Featured
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| Open AccessSystematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples
SARS-CoV-2 coinfections may lead to recombination events which could be important in the emergence of new variants. Here, the authors develop an automated bioinformatics pipeline to identify coinfections in genomic data and test it on >2 million publicly available raw read data sets collected globally.
- Orsolya Anna Pipek
- , Anna Medgyes-Horváth
- & István Csabai
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Article
| Open AccessConvergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China
Bacteria in the same environment can share genetic material but the extent to which this influences development of antimicrobial resistance is unclear. Here, the authors investigate the evidence for co-evolution of antimicrobial resistance in bacteria found coexisting in animals and the environment in chicken farms and slaughterhouses in China.
- Michelle Baker
- , Xibin Zhang
- & Tania Dottorini
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Article
| Open AccessRedirecting antibody responses from egg-adapted epitopes following repeat vaccination with recombinant or cell culture-based versus egg-based influenza vaccines
Here the authors report an exploratory analysis of a clinical trial that tested different influenza virus vaccination platforms. The results show that multiple seasons of recombinant or cell-based influenza vaccinations may be needed to redirect antibody responses away from immune memory to egg-adapted epitopes and refocus on epitopes on the circulating viruses.
- Feng Liu
- , F. Liaini Gross
- & Min Z. Levine
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Article
| Open AccessIncidence and transmission of respiratory syncytial virus in urban and rural South Africa, 2017-2018
Respiratory syncytial virus (RSV) causes a high burden of disease in children, particularly in lower- and middle-income countries. In this prospective household-based observational cohort study in South Africa, the authors estimate the incidence of RSV and identify risk factors for transmission.
- Cheryl Cohen
- , Jackie Kleynhans
- & Stefano Tempia
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Article
| Open AccessQuantitatively assessing early detection strategies for mitigating COVID-19 and future pandemics
Monitoring samples from hospital patients, wastewater, or air travel may enable early detection of pathogens. Here, the authors assess how these surveillance systems could have impacted detection of COVID-19 and their potential benefits for detection of other emerging pathogens.
- Andrew Bo Liu
- , Daniel Lee
- & Michael Springer
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Article
| Open AccessOptimal timing of nirmatrelvir/ritonavir treatment after COVID-19 symptom onset or diagnosis: target trial emulation
Nirmatrelvir/ritonavir can reduce COVID-19 severity when initiated within five days of symptom onset but the optimal timing within this window is unknown. Here, the authors emulate a randomised trial using electronic health records from Hong Kong and find evidence for a benefit of early treatment initiation.
- Carlos K. H. Wong
- , Jonathan J. Lau
- & Joseph T. Wu
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Article
| Open AccessDietary circadian rhythms and cardiovascular disease risk in the prospective NutriNet-Santé cohort
The relation between daily meal and fasting timing with cardiovascular disease incidence remains unclear. Here, authors show that a later daily meal timing is associated with increased cardiovascular disease risk, especially in women. This study suggests that adopting earlier daily eating patterns may be beneficial for cardiovascular prevention.
- Anna Palomar-Cros
- , Valentina A. Andreeva
- & Bernard Srour
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Article
| Open AccessBinge-pattern alcohol consumption and genetic risk as determinants of alcohol-related liver disease
Deaths from alcohol-related liver disease have sharply increased following the Covid-19 pandemic. Here, the authors show that binge-pattern alcohol consumption, genetic factors and the presence of diabetes mellitus confer the greatest risk, allowing targeted interventions for high-risk individuals.
- Chengyi Ding
- , Linda Ng Fat
- & Gautam Mehta
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Article
| Open AccessEffects of accelerometer-based sedentary time and physical activity on DEXA-measured fat mass in 6059 children
Childhood obesity remains a global epidemic. Here, using objective measurements, the authors show that sedentary time increased from 6 h/day in childhood to 9 h/day in young adulthood, and was cumulatively associated with increased total and trunk fat mass. Both light or moderate-to-vigorous physical activity similarly partly reversed risk.
- Andrew O. Agbaje
- , Wei Perng
- & Tomi-Pekka Tuomainen
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Article
| Open AccessTemperature-related death burden of various neurodegenerative diseases under climate warming: a nationwide modelling study
Examining non-optimal temperatures’ influence on neurodegenerative diseases amid climate warming is vital for public health. Here, the authors project a notable net increase of death burden from neurodegenerative diseases after the mid-21st century.
