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Mertens A, Arnold BF, Benjamin-Chung J, Boehm AB, Brown J, Capone D, Clasen T, Fuhrmeister ER, Grembi JA, Holcomb D, Knee J, Kwong LH, Lin A, Luby SP, Nala R, Nelson K, Njenga SM, Null C, Pickering AJ, Rahman M, Reese HE, Steinbaum L, Stewart JR, Thilakaratne R, Cumming O, Colford JM, Ercumen A. Is detection of enteropathogens and human or animal faecal markers in the environment associated with subsequent child enteric infections and growth: an individual participant data meta-analysis. Lancet Glob Health 2024; 12:e433-e444. [PMID: 38365415 PMCID: PMC10882208 DOI: 10.1016/s2214-109x(23)00563-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 11/13/2023] [Accepted: 11/28/2023] [Indexed: 02/18/2024]
Abstract
BACKGROUND Quantifying contributions of environmental faecal contamination to child diarrhoea and growth faltering can illuminate causal mechanisms behind modest health benefits in recent water, sanitation, and hygiene (WASH) trials. We aimed to assess associations between environmental detection of enteropathogens and human or animal microbial source tracking markers (MSTM) and subsequent child health outcomes. METHODS In this individual participant data meta-analysis we searched we searched PubMed, Embase, CAB Direct Global Health, Agricultural and Environmental Science Database, Web of Science, and Scopus for WASH intervention studies with a prospective design and concurrent control that measured enteropathogens or MSTM in environmental samples, or both, and subsequently measured enteric infections, diarrhoea, or height-for-age Z-scores (HAZ) in children younger than 5 years. We excluded studies that only measured faecal indicator bacteria. The initial search was done on Jan 19, 2021, and updated on March 22, 2023. One reviewer (AM) screened abstracts, and two independent reviewers (AM and RT) examined the full texts of short-listed articles. All included studies include at least one author that also contributed as an author to the present Article. Our primary outcomes were the 7-day prevalence of caregiver-reported diarrhoea and HAZ in children. For specific enteropathogens in the environment, primary outcomes also included subsequent child infection with the same pathogen ascertained by stool testing. We estimated associations using covariate-adjusted regressions and pooled estimates across studies. FINDINGS Data from nine published reports from five interventions studies, which included 8603 children (4302 girls and 4301 boys), were included in the meta-analysis. Environmental pathogen detection was associated with increased infection prevalence with the same pathogen and lower HAZ (ΔHAZ -0·09 [95% CI -0·17 to -0·01]) but not diarrhoea (prevalence ratio 1·22 [95% CI 0·95 to 1·58]), except during wet seasons. Detection of MSTM was not associated with diarrhoea (no pooled estimate) or HAZ (ΔHAZ -0·01 [-0·13 to 0·11] for human markers and ΔHAZ -0·02 [-0·24 to 0·21] for animal markers). Soil, children's hands, and stored drinking water were major transmission pathways. INTERPRETATION Our findings support a causal chain from pathogens in the environment to infection to growth faltering, indicating that the lack of WASH intervention effects on child growth might stem from insufficient reductions in environmental pathogen prevalence. Studies measuring enteropathogens in the environment should subsequently measure the same pathogens in stool to further examine theories of change between WASH, faecal contamination, and health. Given that environmental pathogen detection was predictive of infection, programmes targeting specific pathogens (eg, vaccinations and elimination efforts) can environmentally monitor the pathogens of interest for population-level surveillance instead of collecting individual biospecimens. FUNDING The Bill & Melinda Gates Foundation and the UK Foreign and Commonwealth Development Office.
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Affiliation(s)
- Andrew Mertens
- Division of Epidemiology, University of California, Berkeley, CA, USA; Division of Biostatistics, University of California, Berkeley, CA, USA.
