Proteomic analyses of a Listeria monocytogenes mutant lacking σB identify new components of the σB regulon and highlight a role for σB in the utilization of glycerol

In Listeria monocytogenes the alternative sigma factor σB plays important roles in both virulence and stress tolerance. In this study a proteomic approach was used to define components of the σB regulon in L. monocytogenes 10403S (serotype 1/2a). Using two-dimensional gel electrophoresis and the recently developed isobaric tags for relative and absolute quantitation technique, the protein expression profiles of the wild type and an isogenic ΔsigB deletion strain were compared. Overall, this study identified 38 proteins whose expression was σB dependent; 17 of these proteins were found to require the presence of σB for full expression, while 21 were expressed at a higher level in the ΔsigB mutant background. The data obtained with the two proteomic approaches showed limited overlap (four proteins were identified by both methods), a finding that highlights the complementarity of the two technologies. Overall, the proteomic data reaffirmed a role for σB in the general stress response and highlighted a probable role for σB in metabolism, especially in the utilization of alternative carbon sources. Proteomic and physiological data revealed the involvement of σB in glycerol metabolism. Five newly identified members of the σB regulon were shown to be under direct regulation of σB using reverse transcription-PCR (RT-PCR), while random amplification of cDNA ends-PCR was used to map four σB-dependent promoters upstream from lmo0796, lmo1830, lmo2391, and lmo2695. Using RT-PCR analysis of known and newly identified σB-dependent genes, as well as proteomic analyses, σB was shown to play a major role in the stationary phase of growth in complex media.

Distributed hoeffding trees for pocket data mining

Collaborative mining of distributed data streams in a mobile computing environment is referred to as Pocket Data Mining PDM. Hoeffding trees techniques have been experimentally and analytically validated for data stream classification. In this paper, we have proposed, developed and evaluated the adoption of distributed Hoeffding trees for classifying streaming data in PDM applications. We have identified a realistic scenario in which different users equipped with smart mobile devices run a local Hoeffding tree classifier on a subset of the attributes. Thus, we have investigated the mining of vertically partitioned datasets with possible overlap of attributes, which is the more likely case. Our experimental results have validated the efficiency of our proposed model achieving promising accuracy for real deployment.

Contested institutions? Traditional leaders and land access and control in communal areas of Eastern Cape Province, South Africa

The South African government has endeavoured to strengthen property rights in communal areas and develop civil society institutions for community-led development and natural resource management. However, the effectiveness of this remains unclear as the emergence and operation of civil society institutions in these areas is potentially constrained by the persistence of traditional authorities. Focusing on the former Transkei region of Eastern Cape Province, three case study communities are used examine the extent to which local institutions overlap in issues of land access and control. Within these communities, traditional leaders (chiefs and headmen) continue to exercise complete and sole authority over land allocation and use this to entrench their own positions. However, in the absence of effective state support, traditional authorities have only limited power over how land is used and in enforcing land rights, particularly over communal resources such as rangeland. This diminishes their local legitimacy and encourages some groups to contest their authority by cutting fences, ignoring collective grazing decisions and refusing to pay ‘fees’ levied on them. They are encouraged in such activities by the presence of democratically elected local civil society institutions such as ward councillors and farmers’ organisations, which have broad appeal and are increasingly responsible for much of the agrarian development that takes place, despite having no direct mandate over land. Where it occurs at all, interaction between these different institutions is generally restricted to approval being required from traditional leaders for land allocated to development projects. On this basis it is argued that a more radical approach to land reform in communal areas is required, which transfers all powers over land to elected and accountable local institutions and integrates land allocation, land management and agrarian development more effectively.

