bluuebunny/crossref_metadata_2025 huggingface dataset:
Language Socialization into Academic Discourse Communities
Authors: Duff Patricia A.
Published: July 2010

Although much has been written about academic discourse from diverse theoretical perspectives over the past two decades, and especially about English academic discourse, research on socialization into academic discourse or literacies in one's first or subsequently learned languages or into new discourse communities has received far less attention. Academic discourse socialization is a dynamic, socially situated process that in contemporary contexts is often multimodal, multilingual, and highly intertextual as well. The process is characterized by variable amounts of modeling, feedback, and uptake; different levels of investment and agency on the part of learners; by the negotiation of power and identities; and, often, important personal transformations for at least some participants. However, the consequences and outcomes of academic discourse socialization are also quite unpredictable, both in the shorter term and longer term. In this review I provide a brief historical overview of research on language socialization into academic communities and describe, in turn, developments in research on socialization into oral, written, and online discourse and the social practices associated with each mode. I highlight issues of conformity or reproduction to local norms and practices versus resistance and contestation of these. Next, studies of socialization into academic publication and into particular textual identities are reviewed. I conclude with a short discussion of race, culture, gender, and academic discourse socialization, pointing out how social positioning by oneself and others can affect participants’ engagement and performance in their various learning communities.
Usage-Based Approaches to Language and Their Applications to Second Language Learning
Authors: Tyler Andrea
Published: July 2010

Over the past 20 years, many in the field of second language learning and pedagogy have become familiar with models of language that emphasize its communicative nature. These models are often referred to as usage-based because they emphasize the notion that actual language use is a primary shaper of linguistic form. Supporters of these models also argue that making meaning, that is, the use to which language is put, is central to how language is configured. Usage-based models share several other underlying assumptions as well. While these usage models have a number of ideas in common, several distinct approaches have emerged. They often use similar terms, such as cognition and metaphor, but the precise interpretations can vary from model to model. The overall result is that without extensive reading, it is not always clear just how these models differ and what unique insights each offer. This article attempts to address this situation by examining three major usage-based models—systemic functional linguistics, discourse functionalism, and cognitive linguistics. First, the common, underlying tenets shared by the three models are discussed. Second, an overview of the unique tenets and concerns of each approach is presented in order to distinguish key differences among them. Within the discussion of each approach, I also discuss various attempts to apply the model to issues in second language learning.
High-frequency spectral analysis of thin periodic acoustic strips: Theory and numerics
Authors: ADAMS S. D. M. , CHEREDNICHENKO K. D. , CRASTER R. V. , GUENNEAU S.
Published: July 2010

This paper is devoted to the study of the asymptotic behaviour of the high-frequency spectrum of the wave equation with periodic coefficients in a ‘thin’ elastic strip Ση=(0, 1)×(−η/2, η/2), η > 0. The main geometric assumption is that the structure period is of the order of magnitude of the strip thickness η and is chosen in such a way that η−1 is a positive large integer. On the boundary ∂Ση, we set Dirichlet (clamped) or Neumann (traction-free) boundary conditions. Aiming to describe sequences of eigenvalues of order η−2 in the above problem, which correspond to oscillations of high frequencies of order η−1, we study an appropriately rescaled limit of the spectrum. Using a suitable notion of two-scale convergence for bounded operators acting on two-scale spaces, we show that the limiting spectrum consists of two parts: the Bloch (or band) spectrum and the ‘boundary’ spectrum. The latter corresponds to sequences of eigenvectors concentrating on the vertical boundaries of Ση, and is characterised by a problem set in a semi-infinite periodic strip with either clamped or stress-free boundary conditions. Based on the observation that some of the related eigenvalues can be found by solving an appropriate periodic-cell problem, we use modal methods to investigate finite-thickness semi-infinite waveguides. We compare our results with those for finite-thickness infinite waveguides given in Adams et al. (Proc. R. Soc. Lond. A, vol. 464, 2008, pp. 2669–2692). We also study infinite-thickness semi-infinite waveguides in order to gain insight into the finite-height analogue. We develop an asymptotic algorithm making use of the unimodular property of the modal method to demonstrate that in the weak contrast limit, and when wavenumber across the guide is fixed, there is at most one surface wave per gap in the spectrum. Using the monomode property of the waveguide we can consider the gap structure for the nth mode, when doing so, for traction-free boundaries, we find exactly one surface wave in each n-band gap.
The Príncipe Thrush Turdus xanthorhynchus: a newly split, ‘Critically Endangered’, forest flagship species
Authors: DALLIMER MARTIN , MELO MARTIM , COLLAR NIGEL J. , JONES PETER J.
Published: July 2010

