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Article: A new universal system of tree shape indices.

Noble, Robert / Verity, Kimberley

bioRxiv : the preprint server for biology

2023

Abstract: The comparison and categorization of tree diagrams is fundamental to large parts of biology, linguistics, computer science, and other fields, yet the indices currently applied to describing tree shape have important flaws that complicate their ... ...

Abstract	The comparison and categorization of tree diagrams is fundamental to large parts of biology, linguistics, computer science, and other fields, yet the indices currently applied to describing tree shape have important flaws that complicate their interpretation and limit their scope. Here we introduce a new system of indices with no such shortcomings. Our indices account for node sizes and branch lengths and are robust to small changes in either attribute. Unlike currently popular phylogenetic diversity, phylogenetic entropy, and tree balance indices, our definitions assign interpretable values to all rooted trees and enable meaningful comparison of any pair of trees. Our self-consistent definitions further unite measures of diversity, richness, balance, symmetry, effective height, effective outdegree, and effective branch count in a coherent system, and we derive numerous simple relationships between these indices. The main practical advantages of our indices are in 1) quantifying diversity in non-ultrametric trees; 2) assessing the balance of trees that have non-uniform branch lengths or node sizes; 3) comparing the balance of trees with different leaf counts or outdegrees; 4) obtaining a coherent, generic, multidimensional quantification of tree shape that is robust to sampling error and inferential error. We illustrate these features by comparing the shapes of trees representing the evolution of HIV and of Uralic languages, and trees generated by computational models of tumour evolution. Given the ubiquity of tree structures, we identify a wide range of applications across diverse domains.
Language	English
Publishing date	2023-11-27
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.07.17.549219
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Article ; Online: Sampling for malaria molecular surveillance.

Mayor, Alfredo / Ishengoma, Deus S / Proctor, Joshua L / Verity, Robert

Trends in parasitology

2023 Volume 39, Issue 11, Page(s) 954–968

Abstract: Strategic use of Plasmodium falciparum genetic variation has great potential to inform public health actions for malaria control and elimination. Malaria molecular surveillance (MMS) begins with a strategy to identify and collect parasite samples, guided ...

Abstract	Strategic use of Plasmodium falciparum genetic variation has great potential to inform public health actions for malaria control and elimination. Malaria molecular surveillance (MMS) begins with a strategy to identify and collect parasite samples, guided by public-health priorities. In this review we discuss sampling design practices for MMS and point out epidemiological, biological, and statistical factors that need to be considered. We present examples for different use cases, including detecting emergence and spread of rare variants, establishing transmission sources and inferring changes in malaria transmission intensity. This review will potentially guide the collection of samples and data, serve as a starting point for further methodological innovation, and enhance utilization of MMS to support malaria elimination.
MeSH term(s)	Humans ; Antimalarials/pharmacology ; Drug Resistance ; Malaria ; Plasmodium falciparum/genetics ; Malaria, Falciparum/epidemiology ; Malaria, Falciparum/prevention & control ; Malaria, Falciparum/drug therapy
Chemical Substances	Antimalarials
Language	English
Publishing date	2023-09-19
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2036227-4
ISSN	1471-5007 ; 1471-4922
ISSN (online)	1471-5007
ISSN	1471-4922
DOI	10.1016/j.pt.2023.08.007
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Article ; Online: coiaf: Directly estimating complexity of infection with allele frequencies.

Paschalidis, Aris / Watson, Oliver J / Aydemir, Ozkan / Verity, Robert / Bailey, Jeffrey A

PLoS computational biology

2023 Volume 19, Issue 6, Page(s) e1010247

Abstract: In malaria, individuals are often infected with different parasite strains. The complexity of infection (COI) is defined as the number of genetically distinct parasite strains in an individual. Changes in the mean COI in a population have been shown to ... ...

