A fecal score approximation model for analysis of real-time quantitative PCR fecal source identification measurements

Numerous qPCR-based methods are available to estimate the concentration of fecal pollution sources in surface waters. However, qPCR fecal source identification data sets often include a high proportion of non-detections (reactions failing to attain a prespecified minimal signal intensity for detection) and measurements below the assay lower limit of quantification (minimal signal intensity required to estimate target concentration), making it challenging to interpret results in a quantitative manner while accounting for error. In response, a Bayesian statistic based Fecal Score (FS) approach was developed that estimates the weighted average concentration of a fecal source identification genetic marker across a defined group of samples, mathematically incorporating qPCR measurements from all samples. Yet, implementation is technically demanding and computationally intensive requiring specialized training, the use of expert software, and access to high performance computing. To address these limitations, this study reports a novel approximation model for FS determination based on a frequentist approach. The performance of the Bayesian and Frequentist models are compared using fecal source identification qPCR data representative of different 'censored' data scenarios from a recently published study focusing on the impact of stormwater discharge in urban streams. In addition, data set eligibility recommendations for the responsible use of these models are presented. Findings indicate that the Frequentist model can generate similar average concentrations and uncertainty estimates for FS, compared to the original Bayesian approach. The Frequentist model should make calculations less computationally and technically intensive, allowing for the development of easier to use data analysis tools for fecal source identification applications.

Genetic fecal source identification in urban streams impacted by municipal separate storm sewer system discharges

Municipal stormwater systems are designed to collect, transport, and discharge precipitation from a defined catchment area into local surface waters. However, these discharges may contain unsafe levels of fecal waste. Paired measurements of Escherichia coli, precipitation, three land use metrics determined by geographic information system (GIS) mapping, and host-associated genetic markers indicative of human (HF183/BacR287 and HumM2), ruminant (Rum2Bac), dog (DG3), and avian (GFD) fecal sources were assessed in 231 urban stream samples impacted by two or more municipal stormwater outfalls. Receiving water samples were collected twice per month (n = 24) and after rain events (n = 9) from seven headwaters of the Anacostia River in the District of Columbia (United States) exhibiting a gradient of impervious surface, residential, and park surface areas. Almost 50% of stream samples (n = 103) were impaired, exceeding the local E. coli single sample maximum assessment level (410 MPN/100 ml). Fecal scores (average log10 copies per 100 ml) were determined to prioritize sites by pollution source and to evaluate potential links with land use, rainfall, and E. coli levels using a recently developed censored data analysis approach. Dog, ruminant, and avian fecal scores were almost always significantly increased after rain or when E. coli levels exceeded the local benchmark. Human fecal pollution trends showed the greatest variability with detections ranging from 9.1% to 96.7% across sites. Avian fecal scores exhibited the closest connection to land use, significantly increasing in catchments with larger residential areas after rain events (p = 0.038; R2 = 0.62). Overall, results demonstrate that combining genetic fecal source identification methods with GIS mapping complements routine E. coli monitoring to improve management of urban streams impacted by stormwater outfalls.

Interlaboratory performance and quantitative PCR data acceptance metrics for NIST SRM® 2917

Surface water quality quantitative polymerase chain reaction (qPCR) technologies are expanding from a subject of research to routine environmental and public health laboratory testing. Readily available, reliable reference material is needed to interpret qPCR measurements, particularly across laboratories. Standard Reference Material® 2917 (NIST SRM® 2917) is a DNA plasmid construct that functions with multiple water quality qPCR assays allowing for estimation of total fecal pollution and identification of key fecal sources. This study investigates SRM 2917 interlaboratory performance based on repeated measures of 12 qPCR assays by 14 laboratories (n = 1008 instrument runs). Using a Bayesian approach, single-instrument run data are combined to generate assay-specific global calibration models allowing for characterization of within- and between-lab variability. Comparable data sets generated by two additional laboratories are used to assess new SRM 2917 data acceptance metrics. SRM 2917 allows for reproducible single-instrument run calibration models across laboratories, regardless of qPCR assay. In addition, global models offer multiple data acceptance metric options that future users can employ to minimize variability, improve comparability of data across laboratories, and increase confidence in qPCR measurements.

