Cloud-resolving model simulations with one- and two-way couplings via the weak temperature gradient approximation

A cloud-resolving model is modified to implement the weak temperature gradient approximation in order to simulate the interactions between tropical convection and the large-scale tropical circulation. The instantaneous domain-mean potential temperature is relaxed toward a reference profile obtained from a radiative–convective equilibrium simulation of the cloud-resolving model. For homogeneous surface conditions, the model state at equilibrium is a large-scale circulation with its descending branch in the simulated column. This is similar to the equilibrium state found in some other studies, but not all. For this model, the development of such a circulation is insensitive to the relaxation profile and the initial conditions. Two columns of the cloud-resolving model are fully coupled by relaxing the instantaneous domain-mean potential temperature in both columns toward each other. This configuration is energetically closed in contrast to the reference-column configuration. No mean large-scale circulation develops over homogeneous surface conditions, regardless of the relative area of the two columns. The sensitivity to nonuniform surface conditions is similar to that obtained in the reference-column configuration if the two simulated columns have very different areas, but it is markedly weaker for columns of comparable area. The weaker sensitivity can be understood as being a consequence of a formulation for which the energy budget is closed. The reference-column configuration has been used to study the convection in a local region under the influence of a large-scale circulation. The extension to a two-column configuration is proposed as a methodology for studying the influence on local convection of changes in remote convection.

The roles of aerosol, water vapor and cloud in future global dimming/brightening

Observational evidence indicates significant regional trends in solar radiation at the surface in both all-sky and cloud-free conditions. Negative trends in the downwelling solar surface irradiance (SSI) have become known as ‘dimming’ while positive trends have become known as ‘brightening’. We use the Met Office Hadley Centre HadGEM2 climate model to model trends in cloud-free and total SSI from the pre-industrial to the present-day and compare these against observations. Simulations driven by CMIP5 emissions are used to model the future trends in dimming/brightening up to the year 2100. The modeled trends are reasonably consistent with observed regional trends in dimming and brightening which are due to changes in concentrations in anthropogenic aerosols and, potentially, changes in cloud cover owing to the aerosol indirect effects and/or cloud feedback mechanisms. The future dimming/brightening in cloud-free SSI is not only caused by changes in anthropogenic aerosols: aerosol impacts are overwhelmed by a large dimming caused by increases in water vapor. There is little trend in the total SSI as cloud cover decreases in the climate model used here, and compensates the effect of the change in water vapor. In terms of the surface energy balance, these trends in SSI are obviously more than compensated by the increase in the downwelling terrestrial irradiance from increased water vapor concentrations. However, the study shows that while water vapor is widely appreciated as a greenhouse gas, water vapor impacts on the atmospheric transmission of solar radiation and the future of global dimming/brightening should not be overlooked.

AID enzymatic activity is inversely proportional to the size of cytosine C5 orbital cloud

Activation induced deaminase (AID) deaminates cytosine to uracil, which is required for a functional humoral immune system. Previous work demonstrated, that AID also deaminates 5-methylcytosine (5 mC). Recently, a novel vertebrate modification (5-hydroxymethylcytosine - 5 hmC) has been implicated in functioning in epigenetic reprogramming, yet no molecular pathway explaining the removal of 5 hmC has been identified. AID has been suggested to deaminate 5 hmC, with the 5 hmU product being repaired by base excision repair pathways back to cytosine. Here we demonstrate that AID’s enzymatic activity is inversely proportional to the electron cloud size of C5-cytosine - H . F . methyl .. hydroxymethyl. This makes AID an unlikely candidate to be part of 5 hmC removal.

Multispacecraft observation of magnetic cloud erosion by magnetic reconnection during propagation

During propagation, Magnetic Clouds (MC) interact with their environment and, in particular, may reconnect with the solar wind around it, eroding away part of its initial magnetic flux. Here we quantitatively analyze such an interaction using combined, multipoint observations of the same MC flux rope by STEREO A, B, ACE, WIND and THEMIS on November 19–20, 2007. Observation of azimuthal magnetic flux imbalance inside a MC flux rope has been argued to stem from erosion due to magnetic reconnection at its front boundary. The present study adds to such analysis a large set of signatures expected from this erosion process. (1) Comparison of azimuthal flux imbalance for the same MC at widely separated points precludes the crossing of the MC leg as a source of bias in flux imbalance estimates. (2) The use of different methods, associated errors and parametric analyses show that only an unexpectedly large error in MC axis orientation could explain the azimuthal flux imbalance. (3) Reconnection signatures are observed at the MC front at all spacecraft, consistent with an ongoing erosion process. (4) Signatures in suprathermal electrons suggest that the trailing part of the MC has a different large-scale magnetic topology, as expected. The azimuthal magnetic flux erosion estimated at ACE and STEREO A corresponds respectively to 44% and 49% of the inferred initial azimuthal magnetic flux before MC erosion upon propagation. The corresponding average reconnection rate during transit is estimated to be in the range 0.12–0.22 mV/m, suggesting most of the erosion occurs in the inner parts of the heliosphere. Future studies ought to quantify the influence of such an erosion process on geo-effectiveness.

