bluuebunny/crossref_metadata_2025_split huggingface dataset:
The U4 Antibody Epitope on Human Papillomavirus 16 Identified by Cryo-electron Microscopy
Authors: Guan Jian , Bywaters Stephanie M. , Brendle Sarah A. , Lee Hyunwook , Ashley Robert E. , Christensen Neil D. , Hafenstein Susan 
Published: September 2015

ABSTRACT
The human papillomavirus (HPV) major structural protein L1 composes capsomers that are linked together through interactions mediated by the L1 C terminus to constitute a T=7 icosahedral capsid. H16.U4 is a type-specific monoclonal antibody recognizing a conformation-dependent neutralizing epitope of HPV thought to include the L1 protein C terminus. The structure of human papillomavirus 16 (HPV16) complexed with H16.U4 fragments of antibody (Fab) was solved by cryo-electron microscopy (cryo-EM) image reconstruction. Atomic structures of virus and Fab were fitted into the corresponding cryo-EM densities to identify the antigenic epitope. The antibody footprint mapped predominately to the L1 C-terminal arm with an additional contact point on the side of the capsomer. This footprint describes an epitope that is presented capsid-wide. However, although the H16.U4 epitope suggests the presence of 360 potential binding sites exposed in the capsid valley between each capsomer, H16.U4 Fab bound only to epitopes located around the icosahedral five-fold vertex of the capsid. Thus, the binding characteristics of H16.U4 defined in this study showed a distinctive selectivity for local conformation-dependent interactions with specific L1 invading arms between five-fold related capsomers.

IMPORTANCE
Human papillomavirus 16 (HPV16) is the most prevalent oncogenic genotype in HPV-associated anogenital and oral cancers. Here we use cryo-EM reconstruction techniques to solve the structures of the HPV16 capsid complexes using H16.U4 fragment of antibody (Fab). Different from most other antibodies directed against surface loops, H16.U4 monoclonal antibody is unique in targeting the C-terminal arm of the L1 protein. This monoclonal antibody (MAb) is used throughout the HPV research community in HPV serological and vaccine development and to define mechanisms of HPV uptake. The unique binding mode of H16.U4 defined here shows important conformation-dependent interactions within the HPV16 capsid. By targeting an important structural and conformational epitope, H16.U4 may identify subtle conformational changes in different maturation stages of the HPV capsid and provide a key probe to analyze the mechanisms of HPV uptake during the early stages of virus infection. Our analyses precisely define important conformational epitopes on HPV16 capsids that are key targets for successful HPV prophylactic vaccines.
Vpr Enhances Tumor Necrosis Factor Production by HIV-1-Infected T Cells
Authors: Roesch Ferdinand , Richard Léa , Rua Réjane , Porrot Françoise , Casartelli Nicoletta , Schwartz Olivier 
Published: September 2015

ABSTRACTThe HIV-1 accessory protein Vpr displays different activities potentially impacting viral replication, including the arrest of the cell cycle in the G2phase and the stimulation of apoptosis and DNA damage response pathways. Vpr also modulates cytokine production by infected cells, but this property remains partly characterized. Here, we investigated the effect of Vpr on the production of the proinflammatory cytokine tumor necrosis factor (TNF). We report that Vpr significantly increases TNF secretion by infected lymphocytes.De novoproduction of Vpr is required for this effect. Vpr mutants known to be defective for G2cell cycle arrest induce lower levels of TNF secretion, suggesting a link between these two functions. Silencing experiments and the use of chemical inhibitors further implicated the cellular proteins DDB1 and TAK1 in this activity of Vpr. TNF secreted by HIV-1-infected cells triggers NF-κB activity in bystander cells and allows viral reactivation in a model of latently infected cells. Thus, the stimulation of the proinflammatory pathway by Vpr may impact HIV-1 replicationin vivo.IMPORTANCEThe role of the HIV-1 accessory protein Vpr remains only partially characterized. This protein is important for viral pathogenesis in infected individuals but is dispensable for viral replication in most cell culture systems. Some of the functions described for Vpr remain controversial. In particular, it remains unclear whether Vpr promotes or instead prevents proinflammatory and antiviral immune responses. In this report, we show that Vpr promotes the release of TNF, a proinflammatory cytokine associated with rapid disease progression. Using Vpr mutants or inhibiting selected cellular genes, we show that the cellular proteins DDB1 and TAK1 are involved in the release of TNF by HIV-infected cells. This report provides novel insights into how Vpr manipulates TNF production and helps clarify the role of Vpr in innate immune responses and inflammation.
The Lower Old Red Sandstone at Balmaha–Aberfoyle and its bearing on the nature of the Highland Boundary and Gualann Faults
Authors: Bluck B. J. 
Published: September 2015

