bluuebunny/crossref_metadata_2025 huggingface dataset:
The structural parameter optimization of interdigital transducer in single electron transport devices
Authors: Song Li , Yuan Hui , Zhang Chuanyu , Li Ling , Lu Chuan , Gao Jie
Published: November 2009

We investigate the influence of the interdigital transducer (IDT) structure on the amplitude of the surface acoustic wave (SAW) in a SAW device. The SAW amplitude at the entrance of the quantum point contact (QPC) is obtained by using coupling-of-modes theory and p-matrix method. The calculated results indicate that a device with an IDT with a relatively small aperture, large pairs of IDT fingers, and short distance between the active IDT and the QPC, the SAW amplitude is typically enhanced under the same radio frequency (rf) power. Based on these results, we design the corresponding SAW devices, and good agreement is achieved between the experimental data and the numerical results. In experiment, for the devices with optimal IDTs, the rf powers required to observe the quantized acoustoelectric current are reduced; correspondingly, the rf heating effect is reduced. Most importantly, the improvement of the accuracy of the quantized plateau is achieved.
Computational study of thermocompression bonding of carbon nanotubes to metallic substrates
Authors: Song Xiaohui , Gan Zhiyin , Liu Sheng , Yan Han , Lv Qiang
Published: November 2009

Thermocompression bonding of carbon nanotubes (CNTs) to metallic substrates is studied using molecular dynamics. The interaction of the CNT and the metal cluster at high temperature is investigated first. For the diffusion bonding process, the effects of temperature and external pressure are examined. In addition, we apply the tensile loading to examine the mechanical properties and the failure modes during the debonding process. The results show that formation of coalescence structure between the CNT and the metal cluster provides a nanoscale metal surface to facilitate diffusion bonding. Both high temperature and high pressure will enhance the bonding. In addition, the debonding position of the samples under the tensile loading depends on the competition of CNT-metal and metal-metal interface strength. For samples bonded under high temperature and high pressure, the debonding first occurs at the CNT-metal interface. While for samples bonded under low temperature and low pressure, the interdiffusion is not sufficient and therefore the debonding occurs at metal-metal interface. These behaviors indicate that, to obtain larger bonding strength, it is necessary to select the metal with excellent adhesion property to the CNT surface as the medium layer and guarantee full interface contact between the metal cluster and the metallic substrate during the diffusion bonding.
A molecular dynamics study of the influence of ionic charge distribution on the dynamics of a molten salt
Authors: Li Hualin , Kobrak Mark N.
Published: November 2009

The distribution of charge in an ion of a fused salt is known to be an important determinant of liquid dynamics. However, the details of this relationship remain poorly understood. We present the results of molecular dynamics simulations on a model molten salt system and show that changes in the distribution of ionic charge can have a profound effect on liquid dynamics. In particular, we observe complex relationships between the distribution of charge, the rate of ionic rotation, and the translational diffusion of ions in the liquid.
Size and Direction of Distortion in Geometric-Optical Illusions: Conciliation between the Müller-Lyer and Titchener Configurations
Authors: Nemati Farshad
Published: November 2009

Over the past few decades, different theories have been advanced to explain geometric-optical illusions based on various perceptual processes such as assimilation and/or contrast. Consistent with the contradictory effects of assimilation and contrast, Pressey's assimilation theory provided an explanation for the Müller-Lyer illusion, but failed to account for the Titchener (Ebbinghaus) illusion. A model that explains both Müller-Lyer and Titchener illusions according to a common underlying process may outline a unified explanation for a variety of geometric-optical illusions. In order to develop such a model, the concept of empty space is introduced as an area of the illusory figure that is not filled by line drawings. It was predicted that the magnitude of illusion would increase with the area of the empty space around the illusory figures. The effect of empty space on the magnitude of perceptual distortion was measured in Müller-Lyer figures, with outward arrowheads of different length. The results indicated an overestimation of the target stimulus in all of the figures. Nevertheless, consistent with the prediction of the present model, the horizontal line in the Müller-Lyer figure with the longest arrowheads appeared shorter than that with the shortest arrowheads, although the size contrast of these figures was the same. According to the analysis proposed in the present study, the area of empty space not only affects the magnitude of illusion but also serves as a contextual cue for the perceptual system to determine the direction of illusion (orientation). The functional relationships between the size contrast and empty space provide a common explanation for the Müller-Lyer, Titchener, and a variety of other geometric-optical illusions.
How Well Can Theory Predict Addition - Fragmentation Equilibrium Constants in RAFT Polymerization?
Authors: Lin Ching Yeh , Coote Michelle L.
Published: November 2009

High level ab initio molecular orbital calculations are used to study the addition–fragmentation equilibrium constants of S-S’-bis(methyl-2-propionate)-trithiocarbonate mediated polymerization of methyl acrylate in toluene at –30°C. The results, which show strong solvent and chain length effects, are in good order of magnitude agreement with recent experimental results for a closely related system.
Synthesis of Michael Acceptor Ionomers of Poly(4-Sulfonated Styrene-co-Poly(ethylene Glycol) Methyl Ether Acrylate)
Authors: Alconcel Steevens N. S. , Grover Gregory N. , Matsumoto Nicholas M. , Maynard Heather D.
Published: November 2009

