential for new technologies to speed up poliovirus detection and the interpretation of genetic data. At a pivotal point in the eradication campaign with the threat of anti-vaccine sentiment and donor and public fatigue, innovation is critical to maintain drive and overcome the last remaining circulating virus.
Language	English
Publishing date	2020-05-20
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2818949-8
ISSN	2057-1577
ISSN	2057-1577
DOI	10.1093/ve/veaa040
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Article ; Online: Soli-enabled noncontact heart rate detection for sleep and meditation tracking.

Scientific reports

2023 Volume 13, Issue 1, Page(s) 18008

Abstract: Heart rate (HR) is a crucial physiological signal that can be used to monitor health and fitness. Traditional methods for measuring HR require wearable devices, which can be inconvenient or uncomfortable, especially during sleep and meditation. ... ...

Abstract	Heart rate (HR) is a crucial physiological signal that can be used to monitor health and fitness. Traditional methods for measuring HR require wearable devices, which can be inconvenient or uncomfortable, especially during sleep and meditation. Noncontact HR detection methods employing microwave radar can be a promising alternative. However, the existing approaches in the literature usually use high-gain antennas and require the sensor to face the user's chest or back, making them difficult to integrate into a portable device and unsuitable for sleep and meditation tracking applications. This study presents a novel approach for noncontact HR detection using a miniaturized Soli radar chip embedded in a portable device (Google Nest Hub). The chip has a [Formula: see text] dimension and can be easily integrated into various devices. The proposed approach utilizes advanced signal processing and machine learning techniques to extract HRs from radar signals. The approach is validated on a sleep dataset (62 users, 498 h) and a meditation dataset (114 users, 1131 min). The approach achieves a mean absolute error (MAE) of 1.69 bpm and a mean absolute percentage error (MAPE) of [Formula: see text] on the sleep dataset. On the meditation dataset, the approach achieves an MAE of 1.05 bpm and a MAPE of [Formula: see text]. The recall rates for the two datasets are [Formula: see text] and [Formula: see text], respectively. This study represents the first application of the noncontact HR detection technology to sleep and meditation tracking, offering a promising alternative to wearable devices for HR monitoring during sleep and meditation.
MeSH term(s)	Humans ; Heart Rate/physiology ; Meditation ; Sleep ; Monitoring, Physiologic/methods ; Heart Rate Determination
Language	English
Publishing date	2023-10-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-44714-2
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Article: Variability of upper ocean thermohaline structure during a MJO event from DYNAMO aircraft observations

Alappattu, Denny P. / Wang, Qing / Kalogiros, John / Guy, Nick / Jorgensen, David P.

Journal of geophysical research. 2017 Feb., v. 122, no. 2

2017

Abstract: This paper reports upper ocean thermohaline structure and variability observed during the life cycle of an intense Madden Julian Oscillation (MJO) event occurred in the southern tropical Indian Ocean (14°S–Eq, 70°E–81°E). Water column measurements for ... ...

Abstract	This paper reports upper ocean thermohaline structure and variability observed during the life cycle of an intense Madden Julian Oscillation (MJO) event occurred in the southern tropical Indian Ocean (14°S–Eq, 70°E–81°E). Water column measurements for this study were collected using airborne expendable probes deployed from NOAA's WP‐3D Orion aircraft operated as a part of Dynamics of MJO field experiment conducted during November–December 2011. Purpose of the study is twofold; (1) to provide a statistical analysis of the upper ocean properties observed during different phases of MJO and, (2) to investigate how the upper ocean thermohaline structure evolved in the study region in response to the MJO induced perturbation. During the active phase of MJO, mixed layer depth (MLD) had a characteristic bimodal distribution. Primary and secondary modes were at ∼34 m and ∼65 m, respectively. Spatial heterogeneity of the upper ocean response to the MJO forcing was the plausible reason for bimodal distribution. Thermocline and isothermal layer depth deepened, respectively, by 13 and 19 m from the suppressed through the restoring phase of MJO. Thicker (>30 m) barrier layers were found to occur more frequently in the active phase of MJO, associated with convective rainfalls. Additionally, the water mass analysis indicated that, in the active phase of this MJO event the subsurface was dominated by Indonesian throughflow, nonetheless intrusion of Arabian Sea high saline water was also noted near the equator.
Keywords	aircraft ; field experimentation ; research ; saline water ; spatial variation ; statistical analysis ; Arabian Sea ; Indian Ocean
Language	English
Dates of publication	2017-02
Size	p. 1122-1140.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	161667-5
ISSN	2169-9291 ; 2169-9275 ; 0148-0227 ; 0196-2256
ISSN (online)	2169-9291
ISSN	2169-9275 ; 0148-0227 ; 0196-2256
DOI	10.1002/2016JC012137
Database	NAL-Catalogue (AGRICOLA)

