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| 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 AccessHospital load and increased COVID-19 related mortality in Israel
COVID-19 has caused many healthcare systems to become overwhelmed, potentially impacting patient care. Here, the authors show that COVID-19-related in-hospital mortality rates in Israel increased in periods of moderate or high hospital load, independent of patient characteristics.
- Hagai Rossman
- , Tomer Meir
- & Malka Gorfine
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| Open AccessStochastic sampling effects favor manual over digital contact tracing
Contact tracing for a timely isolation of potentially infected individuals can be provided manually or via digital applications. Mancastroppa et al. show that in the combination of both procedures the manual tracing is dominant and allows for better detection of infection super-spreaders.
- Marco Mancastroppa
- , Claudio Castellano
- & Raffaella Burioni
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| Open AccessDigital proximity tracing on empirical contact networks for pandemic control
Digital contact tracing is increasingly considered as one of the tools to control infectious disease outbreaks, in particular the COVID-19 epidemic. Here, the authors present a modeling framework informed by empirical high-resolution contact data to analyze the impact of digital contact tracing apps.
- G. Cencetti
- , G. Santin
- & B. Lepri
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| Open AccessModel-based evaluation of school- and non-school-related measures to control the COVID-19 pandemic
The role of school-based contacts in the epidemiology of SARS-CoV-2 is incompletely understood. Here, the authors use an age-structured transmission model fitted to age-specific seroprevalence and hospital admission data to assess the effects of school-based measures during the COVID-19 pandemic in the Netherlands.
- Ganna Rozhnova
- , Christiaan H. van Dorp
- & Mirjam E. Kretzschmar
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| Open AccessEvaluating the impact of curfews and other measures on SARS-CoV-2 transmission in French Guiana
Identifying effective combinations of control measures in different populations is important for SARS-CoV-2 control. Here, the authors show that in French Guiana, which has a relatively young population, curfews and localised lockdowns appeared to contribute to reducing transmission.
- Alessio Andronico
- , Cécile Tran Kiem
- & Simon Cauchemez
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| Open AccessInfectivity, susceptibility, and risk factors associated with SARS-CoV-2 transmission under intensive contact tracing in Hunan, China
Detailed knowledge of COVID-19 epidemiology is needed to inform public health responses. Here, the authors use large-scale contact tracing data to provide empirical estimates of key parameters, and show that susceptibility increases with age but transmissibility does not vary significantly.
- Shixiong Hu
- , Wei Wang
- & Hongjie Yu
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| Open AccessTropical cyclone exposure is associated with increased hospitalization rates in older adults
Tropical cyclones can cause severe damage and can thus have devastating impacts on societies. Here, the authors use Medicare data to show that tropical cyclone exposure in the United States is associated with increased hospitalization rates for older adults from many different acute causes.
- Robbie M. Parks
- , G. Brooke Anderson
- & Marianthi-Anna Kioumourtzoglou
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Article
| Open AccessOrchestrating performance of healthcare networks subjected to the compound events of natural disasters and pandemic
COVID-19 might occur together with other natural disasters but frameworks to quantify collective effects is lacking. Here, the authors investigated the readiness of a healthcare system in the face of wildfire during an epidemic by assuming the COVID-19 pandemic occurred around the same time with the Camp Fire case in Butte Country California 2018/2019.
- Emad M. Hassan
- & Hussam N. Mahmoud
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Article
| Open AccessMapping ticks and tick-borne pathogens in China
Ticks are an important vector of disease in China, posing threats to humans, livestock and wild animals. Here, Zhao et al. compile a database of the distributions of the 124 tick species known in China and 103 tick-borne pathogens and predict the additional suitable habitats for the predominant vector species.
- Guo-Ping Zhao
- , Yi-Xing Wang
- & Li-Qun Fang
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| Open AccessModelling safe protocols for reopening schools during the COVID-19 pandemic in France
The role of children in the spread of COVID-19 is not fully understood, and the circumstances under which schools should be opened are therefore debated. Here, the authors demonstrate protocols by which schools in France can be safely opened without overwhelming the healthcare system.
