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Synthetic biology is creating genetically engineered organisms at an increasing rate for many potentially valuable applications, but this potential comes with the risk of misuse or accidental release. To begin to address this issue, we have developed a system called GUARDIAN that can automatically detect signatures of engineering in DNA sequencing data, and we have conducted a blinded test of this system using a curated Test and Evaluation (T&E) data set. GUARDIAN uses an ensemble approach based on the guiding principle that no single approach is likely to be able to detect engineering with perfect accuracy. Critically, ensembling enables GUARDIAN to detect sequence inserts in 13 target organisms with a high degree of specificity that requires no subject matter expert (SME) review.
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ADN , Análisis de Secuencia de ADN , ADN/genéticaRESUMEN
Microbacterium sp. BDGP8 is a species of facultative anaerobic gram-positive bacterium of the family Microbacteriaceae. The complete genome consists of a single circular chromosome of 3,293,567 bp with a G + C content of 69.84% and two plasmids of 49,365 bp and 32,884 bp.
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Generating reference maps of interactome networks illuminates genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processes. We apply state-of-the-art methods to identify binary protein-protein interactions (PPIs) for Drosophila melanogaster. Four all-by-all yeast two-hybrid (Y2H) screens of > 10,000 Drosophila proteins result in the 'FlyBi' dataset of 8723 PPIs among 2939 proteins. Testing subsets of data from FlyBi and previous PPI studies using an orthogonal assay allows for normalization of data quality; subsequent integration of FlyBi and previous data results in an expanded binary Drosophila reference interaction network, DroRI, comprising 17,232 interactions among 6511 proteins. We use FlyBi data to generate an autophagy network, then validate in vivo using autophagy-related assays. The deformed wings (dwg) gene encodes a protein that is both a regulator and a target of autophagy. Altogether, these resources provide a foundation for building new hypotheses regarding protein networks and function.
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Proteínas de Drosophila , Mapas de Interacción de Proteínas , Animales , Mapas de Interacción de Proteínas/genética , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Drosophila/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Mapeo de Interacción de Proteínas/métodos , Técnicas del Sistema de Dos HíbridosRESUMEN
Transcription factors (TFs) play a key role in development and in cellular responses to the environment by activating or repressing the transcription of target genes in precise spatial and temporal patterns. In order to develop a catalog of target genes of Drosophila melanogaster TFs, the modERN consortium systematically knocked down the expression of TFs using RNAi in whole embryos followed by RNA-seq. We generated data for 45 TFs which have 18 different DNA-binding domains and are expressed in 15 of the 16 organ systems. The range of inactivation of the targeted TFs by RNAi ranged from log2fold change -3.52 to +0.49. The TFs also showed remarkable heterogeneity in the numbers of candidate target genes identified, with some generating thousands of candidates and others only tens. We present detailed analysis from five experiments, including those for three TFs that have been the focus of previous functional studies (ERR, sens, and zfh2) and two previously uncharacterized TFs (sens-2 and CG32006), as well as short vignettes for selected additional experiments to illustrate the utility of this resource. The RNA-seq datasets are available through the ENCODE DCC (http://encodeproject.org) and the Sequence Read Archive (SRA). TF and target gene expression patterns can be found here: https://insitu.fruitfly.org. These studies provide data that facilitate scientific inquiries into the functions of individual TFs in key developmental, metabolic, defensive, and homeostatic regulatory pathways, as well as provide a broader perspective on how individual TFs work together in local networks during embryogenesis.
