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| Open AccessThe risk of indoor sports and culture events for the transmission of COVID-19
Mass gathering events represent a risk for transmission of SARS-CoV-2. Here, the authors describe an experimental indoor test event in which individual contacts were measured and use aerosol and epidemiological modelling to evaluate transmission risks of different types of restrictions in the arena.
- Stefan Moritz
- , Cornelia Gottschick
- & Rafael Mikolajczyk
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Article
| Open AccessEtiological and epidemiological features of acute respiratory infections in China
China operates a national surveillance program for acute respiratory infections and sampled over 200,000 patients between 2009–2019. Here, the authors present results from this program and describe patterns by age, pathogen type, presence of pneumonia, and season.
- Zhong-Jie Li
- , Hai-Yang Zhang
- & Jun Wang
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Article
| Open AccessHigh COVID-19 transmission potential associated with re-opening universities can be mitigated with layered interventions
Reopening of universities to students following COVID-19 restrictions risks increased transmission due to high numbers of social contacts and the potential for asymptomatic transmission. Here, the authors use a mathematical model with social contact data to estimate the impacts of reopening a typical non-campus based university in the UK.
- Ellen Brooks-Pollock
- , Hannah Christensen
- & Leon Danon
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Article
| Open AccessDeep learning-based transformation of H&E stained tissues into special stains
Performing multiple histological stains on a biopsy can be costly and time consuming. Here the authors present a method for the digital transformation of H&E stained tissue into special stains (e.g., PAS, Masson’s Trichrome and Jones silver stain), and demonstrate that it improves diagnoses over the use of H&E only.
- Kevin de Haan
- , Yijie Zhang
- & Aydogan Ozcan
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Article
| Open AccessTracking the introduction and spread of SARS-CoV-2 in coastal Kenya
SARS-CoV-2 was first detected in Kenya in March 2020 and there was evidence of local transmission in the following months. Here, the authors characterise the early stages of the epidemic in coastal Kenya using phylogenetics and find evidence of multiple strain importations from international points of entry.
- George Githinji
- , Zaydah R. de Laurent
- & Charles N. Agoti
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Article
| Open AccessDetection and characterization of the SARS-CoV-2 lineage B.1.526 in New York
West and colleagues develop the Variant Database software tool for examination of changing Spike mutations in SARS-CoV-2 genomes. The authors use this to detect emerging lineages of SARS-CoV-2 in New York and report the rapid spread of the B.1.526 lineage in the city.
- Anthony P. West Jr.
- , Joel O. Wertheim
- & Pamela J. Bjorkman
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Article
| Open AccessCOVID-19 spread, detection, and dynamics in Bogota, Colombia
Detailed information on SARS-CoV-2 infection rates in Latin America by occupation, socioeconomic group and geographic area are rarely available. Here, the authors provide these estimates for in Bogota, Colombia using data from a sentinel surveillance scheme, and find that over half the population had been infected by March 2021.
- Rachid Laajaj
- , Camilo De Los Rios
- & Duncan Webb
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Article
| Open AccessTime-varying optimization of COVID-19 vaccine prioritization in the context of limited vaccination capacity
In the context of limited supply, strategies for optimising allocation of COVID-19 vaccines are needed. Here, the authors explore time-varying strategies that adapt to the epidemiological situation and simultaneously optimise for multiple objectives including reducing numbers of infections, hospitalisations, and deaths.
- Shasha Han
- , Jun Cai
- & Hongjie Yu
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Article
| Open AccessHeatstroke predictions by machine learning, weather information, and an all-population registry for 12-hour heatstroke alerts
In the context of climate change, heatstroke is expected to become an increasingly relevant public health concern. Here, the authors develop and validate prediction models for the number of all heatstroke cases in different cities in Japan.
- Soshiro Ogata
- , Misa Takegami
- & Kunihiro Nishimura
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Matters Arising
| Open AccessTransplantation of discarded livers: the complementary role of normothermic regional perfusion
- Chris J. C. Johnston
- , Ahmed E. Sherif
- & Gabriel C. Oniscu
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Article
| Open AccessSelf-healing polyurethane-elastomer with mechanical tunability for multiple biomedical applications in vivo
The unique properties of self-healing materials hold great potential in the field of biomedical engineering. Here, the authors designed a series of biodegradable and biocompatible self-healing elastomers with tunable mechanical properties, and apply them to various disease models in vivo, including aortic aneurism, bone fracture and nerve amputation.