Land-atmosphere energy exchange in Arctic tundra and boreal forest: available data and feedbacks to climate

This paper summarizes and analyses available data on the surface energy balance of Arctic tundra and boreal forest. The complex interactions between ecosystems and their surface energy balance are also examined, including climatically induced shifts in ecosystem type that might amplify or reduce the effects of potential climatic change. High latitudes are characterized by large annual changes in solar input. Albedo decreases strongly from winter, when the surface is snow-covered, to summer, especially in nonforested regions such as Arctic tundra and boreal wetlands. Evapotranspiration (QE) of high-latitude ecosystems is less than from a freely evaporating surface and decreases late in the season, when soil moisture declines, indicating stomatal control over QE, particularly in evergreen forests. Evergreen conifer forests have a canopy conductance half that of deciduous forests and consequently lower QE and higher sensible heat flux (QH). There is a broad overlap in energy partitioning between Arctic and boreal ecosystems, although Arctic ecosystems and light taiga generally have higher ground heat flux because there is less leaf and stem area to shade the ground surface, and the thermal gradient from the surface to permafrost is steeper. Permafrost creates a strong heat sink in summer that reduces surface temperature and therefore heat flux to the atmosphere. Loss of permafrost would therefore amplify climatic warming. If warming caused an increase in productivity and leaf area, or fire caused a shift from evergreen to deciduous forest, this would increase QE and reduce QH. Potential future shifts in vegetation would have varying climate feedbacks, with largest effects caused by shifts from boreal conifer to shrubland or deciduous forest (or vice versa) and from Arctic coastal to wet tundra. An increase of logging activity in the boreal forests appears to reduce QE by roughly 50% with little change in QH, while the ground heat flux is strongly enhanced.

Memory as discrimination: what distraction reveals

Recalling information involves the process of discriminating between relevant and irrelevant information stored in memory. Not infrequently, the relevant information needs to be selected from amongst a series of related possibilities. This is likely to be particularly problematic when the irrelevant possibilities are not only temporally or contextually appropriate but also overlap semantically with the target or targets. Here, we investigate the extent to which purely perceptual features which discriminate between irrelevant and target material can be used to overcome the negative impact of contextual and semantic relatedness. Adopting a distraction paradigm, it is demonstrated that when distracters are interleaved with targets presented either visually (Experiment 1) or auditorily (Experiment 2), a within-modality semantic distraction effect occurs; semantically-related distracters impact upon recall more than unrelated distracters. In the semantically-related condition, the number of intrusions in recall is reduced whilst the number of correctly recalled targets is simultaneously increased by the presence of perceptual cues to relevance (color features in Experiment 1 or speaker’s gender in Experiment 2). However, as demonstrated in Experiment 3, even presenting semantically-related distracters in a language and a sensory modality (spoken Welsh) distinct from that of the targets (visual English) is insufficient to eliminate false recalls completely, or to restore correct recall to levels seen with unrelated distracters . Together, the study shows how semantic and non-semantic discriminability shape patterns of both erroneous and correct recall.

A high-resolution near-infrared extraterrestrial solar spectrum derived from ground-based Fourier transform spectrometer measurements

A detailed spectrally-resolved extraterrestrial solar spectrum (ESS) is important for line-by-line radiative transfer modeling in the near-infrared (near-IR). Very few observationally-based high-resolution ESS are available in this spectral region. Consequently the theoretically-calculated ESS by Kurucz has been widely adopted. We present the CAVIAR (Continuum Absorption at Visible and Infrared Wavelengths and its Atmospheric Relevance) ESS which is derived using the Langley technique applied to calibrated observations using a ground-based high-resolution Fourier transform spectrometer (FTS) in atmospheric windows from 2000–10000 cm-1 (1–5 μm). There is good agreement between the strengths and positions of solar lines between the CAVIAR and the satellite-based ACE-FTS (Atmospheric Chemistry Experiment-FTS) ESS, in the spectral region where they overlap, and good agreement with other ground-based FTS measurements in two near-IR windows. However there are significant differences in the structure between the CAVIAR ESS and spectra from semi-empirical models. In addition, we found a difference of up to 8 % in the absolute (and hence the wavelength-integrated) irradiance between the CAVIAR ESS and that of Thuillier et al., which was based on measurements from the Atmospheric Laboratory for Applications and Science satellite and other sources. In many spectral regions, this difference is significant, as the coverage factor k = 2 (or 95 % confidence limit) uncertainties in the two sets of observations do not overlap. Since the total solar irradiance is relatively well constrained, if the CAVIAR ESS is correct, then this would indicate an integrated “loss” of solar irradiance of about 30 W m-2 in the near-IR that would have to be compensated by an increase at other wavelengths.

