Editors’ Picks 2020

Posted on December 31, 2020 by PLoS ONE Editors

This year has seen the scientific community at large come together to better understand and tackle the ongoing pandemic. Along with other PLOS journals, PLOS ONE has been committed to disseminating the resulting research outputs as quickly possible and have collected all published studies in our COVID-19 pandemic (2019-2020) Collection. Alongside this important work on COVID-19, PLOS ONE has continued to publish research from all areas of science. Here, PLOS ONE Staff Editors from the different subject teams reflect on the past year choosing some of their favorite research. From research on plastic pollution to improving prognosis predictions for patients with cancer, we hope that these selections will have something of interest for everyone.

Behavioral and Social Sciences, Neuroscience, Mental Health

Meta-analyses are often conducted to increase the generalizability of results from individual studies and can shed light of the reproducibility of a given effect. However, in an article published in January this year, Maassen and collaborators [1] note concerns about the reproducibility of these meta-analytic methods. They find that almost half of 500 primary study effect sizes drawn from 33 published psychological meta-analyses could not be reproduced. One of the tools often used to assess reproducibility may not be as reproducible as hoped.

Craig-Atkins and colleagues [2] use data from human remains, pottery shards, and animal bones to track dietary changes after the Norman conquest of England. They find that short-term food insecurity was followed by changes in preferences and intensification of the economy.

Gabriel Schwartz and Jaquelyn Jahn [3] analyzed data from Fatal Encounters—the most comprehensive database tracking police-involved deaths in the United States—and uncovered vast differences across metropolitan statistical areas (MSAs) in the overall rates of persons killed by police officers, regional differences (West and South v. Midwest and Northeast), as well as racial inequities in those rates, between 2013 and 2017, for 5,494 police-related fatalities. A formal comment by Nix [4] on this article emphasized the difficulties inherent in such research, such as limitations in the database, and the challenges in interpreting these results.

In this Registered Report Protocol, one of the first ones published at PLOS ONE, Jaffé and Douneva [5] describe three proposed studies to determine how sharing secrets affects the way individuals think about each other. We already know that closeness can make secret-sharing more likely, but these authors plan to investigate whether secret-sharing might in turn increase perceptions of closeness. These studies are expected to be conducted on online platforms and in person with students over this academic year.

Cancer and Medicine

Deep learning is emerging as a potential tool for a range of applications in cancer. Predicting patient prognosis can help to inform monitoring and treatment strategies. In their study, Wulczyn and colleagues [6] demonstrate the feasibility of deep learning systems for predicting survival in multiple cancer types, using histopatholgy images.

When it comes to fighting the global spread of COVID-19, the implementation of preventative measures such as social distancing are paramount. However, it can be challenging to estimate how much of a difference these measures make and how this varies depending on when these measures are put in place or lifted. In their study, Ohsawa and Tsubokura [7] simulate the spread of virus infection using artificial human networks and test how contact between people in different clusters effects the timing and intensity of viral spread. The authors find that releasing a previously imposed constraint too early can lead to a “second wave” of infection that is more intense than the previous wave, and caution against lifting restrictions on social contact too soon.

Ageism’s effects on health may be compounded by individual and structural biases against the elderly. In a systematic review, Chang and colleagues’ [8] synthesis of data from 422 studies showed ageism has a global reach.

Using historical data, this paper looks at gender equity in academic surgical specialties over the past forty years. Linscheid and colleagues [9] present an analysis suggesting that more work needs to be done to ensure female surgical students and trainees are supported to ensure representation across specialties.

Cardiovascular and Public Health, Epidemiology, Sports Science

The epidemiological study by Gosiker and colleagues [10], which is part of Primary and Secondary Prevention of Cardiovascular Disease (CVD) Collection launched in December this year, exemplifies the importance of carefully assessing CVD risk in vulnerable populations. Using data from a large collaboration of clinical sites in the United States, the investigators examined the prevalence of elevated 10-year CVD risk among transgender women with HIV. The approach and main findings from this study contribute to the growing need of calibrated risk prediction tools that support CVD preventive strategies in underrepresented and vulnerable populations.