Ionomers containing sodium 4-styrene sulfonate (4SS) and poly(ethylene glycol) methyl ether acrylate (PEGA) were synthesized by reversible addition–fragmentation chain transfer (RAFT) polymerization. The polymerization was mediated by 1-phenylethyl dithiobenzoate chain transfer agent in a dimethylformamide/water solvent system. Well-defined copolymers of pPEGA-co-4SS were produced with molecular weights ranging from 10 to 40 kDa and polydispersity indices of 1.06–1.18 by gel permeation chromatography against monodisperse poly(methyl methacrylate) standards. After polymerization, the dithioester was reduced and trapped in situ with divinyl sulfone to produce a well-defined, semitelechelic pPEGA-co-4SS Michael acceptor polymer. UV-visible, infrared, and 1H NMR spectroscopy confirmed that the integrity of the polymer backbone was maintained and that the vinyl sulfone was successfully incorporated at the chain end.
Reef exposure to river-borne contaminants: a spatial model
Authors: Maughan M. , Brodie J.
Published: November 2009

Rivers flowing into the Great Barrier Reef carry contaminants such as suspended sediments, dissolved inorganic nitrogen, total phosphorus and pesticides. To measure the extent and direction of the contaminants after they enter the Great Barrier Reef lagoon, a model was created using river volume, flooding variability, contaminant load, distance and direction as inputs. A GIS was used to calculate and visualise the exposure of the contaminants to the reefs for the current day, as well as modelling scenarios for pre-European arrival loads, and land management using realistic targets set by a regional Natural Resource Management board for water quality improvement planning purposes. The results show that a reduction in the dissolved inorganic nitrogen load exiting the Tully and Murray Rivers reduces the exposure of reefs close to the basin, but that reefs further east of the basin are significantly influenced by other rivers, highlighting that management for water quality improvement in neighbouring basins is also required.
Community uses and values of water informing water quality improvement planning: a study from the Great Barrier Reef region, Australia
Authors: Bohnet Iris C. , Kinjun Clarence
Published: November 2009

Community participation has gained widespread recognition in water management and planning for its potential to inform management plans and gain community support for actions that are aligned with the community’s water values. However, the practical application of community participation remains challenging as there is no consensus on who should be involved and why. During a participatory research project to inform the Tully Water Quality Improvement Plan (WQIP), the local community was involved in qualitative interviews and workshops to identify the water uses and values in the Tully basin. The results showed that these waters are extensively used and valued via a wide range of activities and that water is more than an economic good. All participants valued the aquatic ecosystems, which provide the basis for setting the most stringent water quality objectives (WQOs). Moreover, the results showed that many of the current uses and values of waters are under serious threat and that some uses and values have been lost over time. These findings informed the setting of the WQOs for the Tully WQIP to protect and re-establish the water uses and values that the local community supports.
Identifying the land-based sources of suspended sediments, nutrients and pesticides discharged to the Great Barrier Reef from the Tully - Murray Basin, Queensland, Australia
Authors: Bainbridge Zoe T. , Brodie Jon E. , Faithful John W. , Sydes Damon A. , Lewis Stephen E.
Published: November 2009

To assist in the development of the Tully Water Quality Improvement Plan, a subcatchment water quality monitoring program was undertaken to identify the pollutants of concern and their land-based sources. Monitoring of suspended sediments, nutrients and pesticides in subcatchment waterways was conducted during the 2005–06 and 2006–07 wet seasons, which both had above average annual flows. We found distinct water quality signals from the basin’s major land uses (forest, grazing, urban, sugarcane and banana cultivation), except for suspended sediment concentrations, which were low across all land uses when compared with neighbouring river catchments. This reflects the high ground cover of the basin and the location of intensive agriculture on low sloping areas of the floodplain, minimising the potential for erosion. Nitrate concentrations were elevated in streams draining sugarcane, indicating fertiliser export from intensive agricultural landscapes. Residues of the herbicides diuron and atrazine were detected at sites draining sugarcane, and on occasion exceeded national ecological protection trigger values, which highlights a potential threat to downstream wetlands of recognised national significance. Herbicides were also detectable offshore in flood plumes of the Tully–Murray Rivers, with some concentrations of diuron above lowest observable effect concentrations for specific species of seagrass and corals. Run-off of nitrate and diuron were identified as key water quality issues in the Tully–Murray basin.
Target setting for pollutant discharge management of rivers in the Great Barrier Reef catchment area
Authors: Brodie Jon , Lewis Stephen , Bainbridge Zoe , Mitchell Alan , Waterhouse Jane , Kroon Frederieke
Published: November 2009