| | - Benjamin F Arnold
- Francis I Proctor Foundation and Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Jade Benjamin-Chung
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Joe Brown
- Department of Environmental Science and Engineering, University of North Carolina, Gillings School of Global Public Health, Michael Hooker Research Center, Chapel Hill, NC, USA
| | - Drew Capone
- Department of Environmental and Occupational Health, Indiana University, Bloomington, IN, USA
| | - Thomas Clasen
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Erica R Fuhrmeister
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | | | - David Holcomb
- Department of Environmental Science and Engineering, University of North Carolina, Gillings School of Global Public Health, Michael Hooker Research Center, Chapel Hill, NC, USA
| | - Jackie Knee
- Department of Disease Control, London School of Tropical Medicine & Hygiene, London, UK
| | - Laura H Kwong
- Division of Environmental Health Sciences, University of California, Berkeley, CA, USA
| | - Audrie Lin
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, USA
| | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Rassul Nala
- Ministério da Saúde, Instituto Nacional de Saúde Maputo, Maputo, Mozambique
| | - Kara Nelson
- Department of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, CA, USA
| | | | | | - Amy J Pickering
- Department of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, CA, USA
| | - Mahbubur Rahman
- Environmental Interventions Unit, Infectious Diseases Division, Dhaka, Bangladesh
| | - Heather E Reese
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Lauren Steinbaum
- California Department of Toxic Substances Control, Sacramento, CA, USA
| | - Jill R Stewart
- Department of Environmental Science and Engineering, University of North Carolina, Gillings School of Global Public Health, Michael Hooker Research Center, Chapel Hill, NC, USA
| | | | - Oliver Cumming
- Department of Disease Control, London School of Tropical Medicine & Hygiene, London, UK
| | - John M Colford
- Division of Epidemiology, University of California, Berkeley, CA, USA
| | - Ayse Ercumen
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
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Mertens A, Arnold BF, Benjamin-Chung J, Boehm AB, Brown J, Capone D, Clasen T, Fuhrmeister E, Grembi JA, Holcomb D, Knee J, Kwong LH, Lin A, Luby SP, Nala R, Nelson K, Njenga SM, Null C, Pickering AJ, Rahman M, Reese HE, Steinbaum L, Stewart J, Thilakaratne R, Cumming O, Colford JM, Ercumen A. Effects of water, sanitation, and hygiene interventions on detection of enteropathogens and host-specific faecal markers in the environment: a systematic review and individual participant data meta-analysis. Lancet Planet Health 2023; 7:e197-e208. [PMID: 36889861 PMCID: PMC10009758 DOI: 10.1016/s2542-5196(23)00028-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Water, sanitation, and hygiene (WASH) improvements are promoted to reduce diarrhoea in low-income countries. However, trials from the past 5 years have found mixed effects of household-level and community-level WASH interventions on child health. Measuring pathogens and host-specific faecal markers in the environment can help investigate causal pathways between WASH and health by quantifying whether and by how much interventions reduce environmental exposure to enteric pathogens and faecal contamination from human and different animal sources. We aimed to assess the effects of WASH interventions on enteropathogens and microbial source tracking (MST) markers in environmental samples. METHODS We did a systematic review and individual participant data meta-analysis, which included searches from Jan 1, 2000, to Jan 5, 2023, from PubMed, Embase, CAB Direct Global Health, Agricultural and Environmental Science Database, Web of Science, and Scopus, of prospective studies with water, sanitation, or hygiene interventions and concurrent control group that measured pathogens or MST markers in environmental samples and measured child anthropometry, diarrhoea, or pathogen-specific infections. We used covariate-adjusted regression models with robust standard errors to estimate study-specific intervention effects and pooled effect estimates across studies using random-effects models. FINDINGS Few trials have measured the effect of sanitation interventions on pathogens and MST markers in the environment and they mostly focused on onsite sanitation. We extracted individual participant data on nine environmental assessments from five eligible trials. Environmental sampling included drinking water, hand rinses, soil, and flies. Interventions were consistently associated with reduced pathogen detection in the environment but effect estimates in most individual studies could not be distinguished from chance. Pooled across studies, we found a small reduction in the prevalence of any pathogen in any sample type (pooled prevalence ratio [PR] 0·94 [95% CI 0·90-0·99]). Interventions had no effect on the prevalence of MST markers from humans (pooled PR 1·00 [95% CI 0·88-1·13]) or animals (pooled PR 1·00 [95% CI 0·97-1·03]). INTERPRETATION The small effect of these sanitation interventions on pathogen detection and absence of effects on human or animal faecal markers are consistent with the small or null health effects previously reported in these trials. Our findings suggest that the basic sanitation interventions implemented in these studies did not contain human waste and did not adequately reduce exposure to enteropathogens in the environment. FUNDING Bill and Melinda Gates Foundation and the UK Foreign and Commonwealth Development Office.
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Affiliation(s)
- Andrew Mertens
- Division of Epidemiology and Biostatistics, University of California, Berkeley, CA, USA.