- Peng Yin
- , Ya Gao
- & Haidong Kan
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Article
| Open AccessPhylogeny and molecular evolution of the first local monkeypox virus cluster in Guangdong Province, China
The first known local mpox outbreak in Guangdong Province, China occurred in June 2023. Here, the authors perform phylogenetic and molecular evolution analysis of ten mpox virus genome sequences from this outbreak, and place them in the context of other samples detected in surrounding regions.
- Jianhai Yu
- , Xin Zhang
- & Baisheng Li
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Article
| Open AccessInteractions between climate change, urban infrastructure and mobility are driving dengue emergence in Vietnam
The geographic distribution of dengue has been expanding in recent decades, and Vietnam is one of the most severely affected countries. In this study, the authors use Bayesian hierarchical modelling to investigate the socio-environmental and climatic drivers of dengue incidence in Vietnam and how they vary across the country.
- Rory Gibb
- , Felipe J. Colón-González
- & Rachel Lowe
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Article
| Open AccessHigh-throughput target trial emulation for Alzheimer’s disease drug repurposing with real-world data
Target trial emulation (TTE) simulates randomized controlled trials using real world data (RWD). Here, authors show the effectiveness of different TTE strategies to identify drug candidates that could be potentially repurposed to Alzheimer’s disease using two large scale RWD warehouses.
- Chengxi Zang
- , Hao Zhang
- & Fei Wang
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Article
| Open AccessEstimating the potential impact and diagnostic requirements for SARS-CoV-2 test-and-treat programs
Antivirals are now available for treating COVID-19 but must be used early in the course of infection to be effective. Here, the authors use mathematical modelling to assess the potential public health impacts of antiviral use considering different levels of testing and country sociodemographic characteristics.
- Alvin X. Han
- , Emma Hannay
- & Colin A. Russell
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Article
| Open AccessTrue prevalence of long-COVID in a nationwide, population cohort study
Determining the prevalence of Long COVID is challenging because many symptoms attributed to the syndrome could have other causes. Here, the authors estimate the prevalence of Long COVID in Scotland by comparing rates of symptoms reported by people with and without history of SARS-CoV-2 infection.
- Claire E. Hastie
- , David J. Lowe
- & Jill P. Pell
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Article
| Open AccessUtilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems
COVID-19 has impacted health systems unequally and widespread SARS-CoV-2 testing for community surveillance has been limited globally. This work in Malawi highlights how river and wastewater can be used to detect emerging SARS-CoV-2 waves, identify variants of concern, and provide an early warning system.
- Kayla G. Barnes
- , Joshua I. Levy
- & Nicholas Feasey
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Article
| Open AccessPersistent humoral immune response in youth throughout the COVID-19 pandemic: prospective school-based cohort study
Understanding the immune responses of school-aged children to SARS-CoV-2 is important for designing public health measures. Here, the authors report findings from cross-sectional and longitudinal anti-SARS-CoV-2 antibody measurements in a school-based study in Zurich, Switzerland, from 2020-2022.
- Alessia Raineri
- , Thomas Radtke
- & Susi Kriemler
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Article
| Open AccessEpidemiology, mortality, and health service use of local-level multimorbidity patterns in South Spain
Multimorbidity—the occurrence of chronic diseases together—represents a major challenge for healthcare systems. Here, the authors characterise multimorbidity patterns in a large dataset of patients residing in southern Spain and show the unequal distribution of multimorbidity patterns along different socioeconomic areas at the local level.
- Javier Alvarez-Galvez
- , Esther Ortega-Martin
- & Jesus Carretero-Bravo
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Article
| Open AccessAssessing the value of integrating national longitudinal shopping data into respiratory disease forecasting models
Novel indicators of infectious disease prevalence could improve real-time surveillance and support healthcare planning. Here, the authors show that sales data for non-prescription medications from a UK high street retailer can improve the accuracy of models forecasting mortality from respiratory infections.
- Elizabeth Dolan
- , James Goulding
- & Laila J. Tata
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Article
| Open AccessEvaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty
The US COVID-19 Scenario Modeling Hub produced medium to long term projections based on different epidemic scenarios. In this study, the authors evaluate 14 rounds of projections by comparing them to the epidemic trajectories that occurred, and discuss lessons learned for future similar projects.