Building a tropical-extratropical cloud band metbot

An automated cloud band identification procedure is developed that captures the meteorology of such events over southern Africa. This “metbot” is built upon a connected component labelling method that enables blob detection in various atmospheric fields. Outgoing longwave radiation is used to flag candidate cloud band days by thresholding the data and requiring detected blobs to have sufficient latitudinal extent and exhibit positive tilt. The Laplacian operator is used on gridded reanalysis variables to highlight other features of meteorological interest. The ability of this methodology to capture the significant meteorology and rainfall of these synoptic systems is tested in a case study. Usefulness of the metbot in understanding event to event similarities of meteorological features is demonstrated, highlighting features previous studies have noted as key ingredients to cloud band development in the region. Moreover, this allows the presentation of a composite cloud band life cycle for southern Africa events. The potential of metbot to study multiscale interactions is discussed, emphasising its key strength: the ability to retain details of extreme and infrequent events. It automatically builds a database that is ideal for research questions focused on the influence of intraseasonal to interannual variability processes on synoptic events. Application of the method to convergence zone studies and atmospheric river descriptions is suggested. In conclusion, a relation-building metbot can retain details that are often lost with object-based methods but are crucial in case studies. Capturing and summarising these details may be necessary to develop deeper process-level understanding of multiscale interactions.

Cloud bands over southern Africa: seasonality, contribution to rainfall variability, and modulation by the MJO

Tropical-extratropical cloud band systems over southern Africa, known as tropical temperate troughs (TTTs), are known to contribute substantially to South African summer rainfall. This study performs a comprehensive assessment of the seasonal cycle and rainfall contribution of TTTs by using a novel object-based strategy that explicitly tracks these systems for their full life cycle. The methodology incorporates a simple assignment of station rainfall data to each event, thereby creating a database containing detailed rainfall characteristics for each TTT. This is used to explore the importance of TTTs for rain days and climatological rainfall totals in October–March. Average contributions range from 30 to 60 % with substantial spatial heterogeneity observed. TTT rainfall contributions over the Highveld and eastern escarpment are lower than expected. A short analysis of TTT rainfall variability indicates TTTs provide substantial, but not dominant, intraseasonal and interannual variability in station rainfall totals. TTTs are however responsible for a high proportion of heavy rainfall days. Of 52 extreme rainfall events in the 1979–1999 period, 30 are associated with these tropical-extratropical interactions. Cut-off lows were included in the evolution of 6 of these TTTs. The study concludes with an analysis of the question: does the Madden-Julian Oscillation influence the intensity of TTT rainfall over South Africa? Results suggest a weak but significant suppression (enhancement) of intensity during phase 1(6).

Emergence of fluoroquinolone resistance in the native Campylobacter coli population of pigs exposed to enrofloxacin

Objective: The effect of a single 5 day enrofloxacin treatment on the native Campylobacter coli population in conventionally weaned 5-week-old pigs was investigated. Materials: Twelve pigs were split into two groups of six: one group was treated with a therapeutic dose (15 mg/pig/day) of enrofloxacin and the other remained untreated to act as the control. Campylobacter coli were isolated from faecal samples and tested for ciprofloxacin resistance by measuring MIC values. Mutations in the quinolone resistance-determining region (QRDR) of the gyrA gene of resistant isolates were identified by sequencing and denaturing HPLC. Levels of enrofloxacin and its primary metabolite ciprofloxacin in the pig faeces were also measured by HPLC. Results: No quinolone-resistant C. coli (n = 867) were detected in any of the pigs prior to treatment, indicating <0.1% resistance in the group. Resistant C. coli were isolated from pigs for up to 35 days after treatment with a therapeutic dose. These resistant C. coli had MIC values of 128 mg/L and 8-16 mg/L for nalidixic acid and ciprofloxacin, respectively, and the same single point mutation causing a Thr-86 to Ile substitution in the QRDR was identified in each. The concentration of enrofloxacin in the pig faeces was 2-4 mug/g faeces for the duration of the 5 day therapeutic treatment and was detected up to 10 days post-treatment. Ciprofloxacin was also measured and peaked at 0.6 mug/g faeces in the treated group. Conclusion: This study provides evidence that a single course of enrofloxacin treatment contributes directly to the emergence and persistence of fluoroquinolone resistance in C. coli.