The final stages of the emplacement of the Dalradian block into Scotland are recorded in the Old Red Sandstone rocks that lie faulted against the main Dalradian belt. In the case of the Balmaha–Queen Elizabeth Forest sequence this involves the Gualann Fault, a splay of the Highland Boundary Fault, which transects
c
. 6.5 km of Lower Old Red Sandstone conglomerates and sandstones between Balmaha and Aberfoyle. A sequence of coarse conglomerates at Balmaha, near the top of the succession, derived from the SE, was deposited unconformably on the Highland Border Complex. This conglomerate has been studied in detail and the sequence is interpreted as an oblique section through an alluvial fan. Fitting the average dimensions of other alluvial fans to the unfolded cross-section suggests that it once extended some 5 km to the north, over the position of the Dalradian block. The conglomerate–sandstone sequence beneath was also deposited in alluvial fans that accumulated in a strike-slip, extensional basin in which units of conglomerate become progressively younger to the SW. Immediately NW of the Gualann Fault, in the Queen Elizabeth Forest, sub-horizontal red sandstones and breccias rest unconformably on the Highland Border Complex and were probably deposited beyond the reach of the coarse conglomerates.

It is suggested that the Gualann Fault was initially a very low-angle or flat thrust, which was rotated in mid-Devonian times during the development of the steep NW limb of the Strathmore Syncline. It brought sub-horizontal breccias and sandstones, originally deposited 10–15 km to the NW, well out of the influence of the conglomerates on the SE side of the fault, into juxtaposition with folded coarse conglomerates south of the Fault. As the Gualann Fault is a splay of the Highland Boundary Fault this implies that the latter may also be a thrust that brought the Dalradian block over the Highland Border rocks.
The whole sequence, from Balmaha to the Queen Elizabeth Forest, reflects the unroofing of an existing source of conglomerates to eventually erode their quartzite basement. The Highland Boundary Fault, although a fairly straight and prominent feature to the NE, becomes displaced and difficult to follow in the area to the SW where it is accompanied by many splays trending roughly N–S. The area, in and around the Firth of Clyde, has been regarded as the product of a locked phase of the fault movement that produced an extensional basin in Upper Old Red Sandstone times, but is also likely to have generated the more northern basins seen here.
There are a few records of conglomerates and associated rocks cut by the Highland Boundary Fault to the NE, suggesting that Old Red Sandstone basins extended well beyond the present Highland Boundary Fault. These basins may also have relevance to the timing of the incoming of the Dalradian block, absent from Scotland during earlier periods.
Sensitivity to Referential Ambiguity in Discourse: The Role of Attention, Working Memory, and Verbal Ability
Authors: Boudewyn Megan A. , Long Debra L. , Traxler Matthew J. , Lesh Tyler A. , Dave Shruti , Mangun George R. , Carter Cameron S. , Swaab Tamara Y. 
Published: September 2015