Water Quality Improvement Plans (WQIPs) are being developed for individual river basins on the Great Barrier Reef (GBR) catchment associated with the GBR Water Quality Protection Plan. Within each WQIP, marine ecosystem targets are linked to end-of-river pollutant (suspended sediments, nutrients and pesticides) load targets and to farm level management practice targets. The targets are linked through quantitative models; e.g. one model connects GBR chlorophyll concentrations (marine target) to end-of-river nitrate loads, a second connects the end-of-river nitrate loads to fertiliser management targets in the catchment, whereas a third model links fertiliser application to nitrate loss at the farm scale. The difficulties of applying these linked models to derive credible and practical management targets are great, given the high degree of uncertainty in each model. Our understanding of the generation of suspended sediments, nutrients and pesticides in catchments and the relationship to on-farm management, the transport of these materials to the ocean, their transport in coastal waters and their effects on marine ecosystems is incomplete. The challenge is to produce estimates from the models, with known levels of uncertainty, but robust enough for management purposes. Case studies from the Tully–Murray basin and the Burdekin basin in north Queensland are discussed.
Catchment modelling of sediment, nitrogen and phosphorus nutrient loads with SedNet/ANNEX in the Tully - Murray basin
Authors: Armour J. D. , Hateley L. R. , Pitt G. L.
Published: November 2009

A long-term, annual-average catchment biophysical model (SedNet/ANNEX) was used to calculate sediment, nitrogen (N) and phosphorus (P) loads in the Tully–Murray catchment of north-eastern Australia. A total of 119 000 t year–1 of suspended sediment, equivalent to 430 kg ha–1 year–1, was calculated to be exported to the Great Barrier Reef (GBR). Most of the sediment (64%) was generated from hill-slope erosion. The modelled load of dissolved inorganic N (1159 t year–1 or 4.2 kg N ha–1 year–1) was similar to that from other wet tropics catchments in Queensland with similar areas of sugarcane. Sugarcane produced 77% of this load. The annual loads of total N and total P were 2319 t and 244 t, respectively. Simulations (scenarios) were run to evaluate the impact of improved land management on pollutant loads to the GBR. A combination of improved cultivation and fertiliser management of sugarcane and bananas (99% of cropping land) and restoration of the most degraded riparian areas reduced sediment by 23 000 t year–1 (18%) and dissolved inorganic N by 286 t year–1 (25%). However, this reduction is much less than the reduction of 80% that may be needed in the catchment to meet target chlorophyll loads in the marine environment.
Cost-effective water quality improvement in linked terrestrial and marine ecosystems: a spatial environmental - economic modelling approach
Authors: Roebeling P. C. , van Grieken M. E. , Webster A. J. , Biggs J. , Thorburn P.
Published: November 2009

Worldwide, coastal and marine ecosystems are affected by water pollution originating from coastal river catchments, even though ecosystems such as the Great Barrier Reef are vital from an environmental as well as an economic perspective. Improved management of coastal catchment resources is needed to remediate this serious and growing problem through, e.g. agricultural land use and management practice change. This may, however, be very costly and, consequently, there is a need to explore how water quality improvement can be achieved at least cost. In the present paper, we develop an environmental–economic modelling approach that integrates an agricultural production system simulation model and a catchment water quality model into a spatial environmental–economic land-use model to explore patterns of land use and management practice that most cost-effectively achieve specified water quality targets and, in turn, estimate corresponding water pollution abatement cost functions. In a case study of sediment and nutrient water pollution by the sugarcane and grazing industries in the Tully–Murray catchment (Queensland, Australia), it is shown that considerable improvements in water quality can be obtained at no additional cost, or even benefit, to the agricultural industry, whereas larger water quality improvements come at a significant cost to the agricultural industry.
Development and application of the Riparian Mapping Tool to identify priority rehabilitation areas for nitrogen removal in the Tully - Murray basin, Queensland, Australia
Authors: Rassam D. W. , Pagendam D.
Published: November 2009

One feature of riparian zones is their ability to significantly reduce the nitrogen loads entering streams by removing nitrate from the groundwater. A novel GIS model was used to prioritise riparian rehabilitation in catchments. It is proposed that high-priority areas are those with a high potential for riparian denitrification and have nearby land uses that generate high nitrogen loads. For this purpose, we defined the Rehabilitation Index, which is the product of two other indices, the Nitrate Removal Index and the Nitrate Interception Index. The latter identifies the nitrate contamination potential for each raster cell in the riparian zone by examining the extent and proximity of agricultural urban land uses. The former is estimated using a conceptual model for surface–groundwater interactions in riparian zones associated with middle-order gaining perennial streams, where nitrate is removed via denitrification when the base flow interacts with the carbon-rich riparian sediments before discharging to the streams. Riparian zones that are relatively low in the landscape, have a flat topography, and have soils of medium hydraulic conductivity are most conducive to denitrification. In the present study, the model was implemented in the Tully–Murray basin, Queensland, Australia, to produce priority riparian rehabilitation area maps.
A 5′ cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs
Authors: Zhu Deyu , Stumpf Craig R. , Krahn Joseph M. , Wickens Marvin , Hall Traci M. Tanaka
Published: November 2009

