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Article ; Online: A novel benchmark for COVID-19 pandemic testing effectiveness enables the accurate prediction of new Intensive Care Unit admissions.

Nikoloudis, Dimitris / Kountouras, Dimitrios / Hiona, Asimina

2021 Volume 11, Issue 1, Page(s) 20308

Abstract: The positivity rate of testing is currently used both as a benchmark of testing adequacy and for assessing the evolution of the COVID-19 pandemic. However, since the former is a prerequisite for the latter, its interpretation is often conflicting. We ... ...

Abstract	The positivity rate of testing is currently used both as a benchmark of testing adequacy and for assessing the evolution of the COVID-19 pandemic. However, since the former is a prerequisite for the latter, its interpretation is often conflicting. We propose as a benchmark for COVID-19 testing effectiveness a new metric, termed 'Severity Detection Rate' (SDR), that represents the daily needs for new Intensive Care Unit (ICU) admissions, per 100 cases detected (t - i) days ago, per 10,000 tests performed (t - i) days ago. Based on the announced COVID-19 monitoring data in Greece from May 2020 until August 2021, we show that beyond a certain threshold of daily tests, SDR reaches a plateau of very low variability that begins to reflect testing adequacy. Due to the stabilization of SDR, it was possible to predict with great accuracy the daily needs for new ICU admissions, 12 days ahead of each testing data point, over a period of 10 months, with Pearson r = 0.98 (p = 10
MeSH term(s)	Benchmarking/methods ; COVID-19/epidemiology ; COVID-19/immunology ; COVID-19/metabolism ; COVID-19 Testing/methods ; COVID-19 Testing/trends ; Greece/epidemiology ; Humans ; Intensive Care Units/trends ; Models, Theoretical ; Pandemics/prevention & control ; Patient Admission/trends ; SARS-CoV-2/immunology ; SARS-CoV-2/pathogenicity
Language	English
Publishing date	2021-10-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-99543-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The frequency of combined IFITM3 haplotype involving the reference alleles of both rs12252 and rs34481144 is in line with COVID-19 standardized mortality ratio of ethnic groups in England.

Nikoloudis, Dimitris / Kountouras, Dimitrios / Hiona, Asimina

PeerJ

2020 Volume 8, Page(s) e10402

Abstract: Evidence was brought forward in England and the USA that Black, Asian, Latino and Minority Ethnic people exhibit higher mortality risk from COVID-19 than White people. While socioeconomic factors were suggested to contribute to this trend, they arguably ... ...

Abstract	Evidence was brought forward in England and the USA that Black, Asian, Latino and Minority Ethnic people exhibit higher mortality risk from COVID-19 than White people. While socioeconomic factors were suggested to contribute to this trend, they arguably do not explain the range of the differences observed, allowing for possible genetic implications. Almost concurrently, the analysis of a cohort in Chinese COVID-19 patients proposed an association between the severity of the disease and the presence of the minor allele of rs12252 of the Interferon-induced transmembrane protein 3 (IFITM3) gene. This SNP, together with rs34481144, are the two most studied polymorphisms of IFITM3 and have been associated in the past with increased severity in Influenza, Dengue, Ebola, and HIV viruses. IFITM3 is an immune effector protein that is pivotal for the restriction of viral replication, but also for the regulation of cytokine production. Following up on these two developments in the ongoing SARS-CoV-2 pandemic, the present study investigates a possible association between the differences in mortality of ethnic groups in England and the combined haplotypes of rs12252 and rs34481144. The respective allele frequencies were collected for 26 populations from the 1000 Genomes Project and subgroups were pooled wherever possible to create correspondences with ethnic groups in England. A significant correlation (
Language	English
Publishing date	2020-11-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.10402
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Article ; Online: The frequency of combined IFITM3 haplotype involving the reference alleles of both rs12252 and rs34481144 is in line with COVID-19 standardized mortality ratio of ethnic groups in England