Abstract
The establishment of reference is essential to language comprehension. The goal of this study was to examine listeners' sensitivity to referential ambiguity as a function of individual variation in attention, working memory capacity, and verbal ability. Participants listened to stories in which two entities were introduced that were either very similar (e.g., two oaks) or less similar (e.g., one oak and one elm). The manipulation rendered an anaphor in a subsequent sentence (e.g., oak) ambiguous or unambiguous. EEG was recorded as listeners comprehended the story, after which participants completed tasks to assess working memory, verbal ability, and the ability to use context in task performance. Power in the alpha and theta frequency bands when listeners received critical information about the discourse entities (e.g., oaks) was used to index attention and the involvement of the working memory system in processing the entities. These measures were then used to predict an ERP component that is sensitive to referential ambiguity, the Nref, which was recorded when listeners received the anaphor. Nref amplitude at the anaphor was predicted by alpha power during the earlier critical sentence: Individuals with increased alpha power in ambiguous compared with unambiguous stories were less sensitive to the anaphor's ambiguity. Verbal ability was also predictive of greater sensitivity to referential ambiguity. Finally, increased theta power in the ambiguous compared with unambiguous condition was associated with higher working-memory span. These results highlight the role of attention and working memory in referential processing during listening comprehension.
Sustained Splits of Attention within versus across Visual Hemifields Produce Distinct Spatial Gain Profiles
Authors: Walter Sabrina , Keitel Christian , Müller Matthias M. 
Published: September 2015

Abstract
Visual attention can be focused concurrently on two stimuli at noncontiguous locations while intermediate stimuli remain ignored. Nevertheless, behavioral performance in multifocal attention tasks falters when attended stimuli fall within one visual hemifield as opposed to when they are distributed across left and right hemifields. This “different-hemifield advantage” has been ascribed to largely independent processing capacities of each cerebral hemisphere in early visual cortices. Here, we investigated how this advantage influences the sustained division of spatial attention. We presented six isoeccentric light-emitting diodes (LEDs) in the lower visual field, each flickering at a different frequency. Participants attended to two LEDs that were spatially separated by an intermediate LED and responded to synchronous events at to-be-attended LEDs. Task-relevant pairs of LEDs were either located in the same hemifield (“within-hemifield” conditions) or separated by the vertical meridian (“across-hemifield” conditions). Flicker-driven brain oscillations, steady-state visual evoked potentials (SSVEPs), indexed the allocation of attention to individual LEDs. Both behavioral performance and SSVEPs indicated enhanced processing of attended LED pairs during “across-hemifield” relative to “within-hemifield” conditions. Moreover, SSVEPs demonstrated effective filtering of intermediate stimuli in “across-hemifield” condition only. Thus, despite identical physical distances between LEDs of attended pairs, the spatial profiles of gain effects differed profoundly between “across-hemifield” and “within-hemifield” conditions. These findings corroborate that early cortical visual processing stages rely on hemisphere-specific processing capacities and highlight their limiting role in the concurrent allocation of visual attention to multiple locations.
Globalization and Layered Spaces: The Case of Hitec City in Hyderabad, India
Authors: Sam Jillet Sarah 
Published: September 2015

AbstractIn this essay, the area of Hitec City in Hyderabad, India, is analysed through the metaphor of “layered” spaces, in the context of global flows, particularly grobalization—the imperialistic imposition by nation-states and organizations on various geographic areas, involving the transnational expansion of common codes and practices. A layered space refers to multiple layers of actors who share the same space, although not all of them are equally prioritized in its conceptualization. Through a theoretically informed reading of Hitec City, this study highlights spatial polarization in the landscape, where certain actors, theglobal non-persons, are rendered as invisible as possible, so that they do not interfere with a specific global image, thegrobal-as-spectacle, projected through the medium of the landscape. This study draws heavily on the spatial form of Hitec City as a source of data. It is based on observation of this space through detailed mapping, as well as a descriptive analysis of the built forms in the area. While stratification and exclusion are not unique to globalization (or even to the process of grobalization), this study helps to examine particular forms that exclusion and stratification may take in the light of this process.
Observational Evidence of Frontal-Scale Atmospheric Responses to Kuroshio Extension Variability
Authors: Wang Yi-Hui , Liu W. Timothy 
Published: September 2015

