Featured
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Article
| Open AccessMultiplexed ddPCR-amplicon sequencing reveals isolated Plasmodium falciparum populations amenable to local elimination in Zanzibar, Tanzania
Sequencing malaria parasites from low density infections in small amounts of dried blood is important for large-scale genomic surveillance. Here, the authors develop and validate a highly multiplexed droplet digital PCR-based amplicon deep sequencing assay and apply it to data from Zanzibar, Tanzania.
- Aurel Holzschuh
- , Anita Lerch
- & Cristian Koepfli
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Article
| Open AccessSnowflake-inspired and blink-driven flexible piezoelectric contact lenses for effective corneal injury repair
The cornea is susceptible to various injuries with a complicated repair process. Here, the authors propose a snowflake-inspired, blink-driven flexible piezoelectric contact lens for corneal injury repair.
- Guang Yao
- , Xiaoyi Mo
- & Yuan Lin
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Article
| Open AccessNanovesicles loaded with a TGF-β receptor 1 inhibitor overcome immune resistance to potentiate cancer immunotherapy
Targeting the TGF-β signaling pathway has been exploited to relieve immunosuppression in the tumor microenvironment. Here the authors describe the design of a nanoplatform integrating the TGF-β receptor 1 inhibitor LY2157299 and the ROS-responsive JQ1 pro-drug, promoting anti-tumor immune responses in preclinical cancer models.
- Mengxue Zhou
- , Jiaxin Wang
- & Haijun Yu
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Review Article
| Open AccessThe intersection of undernutrition, microbiome, and child development in the first years of life
In this review article, the authors provide an overview of the interrelationships between the microbiome and nutrition in child growth and healthy development and discuss the potential of the microbiome in undernutrition interventions.
- Fanette Fontaine
- , Sondra Turjeman
- & Omry Koren
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Article
| Open AccessNatural history of long-COVID in a nationwide, population cohort study
The long-term natural history of long-COVID is not well understood. In this population-based cohort study from Scotland, the authors describe symptom prevalence and health-related quality of life up to 18 months after a positive SARS-CoV-2 test and compare with matched test-negative controls.
- Claire E. Hastie
- , David J. Lowe
- & Jill P. Pell
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Article
| Open AccessPredicting the antigenic evolution of SARS-COV-2 with deep learning
SARS-CoV-2’s rapid evolution threatens public health. Here, authors present a deep learning approach to forecast high-risk mutations that may appear in the future, aiding vaccine development and enhancing preparedness against future variants.
- Wenkai Han
- , Ningning Chen
- & Xin Gao
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Article
| Open AccessAugmented temperature fluctuation aggravates muscular atrophy through the gut microbiota
Higher diurnal temperature range in humans correlates with the prevalence of sarcopenia. Here, the authors show that fluctuated temperature exposure accelerates muscle atrophy and dampens exercise performance via altering microbiota composition in aged mice.
- Ya Liu
- , Yifan Guo
- & Yan Huang
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Article
| Open AccessScarless wound healing programmed by core-shell microneedles
Effective reprogramming of chronic wound healing remains challenging due to the limited drug delivery efficacy hindered by physiological barriers, as well as the inappropriate dosing timing in distinct healing stages. Here, the authors report a core-shell structured microneedle array patch with programmed functions which dynamically modulates the wound immune microenvironment according to the varied healing phases
- Ying Zhang
- , Shenqiang Wang
- & Zhen Gu
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Article
| Open AccessVitrification and nanowarming enable long-term organ cryopreservation and life-sustaining kidney transplantation in a rat model
The possibility of banking cryopreserved organs could make transplantation medicine much more accessible. Here, the authors show that vitrification and nanowarming—cooling organs to an ice-free state followed by rapid rewarming using nanoparticles and magnetic fields—enables organ cryopreservation, long-term banking, and recovery of full function in a rat kidney transplant model.
- Zonghu Han
- , Joseph Sushil Rao
- & Erik B. Finger
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Article
| Open AccessPregnane X receptor agonist nomilin extends lifespan and healthspan in preclinical models through detoxification functions
The increase in detoxification gene expression is a common transcriptome marker for longevity interventions. Here, the authors show that nomilin extends lifespan and healthspan in animals through activation of PXR regulated detoxification functions.