- Laura Di Domenico
- , Giulia Pullano
- & Vittoria Colizza
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| Open AccessProjecting heat-related excess mortality under climate change scenarios in China
Global warming is expected to increase mortality due to heat stress in many regions. Here, the authors asses how mortality due to high temperatures changes in China changes for different demographic groups and show that heat-related excess mortality is increasing under climate change, a process that is strongly amplified by population ageing.
- Jun Yang
- , Maigeng Zhou
- & Qiyong Liu
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| Open AccessImpact of the COVID-19 nonpharmaceutical interventions on influenza and other respiratory viral infections in New Zealand
New Zealand has been relatively successful in controlling COVID-19 due to implementation of strict non-pharmaceutical interventions. Here, the authors demonstrate a striking decline in reports of influenza and other non-influenza respiratory pathogens over winter months in which the interventions have been in place.
- Q. Sue Huang
- , Tim Wood
- & Richard J. Webby
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Article
| Open AccessMethodological quality of COVID-19 clinical research
During the early phase of the COVID-19 pandemic there was a need for rapid dissemination of clinical findings. Here, Jung, Di Santo et al. perform a systematic review and cohort study providing evidence for lower methodological quality scores and faster time to publication of clinical studies related to COVID-19 than comparable studies.
- Richard G. Jung
- , Pietro Di Santo
- & Benjamin Hibbert
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| Open AccessQuantifying population contact patterns in the United States during the COVID-19 pandemic
Physical distancing measures have been widely adopted to reduce the spread of COVID-19. This study quantifies changes in interpersonal contact patterns in the US and finds an 82% reduction in contacts during early lockdowns in March and steady increases thereafter.
- Dennis M. Feehan
- & Ayesha S. Mahmud
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| Open AccessAssessing the influence of climate on wintertime SARS-CoV-2 outbreaks
Spread of SARS-CoV-2 in the early phase of the pandemic has been driven by high population susceptibility, but virus sensitivity to climate may play a role in future outbreaks. Here, the authors simulate SARS-CoV-2 dynamics in winter assuming climate dependence is similar to an endemic coronavirus strain.
- Rachel E. Baker
- , Wenchang Yang
- & Bryan T. Grenfell
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Article
| Open AccessThe natural history of symptomatic COVID-19 during the first wave in Catalonia
Establishing the natural history of COVID-19 requires longitudinal data from population-based cohorts. Here, the authors use linked primary care, testing, and hospital data to describe the disease in ~100,000 individuals with a COVID-19 diagnosis among a population of ~5.5 million in Catalonia, Spain.
- Edward Burn
- , Cristian Tebé
- & Talita Duarte-Salles
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| Open AccessGenomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy
The Lombardy region of Italy was heavily affected early in the SARS-CoV-2 pandemic. Here, the authors use whole genome sequencing and show that there were multiple introductions into the region, with transmission occurring before the first case was detected.
- Claudia Alteri
- , Valeria Cento
- & Fausto Baldanti
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| Open AccessModelling the global burden of drug-resistant tuberculosis avertable by a post-exposure vaccine
Vaccines preventing tuberculosis disease progression have shown promising results in recent trials. Here, the authors use mathematical modelling to estimate that this type of vaccine could avert 10% of cases of rifampicin-resistant tuberculosis and 7% of deaths from 2020-2035.
- Han Fu
- , Joseph A. Lewnard
- & Nimalan Arinaminpathy
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| Open AccessThe challenges of containing SARS-CoV-2 via test-trace-and-isolate
Test, trace, and isolate programmes are central to COVID-19 control. Here, Viola Priesemann and colleagues evaluate how to allocate scarce resources to keep numbers low, and find that if case numbers exceed test, trace and isolate capacity, there will be a self-accelerating spread.
- Sebastian Contreras
- , Jonas Dehning
- & Viola Priesemann
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| Open AccessInferring high-resolution human mixing patterns for disease modeling
The growing need for realism in addressing complex public health questions calls for accurate models of the human contact patterns that govern disease transmission. Here, the authors generate effective population-level contact matrices by using highly detailed macro (census) and micro (survey) data on key socio-demographic features.