The impact of socioeconomic factors (for example, education level) on health outcomes is widely studied—but do inequality rates vary across different healthcare systems types? Rydland and colleagues [11] contribute to the debate by analysing how educational inequalities found in mortality amenable to healthcare (defined as deaths which are preventable through medical intervention) vary among European countries with different typologies of health systems.

Doshi and colleagues [12] interview providers to analyze the experiences of undocumented Latino(a)/Latinx immigrants seeking healthcare and social services in the United States. By framing the results according to the “Three Delays Model”, the authors provide rich insights on the lived experiences of a marginalized group, and suggest several approaches to improve access to care.

Mental health is a leading cause of disability globally. In their article, Smith and colleagues [13] showcase the use of Implementation Science (IS) tools/principles to deliver and evaluate scale up of much-needed mental health services in the Global South. This is one of a few IS hybrid studies that looked at both: a) implementation outcomes (reach/uptake of the intervention, fidelity) and b) effectiveness outcomes (clinical outcomes, functionality). The authors used elements of the RE-AIM framework/theory and applied simple quasi-experimental design methods for quantitative evaluation.

Life Sciences

Whale sharks, the largest living fish, don’t have much to fear from predators and are known to be docile and and approchable. However, their eyes are exposed to damage from mechanical, chemical and biological hazards. This year, Tomita and colleagues [14] from Japan’s Okinawa Churashima Research Center made the surprising discovery that their retractible eyes are uniquely protected by rows of oakleaf-like denticles. This finding highlights the importance of vision in this species.

Resistin molecules are pleiotropic cytokines associated with inflammatory diseases but their distribution features in human organs remains unexplored. A new anti-human resistin antibody developed by Lin and colleagues [15] is used to explicitly detect the expression pattern of human resistin across normal human tissues. Results show that resistin is broadly distributed, but principally localized in the cytoplasmic granules of macrophages, hematopoietic precursor cells and neuronal cells. This characterization of resistin expression provides a framework for recognition and interpretation of changes in these patterns that may be associated with disease states.

The endemic Giant Senecios of the East African sky islands are an iconic example of the gigantism that has evolved convergently in a number of tropical montane plant lineages. In their new study, Tusiime and colleagues [16] genotyped 460 plants from across the region’s mountains to assess genetic structuring, biogeographic patterns, and taxonomic concepts. They found evidence for rapid recent radiation underpinned by long-distance dispersal and parallel adaptation. They also reported low levels of overall genetic diversity, emphasising the need for enhanced conservation efforts.

PARP proteins play a critical role in the early detection of DNA double-strand breaks, but as yet no structural information on double-strand break detection in the context of chromatin exists. In their study, Gaullier and colleagues [17] use cryo-EM to solve the structure of PARP2 bridging the mimicked double-stranded break of two nucleosomes (Nuc165) reconstituted in vitro with two short linker DNA overhangs. Their model illustrates that by bridging the break, PARP2 acts as a platform for recruitment of other factors involved in DNA repair such as HPF1.

Physical Sciences and Engineering

Understanding long term changes in the ocean can be invaluable not only for elucidating the historical record, but for predicting future scenarios amidst a changing climate. In this study, Simon and colleagues [18] use an unprecedentedly high-resolution record of stable isotopes from a marine core retrieved off western North Iceland to characterize long-term ocean variability. Using foraminifera, they reconstruct the record for the period before instrumentation, as well as overlapping with the period of instrumental observation, and demonstrate a high degree of agreement in predicted and observed data.

Plastic pollution of the natural environment is an ongoing global crisis and plastics which end up in waterways or the ocean can travel vast distances. In this new study, Duncan and colleagues [19] designed their own “bottle tags” which mimicked the characteristics of a half-full 500ml plastic bottle. By installing open-source technology within the bottle and releasing them at various points in the Ganges river system and the Bay of Bengal, the team was able to track the journeys that their bottles made; The longest journey was 2845km over 94 days, illustrating the dispersal processes of plastic pollution.