Cloud droplet size and liquid water path retrievals from zenith radiance measurements: examples from the Atmospheric Radiation Measurement Program and the Aerosol Robotic Network

The ground-based Atmospheric Radiation Measurement Program (ARM) and NASA Aerosol Robotic Net- work (AERONET) routinely monitor clouds using zenith ra- diances at visible and near-infrared wavelengths. Using the transmittance calculated from such measurements, we have developed a new retrieval method for cloud effective droplet size and conducted extensive tests for non-precipitating liquid water clouds. The underlying principle is to combine a liquid-water-absorbing wavelength (i.e., 1640 nm) with a non-water-absorbing wavelength for acquiring information on cloud droplet size and optical depth. For simulated stratocumulus clouds with liquid water path less than 300 g m−2 and horizontal resolution of 201 m, the retrieval method underestimates the mean effective radius by 0.8μm, with a root-mean-squared error of 1.7 μm and a relative deviation of 13%. For actual observations with a liquid water path less than 450 g m−2 at the ARM Oklahoma site during 2007– 2008, our 1.5-min-averaged retrievals are generally larger by around 1 μm than those from combined ground-based cloud radar and microwave radiometer at a 5-min temporal resolution. We also compared our retrievals to those from combined shortwave flux and microwave observations for relatively homogeneous clouds, showing that the bias between these two retrieval sets is negligible, but the error of 2.6 μm and the relative deviation of 22 % are larger than those found in our simulation case. Finally, the transmittance-based cloud effective droplet radii agree to better than 11 % with satellite observations and have a negative bias of 1 μm. Overall, the retrieval method provides reasonable cloud effective radius estimates, which can enhance the cloud products of both ARM and AERONET.

Experimental and modeled UV erthemal irradiance under overcast conditions: the role of cloud optical depth

This paper evaluates the relationship between the cloud modification factor (CMF) in the ultraviolet erythe- mal range and the cloud optical depth (COD) retrieved from the Aerosol Robotic Network (AERONET) "cloud mode" algorithm under overcast cloudy conditions (confirmed with sky images) at Granada, Spain, mainly for non-precipitating, overcast and relatively homogenous water clouds. Empirical CMF showed a clear exponential dependence on experimental COD values, decreasing approximately from 0.7 for COD=10 to 0.25 for COD=50. In addition, these COD measurements were used as input in the LibRadtran radia tive transfer code allowing the simulation of CMF values for the selected overcast cases. The modeled CMF exhibited a dependence on COD similar to the empirical CMF, but modeled values present a strong underestimation with respect to the empirical factors (mean bias of 22 %). To explain this high bias, an exhaustive comparison between modeled and experimental UV erythemal irradiance (UVER) data was performed. The comparison revealed that the radiative transfer simulations were 8 % higher than the observations for clear-sky conditions. The rest of the bias (~14 %) may be attributed to the substantial underestimation of modeled UVER with respect to experimental UVER under overcast conditions, although the correlation between both dataset was high (R2 ~ 0.93). A sensitive test showed that the main reason responsible for that underestimation is the experimental AERONET COD used as input in the simulations, which has been retrieved from zenith radiances in the visible range. In this sense, effective COD in the erythemal interval were derived from an iteration procedure based on searching the best match between modeled and experimental UVER values for each selected overcast case. These effective COD values were smaller than AERONET COD data in about 80 % of the overcast cases with a mean relative difference of 22 %.

Robotic multiwell planar patch-clamp for native and primary mammalian cells

Robotic multiwell planar patch-clamp has become common in drug development and safety programs because it enables efficient and systematic testing of compounds against ion channels during voltage-clamp. It has not, however, been adopted significantly in other important areas of ion channel research, where conventional patch-clamp remains the favored method. Here, we show the wider potential of the multiwell approach with the ability for efficient intracellular solution exchange, describing protocols and success rates for recording from a range of native and primary mammalian cells derived from blood vessels, arthritic joints and the immune and central nervous systems. The protocol involves preparing a suspension of single cells to be dispensed robotically into 4-8 microfluidic chambers each containing a glass chip with a small aperture. Under automated control, giga-seals and whole-cell access are achieved followed by preprogrammed routines of voltage paradigms and fast extracellular or intracellular solution exchange. Recording from 48 chambers usually takes 1-6 h depending on the experimental design and yields 16-33 cell recordings.