Performance of NIST SRM® 2917 with 13 recreational water quality monitoring qPCR assays

Fecal pollution remains a significant challenge for recreational water quality management worldwide. In response, there is a growing interest in the use of real-time quantitative PCR (qPCR) methods to achieve same-day notification of recreational water quality and associated public health risk as well as to characterize fecal pollution sources for targeted mitigation. However, successful widespread implementation of these technologies requires the development of and access to a high-quality standard control material. Here, we report a single laboratory qPCR performance assessment of the National Institute of Standards and Technology Standard Reference Material 2917 (NIST SRM® 2917), a linearized plasmid DNA construct that functions with 13 recreational water quality qPCR assays. Performance experiments indicate the generation of standard curves with amplification efficiencies ranging from 0.95 ± 0.006 to 0.99 ± 0.008 and coefficient of determination values (R2) ≥ 0.980. Regardless of qPCR assay, variability in repeated measurements at each dilution level were very low (quantification threshold standard deviations ≤ 0.657) and exhibited a heteroscedastic trend characteristic of qPCR standard curves. The influence of a yeast carrier tRNA added to the standard control material buffer was also investigated. Findings demonstrated that NIST SRM® 2917 functions with all qPCR methods and suggests that the future use of this control material by scientists and water quality managers should help reduce variability in concentration estimates and make results more consistent between laboratories.

Post-exercise hypotension and skeletal muscle oxygenation is regulated by nitrate-reducing activity of oral bacteria

Post-exercise hypotension (PEH) is a common physiological phenomenon leading to lower blood pressure after acute exercise, but it is not fully understood how this intriguing response occurs. This study investigated whether the nitrate-reducing activity of oral bacteria is a key mechanism to trigger PEH. Following a randomized, double blind and crossover design, twenty-three healthy individuals (15 males/8 females) completed two treadmill trials at moderate intensity. After exercise, participants rinsed their mouth with antibacterial mouthwash to inhibit the activity of oral bacteria or a placebo mouthwash. Blood pressure was measured before, 1h and 2 h after exercise. The microvascular response to a reactive hyperaemia test, as well as blood and salivary samples were taken before and 2 h after exercise to analyse nitrate and nitrite concentrations and the oral microbiome. As expected, systolic blood pressure (SBP) was lower (1 h: -5.2 ± 1.0 mmHg; P < 0.001); 2 h: -3.8 ± 1.1 mmHg, P = 0.005) after exercise compared to baseline in the placebo condition. This was accompanied by an increase of circulatory nitrite 2 h after exercise (2h: 100 ± 13 nM) compared to baseline (59 ± 9 nM; P = 0.013). Additionally, an increase in the peak of the tissue oxygenation index (TOI) during the reactive hyperaemia response was observed after exercise (86.1 ± 0.6%) compared to baseline levels (84.8 ± 0.5%; P = 0.010) in the placebo condition. On the other hand, the SBP-lowering effect of exercise was attenuated by 61% at 1 h in the recovery period, and it was fully attenuated 2 h after exercise with antibacterial mouthwash. This was associated with a lack of changes in circulatory nitrite (P > 0.05), and impaired microvascular response (peak TOI baseline: 85.1 ± 3.1%; peak TOI post-exercise: 84.6 ± 3.2%; P > 0.05). Diversity of oral bacteria did not change after exercise in any treatment. These findings show that nitrite synthesis by oral commensal bacteria is a key mechanism to induce the vascular response to exercise over the first period of recovery thereby promoting lower blood pressure and greater muscle oxygenation.

From statics of composites to acoustic metamaterials

The Hashin-Shtrikman formalism for the static response of a composite is first summarized, in a form applicable to anisotropic media and arbitrary two-point correlations. Its extension to dynamic response is then explained and in particular the extra coupling, for stress with velocity as well as strain, and momentum density with strain as well as velocity that inevitably follows, is highlighted. The more recent dynamical formulations which incorporate extra flexibility through the use of a weighted mean displacement also receive mention. The article is concluded with an explicit analysis of a simple model random composite and some lessons are drawn from the solution, which exposes at least one clear gap in existing knowledge and requires further research. This article is part of the theme issue 'Modelling of dynamic phenomena and localization in structured media (part 1)'.

Repeated low-level formaldehyde exposure produces cross-sensitization to cocaine: possible relevance to chemical sensitivity in humans

Sensitivity to chemicals in humans has been proposed to be an acquired disorder in which individuals become increasingly sensitive to chemicals in the environment. A possible link between the manifestation of psychiatric symptoms in individuals claiming sensitivity to chemicals was investigated based on a leading hypothesis put forth by Bell and co-workers (1992) to explain the amplification of symptoms after chemical exposure. The hypothesis is that chemical sensitivities may be akin to sensitization observed in rodents after repeated psychostimulants. Repeated exposure to psychostimulants enhances behavioral activity and the underlying neurochemical responses in specific limbic pathways; a similar sensitization of limbic pathways has been proposed to occur in individuals who become sensitive to chemicals. To test this hypothesis, female Sprague-Dawley rats were exposed to either air or formaldehyde (Form) for 1 h/day for 7 days or 20 days (5 days/week x 4 weeks). Two to 4 days after the last exposure, rats were given a cocaine challenge (= early withdrawal) followed by an additional cocaine challenge 4-6 weeks later (= late withdrawal). No differences in cocaine-induced locomotor activity were noted between groups after 7 days of exposure. However, after 20 days of exposure to Form, vertical activity was significantly elevated at both early and late withdrawal times. These studies demonstrate that behavioral sensitization occurs after long-term, but not short-term, low-level exposure to Form, and lends support to the limbic system sensitization hypothesis of sensitivity to chemicals in humans.