- Dina Mistry
- , Maria Litvinova
- & Alessandro Vespignani
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| Open AccessEstimating internationally imported cases during the early COVID-19 pandemic
Sparse testing early in the SARS-CoV-2 pandemic hinders estimation of the dates and origins of initial case importations. Here, the authors show that the main source of cases imported from China shifted from Wuhan to other Chinese cities by mid-February, especially for African locations.
- Tigist F. Menkir
- , Taylor Chin
- & Rene Niehus
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| Open AccessMathematical modeling of COVID-19 in 14.8 million individuals in Bahia, Brazil
Low-resource settings can face additional challenges in managing the COVID-19 pandemic. Here, the authors use mathematical modelling to investigate transmission in the state of Bahia, Brazil, and quantify control measures needed to prevent the hospital system becoming overwhelmed.
- Juliane F. Oliveira
- , Daniel C. P. Jorge
- & Roberto F. S. Andrade
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Article
| Open AccessAsynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic
Dengue is endemic in the Dominican Republic, and causes regular outbreaks, whereas Zika and chikungunya are emerging infections in the area. Here, the authors show that outbreaks of the emerging infections could not be predicted by seasonal dengue dynamics.
- Mary E. Petrone
- , Rebecca Earnest
- & Leandro Tapia
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Article
| Open AccessOptimal COVID-19 quarantine and testing strategies
Safely reducing the necessary duration of quarantine for COVID-19 could lessen the economic impacts of the pandemic. Here, the authors demonstrate that testing on exit from quarantine is more effective than testing on entry, and can enable quarantine to be reduced from fourteen to seven days.
- Chad R. Wells
- , Jeffrey P. Townsend
- & Alison P. Galvani
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| Open AccessLongitudinal symptom dynamics of COVID-19 infection
Although many COVID-19 cases are mild, most information about symptoms is derived from hospitalized patients. Here, the authors link self-reported symptom surveys to primary care data to describe the longitudinal dynamics of COVID-19 in non-hospitalized individuals.
- Barak Mizrahi
- , Smadar Shilo
- & Eran Segal
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| Open AccessPost-lockdown SARS-CoV-2 nucleic acid screening in nearly ten million residents of Wuhan, China
Large-scale population screening can provide insights to levels of ongoing SARS-CoV-2 transmission. Here, the authors report a citywide screening of ~10,000,000 residents of Wuhan and show that SARS-CoV-2 infection prevalence was very low five to eight weeks after the end of lockdown.
- Shiyi Cao
- , Yong Gan
- & Zuxun Lu
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| Open AccessRisk of yellow fever virus transmission in the Asia-Pacific region
Yellow fever is absent from the Asia/Pacific region, despite presence of the mosquito vector. Here, the authors demonstrate that mosquitoes collected from field sites across the region are capable of transmitting yellow fever virus, indicating that vector competence is not a barrier to disease spread.
- Lucy de Guilhem de Lataillade
- , Marie Vazeille
- & Pei-Shi Yen
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Article
| Open AccessLow SARS-CoV-2 seroprevalence in blood donors in the early COVID-19 epidemic in the Netherlands
The Netherlands is a country highly affected by the COVID-19 pandemic. In this study, Slot, Hogema and colleagues report a low SARS-CoV-2 seroprevalence one month into the outbreak and provide insights into virus exposure by region and age group when widespread non-pharmaceutical interventions are in place.
- Ed Slot
- , Boris M. Hogema
- & Hans L. Zaaijer
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| Open AccessFull genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel
In this study, Adi Stern and colleagues use full genome sequences of SARS-CoV-2 to look at the rate of infections in Israel. They report that social distancing had a significant effect on minimising the rate of transmission, and find evidence for transmission heterogeneity (superspreading events).
- Danielle Miller
- , Michael A. Martin
- & Adi Stern
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Article
| Open AccessSmell and taste changes are early indicators of the COVID-19 pandemic and political decision effectiveness
Syndromic surveillance for COVID-19 could help to identify areas with increasing transmission. Here, the authors show that increased reports of changes in smell and taste measured at the population level are correlated with the increased COVID-19-related hospital admissions.