| | - Benjamin F Arnold
- Francis I Proctor Foundation and Department of Ophthalmology, University of California, San Francisco, CA, USA
| | - Jade Benjamin-Chung
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Joe Brown
- Department of Environmental Science and Engineering, Gillings School of Global Public Health, Michael Hooker Research Center, University of North Carolina, Chapel Hill, NC, USA
| | - Drew Capone
- Department of Environmental and Occupational Health, Indiana University Bloomington, Bloomington, IN, USA
| | - Thomas Clasen
- Department of Environmental Health, Rollins School of Public Health, Emory University, NE, Atlanta, GA, USA
| | - Erica Fuhrmeister
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | | | - David Holcomb
- Department of Environmental Science and Engineering, Gillings School of Global Public Health, Michael Hooker Research Center, University of North Carolina, Chapel Hill, NC, USA
| | - Jackie Knee
- Department of Disease Control, London School of Tropical Medicine & Hygiene, London, UK
| | - Laura H Kwong
- Division of Environmental Health Sciences, University of California, Berkeley, CA, USA
| | - Audrie Lin
- Department of Biobehavioral Health, Pennsylvania State University, PA, USA
| | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Rassul Nala
- Ministério da Saúde, Instituto Nacional de Saúde Maputo, Maputo, Mozambique
| | - Kara Nelson
- Department of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, CA, USA
| | | | | | - Amy J Pickering
- Department of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, CA, USA
| | - Mahbubur Rahman
- Environmental Interventions Unit, Infectious Diseases Division, Dhaka, Bangladesh
| | - Heather E Reese
- Department of Environmental Health, Rollins School of Public Health, Emory University, NE, Atlanta, GA, USA
| | - Lauren Steinbaum
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Jill Stewart
- Department of Environmental Science and Engineering, Gillings School of Global Public Health, Michael Hooker Research Center, University of North Carolina, Chapel Hill, NC, USA
| | - Ruwan Thilakaratne
- Division of Epidemiology and Biostatistics, University of California, Berkeley, CA, USA
| | - Oliver Cumming
- Department of Disease Control, London School of Tropical Medicine & Hygiene, London, UK
| | - John M Colford
- Division of Epidemiology and Biostatistics, University of California, Berkeley, CA, USA
| | - Ayse Ercumen
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
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Holcomb D, Hamasaki-Katagiri N, Laurie K, Katneni U, Kames J, Alexaki A, Bar H, Kimchi-Sarfaty C. New approaches to predict the effect of co-occurring variants on protein characteristics. Am J Hum Genet 2021; 108:1502-1511. [PMID: 34256028 DOI: 10.1016/j.ajhg.2021.06.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/14/2021] [Indexed: 12/14/2022] Open
Abstract
Predicting the effect of a mutated gene before the onset of symptoms of genetic diseases would greatly facilitate diagnosis and potentiate early intervention. There have been myriad attempts to predict the effects of single-nucleotide variants. However, the applicability of these efforts does not scale to co-occurring variants. Furthermore, an increasing number of protein therapeutics contain co-occurring nucleotide variations, adding uncertainty during development to the safety and efficiency of these drugs. Co-occurring nucleotide variants may often have synergistic, additive, or antagonistic effects on protein attributes, further complicating the task of outcome prediction. We tested four models based on the cooperative and antagonistic effects of co-occurring variants to predict pathogenicity and effectiveness of protein therapeutics. A total of 30 attributes, including amino acid and nucleotide features, as well as existing single-variant effect prediction tools, were considered on the basis of previous studies on single-nucleotide variants. Importantly, the effects of synonymous variants, often seen in protein therapeutics, were also included in our models. We used 12 datasets of people with monogenic diseases and controls with co-occurring genetic variants to evaluate the accuracy of our models, accomplishing a degree of accuracy comparable to that of prediction tools for single-nucleotide variants. More importantly, our framework is generalizable to new, well-curated datasets of monogenic diseases and new variant scoring tools. This approach successfully assists in addressing the challenging task of predicting the effect of co-occurring variants on pathogenicity and protein effectiveness and is applicable for a wide range of protein therapeutics and genetic diseases.
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Capone D, Berendes D, Cumming O, Holcomb D, Knee J, Konstantinidis KT, Levy K, Nalá R, Risk BB, Stewart J, Brown J. Impact of an Urban Sanitation Intervention on Enteric Pathogen Detection in Soils. Environ Sci Technol 2021; 55:9989-10000. [PMID: 34236178 PMCID: PMC8327413 DOI: 10.1021/acs.est.1c02168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Environmental fecal contamination is common in many low-income cities, contributing to a high burden of enteric infections and associated negative sequelae. To evaluate the impact of a shared onsite sanitation intervention in Maputo, Mozambique on enteric pathogens in the domestic environment, we collected 179 soil samples at shared latrine entrances from intervention (n = 49) and control (n = 51) compounds during baseline (preintervention) and after 24 months (postintervention) as part of the Maputo Sanitation Trial. We tested soils for the presence of nucleic acids associated with 18 enteric pathogens using a multiplex reverse transcription qPCR platform. We detected at least one pathogen-associated gene target in 91% (163/179) of soils and a median of 3 (IQR = 1, 5) pathogens. Using a difference-in-difference analysis and adjusting for compound population, visibly wet soil, sun exposure, wealth, temperature, animal presence, and visible feces, we estimate the intervention reduced the probability of detecting ≥1 pathogen gene by 15% (adjusted prevalence ratio, aPR = 0.85; 95% CI: 0.70, 1.0) and the total number of pathogens by 35% (aPR = 0.65; 0.44, 0.95) in soil 24 months following the intervention. These results suggest that the intervention reduced the presence of some fecal contamination in the domestic environment, but pathogen detection remained prevalent 24 months following the introduction of new latrines.