A single regulatory protein can control the fate of many mRNAs with related functions. The Puf3 protein of
Saccharomyces cerevisiae
is exemplary, as it binds and regulates more than 100 mRNAs that encode proteins with mitochondrial function. Here we elucidate the structural basis of that specificity. To do so, we explore the crystal structures of Puf3p complexes with 2 cognate RNAs. The key determinant of Puf3p specificity is an unusual interaction between a distinctive pocket of the protein with an RNA base outside the “core” PUF-binding site. That interaction dramatically affects binding affinity in vitro and is required for regulation in vivo. The Puf3p structures, combined with those of Puf4p in the same organism, illuminate the structural basis of natural PUF-RNA networks. Yeast Puf3p binds its own RNAs because they possess a −2C and is excluded from those of Puf4p which contain an additional nucleotide in the core-binding site.
Recent unprecedented tree-ring growth in bristlecone pine at the highest elevations and possible causes
Authors: Salzer Matthew W. , Hughes Malcolm K. , Bunn Andrew G. , Kipfmueller Kurt F.
Published: November 2009

Great Basin bristlecone pine (
Pinus longaeva
) at 3 sites in western North America near the upper elevation limit of tree growth showed ring growth in the second half of the 20th century that was greater than during any other 50-year period in the last 3,700 years. The accelerated growth is suggestive of an environmental change unprecedented in millennia. The high growth is not overestimated because of standardization techniques, and it is unlikely that it is a result of a change in tree growth form or that it is predominantly caused by CO
2
fertilization. The growth surge has occurred only in a limited elevational band within ≈150 m of upper treeline, regardless of treeline elevation. Both an independent proxy record of temperature and high-elevation meteorological temperature data are positively and significantly correlated with upper-treeline ring width both before and during the high-growth interval. Increasing temperature at high elevations is likely a prominent factor in the modern unprecedented level of growth for
Pinus longaeva
at these sites.
Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire
Authors: Simon Marcelo F. , Grether Rosaura , de Queiroz Luciano P. , Skema Cynthia , Pennington R. Toby , Hughes Colin E.
Published: November 2009

The relative importance of local ecological and larger-scale historical processes in causing differences in species richness across the globe remains keenly debated. To gain insight into these questions, we investigated the assembly of plant diversity in the Cerrado in South America, the world's most species-rich tropical savanna. Time-calibrated phylogenies suggest that Cerrado lineages started to diversify less than 10 Mya, with most lineages diversifying at 4 Mya or less, coinciding with the rise to dominance of flammable C4 grasses and expansion of the savanna biome worldwide. These plant phylogenies show that Cerrado lineages are strongly associated with adaptations to fire and have sister groups in largely fire-free nearby wet forest, seasonally dry forest, subtropical grassland, or wetland vegetation. These findings imply that the Cerrado formed in situ via recent and frequent adaptive shifts to resist fire, rather than via dispersal of lineages already adapted to fire. The location of the Cerrado surrounded by a diverse array of species-rich biomes, and the apparently modest adaptive barrier posed by fire, are likely to have contributed to its striking species richness. These findings add to growing evidence that the origins and historical assembly of species-rich biomes have been idiosyncratic, driven in large part by unique features of regional- and continental-scale geohistory and that different historical processes can lead to similar levels of modern species richness.
Hippocampus-dependent and -independent theta-networks of active maintenance
Authors: Cashdollar Nathan , Malecki Ulrike , Rugg-Gunn Fergus J. , Duncan John S. , Lavie Nilli , Duzel Emrah
Published: November 2009

Recent studies in humans and animals raise the possibility that actively maintaining a detailed memory of a scene within working memory may require the hippocampus, a brain structure better known for its role in long-term memory. We show that the hippocampus is behaviorally and functionally critical for configural-relational (CR) maintenance by orchestrating the synchrony of occipital and temporal brain regions in the theta-frequency range. Using magnetoencephalography in healthy adults and patients with bilateral hippocampal sclerosis, we distinguish this hippocampus-dependent theta-network from one that is independent of the hippocampus and used for non-CR scene maintenance. This non-CR theta-network involved frontal and parietal brain regions. We also show that the functional and topographical dissociation between these two networks cannot be accounted for by perceptual difficulty or the amount of information to be maintained (“load”). Also, we confirm in healthy adults that active maintenance of the CR arrangement of objects within a scene is impaired by task-interference during the delay in a manner akin to working-memory maintenance processes. Together, these findings demand reconsideration of the classical functional-anatomical distinctions between long- and short-term memory.
U94 of human herpesvirus 6 inhibits in vitro angiogenesis and lymphangiogenesis
Authors: Caruso Arnaldo , Caselli Elisabetta , Fiorentini Simona , Rotola Antonella , Prandini Alberto , Garrafa Emirena , Saba Elisa , Alessandri Giulio , Cassai Enzo , Di Luca Dario
Published: November 2009

Human herpesvirus 6 (HHV-6) is a lymphotropic virus, but recent observations showed that also vascular endothelial cells (ECs) are susceptible to infection, both in vivo and in vitro. The observation that lymph nodes are a site of viral persistence suggests that lymphatic ECs (LECs) might be even more relevant for HHV-6 biology than vascular ECs. Here, we provide evidence that HHV-6 can infect LECs in vitro and establish a latent infection. Thus HHV-6 infection induces the loss of angiogenic properties both in LECs and in vascular ECs, as shown by the inability to form capillary-like structures and to seal wound scratches. The antiangiogenic effects observed in infected cells are associated to the expression of HHV-6 U94/
rep
, a latency-associated gene. In fact, transfection of U94/
rep
or addition of recombinant U94/REP protein to ECs inhibits the formation of in vitro capillary-like structures, reduces migration of ECs, and blocks angiogenesis, rendering rat aortic rings insensitive to VEGF-induced vasculogenetic activity. The ability of U94/
rep
to block different angiogenetic steps may lead to approaches in the potential control of the proliferation of blood and lymphatic vessels.
Four-dimensional address topology for circuits with stacked multilayer crossbar arrays
Authors: Strukov Dmitri B. , Williams R. Stanley
Published: November 2009