Native speakers and task performance: comparing effects on complexity, fluency, and lexical diversity

This article argues that a native-speaker baseline is a neglected dimension of studies into second language (L2) performance. If we investigate how learners perform language tasks, we should distinguish what performance features are due to their processing an L2 and which are due to their performing a particular task. Having defined what we mean by “native speaker,” we present the background to a research study into task features on nonnative task performance, designed to include native-speaker data as a baseline for interpreting nonnative-speaker performance. The nonnative results, published in this journal (Tavakoli & Foster, 2008) are recapitulated and then the native-speaker results are presented and discussed in the light of them. The study is guided by the assumption that limited attentional resources impact on L2 performance and explores how narrative design features—namely complexity of storyline and tightness of narrative structure— affect complexity, fluency, accuracy, and lexical diversity in language. The results show that both native and nonnative speakers are prompted by storyline complexity to use more subordinated language, but narrative structure had different effects on native and nonnative fluency. The learners, who were based in either London or Tehran, did not differ in their performance when compared to each other, except in lexical diversity, where the learners in London were close to native-speaker levels. The implications of the results for the applicability of Levelt’s model of speaking to an L2 are discussed, as is the potential for further L2 research using native speakers as a baseline.

Pausing patterns: differences between L2 learners and native speakers

This paper reports on a comparative study of pauses made by L2 learners and native speakers of English while narrating picture stories. The comparison is based on the number of pauses and total amount of silence in themiddle and at the end of clauses in the performance of 40 native speakers and 40 L2 learners of English. The results of the quantitative analyses suggest that, although the L2 learners generally pausemore repeatedly and have longer periods of silence than the native speakers, the distinctive feature of their pausing pattern is that they pause frequently in the middle of clauses rather than at the end. The qualitative analysis of the data suggests that some of the L2 learners’mid-clause pauses are associated with processes such as replacement, reformulation, and online planning. Formulaic sequences, however, contain very few pauses and therefore appear to facilitate the learners’ fluency.

Electrical signature in polar night cloud base variations

Layer clouds are globally extensive. Their lower edges are charged negatively by the fair weather atmospheric electricity current flowing vertically through them. Using polar winter surface meteorological data from Sodankyla ̈ (Finland) and Halley (Antarctica), we find that when meteorological diurnal variations are weak, an appreciable diurnal cycle, on average, persists in the cloud base heights, detected using a laser ceilometer. The diurnal cloud base heights from both sites correlate more closely with the Carnegie curve of global atmospheric electricity than with local meteorological measurements. The cloud base sensitivities are indistinguishable between the northern and southern hemispheres, averaging a (4.0 ± 0.5) m rise for a 1% change in the fair weather electric current density. This suggests that the global fair weather current, which is affected by space weather, cosmic rays and the El Nin ̃o Southern Oscillation, is linked with layer cloud properties.

Projections of UV radiation changes in the 21st century: impact of ozone recovery and cloud effects

Monthly averaged surface erythemal solar irradiance (UV-Ery) for local noon from 1960 to 2100 has been derived using radiative transfer calculations and projections of ozone, temperature and cloud change from 14 chemistry climate models (CCM), as part of the CCMVal-2 activity of SPARC. Our calculations show the influence of ozone depletion and recovery on erythemal irradiance. In addition, we investigate UV-Ery changes caused by climate change due to increasing greenhouse gas concentrations. The latter include effects of both stratospheric ozone and cloud changes. The derived estimates provide a global picture of the likely changes in erythemal irradiance during the 21st century. Uncertainties arise from the assumed scenarios, different parameterizations – particularly of cloud effects on UV-Ery – and the spread in the CCM projections. The calculations suggest that relative to 1980, annually mean UV-Ery in the 2090s will be on average 12% lower at high latitudes in both hemispheres, 3% lower at mid latitudes, and marginally higher (1 %) in the tropics. The largest reduction (16 %) is projected for Antarctica in October. Cloud effects are responsible for 2–3% of the reduction in UV-Ery at high latitudes, but they slightly moderate it at mid-latitudes (1 %). The year of return of erythemal irradiance to values of certain milestones (1965 and 1980) depends largely on the return of column ozone to the corresponding levels and is associated with large uncertainties mainly due to the spread of the model projections. The inclusion of cloud effects in the calculations has only a small effect of the return years. At mid and high latitudes, changes in clouds and stratospheric ozone transport by global circulation changes due to greenhouse gases will sustain the erythemal irradiance at levels below those in 1965, despite the removal of ozone depleting substances.