Last data update: May 06, 2024. (Total: 46732 publications since 2009)
Records 1-11 (of 11 Records) |
Query Trace: Waters KM[original query] |
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A compendium of multi-omics data illuminating host responses to lethal human virus infections
Eisfeld AJ , Anderson LN , Fan S , Walters KB , Halfmann PJ , Westhoff Smith D , Thackray LB , Tan Q , Sims AC , Menachery VD , Schäfer A , Sheahan TP , Cockrell AS , Stratton KG , Webb-Robertson BM , Kyle JE , Burnum-Johnson KE , Kim YM , Nicora CD , Peralta Z , N'Jai A U , Sahr F , van Bakel H , Diamond MS , Baric RS , Metz TO , Smith RD , Kawaoka Y , Waters KM . Sci Data 2024 11 (1) 328 Human infections caused by viral pathogens trigger a complex gamut of host responses that limit disease, resolve infection, generate immunity, and contribute to severe disease or death. Here, we present experimental methods and multi-omics data capture approaches representing the global host response to infection generated from 45 individual experiments involving human viruses from the Orthomyxoviridae, Filoviridae, Flaviviridae, and Coronaviridae families. Analogous experimental designs were implemented across human or mouse host model systems, longitudinal samples were collected over defined time courses, and global multi-omics data (transcriptomics, proteomics, metabolomics, and lipidomics) were acquired by microarray, RNA sequencing, or mass spectrometry analyses. For comparison, we have included transcriptomics datasets from cells treated with type I and type II human interferon. Raw multi-omics data and metadata were deposited in public repositories, and we provide a central location linking the raw data with experimental metadata and ready-to-use, quality-controlled, statistically processed multi-omics datasets not previously available in any public repository. This compendium of infection-induced host response data for reuse will be useful for those endeavouring to understand viral disease pathophysiology and network biology. |
Evaluating predictive relationships between wristbands and urine for assessment of personal PAH exposure.
Dixon HM , Bramer LM , Scott RP , Calero L , Holmes D , Gibson EA , Cavalier HM , Rohlman D , Miller RL , Calafat AM , Kincl L , Waters KM , Herbstman JB , Anderson KA . Environ Int 2022 163 107226 During events like the COVID-19 pandemic or a disaster, researchers may need to switch from collecting biological samples to personal exposure samplers that are easy and safe to transport and wear, such as silicone wristbands. Previous studies have demonstrated significant correlations between urine biomarker concentrations and chemical levels in wristbands. We build upon those studies and use a novel combination of descriptive statistics and supervised statistical learning to evaluate the relationship between polycyclic aromatic hydrocarbon (PAH) concentrations in silicone wristbands and hydroxy-PAH (OH-PAH) concentrations in urine. In New York City, 109 participants in a longitudinal birth cohort wore one wristband for 48 h and provided a spot urine sample at the end of the 48-hour period during their third trimester of pregnancy. We compared four PAHs with the corresponding seven OH-PAHs using descriptive statistics, a linear regression model, and a linear discriminant analysis model. Five of the seven PAH and OH-PAH pairs had significant correlations (Pearson's r = 0.35-0.64, p ≤ 0.003) and significant chi-square tests of independence for exposure categories (p ≤ 0.009). For these five comparisons, the observed PAH or OH-PAH concentration could predict the other concentration within a factor of 1.47 for 50-80% of the measurements (depending on the pair). Prediction accuracies for high exposure categories were at least 1.5 times higher compared to accuracies based on random chance. These results demonstrate that wristbands and urine provide similar PAH exposure assessment information, which is critical for environmental health researchers looking for the flexibility to switch between biological sample and wristband collection. |
CATMoS: Collaborative Acute Toxicity Modeling Suite.
