MALDI MS

Matrix-assisted laser desorption/ionization (MALDI) is a key technique in mass spectrometry (MS)-based proteomics. MALDI MS is extremely sensitive, easy-to-apply, and relatively tolerant to contaminants. Its high-speed data acquisition and large-scale, off-line sample preparation has made it once again the focus for high-throughput proteomic analyses. These and other unique properties of MALDI offer new possibilities in applications such as rapid molecular profiling and imaging by MS. Proteomics and its employment in Systems Biology and other areas that require sensitive and high-throughput bioanalytical techniques greatly depend on these methodologies. This chapter provides a basic introduction to the MALDI methodology and its general application in proteomic research. It describes the basic MALDI sample preparation steps and two easy-to-follow examples for protein identification including extensive notes on these topics with practical tips that are often not available in the Subheadings 2 and 3 of research articles.

Stress-induced changes in the Schizosaccharomyces pombe proteome using two-dimensional difference gel electrophoresis, mass spectrometry and a novel integrated robotics platform

Robotic and manual methods have been used to obtain identification of significantly changing proteins regulated when Schizosaccharomyces pombe is exposed to oxidative stress. Differently treated S. pombe cells were lysed, labelled with CyDye (TM) and analysed by two-dimensional difference gel. electrophoresis. Gel images analysed off-line, using the DeCyder (TM) image analysis software [GE Healthcare, Amersham, UK] allowed selection of significantly regulated proteins. Proteins displaying differential expression were excised robotically for manual digestion and identified by matrix-assisted laser desorption/ionisation - mass spectrometry (MALDI-MS). Additionally the same set of proteins displaying differential expression were automatically cut and digested using a prototype robotic platform. Automated MALDI-MS, peak label assignment and database searching were utilised to identify as many proteins as possible. The results achieved by the robotic system were compared to manual methods. The identification of all significantly altered proteins provides an annotated peroxide stress-related proteome that can be used as a base resource against which other stress-induced proteomic changes can be compared.

Processing of wh-questions in a case of posterior cortical atrophy

Posterior cortical atrophy (PCA) is a type of dementia that is characterized by visuo-spatial and memory deficits, dyslexia and dysgraphia, relatively early onset and preserved insight. Language deficits have been reported in some cases of PCA. Using an off-line grammaticality judgement task, processing of wh-questions is investigated in a case of PCA. Other aspects of auditory language are also reported. It is shown that processing of wh-questions is influenced by syntactic structure, a novel finding in this condition. The results are discussed with reference to accounts of wh-questions in aphasia. An uneven profile of other language abilities is reported with deficits in digit span (forward, backward), story retelling ability, comparative questions but intact abilities in following commands, repetition, concept definition, generative naming and discourse comprehension.

Pronominal and anaphoric reference in agrammatism

Subjects with Broca's aphasia have been shown to display difficulties in on-line and off-line tasks involving personal pronouns and reflexives. Off-line tasks have indicated more errors with pronouns than with reflexives while the reverse has been found in on-line studies. In the present off-line study, the comprehension of sentences containing personal pronouns and reflexives is examined in a group of 10 agrammatic participants. Results indicate that subjects had difficulties with both pronouns and reflexives, particularly with reflexives in sentences that contained a quantificational antecedent, as well as with pronouns in exceptional case marking constructions. It is argued that the low performance that subjects exhibited as a group in pronouns and reflexives indicates two distinct impairments, one that concerns coreference and one that concerns A-dependencies, the latter being a manifestation of a general processing failure to link positions. Poor performance on exceptional case marking constructions compared to simple transitive sentences is claimed to be interpreted within theories for reference assignment that distinguish between the two sentence types. (c) 2007 Elsevier Ltd. All rights reserved.

An oblivious shortest-path routing algorithm for fully connected cubic networks

Fully connected cubic networks (FCCNs) are a class of newly proposed hierarchical interconnection networks for multicomputer systems, which enjoy the strengths of constant node degree and good expandability. The shortest path routing in FCCNs is an open problem. In this paper, we present an oblivious routing algorithm for n-level FCCN with N = 8(n) nodes, and prove that this algorithm creates a shortest path from the source to the destination. At the costs of both an O(N)-parallel-step off-line preprocessing phase and a list of size N stored at each node, the proposed algorithm is carried out at each related node in O(n) time. In some cases the proposed algorithm is superior to the one proposed by Chang and Wang in terms of the length of the routing path. This justifies the utility of our routing strategy. (C) 2006 Elsevier Inc. All rights reserved.