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Book ; Online: Developing .NET web services with XML

Jorgensen, David

2002

Abstract: Prepare for the next generation of the internet with this in-depth, developer's guide to the .Net framework that utilizes XML to achieve greater flexibility of information and increased interoperability. Developing .Net Web Services with XML introduces ...

Institution	ebrary, Inc
Author's details	David Jorgensen
Abstract	"Prepare for the next generation of the internet with this in-depth, developer's guide to the .Net framework that utilizes XML to achieve greater flexibility of information and increased interoperability. Developing .Net Web Services with XML introduces readers to the foundation for the .Net platform. The book covers the history, applications and implementation of the Extensible Markup Language within Microsoft's .NET framework. Readers will be given a thorough introduction to .NET and its XML building blocks while acquiring a firm grasp of how those blocks can be used to build any Web site or service so that it will federate and collaborate seamlessly with others ?Equips developers with the tool necessary to take advantage of the next generation of the internet ?This book will provide web developers with a firm understanding of XML, the building block of the .Net framework ?Includes practical, real-life applications using XML ?Unrivalled web based support: Readers can receive up-to-the minute links, white papers and analysis for two years at solutions@syngress.com."
Keywords	Application software/Development ; Computer network architectures ; Internet programming ; Microsoft .NET Framework ; XML (Document markup language) ; Computer Informatik ; Computer Programmiersprachen
Language	English
Size	Online-Ressource (481 p)
Publisher	Syngress Publishing, Inc
Publishing place	Rockland, Mass
Document type	Book ; Online
Note	Includes index ; Title from title screen
ISBN	1928994814 ; 9780080477213 ; 9781928994817 ; 0080477216
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Article ; Online: Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions.

Ragonnet-Cronin, Manon / Boyd, Olivia / Geidelberg, Lily / Jorgensen, David / Nascimento, Fabricia F / Siveroni, Igor / Johnson, Robert A / Baguelin, Marc / Cucunubá, Zulma M / Jauneikaite, Elita / Mishra, Swapnil / Watson, Oliver J / Ferguson, Neil / Cori, Anne / Donnelly, Christl A / Volz, Erik

Nature communications

2021 Volume 12, Issue 1, Page(s) 2188

Abstract: Unprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but the effectiveness of non-pharmaceutical interventions is still debated. We carried out a phylogenetic ... ...

Abstract	Unprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but the effectiveness of non-pharmaceutical interventions is still debated. We carried out a phylogenetic analysis of more than 29,000 publicly available whole genome SARS-CoV-2 sequences from 57 locations to estimate the time that the epidemic originated in different places. These estimates were examined in relation to the dates of the most stringent interventions in each location as well as to the number of cumulative COVID-19 deaths and phylodynamic estimates of epidemic size. Here we report that the time elapsed between epidemic origin and maximum intervention is associated with different measures of epidemic severity and explains 11% of the variance in reported deaths one month after the most stringent intervention. Locations where strong non-pharmaceutical interventions were implemented earlier experienced much less severe COVID-19 morbidity and mortality during the period of study.
MeSH term(s)	COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/virology ; Communicable Disease Control/methods ; Epidemics ; Humans ; Phylogeny ; Phylogeography/methods ; Public Health/methods ; Public Health/statistics & numerical data ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; SARS-CoV-2/physiology ; Severity of Illness Index
Language	English
Publishing date	2021-04-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-22366-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Sensitive poliovirus detection using nested PCR and nanopore sequencing: a prospective validation study.