Mansouri K , Karmaus AL , Fitzpatrick J , Patlewicz G , Pradeep P , Alberga D , Alepee N , Allen TEH , Allen D , Alves VM , Andrade CH , Auernhammer TR , Ballabio D , Bell S , Benfenati E , Bhattacharya S , Bastos JV , Boyd S , Brown JB , Capuzzi SJ , Chushak Y , Ciallella H , Clark AM , Consonni V , Daga PR , Ekins S , Farag S , Fedorov M , Fourches D , Gadaleta D , Gao F , Gearhart JM , Goh G , Goodman JM , Grisoni F , Grulke CM , Hartung T , Hirn M , Karpov P , Korotcov A , Lavado GJ , Lawless M , Li X , Luechtefeld T , Lunghini F , Mangiatordi GF , Marcou G , Marsh D , Martin T , Mauri A , Muratov EN , Myatt GJ , Nguyen DT , Nicolotti O , Note R , Pande P , Parks AK , Peryea T , Polash AH , Rallo R , Roncaglioni A , Rowlands C , Ruiz P , Russo DP , Sayed A , Sayre R , Sheils T , Siegel C , Silva AC , Simeonov A , Sosnin S , Southall N , Strickland J , Tang Y , Teppen B , Tetko IV , Thomas D , Tkachenko V , Todeschini R , Toma C , Tripodi I , Trisciuzzi D , Tropsha A , Varnek A , Vukovic K , Wang Z , Wang L , Waters KM , Wedlake AJ , Wijeyesakere SJ , Wilson D , Xiao Z , Yang H , Zahoranszky-Kohalmi G , Zakharov AV , Zhang FF , Zhang Z , Zhao T , Zhu H , Zorn KM , Casey W , Kleinstreuer NC . Environ Health Perspect 2021 129 (4) 47013 BACKGROUND: Humans are exposed to tens of thousands of chemical substances that need to be assessed for their potential toxicity. Acute systemic toxicity testing serves as the basis for regulatory hazard classification, labeling, and risk management. However, it is cost- and time-prohibitive to evaluate all new and existing chemicals using traditional rodent acute toxicity tests. In silico models built using existing data facilitate rapid acute toxicity predictions without using animals. OBJECTIVES: The U.S. Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) Acute Toxicity Workgroup organized an international collaboration to develop in silico models for predicting acute oral toxicity based on five different end points: Lethal Dose 50 (LD50 value, U.S. Environmental Protection Agency hazard (four) categories, Globally Harmonized System for Classification and Labeling hazard (five) categories, very toxic chemicals [LD50 (LD50 ≤ 50 mg/kg)], and nontoxic chemicals (LD50 > 2,000 mg/kg). METHODS: An acute oral toxicity data inventory for 11,992 chemicals was compiled, split into training and evaluation sets, and made available to 35 participating international research groups that submitted a total of 139 predictive models. Predictions that fell within the applicability domains of the submitted models were evaluated using external validation sets. These were then combined into consensus models to leverage strengths of individual approaches. RESULTS: The resulting consensus predictions, which leverage the collective strengths of each individual model, form the Collaborative Acute Toxicity Modeling Suite (CATMoS). CATMoS demonstrated high performance in terms of accuracy and robustness when compared with in vivo results. DISCUSSION: CATMoS is being evaluated by regulatory agencies for its utility and applicability as a potential replacement for in vivo rat acute oral toxicity studies. CATMoS predictions for more than 800,000 chemicals have been made available via the National Toxicology Program's Integrated Chemical Environment tools and data sets (ice.ntp.niehs.nih.gov). The models are also implemented in a free, standalone, open-source tool, OPERA, which allows predictions of new and untested chemicals to be made. https://doi.org/10.1289/EHP8495. |
Silicone wristbands compared with traditional polycyclic aromatic hydrocarbon exposure assessment methods
Dixon HM , Scott RP , Holmes D , Calero L , Kincl LD , Waters KM , Camann DE , Calafat AM , Herbstman JB , Anderson KA . Anal Bioanal Chem 2018 410 (13) 3059-3071 Currently there is a lack of inexpensive, easy-to-use technology to evaluate human exposure to environmental chemicals, including polycyclic aromatic hydrocarbons (PAHs). This is the first study in which silicone wristbands were deployed alongside two traditional personal PAH exposure assessment methods: active air monitoring with samplers (i.e., polyurethane foam (PUF) and filter) housed in backpacks, and biological sampling with urine. We demonstrate that wristbands worn for 48 h in a non-occupational setting recover semivolatile PAHs, and we compare levels of PAHs in wristbands to PAHs in PUFs-filters and to hydroxy-PAH (OH-PAH) biomarkers in urine. We deployed all samplers simultaneously for 48 h on 22 pregnant women in an established urban birth cohort. Each woman provided one spot urine sample at the end of the 48-h period. Wristbands recovered PAHs with