Dimitris Nikoloudis / Dimitrios Kountouras / Asimina Hiona

PeerJ, Vol 8, p e

2020 Volume 10402

Abstract	Evidence was brought forward in England and the USA that Black, Asian, Latino and Minority Ethnic people exhibit higher mortality risk from COVID-19 than White people. While socioeconomic factors were suggested to contribute to this trend, they arguably do not explain the range of the differences observed, allowing for possible genetic implications. Almost concurrently, the analysis of a cohort in Chinese COVID-19 patients proposed an association between the severity of the disease and the presence of the minor allele of rs12252 of the Interferon-induced transmembrane protein 3 (IFITM3) gene. This SNP, together with rs34481144, are the two most studied polymorphisms of IFITM3 and have been associated in the past with increased severity in Influenza, Dengue, Ebola, and HIV viruses. IFITM3 is an immune effector protein that is pivotal for the restriction of viral replication, but also for the regulation of cytokine production. Following up on these two developments in the ongoing SARS-CoV-2 pandemic, the present study investigates a possible association between the differences in mortality of ethnic groups in England and the combined haplotypes of rs12252 and rs34481144. The respective allele frequencies were collected for 26 populations from the 1000 Genomes Project and subgroups were pooled wherever possible to create correspondences with ethnic groups in England. A significant correlation (r = 0.9687, p = 0.0003) and a striking agreement was observed between the reported Standardized Mortality Ratios and the frequency of the combined haplotype of both reference alleles, suggesting that the combination of the reference alleles of the specific SNPs may be implicated in more severe outcomes of COVID-19. This study calls for further focus on the role of IFITM3 variants in the mechanism of cellular invasion of SARS-CoV-2, their impact in COVID-19 severity and their possible implications in vaccination efficacy.
Keywords	COVID-19 ; SARS-CoV-2 ; Pandemic ; IFITM3 ; rs12252 ; rs34481144 ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	390
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: An efficient benchmark for COVID-19 pandemic testing effectiveness

Nikoloudis, Dimitris / Kountouras, Dimitrios / Hiona, Asimina

medRxiv

Abstract: Testing for COVID-19 is an important tool that health administrations dispose to adequately monitor and respond to the pandemic, but it is still unclear at which point the number and strategies of testing become effective for these purposes. The ... ...

Abstract	Testing for COVID-19 is an important tool that health administrations dispose to adequately monitor and respond to the pandemic, but it is still unclear at which point the number and strategies of testing become effective for these purposes. The percentage of tests that return a positive result is a metric currently used both as a benchmark of testing adequacy and for assessing the viral spread. However, since the former is a prerequisite for the latter, the interpretation is often conflicting, especially during times of testing scaling-up, or during phases of increasing viral spread. We propose as a benchmark for COVID-19 testing effectiveness a simple metric that creates a link between the cases detected and tests performed, with specific observable outcomes that are actively being monitored in most countries, such as the number of new Intensive Care Unit (ICU) admissions and the number of deaths in the community. This new metric, named "Severity Detection Rate", or SDR, represents the current number of daily needs for new ICU admissions, per 100 cases detected (t-i) days ago, per 10,000 tests performed (t-i) days ago. Based on the announced COVID-19 monitoring data in Greece from May 2020 until end of January 2021, we show that beyond a threshold of daily testing number, SDR reaches a plateau of weak variability that begins to reflect testing adequacy. Because of this stabilization, it was possible to predict with great accuracy the daily needs for new ICU admissions, 12 days ahead of each testing data point, over a period of 6 months that included the second wave of the pandemic in the country, with Pearson r = 0.99 (p = 10^-180), RMSE = 4,34. We suggest the further study of the metric with data from more countries in order to confirm the proposed functionality and utility.
Keywords	covid19
Language	English
Publishing date	2021-02-23
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.02.20.21252138
Database	COVID19

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Article: A complete, multi-level conformational clustering of antibody complementarity-determining regions.