How do you open a historical treasure chest without a key, when the lock may contain any manner of failsafes or protective mechanisms? Zikmundová and colleagues [20] tackle this problem using X-ray computed tomography (CT) scanning. Their technique enabled a detailed exploration of the lock based on a system of levers and bolts handled by a single key, located in a case on the inside of the chest lid, including the dimensions essential for manufacturing of a new key copy. Moreover, two secret protective mechanisms were revealed, as well as all the damages of the object.

References

Maassen E, van Assen MALM, Nuijten MB, Olsson-Collentine A, Wicherts JM (2020) Reproducibility of individual effect sizes in meta-analyses in psychology. PLoS ONE 15(5): e0233107.
Craig-Atkins E, Jervis B, Cramp L, Hammann S, Nederbragt AJ, Nicholson E, et al. (2020) The dietary impact of the Norman Conquest: A multiproxy archaeological investigation of Oxford, UK. PLoS ONE 15(7): e0235005.
Schwartz GL, Jahn JL (2020) Mapping fatal police violence across U.S. metropolitan areas: Overall rates and racial/ethnic inequities, 2013-2017. PLoS ONE 15(6): e0229686.
Nix J (2020) On the challenges associated with the study of police use of deadly force in the United States: A response to Schwartz & Jahn. PLoS ONE 15(7): e0236158.
Jaffé ME, Douneva M (2020) Secretive and close? How sharing secrets may impact perceptions of distance. PLoS ONE 15(6): e0233953.
Wulczyn E, Steiner DF, Xu Z, Sadhwani A, Wang H, Flament-Auvigne I, et al. (2020) Deep learning-based survival prediction for multiple cancer types using histopathology images. PLoS ONE 15(6): e0233678.
Ohsawa Y, Tsubokura M (2020) Stay with your community: Bridges between clusters trigger expansion of COVID-19. PLoS ONE 15(12): e0242766.
Chang E-S, Kannoth S, Levy S, Wang S-Y, Lee JE, Levy BR (2020) Global reach of ageism on older persons’ health: A systematic review. PLoS ONE 15(1): e0220857.
Linscheid LJ, Holliday EB, Ahmed A, Somerson JS, Hanson S, Jagsi R, et al. (2020) Women in academic surgery over the last four decades. PLoS ONE 15(12): e0243308.
Gosiker BJ, Lesko CR, Rich AJ, Crane HM, Kitahata MM, Reisner SL, et al. (2020) Cardiovascular disease risk among transgender women living with HIV in the United States. PLoS ONE 15(7): e0236177.
Rydland HT, Fjær EL, Eikemo TA, Huijts T, Bambra C, Wendt C, et al. (2020) Educational inequalities in mortality amenable to healthcare. A comparison of European healthcare systems. PLoS ONE 15(7): e0234135.
Doshi M, Lopez WD, Mesa H, Bryce R, Rabinowitz E, Rion R, et al. (2020) Barriers & facilitators to healthcare and social services among undocumented Latino(a)/Latinx immigrant clients: Perspectives from frontline service providers in Southeast Michigan. PLoS ONE 15(6): e0233839.
Smith SL, Franke MF, Rusangwa C, Mukasakindi H, Nyirandagijimana B, Bienvenu R, et al. (2020) Outcomes of a primary care mental health implementation program in rural Rwanda: A quasi-experimental implementation-effectiveness study. PLoS ONE 15(2): e0228854.
Tomita T, Murakumo K, Komoto S, Dove A, Kino M, Miyamoto K, et al. (2020) Armored eyes of the whale shark. PLoS ONE 15(6): e0235342.
Lin Q, Price SA, Skinner JT, Hu B, Fan C, Yamaji-Kegan K, et al. (2020) Systemic evaluation and localization of resistin expression in normal human tissues by a newly developed monoclonal antibody. PLoS ONE 15(7): e0235546.
Tusiime FM, Gizaw A, Gussarova G, Nemomissa S, Popp M, Masao CA, et al. (2020) Afro-alpine flagships revisited: Parallel adaptation, intermountain admixture and shallow genetic structuring in the giant senecios (Dendrosenecio). PLoS ONE 15(3): e0228979.
Gaullier G, Roberts G, Muthurajan UM, Bowerman S, Rudolph J, Mahadevan J, et al. (2020) Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1. PLoS ONE 15(11): e0240932.
Simon MH, Muschitiello F, Tisserand AA, Olsen A, Moros M, Perner K, et al. (2020) A multi-decadal record of oceanographic changes of the past ~165 years (1850-2015 AD) from Northwest of Iceland. PLoS ONE 15(9): e0239373.
Duncan EM, Davies A, Brooks A, Chowdhury GW, Godley BJ, Jambeck J, et al. (2020) Message in a bottle: Open source technology to track the movement of plastic pollution. PLoS ONE 15(12): e0242459.
Zikmundová E, Zikmund T, Sládek V, Kaiser J (2020) Non-destructive lock-picking of a historical treasure chest by means of X-ray computed tomography. PLoS ONE 15(7): e0235316