We present a topological framework that provides a simple yet powerful electronic circuit architecture for constructing and using multilayer crossbar arrays, allowing a significantly increased integration density of memristive crosspoint devices beyond the scaling limits of lateral feature sizes. The truly remarkable feature of such circuits, which is an extension of the CMOL (Cmos + MOLecular-scale devices) concept for an area-like interface to a three-dimensional system, is that a large-feature-size complimentary metal-oxide-semiconductor (CMOS) substrate can provide high-density interconnects to multiple crossbar layers through a single set of vertical vias. The physical locations of the memristive devices are mapped to a four-dimensional logical address space such that unique access from the CMOS substrate is provided to every device in a stacked array of crossbars. This hybrid architecture is compatible with digital memories, field-programmable gate arrays, and biologically inspired adaptive networks and with state-of-the-art integrated circuit foundries.
Adenovirus vector vaccination induces expansion of memory CD4 T cells with a mucosal homing phenotype that are readily susceptible to HIV-1
Authors: Benlahrech Adel , Harris Julian , Meiser Andrea , Papagatsias Timos , Hornig Julia , Hayes Peter , Lieber Andre , Athanasopoulos Takis , Bachy Veronique , Csomor Eszter , Daniels Rod , Fisher Kerry , Gotch Frances , Seymour Len , Logan Karen , Barbagallo Romina , Klavinskis Linda , Dickson George , Patterson Steven
Published: November 2009

In the recently halted HIV type 1 (HIV-1) vaccine STEP trial, individuals that were seropositive for adenovirus serotype 5 (Ad5) showed increased rates of HIV-1 infection on vaccination with an Ad5 vaccine. We propose that this was due to activation and expansion of Ad5-specific mucosal-homing memory CD4 T cells. To test this hypothesis, Ad5 and Ad11 antibody titers were measured in 20 healthy volunteers. Dendritic cells (DCs) from these individuals were pulsed with replication defective Ad5 or Ad11 and co-cultured with autologous lymphocytes. Cytokine profiles, proliferative capacity, mucosal migration potential, and susceptibility to HIV infection of the adenovirus-stimulated memory CD4 T cells were measured. Stimulation of T cells from healthy Ad5-seropositive but Ad11-seronegative individuals with Ad5, or serologically distinct Ad11 vectors induced preferential expansion of adenovirus memory CD4 T cells expressing α4β7integrins and CCR9, indicating a mucosal-homing phenotype. CD4 T-cell proliferation and IFN-γ production in response to Ad stimulation correlated with Ad5 antibody titers. However, Ad5 serostatus did not correlate with total cytokine production upon challenge with Ad5 or Ad11. Expanded Ad5 and Ad11 memory CD4 T cells showed an increase in CCR5 expression and higher susceptibility to infection by R5 tropic HIV-1. This suggests that adenoviral-based vaccination against HIV-1 in individuals with preexisting immunity against Ad5 results in preferential expansion of HIV-susceptible activated CD4 T cells that home to mucosal tissues, increases the number of virus targets, and leads to a higher susceptibility to HIV acquisition.
Evidence from intrinsic activity that asymmetry of the human brain is controlled by multiple factors
Authors: Liu Hesheng , Stufflebeam Steven M. , Sepulcre Jorge , Hedden Trey , Buckner Randy L.
Published: November 2009

Cerebral lateralization is a fundamental property of the human brain and a marker of successful development. Here we provide evidence that multiple mechanisms control asymmetry for distinct brain systems. Using intrinsic activity to measure asymmetry in 300 adults, we mapped the most strongly lateralized brain regions. Both men and women showed strong asymmetries with a significant, but small, group difference. Factor analysis on the asymmetric regions revealed 4 separate factors that each accounted for significant variation across subjects. The factors were associated with brain systems involved in vision, internal thought (the default network), attention, and language. An independent sample of right- and left-handed individuals showed that hand dominance affects brain asymmetry but differentially across the 4 factors supporting their independence. These findings show the feasibility of measuring brain asymmetry using intrinsic activity fluctuations and suggest that multiple genetic or environmental mechanisms control cerebral lateralization.
Simple rules can explain discrimination of putative recursive syntactic structures by a songbird species
Authors: van Heijningen Caroline A. A. , de Visser Jos , Zuidema Willem , ten Cate Carel
Published: November 2009