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Affiliation(s)
- Drew Capone
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David Berendes
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Oliver Cumming
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - David Holcomb
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jackie Knee
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Konstantinos T. Konstantinidis
- Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, Georgia, United States of America
| | - Karen Levy
- Environmental and Occupational Health Sciences, University of Washington, 2980 15th Ave NE, Seattle, Washington, United States of America
| | - Rassul Nalá
- Ministério da Saúde, Instituto Nacional de Saúde Maputo, Maputo, Mozambique
| | - Benjamin B. Risk
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, United States of America
| | - Jill Stewart
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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Laurie K, Holcomb D, Kames J, Komar AA, DiCuccio M, Ibla JC, Kimchi-Sarfaty C. In Silico Evaluation of Cyclophilin Inhibitors as Potential Treatment for SARS-CoV-2. Open Forum Infect Dis 2021; 8:ofab189. [PMID: 34109257 PMCID: PMC8083350 DOI: 10.1093/ofid/ofab189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/10/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The advent of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) provoked researchers to propose multiple antiviral strategies to improve patients' outcomes. Studies provide evidence that cyclosporine A (CsA) decreases SARS-CoV-2 replication in vitro and decreases mortality rates of coronavirus disease 2019 (COVID-19) patients. CsA binds cyclophilins, which isomerize prolines, affecting viral protein activity. METHODS We investigated the proline composition from various coronavirus proteomes to identify proteins that may critically rely on cyclophilin's peptidyl-proline isomerase activity and found that the nucleocapsid (N) protein significantly depends on cyclophilin A (CyPA). We modeled CyPA and N protein interactions to demonstrate the N protein as a potential indirect therapeutic target of CsA, which we propose may impede coronavirus replication by obstructing nucleocapsid folding. RESULTS Finally, we analyzed the literature and protein-protein interactions, finding evidence that, by inhibiting CyPA, CsA may impact coagulation proteins and hemostasis. CONCLUSIONS Despite CsA's promising antiviral characteristics, the interactions between cyclophilins and coagulation factors emphasize risk stratification for COVID patients with thrombosis dispositions.
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Affiliation(s)
- Kyle Laurie
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, USA
| | - David Holcomb
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Jacob Kames
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Anton A Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, USA
| | - Michael DiCuccio
- National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Juan C Ibla
- Division of Cardiac Anesthesia, Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Chava Kimchi-Sarfaty
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, USA
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Holcomb D, Palli L, Setty K, Uprety S. Corrigendum to Water and health seminar and special issue highlight ideas that will change the field. [International Journal of Hygiene and Environmental Health 226C (2020) 113529]. Int J Hyg Environ Health 2021. [DOI: 10.1016/j.ijheh.2021.113717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Knee J, Sumner T, Adriano Z, Anderson C, Bush F, Capone D, Casmo V, Holcomb D, Kolsky P, MacDougall A, Molotkova E, Braga JM, Russo C, Schmidt WP, Stewart J, Zambrana W, Zuin V, Nalá R, Cumming O, Brown J. Effects of an urban sanitation intervention on childhood enteric infection and diarrhea in Maputo, Mozambique: A controlled before-and-after trial. eLife 2021; 10:e62278. [PMID: 33835026 PMCID: PMC8121544 DOI: 10.7554/elife.62278] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 04/03/2021] [Indexed: 12/12/2022] Open
Abstract
We conducted a controlled before-and-after trial to evaluate the impact of an onsite urban sanitation intervention on the prevalence of enteric infection, soil transmitted helminth re-infection, and diarrhea among children in Maputo, Mozambique. A non-governmental organization replaced existing poor-quality latrines with pour-flush toilets with septic tanks serving household clusters. We enrolled children aged 1-48 months at baseline and measured outcomes before and 12 and 24 months after the intervention, with concurrent measurement among children in a comparable control arm. Despite nearly exclusive use, we found no evidence that intervention affected the prevalence of any measured outcome after 12 or 24 months of exposure. Among children born into study sites after intervention, we observed a reduced prevalence of Trichuris and Shigella infection relative to the same age group at baseline (<2 years old). Protection from birth may be important to reduce exposure to and infection with enteric pathogens in this setting.
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Affiliation(s)
- Jackie Knee
- London School of Hygiene & Tropical Medicine, Faculty of Infectious Tropical Diseases, Disease Control DepartmentLondonUnited Kingdom
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
| | - Trent Sumner
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
| | | | - Claire Anderson
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
| | - Farran Bush
- Georgia Institute of Technology, School of Chemical and Biomolecular EngineeringAtlantaUnited States
| | - Drew Capone
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of EpidemiologyChapel HillUnited States
| | | | - David Holcomb
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of EpidemiologyChapel HillUnited States
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of Environmental Sciences and EngineeringChapel HillUnited States
| | - Pete Kolsky
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of EpidemiologyChapel HillUnited States
| | - Amy MacDougall
- London School of Hygiene & Tropical Medicine, Faculty of Epidemiology and Population Health, Department of Medical StatisticsLondonUnited Kingdom
| | - Evgeniya Molotkova
- Georgia Institute of Technology, School of Biological SciencesAtlantaUnited States
