Detection of Chlamydia trachomatis mRNA using digital PCR as a more accurate marker of viable organism

© 2018, Springer-Verlag GmbH Germany, part of Springer Nature. Spontaneous resolution of urogenital Chlamydia trachomatis (CT) without treatment has previously been described, but a limitation of these reports is that DNA or RNA-based amplification tests used do not differentiate between viable infection and non-viable DNA. We modified a previously published CT mRNA detection (omp2) method to differentiate between viable infection and non-viable DNA in a sample of CT DNA PCR positive women. We modified a CT mRNA detection (omp2) method from reverse transcriptase qPCR (RTqPCR) to digital PCR (dPCR) and evaluated it in samples from CT DNA positive women. Firstly, CT infected McCoy B cells treated with azithromycin in vitro identified detectable mRNA levels disappeared <2 days, while DNA persisted up to 6 days. We used 55 self-collected vaginal swabs from a cohort of women diagnosed as DNA positive for chlamydia obtained pre- and 7 days of post-azithromycin treatment. Concordance with DNA results was higher for dPCR than RTqPCR (74.5% versus 65.5%). At visit 1, there was a strong linear relationship between DNA and mRNA (r = 0.9, p < 0.000); 24 samples had both mRNA and DNA detected (82.8%) and 5 had only DNA detected with a potential false positive proportion of 17.2% (95%CI: 5.8, 35.8). At visit 2, there was poor correlation between DNA and mRNA (r = 0.14, p = 0.55); eight specimens had only DNA detected (42.1%; 95%CI: 20.25, 66.50) and one had mRNA detected. DNA detection methods alone may detect non-viable DNA. Consideration should be given to further develop mRNA assays as ancillary tests to improve detection of viable chlamydia

Predator Effects in Predator-Free Space: The Remote Effects of Predators on Prey

Predators can have remote effects on prey populations that are connected by migration (i.e. prey metapopulations) because predator-mediated changes in prey behavior and abundance effectively transmit the impact of predators into predator-free prey populations. Behavioral changes in prey that might give rise to remote effects are altered rates of migration or activity in the presence of predation risk (called non-consumptive effects, fear- or μ-driven effects, and risk effects). Changes in prey abundance that may result in remote effects arise from changes in prey density due to direct predation (i.e. consumptive effects, also called N-driven effects and predation effects). Remote effects provide a different perspective on both predator-prey interactions and spatial subsidies, illustrating how the interplay among space, time, behavior, and consumption generates emergent spatial dynamics in places where we might not expect them. We describe how strong remote effects of predators may essentially generate “remote control” over the dynamics of local populations, alter the persistence of metapopulations, shift the importance of particular paradigms of metacommunity structure, alter spatial subsidies, and affect evolutionary dynamics. We suggest how experiments might document remote effects and predict that remote effects will be an important component of prey dynamics under several common scenarios: when predators induce large changes in prey dispersal behavior, when predators dramatically reduce the number of prey available to disperse, when prey movement dynamics occur over greater distances or shorter timescales than predator movement, and when prey abundance is not already limited by competitors or conspecifics

Identifying and Characterizing Impact Melt Outcrops in the Nectaris Basin

The Nectaris Basin is an 820-km diameter, multi-ring impact basin located on the near side of the Moon. Nectaris is a defining stratigraphic horizon based on relationships between ejecta units, giving its name to the Nectarian epoch of lunar history. Lunar basin chronology based on higher resolution LRO imagery and topography, while assigning some important basins like Serenitatis to pre-Nectarian time, were generally consistent with those previously derived. Based on this stratigraphy, at least 11 large basins formed in the time between Nectaris and Imbrium. The absolute age of Nectaris, therefore, is a crucial marker in the lunar time-stratigraphic sequence for understanding the impact flux on the Moon, and by extension, the entire inner solar system. For several decades, workers have attempted to constrain the age of the Nectaris basin through radiometric dating of lunar samples. However, there is little agreement on which samples in our collection represent Nectaris, if any, and what the correct radiometric age of such samples is. The importance of the age of Nectaris goes far beyond assigning a stratigraphic marker to lunar chronology. Several dynamical models use Nectaris as their pin date, so that this date becomes crucial in understanding the time-correlated effects in the rest of the solar system. The importance of the Nectaris basin age, coupled with its nearside, mid-latitude location, make remnants of the impact-melt sheet an attractive target for a future mission, either for in-situ dating or for sample return. We have started exploring this possibility. We have begun a consortium data-analysis effort bringing multiple datasets and analysis methods to bear on these putative impact-melt deposits to characterize their extent, elemental composition and mineralogy, maturity and geologic setting, and to identify potential landing sites that meet both operational safety and science requirements