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Introducing the Photovoltaic Solar Cell Materials – Design, Fabrication and Testing Collection

Posted on May 14, 2020 by PLoS ONE Editors

With the need to shift away from fossil fuel usage, while at the same time supporting increasing global demands for energy, improving efficiency and lowering costs in renewable energy production is critical. Unlike wind energy or hydroelectric energy, solar energy is a relatively reliable source of energy. It is found across all areas of the planet and is the most abundant renewable energy source on earth. Photovoltaics play a pivotal role in harnessing this energy by transforming sunlight to electricity. We are therefore excited to present the PLOS Collection “Photovoltaic Solar Cell Materials – Design, Fabrication and Testing Collection”. This collection highlights the dynamic and multidisciplinary research in this area, showcasing promising new materials, as well as new approaches and techniques to create efficient solar cells.

The collection was curated by a team of Guest
Editors with a wide range of experience and research specializations: Juan-Pablo
Correa-Baena (Georgia Tech), David P. Fenning (University of California San
Diego), Shuxia Tao (Eindhoven University of Technology), Maria Antonietta Loi
(University of Groningen), Graeme Blake (University of Groningen), and Hongxia
Wang (Queensland University of Technology).

Metal halide perovskite-based PV

Metal halide perovskite materials are increasingly demonstrating potential as semiconductor light absorbing materials in solar cells, as cost and energy-efficient alternatives to silicon. In their review, Wieghold and Nienhaus highlight the advantages of perovskite, as well as their current drawbacks with the aim of stimulating this relatively new field. A study by Rivas et al. demonstrates the effective use of cryo-focused ion beam technology to prepare perovskite-based solar cells, while Kirmani et al. investigate ways to improve the optoelectronic properties of perovskite crystals.

SEM cross section image of the full PSC stack obtained by FIB. https://doi.org/10.1371/journal.pone.0227920.g004

New Solar Cell Material Technologies

Sulvanites, with their suitable band gap for solar absorption and relative earth-abundance may also be a promising candidate for solar cell use. In their study, Liu et al. synthesise sulvanite-based materials and evaluate their optoelectronic properties. Meanwhile, Yau et al. present a new method for generating graphene oxide, a material with excellent thermoconductivity and mechanical properties. The authors combined the optimized graphene with titanium oxide, to increase the absorption rate of excited dye in dye-sensitized solar cells.

(A) Low-resolution TEM images. (B) HRTEM images. (C) SEM image of synthesized CVSe NCs. (D-F) SEM–EDS elemental mapping of CVSe NCs. https://doi.org/10.1371/journal.pone.0232184.g002

This multifaceted collection will serve to introduce readers to the world of photovoltaics, while linking the diverse community of researchers who are currently advancing the field.

Guest Editors

David Fenning

David is an Assistant Professor in the Department of NanoEngineering
at UC San Diego, where he directs the Solar Energy Innovation
Laboratory. His research focuses on defect engineering to improve
performance and reliability in silicon and hybrid perovskite solar cells
and on CO₂ electrocatalysis for energy storage and green
fuels. He specializes in the use of synchrotron-based X-ray microscopies
to understand the relationships between local chemistry, structure, and
performance in energy conversion materials.

