Specificity grafting of human antibody frameworks selected from a phage display library: generation of a highly stable humanized anti-CD22 single-chain Fv fragment

A prerequisite for the enrichment of antibodies screened from phage display libraries is their stable expression on a phage during multiple selection rounds. Thus, if stringent panning procedures are employed, selection is simultaneously driven by antigen affinity, stability and solubility. To take advantage of robust pre-selected scaffolds of such molecules, we grafted single-chain Fv (scFv) antibodies, previously isolated from a human phage display library after multiple rounds of in vitro panning on tumor cells, with the specificity of the clinically established murine monoclonal anti-CD22 antibody RFB4. We show that a panel of grafted scFvs retained the specificity of the murine monoclonal antibody, bound to the target antigen with high affinity (6.4-9.6 nM), and exhibited exceptional biophysical stability with retention of 89-93% of the initial binding activity after 6 days of incubation in human serum at 37degreesC. Selection of stable human scaffolds with high sequence identity to both the human germline and the rodent frameworks required only a small number of murine residues to be retained within the human frameworks in order to maintain the structural integrity of the antigen binding site. We expect this approach may be applicable for the rapid generation of highly stable humanized antibodies with low immunogenic potential.

Top single nucleotide polymorphisms affecting carbohydrate metabolism in Metabolic Syndrome: from the LIPGENE study

Rationale:Metabolic Syndrome (MetS) is a high prevalence condition characterized by altered energy metabolism, insulin resistance and elevated cardiovascular risk.Objectives:Although many individual single nucleotide polymorphisms (SNPs) have been linked to certain MetS features, there are few studies analyzing the influence of SNPs on carbohydrate metabolism in MetS.Methods:904 SNPs (tag SNPs and functional SNPs) were tested for influence in eight fasting and dynamic markers of carbohydrate metabolism, performing an intravenous glucose tolerance test in 450 participants of the LIPGENE study.Findings:From 382 initial gene-phenotype associations between SNPs and any phenotypic variables, 61 (a 16 % of the pre-selected) remained significant after Bootstrapping. Top SNPs affecting glucose metabolism variables were as follows: fasting glucose: rs26125 (PPARGC1B); fasting insulin: rs4759277 (LRP1); C peptide: rs4759277 (LRP1); HOMA-IR: rs4759277 (LRP1); QUICKI: rs184003 (AGER); SI: rs7301876 (ABCC9), AIRg: rs290481 (TCF7L2) and DI: rs12691 (CEBPA).Conclusions:We describe here the top SNPs linked to phenotypic features in carbohydrate metabolism among aproximately 1000 candidate gene variations in fasting and postprandial samples of 450 patients with MetS from the LIPGENE study.

The Solar Stormwatch CME catalogue: results from the first space weather citizen science project

Solar Stormwatch was the first space weather citizen science project, the aim of which was to identify and track coronal mass ejections (CMEs) observed by the Heliospheric Imagers aboard the STEREO satellites. The project has now been running for approximately 4 years, with input from >16000 citizen scientists, resulting in a dataset of >38000 time-elongation profiles of CME trajectories, observed over 18 pre-selected position angles. We present our method for reducing this data set into aCME catalogue. The resulting catalogue consists of 144 CMEs over the period January-2007 to February-2010, of which 110 were observed by STEREO-A and 77 were observed by STEREO-B. For each CME, the time-elongation profiles generated by the citizen scientists are averaged into a consensus profile along each position angle that the event was tracked. We consider this catalogue to be unique, being at present the only citizen science generated CME catalogue, tracking CMEs over an elongation range of 4 degrees out to a maximum of approximately 70 degrees. Using single spacecraft fitting techniques, we estimate the speed, direction, solar source region and latitudinal width of each CME. This shows that, at present, the Solar Stormwatch catalogue (which covers only solar minimum years) contains almost exclusively slow CMEs, with a mean speed of approximately 350 kms−1. The full catalogue is available for public access at www.met.reading.ac.uk/spate/stormwatch. This includes, for each event, the unprocessed time-elongation profiles generated by Solar Stormwatch, the consensus time-elongation profiles and a set of summary plots, as well as the estimated CME properties.

Implications for conservation of foraging sites selected by Short-toed Eagles (Circaetus gallicus) in Greece

The major threat to Short-toed Eagles (Circaetus gallicus) is the reduction of suitable foraging habitats, but no quantitative studies have been conducted to understand this process. Here, the spatial distribution of foraging Short-toed Eagles was studied in relation to nine habitat types in Dadia-Lefkimi-Soufli National Park, Greece, during 1996-1998. Compared to the observed occurrence of foraging individuals over a particular habitat type with the expected utilization of that same habitat type, Short-toed Eagles concentrated their foraging efforts on three types of open habitat: intensive and non-intensive cultivation, and grasslands. Forested areas (pine forests, oak forests and mixed oak-pine forests) were largely avoided by foraging individuals. The density of prey items on the ground may not necessarily be a good indicator as to where an eagle individual will forage, as vegetation structure is also highly influential. The results highlight the importance of open habitat types which provide foraging opportunities for the Short-toed Eagle population. Management guidelines that maintain the region as a patchy network of open and wooded habitats are discussed in order to conserve a viable population of Short-toed Eagles, and possibly certain other raptor species that forage over open areas.