- Emily Howerton
- , Lucie Contamin
- & Justin Lessler
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Article
| Open AccessThe burden of post-acute COVID-19 symptoms in a multinational network cohort analysis
Post-acute COVID-19 condition is difficult to quantify because it includes a range of symptoms that may have other causes. In this study, the authors use primary care data from England and Catalonia, Spain, to estimate the incidence of the condition and identify symptoms that occur more frequently following infection than in uninfected controls.
- Kristin Kostka
- , Elena Roel
- & Annika M. Jödicke
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Article
| Open AccessThe metabolic, virulence and antimicrobial resistance profiles of colonising Streptococcus pneumoniae shift after PCV13 introduction in urban Malawi
Pneumococcal vaccination has been shown to promote emergence of non-vaccine S. pneumoniae serotypes. Here, the authors use data from Malawi to investigate whether vaccine introduction also results in changes in metabolic, virulence, and antimicrobial resistance profiles of circulating strains.
- Uri Obolski
- , Todd D. Swarthout
- & Robert S. Heyderman
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Article
| Open AccessCircadian disturbances and frailty risk in older adults
The relationship between circadian function and frailty is not well understood. Here, the authors show that disturbances in circadian rest-activity rhythms were associated with an elevated frailty risk and faster progress of frailty in older adults.
- Ruixue Cai
- , Lei Gao
- & Peng Li
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Article
| Open AccessEvaluation of pragmatic oxygenation measurement as a proxy for Covid-19 severity
There is a need for an accurate measure of pulmonary oxygenation function that can be used as an intermediate endpoint in pragmatic clinical trials, to increase statistical power and efficiency. Here, the authors show that the S/F94, a modification of the S/F ratio, is a simple, meaningful and effective intermediate outcome measure.
- Maaike C. Swets
- , Steven Kerr
- & J. Kenneth Baillie
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Article
| Open AccessImpact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia
In this study, the authors develop a mathematical modelling framework to estimate the impacts of non-pharmaceutical interventions and vaccination on COVID-19 incidence. The model accounts for changes in SARS-CoV-2 variant and population immunity, and here they use it to investigate epidemic dynamics in French Polynesia.
- Lloyd A. C. Chapman
- , Maite Aubry
- & Adam J. Kucharski
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Article
| Open AccessMalaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal
Senegal has initiated a national sentinel surveillance program for malaria parasite genetics. Here, the authors report data from the first year of the program and use it to investigate local malaria incidence, patterns of transmission, and genetic loci under selection.
- Stephen F. Schaffner
- , Aida Badiane
- & Sarah K. Volkman
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Comment
| Open AccessThe counterintuitive implications of superspreading diseases
The superspreading that characterized SARS and now COVID-19 can be rapidly quantified; however, its implications for outbreak control were never well understood. Recent studies point to its profound impact on outbreak dynamics and prospects for effective control of a future Disease X. These insights necessitate research into the mechanisms, impact and different modes of superspreading more widely.
- Bjarke Frost Nielsen
- , Kim Sneppen
- & Lone Simonsen
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Comment
| Open AccessLessons for cross-species viral transmission surveillance from highly pathogenic avian influenza Korean cat shelter outbreaks
In this Comment, the authors describe recent outbreaks of highly pathogenic avian influenza in cat shelters in Seoul, South Korea. They discuss potential routes of transmission and describe implications for surveillance of spillover infections in animals in non-agricultural settings.
- Younjung Kim
- , Guillaume Fournié
- & Pierre Nouvellet
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Article
| Open AccessCumulative effect of PM2.5 components is larger than the effect of PM2.5 mass on child health in India
Health impact of air pollution is estimated using PM2.5 mass as exposure metric. Here authors show that the impacts on child health is underestimated in India using this metric relative to the cumulative impact of the various PM2.5 components.
- Ekta Chaudhary
- , Franciosalgeo George
- & Unnati Mehta
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Article
| Open AccessImpact of COVID-19 on mortality in coastal Kenya: a longitudinal open cohort study
SARS-CoV-2-associated mortality estimates for sub-Saharan Africa are uncertain due to lack of comprehensive surveillance systems. Here, the authors analyse data from a detailed surveillance system in Kilifi, Kenya and find that excess mortality rates were relatively low, except for older adults.