| | | | - Celina Russo
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
| | - Wolf Peter Schmidt
- London School of Hygiene & Tropical Medicine, Faculty of Infectious Tropical Diseases, Disease Control DepartmentLondonUnited Kingdom
| | - Jill Stewart
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of EpidemiologyChapel HillUnited States
| | - Winnie Zambrana
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
| | - Valentina Zuin
- Yale-NUS College, Division of Social ScienceSingaporeSingapore
| | | | - Oliver Cumming
- London School of Hygiene & Tropical Medicine, Faculty of Infectious Tropical Diseases, Disease Control DepartmentLondonUnited Kingdom
| | - Joe Brown
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of EpidemiologyChapel HillUnited States
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Holcomb D, Alexaki A, Hernandez N, Hunt R, Laurie K, Kames J, Hamasaki-Katagiri N, Komar AA, DiCuccio M, Kimchi-Sarfaty C. Gene variants of coagulation related proteins that interact with SARS-CoV-2. PLoS Comput Biol 2021; 17:e1008805. [PMID: 33730015 PMCID: PMC8007013 DOI: 10.1371/journal.pcbi.1008805] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 03/29/2021] [Accepted: 02/15/2021] [Indexed: 12/30/2022] Open
Abstract
Thrombosis is a recognized complication of Coronavirus disease of 2019 (COVID-19) and is often associated with poor prognosis. There is a well-recognized link between coagulation and inflammation, however, the extent of thrombotic events associated with COVID-19 warrants further investigation. Poly(A) Binding Protein Cytoplasmic 4 (PABPC4), Serine/Cysteine Proteinase Inhibitor Clade G Member 1 (SERPING1) and Vitamin K epOxide Reductase Complex subunit 1 (VKORC1), which are all proteins linked to coagulation, have been shown to interact with SARS proteins. We computationally examined the interaction of these with SARS-CoV-2 proteins and, in the case of VKORC1, we describe its binding to ORF7a in detail. We examined the occurrence of variants of each of these proteins across populations and interrogated their potential contribution to COVID-19 severity. Potential mechanisms, by which some of these variants may contribute to disease, are proposed. Some of these variants are prevalent in minority groups that are disproportionally affected by severe COVID-19. Therefore, we are proposing that further investigation around these variants may lead to better understanding of disease pathogenesis in minority groups and more informed therapeutic approaches.
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Affiliation(s)
- David Holcomb
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Aikaterini Alexaki
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Nancy Hernandez
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Ryan Hunt
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Kyle Laurie
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Jacob Kames
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Nobuko Hamasaki-Katagiri
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Anton A. Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Michael DiCuccio
- National Center of Biotechnology Information, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (MD); (CKS)
| | - Chava Kimchi-Sarfaty
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail: (MD); (CKS)
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Holcomb D, Palli L, Setty K, Uprety S. Water and health seminar and special issue highlight ideas that will change the field. Int J Hyg Environ Health 2021; 234:113716. [PMID: 33639583 DOI: 10.1016/j.ijheh.2021.113716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Holcomb D, Palli L, Setty K, Uprety S. Water and health seminar and special issue highlight ideas that will change the field. Int J Hyg Environ Health 2021; 226:113529. [PMID: 32307040 DOI: 10.1016/j.ijheh.2020.113529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Holcomb D, Alexaki A, Hernandez N, Laurie K, Kames J, Hamasaki-Katagiri N, Komar AA, DiCuccio M, Kimchi-Sarfaty C. Potential impact on coagulopathy of gene variants of coagulation related proteins that interact with SARS-CoV-2. bioRxiv 2020. [PMID: 32935103 DOI: 10.1101/2020.09.08.272328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Thrombosis has been one of the complications of the Coronavirus disease of 2019 (COVID-19), often associated with poor prognosis. There is a well-recognized link between coagulation and inflammation, however, the extent of thrombotic events associated with COVID-19 warrants further investigation. Poly(A) Binding Protein Cytoplasmic 4 (PABPC4), Serine/Cysteine Proteinase Inhibitor Clade G Member 1 (SERPING1) and Vitamin K epOxide Reductase Complex subunit 1 (VKORC1), which are all proteins linked to coagulation, have been shown to interact with SARS proteins. We computationally examined the interaction of these with SARS-CoV-2 proteins and, in the case of VKORC1, we describe its binding to ORF7a in detail. We examined the occurrence of variants of each of these proteins across populations and interrogated their potential contribution to COVID-19 severity. Potential mechanisms by which some of these variants may contribute to disease are proposed. Some of these variants are prevalent in minority groups that are disproportionally affected by severe COVID-19. Therefore, we are proposing that further investigation around these variants may lead to better understanding of disease pathogenesis in minority groups and more informed therapeutic approaches. Author summary Increased blood clotting, especially in the lungs, is a common complication of COVID-19. Infectious diseases cause inflammation which in turn can contribute to increased blood clotting. However, the extent of clot formation that is seen in the lungs of COVID-19 patients suggests that there may be a more direct link. We identified three human proteins that are involved indirectly in the blood clotting cascade and have been shown to interact with proteins of SARS virus, which is closely related to the novel coronavirus. We examined computationally the interaction of these human proteins with the viral proteins. We looked for genetic variants of these proteins and examined how these variants are distributed across populations. We investigated whether variants of these genes could impact severity of COVID-19. Further investigation around these variants may provide clues for the pathogenesis of COVID-19 particularly in minority groups.