Shaw, Alexander G / Mampuela, Tresor Kabeya / Lofiko, Emmanuel Lokilo / Pratt, Catherine / Troman, Catherine / Bujaki, Erika / O'Toole, Áine / Akello, Joyce Odeke / Aziza, Adrienne Amuri / Lusamaki, Eddy Kinganda / Makangara, Jean Claude / Akonga, Marceline / Lay, Yvonne / Nsunda, Bibiche / White, Bailey / Jorgensen, David / Pukuta, Elizabeth / Riziki, Yogolelo / Rankin, Kathleen E /

Rambaut, Andrew / Ahuka-Mundeke, Steve / Muyembe, Jean-Jacques / Martin, Javier / Grassly, Nicholas C / Mbala-Kingebeni, Placide

Nature microbiology

2023 Volume 8, Issue 9, Page(s) 1634–1640

Abstract: Timely detection of outbreaks is needed for poliovirus eradication, but gold standard detection in the Democratic Republic of the Congo takes 30 days (median). Direct molecular detection and nanopore sequencing (DDNS) of poliovirus in stool samples is a ... ...

Abstract	Timely detection of outbreaks is needed for poliovirus eradication, but gold standard detection in the Democratic Republic of the Congo takes 30 days (median). Direct molecular detection and nanopore sequencing (DDNS) of poliovirus in stool samples is a promising fast method. Here we report prospective testing of stool samples from suspected polio cases, and their contacts, in the Democratic Republic of the Congo between 10 August 2021 and 4 February 2022. DDNS detected polioviruses in 62/2,339 (2.7%) of samples, while gold standard combination of cell culture, quantitative PCR and Sanger sequencing detected polioviruses in 51/2,339 (2.2%) of the same samples. DDNS provided case confirmation in 7 days (median) in routine surveillance conditions. DDNS enabled confirmation of three serotype 2 circulating vaccine-derived poliovirus outbreaks 23 days (mean) earlier (range 6-30 days) than the gold standard method. The mean sequence similarity between sequences obtained by the two methods was 99.98%. Our data confirm the feasibility of implementing DDNS in a national poliovirus laboratory.
MeSH term(s)	Poliovirus/genetics ; Nanopore Sequencing ; Polymerase Chain Reaction ; Dansyl Compounds
Chemical Substances	dimethylaminonaphthalene-5-sulfonaminoethylmethylamine (74686-82-1) ; Dansyl Compounds
Language	English
Publishing date	2023-08-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-023-01453-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Electrocardiographic Distinction of Left Circumflexand Right Coronary Artery Occlusion in PatientsWith Inferior Acute Myocardial Infarction.

Vives-Borrás, Miquel / Maestro, Alba / García-Hernando, Víctor / Jorgensen, David / Ferrero-Gregori, Andreu / Moustafa, Abdel-Hakim / Solé-González, Eduard / Noriega, Francisco J / Álvarez-García, Jesús / Cinca, Juan

The American journal of cardiology

2019 Volume 123, Issue 7, Page(s) 1019–1025

Abstract: Previously reported electrocardiographic (ECG) criteria to distinguish left circumflex (LCCA) and right coronary artery (RCA) occlusion in patients with acute inferior ST-segment elevation myocardial infarction (STEMI) afford a modest diagnostic accuracy. ...