Enteroscopy-enteroclysis: experience with a combined endoscopic-radiographic technique

BACKGROUND

Video enteroscopy provides high-quality diagnostic and therapeutic capabilities in the proximal small bowel. Enteroclysis remains an essential diagnostic technique in the distal small bowel. We report our experience with the combination of these techniques.

METHODS

Seventy-one patients with obscure gastrointestinal bleeding (group A, 54 patients) or abnormal radiologic studies (group B, 17 patients) were evaluated with enteroscopy. Enteroclysis via a tube inserted on withdrawal of the enteroscope was performed in all patients with nondiagnostic enteroscopy.

RESULTS

Enteroscopy identified bleeding sites in 29 of 54 (54%) group A patients (12 angiodysplasia, 10 ulcers, 7 gastric erosions, 1 vessel, 1 aortoenteric fistula), and lesions in 11 of 17 (65%) group B patients (7 ulcers, 3 benign strictures, 2 radiation enteritis, 1 mass). In group A, 13 (24%) patients had findings detectable by standard esophagogastroduodenoscopy. Enteroclysis identified masses in 2 of 24 (8%) group A patients, and lesions in 5 of 10 (50%) group B patients (3 strictures, 1 mass, 1 large diverticulum). No complications occurred.

CONCLUSIONS

The combination of enteroscopy and enteroclysis is safe and offers quality small bowel examinations in more comfortable and convenient single diagnostic sittings. This combination detected bleeding sources in 57% and lesions in 70% of patients. Though enteroclysis identified bleeding sources in only 8% of patients, this study excluded lesions other than angiodysplasia.

Enteroscopy with enteroclysis

The authors conclude that their experiences support the conclusion that the combination of enteroscopy and enterocysis is safe and offers quality small bowel examinations in a more comfortable and convenient single diagnostic setting. Although enteroclysis has identified bleeding sources in only 8% of patients who underwent this study, other lesions than angiodysplasia were confidently excluded in the remainder of patients. The combined procedure is well tolerated in the outpatient setting, more comfortable, and safer by decreasing radiation exposures than enteroclysis alone. Use of small bowel enteroscopy at an earlier stage in the evaluation of patients with obscure gastrointestinal bleeding increases cost effectiveness without compromising quality.

Proposed animal neurosensitization model for multiple chemical sensitivity in studies with formalin

A potentially promising line of animal research relevant to multiple chemical sensitivity (MCS) is that of sensitization in the central nervous system (CNS), particularly limbic pathways in the brain. Sensitization is the progressive and enduring enhancement in behavioral and neurochemical responses that occurs after repeated exposure to psychostimulants or environmental stressors. Since the onset and progression of sensitization has many parallels with that of MCS, it has been proposed that MCS may be initiated through a mechanism similar to the sensitization of CNS components occurring in the rodent. To test this hypothesis, female Sprague-Dawley rats were exposed to formalin vapors (FORM, 11 ppm) or water vapor (control) 1 h/day for 7 days. The next day, a saline injection was given followed by a cocaine injection (15 mg/kg, i.p.) 24 h later, and locomotor activity was monitored. Animals pretreated with repeated FORM inhalation demonstrated a significantly enhanced locomotor response to cocaine compared to controls, an indicator that specific limbic pathways may have been sensitized. At 4 weeks of withdrawal from FORM exposure, a subset of animals remained sensitized to a cocaine challenge. No differences were found between groups after a saline injection. In a second experiment, animals were screened prior to FORM or water exposure for their response to a novel situation, a measure believed to reflect an animal's general responsiveness to stimuli. Rats were divided into high responders (HR) or low responders (LR), based on their locomotion in a novel cage. Results from three behavioral tests demonstrated that HR and LR were differentially affected by exposure to FORM. In a passive avoidance test, HR and LR appeared to be different in their distribution of responses, while HR and LR responses in the FORM group were nearly identical. On the elevated plus maze test of anxiety, HR spent more time on the open arms than LR in both treatment groups, with significant differences between HR and LR in the FORM, but not water, treated group. On a hot plate test to measure nociceptive levels, no differences occurred between HR and LR in the control group, whereas nociception of LR tended toward an increase compared to HR in the FORM-exposed group. Results from the second experiment suggest that the effects of FORM exposure may be obscured by examining behavior in a heterogeneous population (HR and LR). This approach using animal models may help define neural substrates that mediate the amplification of responses of a subpopulation of individuals to chemicals in the environment.