Recently recognised as specifically distinct, the Príncipe Thrush Turdus xanthorhynchus is endemic to the island of Príncipe in the Gulf of Guinea, West Africa. Formerly treated as conspecific with the more abundant T. olivaceofuscus from the nearby island of São Tomé, the Príncipe Thrush is considered rare and likely to be restricted to primary rainforest. A 2007 survey of Príncipe comprising 177 point transect locations covering 13 sites under different land uses (six in primary forest, three in secondary forest and four in plantations) encountered 18 individuals. Thrushes were found only in primary rainforest, where overall densities were 0.10 birds ha−1, equating to a population size of 435 individuals (95% confidence intervals: 208–913). We adjusted this estimate to take into account the fact that the highest density (0.22 birds ha−1) only occurred above 600 m, giving a final estimated population size of only 364 birds (95% confidence intervals: 186–887). In light of evidence of recent declines, possibly driven by hunting pressure, in the number of mature individuals and the limited area of occurrence of the species, the IUCN Red List category for the Príncipe Thrush should be ‘Critically Endangered’ under both criteria B1a+b(iii and v) and C2a(ii). The recent designation of the primary forests of southern Príncipe as a protected area (Parque Natural d’Obô do Príncipe) provides an opportunity for the conservation of this newly described species, which we recommend is used as a flagship for the forests as a whole.
Real-time qRT-PCR analysis of EGF receptor in cumulus-oocyte complexes recovered by laparoscopy in hormonally treated goats
Authors: Almeida K.C. , Pereira A.F. , Alcântara Neto A.S. , Avelar S.R.G. , Bertolini L.R. , Bertolini M. , Freitas V.J.F. , Melo L.M.
Published: July 2010

Ovarian stimulation with exogenous follicle stimulating hormone (FSH) has been used to increase the number of viable oocytes for laparoscopic oocyte recovery (LOR) in goats. The aim of this study was to evaluate the effect of two FSH protocols for ovarian stimulation in goats on the expression pattern of epidermal growth factor (EGF) receptor (EGFR) in cumulus–oocyte complexes (COCs) recovered by LOR. After real-time qRT-PCR analysis, expression profiles of morphologically graded COCs were compared prior to and afterin vitromaturation (IVM) on a FSH protocol basis. The use of a protocol with higher number of FSH injections at a shorter interval resulted in GI/GII COCs with a higher level of EGFR expression in cumulus cells, but not in the oocyte, which was correlated with an elevated meiotic competence following IVM. Based on the maturation profile and EGFR expression patterns observed between groups, the morphological selection of COCs prior to IVM was not a good predictor of oocyte meiotic competence. Therefore, EGFR may be a good candidate marker for indirect prediction of goat oocyte quality. The IVM process of goat COCs increased the EGFR expression in oocytes and cumulus cells, which seemed to be strongly associated with the resumption of meiosis. In summary, differential EGFR expression in goat cumulus cells was associated with thein vivoprematuration process, and in turn, the upregulation in the entire COC was associated with IVM. Cause-and-effect relationships between such increased expression levels, particularly in the oocyte, and oocyte competence itself still need to be further investigated.
Positive everyday experiences interact with social support to predict depression in multiple sclerosis
Authors: VARGAS GRAY A. , ARNETT PETER A.
Published: July 2010

Both social support and stress predict depression in multiple sclerosis (MS) patients. Little work has been done on the relationship between positive life experiences and depression in this group. Ninety MS patients completed the Social Support Questionnaire (SSQ), the Hassles and Uplifts Scale (HUS), the Chicago Multiscale Depression Inventory (CMDI), and the Affective Reading Span Task (ARST). The Expanded Disability Status Scale (EDSS) was also used. Separate regression analyses were conducted with the EDSS entered at step 1, ARST memory bias score at step 2, SSQ at step 3, either Hassles or Uplifts at step 4, and the interaction term at step 5 to predict depression. Uplifts interacted significantly with social support to predict depression, but hassles did not. After considering disability level, memory bias, and social support and uplifts main effects, the interaction of uplifts and social support accounted for nearly 5% independent variance in depression (p < .05). These results suggest that the absence of uplifts, combined with low levels of social support, is related to depression in MS patients. More generally, these data indicate that it is important to study the absence of positive experiences along with stress and negative experiences in this population. (JINS, 2010, 16, 1039–1046.)
Planetary Trojans – the main source of short period comets?
Authors: Horner J. , Lykawka P. S.
Published: July 2010

One of the key considerations when assessing the potential habitability of telluric worlds will be that of the impact regime experienced by the planet. In this work, we present a short review of our understanding of the impact regime experienced by the terrestrial planets within our own Solar system, describing the three populations of potentially hazardous objects which move on orbits that take them through the inner Solar system. Of these populations, the origins of two (the Near-Earth Asteroids and the Long-Period Comets) are well understood, with members originating in the Asteroid belt and Oort cloud, respectively. By contrast, the source of the third population, the Short-Period Comets, is still under debate. The proximate source of these objects is the Centaurs, a population of dynamically unstable objects that pass perihelion (closest approach to the Sun) between the orbits of Jupiter and Neptune. However, a variety of different origins have been suggested for the Centaur population. Here, we present evidence that at least a significant fraction of the Centaur population can be sourced from the planetary Trojan clouds, stable reservoirs of objects moving in 1:1 mean-motion resonance with the giant planets (primarily Jupiter and Neptune). Focussing on simulations of the Neptunian Trojan population, we show that an ongoing flux of objects should be leaving that region to move on orbits within the Centaur population. With conservative estimates of the flux from the Neptunian Trojan clouds, we show that their contribution to that population could be of order ~3%, while more realistic estimates suggest that the Neptune Trojans could even be the main source of fresh Centaurs. We suggest that further observational work is needed to constrain the contribution made by the Neptune Trojans to the ongoing flux of material to the inner Solar system, and believe that future studies of the habitability of exoplanetary systems should take care not to neglect the contribution of resonant objects (such as planetary Trojans) to the impact flux that could be experienced by potentially habitable worlds.
Haze episodes at Syowa Station, coastal Antarctica: Where did they come from?
Authors: Hara K. , Osada K. , Yabuki M. , Hashida G. , Yamanouchi T. , Hayashi M. , Shiobara M. , Nishita C. , Wada M.
Published: July 2010