Abstract	In malaria, individuals are often infected with different parasite strains. The complexity of infection (COI) is defined as the number of genetically distinct parasite strains in an individual. Changes in the mean COI in a population have been shown to be informative of changes in transmission intensity with a number of probabilistic likelihood and Bayesian models now developed to estimate the COI. However, rapid, direct measures based on heterozygosity or FwS do not properly represent the COI. In this work, we present two new methods that use easily calculated measures to directly estimate the COI from allele frequency data. Using a simulation framework, we show that our methods are computationally efficient and comparably accurate to current approaches in the literature. Through a sensitivity analysis, we characterize how the distribution of parasite densities, the assumed sequencing depth, and the number of sampled loci impact the bias and accuracy of our two methods. Using our developed methods, we further estimate the COI globally from Plasmodium falciparum sequencing data and compare the results against the literature. We show significant differences in the estimated COI globally between continents and a weak relationship between malaria prevalence and COI.
MeSH term(s)	Humans ; Malaria, Falciparum/epidemiology ; Malaria, Falciparum/genetics ; Malaria, Falciparum/parasitology ; Bayes Theorem ; Plasmodium falciparum/genetics ; Gene Frequency/genetics ; Malaria/parasitology
Language	English
Publishing date	2023-06-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1010247
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Article ; Online: Demonstrating core molecular biology principles using GST-GFP in a semester-long laboratory course.

Verity, Nicole / Ulm, Brittany / Pham, Katrina / Evangelista, Baggio / Borgon, Robert

Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology

2021 Volume 50, Issue 1, Page(s) 55–64

Abstract: Undergraduate laboratory courses are essential to teaching core principles in STEM. This course, Quantitative Biological Methods, provides a unique approach to teaching molecular biology research techniques to students, in a laboratory that is delivered ... ...

Abstract	Undergraduate laboratory courses are essential to teaching core principles in STEM. This course, Quantitative Biological Methods, provides a unique approach to teaching molecular biology research techniques to students, in a laboratory that is delivered in a sequence that parallels standard biomedical research laboratory protocols. Students attend a lecture where they are taught the essential principles of biomedical research, and a lab where they learn to use laboratory equipment, perform experiments, and purify and quantify DNA and proteins. The course begins with an introduction to laboratory safety, pipetting, centrifugation, spectrophotometry, and other basic laboratory techniques. Next, the lab focuses on the purification and analysis of glutathione S-transferase (GST) fused to green fluorescent protein (GFP) from an Escherichia coli lysate. Students study this GST-GFP fusion protein and perform protein quantification, enzyme assays, chromatography, fluorescent detection, normalization, SDS-PAGE, and western blotting. Students then learn recombinant DNA technology using the GST-GFP vector that was the source of the fusion protein in the prior labs, and perform ligation, transformation of E. coli cells, blue/white screening, DNA purification via a miniprep, PCR, DNA quantification, restriction enzyme digestion, and agarose gel electrophoresis. Students write laboratory reports to demonstrate an understanding of the principles of the laboratory methods, and they must present and critically analyze their data. The lab methods described herein aim to emphasize the core molecular biology principles and techniques, prepare students for work in a biomedical research laboratory, and introduce students to both GST and GFP, two versatile laboratory proteins.
MeSH term(s)	Curriculum ; DNA ; Escherichia coli/genetics ; Glutathione Transferase/genetics ; Green Fluorescent Proteins/chemistry ; Green Fluorescent Proteins/genetics ; Humans ; Molecular Biology/education
Chemical Substances	Green Fluorescent Proteins (147336-22-9) ; DNA (9007-49-2) ; Glutathione Transferase (EC 2.5.1.18)
Language	English
Publishing date	2021-10-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2039717-3
ISSN	1539-3429 ; 1470-8175
ISSN (online)	1539-3429
ISSN	1470-8175
DOI	10.1002/bmb.21585
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Article ; Online: coiaf

Aris Paschalidis / Oliver J Watson / Ozkan Aydemir / Robert Verity / Jeffrey A Bailey

PLoS Computational Biology, Vol 19, Iss 6, p e

Directly estimating complexity of infection with allele frequencies.

2023 Volume 1010247

Abstract	In malaria, individuals are often infected with different parasite strains. The complexity of infection (COI) is defined as the number of genetically distinct parasite strains in an individual. Changes in the mean COI in a population have been shown to be informative of changes in transmission intensity with a number of probabilistic likelihood and Bayesian models now developed to estimate the COI. However, rapid, direct measures based on heterozygosity or FwS do not properly represent the COI. In this work, we present two new methods that use easily calculated measures to directly estimate the COI from allele frequency data. Using a simulation framework, we show that our methods are computationally efficient and comparably accurate to current approaches in the literature. Through a sensitivity analysis, we characterize how the distribution of parasite densities, the assumed sequencing depth, and the number of sampled loci impact the bias and accuracy of our two methods. Using our developed methods, we further estimate the COI globally from Plasmodium falciparum sequencing data and compare the results against the literature. We show significant differences in the estimated COI globally between continents and a weak relationship between malaria prevalence and COI.
Keywords	Biology (General) ; QH301-705.5
Subject code	310
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
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Article ; Online: Estimating the Number of Subpopulations (K) in Structured Populations.