Nikoloudis, Dimitris / Pitts, Jim E / Saldanha, José W

PeerJ

2014 Volume 2, Page(s) e456

Abstract: Classification of antibody complementarity-determining region (CDR) conformations is an important step that drives antibody modelling and engineering, prediction from sequence, directed mutagenesis and induced-fit studies, and allows inferences on ... ...

Abstract	Classification of antibody complementarity-determining region (CDR) conformations is an important step that drives antibody modelling and engineering, prediction from sequence, directed mutagenesis and induced-fit studies, and allows inferences on sequence-to-structure relations. Most of the previous work performed conformational clustering on a reduced set of structures or after application of various structure pre-filtering criteria. In this study, it was judged that a clustering of every available CDR conformation would produce a complete and redundant repertoire, increase the number of sequence examples and allow better decisions on structure validity in the future. In order to cope with the potential increase in data noise, a first-level statistical clustering was performed using structure superposition Root-Mean-Square Deviation (RMSD) as a distance-criterion, coupled with second- and third-level clustering that employed Ramachandran regions for a deeper qualitative classification. The classification of a total of 12,712 CDR conformations is thus presented, along with rich annotation and cluster descriptions, and the results are compared to previous major studies. The present repertoire has procured an improved image of our current CDR Knowledge-Base, with a novel nesting of conformational sensitivity and specificity that can serve as a systematic framework for improved prediction from sequence as well as a number of future studies that would aid in knowledge-based antibody engineering such as humanisation.
Language	English
Publishing date	2014-07-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.456
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Article: Disjoint combinations profiling (DCP): a new method for the prediction of antibody CDR conformation from sequence.

Nikoloudis, Dimitris / Pitts, Jim E / Saldanha, José W

PeerJ

2014 Volume 2, Page(s) e455

Abstract: The accurate prediction of the conformation of Complementarity-Determining Regions (CDRs) is important in modelling antibodies for protein engineering applications. Specifically, the Canonical paradigm has proved successful in predicting the CDR ... ...

Abstract	The accurate prediction of the conformation of Complementarity-Determining Regions (CDRs) is important in modelling antibodies for protein engineering applications. Specifically, the Canonical paradigm has proved successful in predicting the CDR conformation in antibody variable regions. It relies on canonical templates which detail allowed residues at key positions in the variable region framework or in the CDR itself for 5 of the 6 CDRs. While no templates have as yet been defined for the hypervariable CDR-H3, instead, reliable sequence rules have been devised for predicting the base of the CDR-H3 loop. Here a new method termed Disjoint Combinations Profiling (DCP) is presented, which contributes a considerable advance in the prediction of CDR conformations. This novel method is explained and compared with canonical templates and sequence rules in a 3-way blind prediction. DCP achieved 93% accuracy over 951 blind predictions and showed an improvement in cumulative accuracy compared to predictions with canonical templates or sequence rules. In addition to its overall improvement in prediction accuracy, it is suggested that DCP is open to better implementations in the future and that it can improve as more antibody structures are deposited in the databank. In contrast, it is argued that canonical templates and sequence rules may have reached their peak.
Language	English
Publishing date	2014-07-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.455
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Article ; Online: Disjoint combinations profiling (DCP)