- Chenyu Jiang
- , Luzhi Zhang
- & Xiaofeng Ye
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Perspective
| Open AccessConsensus statement on the role of health systems in advancing the long-term well-being of people living with HIV
- Jeffrey V. Lazarus
- , Kelly Safreed-Harmon
- & Laura Waters
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Article
| Open AccessAdvancing diagnostic performance and clinical usability of neural networks via adversarial training and dual batch normalization
Unmasking the decision making process of machine learning models is essential for implementing diagnostic support systems in clinical practice. Here, the authors demonstrate that adversarially trained models can significantly enhance the usability of pathology detection as compared to their standard counterparts.
- Tianyu Han
- , Sven Nebelung
- & Daniel Truhn
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Article
| Open AccessLineage-specific protection and immune imprinting shape the age distributions of influenza B cases
The earliest infections with influenza A shape the immune responses to future infections, but it is not known if this phenomenon applies to influenza B. Here, the authors use influenza B case data from New Zealand and find evidence for both lineage-specific and imprinting protection.
- Marcos C. Vieira
- , Celeste M. Donato
- & Sarah Cobey
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Article
| Open AccessSensing leg movement enhances wearable monitoring of energy expenditure
Current methods to estimate energy expenditure are either infeasible for everyday use or associated with significant errors. Here the authors present a Wearable System using inertial measurement units worn on the shank and thigh that estimates metabolic energy expenditure in real-time during common steady-state and time-varying activities.
- Patrick Slade
- , Mykel J. Kochenderfer
- & Steven H. Collins
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Article
| Open AccessA clinical deep learning framework for continually learning from cardiac signals across diseases, time, modalities, and institutions
Deep learning algorithms trained on data streamed temporally from different clinical sites and from a multitude of physiological sensors are generally affected by a degradation in performance. To mitigate this, the authors propose a continual learning strategy that employs a replay buffer.
- Dani Kiyasseh
- , Tingting Zhu
- & David Clifton
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Article
| Open AccessThe epidemiology of Plasmodium vivax among adults in the Democratic Republic of the Congo
Plasmodium vivax generally accounts for a low proportion of malaria cases in Africa, but population-level data on the distribution of infections is limited. Here, the authors use data from the Democratic Republic of the Congo and show that the prevalence is low (~3%) and diffusely spread.
- Nicholas F. Brazeau
- , Cedar L. Mitchell
- & Jonathan J. Juliano
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Article
| Open AccessA genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex
Klebsiella pneumoniae is a pathogen of increasing public health concern and antimicrobial resistance is becoming more prevalent. Here, the authors describe a K. pneumoniae genotyping tool, Kleborate, that can be used to identify lineages and detect antimicrobial resistance and virulence loci.
- Margaret M. C. Lam
- , Ryan R. Wick
- & Kathryn E. Holt
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Article
| Open AccessLack of consideration of sex and gender in COVID-19 clinical studies
Sex and gender have been associated with differences in SARS-CoV-2 incidence and clinical outcomes and therefore warrant consideration in study designs. Here, the authors assess registered and published clinical COVID-19 studies and find that sex-disaggregated analyses are infrequently presented or planned.
- Emer Brady
- , Mathias Wullum Nielsen
- & Sabine Oertelt-Prigione
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Article
| Open AccessTemporal trends of SARS-CoV-2 seroprevalence during the first wave of the COVID-19 epidemic in Kenya
The reported burden of SARS-CoV-2 has been relatively low in tropical Africa compared to Europe and the Americas, but estimating true infection rates is challenging. Here, the authors screen blood donors in Kenya for SARS-CoV-2 antibodies and describe spatiotemporal seroprevalence dynamics.