Architecture, sedentism, and social complexity at Pre-Pottery Neolithic A WF16, Southern Jordan

Recent excavations at Pre-Pottery Neolithic A (PPNA) WF16 in southern Jordan have revealed remarkable evidence of architectural developments in the early Neolithic. This sheds light on both special purpose structures and “domestic” settlement, allowing fresh insights into the development of increasingly sedentary communities and the social systems they supported. The development of sedentary communities is a central part of the Neolithic process in Southwest Asia. Architecture and ideas of homes and households have been important to the debate, although there has also been considerable discussion on the role of communal buildings and the organization of early sedentarizing communities since the discovery of the tower at Jericho. Recently, the focus has been on either northern Levantine PPNA sites, such as Jerf el Ahmar, or the emergence of ritual buildings in the Pre-Pottery Neolithic B of the southern Levant. Much of the debate revolves around a division between what is interpreted as domestic space, contrasted with “special purpose” buildings. Our recent evidence allows a fresh examination of the nature of early Neolithic communities.

A novel approach to national technological accumulation and absorptive capacity: aggregating Cohen and Levinthal

The paper develops a more precise specification and understanding of the process of national-level knowledge accumulation and absorptive capabilities by applying the reasoning and evidence from the firm-level analysis pioneered by Cohen and Levinthal (1989, 1990). In doing so, we acknowledge that significant cross-border effects due to the role of both inward and outward FDI exist and that assimilation of foreign knowledge is not only confined to catching-up economies but is also carried out by countries at the frontier-sharing phase. We postulate a non-linear relationship between national absorptive capacity and the technological gap, due to the effects of the cumulative nature of the learning process and the increase in complexity of external knowledge as the country approaches the technological frontier. We argue that national absorptive capacity and the accumulation of knowledge stock are simultaneously determined. This implies that different phases of technological development require different strategies. During the catching-up phase, knowledge accumulation occurs predominately through the absorption of trade and/or inward FDI-related R&D spillovers. At the pre-frontier-sharing phase onwards, increases in the knowledge base occur largely through independent knowledge creation and actively accessing foreign-located technological spillovers, inter alia through outward FDI-related R&D, joint ventures and strategic alliances.

Towards a ‘civic’ narrative: British national identity and the transformation of the British National Party

This article examines the ways in which the BNP utilises the elements of British national identity in its discourse and argues that, during Griffin's leadership, the party has made a discursive choice to shift the emphasis from an ethnic to a civic narrative. We put forward two hypotheses, 1: the modernisation of the discourse of extreme right parties in the British context is likely to be related to the adoption of a predominantly civic narrative and 2: in the context of British party competition the BNP is likely to converge towards UKIP, drawing upon elements of its perceived winning formula, i.e. a predominantly civic rhetoric of national identity. We proceed to empirically test our hypotheses by conducting a twofold comparison. First, we compare the BNP's discourse pre- and post-1999 showing the BNP's progressive adoption of a civic narrative; and second the BNP's post-1999 discourse to that of UKIP in order to illustrate their similarities in terms of civic values.

Fire-free land use in pre-1492 Amazonian savannas

The nature and scale of pre-Columbian land use and the consequences of the 1492 “Columbian Encounter” (CE) on Amazonia are among the more debated topics in New World archaeology and paleoecology. However, pre-Columbian human impact in Amazonian savannas remains poorly understood. Most paleoecological studies have been conducted in neotropical forest contexts. Of studies done in Amazonian savannas, none has the temporal resolution needed to detect changes induced by either climate or humans before and after A.D. 1492, and only a few closely integrate paleoecological and archaeological data. We report a high-resolution 2,150-y paleoecological record from a French Guianan coastal savanna that forces reconsideration of how pre-Columbian savanna peoples practiced raised-field agriculture and how the CE impacted these societies and environments. Our combined pollen, phytolith, and charcoal analyses reveal unexpectedly low levels of biomass burning associated with pre-A.D. 1492 savanna raised-field agriculture and a sharp increase in fires following the arrival of Europeans. We show that pre-Columbian raised-field farmers limited burning to improve agricultural production, contrasting with extensive use of fire in pre-Columbian tropical forest and Central American savanna environments, as well as in present-day savannas. The charcoal record indicates that extensive fires in the seasonally flooded savannas of French Guiana are a post-Columbian phenomenon, postdating the collapse of indigenous populations. The discovery that pre-Columbian farmers practiced fire-free savanna management calls into question the widely held assumption that pre-Columbian Amazonian farmers pervasively used fire to manage and alter ecosystems and offers fresh perspectives on an emerging alternative approach to savanna land use and conservation that can help reduce carbon emissions.