similar detection frequencies to PUFs-filters. Of the 62 PAHs tested for in the 22 wristbands, 51 PAHs were detected in at least one wristband. In this cohort of pregnant women, we found more significant correlations between OH-PAHs and PAHs in wristbands than between OH-PAHs and PAHs in PUFs-filters. Only two comparisons between PAHs in PUFs-filters and OH-PAHs correlated significantly (rs = 0.53 and p = 0.01; rs = 0.44 and p = 0.04), whereas six comparisons between PAHs in wristbands and OH-PAHs correlated significantly (rs = 0.44 to 0.76 and p = 0.04 to <0.0001). These results support the utility of wristbands as a biologically relevant exposure assessment tool which can be easily integrated into environmental health studies. Graphical abstract PAHs detected in samples collected from urban pregnant women. |
Mortality in a combined cohort of uranium enrichment workers
Yiin JH , Anderson JL , Daniels RD , Bertke SJ , Fleming DA , Tollerud DJ , Tseng CY , Chen PH , Waters KM . Am J Ind Med 2016 60 (1) 96-108 OBJECTIVE: To examine the patterns of cause-specific mortality and relationship between internal exposure to uranium and specific causes in a pooled cohort of 29,303 workers employed at three former uranium enrichment facilities in the United States with follow-up through 2011. METHODS: Cause-specific standardized mortality ratios (SMRs) for the full cohort were calculated with the U.S. population as referent. Internal comparison of the dose-response relation between selected outcomes and estimated organ doses was evaluated using regression models. RESULTS: External comparison with the U.S. population showed significantly lower SMRs in most diseases in the pooled cohort. Internal comparison showed positive associations of absorbed organ doses with multiple myeloma, and to a lesser degree with kidney cancer. CONCLUSION: In general, these gaseous diffusion plant workers had significantly lower SMRs than the U.S. POPULATION: The internal comparison however, showed associations between internal organ doses and diseases associated with uranium exposure in previous studies. |
Exposure-response relationships for select cancer and non-cancer health outcomes in a cohort of US firefighters from San Francisco, Chicago and Philadelphia (1950-2009)
Daniels RD , Bertke S , Dahm MM , Yiin JH , Kubale TL , Hales TR , Baris D , Zahm SH , Beaumont JJ , Waters KM , Pinkerton LE . Occup Environ Med 2015 72 (10) 699-706 OBJECTIVES: To examine exposure-response relationships between surrogates of firefighting exposure and select outcomes among previously studied US career firefighters. METHODS: Eight cancer and four non-cancer outcomes were examined using conditional logistic regression. Incidence density sampling was used to match each case to 200 controls on attained age. Days accrued in firefighting assignments (exposed-days), run totals (fire-runs) and run times (fire-hours) were used as exposure surrogates. HRs comparing 75th and 25th centiles of lagged cumulative exposures were calculated using loglinear, linear, log-quadratic, power and restricted cubic spline general relative risk models. Piecewise constant models were used to examine risk differences by time since exposure, age at exposure and calendar period. RESULTS: Among 19 309 male firefighters eligible for the study, there were 1333 cancer deaths and 2609 cancer incidence cases. Significant positive associations between fire-hours and lung cancer mortality and incidence were evident. A similar relation between leukaemia mortality and fire-runs was also found. The lung cancer associations were nearly linear in cumulative exposure, while the association with leukaemia mortality was attenuated at higher exposure levels and greater for recent exposures. Significant negative associations were evident for the exposure surrogates and colorectal and prostate cancers, suggesting a healthy worker survivor effect possibly enhanced by medical screening. CONCLUSIONS: Lung cancer and leukaemia mortality risks were modestly increasing with firefighter exposures. These findings add to evidence of a causal association between firefighting and cancer. Nevertheless, small effects merit cautious interpretation. We plan to continue to follow the occurrence of disease and injury in this cohort. |
Mortality and cancer incidence in a pooled cohort of US firefighters from San Francisco, Chicago and Philadelphia (1950-2009)