- M. Otiende
- , A. Nyaguara
- & J. A. G. Scott
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Article
| Open AccessEffectiveness of the second COVID-19 booster against Omicron: a large-scale cohort study in Chile
This study assesses the effectiveness of a second COVID-19 mRNA booster vaccine against severe disease using data from Chile. The authors find that the effectiveness of the second mRNA booster was high with a range of different background vaccination schemes, but there was evidence of waning over time.
- Alejandro Jara
- , Cristobal Cuadrado
- & Rafael Araos
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Article
| Open AccessUsing drivers and transmission pathways to identify SARS-like coronavirus spillover risk hotspots
Identification of areas with risk factors for spillover of viruses from animals to humans could assist with early detection of emerging infectious diseases. In this study, the authors characterise potential risks for spillover of SARS-like viruses from bats to humans and identify geographical regions in which multiple risk factors cluster together.
- Renata L. Muylaert
- , David A. Wilkinson
- & David T. S. Hayman
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Article
| Open AccessMortality risks from a spectrum of causes associated with sand and dust storms in China
Sand and dust storms pose considerable health risks worldwide. Here, the authors conduct a nationwide multicenter time-series study to examine sand and dust storm-associated mortality risks.
- Can Zhang
- , Meilin Yan
- & Tiantian Li
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Article
| Open AccessLong-term health impacts of COVID-19 among 242,712 adults in England
The duration of symptomatic COVID-19 and its impacts on health and quality of life are not well understood. In this study, the authors report results from a survey of ~275,000 adults in England and find that persistent COVID-19 is relatively rare but is associated with poorer mental health and health-related quality of life.
- Christina J. Atchison
- , Bethan Davies
- & Paul Elliott
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Article
| Open AccessIndividual level analysis of digital proximity tracing for COVID-19 in Belgium highlights major bottlenecks
Digital proximity tracing apps were widely used during the COVID-19 pandemic but have not been thoroughly evaluated. Here, the authors use data from students in Leuven, Belgium and estimate that apps notified only ~4% exposed contacts, had a 1–2 day delay for notification, and identified fewer infected contacts than manual contact tracing.
- Caspar Geenen
- , Joren Raymenants
- & Emmanuel André
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Article
| Open AccessEpidemiology of Plasmodium malariae and Plasmodium ovale spp. in Kinshasa Province, Democratic Republic of Congo
Non-falciparum malaria may cause a significant disease burden in highly endemic regions, but epidemiological data is limited. In this study, the authors estimate the incidence and prevalence of P. malariae, P. ovale spp., in Kinshasa, Democratic Republic of Congo and compare to P. falciparum, which known to be common in the region.
- Rachel Sendor
- , Kristin Banek
- & Jonathan B. Parr
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Article
| Open AccessSARS-CoV-2 genomic surveillance in wastewater as a model for monitoring evolution of endemic viruses
SARS-CoV-2 wastewater surveillance could provide an important means of monitoring population trends as clinical testing decreases. Here, the authors demonstrate the use of wastewater to track variants of concern through a sentinel wastewater surveillance system in South Africa.
- Mukhlid Yousif
- , Said Rachida
- & Kerrigan McCarthy
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Article
| Open AccessA hybrid register and questionnaire study of Covid-19 and post-acute sick leave in Denmark
Authors utilise a questionnaire-based approach to survey self-reported, post-acute sick leave and risk factors in cases of SARS-CoV-2.
- Elisabeth O’Regan
- , Ingrid Bech Svalgaard
- & Anders Hviid
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Article
| Open AccessViral kinetics of sequential SARS-CoV-2 infections
In this study, the authors compare the viral kinetics of first and second SARS-CoV-2 infections using data from an occupational surveillance scheme in the National Basketball League. They find that second infections tend to have a faster clearance time, and that clearance times in first and second infections were positively correlated.
- Stephen M. Kissler
- , James A. Hay
- & Yonatan H. Grad
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Article
| Open AccessGlobal burden of disease due to rifampicin-resistant tuberculosis: a mathematical modeling analysis
Rifampicin-resistant tuberculosis (RR-TB) requires longer, more toxic therapy than rifampicin-sensitive disease and is associated with a higher occurrence of long-term sequelae. In this mathematical modeling study, the authors estimate that incident RR-TB in 2020 will be responsible for ~6.9 million disability-adjusted life years; 44% due to post-tuberculosis sequelae.
