Current controversies in prenatal diagnosis 2: Cell-free DNA prenatal screening should be used to identify all chromosome abnormalities

Noninvasive prenatal testing (NIPT) using cell-free DNA (cfDNA) from maternal serum has been clinically available since 2011. This technology has revolutionized our ability to screen for the common aneuploidies trisomy 21 (Down syndrome), trisomy 18, and trisomy 13. More recently, clinical laboratories have offered screening for other chromosome abnormalities including sex chromosome abnormalities and copy number variants (CNV) without little published data on the sensitivity, specificity, and positive predictive value. In this debate, the pros and cons of performing prenatal screening via cfDNA for all chromosome abnormalities is discussed. At the time of the debate in 2017, the general consensus was that the literature does not yet support using this technology to screen for all chromosome abnormalities and that education is key for both providers and the patients so that the decision-making process is as informed as possible.     

Impact of host community composition on Lyme disease risk

The drivers of variable disease risk in complex multi-host disease systems have proved very difficult to identify. Here we test a model that explains the entomological risk of Lyme disease (LD) in terms of host community composition. The model was parameterized in a continuous forest tract at the Cary Institute of Ecosystem Studies (formerly the Institute of Ecosystem Studies) in New York State, U.S.A. We report the results of continuing longitudinal observations (10 years) at the Cary Institute, and of a shorter-term study conducted in forest fragments in LD endemic areas of Connecticut, New Jersey, and New York, USA. Model predictions were significantly correlated with the observed nymphal infection prevalence (NIP) in both studies, although the relationship was stronger in the longer-term Cary Institute study. Species richness was negatively, albeit weakly, correlated with NIP (logistic regression), and there was no relationship between the Shannon diversity index (H') and NIP. Although these results suggest that LD risk is in fact dependent on host diversity, the relationship relies explicitly on the identities and frequencies of host species such that conventional uses of the term biodiversity (i.e., richness, evenness, H') are less appropriate than are metrics that include species identity. This underscores the importance of constructing interaction webs for vertebrates and exploring the direct and indirect effects of anthropogenic stressors on host community composition.     

Incorporating catastrophic risk assessments into setting conservation goals for threatened Pacific salmon

Catastrophic die-offs can have important consequences for vertebrate population growth and biodiversity, but catastrophic risks are not commonly incorporated into endangered-species recovery planning. Natural (e.g., landslides, floods) and anthropogenic (e.g., toxic leaks and spills) catastrophes pose a challenge for evolutionarily significant units (ESUs) of Pacific salmon listed under the Endangered Species Act and teetering at precariously low population levels. To spread risks among Puget Sound chinook salmon populations, recovery strategies for ESU-wide viability recommend at least two viable populations of historical life-history types in each of five geographic regions. We explored the likelihood of Puget Sound chinook salmon ESU persistence by examining spatial patterns of catastrophic risk and testing ESU viability recommendations for 22 populations of the threatened Puget Sound chinook salmon ESU. We combined geospatial information about catastrophic risks and chinook salmon distribution in Puget Sound watersheds to categorize relative catastrophic risks for each population. We then analyzed similarities in risk scores among regions and compared risk distributions among strategies: (1) population groups selected using the ESU viability recommendations of having populations spread out geographically and including historical life-history diversity, and (2) population groups selected at random. Risks from individual catastrophes varied among populations, but overall risk from catastrophes was similar within geographic regions. Recovery strategies that called for two viable populations in each of five geographic regions had lower risk than random strategies; strategies that included life-history diversity had even lower risks. Geographically distributed populations have varying catastrophic-risks profiles, thus identifying and reinforcing the spatial and life-history diversity critical for populations to respond to environmental change or needed to rescue severely depleted or extirpated populations. Recovery planning can promote viability of Pacific salmon ESUs across the landscape by incorporating catastrophic risk assessments.     