Dimitris Nikoloudis / Jim E. Pitts / José W. Saldanha

PeerJ, Vol 2, p e

a new method for the prediction of antibody CDR conformation from sequence

2014 Volume 455

Abstract	The accurate prediction of the conformation of Complementarity-Determining Regions (CDRs) is important in modelling antibodies for protein engineering applications. Specifically, the Canonical paradigm has proved successful in predicting the CDR conformation in antibody variable regions. It relies on canonical templates which detail allowed residues at key positions in the variable region framework or in the CDR itself for 5 of the 6 CDRs. While no templates have as yet been defined for the hypervariable CDR-H3, instead, reliable sequence rules have been devised for predicting the base of the CDR-H3 loop. Here a new method termed Disjoint Combinations Profiling (DCP) is presented, which contributes a considerable advance in the prediction of CDR conformations. This novel method is explained and compared with canonical templates and sequence rules in a 3-way blind prediction. DCP achieved 93% accuracy over 951 blind predictions and showed an improvement in cumulative accuracy compared to predictions with canonical templates or sequence rules. In addition to its overall improvement in prediction accuracy, it is suggested that DCP is open to better implementations in the future and that it can improve as more antibody structures are deposited in the databank. In contrast, it is argued that canonical templates and sequence rules may have reached their peak.
Keywords	Conformational prediction ; CDR conformation ; Blind test ; Canonical templates ; CDR-H3 sequence rules ; DCP ; Medicine ; R
Subject code	006
Language	English
Publishing date	2014-07-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A complete, multi-level conformational clustering of antibody complementarity-determining regions

Dimitris Nikoloudis / Jim E. Pitts / José W. Saldanha

PeerJ, Vol 2, p e

2014 Volume 456

Abstract	Classification of antibody complementarity-determining region (CDR) conformations is an important step that drives antibody modelling and engineering, prediction from sequence, directed mutagenesis and induced-fit studies, and allows inferences on sequence-to-structure relations. Most of the previous work performed conformational clustering on a reduced set of structures or after application of various structure pre-filtering criteria. In this study, it was judged that a clustering of every available CDR conformation would produce a complete and redundant repertoire, increase the number of sequence examples and allow better decisions on structure validity in the future. In order to cope with the potential increase in data noise, a first-level statistical clustering was performed using structure superposition Root-Mean-Square Deviation (RMSD) as a distance-criterion, coupled with second- and third-level clustering that employed Ramachandran regions for a deeper qualitative classification. The classification of a total of 12,712 CDR conformations is thus presented, along with rich annotation and cluster descriptions, and the results are compared to previous major studies. The present repertoire has procured an improved image of our current CDR Knowledge-Base, with a novel nesting of conformational sensitivity and specificity that can serve as a systematic framework for improved prediction from sequence as well as a number of future studies that would aid in knowledge-based antibody engineering such as humanisation.
Keywords	Antibody structure ; Canonical model ; CDR conformation ; Dynamic hybrid tree-cut ; Humanisation ; Clustering ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	006
Language	English
Publishing date	2014-07-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Clinical validation of cutoff target ranges in newborn screening of metabolic disorders by tandem mass spectrometry: a worldwide collaborative project.

McHugh, David M S / Cameron, Cynthia A / Abdenur, Jose E / Abdulrahman, Mahera / Adair, Ona / Al Nuaimi, Shahira Ahmed / Åhlman, Henrik / Allen, Jennifer J / Antonozzi, Italo / Archer, Shaina / Au, Sylvia / Auray-Blais, Christiane / Baker, Mei / Bamforth, Fiona / Beckmann, Kinga / Pino, Gessi Bentz / Berberich, Stanton L / Binard, Robert / Boemer, François /