- Shengjie Fan
- , Yingxuan Yan
- & Cheng Huang
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Review Article
| Open AccessRadiochemistry for positron emission tomography
Positron emission tomography is widely used to diagnose and monitor different disease states and interest in the technique has led to the demand for the development of new method for radiolabelling. Here the authors review the recent progress in the development of new PET probes.
- Jian Rong
- , Ahmed Haider
- & Steven H. Liang
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Article
| Open AccessNo evidence of sustained nonzoonotic Plasmodium knowlesi transmission in Malaysia from modelling malaria case data
Plasmodium knowlesi is a zoonotic malaria parasite that can infect humans, but whether human-mosquito-human transmission occurs is not known. Here, the authors use data from Malaysia and show, through mathematical modelling, that sustained non-zoonotic transmission is unlikely to be occurring in this setting.
- Kimberly M. Fornace
- , Hillary M. Topazian
- & Chris Drakeley
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Article
| Open AccessNewborn metabolomic signatures of maternal per- and polyfluoroalkyl substance exposure and reduced length of gestation
Mechanisms of the impact of PFAS (also known as forever chemicals) on adverse birth outcomes remain largely unknown. Here, authors identified tissue neogenesis, neuroendocrine function, and redox homeostasis as imprints of prenatal PFAS exposures and reduced gestational age in the newborn metabolome.
- Kaitlin R. Taibl
- , Anne L. Dunlop
- & Donghai Liang
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Article
| Open AccessEvidence-driven spatiotemporal COVID-19 hospitalization prediction with Ising dynamics
Amid the COVID-19 pandemic, accurate hospitalization predictions are vital. Here, the authors show that a deep learning model based on statistical mechanics is able to forecast hospitalizations, supporting targeted vaccination efforts.
- Junyi Gao
- , Joerg Heintz
- & Jimeng Sun
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Article
| Open AccessNeural crest E-cadherin loss drives cleft lip/palate by epigenetic modulation via pro-inflammatory gene–environment interaction
Cleft lip and palate is a common birth defect thought to involve both genetic and environmental components in its etiology. Here they identify a mechanism involving inflammation and E-cadherin mutations that reduces neural crest migration, leading to craniofacial defects.
- Lucas Alvizi
- , Diogo Nani
- & Roberto Mayor
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Article
| Open AccessComparative mRNA booster effectiveness against death or hospitalization with COVID-19 pneumonia across at-risk US Veteran populations
mRNA boosters have been shown to be effective against severe COVID-19 illness. In this work, the authors show that in high-risk populations, three doses of mRNA-1273 vaccine instead of BNT162b2 vaccine conferred a small benefit against death or hospitalization with COVID-19 pneumonia.
- J. Daniel Kelly
- , Samuel Leonard
- & Salomeh Keyhani
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Article
| Open AccessLong COVID risk and pre-COVID vaccination in an EHR-based cohort study from the RECOVER program
The extent to which COVID-19 vaccination protects against long COVID is not well understood. Here, the authors use electronic health record data from the United States and find that, for people who received their vaccination prior to infection, vaccination was associated with lower incidence of long COVID.
- M. Daniel Brannock
- , Robert F. Chew
- & Stuart Katz
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Article
| Open AccessDecentralized federated learning through proxy model sharing
Federated learning enables multi-institutional collaborations on decentralized data with improved privacy protection. Here, authors propose a new scheme for decentralized federated learning with much less communication overhead and stronger privacy.
- Shivam Kalra
- , Junfeng Wen
- & H. R. Tizhoosh
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Article
| Open AccessImpaired humoral immunity to BQ.1.1 in convalescent and vaccinated patients
Dewald et al. show a high Spike-IgG seroprevalence (95%) in a multicenter study with 1,411 participants. They determined a substantially reduced serum neutralization against the SARS-CoV-2 VOCs BA.4/5 and BQ.1.1. and explored predictive factors of neutralizing activity.
- Felix Dewald
- , Martin Pirkl
- & Florian Klein
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Article
| Open AccesssaRNA vaccine expressing membrane-anchored RBD elicits broad and durable immunity against SARS-CoV-2 variants of concern
Vaccines with broad and long-lasting protection against variants of concern are still limited. Here, the authors report a self-amplifying RNA (saRNA) vaccine expressing a membrane-anchored SARS-CoV-2 Spike RBD and show that it elicits broad, durable and protective immunity in small animal models and NHPs.