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Proteínas de Drosophila , Drosophila , Animales , Drosophila/metabolismo , Drosophila melanogaster/metabolismo , Interferencia de ARN , Factores de Transcripción/metabolismo , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Receptores de Estrógenos/genética , Receptores de Estrógenos/metabolismo , Proteínas de Unión al ADN/genéticaRESUMEN
The gut microbiome produces vitamins, nutrients, and neurotransmitters, and helps to modulate the host immune system-and also plays a major role in the metabolism of many exogenous compounds, including drugs and chemical toxicants. However, the extent to which specific microbial species or communities modulate hazard upon exposure to chemicals remains largely opaque. Focusing on the effects of collateral dietary exposure to the widely used herbicide atrazine, we applied integrated omics and phenotypic screening to assess the role of the gut microbiome in modulating host resilience in Drosophila melanogaster. Transcriptional and metabolic responses to these compounds are sex-specific and depend strongly on the presence of the commensal microbiome. Sequencing the genomes of all abundant microbes in the fly gut revealed an enzymatic pathway responsible for atrazine detoxification unique to Acetobacter tropicalis. We find that Acetobacter tropicalis alone, in gnotobiotic animals, is sufficient to rescue increased atrazine toxicity to wild-type, conventionally reared levels. This work points toward the derivation of biotic strategies to improve host resilience to environmental chemical exposures, and illustrates the power of integrative omics to identify pathways responsible for adverse health outcomes.
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Atrazina/toxicidad , Drosophila melanogaster/efectos de los fármacos , Microbioma Gastrointestinal/efectos de los fármacos , Interacciones Microbiota-Huesped/efectos de los fármacos , Insecticidas/toxicidad , Acetobacter/genética , Acetobacter/metabolismo , Animales , Drosophila melanogaster/microbiología , Femenino , Inactivación Metabólica , MasculinoRESUMEN
Lactobacillus brevis Oregon-R-modENCODE strain BDGP6 was isolated from the gut of Drosophila melanogaster for functional host-microbial interaction studies. The bacterial chromosome is a single circular DNA molecule of 2,785,111 bp with a G+C content of 46%.
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Citrobacter freundii is a species of facultative anaerobic Gram-negative bacteria of the family Enterobacteriaceae The complete genome is composed of a single chromosomal circle of 4,957,773 bp with a G+C content of 52%.
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BACKGROUND: Spatial access to primary care has been associated with late-stage and fatal breast cancer, but less is known about its relation to outcomes of other screening-preventable cancers such as colorectal cancer. This population-based retrospective cohort study examined whether spatial access to primary care providers associates with colorectal cancer-specific survival. METHODS: Approximately 26 600 incident colorectal cancers diagnosed between 2000 and 2008 in adults residing in Cook County, Illinois were identified through the state cancer registry and georeferenced to the census tract of residence at diagnosis. An enhanced two-step floating catchment area method measured tract-level access to primary care physicians (PCPs) in the year of diagnosis using practice locations obtained from the American Medical Association. Vital status and underlying cause of death were determined using the National Death Index. Fine-Gray proportional subdistribution hazard models analyzed the association between tract-level PCP access scores and colorectal cancer-specific survival after accounting for tract-level socioeconomic status, case demographics, tumor characteristics, and other factors. RESULTS: Increased tract-level access to PCPs was associated with a lower risk of death from colorectal cancer (hazard ratio [HR], 95% confidence interval [CI]) = 0.87 [0.79, 0.96], P = .008, highest vs lowest quintile), especially among persons diagnosed with regional-stage tumors (HR, 95% CI = 0.80 [0.69, 0.93], P = .004, highest vs lowest quintile). CONCLUSIONS: Spatial access to primary care providers is a predictor of colorectal cancer-specific survival in Cook County, Illinois. Future research is needed to determine which areas within the cancer care continuum are most affected by spatial accessibility to primary care such as referral for screening, accessibility of screening and diagnostic testing, referral for treatment, and access to appropriate survivorship-related care.
