Importance of charge capture in interphase regions during readout of charge-coupled devices

The current understanding of charge transfer dynamics in charge-coupled devices (CCDs) is that charge is moved so quickly from one phase to the next in a clocking sequence and with a density so low that trapping of charge in the interphase regions is negligible. However, simulation capabilities developed at the Centre for Electronic Imaging, which includes direct input of electron density simulations, have made it possible to investigate this assumption further. As part of the radiation testing campaign of the Euclid CCD273 devices, data have been obtained using the trap pumping method, a method that can be used to identify and characterize single defects within CCDs. Combining these data with simulations, we find that trapping during the transfer of charge among phases is indeed necessary to explain the results of the data analysis. This result could influence not only trap pumping theory and how trap pumping should be performed but also how a radiation-damaged CCD is readout in the most optimal way

Representing moisture fluxes and phase changes in glacier debris cover using a reservoir approach

Due to the complexity of treating moisture in supraglacial debris, surface energy balance models to date have neglected moisture infiltration and phase changes in the debris layer. The latent heat flux (QL) is also often excluded due to the uncertainty in determining the surface vapour pressure. To quantify the importance of moisture on the surface energy and climatic mass balance (CMB) of debris-covered glaciers, we developed a simple reservoir parameterization for the debris ice and water content, as well as an estimation of the latent heat flux. The parameterization was incorporated into a CMB model adapted for debris-covered glaciers. We present the results of two point simulations, using both our new “moist” and the conventional “dry” approaches, on the Miage Glacier, Italy, during summer 2008 and fall 2011. The former year coincides with available in situ glaciological and meteorological measurements, including the first eddy-covariance measurements of the turbulent fluxes over supraglacial debris, while the latter contains two refreeze events that permit evaluation of the influence of phase changes. The simulations demonstrate a clear influence of moisture on the glacier energy and mass-balance dynamics. When water and ice are considered, heat transmission to the underlying glacier ice is lower, as the effective thermal diffusivity of the saturated debris layers is reduced by increases in both the density and the specific heat capacity of the layers. In combination with surface heat extraction by QL, subdebris ice melt is reduced by 3.1% in 2008 and by 7.0% in 2011 when moisture effects are included. However, the influence of the parameterization on the total accumulated mass balance varies seasonally. In summer 2008, mass loss due to surface vapour fluxes more than compensates for the reduction in ice melt, such that the total ablation increases by 4.0 %. Conversely, in fall 2011, the modulation of basal debris temperature by debris ice results in a decrease in total ablation of 2.1 %. Although the parameterization is a simplified representation of the moist physics of glacier debris, it is a novel attempt at including moisture in a numerical model of debris-covered glaciers and one that opens up additional avenues for future research

Context dependent substitution biases vary within the human genome

Background: Models of sequence evolution typically assume that different nucleotide positions evolve independently. This assumption is widely appreciated to be an over-simplification. The best known violations involve biases due to adjacent nucleotides. There have also been suggestions that biases exist at larger scales, however this possibility has not been systematically explored. Results: To address this we have developed a method which identifies over- and under-represented substitution patterns and assesses their overall impact on the evolution of genome composition. Our method is designed to account for biases at smaller pattern sizes, removing their effects. We used this method to investigate context bias in the human lineage after the divergence from chimpanzee. We examined bias effects in substitution patterns between 2 and 5 bp long and found significant effects at all sizes. This included some individual three and four base pair patterns with relatively large biases. We also found that bias effects vary across the genome, differing between transposons and non-transposons, between different classes of transposons, and also near and far from genes. Conclusions: We found that nucleotides beyond the immediately adjacent one are responsible for substantial context effects, and that these biases vary across the genome

Two-versus one photon excitation laser scanning microscopy: Critical importance of excitation wavelength

It is often anticipated that two-photon excitation (TPE) laser scanning microscopy should improve cell survival and tissue penetration relative to conventional one-photon excitation (OPE) confocal scanning laser microscopy (CLSM). However few studies have directly compared live cell imaging using one- vs two-photon laser scanning microscopy. We have used calcein-loaded in situ chondrocytes within cartilage as a model for quantitatively comparing these techniques. TPE reduced photo-bleaching and improved cell viability compared to OPE. Using improved detection sensitivity coupled with increased tissue penetration of the near infra-red TPE laser, it was possible to capture images deeper within the cartilage. However, the advantages of TPE vs OPE were strongly dependent on excitation wavelength. We conclude that optimising TPE conditions is essential if the full benefits of this approach are to be realised

