Featured
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| Open AccessA small area model to assess temporal trends and sub-national disparities in healthcare quality
Here, authors present an approach to assess subnational healthcare quality, leveraging health facility survey data. The method jointly estimates indicators over space and time, and may provide insights to decision-makers and health service program managers.
- Adrien Allorant
- , Nancy Fullman
- & Robert C. Reiner Jr
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Article
| Open AccessWastewater-based epidemiology predicts COVID-19-induced weekly new hospital admissions in over 150 USA counties
Wastewater-based epidemiology is increasingly used to predict disease occurrence. Here, the authors use SARS-CoV-2 RNA concentrations in wastewater in machine learning models to predict COVID-19 related hospitalisation in the United States.
- Xuan Li
- , Huan Liu
- & Qilin Wang
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Article
| Open AccessKnowledge-enhanced visual-language pre-training on chest radiology images
Despite the success of multi-modal foundation models in natural language and vision tasks, their use in medical domains is limited. Here, the authors propose to train a foundation model for chest X-ray diagnosis that combines medical domain knowledge with vision-language representation learning.
- Xiaoman Zhang
- , Chaoyi Wu
- & Yanfeng Wang
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Article
| Open AccessEstimating long-term vaccine effectiveness against SARS-CoV-2 variants: a model-based approach
Evaluation of the effectiveness of COVID-19 vaccines is increasingly challenging due to high levels of exposure to infection and vaccination. Here, the authors use a model-based approach incorporating these factors and estimate that using a variant-matched rather than ancestral booster could prevent nearly twice as many hospitalisations and deaths over one year.
- Alexandra B. Hogan
- , Patrick Doohan
- & Azra C. Ghani
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Article
| Open AccessMolecular and phenotypic characteristics of RSV infections in infants during two nirsevimab randomized clinical trials
Nirsevimab binds the respiratory syncytial virus (RSV) fusion protein and has been tested for RSV prevention in clinical trials. Here, the authors analyse RSV from infections and show that binding site substitutions are rare and that over 99% of isolates remain susceptible to nirsevimab.
- Bahar Ahani
- , Kevin M. Tuffy
- & Tonya Villafana
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Article
| Open AccessHerpes zoster vaccine safety in the Aotearoa New Zealand population: a self-controlled case series study
The herpes zoster vaccine live was approved in New Zealand in 2018 for use in older adults. This self-controlled case-series study uses whole-country electronic health record data to assess the risk of serious adverse events associated with the vaccine, with results supporting its safety.
- James F. Mbinta
- , Alex X. Wang
- & Colin R. Simpson
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Article
| Open AccessDetecting shortcut learning for fair medical AI using shortcut testing
Diagnosing shortcut learning in clinical models is difficult, as sensitive attributes may be causally linked with disease. Using multitask learning, the authors propose a method to directly test for the presence of shortcut learning in clinical ML systems.
- Alexander Brown
- , Nenad Tomasev
- & Jessica Schrouff
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Article
| Open AccessPrevalence of diabetic retinopathy and vision-threatening diabetic retinopathy in adults with diabetes in China
Current data on the national distribution of diabetic retinopathy (DR) is lacking. Here, the authors show the national distribution, associated multi-level factors, and visual impairment of DR and vision-threatening DR in Chinese adults with diabetes.
- Xuhong Hou
- , Limin Wang
- & Weiping Jia
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Article
| Open AccessEpidemiological drivers of transmissibility and severity of SARS-CoV-2 in England
The COVID-19 pandemic has been characterised by periods of dominance of different SARS-CoV-2 variants. In this mathematical modelling study, the authors investigate the epidemiological properties of successive variants in England until early 2022 and quantify the impacts of control measures.
- Pablo N. Perez-Guzman
- , Edward Knock
- & Marc Baguelin
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Article
| Open AccessThe role of vaccination and public awareness in forecasts of Mpox incidence in the United Kingdom
An outbreak of Mpox in the UK began in May 2022 and peaked in July. In this modelling study, the authors show that the decline in cases was likely due to behavioural changes among high-risk populations, whilst vaccination could prevent a rebound.