Daniels RD , Kubale TL , Yiin JH , Dahm MM , Hales TR , Baris D , Zahm SH , Beaumont JJ , Waters KM , Pinkerton LE . Occup Environ Med 2013 71 (6) 388-97 OBJECTIVES: To examine mortality patterns and cancer incidence in a pooled cohort of 29 993 US career firefighters employed since 1950 and followed through 2009. METHODS: Mortality and cancer incidence were evaluated by life table methods with the US population referent. Standardised mortality (SMR) and incidence (SIR) ratios were determined for 92 causes of death and 41 cancer incidence groupings. Analyses focused on 15 outcomes of a priori interest. Sensitivity analyses were conducted to examine the potential for significant bias. RESULTS: Person-years at risk totalled 858 938 and 403 152 for mortality and incidence analyses, respectively. All-cause mortality was at expectation (SMR=0.99, 95% CI 0.97 to 1.01, n=12 028). There was excess cancer mortality (SMR=1.14, 95% CI 1.10 to 1.18, n=3285) and incidence (SIR=1.09, 95% CI 1.06 to 1.12, n=4461) comprised mainly of digestive (SMR=1.26, 95% CI 1.18 to 1.34, n=928; SIR=1.17, 95% CI 1.10 to 1.25, n=930) and respiratory (SMR=1.10, 95% CI 1.04 to 1.17, n=1096; SIR=1.16, 95% CI 1.08 to 1.24, n=813) cancers. Consistent with previous reports, modest elevations were observed in several solid cancers; however, evidence of excess lymphatic or haematopoietic cancers was lacking. This study is the first to report excess malignant mesothelioma (SMR=2.00, 95% CI 1.03 to 3.49, n=12; SIR=2.29, 95% CI 1.60 to 3.19, n=35) among US firefighters. Results appeared robust under differing assumptions and analytic techniques. CONCLUSIONS: Our results provide evidence of a relation between firefighting and cancer. The new finding of excess malignant mesothelioma is noteworthy, given that asbestos exposure is a known hazard of firefighting. |
Risk of leukaemia mortality from exposure to ionising radiation in US nuclear workers: a pooled case-control study
Daniels RD , Bertke S , Waters KM , Schubauer-Berigan MK . Occup Environ Med 2012 70 (1) 41-8 OBJECTIVE: To follow-up on earlier studies of the leukaemogenicity of occupational ionising radiation exposure. METHODS: We conducted a nested case-control analysis of leukaemia mortality in a pooled cohort of US nuclear workers followed through 2005. Each case was matched to four controls on attained age. Exposures were estimated from available records. General relative risk models were used to estimate the excess relative risk (ERR) of leukaemia, excluding chronic lymphocytic (CLL), acute myeloid leukaemia, chronic myeloid leukaemia and CLL while controlling for potential confounders. Preferred exposure lags and time-windows of risks were calculated using joint maximum likelihood. Dose-response was also examined using linear, linear-quadratic, categorical and restricted cubic spline models. RESULTS: There were 369 leukaemia deaths in 105 245 US nuclear workers. The adjusted ERR for non-CLL leukaemia was 0.09 (95% CI -0.17 to 0.65) per 100 mGy. Elevated non-CLL risks were observed from exposures occurring 6-14 years prior to attained age of cases (ERR per 100 mGy=1.9; 95% CI <0 to 8.0). Lagged models indicated non-linearity of risk at very low (<10 mGy) and high (>100 mGy) doses, which contributed to the imprecision of results in linear models. Similar risk attenuation was not evident in time-windows-based models. CONCLUSIONS: Risk estimates were in reasonable agreement with previous estimates, with the temporality of non-CLL leukaemia risk as a dominant factor in dose-response analyses. Future research should focus on methods that improve evaluations of the dose-response, particularly in the low-dose range. |
The Upper Midwest Health Study: industry and occupation of glioma cases and controls
Ruder AM , Waters MA , Carreon T , Butler MA , Calvert GM , Davis-King KE , Waters KM , Schulte PA , Mandel JS , Morton RF , Reding DJ , Rosenman KD . Am J Ind Med 2012 55 (9) 747-55 BACKGROUND: Understanding glioma etiology requires determining which environmental factors are associated with glioma. Upper Midwest Health Study case-control participant work histories collected 1995-1998 were evaluated for occupational associations with glioma. "Exposures of interest" from our study protocol comprise our a priori hypotheses. MATERIALS AND METHODS: Year-long or longer jobs for 1,973 participants were assigned Standard Occupational Classifications (SOC) and Standard Industrial Classifications (SIC). The analysis file includes 8,078 SIC- and SOC-coded jobs. For each individual, SAS 9.2 programs collated employment with identical SIC-SOC coding. Distributions of longest "total employment duration" (total years worked in jobs with identical industry and occupation codes, including multiple jobs, and non-consecutive jobs) were compared between cases and controls, using an industrial hygiene algorithm to group occupations. RESULTS: Longest employment