bluuebunny/crossref_metadata_2025 huggingface dataset:
Strain effect in PbTiO3/PbZr0.2Ti0.8O3 superlattices: From polydomain to monodomain structures
Authors: Hubault C. , Davoisne C. , Boulle A. , Dupont L. , Demange V. , Perrin A. , Gautier B. , Holc J. , Kosec M. , Karkut M.G. , Lemée N.
Published: December 2012

Ferroelectric symmetric superlattices consisting of alternating layers of PbTiO3 and PbZr0.2Ti0.8O3, were grown by pulsed laser deposition on SrTiO3 and SrRuO3-coated SrTiO3 substrates. The superlattices, with wavelengths Λ ranging from 20 Å to 200 Å, were analyzed using x-ray diffraction (θ−2θ diffraction scans, rocking curves, and reciprocal space mapping), high resolution transmission electron microscopy, and piezoforce scanning microscopy. For large-period superlattices, the strain is relieved by the formation of an a/c polydomain structure which propagates through the whole film. We investigate the influence of the wavelength on the a-domain volume fraction, the lattice parameters, the in-plane strain εxx, and the mosaicity of the samples. We show that with decreasing the wavelength, a reduction of the a-domain volume fraction is observed as well as a reduced tensile in-plane strain and a lower mosaicity. A concomitant improvement of the local ferroelectric response is detected. Below a critical wavelength of about 30 Å and a critical sample thickness of 500 Å, the formation of 90° a/c domains is inhibited and the superlattices are completely c oriented. Thus the reduced wavelength induces compressive strain which dominates over the tensile clamping due to the thermal expansion mismatch between the substrate and the superlattice. This compressive strain favors a c-oriented structure in the PbTiO3/PbZr0.2Ti0.8O3 superlattices.
Structural stability and electronic properties of sp3 type silicon nanotubes
Authors: Hever Alon , Bernstein Jonathan , Hod Oded
Published: December 2012

A density functional theory study of the structural and electronic properties and relative stability of narrow hydrogen passivated sp3 silicon nanotubes of different growth orientations is presented. All nanotubes studied and their corresponding wire structures are found to be meta-stable with the wires being more energetically stable. Silicon nanotubes show a dramatic bandgap increase of up to 68% with respect to the corresponding wires. Furthermore, a direct relation between the bandgap of the system and the molar fraction of the passivating hydrogen contents is found. These results suggest that by careful control over their crystallographic growth orientation, dimensions, and chemical composition it should be possible to design and fabricate silicon nanotubes with desired electronic properties.
Inertness and degradation of (0001) surface of Bi2Se3 topological insulator
Authors: Golyashov V. A. , Kokh K. A. , Makarenko S. V. , Romanyuk K. N. , Prosvirin I. P. , Kalinkin A. V. , Tereshchenko O. E. , Kozhukhov A. S. , Sheglov D. V. , Eremeev S. V. , Borisova S. D. , Chulkov E. V.
Published: December 2012

Inertness of the cleaved (0001) surface of the Bi2Se3 single crystal, grown by modified Bridgman method, to oxidation has been demonstrated by X-ray photoelectron spectroscopy, scanning tunneling microscopy, and by ab initio DFT calculations. No intrinsic bismuth and selenium oxides are formed on the low-defect, atomically flat Bi2Se3(0001)-(1×1) surface after a long-time air exposure. The inertness of Bi2Se3(0001) to O2 and NO2, as well as bismuth-oxygen bonding formation under molecular adsorption in the Se vacancy was supported by DFT calculations.
Crystal-structure prediction via the Floppy-Box Monte Carlo algorithm: Method and application to hard (non)convex particles
Authors: de Graaf Joost , Filion Laura , Marechal Matthieu , van Roij René , Dijkstra Marjolein
Published: December 2012

In this paper, we describe the way to set up the floppy-box Monte Carlo (FBMC) method [L. Filion, M. Marechal, B. van Oorschot, D. Pelt, F. Smallenburg, and M. Dijkstra, Phys. Rev. Lett. 103, 188302 (2009)10.1103/PhysRevLett.103.188302] to predict crystal-structure candidates for colloidal particles. The algorithm is explained in detail to ensure that it can be straightforwardly implemented on the basis of this text. The handling of hard-particle interactions in the FBMC algorithm is given special attention, as (soft) short-range and semi-long-range interactions can be treated in an analogous way. We also discuss two types of algorithms for checking for overlaps between polyhedra, the method of separating axes and a triangular-tessellation based technique. These can be combined with the FBMC method to enable crystal-structure prediction for systems composed of highly shape-anisotropic particles. Moreover, we present the results for the dense crystal structures predicted using the FBMC method for 159 (non)convex faceted particles, on which the findings in [J. de Graaf, R. van Roij, and M. Dijkstra, Phys. Rev. Lett. 107, 155501 (2011)10.1103/PhysRevLett.107.155501] were based. Finally, we comment on the process of crystal-structure prediction itself and the choices that can be made in these simulations.
Effects of space charge distribution on ferroelectric hysteresis loops considering the inhomogeneous built-in electric field: A phase field simulation
Authors: Wang X. L. , Li B. , Zhong X. L. , Zhang Y. , Wang J. B. , Zhou Y. C.
Published: December 2012