During our aerosol measurement program at Syowa Station, Antarctica, in 2004–2007, some low‐visibility (haze) phenomena were observed during winter–spring under conditions with low winds and without drifting snow and fog. During “Antarctic haze” phenomena, the number concentration of aerosol particles and black carbon concentration increased by 1 to 2 orders higher relative to background conditions at Syowa Station, whereas surface O3 concentration dropped simultaneously, especially after polar sunrise. Chemical analysis showed that major aerosol constituents in the haze phenomena were sea salt (e.g., Na+, Cl−). Trajectory analysis and the Navy Aerosol Analysis and Prediction System model showed that plumes from biomass burning in South America and southern Africa were transported to Syowa Station, on the Antarctic coast, because of the eastward (occasionally westward) approach of cyclones in the Southern Ocean and subsequent poleward flow. This poleward flow from midlatitudes of the plume and injection of sea‐salt particles during the transport might engender Antarctic haze phenomena at Syowa Station. Differences of O3 concentration between the background and the haze conditions tended to be larger in spring (after polar sunrise) than in winter. Enhancement of sea‐salt particles in the haze events can serve important roles in providing additional sources of reactive halogen species.
On the spectral dependence of backscatter from cirrus clouds: Assessing CALIOP's 1064 nm calibration assumptions using cloud physics lidar measurements
Authors: Vaughan Mark A. , Liu Zhaoyan , McGill Matthew J. , Hu Yongxiang , Obland Michael D.
Published: July 2010

Recent space‐based lidar missions rely on assumptions about the spectral dependence of the backscatter signals from cirrus clouds to calibrate measurements made at 1064 nm. In particular, the calibration procedure employed by the Cloud Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) mission assumes that the backscatter color ratio, defined as the ratio of particulate backscatter coefficients at 1064 nm and 532 nm, has a value of 1.00, with an expected standard deviation on the order of 0.04. This work assesses the accuracy of this assumption, and its implications for the CALIPSO 1064 nm calibration scheme, using over 400 h of lidar measurements acquired in the northern hemisphere between 2002 and 2007 by the Cloud Physics Lidar (CPL). For the strongly scattering cirrus clouds typically used for CALIPSO calibrations, the uncorrected CPL‐derived backscatter color ratio is 0.83 ± 0.19. Accounting for computational biases introduced by the CPL assumption of pristine air in the calibration region yields a best estimate cirrus cloud color ratio of 1.01 ± 0.25.
Regional climate simulation over Australia's Murray‐Darling basin: A multitemporal assessment
Authors: Evans J. P. , McCabe M. F.
Published: July 2010

The climate of the Murray‐Darling basin (MDB) has been simulated using the Weather Research and Forecasting (WRF) model. WRF was implemented using a 10 km horizontal grid and run for 24 years from 1985 through 2008. The model simulated climate was evaluated against gridded precipitation and temperature observations from the Australian Water Availability Project (AWAP) at daily, monthly, interannual and multiannual time scales. WRF successfully reproduced daily statistics when compared to AWAP observations. It also improves almost all monthly and interannual statistics relative to those of the National Oceanic and Atmospheric Administrations Centers for Environmental Prediction (NCEP)/National Center for Atmospheric Research (NCAR) Reanalysis, which supplied the lateral boundary conditions. WRF simulations were able to capture the drought experienced over the basin in recent years, except for an overestimation of the negative anomaly in the northernmost part of the domain. Examining ENSO cycles showed WRF has good skill at capturing the correct spatial distribution of precipitation anomalies associated with El Niño/La Niña events during this 24 year period. The high‐resolution simulation developed here allows for improved characterization of land‐atmosphere coupling within the basin, including identification of the dominant water vapor source regions for events and seasons and provides insight into the quantification of precipitation recycling.
Early activation of mucosal mast cells during the primary immune response in a rodent model of neonatal asthma
Authors: Liu Shuang , Shudou Masachika , Maeyama Kazutaka
Published: July 2010