Phonological therapy in jargon aphasia: effects on naming and neologisms

Background: Jargon aphasia is one of the most intractable forms of aphasia with limited recommendation on amelioration of associated naming difficulties and neologisms. The few naming therapy studies that exist in jargon aphasia have utilized either semantic or phonological approaches but the results have been equivocal. Moreover, the effect of therapy on characteristics of neologisms is less explored. Aims: This study investigates the effectiveness of a phonological naming therapy (i.e., phonological component analysis, PCA) on picture naming abilities and on quantitative and qualitative changes in neologisms for an individual with jargon aphasia (FF). Methods: FF showed evidence of jargon aphasia with severe naming difficulties and produced a very high proportion of neologisms. A single-subject multiple probe design across behaviors was employed to evaluate the effects of PCA therapy on the accuracy for three sets of words. In therapy, a phonological components analysis chart was used to identify five phonological components (i.e., rhymes, first sound, first sound associate, final sound, number of syllables) for each target word. Generalization effects—change in percent accuracy and error pattern—were examined comparing pre-and post-therapy responses on the Philadelphia Naming Test and these responses were analyzed to explore the characteristics of the neologisms. The quantitative change in neologisms was measured by change in the proportion of neologisms from pre- to post-therapy and the qualitative change was indexed by the phonological overlap between target and neologism. Results: As a consequence of PCA therapy, FF showed a significant improvement in his ability to name the treated items. His performance in maintenance and follow-up phases remained comparable to his performance during the therapy phases. Generalization to other naming tasks did not show a change in accuracy but distinct differences in error pattern (an increase in proportion of real word responses and a decrease in proportion of neologisms) were observed. Notably, the decrease in neologisms occurred with a corresponding trend for increase in the phonological similarity between the neologisms and the targets. Conclusions: This study demonstrated the effectiveness of a phonological therapy for improving naming abilities and reducing the amount of neologisms in an individual with severe jargon aphasia. The positive outcome of this research is encouraging, as it provides evidence for effective therapies for jargon aphasia and also emphasizes that use of the quality and quantity of errors may provide a sensitive outcome measure to determine therapy effectiveness, in particular for client groups who are difficult to treat.

Deriving a sea surface temperature record suitable for climate change research from the along-track scanning radiometers

We describe the approach to be adopted for a major new initiative to derive a homogeneous record of sea surface temperature for 1991–2007 from the observations of the series of three along-track scanning radiometers (ATSRs). This initiative is called (A)RC: (Advanced) ATSR Re-analysis for Climate. The main objectives are to reduce regional biases in retrieved sea surface temperature (SST) to less than 0.1 K for all global oceans, while creating a very homogenous record that is stable in time to within 0.05 K decade−1, with maximum independence of the record from existing analyses of SST used in climate change research. If these stringent targets are achieved, this record will enable significantly improved estimates of surface temperature trends and variability of sufficient quality to advance questions of climate change attribution, climate sensitivity and historical reconstruction of surface temperature changes. The approach includes development of new, consistent estimators for SST for each of the ATSRs, and detailed analysis of overlap periods. Novel aspects of the approach include generation of multiple versions of the record using alternative channel sets and cloud detection techniques, to assess for the first time the effect of such choices. There will be extensive effort in quality control, validation and analysis of the impact on climate SST data sets. Evidence for the plausibility of the 0.1 K target for systematic error is reviewed, as is the need for alternative cloud screening methods in this context.