- Samuel P. C. Brand
- , Massimo Cavallaro
- & Matt J. Keeling
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Article
| Open AccessReal-time environmental surveillance of SARS-CoV-2 aerosols
Rapid detection of respiratory pathogens circulating in indoor environments could facilitate improved infection prevention responses. In this proof-of-concept study, the authors develop a pathogen air quality monitor for real-time direct detection of SARS-CoV-2 aerosols and demonstrate its application in rooms of people with SARS-CoV-2 infections.
- Joseph V. Puthussery
- , Dishit P. Ghumra
- & Rajan K. Chakrabarty
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Article
| Open AccessInduction of lysosomal exocytosis and biogenesis via TRPML1 activation for the treatment of uranium-induced nephrotoxicity
The roles of lysosomes in uranium (U) decorporation and detoxification remain to be elucidated. Here, the authors demonstrate that TRPML1 activation is an attractive therapeutic strategy to induce lysosomal exocytosis and biogenesis for the treatment of U-induced nephrotoxicity.
- Dengqin Zhong
- , Ruiyun Wang
- & Honghong Chen
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Article
| Open AccessDetecting temporal and spatial malaria patterns from first antenatal care visits
Pregnant people visiting antenatal clinics may represent a useful sentinel surveillance population for monitoring infections such as malaria. Here, the authors investigate the potential of this approach by comparing malaria prevalence in pregnant people and children living in the same area of southern Mozambique.
- Arnau Pujol
- , Nanna Brokhattingen
- & Alfredo Mayor
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Article
| Open AccessLongitudinal body mass index and cancer risk: a cohort study of 2.6 million Catalan adults
Here, the authors show that longer duration and greater degree of overweight and obesity during early adulthood as well as younger age of onset of a high body mass index are associated with a higher risk of 18 cancer types.
- Martina Recalde
- , Andrea Pistillo
- & Talita Duarte-Salles
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Article
| Open AccessUsing mortuary and burial data to place COVID-19 in Lusaka, Zambia within a global context
Estimates of COVID-19 impacts in many low- and middle-income countries remain very uncertain, with lack of high-quality data. Here, the authors reconstruct epidemic dynamics in Lusaka, Zambia and estimate that, when accounting for demographic patterns, the epidemic severity is comparable with global norms.
- Richard J. Sheppard
- , Oliver J. Watson
- & Christopher J. Gill
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Article
| Open AccessA randomized non-inferiority trial of therapeutic strategy with immunosuppressants versus biologics for Vogt-Koyanagi-Harada disease
Different classes of biologic therapeutics have been assessed in the context of Vogt-Koyanagi-Harada disease. Here the authors compared cyclosporine immunosuppression or adalimumab in a randomised clinical trial for the treatment of patients with Vogt-Koyanagi-Harada disease and found non-inferiority upon treatment with cyclosporine.
- Zhenyu Zhong
- , Lingyu Dai
- & Peizeng Yang
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Article
| Open AccessGenomic epidemiology of Vibrio cholerae during a mass vaccination campaign of displaced communities in Bangladesh
The Cox’s Bazar area of Bangladesh has received a large number of Forcibly Displaced Myanmar Nationals. Cholera outbreaks have been detected in the area, and here, the authors perform genomic surveillance of cholera in the refugee and non-refugee population to infer the risk of epidemic spread.
- Alyce Taylor-Brown
- , Mokibul Hassan Afrad
- & Firdausi Qadri
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Article
| Open AccessPractical intelligent diagnostic algorithm for wearable 12-lead ECG via self-supervised learning on large-scale dataset
Intelligent diagnostic algorithms for ECG are becoming increasingly important to reduce the workload of cardiologists, enable telemedicine and real-time monitoring. Here, the authors show a model based on self-supervised learning that can classify 60 diagnostic terms for ECG.
- Jiewei Lai
- , Huixin Tan
- & Wei Yang
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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