During an allergic inflammatory response in the airway, if a failure of the epithelial cell barrier occurs before the systemic immune response is triggered by allergens, more allergens can invade. Using a rat model of asthma, we previously found that mucosal mast cells, which localise to the epithelial layer of the airways, are activated to promote a pro‐asthmatic immune response. In this study, we developed a neonatal rat model of allergic airway hypersensitivity that mimics some features of childhood asthma. Airway hypersensitivity was measured using unrestrained whole‐body plethysmography after analysis of the serum IgE titre. Inflammatory cells and inflammatory mediators in bronchoalveolar lavage fluid samples were examined. Two mast cell‐specific proteases were detected using PCR. In addition, we analysed the phenotype and the number of mast cells in the airways by immunohistochemistry, and we found that the number of mucosal mast cells and the expression level of the proteases increased 2 weeks after sensitisation. Changes in the IgE titre, airway hypersensitivity and the activation of other inflammatory cells were delayed, appearing during the 4 weeks after sensitisation. Our results indicate that the activation of mucosal mast cells contributes to the pro‐asthmatic immune response. This activation may be a biomarker allowing early intervention that could help prevent allergic airway inflammation.
Interaction proteomics: characterization of protein complexes using tandem affinity purification–mass spectrometry
Authors: Völkel Pamela , Le Faou Perrine , Angrand Pierre-Olivier
Published: July 2010

Most cellular processes are carried out by a multitude of proteins that assemble into multimeric complexes. Thus a precise understanding of the biological pathways that control cellular events relies on the identification and on the biochemical characterization of the proteins involved in such multimeric assemblies. Advances in MS have made possible the identification of multisubunit protein complexes isolated from cell lysates with high sensitivity and accuracy, whereas the TAP (tandem affinity purification) methodology efficiently isolates native protein complexes from cells for proteomics analysis. TAP is a generic method based on the sequential utilization of two affinity tags to purify protein assemblies. During the first purification step, the Protein A moiety of the TAP tag is bound to IgG beads, and protein components associated with the TAP-tagged protein are retrieved by TEV (tobacco etch virus) protease cleavage. This enzyme is a sequence-specific protease cleaving a seven-amino-acid recognition site located between the first and second tags. In the second affinity step, the protein complex is immobilized to calmodulin-coated beads via the CBP (calmodulin-binding peptide) of the TAP tag. The CBP–calmodulin interaction is calcium-dependent and calcium-chelating agents are used in the second elution step to release the final protein complex preparation used for protein identification by MS. The TAP–MS approach has proven to efficiently permit the characterization of protein complexes from bacteria, yeast and mammalian cells, as well as from multicellular organisms such as Caenorhabditis elegans, Drosophila and mice.
Single-molecule two-colour coincidence detection to probe biomolecular associations
Authors: Orte Angel , Clarke Richard , Klenerman David
Published: July 2010

Two-colour coincidence detection (TCCD) is a form of single-molecule fluorescence developed to sensitively detect and characterize associated biomolecules without any separation, in solution, on the cell membrane and in live cells. In the present short review, we first explain the principles of the method and then describe the application of TCCD to a range of biomedical problems and how this method may be developed further in the future to try to monitor biological processes in live cells.
Interactions of caeruloplasmin with other proteins participating in inflammation
Authors: Vasilyev Vadim B.
Published: July 2010

The first detailed report of a specific interaction of CP (caeruloplasmin) with another protein described its complex with LF (lactoferrin) in 2000. Since then, several protein–protein interactions involving CP have been reported, mostly concerning iron-containing proteins. The CP–LF complex was studied thoroughly, and evidence of reciprocal effects of CP and LF was obtained. Another specific interaction investigated in detail occurs between CP and MPO (myeloperoxidase). CP–LF, CP–MPO and CP–LF–MPO complexes were found in sera of patients with inflammation. Modelling in vitro allowed understanding of which structural peculiarities of CP and partners allow the modification of their functions in a complex. The present paper reviews the latest data on complexes of CP with LF and MPO, and advances some suggestions about their role in health and disease.
From tau phosphorylation to tau aggregation: what about neuronal death?
Authors: Buée Luc , Troquier Laëtitia , Burnouf Sylvie , Belarbi Karim , Van der Jeugd Anneke , Ahmed Tariq , Fernandez-Gomez Francisco , Caillierez Raphaelle , Grosjean Marie-Eve , Begard Séverine , Barbot Bérangère , Demeyer Dominique , Obriot Hélène , Brion Ingrid , Buée-Scherrer Valérie , Maurage Claude-Alain , Balschun Detlef , D'Hooge Rudi , Hamdane Malika , Blum David , Sergeant Nicolas
Published: July 2010

Tau pathology is characterized by intracellular aggregates of abnormally and hyperphosphorylated tau proteins. It is encountered in many neurodegenerative disorders, but also in aging. These neurodegenerative disorders are referred to as tauopathies. Comparative biochemistry of the tau aggregates shows that they differ in both tau isoform phosphorylation and content, which enables a molecular classification of tauopathies. In conditions of dementia, NFD (neurofibrillary degeneration) severity is correlated to cognitive impairment and is often considered as neuronal death. Using tau animal models, analysis of the kinetics of tau phosphorylation, aggregation and neuronal death in parallel to electrophysiological and behavioural parameters indicates a disconnection between cognition deficits and neuronal cell death. Tau phosphorylation and aggregation are early events followed by cognitive impairment. Neuronal death is not observed before the oldest ages. A sequence of events may be the formation of toxic phosphorylated tau species, their aggregation, the formation of neurofibrillary tangles (from pre-tangles to ghost tangles) and finally neuronal cell death. This sequence will last from 15 to 25 years and one can ask whether the aggregation of toxic phosphorylated tau species is a protection against cell death. Apoptosis takes 24 h, but NFD lasts for 24 years to finally kill the neuron or rather to protect it for more than 20 years. Altogether, these data suggest that NFD is a transient state before neuronal death and that therapeutic interventions are possible at that stage.
Human pluripotent stem cells in drug discovery and predictive toxicology
Authors: Laustriat Delphine , Gide Jacqueline , Peschanski Marc
Published: July 2010