Abstract
This study investigates the regional atmospheric response to the Kuroshio Extension (KE) using a combination of multiple satellite observations and reanalysis data from boreal winter over a period of at least a decade. The goal is to understand the relationship between KE variations and atmospheric responses at low frequencies. A climate index is used to measure the interannual to decadal KE variability, which leaves remarkable imprints on the mesoscale sea surface temperature (SST). Clear spatial coherence between the SST signals and frontal-scale atmospheric variables, including surface wind convergence, vertical velocity, precipitation, and clouds, is identified by linear regression analysis. Consistent with previous studies, the penetrating effect of the KE variability on the free atmosphere is found. The westward tilt of the atmospheric response above the KE near 500 hPa is revealed. The difference in the associations of frontal-scale air temperature and geopotential height with the KE variability between the satellite observations and the reanalysis data suggests an imperfect interpretation of frontal-scale oceanic forcing on the overlying atmosphere in the reanalysis assimilation system.
Dynamical Downscaling–Based Projections of Great Lakes Water Levels*+
Authors: Notaro Michael , Bennington Val , Lofgren Brent 
Published: September 2015

Abstract
Projections of regional climate, net basin supply (NBS), and water levels are developed for the mid- and late twenty-first century across the Laurentian Great Lakes basin. Two state-of-the-art global climate models (GCMs) are dynamically downscaled using a regional climate model (RCM) interactively coupled to a one-dimensional lake model, and then a hydrologic routing model is forced with time series of perturbed NBS. The dynamical downscaling and coupling with a lake model to represent the Great Lakes create added value beyond the parent GCM in terms of simulated seasonal cycles of temperature, precipitation, and surface fluxes. However, limitations related to this rudimentary treatment of the Great Lakes result in warm summer biases in lake temperatures, excessive ice cover, and an abnormally early peak in lake evaporation. While the downscaling of both GCMs led to consistent projections of increases in annual air temperature, precipitation, and all NBS components (overlake precipitation, basinwide runoff, and lake evaporation), the resulting projected water level trends are opposite in sign. Clearly, it is not sufficient to correctly simulate the signs of the projected change in each NBS component; one must also account for their relative magnitudes. The potential risk of more frequent episodes of lake levels below the low water datum, a critical shipping threshold, is explored.
Predictors of rapid reincarceration in mentally ill young offenders
Authors: Kasinathan John 
Published: September 2015

Objective: Describe characteristics of mentally ill young offenders released from custody and predictors of those who rapidly returned to custody. Method: Ambidirectional cohort study of 51 young males with mental disorders released from the largest New South Wales Juvenile Justice Centre (2005–2007), a health file audit at time of release and prospective determination of reincarceration. Results: Overall 47% were Aboriginal, 43% originated from regional communities, substance disorders were highly prevalent and only 12% accessed prior community mental health care. Over half (57%) satisfied diagnostic criteria for schizophrenia spectrum disorder. In custody, 39% were suicidal and 18% were homicidal. A majority (90%) returned to custody over a median of 28 months; half within five months of release. Schizophrenia/schizophreniform disorder ( p<.001), bipolar disorder ( p=.001) and schizoaffective disorder ( p=.005) predicted rapid reincarceration, with shorter community survival than those without those diagnoses ( p=.009). Antipsychotic treatment ( p=.006) and treatment duration in custody ( p=.006) predicted longer community survival. Aboriginality, younger age, prior incarceration and substance disorders were not predictive of rapid reincarceration. Conclusions: Serious mental illness was a significant predictor of rapid reincarceration in young offenders. Treatment improved community survival. The findings highlight the need for optimal psychiatric treatment and post-release care for young offenders with mental illness.
ATM deficiency promotes development of murine B-cell lymphomas that resemble diffuse large B-cell lymphoma in humans
Authors: Hathcock Karen S. , Padilla-Nash Hesed M. , Camps Jordi , Shin Dong-Mi , Triner Daniel , Shaffer Arthur L. , Maul Robert W. , Steinberg Seth M. , Gearhart Patricia J. , Staudt Louis M. , Morse Herbert C. , Ried Thomas , Hodes Richard J. 
Published: September 2015

Key PointsATM deficiency promotes the development of murine B-cell lymphomas that model human ABC DLBCL. T cell–dependent immune surveillance may be important to prevent emergence of ATM-deficient B-cell lymphomas.
Condensation of Indoles and Aldehydes in Subcritical Water without the Addition of Catalysts
Authors: Hirashita Tsunehisa , Ogawa Masaki , Hattori Reina , Okochi Sota , Araki Shuki 
Published: September 2015