According to a controversial hypothesis, a characteristic unique to human language is recursion. Contradicting this hypothesis, it has been claimed that the starling, one of the two animal species tested for this ability to date, is able to distinguish acoustic stimuli based on the presence or absence of a center-embedded recursive structure. In our experiment we show that another songbird species, the zebra finch, can also discriminate between artificial song stimuli with these structures. Zebra finches are able to generalize this discrimination to new songs constructed using novel elements belonging to the same categories, similar to starlings. However, to demonstrate that this is based on the ability to detect the putative recursive structure, it is critical to test whether the birds can also distinguish songs with the same structure consisting of elements belonging to unfamiliar categories. We performed this test and show that seven out of eight zebra finches failed it. This suggests that the acquired discrimination was based on phonetic rather than syntactic generalization. The eighth bird, however, must have used more abstract, structural cues. Nevertheless, further probe testing showed that the results of this bird, as well as those of others, could be explained by simpler rules than recursive ones. Although our study casts doubts on whether the rules used by starlings and zebra finches really provide evidence for the ability to detect recursion as present in “context-free” syntax, it also provides evidence for abstract learning of vocal structure in a songbird.
Dynamic structure of lipid-bound synaptobrevin suggests a nucleation-propagation mechanism for trans-SNARE complex formation
Authors: Ellena Jeffrey F. , Liang Binyong , Wiktor Maciej , Stein Alexander , Cafiso David S. , Jahn Reinhard , Tamm Lukas K.
Published: November 2009

The synaptic vesicle protein synaptobrevin engages with syntaxin and SNAP-25 to form the SNARE complex, which drives membrane fusion in neuronal exocytosis. In the SNARE complex, the SNARE motif of synaptobrevin forms a 55-residue helix, but it has been assumed to be mostly unstructured in its prefusion form. NMR data for full-length synaptobrevin in dodecylphosphocholine micelles reveals two transient helical segments flanked by natively disordered regions and a third more stable helix. Transient helix I comprises the most N-terminal part of the SNARE motif, transient helix II extends the SNARE motif into the juxtamembrane region, and the more stable helix III is the transmembrane domain. These helices may have important consequences for SNARE complex folding and fusion: helix I likely forms a nucleation site, the C-terminal disordered SNARE motif may act as a folding arrest signal, and helix II likely couples SNARE complex folding and fusion.
Crystal structure of the catalytic domain of Haspin, an atypical kinase implicated in chromatin organization
Authors: Villa Fabrizio , Capasso Paola , Tortorici Marcello , Forneris Federico , de Marco Ario , Mattevi Andrea , Musacchio Andrea
Published: November 2009

Haspin, a nuclear and chromosome-associated serine/threonine (S/T) kinase, is responsible for mitotic phosphorylation of Thr-3 of histone H3. Haspin bears recognizable similarity to the eukaryotic protein kinase (ePK) fold, but its sequence is highly divergent and there is therefore considerable interest in its structural organization. We report the 2.15-Å crystal structure of the kinase domain of human Haspin. The ePK fold of Haspin contains an array of insertions and deletions. The structure illustrates how Haspin escapes the classical activation scheme of most other kinases. The αC helix, which bears a conserved glutamate that is essential for catalysis, adopts its final active conformation within the small lobe of the kinase. It is sandwiched between an α-helical insertion that precedes the kinase domain, and the activation segment, which adopts an unprecedented conformation. The activation segment, which does not contain phosphorylatable residues, packs against an unusually structured αEF helix. Significantly extruded from the core of the fold, it forms an extensive plateau, hosting several residues implicated in substrate binding. Overall, the structure of the Haspin kinase domain reveals an active conformation that is poised for substrate recognition and phosphorylation in the absence of external regulators.
Necrotic cells trigger a sterile inflammatory response through the Nlrp3 inflammasome
Authors: Iyer Shankar S. , Pulskens Wilco P. , Sadler Jeffrey J. , Butter Loes M. , Teske Gwendoline J. , Ulland Tyler K. , Eisenbarth Stephanie C. , Florquin Sandrine , Flavell Richard A. , Leemans Jaklien C. , Sutterwala Fayyaz S.
Published: November 2009

Dying cells are capable of activating the innate immune system and inducing a sterile inflammatory response. Here, we show that necrotic cells are sensed by the Nlrp3 inflammasome resulting in the subsequent release of the proinflammatory cytokine IL-1β. Necrotic cells produced by pressure disruption, hypoxic injury, or complement-mediated damage were capable of activating the Nlrp3 inflammasome. Nlrp3 inflammasome activation was triggered in part through ATP produced by mitochondria released from damaged cells. Neutrophilic influx into the peritoneum in response to necrotic cells in vivo was also markedly diminished in the absence of Nlrp3. Nlrp3-deficiency moreover protected animals against mortality, renal dysfunction, and neutrophil influx in an in vivo renal ischemic acute tubular necrosis model. These findings suggest that the inhibition of Nlrp3 inflammasome activity can diminish the acute inflammation and damage associated with tissue injury.
Dual blockade of FAAH and MAGL identifies behavioral processes regulated by endocannabinoid crosstalk in vivo
Authors: Long Jonathan Z. , Nomura Daniel K. , Vann Robert E. , Walentiny D. Matthew , Booker Lamont , Jin Xin , Burston James J. , Sim-Selley Laura J. , Lichtman Aron H. , Wiley Jenny L. , Cravatt Benjamin F.
Published: November 2009