- Denis Pierron
- , Veronica Pereda-Loth
- & Moustafa Bensafi
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Article
| Open AccessReductions in commuting mobility correlate with geographic differences in SARS-CoV-2 prevalence in New York City
New York City is one of the areas most affected by the SARS-CoV-2 pandemic in the United States, and there has been large variation in rates of hospitalisation and death by city borough. Here, the authors show that boroughs with the largest reduction in daily commutes also had the lowest SARS-CoV-2 prevalence.
- Stephen M. Kissler
- , Nishant Kishore
- & Yonatan H. Grad
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Article
| Open AccessDeveloping a COVID-19 mortality risk prediction model when individual-level data are not available
Identification of individuals at risk of severe COVID-19 disease could inform treatment and public health planning. Here, the authors develop and validate a risk prediction model for COVID-19 mortality in Israel by building a model for severe respiratory infection and recalibrating it using COVID-19 case fatality rates.
- Noam Barda
- , Dan Riesel
- & Noa Dagan
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Article
| Open AccessThe geography of COVID-19 spread in Italy and implications for the relaxation of confinement measures
Releasing COVID-19 lockdown measures risks increases in transmission. Here, the authors estimate the increase in transmission rate for different regions in Italy and estimate that isolation of 5.5% exposed and highly infectious individuals would be needed to compensate for a 40% increase in transmission.
- Enrico Bertuzzo
- , Lorenzo Mari
- & Andrea Rinaldo
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Article
| Open AccessModelling the incremental benefit of introducing malaria screening strategies to antenatal care in Africa
Plasmodium falciparum infection in pregnancy is a major cause of adverse pregnancy outcomes. Here, the authors combine performance estimates of standard rapid diagnostic tests with modelling to assess whether screening at antenatal visits improves upon current intermittent preventative therapy.
- Patrick G. T. Walker
- , Matt Cairns
- & Feiko O. ter Kuile
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Article
| Open AccessEfficient polygenic risk scores for biobank scale data by exploiting phenotypes from inferred relatives
Genetic data from large cohorts of unrelated individuals can be used to create polygenic risk scores, which could be used to predict individual risk of developing a specific disease. Here the authors show that smaller cohorts of related individuals can provide similarly powerful predictive ability.
- Buu Truong
- , Xuan Zhou
- & S. Hong Lee
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Article
| Open AccessComprehensive aptamer-based screening identifies a spectrum of urinary biomarkers of lupus nephritis across ethnicities
Developing noninvasive diagnostic biomarkers for lupus nephritis (LN) diagnosis is an important clinical goal. Here the authors identify urinary proteins correlated with active LN and disease severity, which differ across ethnicities but collectively outperform the current clinical method.
- Samantha Stanley
- , Kamala Vanarsa
- & Chandra Mohan
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Article
| Open AccessAntimicrobial resistant enteric bacteria are widely distributed amongst people, animals and the environment in Tanzania
Spread of antimicrobial-resistant (AR) bacteria is a global concern, but contributing factors remain unclear. Here, authors analyze distribution of AR bacteria in households from three ethnic groups in Tanzania and find that livelihood factors are more strongly associated with AR prevalence than antibiotic use.
- Murugan Subbiah
- , Mark A. Caudell
- & Douglas R. Call
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Article
| Open AccessAgricultural land-uses consistently exacerbate infectious disease risks in Southeast Asia
Here, Shah et al. perform a meta-analysis and show that people who live or work in agricultural land in Southeast Asia are on average 1.7 times more likely to be infected with a pathogen than controls, suggesting that agricultural land-use increases infectious disease risk.
- Hiral A. Shah
- , Paul Huxley
- & Kris A. Murray
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Article
| Open AccessOpen data on industry payments to healthcare providers reveal potential hidden costs to the public
Industry payments to healthcare providers for non-research costs are common in the US. Linking Medicare and Open Payments data, the authors find that providers receiving more industry payments tend to bill higher drug and medical costs, and this association is stronger in more conservative states.