Abstract
A series of 3,3′-diindolylmethanes were prepared in high yields from indoles and aldehydes under subcritical water conditions without the addition of catalysts. 3-Alkenylindoles were also obtained in good yields from aldehydes bearing benzylic hydrogen atoms.
Long-term high frequency measurements of ethane, benzene and methyl chloride at Ragged Point, Barbados: Identification of long-range transport events
Authors: Archibald A.T. , Witham C.S. , Ashfold M.J. , Manning A.J. , O’Doherty S. , Greally B.R. , Young D. , Shallcross D.E. 
Published: September 2015

Abstract
Here we present high frequency long-term observations of ethane, benzene and methyl chloride from the AGAGE Ragged Point, Barbados, monitoring station made using a custom built GC-MS system. Our analysis focuses on the first three years of data (2005–2007) and on the interpretation of periodic episodes of high concentrations of these compounds. We focus specifically on an exemplar episode during September 2007 to assess if these measurements are impacted by long-range transport of biomass burning and biogenic emissions. We use the Lagrangian Particle Dispersion model, NAME, run forwards and backwards in time to identify transport of air masses from the North East of Brazil during these events. To assess whether biomass burning was the cause we used hot spots detected using the MODIS instrument to act as point sources for simulating the release of biomass burning plumes. Excellent agreement for the arrival time of the simulated biomass burning plumes and the observations of enhancements in the trace gases indicates that biomass burning strongly influenced these measurements. These modelling data were then used to determine the emissions required to match the observations and compared with bottom up estimates based on burnt area and literature emission factors. Good agreement was found between the two techniques highlight the important role of biomass burning. The modelling constrained by in situ observations suggests that the emission factors were representative of their known upper limits, with the in situ data suggesting slightly greater emissions of ethane than the literature emission factors account for. Further analysis was performed concluding only a small role for biogenic emissions of methyl chloride from South America impacting measurements at Ragged Point.
These results highlight the importance of long-term high frequency measurements of NMHC and ODS and highlight how these data can be used to determine sources of emissions 1000’s km away.
The need for space in art practice
Authors: Solomons Ruth 
Published: September 2015

Abstract
This article starts with the premise that artists have an intrinsic understanding of visual space through a theoretical awareness of spatial discourses in art, including the ‘gesture’, objecthood and post-studio debates. This understanding then becomes interwoven into the practical aspects of sustaining an art practice, and expanded within the broader context of the socially felt space within which artists make work. The article looks at practices that exemplify the artist’s need for space, in relation to: spaces in which artworks are produced, stored and distributed; the depicted studio; occupations which deny headspace; and gendered containment of domestic space. Lastly, the article asks whether practices with varying adaptability to spatial resources are then varyingly resilient when there is a lack of space, resulting in different levels of sustainability for different types of practice.
Exploded diagrams and faulty parts
Authors: Charlton James 
Published: September 2015

Abstract
CDD – Compulsive Dismantling Disorder, is a quasi-diagnosis for the systematic and obsessive dissembling of objects, whereby an object becomes an exploded diagram of its parts. This is analogous to empirical research methods, whereby a human analyses an object in terms of its cumulative parts. Taken as an ontological perspective, questions of operation and dependence arise in relation to the theories of Tristan Garcia and Graham Harman. When considering the Journal of Artistic Research (JAR) in this context, an irreducible issue of potentiality is identified: selfexposition prohibits art from functioning as art-research.
Beyond deconstruction: Desire in postmodern American appropriation art
Authors: Vranou Sofia 
Published: September 2015

Abstract
Towards the end of the 1970s the American art scene welcomed a new era: postmodernism. The new radical practices and ideas concerning representation were central in the photo-conceptual art of this period, and appropriation became the key deconstructive method. This is an article about the Pictures Generation, the way postmodernism was initially theorized, and deconstructed, and the notion of desire through the analysis of significant artworks of that period.