Δ9-Tetrahydrocannabinol (THC), the psychoactive component of marijuana, and other direct cannabinoid receptor (CB1) agonists produce a number of neurobehavioral effects in mammals that range from the beneficial (analgesia) to the untoward (abuse potential). Why, however, this full spectrum of activities is not observed upon pharmacological inhibition or genetic deletion of either fatty acid amide hydrolase (FAAH) or monoacylglycerol lipase (MAGL), enzymes that regulate the two major endocannabinoids anandamide (AEA) and 2-arachidonoylglycerol (2-AG), respectively, has remained unclear. Here, we describe a selective and efficacious dual FAAH/MAGL inhibitor, JZL195, and show that this agent exhibits broad activity in the tetrad test for CB1 agonism, causing analgesia, hypomotilty, and catalepsy. Comparison of JZL195 to specific FAAH and MAGL inhibitors identified behavioral processes that were regulated by a single endocannabinoid pathway (e.g., hypomotility by the 2-AG/MAGL pathway) and, interestingly, those where disruption of both FAAH and MAGL produced additive effects that were reversed by a CB1 antagonist. Falling into this latter category was drug discrimination behavior, where dual FAAH/MAGL blockade, but not disruption of either FAAH or MAGL alone, produced THC-like responses that were reversed by a CB1 antagonist. These data indicate that AEA and 2-AG signaling pathways interact to regulate specific behavioral processes in vivo, including those relevant to drug abuse, thus providing a potential mechanistic basis for the distinct pharmacological profiles of direct CB1 agonists and inhibitors of individual endocannabinoid degradative enzymes.
The antioxidant role of thiocyanate in the pathogenesis of cystic fibrosis and other inflammation-related diseases
Authors: Xu Yanping , Szép Szilvia , Lu Zhe
Published: November 2009

Cystic fibrosis (CF) is a pleiotropic disease, originating from mutations in the CF transmembrane conductance regulator (CFTR). Lung injuries inflicted by recurring infection and excessive inflammation cause ≈90% of the morbidity and mortality of CF patients. It remains unclear how CFTR mutations lead to lung illness. Although commonly known as a Cl−channel, CFTR also conducts thiocyanate (SCN−) ions, important because, in several ways, they can limit potentially harmful accumulations of hydrogen peroxide (H2O2) and hypochlorite (OCl−). First, lactoperoxidase (LPO) in the airways catalyzes oxidation of SCN−to tissue-innocuous hypothiocyanite (OSCN−), while consuming H2O2. Second, SCN−even at low concentrations competes effectively with Cl−for myeloperoxidase (MPO) (which is released by white blood cells), thus limiting OCl−production by the enzyme. Third, SCN−can rapidly reduce OCl−without catalysis. Here, we show that SCN−and LPO protect a lung cell line from injuries caused by H2O2; and that SCN−protects from OCl−made by MPO. Of relevance to inflammation in other diseases, we find that in three other tested cell types (arterial endothelial cells, a neuronal cell line, and a pancreatic β cell line) SCN−at concentrations of ≥100 μM greatly attenuates the cytotoxicity of MPO. Humans naturally derive SCN−from edible plants, and plasma SCN−levels of the general population vary from 10 to 140 μM. Our findings raise the possibility that insufficient levels of antioxidant SCN−provide inadequate protection from OCl−, thus worsening inflammatory diseases, and predisposing humans to diseases linked to MPO activity, including atherosclerosis, neurodegeneration, and certain cancers.
Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi
Authors: Chen Chen , Jin Jing , James D. Andrew , Adams-Cioaba Melanie A. , Park Jin Gyoon , Guo Yahong , Tenaglia Enrico , Xu Chao , Gish Gerald , Min Jinrong , Pawson Tony
Published: November 2009

Tudor domains are protein modules that mediate protein–protein interactions, potentially by binding to methylated ligands. A group of germline specific single and multiTudor domain containing proteins (TDRDs) represented by
drosophila
Tudor and its mammalian orthologs Tdrd1, Tdrd4/RNF17, and Tdrd6 play evolutionarily conserved roles in germinal granule/nuage formation and germ cell specification and differentiation. However, their physiological ligands, and the biochemical and structural basis for ligand recognition, are largely unclear. Here, by immunoprecipitation of endogenous murine Piwi proteins (Miwi and Mili) and proteomic analysis of complexes related to the piRNA pathway, we show that the TDRD group of Tudor proteins are physiological binding partners of Piwi family proteins. In addition, mass spectrometry indicates that arginine residues in RG repeats at the N-termini of Miwi and Mili are methylated in vivo. Notably, we found that Tdrkh/Tdrd2, a novel single Tudor domain containing protein identified in the Miwi complex, is expressed in the cytoplasm of male germ cells and directly associates with Miwi. Mutagenesis studies mapped the Miwi–Tdrkh interaction to the very N-terminal RG/RA repeats of Miwi and showed that the Tdrkh Tudor domain is critical for binding. Furthermore, we have solved the crystal structure of the Tdrkh Tudor domain, which revealed an aromatic binding pocket and negatively charged binding surface appropriate for accommodating methylated arginine. Our findings identify a methylation-directed protein interaction mechanism in germ cells mediated by germline Tudor domains and methylated Piwi family proteins, and suggest a complex mode of regulating the organization and function of Piwi proteins in piRNA silencing pathways.
Constructing Neoliberal Urban Democracy in the American Inner-city
Authors: Addie Jean-Paul D.
Published: November 2009

