Real-time kinetics and high-resolution melt curves in single-molecule digital LAMP to differentiate and study specific and non-specific amplification

Isothermal amplification assays, such as loop-mediated isothermal amplification (LAMP), show great utility for the development of rapid diagnostics for infectious diseases because they have high sensitivity, pathogen-specificity and potential for implementation at the point of care. However, elimination of non-specific amplification remains a key challenge for the optimization of LAMP assays. Here, using chlamydia DNA as a clinically relevant target and high-throughput sequencing as an analytical tool, we investigate a potential mechanism of non-specific amplification. We then develop a real-time digital LAMP (dLAMP) with high-resolution melting temperature (HRM) analysis and use this single-molecule approach to analyze approximately 1.2 million amplification events. We show that single-molecule HRM provides insight into specific and non-specific amplification in LAMP that are difficult to deduce from bulk measurements. We use real-time dLAMP with HRM to evaluate differences between polymerase enzymes, the impact of assay parameters (e.g. time, rate or florescence intensity), and the effect background human DNA. By differentiating true and false positives, HRM enables determination of the optimal assay and analysis parameters that leads to the lowest limit of detection (LOD) in a digital isothermal amplification assay

Atomic and molecular interstellar absorption lines toward the high galactic latitude stars HD~141569 and HD~157841 at ultra-high resolution

We present ultra-high resolution (0.32 km/s) spectra obtained with the 3.9m Anglo-Australian Telescope (AAT) and Ultra-High-Resolution Facility (UHRF), of interstellar NaI D1, D2, Ca II K, K I and CH absorption toward two high galactic latitude stars HD141569 and HD157841. We have compared our data with 21-cm observations obtained from the Leiden/Dwingeloo HI survey. We derive the velocity structure, column densities of the clouds represented by the various components and identify the clouds with ISM structures seen in the region at other wavelengths. We further derive abundances, linear depletions and H2 fractional abundances for these clouds, wherever possible. Toward HD141569, we detect two components in our UHRF spectra : a weak, broad component at - 15 km/s, seen only in CaII K absorption and another component at 0 km/s, seen in NaI D1, D2, Ca II K, KI and CH absorption. In the case of the HD157841 sightline, a total of 6 components are seen on our UHRF spectra in NaI D1, D2 Ca II K, K I and CH absorption. 2 of these 6 components are seen only in a single species.Comment: 16 pages, Latex, 4 figures, ps files Astrophysical Journal (in press

Remarkable dynamics of nanoparticles in the urban atmosphere

Nanoparticles emitted from road traffic are the largest source of respiratory exposure for the general public living in urban areas. It has been suggested that the adverse health effects of airborne particles may scale with the airborne particle number, which if correct, focuses attention on the nanoparticle (less than 100 nm) size range which dominates the number count in urban areas. Urban measurements of particle size distributions have tended to show a broadly similar pattern dominated by a mode centred on 20–30 nm diameter particles emitted by diesel engine exhaust. In this paper we report the results of measurements of particle number concentration and size distribution made in a major London park as well as on the BT Tower, 160 m high. These measurements taken during the REPARTEE project (Regents Park and BT Tower experiment) show a remarkable shift in particle size distributions with major losses of the smallest particle class as particles are advected away from the traffic source. In the Park, the traffic related mode at 20–30 nm diameter is much reduced with a new mode at <10 nm. Size distribution measurements also revealed higher number concentrations of sub-50 nm particles at the BT Tower during days affected by higher turbulence as determined by Doppler Lidar measurements and indicate a loss of nanoparticles from air aged during less turbulent conditions. These results suggest that nanoparticles are lost by evaporation, rather than coagulation processes. The results have major implications for understanding the impacts of traffic-generated particulate matter on human health

Drivers of European bat population change: a review reveals evidence gaps

Bat populations are thought to have suffered significant declines in the past century throughout Europe. Fortunately, there are some signs of recovery; for instance, of the 11 species monitored in the UK, population trends of five are increasing. The drivers of past losses and recent trends are unclear; identifying them will enable targeted conservation strategies to support further recovery. We review the evidence linking proposed drivers to impacts on bat populations in Europe, using the results of a previous cross‐taxa semi‐quantitative assessment as a framework. Broadly, the drivers reviewed relate to land‐use practices, climate change, pollution, development and infrastructure, and human disturbance. We highlight where evidence gaps or conflicts present barriers to successful conservation and review emerging opportunities to address these gaps. We find that the relative importance or impacts of the potential drivers of bat population change are not well understood or quantified, with conflicting evidence in many cases. To close key gaps in the evidence for responses of bat populations to environmental change, future studies should focus on the impacts of climate change, urbanisation, offshore wind turbines, and water pollution, as well as on mitigation measures and the synergistic effects of putative drivers. To increase available evidence of drivers of bat population change, we propose utilising advances in monitoring tools and statistical methods, together with robust quantitative assessment of conservation interventions to mitigate threats and enable the effective conservation of these protected species