Abstract	Previously reported electrocardiographic (ECG) criteria to distinguish left circumflex (LCCA) and right coronary artery (RCA) occlusion in patients with acute inferior ST-segment elevation myocardial infarction (STEMI) afford a modest diagnostic accuracy. We aimed to develop a new algorithm overcoming limitations of previous studies. Clinical, ECG, and coronary angiographic data were analyzed in 230 nonselected patients with acute inferior STEMI who underwent primary percutaneous coronary intervention. A decision-tree analysis was used to develop a new ECG algorithm. The diagnostic accuracy of reported ECG criteria was reviewed. LCCA occlusion occurred in 111 cases and RCA in 119. We developed a 3-step algorithm that identified LCCA and RCA occlusion with a sensitivity of 77%, specificity of 86%, accuracy of 82%, and Youden index of 0.63. The area under the ROC curve was 0.85 and resulted 0.82 after a 10-fold cross validation. The key leads for LCCA occlusion were V3 (ST depression in V3/ST elevation in III >1.2) and V6 (ST elevation ≥0.1 mV or greater than III). The key leads for RCA occlusion were I and aVL (ST depression ≥ 0.1 mV). Fifteen of 21 reviewed studies had less than 20 cases of LCCA occlusion, only 48% performed primary percutaneous coronary intervention, and previous infarction or multivessel disease were often excluded. The diagnostic accuracy of reported ECG criteria decreased when applied to our study population. In conclusion, we report a simple and highly discriminative 3-step ECG algorithm to differentiate LCCA and RCA occlusion in an "all comers" population of patients with acute inferior STEMI. The diagnostic key ECG leads were V3 and V6 for LCCA and I and aVL for RCA occlusion.
MeSH term(s)	Algorithms ; Case-Control Studies ; Coronary Angiography ; Coronary Occlusion/complications ; Coronary Occlusion/diagnosis ; Coronary Vessels/diagnostic imaging ; Electrocardiography/methods ; Female ; Follow-Up Studies ; Humans ; Inferior Wall Myocardial Infarction/diagnosis ; Inferior Wall Myocardial Infarction/etiology ; Male ; Middle Aged ; Reproducibility of Results ; Retrospective Studies ; ST Elevation Myocardial Infarction/diagnosis ; ST Elevation Myocardial Infarction/etiology
Language	English
Publishing date	2019-01-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80014-4
ISSN	1879-1913 ; 0002-9149
ISSN (online)	1879-1913
ISSN	0002-9149
DOI	10.1016/j.amjcard.2018.12.026
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Article: Genomic epidemiology of a densely sampled COVID-19 outbreak in China.

Virus evolution

2021 Volume 7, Issue 1, Page(s) veaa102

Abstract: Analysis of genetic sequence data from the SARS-CoV-2 pandemic can provide insights into epidemic origins, worldwide dispersal, and epidemiological history. With few exceptions, genomic epidemiological analysis has focused on geographically distributed ... ...

Abstract	Analysis of genetic sequence data from the SARS-CoV-2 pandemic can provide insights into epidemic origins, worldwide dispersal, and epidemiological history. With few exceptions, genomic epidemiological analysis has focused on geographically distributed data sets with few isolates in any given location. Here, we report an analysis of 20 whole SARS- CoV-2 genomes from a single relatively small and geographically constrained outbreak in Weifang, People's Republic of China. Using Bayesian model-based phylodynamic methods, we estimate a mean basic reproduction number (
Language	English
Publishing date	2021-03-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2818949-8
ISSN	2057-1577
ISSN	2057-1577
DOI	10.1093/ve/veaa102
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Article ; Online: SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load.

Mourier, Tobias / Shuaib, Muhammad / Hala, Sharif / Mfarrej, Sara / Alofi, Fadwa / Naeem, Raeece / Alsomali, Afrah / Jorgensen, David / Subudhi, Amit Kumar / Ben Rached, Fathia / Guan, Qingtian / Salunke, Rahul P / Ooi, Amanda / Esau, Luke / Douvropoulou, Olga / Nugmanova, Raushan / Perumal, Sadhasivam / Zhang, Huoming / Rajan, Issaac /

Al-Omari, Awad / Salih, Samer / Shamsan, Abbas / Al Mutair, Abbas / Taha, Jumana / Alahmadi, Abdulaziz / Khotani, Nashwa / Alhamss, Abdelrahman / Mahmoud, Ahmed / Alquthami, Khaled / Dageeg, Abdullah / Khogeer, Asim / Hashem, Anwar M / Moraga, Paula / Volz, Eric / Almontashiri, Naif / Pain, Arnab

Nature communications

2022 Volume 13, Issue 1, Page(s) 601

Abstract: Monitoring SARS-CoV-2 spread and evolution through genome sequencing is essential in handling the COVID-19 pandemic. Here, we sequenced 892 SARS-CoV-2 genomes collected from patients in Saudi Arabia from March to August 2020. We show that two consecutive ...