Maria Antonietta Loi

Maria Antonietta studied physics at the University of Cagliari in
Italy where she received a PhD in 2001. In the same year, she joined the
Linz Institute for Organic Solar cells, of the University of Linz,
Austria as a postdoctoral fellow. Later she worked as a researcher at
the Institute for Nanostructured Materials of the Italian National
Research Council in Bologna, Italy. In 2006, she became an assistant
professor and Rosalind Franklin Fellow at the Zernike Institute for
Advanced Materials of the University of Groningen, The Netherlands,
where she is now full professor and chair of the Photophysics and
OptoElectronics group. In 2018 she received the Physicaprijs from the
Dutch physics association for her outstanding work on organic-inorganic
hybrid materials

Hongxia Wang

Hongxia has a PhD degree in Condensed Matter Physics from the
Institute of Physics, Chinese Academy of Science, Master’s degree and
Bachelor’s degree in Chemistry from the Central South University, China.
She is currently a full Professor at Queensland University of
Technology (QUT), Australia. Her research group is dedicated to the
development of new routes to enhance the performance and stability of
next generation solar cells, in particular perovskite solar cells and
energy storage devices such as supercapacitors, through innovative
material and device engineering. She was the recipient of several
prestigious fellowships including the “Australian Research Council (ARC)
Future Fellowship” and the “Australian Postdoctoral Fellowship
(Industry)”.

Graeme Blake

Graeme is an Assistant Professor at the Zernike Institute for Advanced Materials, University of Groningen, Netherlands. He received his PhD in inorganic chemistry at the University of Oxford, then worked as a postdoc split between Argonne National Laboratory and the ISIS neutron scattering facility, UK, before joining the faculty at the University of Groningen. His research interests include the chemical synthesis and characterisation of hybrid perovskite-related materials, with a special focus on their crystallography. He is also interested in magnetic materials, especially multiferroic order, skyrmion phases, and magnetism arising from p-electrons in oxygen, and in addition, investigates the chemistry and physics of thermoelectric materials such as chalcogenides.

Want to find out more about the Guest Editors and their interests in this field? Read our interview with them here.

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Stem Cell Plasticity in Tissue Repair and Regeneration Collection

Posted on April 23, 2020 by PLoS ONE Editors

We are excited to publish a collection entitled Stem Cell Plasticity in Tissue Repair and Regeneration, which results from a PLOS ONE’s call for papers announced last year. We encouraged submissions spanning a broad

Stem Cell Plasticity in Tissue Repair and Regeneration Collection

Posted on April 23, 2020 by PLoS ONE Editors

We are excited to publish a collection entitled Stem Cell Plasticity in Tissue Repair and Regeneration, which results from a PLOS ONE’s call for papers announced last year. We encouraged submissions spanning a broad range of biomedical topics, including basic stem cell biology, preclinical research and biomedical engineering. The papers included in the collection provide examples of how the dynamic functions of stem cells can be harnessed to regenerate damaged or lost tissues. Regenerative approaches may offer a unique therapeutic opportunity for diseases where with no established treatments exist.

In line with PLOS ONE publication ethos, we welcomed solid and clearly reported studies regardless of the perceived impact and positive nature of the main findings. We think that in the fast-paced field of stem cell research, addressing publication bias is particularly important to advance knowledge and bring new therapies to the clinic.

Two studies included in the collection reported the role and regenerative ability of adult mesenchymal stem cells (MSCs). Chung et al. showed the regenerative potential of human MSCs in a rat model of bladder disease. They also identified the bladder submucosa as the most effective route of MSC administration. In a clinical study among patients with acute respiratory distress syndrome, Patry et al. found that extracorporeal membrane oxygenation increased the number of circulating MSCs, although further research is needed to establish the regenerative potential of these cells in the context of pulmonary disease.