- Jorge Mejia
- , Amanda Mejia
- & Franco Pestilli
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Article
| Open AccessAmbient black carbon particles reach the fetal side of human placenta
Exposure to air pollution during pregnancy has been associated with impaired birth outcomes. Here, Bové et al. report evidence of black carbon particle deposition on the fetal side of human placentae, including at early stages of pregnancy, suggesting air pollution could affect birth outcome through direct effects on the fetus.
- Hannelore Bové
- , Eva Bongaerts
- & Tim S. Nawrot
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Perspective
| Open AccessLessons from the reestablishment of Public Health Laboratory activities in Puerto Rico after Hurricane Maria
Hurricane Maria hit Puerto Rico in 2017 and resulted in a complete loss of activity of the Public Health Laboratories. Here, the authors discuss the approach taken and tools developed to re-establish activity in these laboratories using a quality management system and the lessons learned in this process.
- Margaret C. Hardy
- , Rita C. Stinnett
- & Eduardo O’Neill
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Article
| Open AccessMicrobial and metabolic succession on common building materials under high humidity conditions
Microbes inhabit built environments and could contribute to degradation of surfaces especially in damp conditions. Here the authors explore how communities of microbes and their metabolites affect four types of built surfaces under varying environmental conditions.
- Simon Lax
- , Cesar Cardona
- & Jack A. Gilbert
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Article
| Open AccessGenome-wide association study of alcohol consumption and use disorder in 274,424 individuals from multiple populations
The genetic underpinnings of alcohol use disorder and consumption are incompletely understood. Here, the authors perform GWAS for Alcohol Use Disorder (AUD) Identification Test-Consumption scores and AUD diagnosis from electronic health records of 274,424 individuals and identify a total of 18 associated loci.
- Henry R. Kranzler
- , Hang Zhou
- & Joel Gelernter
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Article
| Open AccessEffects of infection history on dengue virus infection and pathogenicity
Lack of knowledge of individual infection history hinders understanding of immunological interactions among DENV serotypes. Here, the authors introduce a framework to infer the relationship between unobserved infection history and subsequent infection and disease risk, and find complex dependencies.
- Tim K. Tsang
- , Samson L. Ghebremariam
- & Yang Yang
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Article
| Open AccessInter-annual variation in seasonal dengue epidemics driven by multiple interacting factors in Guangzhou, China
In 2014 Guangzhou, China experienced its worse dengue epidemic on record. To determine the reasons for this the authors model historical data under combinations of four time-varying factors and find that past epidemics were limited by one or more unfavourable conditions, but the 2014 epidemic faced none of these restraints.
- Rachel J. Oidtman
- , Shengjie Lai
- & Hongjie Yu
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Article
| Open AccessMulti-cohort study identifies social determinants of systemic inflammation over the life course
Here, the authors explore the relationship between socioeconomic position (SEP) across the life course and inflammation in a multi-cohort study and show that educational attainment is most strongly related to inflammation, suggesting that socioeconomic disadvantage in young adulthood is independently associated with later life inflammation.
- Eloïse Berger
- , Raphaële Castagné
- & Michelle Kelly-Irving
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Article
| Open AccessSuicide among cancer patients
Cancer patients are at an increased risk of suicide: elderly, white, unmarried males with localized disease are at highest risk vs other cancer patients. Among those diagnosed at < 50 years of age, the plurality of suicides is from hematologic and testicular tumors; if > 50, from prostate, lung, and colorectal cancer patients.
- Nicholas G. Zaorsky
- , Ying Zhang
- & Vernon M. Chinchilli
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Article
| Open AccessImproved state-level influenza nowcasting in the United States leveraging Internet-based data and network approaches
Real-time disease surveillance can aid mitigation of outbreaks. Here, Lu et al. combine an approach using Google search and EHR data with an approach leveraging spatiotemporal synchronicities of influenza activity across states to improve state-level influenza activity estimates in the US.
- Fred S. Lu
- , Mohammad W. Hattab
- & Mauricio Santillana