- Mai Komori
- , Takuto Nogimori
- & Wataru Akahata
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Article
| Open AccessModelling the economic burden of SARS-CoV-2 infection in health care workers in four countries
Health care workers were at high risk of SARS-CoV-2 infection in the early stage of the pandemic, and this had knock-on effects including secondary infections and disruptions in health service delivery. Here, the authors estimate the economic impacts of SARS-CoV-2 infections in health care workers at the society level in five low- and middle-income country settings.
- Huihui Wang
- , Wu Zeng
- & Mickey Chopra
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Article
| Open AccessDeep learning to estimate lung disease mortality from chest radiographs
Risk assessment of lung disease mortality is currently limited. Here, authors show that deep learning can estimate lung disease mortality from a chest x-ray beyond risk factors, which may help to identify individuals at risk in screening and cancer populations.
- Jakob Weiss
- , Vineet K. Raghu
- & Hugo J.W.L. Aerts
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Article
| Open AccessModelling the impact of interventions on imported, introduced and indigenous malaria infections in Zanzibar, Tanzania
Malaria elimination is defined by WHO as the absence of recent indigenous cases in an area. In this study, the authors develop a metapopulation model that identifies indigenous cases and use it to investigate the likelihood of malaria elimination in Zanzibar under different intervention scenarios.
- Aatreyee M. Das
- , Manuel W. Hetzel
- & Nakul Chitnis
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Article
| Open AccessThe impact of introduction of the 10-valent pneumococcal conjugate vaccine on pneumococcal carriage in Nigeria
Nigeria has the highest incidence of pneumococcal disease in Africa and introduced the 10-valent pneumococcal vaccine for infants between 2014 and 2016. Here, the authors conduct repeated cross-sectional surveys to analyse the impact of the vaccination campaign on pneumococcal carriage and serotype distribution.
- Aishatu L. Adamu
- , J. Ojal
- & Ifedayo M. O. Adetifa
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Article
| Open AccessVirus diversity, wildlife-domestic animal circulation and potential zoonotic viruses of small mammals, pangolins and zoo animals
Monitoring the diversity of viruses infecting animals is important for assessing zoonotic risk. Here, the authors use metatranscriptomics to characterise the viromes of small mammals, pangolins, and zoo animals in China to identify potentially zoonotic viruses.
- Xinyuan Cui
- , Kewei Fan
- & Yongyi Shen
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Article
| Open AccessAn aptamer-based depot system for sustained release of small molecule therapeutics
Controlled delivery of small molecule therapeutics is challenging. Here the authors report a simple and effective aptamer-based depot system where the formation of aptamer/drug complexes leads to sustained release, and using this approach demonstrate improved in vivo delivery of channel blockers.
- Dali Wang
- , Yang Li
- & Christopher B. Weldon
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Perspective
| Open AccessLess is more: Antibiotics at the beginning of life
Fear of missing neonatal sepsis has led to early in life antibiotic administration, even without culture-proven sepsis. Here, the authors discuss the potential impact on antimicrobial resistance, and chronic disease later in life, due to effect on the developing microbiome, suggesting a factual based approach in quantifying burden of treatment in relation to the burden of disease.
- Martin Stocker
- , Claus Klingenberg
- & Eric Giannoni
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Article
| Open AccessResurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong
Hong Kong experienced a large wave of COVID-19 in early 2022 driven by Omicron BA.2. Here, the authors describe the epidemiological dynamics of this wave and show discordant inferences based on genomic and epidemiological data that underscore the need to improve near real-time epidemic growth estimates.
- Ruopeng Xie
- , Kimberly M. Edwards
- & Vijaykrishna Dhanasekaran
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Article
| Open AccessBridging clinic and wildlife care with AI-powered pan-species computational pathology
Artificial Intelligence (AI) has the potential of assisting the study and diagnosis of veterinary cancers. Here, the authors build a cancer digital pathology atlas encompassing multiple animal species and demonstrate an AI approach for comparative pathology, which yields insights about immune response and morphological similarities.
- Khalid AbdulJabbar
- , Simon P. Castillo
- & Yinyin Yuan
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Article
| Open AccessSample-to-answer platform for the clinical evaluation of COVID-19 using a deep learning-assisted smartphone-based assay
The lateral flow assay (LFA) has been considered a rapid test tool but with low sensitivity hampering the precise diagnosis. Here, the authors report bioengineered enrichment tools for LFAs with enhanced sensitivity and specificity that can reinforce LFA’s clinical performance.