Human pluripotent stem cells are a biological resource most commonly considered for their potential in cell therapy or, as it is now called, ‘regenerative medicine’. However, in the near future, their most important application for human health may well be totally different, as they are more and more envisioned as opening new routes for pharmacological research. Pluripotent stem cells indeed possess the main attributes that make them theoretically fully equipped for the development of cell-based assays in the fields of drug discovery and predictive toxicology. These cells are characterized by: (i) an unlimited self-renewal capacity, which make them an inexhaustible source of cells; (ii) the potential to differentiate into any cell phenotype of the body at any stage of differentiation, with probably the notable exception, however, of the most mature forms of many lineages; and (iii) the ability to express genotypes of interest via the selection of donors, whether they be of embryonic origin, through pre-implantation genetic diagnosis, or adults, by genetic reprogramming of somatic cells, so-called iPSCs (induced pluripotent stem cells). In the present review, we provide diverse illustrations of the use of pluripotent stem cells in drug discovery and predictive toxicology, using either human embryonic stem cell lines or iPSC lines.
Alternative polyadenylation of antisense RNAs and flowering time control
Authors: Hornyik Csaba , Duc Céline , Rataj Katarzyna , Terzi Lionel C. , Simpson Gordon G.
Published: July 2010

Flowering time is controlled by precision in gene regulation mediated by different pathways. Two Arabidopsis thaliana components of the autonomous flowering pathway, FCA and FPA, function as genetically independent trans-acting regulators of alternative cleavage and polyadenylation. FCA and FPA directly associate with chromatin at the locus encoding the floral repressor FLC, but appear to control FLC transcription by mediating alternative polyadenylation of embedded non-coding antisense RNAs. These findings prompt the re-examination of how other factors control FLC expression, as it is formally possible that they function primarily to control alternative processing of antisense RNAs. As co-expressed sense and antisense gene pairs are widespread in eukaryotes, alternative processing of antisense RNAs may represent a significant form of gene regulation.
Rrp47 and the function of the Sas10/C1D domain
Authors: Mitchell Phil
Published: July 2010

The Sas10/C1D domain is found in a small group of eukaryotic proteins that have functions in RNA processing events, translational control and DNA repair mechanisms. The domain is predicted to be α-helical in nature and comprises approx. 80 amino acid residues. Whereas the Sas10/C1D domain has yet to be functionally characterized, available results suggest that this domain forms a binding surface for specific interactions with other proteins and can concomitantly interact with RNA or DNA. This property of the Sas10/C1D domain may facilitate this family of proteins to dock other proteins on to nucleic acid substrates.
The function of the NineTeen Complex (NTC) in regulating spliceosome conformations and fidelity during pre-mRNA splicing
Authors: Hogg Rebecca , McGrail Joanne C. , O'Keefe Raymond T.
Published: July 2010

The NineTeen Complex (NTC) of proteins associates with the spliceosome during pre-mRNA splicing and is essential for both steps of intron removal. The NTC and other NTC-associated proteins are recruited to the spliceosome where they participate in regulating the formation and progression of essential spliceosome conformations required for the two steps of splicing. It is now clear that the NTC is an integral component of active spliceosomes from yeast to humans and provides essential support for the spliceosomal snRNPs (small nuclear ribonucleoproteins). In the present article, we discuss the identification and characterization of the yeast NTC and review recent work in yeast that supports the essential role for this complex in the regulation and fidelity of splicing.
Midfacial Reconstruction and Radiation: Case Report and Review of the Literature
Authors: Evans Gregory R.D. , Salibian Ara , Scholz Thomas
Published: July 2010

Midfacial radiation-induced defects usually involve the bony structures and require composite reconstruction. A 36-year-old male patient with a midfacial defect due to radiation and failure of local flaps was referred to us and treated successfully with a microvascular flap. This case is reported in correspondence with a literature review of the classification of midfacial defects, choice of treatments, and outcomes of different reconstructive options. The deleterious effects of radiation on tissue healing and the functional and aesthetic outcome of reconstruction are discussed. Midfacial defects that are refractory to treatment with local flaps are best treated with microvascular free tissue transfer.
Managing the Difficult Airway in Craniomaxillofacial Trauma
Authors: Lock Richard
Published: July 2010

Securing the airway in the patient with craniomaxillofacial trauma can be an extremely difficult challenge for health care practitioners. This article provides several approaches to airway management. Presented here are several options for securing the airway under a variety of conditions and scenarios.
‘Vertebrating’ the Region as Networked Space of Flows: Learning from the Spatial Grammar of Catalanist Territoriality
Authors: Prytherch David L
Published: July 2010