A phase field model based on the time-dependent Ginsburg-Landau equation is developed to investigate the space charge distribution effects on the ferroelectric hysteresis characteristics of the ferroelectric thin film, in which the inhomogeneity of the built-in electric field (Eib) distribution along the vertical direction of ferroelectric thin film and the corresponding effect on the domain kinetics are taken into account. The hysteresis loops of the ferroelectric thin films with different space charge distributions are calculated by using this model. The results indicate that symmetrically (including homogeneously) distributed space charges lead to the hysteresis loop constriction because the Eib weakens the total electric field to make the ferroelectric film form a stable monodomain structure or the 180° strip domain. However, asymmetrically distributed space charges cause not only the shift but also the distortion of the hysteresis loop which is pinched in one head and loses its centrosymmetry. This is attributed to that the negative Eib changes the total electric field and activates domain nucleation at the interface.
Magnon scattering in single and bilayer graphene intercalates
Authors: Hiranandani Dharmendra , Salimath Akshaykumar , Bishnoi Bhupesh , Nandal Vikas , Akram M. W. , Jayanthi Aditya , Kumar Yada Mahesh , Ghosh Bahniman
Published: December 2012

Semi-classical Monte Carlo simulation is used to determine the effect of magnetic substance as intercalated layer in single layer and bilayer graphene intercalates on spin relaxation length. Spin relaxation lengths are studied with spin density matrix calculation under the effect of one magnon scattering mechanisms. Spin relaxation lengths are simulated and made comparisons by including magnon scattering with phonon scattering. The results are simulated with varying temperatures below Curie temperature.
Simulation of inhomogeneous magnetoelastic anisotropy in ferroelectric/ferromagnetic nanocomposites
Authors: Aimon Nicolas M. , Liao Jiexi , Ross C. A.
Published: December 2012

The magnetic response of CoFe2O4/BiFeO3 (CFO/BFO) nanocomposite thin films, in which ferromagnetic CFO nanopillars are embedded in a ferroelectric BFO matrix, has been modeled by including the position-dependent magnetoelastic anisotropy of the CFO. A finite element simulation of the strain state of an arrangement of CFO pillars was performed in which the BFO matrix surrounding one or all of the pillars was subject to a piezoelectric strain. The strain transferred to the CFO pillars was calculated and transformed into a spatially varying magnetoelastic anisotropy in the CFO, and a micromagnetic model was then used to calculate the hysteresis of the pillar, which differed significantly from a macrospin model. The position-dependent anisotropy led to a complex reversal process and to a reorientation of the easy axis to the in-plane direction at sufficient applied electric fields.
Lattice strains and polarized luminescence in homoepitaxial growth of a-plane ZnO
Authors: Matsui Hiroaki , Tabata Hitoshi
Published: December 2012

In-plane lattice strains in a-plane zinc oxide (ZnO) homoepitaxial layers were selectively introduced by changing substrate type and growth conditions. Strain-free layers were observed when using a Crystec ZnO substrate, which resulted in atomically flat surfaces with nano-facets consisting of the m-plane (10-10) at atomic scale. In contrast, ZnO layers on Goodwill ZnO substrates possessed in-plane lattice strains due to generation of basal-plane stacking faults. The degree of lattice strains was systematically changed by the oxygen pressure, which clarified the close correlation between photoluminescence (PL) polarization and lattice strains. The polarization ratio of PL enhanced with the lattice strains.
Efficient counter-propagating wave acoustic micro-particle manipulation
Authors: Grinenko A. , Ong C. K. , Courtney C. R. P. , Wilcox P. D. , Drinkwater B. W.
Published: December 2012

A simple acoustic system consisting of a pair of parallel singe layered piezoelectric transducers submerged in a fluid used to form standing waves by a superposition of two counter-propagating waves is reported. The nodal positions of the standing wave are controlled by applying a variable phase difference to the transducers. This system was used to manipulate polystyrene micro-beads trapped at the nodal positions of the standing wave. The demonstrated good manipulation capability of the system is based on a lowering of the reflection coefficient in a narrow frequency band near the through-thickness resonance of the transducer plates.
TiO2 nanofibrous interface development for Raman detection of environmental pollutants
Authors: Maznichenko D. , Selvaganapathy P. R. , Venkatakrishnan K. , Tan B.
Published: December 2012

Sensor development has been reliant on planar Au and Ag nanoparticle research. The current findings explored a unique 3-D network of crystalline TiO2 nanoparticles linked as nanofibers. In addition to the favorability of using TiO2 for chemical and bio-molecular sensing, the nanofiber network provides molecular diffusion control and an increased confocal volume signal. Controlled femtosecond laser synthesis is also demonstrated that directly impacts surface-enhanced Raman spectroscopy detection of two common environmentally harmful chemicals: bisphenol A and diclofenac sodium salt. These findings assert that 3-D nanofibrous network porosity optimization is crucial for Raman monitoring of drinking water.
Male traits and herd reproductive capability in tropical beef cattle. 1. Experimental design and animal measures
Authors: Burns B. M. , Corbet N. J. , Corbet D. H. , Crisp J. M. , Venus B. K. , Johnston D. J. , Li Y. , McGowan M. R. , Holroyd R. G.
Published: December 2012