Verity, Robert / Nichols, Richard A

Genetics

2016 Volume 203, Issue 4, Page(s) 1827–1839

Abstract: A key quantity in the analysis of structured populations is the parameter K, which describes the number of subpopulations that make up the total population. Inference of K ideally proceeds via the model evidence, which is equivalent to the likelihood of ... ...

Abstract	A key quantity in the analysis of structured populations is the parameter K, which describes the number of subpopulations that make up the total population. Inference of K ideally proceeds via the model evidence, which is equivalent to the likelihood of the model. However, the evidence in favor of a particular value of K cannot usually be computed exactly, and instead programs such as Structure make use of heuristic estimators to approximate this quantity. We show-using simulated data sets small enough that the true evidence can be computed exactly-that these heuristics often fail to estimate the true evidence and that this can lead to incorrect conclusions about K Our proposed solution is to use thermodynamic integration (TI) to estimate the model evidence. After outlining the TI methodology we demonstrate the effectiveness of this approach, using a range of simulated data sets. We find that TI can be used to obtain estimates of the model evidence that are more accurate and precise than those based on heuristics. Furthermore, estimates of K based on these values are found to be more reliable than those based on a suite of model comparison statistics. Finally, we test our solution in a reanalysis of a white-footed mouse data set. The TI methodology is implemented for models both with and without admixture in the software MavericK1.0.
MeSH term(s)	Animals ; Computer Simulation ; Genetics, Population ; Mice ; Models, Statistical ; Pigments, Biological/genetics ; Probability ; Software
Chemical Substances	Pigments, Biological
Language	English
Publishing date	2016-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.115.180992
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Article ; Online: Reassessing Reported Deaths and Estimated Infection Attack Rate during the First 6 Months of the COVID-19 Epidemic, Delhi, India.

Pons-Salort, Margarita / John, Jacob / Watson, Oliver J / Brazeau, Nicholas F / Verity, Robert / Kang, Gagandeep / Grassly, Nicholas C

Emerging infectious diseases

2022 Volume 28, Issue 4, Page(s) 759–766

Abstract: India reported >10 million coronavirus disease (COVID-19) cases and 149,000 deaths in 2020. To reassess reported deaths and estimate incidence rates during the first 6 months of the epidemic, we used a severe acute respiratory syndrome coronavirus 2 ... ...

Abstract	India reported >10 million coronavirus disease (COVID-19) cases and 149,000 deaths in 2020. To reassess reported deaths and estimate incidence rates during the first 6 months of the epidemic, we used a severe acute respiratory syndrome coronavirus 2 transmission model fit to data from 3 serosurveys in Delhi and time-series documentation of reported deaths. We estimated 48.7% (95% credible interval 22.1%-76.8%) cumulative infection in the population through the end of September 2020. Using an age-adjusted overall infection fatality ratio based on age-specific estimates from mostly high-income countries, we estimated that just 15.0% (95% credible interval 9.3%-34.0%) of COVID-19 deaths had been reported, indicating either substantial underreporting or lower age-specific infection-fatality ratios in India than in high-income countries. Despite the estimated high attack rate, additional epidemic waves occurred in late 2020 and April-May 2021. Future dynamics will depend on the duration of natural and vaccine-induced immunity and their effectiveness against new variants.
MeSH term(s)	COVID-19 ; Epidemics ; Humans ; Incidence ; India/epidemiology ; SARS-CoV-2
Language	English
Publishing date	2022-02-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2804.210879
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Article ; Online: Emergency fasciotomy in an anticoagulated patient with low energy posterior thigh injury.

Brooker, Verity / Brown, Robert / Thornton, Luke / Wood, Edward

BMJ case reports

2020 Volume 13, Issue 9

Abstract: We present a case of a 58-year-old patient with a low energy trauma developing compartment syndrome. He required multiple surgeries, including fasciotomy and removal of a large haematoma. He continued to bleed with a vacuum-assisted closure dressing in ... ...