For decades theoretical debates about political restructuring have resorted to and coconstructed geographical concepts of territory and scale, interpreting ‘new’ and ‘Euro’ regionalisms as processes of reterritorialization and rescaling (and the politics thereof). But nested and hierarchical theories of scale have been severely critiqued, and bounded notions of territory opened to question. How then to develop a more relational understanding of the region without trading one limiting theoretical master narrative for another? Drawing inspiration from recent attempts to do just this, in this paper I ask: what can we learn about the complex and relational spatiality of the region, and thus scale and territory, through the spatial vocabularies of regionalists themselves? Using the case study of the Northwestern Mediterranean, I explore the imaginaries and stratagems of Catalan regionalism and transboundary macroregionalism, particularly in the neighboring regions of Catalunya and the Comunitat Valenciana and their proposed integration in a Euroregion called the Arc Mediterrani. While Catalanists increasingly emphasize networked economic relationships and flows, they do so within a structured, territorial, and in many ways bounded understanding of Mediterranean spatial relations. How Catalanists vertebrar territori (articulate or structurate territory, in Catalan) offers an alternative spatial grammar for thinking about how various spatialities—including network and geographical scale—are distinct yet co-implicated in the social production of regional and macroregional territory.
Transecting Security and Space in Maputo
Authors: Paasche Till F , Sidaway James D
Published: July 2010

Over the past four decades, the Mozambican capital city of Maputo has undergone rapid changes. Although still governed by the (formerly socialist) party that inherited the city from a collapsing Portuguese colonial state in 1975, postsocialist Maputo recasts disparities in class and power. This paper negotiates these fractures, based on two walking transects through the central areas of the city conducted by the coauthors. Initially informed by ‘psychogeography’ literatures on negotiating and representing cities, these were supplemented by and enacted through a focus on security and policing. While the state uses police to secure vital interests, other sites and spaces experience limited policing. To bridge this security gap, commercial and ad hoc security providers are contracted to secure private homes and enterprises. We describe an increased and uneven commoditisation of security. The security landscape of central Maputo thus comprises a complex patchwork of privately secured micro enclaves that relay and rework enclaving on larger scales.
Beta toxin catalyzes formation of nucleoprotein matrix in staphylococcal biofilms
Authors: Huseby Medora J. , Kruse Andrew C. , Digre Jeff , Kohler Petra L. , Vocke Jillian A. , Mann Ethan E. , Bayles Kenneth W. , Bohach Gregory A. , Schlievert Patrick M. , Ohlendorf Douglas H. , Earhart Cathleen A.
Published: July 2010

Biofilms are surface-associated communities of microbes encompassed by an extracellular matrix. It is estimated that 80% of all bacterial infections involve biofilm formation, but the structure and regulation of biofilms are incompletely understood. Extracellular DNA (eDNA) is a major structural component in many biofilms of the pathogenic bacterium
Staphylococcus aureus
, but its role is enigmatic. Here, we demonstrate that beta toxin, a neutral sphingomyelinase and a virulence factor of
S. aureus
, forms covalent cross-links to itself in the presence of DNA (we refer to this as biofilm ligase activity, independent of sphingomyelinase activity) producing an insoluble nucleoprotein matrix in vitro. Furthermore, we show that beta toxin strongly stimulates biofilm formation in vivo as demonstrated by a role in causation of infectious endocarditis in a rabbit model. Together, these results suggest that beta toxin cross-linking in the presence of eDNA assists in forming the skeletal framework upon which staphylococcal biofilms are established.
Bone marrow transplantation restores epidermal basement membrane protein expression and rescues epidermolysis bullosa model mice
Authors: Fujita Yasuyuki , Abe Riichiro , Inokuma Daisuke , Sasaki Mikako , Hoshina Daichi , Natsuga Ken , Nishie Wataru , McMillan James R. , Nakamura Hideki , Shimizu Tadamichi , Akiyama Masashi , Sawamura Daisuke , Shimizu Hiroshi
Published: July 2010

Attempts to treat congenital protein deficiencies using bone marrow-derived cells have been reported. These efforts have been based on the concepts of stem cell plasticity. However, it is considered more difficult to restore structural proteins than to restore secretory enzymes. This study aims to clarify whether bone marrow transplantation (BMT) treatment can rescue epidermolysis bullosa (EB) caused by defects in keratinocyte structural proteins. BMT treatment of adult collagen XVII (Col17) knockout mice induced donor-derived keratinocytes and Col17 expression associated with the recovery of hemidesmosomal structure and better skin manifestations, as well improving the survival rate. Both hematopoietic and mesenchymal stem cells have the potential to produce Col17 in the BMT treatment model. Furthermore, human cord blood CD34
+
cells also differentiated into keratinocytes and expressed human skin component proteins in transplanted immunocompromised (NOD/SCID/γ
c
null
) mice. The current conventional BMT techniques have significant potential as a systemic therapeutic approach for the treatment of human EB.
Autophagy inhibition and antimalarials promote cell death in gastrointestinal stromal tumor (GIST)
Authors: Gupta Anu , Roy Srirupa , Lazar Alexander J. F. , Wang Wei-Lien , McAuliffe John C. , Reynoso David , McMahon James , Taguchi Takahiro , Floris Giuseppe , Debiec-Rychter Maria , Schőffski Patrick , Trent Jonathan A. , Debnath Jayanta , Rubin Brian P.
Published: July 2010