- Nicolas A. Menzies
- , Brian W. Allwood
- & Ted Cohen
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Article
| Open AccessSugar-sweetened beverage intakes among adults between 1990 and 2018 in 185 countries
Recent estimates of sugar-sweetened beverages (SSBs) intake are generally unavailable. Here the authors show a global SSBs intake of 2.7 servings/week in 2018 in adults (range: 0.7 South Asia, 7.8 Latin America/Caribbean); intakes were higher among males, younger, more educated, and urban adults.
- Laura Lara-Castor
- , Renata Micha
- & Rubina Hakeem
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Article
| Open AccessUncovering the complex relationship between balding, testosterone and skin cancers in men
Male-pattern baldness (MPB) is related to dysregulation of androgens. Here, authors show that MPB (but not androgens) is associated with skin cancer risk, particularly in the scalp region, suggesting that sun exposure, rather than androgens, is the main driver.
- Jue-Sheng Ong
- , Mathias Seviiri
- & Matthew H. Law
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Article
| Open AccessSelf-sampling monkeypox virus testing in high-risk populations, asymptomatic or with unrecognized Mpox, in Spain
The monkeypox outbreak in 2022 was of global concern. Here the authors present results from an observational study providing self-sampling testing to a high-risk population in a community center in Spain and diagnose monkeypox infection in asymptomatic individuals.
- Cristina Agustí
- , Héctor Martínez-Riveros
- & Jordi Casabona
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Article
| Open AccessPredictors of the post-COVID condition following mild SARS-CoV-2 infection
In this study, the authors investigate the incidence and risk factors for post-COVID condition among people who had a mild initial SARS-CoV-2 infection in Norway. They use national linked registry data including ~215,000 individuals with a positive SARS-CoV-2 test who were not hospitalised and followed them up for 180 days after infection.
- B-A. Reme
- , J. Gjesvik
- & K. Magnusson
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Article
| Open AccessDisentangling age, gender, and racial/ethnic disparities in multiple myeloma burden: a modeling study
Multiple myeloma (MM) is a haematological malignancy that is preceded by monoclonal gammopathy of undetermined significance (MGUS). Here, the authors use a mechanistic model fitted to surveillance data from the United States to investigate whether variation in MM is best explained by incidence of MGUS or rate of progression to MM.
- John H. Huber
- , Mengmeng Ji
- & Su-Hsin Chang
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Article
| Open AccessmRNA-1273 bivalent (original and Omicron) COVID-19 vaccine effectiveness against COVID-19 outcomes in the United States
Bivalent mRNA COVID-19 vaccines have been developed to provide broader protection against SARS-CoV-2 variants. In this cohort study based on electronic health records from the United States, the authors estimate the effectiveness of bivalent, compared to monovalent, vaccines and no vaccination against a range of COVID-19-related outcomes.
- Hung Fu Tseng
- , Bradley K. Ackerson
- & Lei Qian
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Article
| Open AccessBreastfeeding and impact on childhood hospital admissions: a nationwide birth cohort in South Korea
Benefits of breastfeeding are well established, but a comprehensive study about its impacts on hospitalizations is lacking. Here, the authors use Korean nationwide birth cohort data (n = 1,608,540) and find that breastfeeding for at least 6 months was associated with a lower risk for subsequent hospital admissions.
- Jeong-Seon Lee
- , Jae Il Shin
- & Dong Keon Yon
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Comment
| Open AccessZoonotic malaria requires new policy approaches to malaria elimination
WHO guidelines for classification of malaria elimination in a country require that the risk of human infection from zoonotic, as well as nonzoonotic, malaria parasites is negligible. In this Comment, the authors discuss the implications of this policy for countries, such as Malaysia, with no recent reported nonzoonotic cases but ongoing zoonotic transmission.
- Kimberly M. Fornace
- , Chris J. Drakeley
- & Kamruddin Ahmed
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Article
| Open AccessPlasma metabolomic profiles associated with mortality and longevity in a prospective analysis of 13,512 individuals
The metabolic alterations underpinning aging processes and mortality in humans are not well understood. Here, the authors show that differences in levels of nucleosides, amino acids, and several lipid subclasses can predict mortality and longevity.
- Fenglei Wang
- , Anne-Julie Tessier
- & Marta Guasch-Ferré