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Neoplasias Colorrectales/mortalidad , Personal de Salud/estadística & datos numéricos , Accesibilidad a los Servicios de Salud/tendencias , Atención Primaria de Salud/estadística & datos numéricos , Adolescente , Adulto , Anciano , Niño , Preescolar , Neoplasias Colorrectales/epidemiología , Neoplasias Colorrectales/patología , Femenino , Estudios de Seguimiento , Humanos , Illinois/epidemiología , Masculino , Persona de Mediana Edad , Pronóstico , Factores Socioeconómicos , Análisis Espacial , Tasa de Supervivencia , Adulto JovenRESUMEN
Parental occupational exposures to pesticides, animals and organic dust have been associated with an increased risk of childhood cancer based mostly on case-control studies. We prospectively evaluated parental occupational exposures and risk of childhood leukemia and central nervous system (CNS) tumors in the International Childhood Cancer Cohort Consortium. We pooled data on 329,658 participants from birth cohorts in five countries (Australia, Denmark, Israel, Norway and United Kingdom). Parental occupational exposures during pregnancy were estimated by linking International Standard Classification of Occupations-1988 job codes to the ALOHA+ job exposure matrix. Risk of childhood (<15 years) acute lymphoblastic leukemia (ALL; n = 129), acute myeloid leukemia (AML; n = 31) and CNS tumors (n = 158) was estimated using Cox proportional hazards models to generate hazard ratios (HR) and 95% confidence intervals (CI). Paternal exposures to pesticides and animals were associated with increased risk of childhood AML (herbicides HR = 3.22, 95% CI = 0.97-10.68; insecticides HR = 2.86, 95% CI = 0.99-8.23; animals HR = 3.89, 95% CI = 1.18-12.90), but not ALL or CNS tumors. Paternal exposure to organic dust was positively associated with AML (HR = 2.38 95% CI = 1.12-5.07), inversely associated with ALL (HR = 0.55, 95% CI = 0.31-0.99) and not associated with CNS tumors. Low exposure prevalence precluded evaluation of maternal pesticide and animal exposures; we observed no significant associations with organic dust exposure. This first prospective analysis of pooled birth cohorts and parental occupational exposures provides evidence for paternal agricultural exposures as childhood AML risk factors. The different risks for childhood ALL associated with maternal and paternal organic dust exposures should be investigated further.
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Neoplasias del Sistema Nervioso Central/epidemiología , Leucemia Mieloide Aguda/epidemiología , Exposición Materna/efectos adversos , Exposición Profesional/efectos adversos , Exposición Paterna/efectos adversos , Leucemia-Linfoma Linfoblástico de Células Precursoras/epidemiología , Efectos Tardíos de la Exposición Prenatal/epidemiología , Adolescente , Adulto , Animales , Animales Domésticos , Australia/epidemiología , Neoplasias del Sistema Nervioso Central/etiología , Niño , Preescolar , Dinamarca/epidemiología , Polvo , Femenino , Estudios de Seguimiento , Humanos , Lactante , Recién Nacido , Israel/epidemiología , Leucemia Mieloide Aguda/etiología , Masculino , Noruega/epidemiología , Plaguicidas/toxicidad , Leucemia-Linfoma Linfoblástico de Células Precursoras/etiología , Embarazo , Efectos Tardíos de la Exposición Prenatal/etiología , Estudios Prospectivos , Factores de Riesgo , Reino Unido/epidemiología , Adulto JovenRESUMEN
Identifying functional enhancer elements in metazoan systems is a major challenge. Large-scale validation of enhancers predicted by ENCODE reveal false-positive rates of at least 70%. We used the pregrastrula-patterning network of Drosophila melanogaster to demonstrate that loss in accuracy in held-out data results from heterogeneity of functional signatures in enhancer elements. We show that at least two classes of enhancers are active during early Drosophila embryogenesis and that by focusing on a single, relatively homogeneous class of elements, greater than 98% prediction accuracy can be achieved in a balanced, completely held-out test set. The class of well-predicted elements is composed predominantly of enhancers driving multistage segmentation patterns, which we designate segmentation driving enhancers (SDE). Prediction is driven by the DNA occupancy of early developmental transcription factors, with almost no additional power derived from histone modifications. We further show that improved accuracy is not a property of a particular prediction method: after conditioning on the SDE set, naïve Bayes and logistic regression perform as well as more sophisticated tools. Applying this method to a genome-wide scan, we predict 1,640 SDEs that cover 1.6% of the genome. An analysis of 32 SDEs using whole-mount embryonic imaging of stably integrated reporter constructs chosen throughout our prediction rank-list showed >90% drove expression patterns. We achieved 86.7% precision on a genome-wide scan, with an estimated recall of at least 98%, indicating high accuracy and completeness in annotating this class of functional elements.