Although gastrointestinal stromal tumors (GISTs) harboring activating
KIT
or platelet-derived growth factor receptor A (
PDGFRA
) mutations respond to treatment with targeted KIT/PDGFRA inhibitors such as imatinib mesylate, these treatments are rarely curative. Most often, a sizeable tumor cell subpopulation survives and remains quiescent for years, eventually resulting in acquired resistance and treatment failure. Here, we report that imatinib induces autophagy as a survival pathway in quiescent GIST cells. Inhibiting autophagy, using RNAi-mediated silencing of autophagy regulators (ATGs) or antimalarial lysosomotrophic agents, promotes the death of GIST cells both in vitro and in vivo. Thus, combining imatinib with autophagy inhibition represents a potentially valuable strategy to promote GIST cytotoxicity and to diminish both cellular quiescence and acquired resistance in GIST patients.
Identification of a third variable lymphocyte receptor in the lamprey
Authors: Kasamatsu Jun , Sutoh Yoichi , Fugo Kazunori , Otsuka Noriyuki , Iwabuchi Kazuya , Kasahara Masanori
Published: July 2010

Jawless vertebrates such as lamprey and hagfish lack T-cell and B-cell receptors; instead, they have unique antigen receptors known as variable lymphocyte receptors (VLRs). VLRs generate diversity by recombining highly diverse leucine-rich repeat modules and are expressed clonally on lymphocyte-like cells (LLCs). Thus far, two types of receptors, VLRA and VLRB, have been identified in lampreys and hagfish. Recent evidence indicates that VLRA and VLRB are expressed on distinct populations of LLCs that resemble T cells and B cells of jawed vertebrates, respectively. Here we identified a third VLR, designated VLRC, in the lamprey. None of the ≈100 VLRC cDNA clones subjected to sequencing had an identical sequence, indicating thatVLRCcan generate sufficient diversity to function as antigen receptors. Notably, the C-terminal cap of VLRC exhibits only limited diversity and has important structural differences relative to VLRA and VLRB. Single-cell PCR analysis identified LLCs that rearrangedVLRCbut notVLRAorVLRB, suggesting the presence of a unique population of LLCs that express only VLRC.
Inducible response required for repair of low-dose radiation damage in human fibroblasts
Authors: Grudzenski Saskia , Raths Antonia , Conrad Sandro , Rübe Claudia E. , Löbrich Markus
Published: July 2010

Ionizing radiation (IR) induces a variety of DNA lesions among which DNA double-strand breaks (DSBs) are the biologically most significant. It is currently unclear if DSB repair is equally efficient after low and high doses. Here, we use γ-H2AX, phospho-ATM (pATM), and 53BP1 foci analysis to monitor DSB repair. We show, consistent with a previous study, that the kinetics of γ-H2AX and pATM foci loss in confluent primary human fibroblasts are substantially compromised after doses of 10 mGy and lower. Following 2.5 mGy, cells fail to show any foci loss. Strikingly, cells pretreated with 10 μM H
2
O
2
efficiently remove all γ-H2AX foci induced by 10 mGy. At the concentration used, H
2
O
2
produces single-strand breaks and base damages via the generation of oxygen radicals but no DSBs. Moreover, 10 μM H
2
O
2
up-regulates a set of genes that is also up-regulated after high (200 mGy) but not after low (10 mGy) radiation doses. This suggests that low radical levels induce a response that is required for the repair of radiation-induced DSBs when the radiation damage is too low to cause the induction itself. To address the in vivo significance of this finding, we established γ-H2AX and 53BP1 foci analysis in various mouse tissues. Although mice irradiated with 100 mGy or 1 Gy show efficient γ-H2AX and 53BP1 foci removal during 24 h post-IR, barely any foci loss was observed after 10 mGy. Our data suggest that the cellular response to DSBs is substantially different for low vs. high radiation doses.
Stereotype threat prevents perceptual learning
Authors: Rydell Robert J. , Shiffrin Richard M. , Boucher Kathryn L. , Van Loo Katie , Rydell Michael T.
Published: July 2010

Stereotype threat (ST) refers to a situation in which a member of a group fears that her or his performance will validate an existing negative performance stereotype, causing a decrease in performance. For example, reminding women of the stereotype “women are bad at math” causes them to perform more poorly on math questions from the SAT and GRE. Performance deficits can be of several types and be produced by several mechanisms. We show that ST prevents perceptual learning, defined in our task as an increasing rate of search for a target Chinese character in a display of such characters. Displays contained two or four characters and half of these contained a target. Search rate increased across a session of training for a control group of women, but not women under ST. Speeding of search is typically explained in terms of learned “popout” (automatic attraction of attention to a target). Did women under ST learn popout but fail to express it? Following training, the women were shown two colored squares and asked to choose the one with the greater color saturation. Superimposed on the squares were task-irrelevant Chinese characters. For women not trained under ST, the presence of a trained target on one square slowed responding, indicating that training had caused the learning of an attention response to targets. Women trained under ST showed no slowing, indicating that they had not learned such an attention response.
Neural mechanisms of observational learning
Authors: Burke Christopher J. , Tobler Philippe N. , Baddeley Michelle , Schultz Wolfram
Published: July 2010