A model for the generic alpha relaxation of viscous liquids

Dielectric measurements on molecular liquids just above the glass transition indicate that alpha relaxation is characterized by a generic high-frequency loss varying as $\omega^{-1/2}$, whereas deviations from this come from one or more low-lying beta processes [Olsen et al, Phys. Rev. Lett. {\bf 86} (2001) 1271]. Assuming that long-wavelength fluctuations dominate the dynamics, a model for the dielectric alpha relaxation based on the simplest coupling between the density and dipole density fields is proposed here. The model, which is solved in second order perturbation theory in the Gaussian approximation, reproduces the generic features of alpha relaxation

Assessing methods to extrapolate the vertical wind-speed profile from surface observations in a city centre during strong winds

Knowledge of the vertical wind-speed profile in cities is important for the construction and insurance industries, wind energy predictions, and simulations of pollutant and toxic gas release. Here, five methods to estimate the spatially- and temporally- averaged wind-speed profile are compared in London: the logarithmic wind law (LOG); the Deaves and Harris equilibrium (DHe) and non-equilibrium (DHv) models; an adaptation of the power law (PL) and the Gryning et al. (GR) profile. Using measurements at 2.5 times the average building height, a source area model is used to determine aerodynamic roughness parameters using two morphometric methods, which assume homogeneous and variable roughness-element heights, respectively. Hourly-averaged wind speeds are extrapolated to 200 m above the canopy during strong wind conditions, and compared to wind speeds observed with Doppler lidar. Wind speeds are consistently underestimated if roughness-element height variability is not considered during aerodynamic parameter determination. Considering height variability, the resulting estimations with the DHe and GR profiles are marginally more similar to observations than the DHv profile, which is more accurate than the LOG and PL methods. An exception is in directions with more homogeneous fetch and a gradual reduction in upwind roughness, where the LOG and PL profiles are more appropriate

Volume for pollution dispersion: London’s atmospheric boundary layer during ClearfLo observed with two ground-based lidar types

In urban areas with high air pollution emissions, the boundary layer volume within which gases and particles are diluted is critical to air quality impacts. With advances in ground-based remote sensing technologies and data processing algorithms, observations of layers forming the atmospheric boundary layer (ABL) are becoming increasingly available at high temporal resolution. Here, mixing height (MH) estimates determined from turbulence measurements of Doppler lidars and aerosol derived mixed layer height (MLH) based on automatic lidar and ceilometer (ALC) observations within the centre of London are assessed. While MH uncertainty increases with shorter duration of vertical stare sampling within the Doppler lidar scan pattern, instrument-related noise of the ALC may result in large MLH errors due to the challenging task of layer attribution. However, when long time series are assessed most of the algorithm- and instrument-related uncertainties average out and therefore become less critical to overall climatological analyses. Systematic differences occur in nocturnal MH from two nearby (3-4 km) sites but MLH estimates at both sites generally agree with MH obtained at the denser urban setting. During daytime, most spatial variations in ABL structure induced by synoptic conditions or land cover heterogeneity at this scale do not exceed measurement uncertainty. Agreement between MH and MLH is clearly affected by ABL aerosol content and cloud 28 conditions. Discrepancies increase with cloud complexity. On average, MH rises ahead of MLH during the morning growth period and peaks earlier in the day. There is a faster afternoon decay of MLH so that MLH and MH converge again around sunset and often have similar nocturnal values. Results demonstrate that turbulence-derived MH and aerosol-derived MLH should not be used inter32 changeably for purposes of model evaluation, interpretation of surface air quality observations or 33 initialisation of chemical transport models

The Very Highly Ionized Broad Absorption Line System of the QSO SBS1542+541

We have analyzed the broad absorption line system of the bright (V=16.5) high-redshift (z=2.361) QSO SBS1542+541 using UV spectra from the HST FOS along with optical data from the MMT and the Steward Observatory 2.3m telescope. These spectra give continuous wavelength coverage from 1200 to 8000 Angstroms, corresponding to 340 to 2480 Angstroms in the QSO rest frame. This object therefore offers a rare opportunity to study broad absorption lines in the rest-frame extreme UV. We find that the absorption system is dominated by very high-ionization species, including O VI, NeVIII, and SiXII. We also identify apparently saturated broad Lyman-series lines of order Ly-gamma and higher. There is strong evidence for partial occultation of the QSO emission source, particularly from the higher-order Lyman lines which indicate a covered fraction less than 0.2. Overall, the data suggest a correlation between a larger covered fraction and a higher state of ionization. We suggest that the different covered fractions can be explained by either a special line of sight through a disk-like geometry or by the existence of density fluctuations of a factor >2 in the BAL gas. Our photoionization models of the system indicate a large column density and high ionization state similar to that found in X-ray ``warm absorbers''.Comment: 31 pages, 13 figures, to be published in Ap