- Ifedayo M. O. Adetifa
- , Sophie Uyoga
- & George M. Warimwe
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Article
| Open AccessGut microbiota mediate the FGF21 adaptive stress response to chronic dietary protein-restriction in mice
Dietary protein restriction induces a hepatic stress response mediated by the endocrine molecule FGF21, which triggers host adaptive pathways. Here the authors demonstrate that the gut microbiome is required to trigger the FGF21 response and can be manipulated through dietary fiber supplementation.
- Anthony Martin
- , Gertrude Ecklu-Mensah
- & Suzanne Devkota
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Article
| Open AccessDesign of COVID-19 staged alert systems to ensure healthcare capacity with minimal closures
Selection of COVID-19 mitigation measures requires balancing health outcomes with economic impacts. Here, the authors derive a system to set triggers for increasing mitigation measures to preserve healthcare capacity, and describe how it has been used to support public health decision making in Austin, Texas.
- Haoxiang Yang
- , Özge Sürer
- & Lauren Ancel Meyers
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Article
| Open AccessAssociation of social distancing and face mask use with risk of COVID-19
Estimating the effectiveness of COVID-19 control measures requires large prospective data including symptoms and personal risk factors. Here, the authors used data from smartphone-based application and found that individual face mask use was associated with a 64% reduced risk of COVID-19 symptoms.
- Sohee Kwon
- , Amit D. Joshi
- & Andrew T. Chan
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Article
| Open AccessPreventing corneal blindness caused by keratitis using artificial intelligence
Keratitis is the main cause of corneal blindness worldwide, but most vision loss caused by keratitis can be avoidable via early detection and treatment, which are challenging in resource-limited settings. Here, the authors develop a deep learning system for the automated classification of keratitis and other cornea abnormalities.
- Zhongwen Li
- , Jiewei Jiang
- & Wei Chen
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Article
| Open AccessControlling the pandemic during the SARS-CoV-2 vaccination rollout
Despite the consensus that mass vaccination against SARS-CoV-2 will ultimately end the pandemic, it is not clear when and which control measures can be relaxed during the rollout of vaccination programmes. Here, the authors investigate relaxation scenarios using an age-structured transmission model that has been fitted to data for Portugal.
- João Viana
- , Christiaan H. van Dorp
- & Ganna Rozhnova
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Article
| Open AccessMolecular benchmarks of a SARS-CoV-2 epidemic
The concentration of SARS-CoV-2 changes during an individual’s infection, and mutations accumulate as viruses are transmitted between people. Here, the authors use data from Iceland to demonstrate how this information can be exploited at the population-level to determine the phase of the epidemic.
- Hakon Jonsson
- , Olafur T. Magnusson
- & Kari Stefansson
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Article
| Open AccessInsights into household transmission of SARS-CoV-2 from a population-based serological survey
Household-based studies can provide insights into SARS-CoV-2 transmission. Here, the authors fit transmission models to serological data from Geneva, Switzerland, and estimate that the risk of infection from single household exposure (17.3%) was higher than for extra-household exposure (5.1%).
- Qifang Bi
- , Justin Lessler
- & Didier Trono
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Article
| Open AccessRole of meteorological factors in the transmission of SARS-CoV-2 in the United States
The role of meteorological factors in SARS-COV-2 transmission is not well understood. Here, the authors use county-level data from the United States to the end of 2020 and find evidence of a moderate association between increased transmissibility and cold, dry weather and low ultraviolet radiation.
- Yiqun Ma
- , Sen Pei
- & Kai Chen
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Article
| Open AccessMaps and metrics of insecticide-treated net access, use, and nets-per-capita in Africa from 2000-2020
Insecticide treated nets (ITNs) are an important part of malaria control in Africa and WHO targets aim for 80% coverage. This study estimates the spatio-temporal access and use of ITNs in Africa from 2000-2020, and shows that both metrics have improved over time but access remains below WHO targets.
- Amelia Bertozzi-Villa
- , Caitlin A. Bever
- & Samir Bhatt
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Article
| Open AccessEffect of specific non-pharmaceutical intervention policies on SARS-CoV-2 transmission in the counties of the United States
Disentangling the impacts of non-pharmaceutical interventions on COVID-19 transmission is challenging as they have been used in different combinations across time and space. This study shows that, early in the epidemic, school/daycare closures and stopping nursing home visits were associated with the biggest reduction in transmission in the United States.