Bonham, Jim / Breen, Nancy N / Bryant, Sandra C / Caggana, Michele / Caldwell, S Graham / Camilot, Marta / Campbell, Carlene / Carducci, Claudia / Cariappa, Rohit / Carlisle, Clover / Caruso, Ubaldo / Cassanello, Michela / Castilla, Ane Miren / Ramos, Daisy E Castiñeiras / Chakraborty, Pranesh / Chandrasekar, Ram / Ramos, Alfredo Chardon / Cheillan, David / Chien, Yin-Hsiu / Childs, Thomas A / Chrastina, Petr / Sica, Yuri Cleverthon / de Juan, Jose Angel Cocho / Colandre, Maria Elena / Espinoza, Veronica Cornejo / Corso, Gaetano / Currier, Robert / Cyr, Denis / Czuczy, Noemi / D'Apolito, Oceania / Davis, Tim / de Sain-Van der Velden, Monique G / Delgado Pecellin, Carmen / Di Gangi, Iole Maria / Di Stefano, Cristina Maria / Dotsikas, Yannis / Downing, Melanie / Downs, Stephen M / Dy, Bonifacio / Dymerski, Mark / Rueda, Inmaculada / Elvers, Bert / Eaton, Roger / Eckerd, Barbara M / El Mougy, Fatma / Eroh, Sarah / Espada, Mercedes / Evans, Catherine / Fawbush, Sandy / Fijolek, Kristel F / Fisher, Lawrence / Franzson, Leifur / Frazier, Dianne M / Garcia, Luciana R C / Bermejo, Maria Sierra García-Valdecasas / Gavrilov, Dimitar / Gerace, Rosemarie / Giordano, Giuseppe / Irazabal, Yolanda González / Greed, Lawrence C / Grier, Robert / Grycki, Elyse / Gu, Xuefan / Gulamali-Majid, Fizza / Hagar, Arthur F / Han, Lianshu / Hannon, W Harry / Haslip, Christa / Hassan, Fayza Abdelhamid / He, Miao / Hietala, Amy / Himstedt, Leslie / Hoffman, Gary L / Hoffman, William / Hoggatt, Philis / Hopkins, Patrick V / Hougaard, David M / Hughes, Kerie / Hunt, Patricia R / Hwu, Wuh-Liang / Hynes, June / Ibarra-González, Isabel / Ingham, Cindy A / Ivanova, Maria / Jacox, Ward B / John, Catharine / Johnson, John P / Jónsson, Jón J / Karg, Eszter / Kasper, David / Klopper, Brenda / Katakouzinos, Dimitris / Khneisser, Issam / Knoll, Detlef / Kobayashi, Hirinori / Koneski, Ronald / Kozich, Viktor / Kouapei, Rasoul / Kohlmueller, Dirk / Kremensky, Ivo / la Marca, Giancarlo / Lavochkin, Marcia / Lee, Soo-Youn / Lehotay, Denis C / Lemes, Aida / Lepage, Joyce / Lesko, Barbara / Lewis, Barry / Lim, Carol / Linard, Sharon / Lindner, Martin / Lloyd-Puryear, Michele A / Lorey, Fred / Loukas, Yannis L / Luedtke, Julie / Maffitt, Neil / Magee, J Fergall / Manning, Adrienne / Manos, Shawn / Marie, Sandrine / Hadachi, Sônia Marchezi / Marquardt, Gregg / Martin, Stephen J / Matern, Dietrich / Mayfield Gibson, Stephanie K / Mayne, Philip / McCallister, Tonya D / McCann, Mark / McClure, Julie / McGill, James J / McKeever, Christine D / McNeilly, Barbara / Morrissey, Mark A / Moutsatsou, Paraskevi / Mulcahy, Eleanor A / Nikoloudis, Dimitris / Norgaard-Pedersen, Bent / Oglesbee, Devin / Oltarzewski, Mariusz / Ombrone, Daniela / Ojodu, Jelili / Papakonstantinou, Vagelis / Reoyo, Sherly Pardo / Park, Hyung-Doo / Pasquali, Marzia / Pasquini, Elisabetta / Patel, Pallavi / Pass, Kenneth A / Peterson, Colleen / Pettersen, Rolf D / Pitt, James J / Poh, Sherry / Pollak, Arnold / Porter, Cory / Poston, Philip A / Price, Ricky W / Queijo, Cecilia / Quesada, Jonessy / Randell, Edward / Ranieri, Enzo / Raymond, Kimiyo / Reddic, John E / Reuben, Alejandra / Ricciardi, Charla / Rinaldo, Piero / Rivera, Jeff D / Roberts, Alicia / Rocha, Hugo / Roche, Geraldine / Greenberg, Cheryl Rochman / Mellado, José María Egea / Juan-Fita, María Jesús / Ruiz, Consuelo / Ruoppolo, Margherita / Rutledge, S Lane / Ryu, Euijung / Saban, Christine / Sahai, Inderneel / García-Blanco, Maria Isabel Salazar / Santiago-Borrero, Pedro / Schenone, Andrea / Schoos, Roland / Schweitzer, Barb / Scott, Patricia / Seashore, Margretta R / Seeterlin, Mary A / Sesser, David E / Sevier, Darrin W / Shone, Scott M / Sinclair, Graham / Skrinska, Victor A / Stanley, Eleanor L / Strovel, Erin T / Jones, April L Studinski / Sunny, Sherlykutty / Takats, Zoltan / Tanyalcin, Tijen / Teofoli, Francesca / Thompson, J Robert / Tomashitis, Kathy / Domingos, Mouseline Torquado / Torres, Jasmin / Torres, Rosario / Tortorelli, Silvia / Turi, Sandor / Turner, Kimberley / Tzanakos, Nick / Valiente, Alf G / Vallance, Hillary / Vela-Amieva, Marcela / Vilarinho, Laura / von Döbeln, Ulrika / Vincent, Marie-Francoise / Vorster, B Chris / Watson, Michael S / Webster, Dianne / Weiss, Sheila / Wilcken, Bridget / Wiley, Veronica / Williams, Sharon K / Willis, Sharon A / Woontner, Michael / Wright, Katherine / Yahyaoui, Raquel / Yamaguchi, Seiji / Yssel, Melissa / Zakowicz, Wendy M