Abstract	We present a case of a 58-year-old patient with a low energy trauma developing compartment syndrome. He required multiple surgeries, including fasciotomy and removal of a large haematoma. He continued to bleed with a vacuum-assisted closure dressing in situ, requiring prothrombin complex Concentrate and blood transfusion. This case highlights the need for an increased awareness of possible development of compartment syndrome following low impact trauma in a patient who is anticoagulated and raises the question of a possible period of observation for those who may be at risk.
MeSH term(s)	Anticoagulants/therapeutic use ; Emergency Treatment ; Fasciotomy ; Hematoma/etiology ; Hematoma/surgery ; Humans ; Male ; Middle Aged ; Thigh/injuries ; Thigh/surgery ; Wounds, Nonpenetrating/complications ; Wounds, Nonpenetrating/surgery
Chemical Substances	Anticoagulants
Keywords	covid19
Language	English
Publishing date	2020-09-07
Publishing country	England
Document type	Case Reports ; Journal Article
ISSN	1757-790X
ISSN (online)	1757-790X
DOI	10.1136/bcr-2019-232709
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Article ; Online: A Longitudinal Cohort Study of Factors Impacting Healthcare Worker Burnout in New York City During the COVID-19 Pandemic.

Peccoralo, Lauren A / Pietrzak, Robert H / Tong, Michelle / Kaplan, Sabrina / Feingold, Jordyn H / Feder, Adriana / Chan, Chi / Verity, Jaclyn / Charney, Dennis / Ripp, Jonathan

Journal of occupational and environmental medicine

2023 Volume 65, Issue 5, Page(s) 362–369

Abstract: Objective: This study aimed to longitudinally examine the prevalence and correlates of burnout in frontline healthcare workers (FHCWs) during COVID-19 in New York City.: Methods: A prospective cohort study of 786 FHCWs at Mount Sinai Hospital was ... ...

Abstract	Objective: This study aimed to longitudinally examine the prevalence and correlates of burnout in frontline healthcare workers (FHCWs) during COVID-19 in New York City. Methods: A prospective cohort study of 786 FHCWs at Mount Sinai Hospital was conducted during the initial COVID surge in April to May 2020 (T1) and November 2020 to January 2021 (T2) to assess factors impacting burnout. Results: Burnout increased from 38.9% to 44.8% ( P = 0.002); 222 FHCWs (28.3%) had persistent burnout, 82 (10.5%) had early burnout, and 129 (16.5%) had delayed burnout. Relative to FHCWs with no burnout ( n = 350; 44.7%), those with persistent burnout reported more prepandemic burnout (relative risk [RR], 6.67), less value by supervisors (RR, 1.79), and lower optimism (RR, 0.82), whereas FHCWs with delayed burnout reported more prepandemic burnout (RR, 1.75) and caring for patients who died (RR, 3.12). Conclusion: FHCW burnout may be mitigated through increasing their sense of value, support, and optimism; treating mental health symptoms; and counseling regarding workplace distress.
MeSH term(s)	Humans ; Longitudinal Studies ; New York City/epidemiology ; Pandemics ; Prospective Studies ; COVID-19/epidemiology ; Cohort Studies ; Health Personnel
Language	English
Publishing date	2023-01-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	1223932-x
ISSN	1536-5948 ; 1076-2752
ISSN (online)	1536-5948
ISSN	1076-2752
DOI	10.1097/JOM.0000000000002790
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Article: Strong isolation by distance and evidence of population microstructure reflect ongoing

Connelly, Sean V / Brazeau, Nicholas F / Msellem, Mwinyi / Ngasala, Billy E / Aydemir, Özkan / Goel, Varun / Niaré, Karamoko / Giesbrecht, David J / Popkin-Hall, Zachary R / Hennelly, Christopher M / Park, Zackary / Moormann, Ann M / Ong'echa, John Michael / Verity, Robert / Mohammed, Safia / Shija, Shija J / Mhamilawa, Lwidiko E / Morris, Ulrika / Mårtensson, Andreas /

Lin, Jessica T / Björkman, Anders / Juliano, Jonathan J / Bailey, Jeffrey A

medRxiv : the preprint server for health sciences

2024

Abstract: The Zanzibar archipelago of Tanzania has become a low-transmission area ... ...

Abstract	The Zanzibar archipelago of Tanzania has become a low-transmission area for
Language	English
Publishing date	2024-02-13
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.02.15.23285960
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