Abstract	Monitoring SARS-CoV-2 spread and evolution through genome sequencing is essential in handling the COVID-19 pandemic. Here, we sequenced 892 SARS-CoV-2 genomes collected from patients in Saudi Arabia from March to August 2020. We show that two consecutive mutations (R203K/G204R) in the nucleocapsid (N) protein are associated with higher viral loads in COVID-19 patients. Our comparative biochemical analysis reveals that the mutant N protein displays enhanced viral RNA binding and differential interaction with key host proteins. We found increased interaction of GSK3A kinase simultaneously with hyper-phosphorylation of the adjacent serine site (S206) in the mutant N protein. Furthermore, the host cell transcriptome analysis suggests that the mutant N protein produces dysregulated interferon response genes. Here, we provide crucial information in linking the R203K/G204R mutations in the N protein to modulations of host-virus interactions and underline the potential of the nucleocapsid protein as a drug target during infection.
MeSH term(s)	COVID-19/enzymology ; COVID-19/genetics ; COVID-19/virology ; Coronavirus Nucleocapsid Proteins/genetics ; Coronavirus Nucleocapsid Proteins/metabolism ; Genome, Viral ; Glycogen Synthase Kinase 3/genetics ; Glycogen Synthase Kinase 3/metabolism ; Host-Pathogen Interactions ; Humans ; Mutation, Missense ; Nucleocapsid/genetics ; Nucleocapsid/metabolism ; Phosphorylation ; Phylogeny ; Protein Binding ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; SARS-CoV-2/physiology ; Saudi Arabia ; Viral Load ; Virus Replication
Chemical Substances	Coronavirus Nucleocapsid Proteins ; Glycogen Synthase Kinase 3 (EC 2.7.11.26)
Language	English
Publishing date	2022-02-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-28287-8
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Article: Square not a running knot.

Aanning, Harald L / Haas, Tara / Jorgensen, David R / Wulf, Corey A

Journal of the American College of Surgeons

2007 Volume 204, Issue 3, Page(s) 422–425

Abstract: Background: The tensile strength of running monofilament polypropylene sutures anchored with square knots was compared with the strength of the same size sutures anchored with half hitches.: Study design: Polypropylene (Prolene; Ethicon) 0, 2-0, 3-0, ...

Abstract	Background: The tensile strength of running monofilament polypropylene sutures anchored with square knots was compared with the strength of the same size sutures anchored with half hitches. Study design: Polypropylene (Prolene; Ethicon) 0, 2-0, 3-0, 4-0, and 5-0 sutures were secured to a tensionometer with either square knots or half hitches. As tension was applied to the running suture end, the force required to break the suture and the point at which the break occurred were recorded. Results: The sutures anchored with square knots showed only 75% of the strength of the sutures secured with half hitches (p=<0.001). Every suture tied with square knots broke precisely at the point where the last two squared throws invariably tumbled into half hitches with increased tension on the running end. The resulting stress transformation distorted and weakened the suture, as documented by electron microscopy scanning. The sutures secured with half hitches did not show any surface defects, and none of the running sutures tied down with half hitches broke at the knots. Conclusions: A running polypropylene suture initially anchored with half hitches is stronger and safer than a running suture tied down with square knots.
MeSH term(s)	Humans ; In Vitro Techniques ; Microscopy, Electron ; Polypropylenes/chemistry ; Polypropylenes/standards ; Surface Properties ; Suture Techniques/instrumentation ; Suture Techniques/standards ; Tensile Strength
Chemical Substances	Polypropylenes
Language	English
Publishing date	2007-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	1181115-8
ISSN	1879-1190 ; 1072-7515
ISSN (online)	1879-1190
ISSN	1072-7515
DOI	10.1016/j.jamcollsurg.2006.12.024
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