Bladder tissue regeneration identified via IHC staining pone.0226390

Two methodological papers focused on the differentiation of human induced pluripotent stem cells (hiPSCs) into cardiac cells. This rapidly evolving research area aims at overcoming the current challenges in generating mature cells in large quantity and high purity for tissue engineering applications. Rupert et al. described practical methods for the optimization of hiPSC-cardiomyocyte differentiation, highlighting the key role of metabolic selection. Chu et al. demonstrated that cardiac differentiation can be achieved by co-culturing hiPSCs with mature cardiomyocytes, without the addition of exogenous pharmacological agents.

Workflows for cardiac differentiation of stem cells pone.0230001

This collection was made possible thanks to the fantastic work of our Guest Editors – Michelina Iacovino, Scott D. Olson and Che Connon – who helped develop the scope of the call for papers and evaluated all submitted research for inclusion in the collection. We are also extremely grateful to the members of our editorial board and external peer-reviewers for dedicating their time and expertise to the evaluation of submissions.

We will add new papers to the Collection as they are published, so we invite you to check back the collection webpage in the coming weeks. If you are interested in keeping up to date with the latest stem cell research from the broader literature, check out our PLOS Channel too.

Guest Editors

Scott D. Olson

Scott Olson is a mesenchymal stem cell (MSC) Biologist working in the Children’s Program in Regenerative Medicine in the Department of Pediatric Surgery at McGovern School of Medicine. Dr. Olson completed his doctorate in the lab of Dr. Darwin Prockop at Tulane University’s Center for Gene Therapy studying novel methods by which MSCs can contribute to tissue repair. At University of California at Davis’s Health Sciences Institute for Regenerative Cures with Dr. Jan Nolta, Dr. Olson worked to apply MSCs as a platform to develop new treatments for Huntington’s Disease. Dr. Olson joined UTHealth in September 2011.

Dr. Olson is involved in developing and transitioning studies with direct translational applications. At UT Health, his primary focus is bringing his expertise in the field of adult stem cells, specifically MSCs, to explore their potential in the treatment of Traumatic Brain Injury (TBI) and in trauma-associated neuroinflammation in general. MSCs have been used in a number of completed, ongoing, and proposed clinical trials with reported therapeutic benefits. Dr. Olson strives to better describe the role of MSCs in injuries of the central nervous system, highlighting their innate therapeutic abilities in an effort to create an improved treatment for TBI.

Michelina Iacovino

Michelina Iacovino is an Assistant Professor at the David Geffen School of Medicine at The University of California, Los Angeles (UCLA), and a Principal Investigator at Los Angeles Biomedical Research Institute (LABioMed) at Harbor-UCLA in the Pediatrics Department.

She obtained her Doctorate in Italy in Biochemistry and Applied Chemistry working on mitochondrial DNA inheritance in yeast in collaboration with Dr. Ronal Butow at the University of Texas Southwestern Medical Center. She then trained in the field of hematopoietic stem cells with Dr. Michael Kyba during her postdoctoral fellowship, studying the role of Hox genes during blood development. She joined LABioMed in 2012, extending her expertise of stem cell biology to develop treatments for rare lysosomal disorders that affect brain function. She is currently developing a stem cell therapy for Sanfilippo syndrome, an incurable and rare lysosomal disorder, using neural progenitor cells.

Che Connon

Che Connon obtained his PhD in Biophysics from the Open University Oxford Research Unit in 2000, during which time (under the supervision of Professor Keith Meek) he investigated corneal wound healing and transparency. He subsequently obtained a JSPS post-doctoral fellowship to work with Professor Shigeru Kinoshita in Kyoto, Japan for two years studying corneal stem cell transplantation. Upon his return to the UK he was awarded a Royal Society Fellowship to investigate the use of biomaterials in stem cell therapies. He obtained his first permanent position in 2007 at University of Reading, School of Pharmacy and since 2014 he has held the position of Professor of Tissue Engineering at Newcastle University.

Professor Connon’s research team seeks to engineer functional replacement and temporary ‘bridge’ tissues using a modular approach while also developing model systems to study physiological and pathophysiological corneal tissue formation. He is currently working with smart (cell responsive) biomaterials, characterizing the mechanical and geometric environment of the corneal stem cell niche and 3D printing the corneal stroma.