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Hunt R, Hettiarachchi G, Katneni U, Hernandez N, Holcomb D, Kames J, Alnifaidy R, Lin B, Hamasaki-Katagiri N, Wesley A, Kafri T, Morris C, Bouché L, Panico M, Schiller T, Ibla J, Bar H, Ismail A, Morris H, Komar A, Kimchi-Sarfaty C. A Single Synonymous Variant (c.354G>A [p.P118P]) in ADAMTS13 Confers Enhanced Specific Activity. Int J Mol Sci 2019; 20:ijms20225734. [PMID: 31731663 PMCID: PMC6888508 DOI: 10.3390/ijms20225734] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/09/2019] [Accepted: 11/13/2019] [Indexed: 12/18/2022] Open
Abstract
Synonymous variants within coding regions may influence protein expression and function. We have previously reported increased protein expression levels ex vivo (~120% in comparison to wild-type) from a synonymous polymorphism variant, c.354G>A [p.P118P], of the ADAMTS13 gene, encoding a plasma protease responsible for von Willebrand Factor (VWF) degradation. In the current study, we investigated the potential mechanism(s) behind the increased protein expression levels from this variant and its effect on ADAMTS13 physico-chemical properties. Cell-free assays showed enhanced translation of the c.354G>A variant and the analysis of codon usage characteristics suggested that introduction of the frequently used codon/codon pair(s) may have been potentially responsible for this effect. Limited proteolysis, however, showed no substantial influence of altered translation on protein conformation. Analysis of post-translational modifications also showed no notable differences but identified three previously unreported glycosylation markers. Despite these similarities, p.P118P variant unexpectedly showed higher specific activity. Structural analysis using modeled interactions indicated that subtle conformational changes arising from altered translation kinetics could affect interactions between an exosite of ADAMTS13 and VWF resulting in altered specific activity. This report highlights how a single synonymous nucleotide variation can impact cellular expression and specific activity in the absence of measurable impact on protein structure.
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Affiliation(s)
- Ryan Hunt
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Gaya Hettiarachchi
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Upendra Katneni
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Nancy Hernandez
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - David Holcomb
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Jacob Kames
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Redab Alnifaidy
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Brian Lin
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Nobuko Hamasaki-Katagiri
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Aaron Wesley
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Present Address: Department of Emergency Medicine, Banner University Medical Center, The University of Arizona, Tucson, AZ 85724, USA
| | - Tal Kafri
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Laura Bouché
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
- Present Address: Antikor Biopharma Ltd., Stevenage Bioscience Catalyst, Gunnels Wood Road, Stevenage SG1 2FX, UK
| | - Maria Panico
- BioPharmaSpec Ltd., St. Saviour JE2 7LA, UK or or
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Tal Schiller
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Juan Ibla
- Departments of Cardiac Surgery and Anesthesiology, Perioperative and Pain Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Haim Bar
- Department of Statistics, University of Connecticut, Storrs, CT 06269, USA
| | - Amra Ismail
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological & Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - Howard Morris
- BioPharmaSpec Ltd., St. Saviour JE2 7LA, UK or or
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Anton Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological & Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
- Correspondence: ; Tel.: +1-(240)-402-8203
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Katneni UK, Liss A, Holcomb D, Katagiri NH, Hunt R, Bar H, Ismail A, Komar AA, Kimchi-Sarfaty C. Splicing dysregulation contributes to the pathogenicity of several F9 exonic point variants. Mol Genet Genomic Med 2019; 7:e840. [PMID: 31257730 PMCID: PMC6687662 DOI: 10.1002/mgg3.840] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/10/2019] [Indexed: 12/27/2022] Open
Abstract
Background Pre‐mRNA splicing is a complex process requiring the identification of donor site, acceptor site, and branch point site with an adjacent polypyrimidine tract sequence. Splicing is regulated by splicing regulatory elements (SREs) with both enhancer and suppressor functions. Variants located in exonic regions can impact splicing through dysregulation of native splice sites, SREs, and cryptic splice site activation. While splicing dysregulation is considered primary disease‐inducing mechanism of synonymous variants, its contribution toward disease phenotype of non‐synonymous variants is underappreciated. Methods In this study, we analyzed 415 disease‐causing and 120 neutral F9 exonic point variants including both synonymous and non‐synonymous for their effect on splicing using a series of in silico splice site prediction tools, SRE prediction tools, and in vitro minigene assays. Results The use of splice site and SRE prediction tools in tandem provided better prediction but were not always in agreement with the minigene assays. The net effect of splicing dysregulation caused by variants was context dependent. Minigene assays revealed that perturbed splicing can be found. Conclusion Synonymous variants primarily cause disease phenotype via splicing dysregulation while additional mechanisms such as translation rate also play an important role. Splicing dysregulation is likely to contribute to the disease phenotype of several non‐synonymous variants.