Unconscious effects of language-specific terminology on pre-attentive colour perception

It is now established that native language affects one's perception of the world. However, it is unknown whether this effect is merely driven by conscious, language-based evaluation of the environment or whether it reflects fundamental differences in perceptual processing between individuals speaking different languages. Using brain potentials, we demonstrate that the existence in Greek of 2 color terms—ghalazio and ble—distinguishing light and dark blue leads to greater and faster perceptual discrimination of these colors in native speakers of Greek than in native speakers of English. The visual mismatch negativity, an index of automatic and preattentive change detection, was similar for blue and green deviant stimuli during a color oddball detection task in English participants, but it was significantly larger for blue than green deviant stimuli in native speakers of Greek. These findings establish an implicit effect of language-specific terminology on human color perception.

Perceptual shift in bilingualism: brain potentials reveal plasticity in pre-attentive colour perception

The validity of the linguistic relativity principle continues to stimulate vigorous debate and research. The debate has recently shifted from the behavioural investigation arena to a more biologically grounded field, in which tangible physiological evidence for language effects on perception can be obtained. Using brain potentials in a colour oddball detection task with Greek and English speakers, a recent study suggests that language effects may exist at early stages of perceptual integration [Thierry, G., Athanasopoulos, P., Wiggett, A., Dering, B., & Kuipers, J. (2009). Unconscious effects of language-specific terminology on pre-attentive colour perception. Proceedings of the National Academy of Sciences, 106, 4567–4570]. In this paper, we test whether in Greek speakers exposure to a new cultural environment (UK) with contrasting colour terminology from their native language affects early perceptual processing as indexed by an electrophysiological correlate of visual detection of colour luminance. We also report semantic mapping of native colour terms and colour similarity judgements. Results reveal convergence of linguistic descriptions, cognitive processing, and early perception of colour in bilinguals. This result demonstrates for the first time substantial plasticity in early, pre-attentive colour perception and has important implications for the mechanisms that are involved in perceptual changes during the processes of language learning and acculturation.

Environmental impact of geometric earthwork construction in pre-Columbian Amazonia

There is considerable controversy over whether pre-Columbian (pre-A.D. 1492) Amazonia was largely “pristine” and sparsely populated by slash-and-burn agriculturists, or instead a densely populated, domesticated landscape, heavily altered by extensive deforestation and anthropogenic burning. The discovery of hundreds of large geometric earthworks beneath intact rainforest across southern Amazonia challenges its status as a pristine landscape, and has been assumed to indicate extensive pre-Columbian deforestation by large populations. We tested these assumptions using coupled local- and regional-scale paleoecological records to reconstruct land use on an earthwork site in northeast Bolivia within the context of regional, climate-driven biome changes. This approach revealed evidence for an alternative scenario of Amazonian land use, which did not necessitate labor-intensive rainforest clearance for earthwork construction. Instead, we show that the inhabitants exploited a naturally open savanna landscape that they maintained around their settlement despite the climatically driven rainforest expansion that began ∼2,000 y ago across the region. Earthwork construction and agriculture on terra firme landscapes currently occupied by the seasonal rainforests of southern Amazonia may therefore not have necessitated large-scale deforestation using stone tools. This finding implies far less labor—and potentially lower population density—than previously supposed. Our findings demonstrate that current debates over the magnitude and nature of pre-Columbian Amazonian land use, and its impact on global biogeochemical cycling, are potentially flawed because they do not consider this land use in the context of climate-driven forest–savanna biome shifts through the mid-to-late Holocene.

Information and punitiveness: trial reconstruction in Ireland

Purpose – The purpose of this paper is to report results from a rape trial reconstruction in Ireland. Design/methodology/approach – A studio audience of 100 members of the Irish public were selected to attend a TV programme by the Republic of Ireland’s national broadcasting organisation. This involved the examination of the sentencing of a rape case. The audience’s sentencing preferences were measured at the outset, when they had been given only summary information about the case, and later, when full details had been disclosed. Findings – Previous research examining changes in public attitudes to crime and punishment has shown that deliberation, including the provision of new information and discussion with others and experts, tends to decrease public punitiveness and increase public leniency towards sentencing. An experiment in Ireland, however, showed that providing information does not invariably and necessarily moderate punitive attitudes. This paper presents the results, and offers some explanations for the anomalous outcome. Research limitations/implications – The pre/post design, in which the audience served as their own controls, is a weak one, and participants may have responded to what they took to be the agenda of the producers. Due to the quality of the sample, the results may not be generalisable to the broader Irish population. Practical implications – Policy makers should recognise that the public is not uniformly punitive for all crimes. There is good research evidence to show that the apparent public appetite for tough punishment is illusory, and is a function of the way that polls measure public attitudes to punishment. Sentencers and those responsible for sentencing policy would benefit from a fuller understanding of the sorts of cases which illicit strong punitive responses from the public, and the reasons for this response. However any such understanding should not simply translate into responsiveness to the public’s punitive sentiments – where these exist. Innovative survey methods – like this experiment – which attempt to look beyond the top-of-the-head opinions by providing information and opportunities for deliberation should be welcomed and used more widely. Originality/value – There have been limited research studies which reports factors which may increase punitiveness through the provision of information and deliberation.