Research into the genetics of whole herd profitability has been a focus of the Beef Cooperative Research Centre for Beef Genetic Technologies over the past decade and it has been identified that measures of male reproduction may offer a potential indirect means of selecting for improved female reproduction. This paper describes the experimental design and provides a descriptive analysis of an array of male traits in Brahman and Tropical Composite genotypes managed under the medium to high stress, semi-extensive to extensive production systems of northern Australia. A total of 1639 Brahman and 2424 Tropical Composite bulls with known pedigrees, bred and raised in northern Australia, were evaluated for a comprehensive range of productive and reproductive traits. These included blood hormonal traits (luteinising hormone, inhibin and insulin-like growth factor-I); growth and carcass traits (liveweight, body condition score, ultrasound scanned 12–13th rib fat, rump P8 fat, eye muscle area and hip height); adaptation traits (flight time and rectal temperature); and a bull breeding soundness evaluation (leg and hoof conformation, sheath score, length of everted prepuce, penile anatomy, scrotal circumference, semen mass activity, sperm motility and sperm morphology). Large phenotypic variation was evident for most traits, with complete overlap between genotypes, indicating that there is likely to be a significant opportunity to improve bull fertility traits through management and bull selection.
Male great bowerbirds create forced perspective illusions with consistently different individual quality
Authors: Kelley Laura A. , Endler John A.
Published: December 2012

Males often produce elaborate displays that increase their attractiveness to females, and some species extend their displays to include structures or objects that are not part of their body. Such “extended phenotypes” may communicate information that cannot be transmitted by bodily signals or may provide a more reliable signal than bodily signals. However, it is unclear whether these signals are individually distinct and whether they are consistent over long periods of time. Male bowerbirds construct and decorate bowers that function in mate choice. Bower display courts constructed by male great bowerbirds (
Ptilonorhynchus nuchalis
) induce a visual illusion known as forced perspective for the female viewing the male’s display over the court, and the quality of illusion is associated with mating success. We improved the quality of the forced perspective to determine whether males maintained it at the new higher level, decreased the perspective quality back to its original value, or allowed it to decay at random over time. We found that the original perspective quality was actively recovered to individual original values within 3 d. We measured forced perspective over the course of one breeding season and compared the forced perspective of individual males between two successive breeding seasons. We found that differences in the quality of visual illusion among males were consistent within and between two breeding seasons. This suggests that forced perspective is actively and strongly maintained at a different level by each individual male.
Different secretory repertoires control the biomineralization processes of prism and nacre deposition of the pearl oyster shell
Authors: Marie Benjamin , Joubert Caroline , Tayalé Alexandre , Zanella-Cléon Isabelle , Belliard Corinne , Piquemal David , Cochennec-Laureau Nathalie , Marin Frédéric , Gueguen Yannick , Montagnani Caroline
Published: December 2012

Mollusca evolutionary success can be attributed partly to their efficiency to sustain and protect their soft body with an external biomineralized structure, the shell. Current knowledge of the protein set responsible for the formation of the shell microstructural polymorphism and unique properties remains largely patchy. In
Pinctada margaritifera
and
Pinctada maxima
, we identified 80 shell matrix proteins, among which 66 are entirely unique. This is the only description of the whole “biomineralization toolkit” of the matrices that, at least in part, is thought to regulate the formation of the prismatic and nacreous shell layers in the pearl oysters. We unambiguously demonstrate that prisms and nacre are assembled from very different protein repertoires. This suggests that these layers do not derive from each other.
Great majority of recombination events in
Arabidopsis
are gene conversion events
Authors: Yang Sihai , Yuan Yang , Wang Long , Li Jing , Wang Wen , Liu Haoxuan , Chen Jian-Qun , Hurst Laurence D. , Tian Dacheng
Published: December 2012

The evolutionary importance of meiosis may not solely be associated with allelic shuffling caused by crossing-over but also have to do with its more immediate effects such as gene conversion. Although estimates of the crossing-over rate are often well resolved, the gene conversion rate is much less clear. In
Arabidopsis
, for example, next-generation sequencing approaches suggest that the two rates are about the same, which contrasts with indirect measures, these suggesting an excess of gene conversion. Here, we provide analysis of this problem by sequencing 40 F
2
Arabidopsis
plants and their parents. Small gene conversion tracts, with biased gene conversion content, represent over 90% (probably nearer 99%) of all recombination events. The rate of alteration of protein sequence caused by gene conversion is over 600 times that caused by mutation. Finally, our analysis reveals recombination hot spots and unexpectedly high recombination rates near centromeres. This may be responsible for the previously unexplained pattern of high genetic diversity near
Arabidopsis
centromeres.
Morphing between expressions dissociates continuous from categorical representations of facial expression in the human brain
Authors: Harris Richard J. , Young Andrew W. , Andrews Timothy J.
Published: December 2012