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Affiliation(s)
- Upendra K Katneni
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, Maryland
| | - Aaron Liss
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, Maryland
| | - David Holcomb
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, Maryland
| | - Nobuko H Katagiri
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, Maryland
| | - Ryan Hunt
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, Maryland
| | - Haim Bar
- Department of Statistics, University of Connecticut, Storrs, Connecticut
| | - Amra Ismail
- Department of Biological, Geological and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, Ohio
| | - Anton A Komar
- Department of Biological, Geological and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, Ohio
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, Maryland
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Ezell NDB, Britton C, Ericson N, Holcomb D, Roberts MJ, Djouadi S, Wood R. A Novel Technique Applying Spectral Estimation to Johnson Noise Thermometry. NUCL TECHNOL 2018. [DOI: 10.1080/00295450.2018.1452498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- N. Dianne Bull Ezell
- Oak Ridge National Laboratories, Electrical Engineering Systems Research Division, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830
| | - Chuck Britton
- Oak Ridge National Laboratories, Electrical Engineering Systems Research Division, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830
| | - Nance Ericson
- Oak Ridge National Laboratories, Electrical Engineering Systems Research Division, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830
| | - David Holcomb
- Oak Ridge National Laboratories, Electrical Engineering Systems Research Division, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830
| | - M. J. Roberts
- University of Tennessee, Electrical Engineering Department, 1520 Middle Drive, Knoxville, Tennessee 37996
| | - Seddik Djouadi
- University of Tennessee, Electrical Engineering Department, 1520 Middle Drive, Knoxville, Tennessee 37996
| | - Richard Wood
- University of Tennessee, Nuclear Engineering Department, 308 Pasqua Engineering Building, Knoxville, Tennessee 37996
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Zhang R, Jiang H, Wang ZR, Lin P, Zhuo Y, Holcomb D, Zhang DH, Yang JJ, Xia Q. Nanoscale diffusive memristor crossbars as physical unclonable functions. Nanoscale 2018; 10:2721-2726. [PMID: 29419836 DOI: 10.1039/c7nr06561b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Physical unclonable functions have emerged as promising hardware security primitives for device authentication and key generation in the era of the Internet of Things. Herein, we report novel physical unclonable functions built upon the crossbars of nanoscale diffusive memristors that translate the stochastic distribution of Ag clusters in a SiO2 matrix into a random binary bitmap that serves as a device fingerprint. The random dispersion of Ag led to an uneven number of clusters at each cross-point, which in turn resulted in a stochastic ability to switch in the Ag:SiO2 diffusive memristors in an array. The randomness of the dispersion was a barrier to fingerprint cloning and the unique fingerprints of each device were persistent after fabrication. Using an optimized fabrication procedure, we maximized the randomness and achieved an inter-class Hamming distance of 50.68%. We also discovered that the bits were not flipping after over 104 s at 400 K, suggesting superior reliability of our physical unclonable functions. In addition, our diffusive memristor-based physical unclonable functions were easy to fabricate and did not require complicated post-processing for digitization and thus, provide new opportunities in hardware security applications.
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Affiliation(s)
- R Zhang
- State Key Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin, 300072, China.
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Brown J, Cumming O, Bartram J, Cairncross S, Ensink J, Holcomb D, Knee J, Kolsky P, Liang K, Liang S, Nala R, Norman G, Rheingans R, Stewart J, Zavale O, Zuin V, Schmidt WP. A controlled, before-and-after trial of an urban sanitation intervention to reduce enteric infections in children: research protocol for the Maputo Sanitation (MapSan) study, Mozambique. BMJ Open 2015; 5:e008215. [PMID: 26088809 PMCID: PMC4480002 DOI: 10.1136/bmjopen-2015-008215] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
INTRODUCTION Access to safe sanitation in low-income, informal settlements of Sub-Saharan Africa has not significantly improved since 1990. The combination of a high faecal-related disease burden and inadequate infrastructure suggests that investment in expanding sanitation access in densely populated urban slums can yield important public health gains. No rigorous, controlled intervention studies have evaluated the health effects of decentralised (non-sewerage) sanitation in an informal urban setting, despite the role that such technologies will likely play in scaling up access. METHODS AND ANALYSIS We have designed a controlled, before-and-after (CBA) trial to estimate the health impacts of an urban sanitation intervention in informal neighbourhoods of Maputo, Mozambique, including an assessment of whether exposures and health outcomes vary by localised population density. The intervention consists of private pour-flush latrines (to septic tank) shared by multiple households in compounds or household clusters. We will measure objective health outcomes in approximately 760 children (380 children with household access to interventions, 380 matched controls using existing shared private latrines in poor sanitary conditions), at 2 time points: immediately before the intervention and at follow-up after 12 months. The primary outcome is combined prevalence of selected enteric infections among children under 5 years of age. Secondary outcome measures include soil-transmitted helminth (STH) reinfection in children following baseline deworming and prevalence of reported diarrhoeal disease. We will use exposure assessment, faecal source tracking, and microbial transmission modelling to examine whether and how routes of exposure for diarrhoeagenic pathogens and STHs change following introduction of effective sanitation. ETHICS Study protocols have been reviewed and approved by human subjects review boards at the London School of Hygiene and Tropical Medicine, the Georgia Institute of Technology, the University of North Carolina at Chapel Hill, and the Ministry of Health, Republic of Mozambique. TRIAL REGISTRATION NUMBER NCT02362932.