Disaster journalism: fostering citizen and community disaster mitigation,preparedness, response,recovery, and resilience across the disaster cycle

Natural and human‐caused disasters pose a significant risk to the health and well‐being of people. Journalists and news organisations can fulfil multiple roles related to disasters, ranging from providing warnings, assessing disaster mitigation and preparedness, and reporting on what occurs, to aiding long‐term recovery and fostering disaster resilience. This paper considers these possible functions of disaster journalism and draws on semi‐structured interviews with 24 journalists in the United States to understand better their approach to the discipline. A thematic analysis was employed, which resulted in the identification of five main themes and accompanying subthemes: (i) examining disaster mitigation and preparedness; (ii) facilitating recovery; (iii) self‐care and care of journalists; (iv) continued spread of social media; and (v) disaster journalism ethics. The paper concludes that disaster journalism done poorly can result in harm, but done well, it can be an essential instrument with respect to public disaster planning, management, response, and recovery.     

A Bayesian mixture model for missing data in marine mammal growth analysis

Much of what is known about bottle nose dolphin (Tursiops truncatus) anatomy and physiology is based on necropsies from stranding events. Measurements of total body length, total body mass, and age are used to estimate growth. It is more feasible to retrieve and transport smaller animals for total body mass measurement than larger animals, introducing a systematic bias in sampling. Adverse weather events, volunteer availability, and other unforeseen circumstances also contribute to incomplete measurement. We have developed a Bayesian mixture model to describe growth in detected stranded animals using data from both those that are fully measured and those not fully measured. Our approach uses a shared random effect to link the missingness mechanism (i.e. full/partial measurement) to distinct growth curves in the fully and partially measured populations, thereby enabling drawing of strength for estimation. We use simulation to compare our model to complete case analysis and two common multiple imputation methods according to model mean square error. Results indicate that our mixture model provides better fit both when the two populations are present and when they are not. The feasibility and utility of our new method is demonstrated by application to South Carolina strandings data.     

The impact of the invasive shrub Lonicera maackii on the decomposition dynamics of a native plant community

Invasive plants may have variable effects within a given environment depending on their interactions with the dominant native species, yet little research has examined such species-species interactions within a site. Savanna trees with nonoverlapping canopies offer an ideal opportunity to assess associated changes in the ecosystem processes that result from interactions between an invasive species and different native tree species. We examined the influence of the exotic invasive shrub Lonicera maackii on decomposition dynamics under three native tree species: Fraxinus quadrangulata, Quercus muehlenbergii, and Carya ovata. Litter decomposition rates and litter C and N were evaluated over two years using single- and mixed-species litterbags (L. maackii and individual tree species litter); microarthropod abundance was measured at 6 weeks using Tulgren funnels. Litter from the invasive L. maackii decomposed and lost N more rapidly than the litter of the three native tree species. The rate at which L. maackii decomposed depended on its location, with L. maackii litter decomposing and losing N more rapidly under C. ovata than under the other two native tree species. Mixing L. maackii with the native species' litter did not accelerate litter mass loss overall but did result in synergistic N losses at variable times throughout the experiment, further highlighting the variable interaction between native species and L. maackii. Nitrogen loss was significantly higher than expected in mixtures of C. ovata + L. maackii litter at 6 weeks, in F. quadrangulata + L. maackii litter at 12 weeks, and in Q. muehlenbergii + L. maackii litter at 24 weeks. If the effects of invasive species on certain ecosystem processes, such as litter decomposition, are strongly influenced by their association with native species, this could suggest the need for a more nuanced understanding of the vulnerability of ecosystem processes to invasions of L. maackii and potentially other invasive species.     