Whether the brain represents facial expressions as perceptual continua or as emotion categories remains controversial. Here, we measured the neural response to morphed images to directly address how facial expressions of emotion are represented in the brain. We found that face-selective regions in the posterior superior temporal sulcus and the amygdala responded selectively to changes in facial expression, independent of changes in identity. We then asked whether the responses in these regions reflected categorical or continuous neural representations of facial expression. Participants viewed images from continua generated by morphing between faces posing different expressions such that the expression could be the same, could involve a physical change but convey the same emotion, or could differ by the same physical amount but be perceived as two different emotions. We found that the posterior superior temporal sulcus was equally sensitive to all changes in facial expression, consistent with a continuous representation. In contrast, the amygdala was only sensitive to changes in expression that altered the perceived emotion, demonstrating a more categorical representation. These results offer a resolution to the controversy about how facial expression is processed in the brain by showing that both continuous and categorical representations underlie our ability to extract this important social cue.
Mineral dust photochemistry induces nucleation events in the presence of SO2
Authors: Dupart Yoan , King Stephanie M. , Nekat Bettina , Nowak Andreas , Wiedensohler Alfred , Herrmann Hartmut , David Gregory , Thomas Benjamin , Miffre Alain , Rairoux Patrick , D’Anna Barbara , George Christian
Published: December 2012

Large quantities of mineral dust particles are frequently ejected into the atmosphere through the action of wind. The surface of dust particles acts as a sink for many gases, such as sulfur dioxide. It is well known that under most conditions, sulfur dioxide reacts on dust particle surfaces, leading to the production of sulfate ions. In this report, for specific atmospheric conditions, we provide evidence for an alternate pathway in which a series of reactions under solar UV light produces first gaseous sulfuric acid as an intermediate product before surface-bound sulfate. Metal oxides present in mineral dust act as atmospheric photocatalysts promoting the formation of gaseous OH radicals, which initiate the conversion of SO2to H2SO4in the vicinity of dust particles. Under low dust conditions, this process may lead to nucleation events in the atmosphere. The laboratory findings are supported by recent field observations near Beijing, China, and Lyon, France.
Vocal learning is constrained by the statistics of sensorimotor experience
Authors: Sober Samuel J. , Brainard Michael S.
Published: December 2012

The brain uses sensory feedback to correct behavioral errors. Larger errors by definition require greater corrections, and many models of learning assume that larger sensory feedback errors drive larger motor changes. However, an alternative perspective is that larger errors drive learning less effectively because such errors fall outside the range of errors normally experienced and are therefore unlikely to reflect accurate feedback. This is especially crucial in vocal control because auditory feedback can be contaminated by environmental noise or sensory processing errors. A successful control strategy must therefore rely on feedback to correct errors while disregarding aberrant auditory signals that would lead to maladaptive vocal corrections. We hypothesized that these constraints result in compensation that is greatest for smaller imposed errors and least for larger errors. To test this hypothesis, we manipulated the pitch of auditory feedback in singing Bengalese finches. We found that learning driven by larger sensory errors was both slower than that resulting from smaller errors and showed less complete compensation for the imposed error. Additionally, we found that a simple principle could account for these data: the amount of compensation was proportional to the overlap between the baseline distribution of pitch production and the distribution experienced during the shift. Correspondingly, the fraction of compensation approached zero when pitch was shifted outside of the song’s baseline pitch distribution. Our data demonstrate that sensory errors drive learning best when they fall within the range of production variability, suggesting that learning is constrained by the statistics of sensorimotor experience.
Topographically induced hierarchical assembly and geometrical transformation of focal conic domain arrays in smectic liquid crystals
Authors: Honglawan Apiradee , Beller Daniel A. , Cavallaro Marcello , Kamien Randall D. , Stebe Kathleen J. , Yang Shu
Published: December 2012

Controlling topological defects in 3D liquid crystal phases is a crucial element in the development of novel devices, from blue-phase displays to passive biochemical sensors. However, it remains challenging to realize the 3D topological conditions necessary to robustly and arbitrarily direct the formation of defects. Here, using a series of short pillar arrays as topological templates, we demonstrate the hierarchical assembly of focal conic domains (FCDs) in smectic-A liquid crystals that break the underlying symmetry of the pillar lattice, exhibit tunable eccentricity, and together develop a nontrivial yet organized array of defects. The key to our approach lies in the selection of the appropriate ratio of the size of focal domain to the dimension of pillars such that the system favors the “pinning” of FCD centers near pillar edges while avoiding the opposing effect of confinement. Our study unequivocally shows that the arrangement of FCDs is strongly influenced by the height and shape of the pillars, a feature that promotes both a variety of nontrivial self-assembled lattice types and the attraction of FCD centers to pillar edges, especially at regions of high curvature. Finally, we propose a geometric model to reconstruct the smectic layer structure in the gaps between neighboring FCDs to estimate the energetic effects of nonzero eccentricity and assess their thermodynamic stability.
In vivo localization and identification of SUMOylated proteins in the brain of His
6
-HA-SUMO1 knock-in mice
Authors: Tirard Marilyn , Hsiao He-Hsuan , Nikolov Miroslav , Urlaub Henning , Melchior Frauke , Brose Nils
Published: December 2012