Tandem quadruplication of HMA4 in the zinc (Zn) and cadmium (Cd) hyperaccumulator Noccaea caerulescens

Zinc (Zn) and cadmium (Cd) hyperaccumulation may have evolved twice in the Brassicaceae, in Arabidopsis halleri and in the Noccaea genus. Tandem gene duplication and deregulated expression of the Zn transporter, HMA4, has previously been linked to Zn/Cd hyperaccumulation in A. halleri. Here, we tested the hypothesis that tandem duplication and deregulation of HMA4 expression also occurs in Noccaea. A Noccaea caerulescens genomic library was generated, containing 36,864 fosmid pCC1FOS (TM) clones with insert sizes similar to 20-40 kbp, and screened with a PCR-generated HMA4 genomic probe. Gene copy number within the genome was estimated through DNA fingerprinting and pooled fosmid pyrosequencing. Gene copy numbers within individual clones was determined by PCR analyses with novel locus specific primers. Entire fosmids were then sequenced individually and reads equivalent to 20-fold coverage were assembled to generate complete whole contigs. Four tandem HMA4 repeats were identified in a contiguous sequence of 101,480 bp based on sequence overlap identities. These were flanked by regions syntenous with up and downstream regions of AtHMA4 in Arabidopsis thaliana. Promoter-reporter beta-glucuronidase (GUS) fusion analysis of a NcHMA4 in A. thaliana revealed deregulated expression in roots and shoots, analogous to AhHMA4 promoters, but distinct from AtHMA4 expression which localised to the root vascular tissue. This remarkable consistency in tandem duplication and deregulated expression of metal transport genes between N. caerulescens and A. halleri, which last shared a common ancestor > 40 mya, provides intriguing evidence that parallel evolutionary pathways may underlie Zn/Cd hyperaccumulation in Brassicaceae.

Settlement patterns in the late Mesolithic of western Scotland: the implications of Bayesian analysis of radiocarbon dates and inter-site technological comparisons

The character of settlement patterns within the late Mesolithic communities of north-west Europe is a topic of substantial debate. An important case study concerns the five shell middens on the island of Oronsay, Inner Hebrides, western Scotland. Two conflicting interpretations have been proposed: the evidence from seasonality indicators and stable isotope analysis of human bones has been used to support a model of year-round settlement on this small island; alternatively, the middens have been interpreted as resulting from short-term intermittent visits to Oronsay within a regionally mobile settlement pattern. We contribute to this debate by describing Storakaig, a newly discovered site on the nearby island of Islay, undertaking a Bayesian chronological analysis and providing evidence for technological continuity between Oronsay and sites elsewhere in the region. While this new evidence remains open to alternative interpretation, we suggest that it makes regional mobility rather than year-round settlement on Oronsay a more viable interpretation for the Oronsay middens. Our analysis also confirms the likely overlap of the late Mesolithic with the earliest Neolithic within western Scotland.

Radiative forcing of climate by hydrochlorofluorocarbons and hydrofluorocarbons

We measure infrared absorption spectra of 18 hydrochlorofluorocarbons and hydrofluorocarbons, seven of which do not yet appear in the literature. The spectra are used in a narrowband model of the terrestrial infrared radiation to calculate radiative forcing and global warming potentials. We investigate the sensitivity of the radiative forcing to the absorption spectrum temperature dependence, halocarbon vertical profile, stratospheric adjustment, cloudiness, spectral overlap, and latitude, and we make some recommendations for the reporting of radiative forcings that would help to resolve discrepancies between assessments. We investigate simple methods of estimating instantaneous radiative forcing directly from a molecule's absorption spectrum and we present a new method that agrees to within 0.3% with our narrowband model results.

Essays on labour market dualisation in Western Europe: active labour market policies, temporary work regulation and inequality