A typology of internet users based on comparative affective states: evidence from eight countries

Purpose - The role of affective states in consumer behaviour is well established. However, no study to date has empirically examined online affective states as a basis for constructing typologies of internet users and for assessing the invariance of clusters across national cultures. Design/methodology/approach - Four focus groups with internet users were carried out to adapt a set of affective states identified from the literature to the online environment. An online survey was then designed to collect data from internet users in four Western and four East Asian countries. Findings - Based on a cluster analysis, six cross-national market segments are identified and labelled "Positive Online Affectivists", "Offline Affectivists", "On/Off-line Negative Affectivists", "Online Affectivists", "Indistinguishable Affectivists", and "Negative Offline Affectivists". The resulting clusters discriminate on the basis of national culture, gender, working status and perceptions towards online brands. Practical implications - Marketers may use this typology to segment internet users in order to predict their perceptions towards online brands. Also, a standardised approach to e-marketing is not recommended on the basis of affective state-based segmentation. Originality/value - This is the first study proposing affective state-based typologies of internet users using comparable samples from four Western and four East Asian countries.

The effect of regional changes in anthropogenic aerosols on rainfall of the East Asian summer monsoon

The response of East Asian Summer Monsoon (EASM) precipitation to long term changes in regional anthropogenic aerosols (sulphate and black carbon) is explored in an atmospheric general circulation model, the atmospheric component of the UK High-Resolution Global Environment Model v1.2 (HiGAM). Separately, sulphur dioxide (SO2) and black carbon (BC) emissions in 1950 and 2000 over East Asia are used to drive model simulations, while emissions are kept constant at year 2000 level outside this region. The response of the EASM is examined by comparing simulations driven by aerosol emissions representative of 1950 and 2000. The aerosol radiative effects are also determined using an off-line radiative transfer model. During June, July and August, the EASM was not significantly changed as either SO2 or BC emissions increased from 1950 to 2000 levels. However, in September, precipitation is significantly decreased by 26.4% for sulphate aerosol and 14.6% for black carbon when emissions are at the 2000 level. Over 80% of the decrease is attributed to changes in convective precipitation. The cooler land surface temperature over China in September (0.8 °C for sulphate and 0.5 °C for black carbon) due to increased aerosols reduces the surface thermal contrast that supports the EASM circulation. However, mechanisms causing the surface temperature decrease in September are different between sulphate and BC experiments. In the sulphate experiment, the sulphate direct and the 1st indirect radiative effects contribute to the surface cooling. In the BC experiment, the BC direct effect is the main driver of the surface cooling, however, a decrease in low cloud cover due to the increased heating by BC absorption partially counteracts the direct effect. This results in a weaker land surface temperature response to BC changes than to sulphate changes. The resulting precipitation response is also weaker, and the responses of the monsoon circulation are different for sulphate and black carbon experiments. This study demonstrates a mechanism that links regional aerosol emission changes to the precipitation changes of the EASM, and it could be applied to help understand the future changes in EASM precipitation in CMIP5 simulations.

Parsing the passive: comparing children with Specific Language Impairment to sequential bilingual children

25 monolingual (L1) children with Specific Language Impairment (SLI), 32 sequential bilingual (L2) children, and 29 L1 controls completed the Test of Active & Passive Sentences-Revised (van der Lely, 1996) and the self-paced listening task with picture verification for actives and passives (Marinis, 2007). These revealed important between-group differences in both tasks. The children with SLI showed difficulties in both actives and passives when they had to reanalyse thematic roles on-line. Their error pattern provided evidence for working memory limitations. The L2 children showed difficulties only in passives both on-line and off-line. We suggest that these relate to the complex syntactic algorithm in passives and reflect an earlier developmental stage due to reduced exposure to the L2. The results are discussed in relation to theories of SLI and can be best accommodated within accounts proposing that difficulties in the comprehension of passives stem from processing limitations.

Evaluation of regional climate simulations for air quality modelling purposes

In order to evaluate the future potential benefits of emission regulation on regional air quality, while taking into account the effects of climate change, off-line air quality projection simulations are driven using weather forcing taken from regional climate models. These regional models are themselves driven by simulations carried out using global climate models (GCM) and economical scenarios. Uncertainties and biases in climate models introduce an additional “climate modeling” source of uncertainty that is to be added to all other types of uncertainties in air quality modeling for policy evaluation. In this article we evaluate the changes in air quality-related weather variables induced by replacing reanalyses-forced by GCM-forced regional climate simulations. As an example we use GCM simulations carried out in the framework of the ERA-interim programme and of the CMIP5 project using the Institut Pierre-Simon Laplace climate model (IPSLcm), driving regional simulations performed in the framework of the EURO-CORDEX programme. In summer, we found compensating deficiencies acting on photochemistry: an overestimation by GCM-driven weather due to a positive bias in short-wave radiation, a negative bias in wind speed, too many stagnant episodes, and a negative temperature bias. In winter, air quality is mostly driven by dispersion, and we could not identify significant differences in either wind or planetary boundary layer height statistics between GCM-driven and reanalyses-driven regional simulations. However, precipitation appears largely overestimated in GCM-driven simulations, which could significantly affect the simulation of aerosol concentrations. The identification of these biases will help interpreting results of future air quality simulations using these data. Despite these, we conclude that the identified differences should not lead to major difficulties in using GCM-driven regional climate simulations for air quality projections.