SUMOylation, an essential posttranslational protein modification, is involved in many eukaryotic cellular signaling pathways. The identification of SUMOylated proteins is difficult, because SUMOylation sites in proteins are hard to predict, SUMOylated protein states are transient in vivo and labile in vitro, only a small substrate fraction is SUMOylated in vivo, and identification tools for natively SUMOylated proteins are rare. To solve these problems, we generated knock-in mice expressing His
6
-HA-SUMO1. By anti-HA immunostaining, we show that SUMO1 conjugates in neurons are only detectable in nuclei and annulate lamellae. By anti-HA affinity purification, we identified several hundred candidate SUMO1 substrates, of which we validated Smchd1, Ctip2, TIF1γ, and Zbtb20 as novel substrates. The knock-in mouse represents an excellent mammalian model for studies on SUMO1 localization and screens for SUMO1 conjugates in vivo.
Human macrophage and dendritic cell-specific silencing of high-mobility group protein B1 ameliorates sepsis in a humanized mouse model
Authors: Ye Chunting , Choi Jang-Gi , Abraham Sojan , Wu Haoquan , Diaz Dolores , Terreros Daniel , Shankar Premlata , Manjunath N.
Published: December 2012

Hypersecretion of cytokines by innate immune cells is thought to initiate multiple organ failure in murine models of sepsis. Whether human cytokine storm also plays a similar role is not clear. Here, we show that human hematopoietic cells are required to induce sepsis-induced mortality following cecal ligation and puncture (CLP) in the severely immunodeficient nonobese diabetic (NOD)/SCID/IL2Rγ
−/−
mice, and siRNA treatment to inhibit HMGB1 release by human macrophages and dendritic cells dramatically reduces sepsis-induced mortality. Following CLP, compared with immunocompetent WT mice, NOD/SCID/IL2Rγ
−/−
mice did not show high levels of serum HMGB1 or murine proinflammatory cytokines and were relatively resistant to sepsis-induced mortality. In contrast, NOD/SCID/IL2Rγ
−/−
mice transplanted with human hematopoietic stem cells [humanized bone marrow liver thymic mice (BLT) mice] showed high serum levels of HMGB1, as well as multiple human but not murine proinflammatory cytokines, and died uniformly, suggesting human cytokines are sufficient to induce organ failure in this model. Moreover, targeted delivery of HMGB1 siRNA to human macrophages and dendritic cells using a short acetylcholine receptor (AchR)-binding peptide [rabies virus glycoprotein (RVG)-9R] effectively suppressed secretion of HMGB1, reduced the human cytokine storm, human lymphocyte apoptosis, and rescued humanized mice from CLP-induced mortality. siRNA treatment was also effective when started after the appearance of sepsis symptoms. These results show that CLP in humanized mice provides a model to study human sepsis, HMGB1 siRNA might provide a treatment strategy for human sepsis, and RVG-9R provides a tool to deliver siRNA to human macrophages and dendritic cells that could potentially be used to suppress a variety of human inflammatory diseases.
Foxn1 maintains thymic epithelial cells to support T-cell development via
mcm2
in zebrafish
Authors: Ma Dongyuan , Wang Lu , Wang Sifeng , Gao Ya , Wei Yonglong , Liu Feng
Published: December 2012

The thymus is mainly comprised of thymic epithelial cells (TECs), which form the unique thymic epithelial microenvironment essential for intrathymic T-cell development. Foxn1, a member of the forkhead transcription factor family, is required for establishing a functional thymic rudiment. However, the molecular mechanisms underlying the function of Foxn1 are still largely unclear. Here, we show that Foxn1 functions in thymus development through Mcm2 in the zebrafish. We demonstrate that, in
foxn1
knockdown embryos, the thymic rudiment is reduced and T-cell development is impaired. Genome-wide expression profiling shows that a number of genes, including some known thymopoiesis genes, are dysregulated during the initiation of the thymus primordium and immigration of T-cell progenitors to the thymus. Functional and epistatic studies show that
mcm2
and
cdca7
are downstream of Foxn1, and
mcm2
is a direct target gene of Foxn1 in TECs. Finally, we find that the thymus defects in
foxn1
and
mcm2
morphants might be attributed to reduced cell proliferation rather than apoptosis. Our results reveal that the
foxn1
-
mcm2
axis plays a central role in the genetic regulatory network controlling thymus development in zebrafish.
Identification and elimination of an immunodominant T-cell epitope in recombinant immunotoxins based onPseudomonasexotoxin A
Authors: Mazor Ronit , Vassall Aaron N. , Eberle Jaime A. , Beers Richard , Weldon John E. , Venzon David J. , Tsang Kwong Y. , Benhar Itai , Pastan Ira
Published: December 2012