- Bingyi Yang
- , Angkana T. Huang
- & Derek A. T. Cummings
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Article
| Open AccessThe geometry of clinical labs and wellness states from deeply phenotyped humans
Longitudinal multi-omics measurements are highly valuable in studying heterogeneity in health and disease phenotypes. Here, the authors apply Pareto Task Inference to analyze the clinical lab tests of 3094 individuals and find three wellness states, and one aberrant health state defining this cohort.
- Anat Zimmer
- , Yael Korem
- & Nathan D. Price
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Article
| Open AccessImpact of COVID-19 outbreaks and interventions on influenza in China and the United States
Non-pharmaceutical interventions (NPIs) implemented to interrupt COVID-19 transmission may also impact the spread of other infectious diseases. Here, the authors estimate that influenza activity in China and the United States reduced by up to 80% when NPIs were in place in the 2019–2020 season.
- Luzhao Feng
- , Ting Zhang
- & George F. Gao
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Article
| Open AccessImpacts of social distancing policies on mobility and COVID-19 case growth in the US
In response to COVID-19, many states have implemented social distancing orders, but the effect of these orders on population mobility has not been fully quantified. Here, the authors use data from the US to show that state-level social distancing orders substantially reduced mobility and limited the spread of disease.
- Gregory A. Wellenius
- , Swapnil Vispute
- & Evgeniy Gabrilovich
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Article
| Open AccessHealth improvement framework for actionable treatment planning using a surrogate Bayesian model
Clinical decision-making regarding treatments based on personal characteristics leads to effective health improvements. Here, the authors introduce a modeling framework to evaluate the actionability of treatment pathways.
- Kazuki Nakamura
- , Ryosuke Kojima
- & Yasushi Okuno
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Article
| Open AccessThe effect of generic market entry on antibiotic prescriptions in the United States
Generics contribute to increased availability of antibiotics, benefiting healthcare systems but potentially leading to increased consumption with implications for antibiotic stewardship and resistance. Here, the authors found no consistent changes in prescribing patterns of the 13 antibiotics that entered the US market as generics from 2000–2012.
- Cecilia Kållberg
- , Jemma Hudson
- & Ramanan Laxminarayan
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Article
| Open AccessA global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch
Whole genome sequencing data are increasingly becoming routinely available but generating actionable insights is challenging. Here, the authors describe Pathogenwatch, a web tool for genomic surveillance of S. Typhi, and demonstrate its use for antimicrobial resistance assignment and strain risk assessment.
- Silvia Argimón
- , Corin A. Yeats
- & David M. Aanensen
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Article
| Open AccessCirculation of pertussis and poor protection against diphtheria among middle-aged adults in 18 European countries
Recent outbreaks of pertussis have highlighted the importance of surveillance of vaccine-preventable diseases. Here, the authors performed a cross-sectional seroprevalence study of pertussis, diphtheria, and tetanus in Europe and found evidence of circulation of pertussis in middle-aged adults.
- Guy Berbers
- , Pieter van Gageldonk
- & Jussi Mertsola
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Article
| Open AccessUsing mobile phone data to reveal risk flow networks underlying the HIV epidemic in Namibia
Human mobility influences the spatial distribution of infectious diseases such as HIV. Here, the authors use call data records from mobile phones to model HIV networks in Namibia and estimate that ~40% of the risk of HIV acquisition is driven by mobility.
- Eugenio Valdano
- , Justin T. Okano
- & Sally Blower
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Article
| Open AccessEstimating COVID-19 mortality in Italy early in the COVID-19 pandemic
Estimates of COVID-19-related mortality are limited by incomplete testing. Here, the authors perform counterfactual analyses and estimate that there were 59,000–62,000 deaths from COVID-19 in Italy until 9th September 2020, approximately 1.5 times higher than official statistics.
- Chirag Modi
- , Vanessa Böhm
- & Uroš Seljak
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Article
| Open AccessThe impact of stopping and starting indoor residual spraying on malaria burden in Uganda
Indoor residual spraying (IRS) of insecticide is one of the primary malaria vector control initiatives, but implementation is limited. Here, the authors show that discontinuation of IRS in Uganda was associated with increased malaria incidence, and introduction of IRS was associated with decreased incidence.