Accuracy of Immunofluorescence in the Diagnosis of Primary Ciliary Dyskinesia

RATIONALE The standard approach to diagnosis of primary ciliary dyskinesia (PCD) in the UK consists of assessing ciliary function by high-speed-microscopy and ultrastructure by election microscopy, but equipment and expertise is not widely available internationally. The identification of bi-allelic disease causing mutations is also diagnostic, but many disease causing genes are unknown, and testing is not widely available outside the USA. Fluorescent antibodies to ciliary proteins are used to validate research genetic studies, but diagnostic utility in this disease has not been systematically evaluated. OBJECTIVES: Determine utility of a panel of six fluorescent labelled antibodies as a diagnostic tool for PCD. METHODS: Immunofluorescent labelling of nasal brushings from a discovery cohort of 35 patients diagnosed with PCD by ciliary ultrastructure, and a diagnostic accuracy cohort of 386 patients referred with symptoms suggestive of disease. The results were compared to diagnostic outcome. MEASUREMENTS AND MAIN RESULTS: Immunofluorescence correctly identified mislocalised or absent staining in 100% of the discovery cohort. In the diagnostic cohort immunofluorescence successfully identified 22 of 25 patients with PCD and normal staining in all 252 in whom PCD was considered highly unlikely. Immunofluorescence additionally provided a result in 55% (39) of cases which were previously inconclusive. Immunofluorescence results were available within 14 days, costing $187 per sample compared to electron microscopy (27 days, cost$1452). CONCLUSIONS: Immunofluorescence is a highly specific diagnostic test for PCD, and improves the speed and availability of diagnostic testing, however, sensitivity is limited and immunofluorescence is not suitable as a stand-alone test

Is a community still a community? Reviewing definitions of key terms in community ecology

Community ecology is an inherently complicated field, confounded by the conflicting use of fundamental terms. Nearly two decades ago, Fauth etal. (1996) demonstrated that imprecise language led to the virtual synonymy of important terms and so attempted to clearly define four keywords in community ecology; community, assemblage, guild, and ensemble. We revisit Fauth etal.\u27s conclusion and discuss how the use of these terms has changed over time since their review. An updated analysis of term definition from a selection of popular ecological textbooks suggests that definitions have drifted away from those encountered pre-1996, and slightly disagreed with results from a survey of 100 ecology professionals (comprising of academic professors, nonacademic PhDs, graduate and undergraduate biology students). Results suggest that confusion about these terms is still widespread in ecology. We conclude with clear suggestions for definitions of each term to be adopted hereafter to provide greater cohesion among research groups

Impact of calcium on salivary α-amylase activity, starch paste apparent viscosity and thickness perception

Thickness perception of starch-thickened products during eating has been linked to starch viscosity and salivary amylase activity. Calcium is an essential cofactor for α-amylase and there is anecdotal evidence that adding extra calcium affects amylase activity in processes like mashing of beer. The aims of this paper were to (1) investigate the role of salivary calcium on α-amylase activity and (2) to measure the effect of calcium concentration on apparent viscosity and thickness perception when interacting with salivary α-amylase in starch-based samples. α-Amylase activity in saliva samples from 28 people was assessed using a typical starch pasting cycle (up to 95 °C). The activity of the enzyme (as measured by the change in starch apparent viscosity) was maintained by the presence of calcium, probably by protecting the enzyme from heat denaturation. Enhancement of α-amylase activity by calcium at 37 °C was also observed although to a smaller extent. Sensory analysis showed a general trend of decreased thickness perception in the presence of calcium, but the result was only significant for one pair of samples, suggesting a limited impact of calcium enhanced enzyme activity on perceived thickness

Primary ciliary dyskinesia with normal ultrastructure:three-dimensional tomography detects absence of DNAH11

In primary ciliary dyskinesia (PCD), motile ciliary dysfunction arises from ciliary defects usually confirmed by transmission electron microscopy (TEM). In 30% of patients, such as those with DNAH11 mutations, apparently normal ultrastructure makes diagnosis difficult. Genetic analysis supports diagnosis, but may not identify definitive causal variants. Electron tomography, an extension of TEM, produces three-dimensional ultrastructural ciliary models with superior resolution to TEM. Our hypothesis is that tomography using existing patient samples will enable visualisation of DNAH11-associated ultrastructural defects. Dual axis tomograms from araldite-embedded nasal cilia were collected in 13 PCD patients with normal ultrastructure (DNAH11 n=7, HYDIN n=2, CCDC65 n=3 and DRC1 n=1) and six healthy controls, then analysed using IMOD and Chimera software. DNAH11 protein is localised to the proximal ciliary region. Within this region, electron tomography indicated a deficiency of >25% of proximal outer dynein arm volume in all patients with DNAH11 mutations (n=7) compared to other patients with PCD and normal ultrastructure (n=6) and healthy controls (n=6). DNAH11 mutations cause a shared abnormality in ciliary ultrastructure previously undetectable by TEM. Advantageously, electron tomography can be used on existing diagnostic samples and establishes a structural abnormality where ultrastructural studies were previously normal