Recombinant immunotoxins (RITs) are chimeric proteins that are being developed for cancer treatment. We have produced RITs that contain PE38, a portion of the bacterial proteinPseudomonasexotoxin A. Because the toxin is bacterial, it often induces neutralizing antibodies, which limit the number of treatment cycles and the effectiveness of the therapy. Because T cells are essential for antibody responses to proteins, we adopted an assay to map the CD4+T-cell epitopes in PE38. We incubated peripheral blood mononuclear cells with an immunotoxin to stimulate T-cell expansion, followed by exposure to overlapping peptide fragments of PE38 and an IL-2 ELISpot assay to measure responses. Our observation of T-cell responses in 50 of 50 individuals correlates with the frequency of antibody formation in patients with normal immune systems. We found a single, highly immunodominant epitope in 46% (23/50) of the donors. The immunodominant epitope is DRB1-restricted and was observed in subjects with different HLA alleles, indicating promiscuity. We identified two amino acids that, when deleted or mutated to alanine, eliminated the immunodominant epitope, and we used this information to construct mutant RITs that are highly cytotoxic and do not stimulate T-cell responses in many donors.
Maximum entropy production, carbon assimilation, and the spatial organization of vegetation in river basins
Authors: del Jesus Manuel , Foti Romano , Rinaldo Andrea , Rodriguez-Iturbe Ignacio
Published: December 2012

The spatial organization of functional vegetation types in river basins is a major determinant of their runoff production, biodiversity, and ecosystem services. The optimization of different objective functions has been suggested to control the adaptive behavior of plants and ecosystems, often without a compelling justification. Maximum entropy production (MEP), rooted in thermodynamics principles, provides a tool to justify the choice of the objective function controlling vegetation organization. The application of MEP at the ecosystem scale results in maximum productivity (i.e., maximum canopy photosynthesis) as the thermodynamic limit toward which the organization of vegetation appears to evolve. Maximum productivity, which incorporates complex hydrologic feedbacks, allows us to reproduce the spatial macroscopic organization of functional types of vegetation in a thoroughly monitored river basin, without the need for a reductionist description of the underlying microscopic dynamics. The methodology incorporates the stochastic characteristics of precipitation and the associated soil moisture on a spatially disaggregated framework. Our results suggest that the spatial organization of functional vegetation types in river basins naturally evolves toward configurations corresponding to dynamically accessible local maxima of the maximum productivity of the ecosystem.
Knowledge of English verb phrase ellipsis by speakers of Arabic and Chinese
Authors: Hawkins Roger
Published: December 2012

English verb phrase ellipsis (VPE) involves both syntactic and discourse information. The present study investigates knowledge of these properties by L1 speakers of Arabic and Mandarin Chinese. Three issues are addressed. Can the participants acquire syntactic properties of VPE that differ from their L1s and are under-determined by positive evidence? Can they acquire all of the syntactic properties of VPE that differ from their L1s? Can they successfully integrate their knowledge of the syntax of VPE with discourse information determining felicity? Results from a sentence completion judgement task are broadly consistent with the L2 participants having Universal Grammar (UG)-constrained grammars for VPE, and with their being able to successfully integrate syntactic representations with discourse information. A persistent problem with an uninterpretable feature is discussed, as are the implications of the findings for the claim that VPE involves gradient grammaticality.
Persistent Organic Pollutants in Juvenile Chinook Salmon in the Columbia River Basin: Implications for Stock Recovery
Authors: Johnson Lyndal , Anulacion Bernadita , Arkoosh Mary , Olson O. Paul , Sloan Catherine , Sol Sean Y. , Spromberg Julann , Teel David J. , Yanagida Gladys , Ylitalo Gina
Published: December 2012

Among the populations of Pacific salmon and steelhead Oncorhynchus mykiss (anadromous Rainbow Trout) that inhabit the Columbia River basin there are currently 13 Evolutionarily Significant Units listed as threatened or endangered under the U.S. Endangered Species Act. While habitat loss, dams, overharvest, and climate change have been implicated in declining abundance of Chinook Salmon O. tshawytscha in the Columbia River, chemical contaminants represent an additional, yet poorly understood, conservation threat. In this study we measured concentrations of persistent organic pollutants in juvenile Chinook Salmon from various Columbia River stocks and life history types to evaluate the potential for adverse effects in these threatened and endangered fish. Polychlorinated biphenyls (PCBs) and dichlorodiphenyltrichloroethane (DDTs), recognized contaminants of concern in the Columbia basin, are the primary focus of this paper; other contaminants found in these fish, such as polybrominated diphenyl ethers and polycyclic aromatic hydrocarbons, are described in other publications. We frequently detected PCBs and DDTs in juvenile salmon and salmon diet samples from the lower Columbia River and estuary. In some cases, concentrations in salmon were above estimated thresholds for effects on growth and survival. The tidal freshwater portion of the estuary, between Portland, Oregon, and Longview, Washington, appeared to be an important source of contaminants for juvenile salmon and a region in which salmon were exposed to toxicants associated with urban development and industrial activity. Highest concentrations of PCBs were found in fall Chinook Salmon stocks with subyearling life histories, including populations from the upper Columbia and Snake rivers, which feed and rear in the tidal freshwater and estuarine portions of the river for extended periods. Spring Chinook Salmon stocks with yearling life histories that migrate more rapidly through the estuary generally had low PCB concentrations, but high concentrations of DDTs. Lipid content was low (<1%) in many of the fish examined, contributing to high lipid‐adjusted contaminants concentrations in some samples.
The novel synaptogenic protein Farp1 links postsynaptic cytoskeletal dynamics and transsynaptic organization
Authors: Cheadle Lucas , Biederer Thomas
Published: December 2012