- Seungmin Lee
- , Sunmok Kim
- & Jeong Hoon Lee
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Article
| Open AccessMachine learning prediction of the degree of food processing
Evidence suggests that increased consumption of ultra-processed food has adverse health implications, however, it remains difficult to classify processed food. Here, the authors introduce FPro, a machine learning-based score predicting the degree of food processing.
- Giulia Menichetti
- , Babak Ravandi
- & Albert-László Barabási
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Article
| Open AccessInterstitial lung disease diagnosis and prognosis using an AI system integrating longitudinal data
Accurate diagnosis of interstitial lung disease subtypes and prediction of patient survival rates remains challenging. Here, the authors develop AI algorithms to combine patient’s clinical history and longitudinal CT images to help clinicians diagnose and classify subtypes and dynamically predict disease progression and prognosis.
- Xueyan Mei
- , Zelong Liu
- & Yang Yang
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Article
| Open AccessHealth disparities among older adults following tropical cyclone exposure in Florida
Tropical cyclones pose a significant threat to human health. Here, authors show associations between tropical cyclones and risk of cause-specific hospitalizations, with elevated risks according to neighborhood-level poverty, homeownership and urbanicity.
- K. Burrows
- , G. B. Anderson
- & M. L. Bell
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Article
| Open AccessAccounting for assay performance when estimating the temporal dynamics in SARS-CoV-2 seroprevalence in the U.S.
SARS-CoV-2 seroprevalence surveys aim to estimate the proportion of the population that has been infected, but their accuracy depends on the characteristics of the test assay used. Here, the authors use statistical models to assess the impact of the use of different assays on estimates of seroprevalence in the United States.
- Bernardo García-Carreras
- , Matt D. T. Hitchings
- & Derek A. T. Cummings
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Article
| Open AccessDrivers of SARS-CoV-2 testing behaviour: a modelling study using nationwide testing data in England
SARS-CoV-2 testing rates have varied during the pandemic but the drivers of changes in testing behaviour are unclear. Here, the authors link national testing data from England to indicators of epidemic trends to describe how testing varies according to level of virus transmission, disease susceptibility/severity, public health measures, and risk perception.
- Younjung Kim
- , Christl A. Donnelly
- & Pierre Nouvellet
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Article
| Open AccessComparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in the Brazilian State of Amazonas
The Amazonas region has been the most heavily affected by COVID-19 in Brazil. In this study, the authors conduct phylodynamic analyses to assess SARS-CoV-2 lineage replacement dynamics in the region and infer the impact of population immunity on the spread and severity of the Delta and Omicron variants.
- Ighor Arantes
- , Gonzalo Bello
- & Felipe Gomes Naveca
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Article
| Open AccessEffectiveness of inactivated COVID-19 vaccines among older adults in Shanghai: retrospective cohort study
Inactivated COVID-19 vaccines have been widely used in China, but there is limited real-world evidence for their effectiveness in this setting. Here, the authors estimate effectiveness of inactivated vaccines for people aged 60 or older in Shanghai during a period when Omicron was the dominant circulating variant.
- Zhuoying Huang
- , Shuangfei Xu
- & Weibing Wang
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Article
| Open AccessThe evolution and international spread of extensively drug resistant Shigella sonnei
An increase in shigellosis cases among men who have sex with men in the United Kingdom has been linked to an extensively drug-resistant strain of Shigella sonnei. In this genomic epidemiology study, the authors investigate the genetic basis, evolutionary history, and international dissemination of the outbreak strain.
- Lewis C. E. Mason
- , David R. Greig
- & Kate S. Baker
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Article
| Open AccessData-driven analysis to understand long COVID using electronic health records from the RECOVER initiative
In this study, the authors characterise post-acute sequelae of SARS-CoV-2 (PASC) in two large cohorts based on electronic health records from the USA. They identify a broad range of PASC-related conditions which were only partially replicated across the two cohorts, indicating possible heterogeneity between populations.