Genetics in medicine : official journal of the American College of Medical Genetics

2011 Volume 13, Issue 3, Page(s) 230–254

Abstract: Purpose: To achieve clinical validation of cutoff values for newborn screening by tandem mass spectrometry through a worldwide collaborative effort.: Methods: Cumulative percentiles of amino acids and acylcarnitines in dried blood spots of ... ...

Abstract	Purpose: To achieve clinical validation of cutoff values for newborn screening by tandem mass spectrometry through a worldwide collaborative effort. Methods: Cumulative percentiles of amino acids and acylcarnitines in dried blood spots of approximately 25–30 million normal newborns and 10,742 deidentified true positive cases are compared to assign clinical significance, which is achieved when the median of a disorder range is, and usually markedly outside, either the 99th or the 1st percentile of the normal population. The cutoff target ranges of analytes and ratios are then defined as the interval between selected percentiles of the two populations. When overlaps occur, adjustments are made to maximize sensitivity and specificity taking all available factors into consideration. Results: As of December 1, 2010, 130 sites in 45 countries have uploaded a total of 25,114 percentile data points, 565,232 analyte results of true positive cases with 64 conditions, and 5,341 cutoff values. The average rate of submission of true positive cases between December 1, 2008, and December 1, 2010, was 5.1 cases/day. This cumulative evidence generated 91 high and 23 low cutoff target ranges. The overall proportion of cutoff values within the respective target range was 42% (2,269/5,341). Conclusion: An unprecedented level of cooperation and collaboration has allowed the objective definition of cutoff target ranges for 114 markers to be applied to newborn screening of rare metabolic disorders.
MeSH term(s)	Amino Acids/blood ; Carnitine/analogs & derivatives ; Carnitine/blood ; Humans ; Infant, Newborn ; International Cooperation ; Metabolic Diseases/diagnosis ; Neonatal Screening ; Reference Values ; Sensitivity and Specificity ; Software ; Tandem Mass Spectrometry
Chemical Substances	Amino Acids ; acylcarnitine ; Carnitine (S7UI8SM58A)
Language	English
Publishing date	2011-02-08
Publishing country	United States
Document type	Journal Article ; Multicenter Study ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S. ; Validation Study
ZDB-ID	1455352-1
ISSN	1530-0366 ; 1098-3600
ISSN (online)	1530-0366
ISSN	1098-3600
DOI	10.1097/GIM.0b013e31820d5e67
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