- Jane F. Namuganga
- , Adrienne Epstein
- & Isabel Rodriguez-Barraquer
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Article
| Open AccessEtiological, epidemiological, and clinical features of acute diarrhea in China
Diarrhoea is a major cause of morbidity and mortality in China. Here, the authors present results from a large sentinel surveillance scheme from 217 hospitals in all 31 provinces in mainland China, including ~150,000 patients with acute diarrhoea and covering years 2009-2018.
- Li-Ping Wang
- , Shi-Xia Zhou
- & Jun Wang
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Comment
| Open AccessBreaking new ground in antimicrobial stewardship in companion animal veterinary practice
Singleton and colleagues publish in Nature Communications an intervention study to reduce antimicrobial usage in companion animal practice. They identify significant reductions in antimicrobial usage with their more active intervention group over approximately a 6-month period. The study offers an exciting way forward to explore further the trial interventions and assess alternative methods to improve antimicrobial stewardship in veterinary practice.
- David Brodbelt
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Article
| Open AccessLeveraging community mortality indicators to infer COVID-19 mortality and transmission dynamics in Damascus, Syria
Reported COVID-19 mortality rates have been relatively low in Syria, but there has been concern about overwhelmed health systems. Here, the authors use community mortality indicators and estimate that <3% of COVID-19 deaths in Damascus were reported as of 2 September 2020.
- Oliver J. Watson
- , Mervat Alhaffar
- & Patrick Walker
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Article
| Open AccessAssociation of sleep duration in middle and old age with incidence of dementia
Sleep dysregulation has been linked to dementia, but it is unknown whether sleep duration earlier in life is associated with dementia risk. Here, the authors show higher dementia risk associated with short sleep duration (six hours or less) in a longitudinal study of middle and older age adults.
- Séverine Sabia
- , Aurore Fayosse
- & Archana Singh-Manoux
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Article
| Open AccessReal-world stress resilience is associated with the responsivity of the locus coeruleus
Individuals vary considerably in how they are affected by stress. Here, the authors show that the severity of psychopathological symptoms triggered by prolonged real-life stress relate to fMRI-measured responsivity of the human brainstem arousal system and associated pupil responses.
- Marcus Grueschow
- , Nico Stenz
- & Birgit Kleim
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Article
| Open AccessGenetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions
Estimating the effects of non-pharmaceutical interventions for COVID-19 is challenging, partly due to variations in testing. Here, the authors use viral sequence data as an alternative means of inferring intervention effects, and show that delays in implementation resulted in more severe epidemics.
- Manon Ragonnet-Cronin
- , Olivia Boyd
- & Erik Volz
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Article
| Open AccessIncreased respiratory morbidity associated with exposure to a mature volcanic plume from a large Icelandic fissure eruption
Large fissure eruptions can cause air pollution events when the volcanic plume returns to the same area after the initial advisory has been lifted. Here, the authors show that these events had a significant impact on health care usage in Iceland, and the impact was exacerbated when advisories were not issued successfully.
- Hanne Krage Carlsen
- , Evgenia Ilyinskaya
- & Thorolfur Gudnason
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Article
| Open AccessSeroprevalence and correlates of SARS-CoV-2 neutralizing antibodies from a population-based study in Bonn, Germany
Population-based studies of SARS-CoV-2 seroprevalence are needed to understand levels of immunity and antibody dynamics. Here, the authors show that the seroprevalence in Bonn, Germany was low (<1%) following the first epidemic wave, and that neutralising antibodies waned within a few months.
- N. Ahmad Aziz
- , Victor M. Corman
- & Monique M. B. Breteler
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Article
| Open AccessOntology-driven weak supervision for clinical entity classification in electronic health records
In the electronic health record, using clinical notes to identify entities such as disorders and their temporality can inform many important analyses. Here, the authors present a framework for weakly supervised entity classification using medical ontologies and expert-generated rules.
- Jason A. Fries
- , Ethan Steinberg
- & Nigam H. Shah