Parameterised diabatic processes in numerical simulations of an extratropical cyclone

The parameterisation of diabatic processes in numerical models is critical for the accuracy of weather forecasts and for climate projections. A novel approach to the evaluation of these processes in models is introduced in this contribution. The approach combines a suite of on-line tracer diagnostics with off-line trajectory calculations. Each tracer tracks accumulative changes in potential temperature associated with a particular parameterised diabatic process in the model. A comparison of tracers therefore allows the identification of the most active diabatic processes and their downstream impacts. The tracers are combined with trajectories computed using model-resolved winds, allowing the various diabatic contributions to be tracked back to their time and location of occurrence. We have used this approach to investigate diabatic processes within a simulated extratropical cyclone. We focus on the warm conveyor belt, in which the dominant diabatic contributions come from large-scale latent heating and parameterised convection. By contrasting two simulations, one with standard convection parameterisation settings and another with reduced parameterised convection, the effects of parameterised convection on the structure of the cyclone have been determined. Under reduced parameterised convection conditions, the large-scale latent heating is forced to release convective instability that would otherwise have been released by the convection parameterisation. Although the spatial distribution of precipitation depends on the details of the split between parameterised convection and large-scale latent heating, the total precipitation amount associated with the cyclone remains largely unchanged. For reduced parameterised convection, a more rapid and stronger latent heating episode takes place as air ascends within the warm conveyor belt.

The dichotomous structure of the warm conveyor belt

The warm conveyor belt (WCB) of an extratropical cyclone generally splits into two branches. One branch (WCB1) turns anticyclonically into the downstream upper-level tropospheric ridge, while the second branch (WCB2) wraps cyclonically around the cyclone centre. Here, the WCB split in a typical North Atlantic cold-season cyclone is analysed using two numerical models: the Met Office Unified Model and the COSMO model. The WCB flow is defined using off-line trajectory analysis. The two models represent the WCB split consistently. The split occurs early in the evolution of the WCB with WCB1 experiencing maximum ascent at lower latitudes and with higher moisture content than WCB2. WCB1 ascends abruptly along the cold front where the resolved ascent rates are greatest and there is also line convection. In contrast, WCB2 remains at lower levels for longer before undergoing saturated large-scale ascent over the system's warm front. The greater moisture in WCB1 inflow results in greater net potential temperature change from latent heat release, which determines the final isentropic level of each branch. WCB1 also exhibits lower outflow potential vorticity values than WCB2. Complementary diagnostics in the two models are utilised to study the influence of individual diabatic processes on the WCB. Total diabatic heating rates along the WCB branches are comparable in the two models with microphysical processes in the large-scale cloud schemes being the major contributor to this heating. However, the different convective parameterisation schemes used by the models cause significantly different contributions to the total heating. These results have implications for studies on the influence of the WCB outflow in Rossby wave evolution and breaking. Key aspects are the net potential temperature change and the isentropic level of the outflow which together will influence the relative mass going into each WCB branch and the associated negative PV anomalies at the tropopause-level flow.

Multi-site evaluation of an urban land-surface model: intra-urban heterogeneity, seasonality and parameter complexity requirements

An extensive off-line evaluation of the Noah/Single Layer Urban Canopy Model (Noah/SLUCM) urban land-surface model is presented using data from 15 sites to assess (1) the ability of the scheme to reproduce the surface energy balance observed in a range of urban environments, including seasonal changes, and (2) the impact of increasing complexity of input parameter information. Model performance is found to be most dependent on representation of vegetated surface area cover; refinement of other parameter values leads to smaller improvements. Model biases in net all-wave radiation and trade-offs between turbulent heat fluxes are highlighted using an optimization algorithm. Here we use the Urban Zones to characterize Energy partitioning (UZE) as the basis to assign default SLUCM parameter values. A methodology (FRAISE) to assign sites (or areas) to one of these categories based on surface characteristics is evaluated. Using three urban sites from the Basel Urban Boundary Layer Experiment (BUBBLE) dataset, an independent evaluation of the model performance with the parameter values representative of each class is performed. The scheme copes well with both seasonal changes in the surface characteristics and intra-urban heterogeneities in energy flux partitioning, with RMSE performance comparable to similar state-of-the-art models for all fluxes, sites and seasons. The potential of the methodology for high-resolution atmospheric modelling application using the Weather Research and Forecasting (WRF) model is highlighted. This analysis supports the recommendations that (1) three classes are appropriate to characterize the urban environment, and (2) that the parameter values identified should be adopted as default values in WRF.