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Introducing the Mathematical Modelling of Infectious Disease Dynamics Collection

Posted on February 20, 2020 by PLoS ONE Editors

Introducing the Mathematical Modelling of Infectious Disease Dynamics Collection

Posted on February 20, 2020 by PLoS ONE Editors

In recent months, the words “infection” and “outbreak” have not been far from anyone’s mind as we’ve faced the emergence of a new coronavirus, COVID-19. Across the globe, efforts are underway to control and limit the spread of the virus, and to find ways to treat those infected. As we watch these events unfurl, it is evident that there is still a lot that we, as a global community, do not yet understand about the dynamics of infectious diseases. The ways in which diseases spread are a concern that we all have a stake in?research that helps further our understanding of infectious diseases can influence each of our lives.

One distinct community of researchers working on understanding infectious disease dynamics is the mathematical modelling community, consisting of scientists from many different disciplines coming together to tackle a common problem through the use of mathematical models and computer simulations. Mathematics may sound like an unlikely hero to help us overcome a global epidemic; however, the insights we gain from studying the dynamics of infectious diseases by using equations describing fundamental variables are not to be underestimated. By approaching infectious diseases from a mathematical perspective, we can identify patterns and common systems in disease function, and it enables us to find some of the underlying structures that govern outbreaks and epidemics. Mathematical modellers make use of available data from current and previous outbreaks to predict who may get infected, where vaccination efforts will be most effective, and how to limit the spread of the disease.

Today at PLOS, we are launching a collection of new research papers submitted to a call for papers during the latter half of 2019 entitled “Mathematical Modelling of Infectious Disease Dynamics”, hosted by PLOS Biology, PLOS Computational Biology and PLOS ONE. The aim of this collection is to bring together different disciplines such as mathematics, biology, medicine and physics in order to shed light on the important topic of how mathematical models can help us understand infectious disease dynamics, and to present this research to the broad readership of these three journals and beyond. The accumulation of vital new research in a comprehensive collection will be a useful resource for understanding how infectious diseases operate, and how we can tackle them in real-time as well as in the future.

At PLOS we remain committed to our primary Open Access mission?ensuring that science is made as widely available as possible, and not locked behind paywalls. This is especially important in outbreak scenarios, such as the current COVID-19 epidemic, where it is critical that any new and relevant research be made easily accessible around the world, immediately at the time of publication.

Novel Coronavirus SARS-CoV-2 NIAID CC-BY

Several of the papers in this collection present new methods that can be utilized in a range of scenarios. For instance, Patel and Sprouge developed a new estimator for predicting the basic reproduction number R₀, which is the expected number of host cells infected by a single infected cell. This can be used for instance to understand the early stages of HIV infections, and for assessing the effectiveness of various therapies.

If two pathogen species, strains, or clones don’t interact, surely we can estimate the proportion of coinfected hosts as the simple product of the individual prevalences? A paper in PLOS Biology by Frédéric Hamelin, Nik Cunniffe and co-workers shows that this assumption is false; even if pathogens don’t interact, death of coinfected hosts causes net prevalences of individual pathogens to decrease simultaneously. The authors reinterpret data from previous studies accordingly.

Unusually large outbreaks of mumps across the United States in 2016 and 2017 raised questions about the extent of mumps circulation and the relationship between these and prior outbreaks. In this PLOS Biology paper, Shirlee Wohl, Pardis Sabeti and co-authors paired epidemiological data from public health investigations with analysis of mumps virus whole-genome sequences from 201 infected individuals. This allowed them to reconstruct mumps transmission links not evident from more traditional approaches and also revealed connections between apparently unrelated mumps outbreaks.

Endo and colleagues present a model of a phenomenon to which we can all relate, but which is still not well understood – the spread of infection within the household. They modelled the fine structures of family life to understand how disease typically enters and spreads through the household. Their findings support the idea that children are the most likely culprits of bringing disease into the household, and showed that there is a high level of transmission within generations, as well as between mother and child.