- Chengxi Zang
- , Yongkang Zhang
- & Rainu Kaushal
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Article
| Open AccessAssociations between mental health, blood pressure and the development of hypertension
Mental and cardiovascular health interact in complex ways. Here, the authors demonstrate an association of blood pressure with depressive symptoms, well-being, and emotion-related brain activity that may be relevant to the development of hypertension.
- H. Lina Schaare
- , Maria Blöchl
- & Arno Villringer
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Article
| Open AccessEffectiveness of BNT162b2 after extending the primary series dosing interval in children and adolescents aged 5–17
Extending the interval between doses of mRNA Covid-19 vaccines has been linked with a reduced risk of myocarditis in children and adolescents, but impacts on vaccine effectiveness are not known. Here, the authors perform a nested case-control study using data from Hong Kong and find evidence of reduced risk of infection following a longer dosing interval.
- Francisco Tsz Tsun Lai
- , Min Fan
- & Esther Wai Yin Chan
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Article
| Open AccessLong-term measles antibody profiles following different vaccine schedules in China, a longitudinal study
The timing of measles vaccination in infants affects the risk of infection in young children and the duration of protection provided. Here, the authors investigate optimal vaccination timing by characterising antibody kinetics following different vaccine schedules in two cohorts of children in southern China.
- Qianli Wang
- , Wei Wang
- & Hongjie Yu
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Article
| Open AccessRisk of death following COVID-19 vaccination or positive SARS-CoV-2 test in young people in England
Rare but serious cardiac disease side effects have been linked to COVID-19 vaccinations, especially in young people. Here, the authors find very little evidence of an association between vaccination and mortality, except for in females after a non mRNA vaccine, but show an increased risk of death following COVID-19 infection
- Vahé Nafilyan
- , Charlotte R. Bermingham
- & James C. Doidge
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Article
| Open AccessThe genomic epidemiology of Escherichia albertii infecting humans and birds in Great Britain
Escherichia albertii is an emerging gastrointestinal pathogen that causes disease in humans and animals, notably birds. In this genomic epidemiology study, the authors investigate characteristics of isolates sampled from humans and birds in Great Britain and find that they tend to cluster separately.
- Rebecca J. Bengtsson
- , Kate S. Baker
- & Becki Lawson
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Article
| Open AccessTransmission modeling to infer tuberculosis incidence prevalence and mortality in settings with generalized HIV epidemics
Accurately estimating the burden of tuberculosis is challenging due to incomplete registration systems and the relationship with HIV. Here, the authors develop a Bayesian modelling strategy accounting for these factors that estimates age- and country-specific annual risks of infection and the proportion resulting from recent infection.
- Peter J. Dodd
- , Debebe Shaweno
- & Helen Ayles
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Article
| Open AccessPredicting vaccine effectiveness against severe COVID-19 over time and against variants: a meta-analysis
In this study, the authors perform a meta-analysis of COVID-19 vaccine effectiveness studies and compare observed protection against severe disease with model-based estimates of neutralising antibody titres. Their results show that SARS-CoV-2 antibody titres are predictive of protection against severe COVID-19 disease.
- Deborah Cromer
- , Megan Steain
- & Miles P. Davenport
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Article
| Open AccessSingle test-based diagnosis of multiple cancer types using Exosome-SERS-AI for early stage cancers
Early detection of multiple cancers through a single method could be clinically important. Here the authors report the diagnostic performance for early detection for multiple cancers using surface-enhanced Raman spectroscopy (SERS) profiles of exosomes from a single blood test and artificial intelligence in a retrospective study design.
- Hyunku Shin
- , Byeong Hyeon Choi
- & Yeonho Choi
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Article
| Open AccessInteroperable slide microscopy viewer and annotation tool for imaging data science and computational pathology
There is a lack of standardisation in slide microscopy imaging data. Here the authors report Slim, an open-source, web-based slide microscopy viewer implementing the Digital Imaging and Communications in Medicine (DICOM) standard to achieve interoperability with a range of existing medical imaging systems.
- Chris Gorman
- , Davide Punzo
- & Markus D. Herrmann
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Article
| Open AccessSpatial immunization to abate disease spreading in transportation hubs
Efficient spatial targeting of interventions could reduce the spread of infections in transportation hubs. Here, the authors assess the optimal locations to target in Heathrow airport using disease transmission models informed by a contact network based on anonymised location data from 200,000 individuals.
- Mattia Mazzoli
- , Riccardo Gallotti
- & José J. Ramasco