The impact of number mismatch and passives on the real-time processing of relative clauses

Language processing plays a crucial role in language development, providing the ability to assign structural representations to input strings (e.g., Fodor, 1998). In this paper we aim at contributing to the study of children's processing routines, examining the operations underlying the auditory processing of relative clauses in children compared to adults. English-speaking children (6–8;11) and adults participated in the study, which employed a self-paced listening task with a final comprehension question. The aim was to determine (i) the role of number agreement in object relative clauses in which the subject and object NPs differ in terms of number properties, and (ii) the role of verb morphology (active vs. passive) in subject relative clauses. Even though children's off-line accuracy was not always comparable to that of adults, analyses of reaction times results support the view that children have the same structural processing reflexes observed in adults.

Representation errors and retrievals in linear and nonlinear data assimilation

This article shows how one can formulate the representation problem starting from Bayes’ theorem. The purpose of this article is to raise awareness of the formal solutions,so that approximations can be placed in a proper context. The representation errors appear in the likelihood, and the different possibilities for the representation of reality in model and observations are discussed, including nonlinear representation probability density functions. Specifically, the assumptions needed in the usual procedure to add a representation error covariance to the error covariance of the observations are discussed,and it is shown that, when several sub-grid observations are present, their mean still has a representation error ; socalled ‘superobbing’ does not resolve the issue. Connection is made to the off-line or on-line retrieval problem, providing a new simple proof of the equivalence of assimilating linear retrievals and original observations. Furthermore, it is shown how nonlinear retrievals can be assimilated without loss of information. Finally we discuss how errors in the observation operator model can be treated consistently in the Bayesian framework, connecting to previous work in this area.

The neurological underpinnings of cluttering: some initial findings

Background Cluttering is a fluency disorder characterised by overly rapid or jerky speech patterns that compromise intelligibility. The neural correlates of cluttering are unknown but theoretical accounts implicate the basal ganglia and medial prefrontal cortex. Dysfunction in these brain areas would be consistent with difficulties in selection and control of speech motor programs that are characteristic of speech disfluencies in cluttering. There is a surprising lack of investigation into this disorder using modern imaging techniques. Here, we used functional MRI to investigate the neural correlates of cluttering. Method We scanned 17 adults who clutter and 17 normally fluent control speakers matched for age and sex. Brain activity was recorded using sparse-sampling functional MRI while participants viewed scenes and either (i) produced overt speech describing the scene or (ii) read out loud a sentence provided that described the scene. Speech was recorded and analysed off line. Differences in brain activity for each condition compared to a silent resting baseline and between conditions were analysed for each group separately (cluster-forming threshold Z > 3.1, extent p < 0.05, corrected) and then these differences were further compared between the two groups (voxel threshold p < 0.01, extent > 30 voxels, uncorrected). Results In both conditions, the patterns of activation in adults who clutter and control speakers were strikingly similar, particularly at the cortical level. Direct group comparisons revealed greater activity in adults who clutter compared to control speakers in the lateral premotor cortex bilaterally and, as predicted, on the medial surface (pre-supplementary motor area). Subcortically, adults who clutter showed greater activity than control speakers in the basal ganglia. Specifically, the caudate nucleus and putamen were overactive in adults who clutter for the comparison of picture description with sentence reading. In addition, adults who clutter had reduced activity relative to control speakers in the lateral anterior cerebellum bilaterally. Eleven of the 17 adults who clutter also stuttered. This comorbid diagnosis of stuttering was found to contribute to the abnormal overactivity seen in the group of adults who clutter in the right ventral premotor cortex and right anterior cingulate cortex. In the remaining areas of abnormal activity seen in adults who clutter compared to controls, the subgroup who clutter and stutter did not differ from the subgroup who clutter but do not stutter. Conclusions Our findings were in good agreement with theoretical predictions regarding the neural correlates of cluttering. We found evidence for abnormal function in the basal ganglia and their cortical output target, the medial prefrontal cortex. The findings are discussed in relation to models of cluttering that point to problems with motor control of speech.