Rotavirus, the leading cause of diarrhea globally in children under 5, shows a biennial pattern of emergence in the US, while in many other high-income countries it exhibits an annual pattern. Ai and colleagues modelled the effect that higher vaccine coverage may have on this phenomenon, and found that increasing vaccine coverage from the current 70-75% to 85% would not only reduce the number of rotavirus cases, but also shift occurance to a more predictable annual epidemic pattern.

Two of the papers published in the collection are concerned with malaria. Kim and colleagues modelled the effectiveness of relapse control methods for Plasmodium vivax, finding that current vector control methods may have a negative effect on controlling disease prevalence, but that a shift towards control at a higher vector control level may be more efficient. Meanwhile, Wang and colleagues have constructed a stacking model for malaria prediction by combining two traditional time series models and two deep learning methods. Utilising malaria incidence data from Yunnan Province, China, they find that the ensemble architecture outperforms each of the sub-structure models in predicting malaria cases.

Predicted dengue importations for August 2015 pone.0225193 CC-BY

There are two papers in the collection that look at improving prediction of dengue infections. Leibig and colleagues present a network model of how international air travel can affect the spread of dengue across the world. By modelling the number of dengue-infected passengers arriving at various airports each month, the authors were able to study how dengue may be imported into different countries, and which routes would be the most likely for dengue-infected passengers to arrive by. Secondly, Liu and colleagues developed a model for predicting the spread of dengue infections that incorporates climate factors such as mean temperature, relative humidity and precipitation and applied this to data from dengue infections in Guangzhou, China, in order to help inform best practices in the early stages of a dengue outbreak.

The development of diseases can be influenced by personal factors such as age, which two of the papers in the collection address. Ku and Dodd developed a model for accounting for population aging when looking at tuberculosis incidence, as the impact of demographic change on disease forecasting is still not well understood. They applied the model to historical data of TB cases in Taiwan from 2005-2018, and used this to forecast what the incidence may look like until 2035. On the other end of the age spectrum, Rostgaard and colleagues used a Markov model to study the relationship between Epstein-Barr virus and infectious mononucleosis. Most people are typically infected with Epstein-Barr virus in early childhood, while infectious mononucleosis can sometimes follow in adolescence or later in life. The authors developed a statistical model to probe some of the uncertainties surrounding the origin and dynamics of infectious mononucleosis.

Some of the papers in the collection address new and emerging diseases. Dodero-Rojas and colleagues used the SEIR model to study the last three Chikungunya outbreaks in Rio de Janeiro, Brazil, and estimated their respective Basic Reproduction Numbers, R₀. They also expanded their findings to include predictions for the Mayaro virus, which is an emerging disease in South America, and found that it has the possibility to become an epidemic disease in Rio de Janeiro.

The ability to accurately forecast disease patterns is crucial for ensuring that the right resources are in place to handle outbreaks. Morbey and colleagues looked at seasonal patterns in respiratory disease in England, and found that although syndromic indicators were affected by the timing of the peaks in seasonal disease, the demand for hospital beds was the highest on either 29th or 30th December, regardless of the timing of the syndromic peaks. Asadgol and colleagues also addressed seasonal patterns, this time in cholera in Iran, and predicted the effect of climate change on cholera incidence from 2020-2050 using an artificial neural network.

Given the interdisciplinary nature of the topic, we are grateful to countless authors, reviewers, Academic Editors and Guest Editors for making this collection a reality. We are especially grateful to our Guest Editor team, Konstantin Blyuss (University of Sussex), Sara Del Valle (Los Alamos National Laboratory), Jennifer Flegg (University of Melbourne), Louise Matthews (University of Glasgow) and Jane Heffernan (York University) for curating the collection. While 14 papers are included in this collection today, we’ll keep adding new papers as they are published, so please keep checking back for updates.

Guest Editor Konstantin Blyuss sums up the importance of this collection: “A recent and ongoing outbreak of coronavirus COVID-19 has highlighted the enormous significance of mathematical models for understanding the dynamics of infectious diseases and developing appropriate strategies for mitigating them. Mathematical models have helped identify the important factors affecting the spread of this infection both globally, and locally using country-specific information. They have also elucidated the effectiveness of different containment strategies and provided quantitative measures of disease severity”.