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Proteínas de Drosophila , Embrión no Mamífero/embriología , Desarrollo Embrionario/fisiología , Elementos de Facilitación Genéticos/fisiología , Análisis de Secuencia de ADN , Factores de Transcripción , Animales , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Drosophila melanogaster , Estudio de Asociación del Genoma Completo , Factores de Transcripción/genética , Factores de Transcripción/metabolismoRESUMEN
BACKGROUND: Virtually all anesthesiologists care for patients who sustain traumatic injuries; however, the frequency with which operative anesthesia care is provided to this specific patient population is unclear. We sought to better understand the degree to which anesthesia providers participate in operative trauma care and how this differs by trauma center designation (levels I-V), using data from a comprehensive, regional database-the Washington State Trauma Registry (WSTR). We also sought to specifically assess operative anesthesia care frequency vis a vis the American College of Surgeons guidelines for continuous anesthesiology coverage for Level II trauma center accreditation. METHODS: We conducted a retrospective analysis measuring the frequency of operative anesthesia care among patients enrolled in the WSTR. Univariate comparisons were made between trauma patients who had surgery during their admission and those who did not (medical management only). In addition, clinical factors associated with surgical intervention were measured. We also measured the average times from hospital admission to surgery and compared these times across trauma centers, grouped level I, II, and III-V. RESULTS: From 2004 to 2014, there were approximately 176,000 encounters meeting WSTR inclusion criteria. Approximately 60% of these trauma encounters included exposure to operative anesthesia during the admission. Among all surgical procedures during the trauma admission, approximately 33% occurred within a level I trauma center, 23% occurred within a level II trauma center, and 44% occurred in a trauma center with a III, IV, or V designation. The predominant procedure category during a trauma admission was orthopedic. The presence of hypotension on admission (P < .01), increasing injury severity score (P < .01) and higher emergency department Glasgow Coma Score (P < .01) were all associated with surgical intervention during the trauma hospitalization, after adjustment for potential confounders. In level I trauma centers, for general surgical procedures, the median time to surgery was 2.5 hours; in level II trauma centers, the median time was 1.7 hours. CONCLUSIONS: This study highlights the frequent role anesthesiologists play in caring for patients who sustain traumatic injuries, in trauma centers levels I-V. In level II trauma centers, in-house anesthesiology coverage might have benefit for those patients requiring surgery within 1 hour, whereas the former American College of Surgeons requirement of 30-minute response time for out-of-hospital anesthesiology coverage is likely sufficient to provide satisfactory care to patients requiring surgery within 3 hours. Whether the increased cost of such in-house anesthesiology coverage at level II trauma centers is justified by its clinical benefit remains an unanswered question.