Individuals can learn by interacting with the environment and experiencing a difference between predicted and obtained outcomes (prediction error). However, many species also learn by observing the actions and outcomes of others. In contrast to individual learning, observational learning cannot be based on directly experienced outcome prediction errors. Accordingly, the behavioral and neural mechanisms of learning through observation remain elusive. Here we propose that human observational learning can be explained by two previously uncharacterized forms of prediction error, observational action prediction errors (the actual minus the predicted choice of others) and observational outcome prediction errors (the actual minus predicted outcome received by others). In a functional MRI experiment, we found that brain activity in the dorsolateral prefrontal cortex and the ventromedial prefrontal cortex respectively corresponded to these two distinct observational learning signals.
Investigation of protein conformation and interactions with salts via X-ray absorption spectroscopy
Authors: Schwartz Craig P. , Uejio Janel S. , Duffin Andrew M. , England Alice H. , Kelly Daniel N. , Prendergast David , Saykally Richard J.
Published: July 2010

Nitrogen K-edge spectra of aqueous triglycine were measured using liquid microjets, and the effects of Hofmeister-active salts on the spectra were observed. Spectra simulated using density functional theory, sampled from room temperature classical molecular dynamics trajectories, capture all major features in the measured spectra. The spectrum of triglycine in water is quite similar to that in the presence of chaotropic sodium bromide (and other halides), which raises the solubility of proteins. However, a new feature is found when kosmotropic Na
2
SO
3
, which lowers solubility, is present; this feature results from excitations of the nitrogen atom in the terminal amino group of triglycine. Both direct interactions between this salt and the protonated amino terminus, as well as corresponding changes in the conformational dynamics of the system, contribute to this new feature. These molecular measurements support a different mechanism for the Hofmeister effect than has previously been suggested based on thermodynamic measurements. It is also shown that near edge X-ray absorption fine structure (NEXAFS) is sensitive to strong direct interaction between certain salts and charged peptides. However, by investigating the sensitivity of NEXAFS to the extreme structural differences between model β-sheets and α-helices, we conclude that this technique is relatively insensitive to secondary structure of peptides and proteins.
Gene cooption and convergent evolution of oxygen transport hemoglobins in jawed and jawless vertebrates
Authors: Hoffmann Federico G. , Opazo Juan C. , Storz Jay F.
Published: July 2010

Natural selection often promotes evolutionary innovation by coopting preexisting genes for new functions, and this process may be greatly facilitated by gene duplication. Here we report an example of cooptive convergence where paralogous members of the globin gene superfamily independently evolved a specialized O2transport function in the two deepest branches of the vertebrate family tree. Specifically, phylogenetic evidence demonstrates that erythroid-specific O2transport hemoglobins evolved independently from different ancestral precursor proteins in jawed vertebrates (gnathostomes) and jawless fish (cyclostomes, represented by lamprey and hagfish). A comprehensive phylogenetic analysis of the vertebrate globin gene superfamily revealed that the erythroid hemoglobins of cyclostomes are orthologous to the cytoglobin protein of gnathostome vertebrates, a hexacoordinate globin that has no O2transport function and that is predominantly expressed in fibroblasts and related cell types. The phylogeny reconstruction also revealed that vertebrate-specific globins are grouped into four main clades: (i) cyclostome hemoglobin + cytoglobin, (ii) myoglobin + globin E, (iii) globin Y, and (iv) the α- and β-chain hemoglobins of gnathostomes. In the hemoglobins of gnathostomes and cyclostomes, multisubunit quaternary structures provide the basis for cooperative O2binding and allosteric regulation by coupling the effects of ligand binding at individual subunits with interactions between subunits. However, differences in numerous structural details belie their independent origins. This example of convergent evolution of protein function provides an impressive demonstration of the ability of natural selection to cobble together complex design solutions by tinkering with different variations of the same basic protein scaffold.
Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain
Authors: Brannigan Grace , LeBard David N. , Hénin Jérôme , Eckenhoff Roderic G. , Klein Michael L.
Published: July 2010

An extensive search for isoflurane binding sites in the nicotinic acetylcholine receptor (nAChR) and the proton gated ion channel fromGloebacter violaceus(GLIC) has been carried out based on molecular dynamics (MD) simulations in fully hydrated lipid membrane environments. Isoflurane introduced into the aqueous phase readily partitions into the lipid membrane and the membrane-bound protein. Specifically, isoflurane binds persistently to three classes of sites in the nAChR transmembrane domain: (i) An isoflurane dimer occludes the pore, contacting residues identified by previous mutagenesis studies; analogous behavior is observed in GLIC. (ii) Several nAChR subunit interfaces are also occupied, in a site suggested by photoaffinity labeling and thought to positively modulate the receptor; these sites are not occupied in GLIC. (iii) Isoflurane binds to the subunit centers of both nAChR α chains and one of the GLIC chains, in a site that has had little experimental targeting. Interpreted in the context of existing structural and physiological data, the present MD results support a multisite model for the mechanism of receptor-channel modulation by anesthetics.