The neoliberalization of urban governance has profoundly problematized issues of ‘local’ and ‘urban’ democracy on both sides of the Atlantic. This paper explores the changing modalities of urban democracy under neoliberalism through a case study of Over-the-Rhine, Cincinnati. A historically maligned inner-city neighbourhood, Over-the-Rhine is the locus for a concerted neoliberalizing gentrification drive and site of a coordinated resistance to market-oriented redevelopment. Three key processes of neoliberal restructuring are analyzed to highlight the centrality of contestations over local democracy for local economic development. Governance restructuring and the implementation of key spatial imaginaries are argued to produce a neoliberal articulation of urban democracy that discursively legitimizes development from above via an understanding of the neighbourhood as a physical environment, usurping pre-existing grassroots organizations conceptualizing Over-the-Rhine as a social structure.
The processes underlying flexibility in childhood
Authors: Cragg Lucy , Chevalier Nicolas
Published: November 2009

It is now well established in the adult literature that the ability to engage in flexible thought and action is a complex skill that relies on a number of underlying processes. The development of this skill has received growing interest in recent years. However, theories explaining children's ability to switch between different tasks typically focus on a single underlying process and are rarely extended to explain development beyond the preschool years. This article reviews the current literature on set shifting in children in comparison with task switching in adults, in order to highlight the range of factors that impact on children's ability to flexibly shift between tasks. In doing this we hope to set the scene for future research that can begin to establish the relationships between these processes and how they change with age.
Visuospatial bootstrapping: Evidence for binding of verbal and spatial information in working memory
Authors: Darling Stephen , Havelka Jelena
Published: November 2009

Traditionally, working memory is held to comprise separate subcomponents dedicated to the temporary storage of visuospatial and verbal information. More recently, the addition of an episodic buffer has been proposed where information from multiple memory systems is integrated. We report an experiment designed to investigate the effects of providing additional visuospatial information in a verbal working memory task. When to-be-remembered digits were arranged in a horizontal line, performance was no better than when digits were presented in a single location. However, when digits were presented in a keyboard array, performance was significantly better. It is argued that this pattern is hard to reconcile with the traditional model of working memory, and that the “spatial bootstrapping” effect provides evidence towards models of working memory that incorporate an episodic buffer.
Do people reason on the Wason selection task? A new look at the data of Ball et al. (2003)
Authors: Evans Jonathan St. B. T. , Ball Linden J.
Published: November 2009

Despite the popularity of the Wason selection task in the psychology of reasoning, doubt remains as to whether card choices actually reflect a process of reasoning. One view is that while participants reason about the cards and their hidden sides—as indicated by protocol analysis—this reasoning merely confabulates explanations for cards that were preconsciously cued. This hypothesis has apparently been supported by studies that show that participants predominantly inspect cards which they end up selecting. In this paper, we reanalyse the data of one such study, which used eye-movement tracking to record card inspection times (Ball, Lucas, Miles, & Gale, 2003). We show that while cards favoured by matching bias are inspected for roughly equal lengths of times, their selection rates are strongly affected by their logical status. These findings strongly support a two-stage account in which attention is necessary but not sufficient for card selections. Hence, reasoning does indeed affect participants’ choices on this task.
The G protein βγ subunit mediates reannealing of adherens junctions to reverse endothelial permeability increase by thrombin
Authors: Knezevic Nebojsa , Tauseef Mohammad , Thennes Tracy , Mehta Dolly
Published: November 2009

The inflammatory mediator thrombin proteolytically activates protease-activated receptor (PAR1) eliciting a transient, but reversible increase in vascular permeability. PAR1-induced dissociation of Gα subunit from heterotrimeric Gq and G12/G13 proteins is known to signal the increase in endothelial permeability. However, the role of released Gβγ is unknown. We now show that impairment of Gβγ function does not affect the permeability increase induced by PAR1, but prevents reannealing of adherens junctions (AJ), thereby persistently elevating endothelial permeability. We observed that in the naive endothelium Gβ1, the predominant Gβ isoform is sequestered by receptor for activated C kinase 1 (RACK1). Thrombin induced dissociation of Gβ1 from RACK1, resulting in Gβ1 interaction with Fyn and focal adhesion kinase (FAK) required for FAK activation. RACK1 depletion triggered Gβ1 activation of FAK and endothelial barrier recovery, whereas Fyn knockdown interrupted with Gβ1-induced barrier recovery indicating RACK1 negatively regulates Gβ1-Fyn signaling. Activated FAK associated with AJ and stimulated AJ reassembly in a Fyn-dependent manner. Fyn deletion prevented FAK activation and augmented lung vascular permeability increase induced by PAR1 agonist. Rescuing FAK activation in fyn−/− mice attenuated the rise in lung vascular permeability. Our results demonstrate that Gβ1-mediated Fyn activation integrates FAK with AJ, preventing persistent endothelial barrier leakiness.