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Anestesia/tendencias , Anestesiólogos/tendencias , Cuidados Intraoperatorios/tendencias , Grupo de Atención al Paciente/tendencias , Pautas de la Práctica en Medicina/tendencias , Heridas y Lesiones/cirugía , Adulto , Anciano , Anestesia/efectos adversos , Femenino , Humanos , Cuidados Intraoperatorios/efectos adversos , Masculino , Persona de Mediana Edad , Quirófanos , Tempo Operativo , Rol del Médico , Sistema de Registros , Estudios Retrospectivos , Factores de Riesgo , Cirujanos , Factores de Tiempo , Centros Traumatológicos , Resultado del Tratamiento , WashingtónRESUMEN
BACKGROUND: Initial results of Washington State's quality improvement initiative addressing the management of blunt traumatic pediatric spleen injuries were published in 2008. In this update, we evaluated whether these effects were sustained over time. METHODS: Data from the Washington Trauma Registry for years 1999-2001 (pre-intervention), 2003-2005 (post-intervention), and 2012-2014 (follow-up) were used in a retrospective cohort study. Children between ages 0 to 14â¯years who were hospitalized with a traumatic blunt spleen injury were included. Multivariable logistic regression was used to account for patient, injury, and hospital characteristics. RESULTS: Overall, splenectomies continued to be less common with 8.3% of pediatric patients receiving splenectomies in the follow-up period compared with 14.3% and 7.2% in the preintervention and post-intervention periods (pâ¯=â¯0.034). After adjustment, splenectomies remained less likely to be performed in both post-intervention (ORâ¯=â¯0.37; 95% CIâ¯=â¯0.16-0.90) and follow-up periods (ORâ¯=â¯0.29; 95% CIâ¯=â¯0.12-0.70) compared to pre-intervention. Children were much more likely to be cared for at pediatric trauma hospitals in the follow-up period (ORâ¯=â¯5.13; 95% CIâ¯=â¯2.79-9.43) after adjustment. CONCLUSIONS: Evaluation of this statewide quality improvement initiative showed that positive changes in management practices persist. This evidence suggests that statewide quality improvement initiatives can be sustainable with minimal ongoing effort. LEVEL OF EVIDENCE: Level III.
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Traumatismos Abdominales/terapia , Mejoramiento de la Calidad , Bazo , Esplenectomía/estadística & datos numéricos , Adolescente , Niño , Preescolar , Hospitales Pediátricos , Humanos , Lactante , Recién Nacido , Estudios Retrospectivos , Bazo/lesiones , Bazo/cirugía , WashingtónRESUMEN
High-content image acquisition is generally limited to cells grown in culture, requiring complex hardware and preset imaging modalities. Here we report an open source software package, OpenHiCAMM (Open Hi Content Acquisition for µManager), that provides a flexible framework for integration of generic microscope-associated robotics and image processing with sequential work-flows. As an example, we imaged Drosophila embryos, detecting the embryos at low resolution, followed by re-imaging the detected embryos at high resolution, suitable for computational analysis and screening. The OpenHiCAMM package is easy to use and adapt for automating complex microscope image tasks. It expands our abilities for high-throughput image-based screens to a new range of biological samples, such as organoids, and will provide a foundation for bioimaging systems biology.
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Acetobacter pomorum Oregon-R-modENCODE strain BDGP5 was isolated from Drosophila melanogaster for functional host-microbe interaction studies. The complete genome is composed of a single chromosomal circle of 2,848,089 bp, with a G+C content of 53% and three plasmids of 131,455 bp, 19,216 bp, and 9,160 bp.
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Acetobacter tropicalis Oregon-R-modENCODE strain BDGP1 was isolated from Drosophila melanogaster for functional host-microbe interaction studies. The complete genome comprises a single chromosomal circle of 3,988,649 bp with a G+C content of 56% and a conjugative plasmid of 151,013 bp.
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Enterococcus durans Oregon-R-modENCODE strain BDGP3 was isolated from the Drosophila melanogaster gut for functional host-microbe interaction studies. The complete genome is composed of a single circular genome of 2,983,334 bp, with a G+C content of 38%, and a single plasmid of 5,594 bp.
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Bacillus kochii Oregon-R-modENCODE strain BDGP4 was isolated from the gut of Drosophila melanogaster for functional host microbial interaction studies. The complete genome comprised a single chromosomal circle of 4,557,232 bp with a G+C content of 37% and a single plasmid of 137,143 bp.
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Lactobacillus plantarum Oregon-R-modENCODE strain BDGP2 was isolated from the gut of Drosophila melanogaster for functional host microbial interaction studies. The complete genome comprised a single circular genome of 3,407,160 bp, with a G+C content of 44%, and four plasmids.