European labour markets are increasingly divided between insiders in full-time permanent employment and outsiders in precarious work or unemployment. Using quantitative as well as qualitative methods, this thesis investigates the determinants and consequences of labour market policies that target these outsiders in three separate papers. The first paper looks at Active Labour Market Policies (ALMPs) that target the unemployed. It shows that left and right-wing parties choose different types of ALMPs depending on the policy and the welfare regime in which the party is located. These findings reconcile the conflicting theoretical expectations from the Power Resource approach and the insider-outsider theory. The second paper considers the regulation and protection of the temporary work sector. It solves the puzzle of temporary re-regulation in France, which contrasts with most other European countries that have deregulated temporary work. Permanent workers are adversely affected by the expansion of temporary work in France because of general skills and low wage coordination. The interests of temporary and permanent workers for re-regulation therefore overlap in France and left governments have an incentive to re-regulate the sector. The third paper then investigates what determines inequality between median and bottom income workers. It shows that non-inclusive economic coordination increases inequality in the absence of compensating institutions such as minimum wage regulation. The deregulation of temporary work as well as spending on employment incentives and rehabilitation also has adverse effects on inequality. Thus, policies that target outsiders have important economic effects on the rest of the workforce. Three broader contributions can be identified. First, welfare state policies may not always be in the interests of labour, so left parties may not always promote them. Second, the interests of insiders and outsiders are not necessarily at odds. Third, economic coordination may not be conducive to egalitarianism where it is not inclusive.

Climate-driven spatial mismatches between British orchards and their pollinators: increased risks of pollination deficits

Understanding how climate change can affect crop-pollinator systems helps predict potential geographical mismatches between a crop and its pollinators, and therefore identify areas vulnerable to loss of pollination services. We examined the distribution of orchard species (apples, pears, plums and other top fruits) and their pollinators in Great Britain, for present and future climatic conditions projected for 2050 under the SRES A1B Emissions Scenario. We used a relative index of pollinator availability as a proxy for pollination service. At present there is a large spatial overlap between orchards and their pollinators, but predictions for 2050 revealed that the most suitable areas for orchards corresponded to low pollinator availability. However, we found that pollinator availability may persist in areas currently used for fruit production, but which are predicted to provide sub-optimal environmental suitability for orchard species in the future. Our results may be used to identify mitigation options to safeguard orchard production against the risk of pollination failure in Great Britain over the next 50 years; for instance choosing fruit tree varieties that are adapted to future climatic conditions, or boosting wild pollinators through improving landscape resources. Our approach can be readily applied to other regions and crop systems, and expanded to include different climatic scenarios.

In optics humidity compensation in NDIR exhaust gas measurements of NO2

NDIR is proposed for monitoring of air pollutants emitted by ship engines. Careful optical filtering overcomes the challenge of optical detection of NO2 in humid exhaust gas, despite spectroscopic overlap with the water vapour band.

Derivation of an urban materials spectral library through emittance and reflectance spectroscopy

Recent advances in thermal infrared remote sensing include the increased availability of airborne hyperspectral imagers (such as the Hyperspectral Thermal Emission Spectrometer, HyTES, or the Telops HyperCam and the Specim aisaOWL), and it is planned that an increased number spectral bands in the long-wave infrared (LWIR) region will soon be measured from space at reasonably high spatial resolution (by imagers such as HyspIRI). Detailed LWIR emissivity spectra are required to best interpret the observations from such systems. This includes the highly heterogeneous urban environment, whose construction materials are not yet particularly well represented in spectral libraries. Here, we present a new online spectral library of urban construction materials including LWIR emissivity spectra of 74 samples of impervious surfaces derived using measurements made by a portable Fourier Transform InfraRed (FTIR) spectrometer. FTIR emissivity measurements need to be carefully made, else they are prone to a series of errors relating to instrumental setup and radiometric calibration, which here relies on external blackbody sources. The performance of the laboratory-based emissivity measurement approach applied here, that in future can also be deployed in the field (e.g. to examine urban materials in situ), is evaluated herein. Our spectral library also contains matching short-wave (VIS–SWIR) reflectance spectra observed for each urban sample. This allows us to examine which characteristic (LWIR and) spectral signatures may in future best allow for the identification and discrimination of the various urban construction materials, that often overlap with respect to their chemical/mineralogical constituents. Hyperspectral or even strongly multi-spectral LWIR information appears especially useful, given that many urban materials are composed of minerals exhibiting notable reststrahlen/absorption effects in this spectral region. The final spectra and interpretations are included in the London Urban Micromet data Archive (LUMA; http://LondonClimate.info/LUMA/SLUM.html).