Synaptic adhesion organizes synapses, yet the signaling pathways that drive and integrate synapse development remain incompletely understood. We screened for regulators of these processes by proteomically analyzing synaptic membranes lacking the synaptogenic adhesion molecule SynCAM 1. This identified FERM, Rho/ArhGEF, and Pleckstrin domain protein 1 (Farp1) as strongly reduced in SynCAM 1 knockout mice. Farp1 regulates dendritic filopodial dynamics in immature neurons, indicating roles in synapse formation. Later in development, Farp1 is postsynaptic and its 4.1 protein/ezrin/radixin/moesin (FERM) domain binds SynCAM 1, assembling a synaptic complex. Farp1 increases synapse number and modulates spine morphology, and SynCAM 1 requires Farp1 for promoting spines. In turn, SynCAM 1 loss reduces the ability of Farp1 to elevate spine density. Mechanistically, Farp1 activates the GTPase Rac1 in spines downstream of SynCAM 1 clustering, and promotes F-actin assembly. Farp1 furthermore triggers a retrograde signal regulating active zone composition via SynCAM 1. These results reveal a postsynaptic signaling pathway that engages transsynaptic interactions to coordinate synapse development.
Local phosphocycling mediated by LOK/SLK restricts ezrin function to the apical aspect of epithelial cells
Authors: Viswanatha Raghuvir , Ohouo Patrice Y. , Smolka Marcus B. , Bretscher Anthony
Published: December 2012

In this paper, we describe how a dynamic regulatory process is necessary to restrict microvilli to the apical aspect of polarized epithelial cells. We found that local phosphocycling regulation of ezrin, a critical plasma membrane–cytoskeletal linker of microvilli, was required to restrict its function to the apical membrane. Proteomic approaches and ribonucleic acid interference knockdown identified lymphocyte-oriented kinase (LOK) and SLK as the relevant kinases. Using drug-resistant LOK and SLK variants showed that these kinases were sufficient to restrict ezrin function to the apical domain. Both kinases were enriched in microvilli and locally activated there. Unregulated kinase activity caused ezrin mislocalization toward the basolateral domain, whereas expression of the kinase regulatory regions of LOK or SLK resulted in local inhibition of ezrin phosphorylation by the endogenous kinases. Thus, the domain-specific presence of microvilli is a dynamic process requiring a localized kinase driving the phosphocycling of ezrin to continually bias its function to the apical membrane.
Evolutionary rescue and the limits of adaptation
Authors: Bell Graham
Published: December 2012

Populations subject to severe stress may be rescued by natural selection, but its operation is restricted by ecological and genetic constraints. The cost of natural selection expresses the limited capacity of a population to sustain the load of mortality or sterility required for effective selection. Genostasis expresses the lack of variation that prevents many populations from adapting to stress. While the role of relative fitness in adaptation is well understood, evolutionary rescue emphasizes the need to recognize explicitly the importance of absolute fitness. Permanent adaptation requires a range of genetic variation in absolute fitness that is broad enough to provide a few extreme types capable of sustained growth under a stress that would cause extinction if they were not present. This principle implies that population size is an important determinant of rescue. The overall number of individuals exposed to selection will be greater when the population declines gradually under a constant stress, or is progressively challenged by gradually increasing stress. In gradually deteriorating environments, survival at lethal stress may be procured by prior adaptation to sublethal stress through genetic correlation. Neither the standing genetic variation of small populations nor the mutation supply of large populations, however, may be sufficient to provide evolutionary rescue for most populations.
How competition affects evolutionary rescue
Authors: Osmond Matthew Miles , de Mazancourt Claire
Published: December 2012

Populations facing novel environments can persist by adapting. In nature, the ability to adapt and persist will depend on interactions between coexisting individuals. Here we use an adaptive dynamic model to assess how the potential for evolutionary rescue is affected by intra- and interspecific competition. Intraspecific competition (negative density-dependence) lowers abundance, which decreases the supply rate of beneficial mutations, hindering evolutionary rescue. On the other hand, interspecific competition can aid evolutionary rescue when it speeds adaptation by increasing the strength of selection. Our results clarify this point and give an additional requirement: competition must increase selection pressure enough to overcome the negative effect of reduced abundance. We therefore expect evolutionary rescue to be most likely in communities which facilitate rapid niche displacement. Our model, which aligns to previous quantitative and population genetic models in the absence of competition, provides a first analysis of when competitors should help or hinder evolutionary rescue.
Evolutionary rescue: an emerging focus at the intersection between ecology and evolution
Authors: Gonzalez Andrew , Ronce Ophélie , Ferriere Regis , Hochberg Michael E.
Published: December 2012