Impact of consistent boundary layer mixing approaches between NAM and CMAQ

Discrepancies in grid structure, dynamics and physics packages in the offline coupled NWS/NCEP NAM meteorological model with the U.S. Environmental Protection Agency Community Multiscale Air Quality (CMAQ) model can give rise to inconsistencies. This study investigates the use of three vertical mixing schemes to drive chemistry tracers in the National Air Quality Forecast Capability (NAQFC). The three schemes evaluated in this study represent various degrees of coupling to improve the commonality in turbulence parameterization between the meteorological and chemistry models. The methods tested include: (1) using NAM predicted TKE-based planetary boundary height, h, as the prime parameter to derive CMAQ vertical diffusivity; (2) using the NAM mixed layer depth to determine h and then proceeding as in (1); and (3) using NAM predicted vertical diffusivity directly to parameterize turbulence mixing within CMAQ. A two week period with elevated surface O₃ concentrations during the summer 2006 has been selected to test these schemes in a sensitivity study. The study results are verified and evaluated using the EPA AIRNow monitoring network and other ozonesonde data. The third method is preferred a priori as it represents the tightest coupling option studied in this work for turbulent mixing processes between the meteorological and air quality models. It was found to accurately reproduce the upper bounds of turbulent mixing and provide the best agreement between predicted h and ozonesonde observed relative humidity profile inferred h for sites investigated in this study. However, this did not translate into the best agreement in surface O₃ concentrations. Overall verification results during the test period of two weeks in August 2006, did not show superiority of this method over the other 2 methods in all regions of the continental U.S. Further efforts in model improvement for the parameterizations of turbulent mixing and other surface O₃ forecast related processes are warranted.     

Reactions of the amine-containing drugs fluoxetine and metoprolol during chlorination and dechlorination processes used in wastewater treatment

The reactivities of the amine-containing pharmaceuticals fluoxetine and metoprolol with hypochlorite were studied using conditions that simulate wastewater disinfection including neutral pH (7.0), a range of reaction times (2–60 min), and a molar excess of hypochlorite relative to the pharmaceutical concentration (5.7 times). The reactions were monitored using liquid chromatography (LC) with several detection modes including ultraviolet absorbance (UV), mass spectrometry (MS), and post-column reaction/reductive electrochemistry (EC) for determining active chlorine products. At levels of 10 μM, both compounds reacted rapidly (<2 min) to form principally N-chloramine products that were stable in aqueous solution for at least 1 h. The reaction was also studied in wastewater, and similar reactivity was noted. These results demonstrate that the cations fluoxetine and metoprolol are likely to be rapidly transformed into neutral N-chloramines during wastewater disinfection. The reactivity of the N-chloramines was also studied with sulfite to simulate dechlorination, which is often employed in wastewater treatment. Both N-chloramines reacted slowly with sulfite. In the pure water dechlorination experiments, it was estimated that 70% and 10% of the peak areas remained after 2 min reaction time for fluoxetine and metoprolol, respectively. At longer reaction times both N-chloramines had been completely reduced by sulfite, and the product of the sulfite reduction reaction was the parent pharmaceutical amine. Since typical dechlorination times in wastewater treatment are on the order of seconds, this suggests the chloramines formed from these two basic drugs might evade dechlorination and be released into the environment. The implications of chloramine release are discussed.     

Seasonal and decadal changes in distribution patterns of Halobates (Hemiptera: Gerridae) populations in the eastern tropical Pacific

Five species of the marine insect Halobates share similar ecology but have distinct biogeographic ranges in the eastern tropical Pacific, a region from approximately 75°W–160°W and 10°S–35°N. Between 2001 and 2010, the Sea Education Association collected Halobates from 682 neuston tows (surface net 1 m × 0.5 m, 335-μm mesh) during fifteen cruises between San Diego, USA, Mexico and Tahiti. Total Halobates spp. densities varied substantially from year to year, but our data do not show a sustained change from a data set collected 40 years earlier from 1967 to 1968 (Cheng and Shulenberger in Fish Bull 78(3):579–591, 1980). Halobates are sensitive to sea surface temperature and we observed significant differences in species distributions over time, but these were not due to differences in water temperature or climate change. Our analyses show that the patterns observed are attributable to substantial but previously undescribed seasonal shifts that occur each year in the ranges for both Halobates sobrinus and Halobates micans. There is substantial overlap in ranges during seasonal shifts, but very little co-occurrence of H. sobrinus and H. micans in individual net tows, suggesting biological mechanisms rather than physical factors are restricting distribution and co-occurrence of these two species.