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Affiliation(s)
- Joe Brown
- School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Oliver Cumming
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, UK
| | - Jamie Bartram
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sandy Cairncross
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, UK
| | - Jeroen Ensink
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, UK
| | - David Holcomb
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jackie Knee
- School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Peter Kolsky
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kaida Liang
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Song Liang
- Department of Environmental and Global Health, University of Florida, Gainesville, Florida, USA
| | - Rassul Nala
- Ministry of Health, Republic of Mozambique, Maputo, Mozambique
| | - Guy Norman
- Water and Sanitation for the Urban Poor, London, UK
| | - Richard Rheingans
- Department of Environmental and Global Health, University of Florida, Gainesville, Florida, USA
| | - Jill Stewart
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Valentina Zuin
- Emmett Interdisciplinary Program in Environment and Resources, Stanford University, Palo Alto, California, USA
| | - Wolf-Peter Schmidt
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, UK
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Serp J, Allibert M, Beneš O, Delpech S, Feynberg O, Ghetta V, Heuer D, Holcomb D, Ignatiev V, Kloosterman JL, Luzzi L, Merle-Lucotte E, Uhlíř J, Yoshioka R, Zhimin D. The molten salt reactor (MSR) in generation IV: Overview and perspectives. Progress in Nuclear Energy 2014. [DOI: 10.1016/j.pnucene.2014.02.014] [Citation(s) in RCA: 444] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Haselow DT, Safi H, Holcomb D, Smith N, Wagner KD, Bolden BB, Harik NS. Histoplasmosis associated with a bamboo bonfire--Arkansas, October 2011. MMWR Morb Mortal Wkly Rep 2014; 63:165-8. [PMID: 24572611 PMCID: PMC4584522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
On October 27, 2011, the Arkansas Department of Health (ADH) was notified by a northeast Arkansas primary care provider of a cluster of three histoplasmosis cases. On November 4, ADH was notified by a pediatric infectious diseases specialist regarding seven potential cases of pulmonary histoplasmosis associated with a family gathering that included a bonfire that burned bamboo from a grove that had been a red-winged blackbird roost. These reports prompted an outbreak investigation to ensure that the persons involved received appropriate medical care, to identify whether any novel exposures were associated with illness, and to determine whether any factors were associated with hospitalization. The investigation found that, among the 19 attendees at the family gathering, seven were confirmed with histoplasmosis, 11 were probable, and one did not have histoplasmosis.
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Affiliation(s)
- Dirk T. Haselow
- Arkansas Department of Health,Corresponding author: Dirk T. Haselow, 501-537-8969,
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Yoder GL, Aaron A, Cunningham B, Fugate D, Holcomb D, Kisner R, Peretz F, Robb K, Wilgen J, Wilson D. An experimental test facility to support development of the fluoride-salt-cooled high-temperature reactor. ANN NUCL ENERGY 2014. [DOI: 10.1016/j.anucene.2013.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Freeman VS, Holcomb D, Brickell J, Chandler K, Muellenberg P. Faculty members acceptance of web-based education. Clin Lab Sci 2004; 17:88-94. [PMID: 15168889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
OBJECTIVE To assess the effect of the WebCLS project on clinical laboratory science (CLS) faculty members including improvement of participating CLS educators' skills in designing, developing, delivering, and evaluating interactive, Web-based instructional programs. DESIGN A survey was developed that included 24 statements related to respondents' perceptions of how their participation in the project: a) improved their course development skills, b) developed their evaluation skills, and c) affected them personally. Four open-ended questions asked the respondents to comment on the project's effect on their traditional course development skills, plans for future usage of WebCLS-produced course materials, the most beneficial outcomes of their participation, any problems that participation in the project caused them, and any unexpected positive or negative outcomes that could be attributed to their participation. SETTING The survey was sent to 27 individuals who had participated in the project. RESULTS Twenty-four participants completed the survey for an 89% response rate. The mean response was 6.82 (S.D. 2.32) with sixteen respondents' (73%) reporting participation at the mean or above. CONCLUSION Overall, the WebCLS project accomplished its objective of improving CLS educators' Web-based, distance education course development skills. One of the most positive outcomes of the project was the survey respondents' belief that their participation in the project expanded their contacts with colleagues in CLS education as well as with instructional design experts, computer programmers, and other technical support personnel. Furthermore, this outcome prompted several participating faculty to report that this enhanced collegial relationship will sustain their interest in curriculum development over time.
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Affiliation(s)
- Vicki S Freeman
- Department of Clinical Laboratory Sciences, School of Allied Health Sciences, University of Texas Medical Branch, Galveston, TX 77555-1140, USA.
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Norwood RA, Sounik JR, Holcomb D, Popolo J, Swanson D, Spitzer R, Hansen G. Nonlinear Bragg mirror made from a silicon phthalocyanine/methyl methacrylate copolymer. Opt Lett 1992; 17:577-579. [PMID: 19794563 DOI: 10.1364/ol.17.000577] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A nonlinear Bragg mirror based on saturably absorbing nonlinear-optical polymers is proposed and demonstrated. The saturable absorber is a copolymer of silicon phthalocyanine with methyl methacrylate, which exhibits its largest nonlinear absorption near 670 nm. A 23-layer stack was made by spin coating, with polymethyl methacrylate as the low-index layer, and the linear-optical performance was found to agree reasonably well with predictions based on a modified two-level model of the optical properties of the copolymer. Optical limiting at an intensity of 5-10 MW/cm(2) was demonstrated for 6-ns pulses at a wavelength of 688 nm.
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