There is concern that the rate of environmental change is now exceeding the capacity of many populations to adapt. Mitigation of biodiversity loss requires science that integrates both ecological and evolutionary responses of populations and communities to rapid environmental change, and can identify the conditions that allow the recovery of declining populations. This special issue focuses on evolutionary rescue (ER), the idea that evolution might occur sufficiently fast to arrest population decline and allow population recovery before extinction ensues. ER emphasizes a shift to a perspective on evolutionary dynamics that focuses on short time-scales, genetic variants of large effects and absolute rather than relative fitness. The contributions in this issue reflect the state of field; the articles address the latest conceptual developments, and report novel theoretical and experimental results. The examples in this issue demonstrate that this burgeoning area of research can inform problems of direct practical concern, such as the conservation of biodiversity, adaptation to climate change and the emergence of infectious disease. The continued development of research on ER will be necessary if we are to understand the extent to which anthropogenic global change will reduce the Earth's biodiversity.
Efficacy of the Bilateral Ilioinguinal-Iliohypogastric Block with Intrathecal Morphine for Postoperative Cesarean Delivery Analgesia
Authors: Vallejo Manuel C. , Steen Talora L. , Cobb Benjamin T. , Phelps Amy L. , Pomerantz Joel M. , Orebaugh Steven L. , Chelly Jacques E.
Published: December 2012

The ilioinguinal-iliohypogastric (IIIH) block is frequently used as multimodal analgesia for lower abdominal surgeries. The aim of this study is to compare the efficacy of IIIH block using ultrasound visualization for reducing postoperative pain after caesarean delivery (CD) in patients receiving intrathecal morphine (ITM) under spinal anesthesia. Participants were randomly assigned to 1 of 3 treatment groups for the bilateral IIIH block: Group A = 10 mL of 0.5% bupivacaine, Group B = 10 mL of 0.5% bupivacaine on one side and 10 mL of a normal saline (NSS) placebo block on the opposite side, and Group C = 10 mL of NSS placebo per side. Pain and nausea scores, treatment for pain and nausea, and patient satisfaction were recorded for 48 hours after CD. No differences were noted with respect to pain scores or treatment for pain over the 48 hours. There were no differences to the presence of nausea (P=0.64), treatment for nausea (P=0.21), pruritus (P=0.39), emesis (P=0.35), or patient satisfaction (P=0.29). There were no differences in pain and nausea scores over the measured time periods (MANOVA,P>0.05). In parturients receiving ITM for elective CD, IIIH block offers no additional postoperative benefit for up to 48 hours.
The SWI2/SNF2 Chromatin Remodeling ATPase BRAHMA Represses Abscisic Acid Responses in the Absence of the Stress Stimulus inArabidopsis
Authors: Han Soon-Ki , Sang Yi , Rodrigues Americo ,   BIOL425 F2010, Wu Miin-Feng , Rodriguez Pedro L. , Wagner Doris
Published: December 2012

The survival of plants as sessile organisms depends on their ability to cope with environmental challenges. Of key importance in this regard is the phytohormone abscisic acid (ABA). ABA not only promotes seed dormancy but also triggers growth arrest in postgermination embryos that encounter water stress. This is accompanied by increased desiccation tolerance. Postgermination ABA responses in Arabidopsis thaliana are mediated in large part by the ABA-induced basic domain/leucine zipper transcription factor ABA INSENSITIVE5 (ABI5). Here, we show that loss of function of the SWI2/SNF2 chromatin remodeling ATPase BRAHMA (BRM) causes ABA hypersensitivity during postgermination growth arrest. ABI5 expression was derepressed in brm mutants in the absence of exogenous ABA and accumulated to high levels upon ABA sensing. This effect was likely direct; chromatin immunoprecipitation revealed BRM binding to the ABI5 locus. Moreover, loss of BRM activity led to destabilization of a nucleosome likely to repress ABI5 transcription. Finally, the abi5 null mutant was epistatic to BRM in postgermination growth arrest. In addition, vegetative growth defects typical of brm mutants in the absence of ABA treatment could be partially overcome by reduction of ABA responses, and brm mutants displayed increased drought tolerance. We propose a role for BRM in the balance between growth or stress responses.
To scavenge or not to scavenge, that is STILL the question
Authors: Allan Elizabeth G. , Kander Melissa C. , Carmichael Ian , Garman Elspeth F.
Published: December 2012

An extensive radiation chemistry literature would suggest that the addition of certain radical scavengers might mitigate the effects of radiation damage during protein crystallography diffraction data collection. However, attempts to demonstrate and quantify such an amelioration and its dose dependence have not yielded consistent results, either at room temperature (RT) or 100 K. Here the information thus far available is summarized and reasons for this lack of quantitative success are identified. Firstly, several different metrics have been used to monitor and quantify the rate of damage, and, as shown here, these can give results which are in conflict regarding scavenger efficacy. In addition, significant variation in results from data collected from crystals treated in nominally the same way has been observed. Secondly, typical crystallization conditions contain substantial concentrations of chemical species which already interact strongly with some of the X-ray-induced radicals that the added scavengers are intended to intercept. These interactions are probed here by the complementary technique of on-line microspectrophotometry carried out on solutions and crystals held both at 100 K and RT, the latter enabled by the use of a beamline-mounted humidifying device. With the help of computational chemistry, attempts are made to assign some of the characteristic spectral features observed experimentally. A further source of uncertainty undoubtedly lies in the challenge of reliably measuring the parameters necessary for the accurate calculation of the absorbed dose (e.g.crystal size and shape, beam profile) and its distribution within the volume of the crystal (an issue addressed in detail in another article in this issue). While microspectrophotometry reveals that the production of various species can be quenched by the addition of scavengers, it is less clear that this observation can be translated into a significant gain in crystal dose tolerance for macromolecular crystallographers.