duration was calculated for 780 cases and 1,156 controls. More case than control longest total employment duration was in the "engineer, architect" occupational group [16 cases, 10 controls, odds ratio (OR) 2.50, adjusted for age group, sex, age and education, 95% confidence interval (CI) 1.12-5.60]. Employment as a food processing worker [mostly butchers and meat cutters] was of borderline significance (27 cases, 21 controls, adjusted OR: 1.78, CI: 0.99-3.18). CONCLUSIONS: Among our exposures of interest work as engineers or as butchers and meat cutters was associated with increased glioma risk. Significant associations could be due to chance, because of multiple comparisons, but similar findings have been reported for other glioma studies. Our results suggest some possible associations but by themselves could not provide conclusive evidence. (Am. J. Ind. Med. (c) 2012 Wiley Periodicals, Inc.) |
Update of the NIOSH life table analysis system: a person-years analysis program for the windows computing environment
Schubauer-Berigan MK , Hein MJ , Raudabaugh WM , Ruder AM , Silver SR , Spaeth S , Steenland K , Petersen MR , Waters KM . Am J Ind Med 2011 54 (12) 915-24 BACKGROUND: Person-years analysis is a fundamental tool of occupational epidemiology. A life table analysis system (LTAS), previously developed by the National Institute for Occupational Safety and Health, was limited by its platform and analysis and reporting capabilities. We describe the updating of LTAS for the Windows operating system (LTAS.NET) with improved properties. SOFTWARE DEVELOPMENT PROCESS: A group of epidemiologists, programmers, and statisticians developed software, platform, and computing requirements. Statistical methods include the use of (indirectly) standardized mortality ratios, (directly) standardized rate ratios, confidence intervals, and P values based on the normal approximation and exact Poisson methods, and a trend estimator for linear exposure-response associations. SOFTWARE FEATURES: We show examples using LTAS.NET to stratify and analyze multiple fixed and time-dependent variables. Data import, stratification, and reporting options are highly flexible. Users may export stratified data for Poisson regression modeling. CONCLUSIONS: LTAS.NET incorporates improvements that will facilitate more complex person-years analysis of occupational cohort data. |
Comparative proteomics and pulmonary toxicity of instilled single-walled carbon nanotubes, crocidolite asbestos, and ultrafine carbon black in mice
Teeguarden JG , Webb-Robertson BJ , Waters KM , Murray AR , Kisin ER , Varnum SM , Jacobs JM , Pounds JG , Zanger RC , Shvedova AA . Toxicol Sci 2011 120 (1) 123-135 Reflecting their exceptional potential to advance a range of biomedical, aeronautic, and other industrial products, carbon nanotube (CNT) production and the potential for human exposure to aerosolized CNTs are increasing. CNTs have toxicologically significant structural and chemical similarities to asbestos (AB) and have repeatedly been shown to cause pulmonary inflammation, granuloma formation, and fibrosis after inhalation/instillation/aspiration exposure in rodents, a pattern of effects similar to those observed following exposure to AB. To determine the degree to which responses to single-walled CNTs (SWCNT) and AB are similar or different, the pulmonary response of C57BL/6 mice to repeated exposures to SWCNTs, crocidolite AB, and ultrafine carbon black (UFCB) were compared using high-throughput global high performance liquid chromatography fourier transform ion cyclotron resonance mass spectrometry (HPLC-FTICR-MS) proteomics, histopathology, and bronchoalveolar lavage cytokine analyses. Mice were exposed to material suspensions (40 micrograms per mouse) twice a week for 3 weeks by pharyngeal aspiration. Histologically, the incidence and severity of inflammatory and fibrotic responses were greatest in mice treated with SWCNTs. SWCNT treatment affected the greatest changes in abundance of identified lung tissue proteins. The trend in number of proteins affected (SWCNT [376] > AB [231] > UFCB [184]) followed the potency of these materials in three biochemical assays of inflammation (cytokines). SWCNT treatment uniquely affected the abundance of 109 proteins, but these proteins largely represent cellular processes affected by AB treatment as well, further evidence of broad similarity in the tissue-level response to AB and SWCNTs. Two high-sensitivity markers of inflammation, one (S100a9) observed in humans exposed to AB, were found and may be promising biomarkers of human response to SWCNT exposure. |
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