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BACKGROUND: Parental occupational and childhood exposures to farm animals have been positively associated with childhood brain tumors, whereas associations with childhood leukemia are equivocal. The developing immune system may be influenced by allergen, virus, or other exposures from animal sources, which may contribute to childhood cancer incidence. METHODS: Incident cancers (acute lymphoblastic leukemia [ALL], acute myeloid leukemia [AML], central nervous system [CNS], peripheral nervous system [PNS]) for children aged 0-4 diagnosed between 2003 and 2008 were obtained from nine National Cancer Institute Surveillance, Epidemiology and End Results (SEER) registries and were linked to U.S. Census of Agriculture data from 2002 and 2007 by county of diagnosis. Animal densities (animal units [AU]/km2; one animal unit is 1000 pounds of animal weight) were estimated for hogs, cattle, chickens (layers and broilers, separately), equine (horses, ponies, mules, burros, donkeys), goats, sheep, turkeys, and total animals. Animal density was examined in models as both continuous (AU per km2) and categorical variables (quartiles). Animal operation densities (per km2) by size of operation (cattle, hogs, chickens, sheep) were modeled continuously. Rate ratios and 95% confidence intervals were estimated using Poisson regression. RESULTS: We found positive associations between AML and broiler chicken densities (RRper 10AU/km2 = 1.14, 95% CI = 1.02-1.26). ALL rates increased with densities of hog operations (RRper operation/100km2 = 1.06, 95% CI = 1.02-1.11). PNS cancer rates were inversely associated with layer chicken density (RRper log of AU/km2 = 0.94, 95% CI = 0.89-0.99). No association was found between any cancer type and densities of cattle, equine, or goats. CONCLUSIONS: Although limited by the ecologic study design, some of our findings are novel and should be examined in epidemiological studies with individual level data.
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Ganado , Neoplasias/epidemiología , Aves de Corral , Animales , Neoplasias del Sistema Nervioso Central/epidemiología , Preescolar , Femenino , Humanos , Incidencia , Lactante , Recién Nacido , Leucemia Mieloide Aguda/epidemiología , Masculino , Neoplasias del Sistema Nervioso Periférico/epidemiología , Densidad de Población , Leucemia-Linfoma Linfoblástico de Células Precursoras/epidemiología , Características de la Residencia , Estados Unidos/epidemiologíaRESUMEN
BACKGROUND: Few studies have evaluated environmental chemical exposures in relation to ovarian cancer. We previously found an increased risk of ovarian cancer among postmenopausal women in Iowa associated with higher nitrate levels in public water supplies (PWS). However, elevated nitrate levels may reflect the presence of other agricultural chemicals, such as atrazine, one of the most commonly detected pesticides in Iowa PWS. METHODS: We evaluated the association between atrazine in drinking water and incident ovarian cancer (N=145, 1986-2010) among 13â 041 postmenopausal women in the Iowa Women's Health Study who used their PWS for ≥11â years as reported in 1989. Average levels of atrazine (1986-1987), nitrate-nitrogen (NO3-N, 1955-1988) and estimated levels of total trihalomethanes (TTHM, 1955-1988) from PWS monitoring data were linked to the participants' cities of residence. We computed HRs and 95% CIs by categories of the average atrazine level (not detected, ≤ or >0.37 parts per billion=median) using Cox proportional hazards regression adjusting for ovarian cancer risk factors. RESULTS: Atrazine was detected in water samples from 69 cities where 4155 women (32%) lived and levels were moderately correlated with NO3-N (ρ=0.35) and TTHM (ρ=0.24). Atrazine levels were not associated with ovarian cancer risk with or without adjusting for NO3-N and TTHM levels (p-trend=0.50 and 0.81, respectively). Further, there was no evidence for effect modification of the atrazine association by NO3-N or TTHM levels. CONCLUSIONS: In our study with low atrazine detection rates, we found no association between atrazine in PWS and postmenopausal ovarian cancer risk.