Managing contested spaces: Public managers, obscured mechanisms and the legacy of the past in Northern Ireland

Societies emerging from ethno-political and inter-communal conflict face a range of complex problems that stem directly from the recent lived experience of bloodshed and injury, militarisation, securitisation and segregation. As institutional agents in such an environment, public managers perform the dual role of both interpreting public policy and implementing it within a politically contested space and place. In this article we address how managers cope with the outworking of ethno-nationalist conflict and peace building within government processes and policy implementation and contend this is a subject of emerging concern within the wider public administration, urban studies and conflict literature. Using data from a witness seminar initiative on the Northern Ireland conflict transformation experience, we explain how public sector managers make sense of their role in post-agreement public management and highlight the importance of three identified mechanisms; ‘bricolage’, ‘diffusion’ and ‘translation’ in the management of public sector organisations and urban spaces in a context of entrenched conflict and an uncertain path to peace

Documenting the NICU design dilemma: comparative patient progress in open-ward and single family room units

Objective:To test the efficacy of single family room (SFR) neonatal intensive care unit (NICU) designs, questions regarding patient medical progress and relative patient safety were explored. Addressing these questions would be of value to hospital staff, administrators and designers alike. Study Design:This prospective study documented, by means of Institution Review Board-approved protocols, the progress of patients in two contrasting NICU designs. Noise levels, illumination and air quality measurements were included to define the two NICU physical environments. Result:Infants in the SFR unit had fewer apneic events, reduced nosocomial sepsis and mortality, as well as earlier transitions to enteral nutrition. More mothers sustained stage III lactation, and more infants were discharged breastfeeding in the SFR. Conclusion:This study showed the SFR to be more conducive to family-centered care, and to enhance infant medical progress and breastfeeding success over that of an open ward

The role of high frequency intra-daily data, daily range and implied volatility in multi-period Value-at-Risk forecasting

In this paper, we assess the informational content of daily range, realized variance, realized bipower variation, two time scale realized variance, realized range and implied volatility in daily, weekly, biweekly and monthly out-of-sample Value-at-Risk (VaR) predictions. We use the recently proposed Realized GARCH model combined with the skewed student distribution for the innovations process and a Monte Carlo simulation approach in order to produce the multi-period VaR estimates. The VaR forecasts are evaluated in terms of statistical and regulatory accuracy as well as capital efficiency. Our empirical findings, based on the S&P 500 stock index, indicate that almost all realized and implied volatility measures can produce statistically and regulatory precise VaR forecasts across forecasting horizons, with the implied volatility being especially accurate in monthly VaR forecasts. The daily range produces inferior forecasting results in terms of regulatory accuracy and Basel II compliance. However, robust realized volatility measures such as the adjusted realized range and the realized bipower variation, which are immune against microstructure noise bias and price jumps respectively, generate superior VaR estimates in terms of capital efficiency, as they minimize the opportunity cost of capital and the Basel II regulatory capital. Our results highlight the importance of robust high frequency intra-daily data based volatility estimators in a multi-step VaR forecasting context as they balance between statistical or regulatory accuracy and capital efficiency

Ruminal degradation and intestinal digestibility of camelina meal and carinata meal compared to other protein sources.

Production of reneweable feedstocks for biodiesel have drawn attention to alternative oilseed crops. Our objective was to determine DM and CP ruminal degradability and intestinal digestibility of camelina meal (CAM) and carinata meal (CAR), compared with canola meal (CAN), linseed meal (LIN), soybean meal (SBM), and distillers dried grains with solubles (DDGS) as controls. In situ degradability measurements were done using 3 multiparous, mid-late lactation ruminally cannulated Holstein cows. Sample bags were ruminally incubated in duplicate for each cow and feedstuff for 0, 2, 4, 8, and 12 h and in triplicate for 24 and 48 h. Eight bags of each feed were incubated at 12 h for use of the residues in determination of in vitro intestinal digestibility. Ruminal particulate passage rate averaged 6.0%/h. Rate of DM degradation was greatest (P \u3c 0.05) for CAM and LIN and least for DDGS, whereas CAR and SBM were similar. Ruminally degradable DM was greatest (P \u3c 0.01) in CAM, CAR, and SBM. The CAM and CAR had the greatest (P \u3c 0.05) RDP and least RUP. Intestinal digestible protein was similar (P \u3e 0.05) for LIN, CAM, and CAR, which was greater (P \u3c 0.05) than CAN and DDGS. Intestinally absorbable digestible protein was least for CAM and CAR (P \u3c 0.01) compared with the other feeds. Total digestible protein was similar (P \u3e 0.05) for CAM and CAR compared with SBM and LIN. Results indicate that CAM and CAR are highly degradable and comparable to SBM and LIN for protein utilization