bluuebunny/crossref_metadata_2025 huggingface dataset:
Surface effect on electronic and optical properties of Bi2Ti2O7 nanowires for visible light photocatalysis
Authors: Fu Q. , He T. , Li J. L. , Yang G. W.
Published: June 2012

We theoretically performed the structural, electronic, and optical properties of the pyrochlore Bi2Ti2O7 nanowires for photocatalytic applications using pseudopotential density-functional theory calculations. The groundwork of electronic structure calculations showed a possible band gap modification of the Bi2Ti2O7 nanowires compared to that of the bulk. The midband states induced by the oxygen atoms and bismuth atoms on the surface of nanowires leads to a shift in the valence band toward the conduction band, which enables reduction of the band gap. The calculated optical results indicated that the absorption edges shift of nanowires towards the red-light region. These theoretical results suggested that the pyrochlore Bi2Ti2O7 nanowires can be expected to be a promising candidate for photocatalytic applications such as solar-assisted water splitting reactions.
High mobility two-dimensional hole system on hydrogen-terminated silicon (111) surfaces
Authors: Hu Binhui , Kott Tomasz M. , McFarland Robert N. , Kane B. E.
Published: June 2012

We have realized a two-dimensional hole system (2DHS), in which the 2DHS is induced at an atomically flat hydrogen-terminated Si(111) surface by a negative gate voltage applied across a vacuum cavity. Hole densities up to 7.5 × 1011 cm−2 are obtained, and the peak hole mobility is about 104 cm2/Vs at 70 mK. The quantum Hall effect is observed. Shubnikov-de Haas oscillations show a beating pattern due to the spin-orbit effects, and the inferred zero-field spin splitting can be tuned by the gate voltage.
Room temperature electroluminescence from light-emitting diodes based on In0.5Ga0.5As/GaP self-assembled quantum dots
Authors: Song Yuncheng , Larry Lee Minjoo
Published: June 2012

Room-temperature electroluminescence from In0.5Ga0.5As/GaP(001) self-assembled quantum dot light emitting diodes is demonstrated. Output light versus input current measurements indicate that stacking multiple periods of self-assembled quantum dots can substantially increase the electroluminescence intensity. Aside from potential applications in transparent-substrate light emitting diodes, InxGa1-xAs/GaP self-assembled quantum dots could be a possible candidate for monolithic integration of optoelectronics with Si due to recent advances in the growth of high-quality GaP on Si.
Experimental reduction of laser imprinting and Rayleigh–Taylor growth in spherically compressed, medium-Z-doped plastic targets
Authors: Fiksel G. , Hu S. X. , Goncharov V. A. , Meyerhofer D. D. , Sangster T. C. , Smalyuk V. A. , Yaakobi B. , Bonino M. J. , Jungquist R.
Published: June 2012

The effect of medium-Z doping of plastic ablators on laser imprinting and Rayleigh–Taylor (RT) instability growth was studied using spherical direct-drive implosions on the OMEGA Laser System [T. R. Boehly et al., Opt. Commun. 133, 495 (1977)]. The targets were spherical plastic (CH) shells, with an outer diameter of 860 μm and a thickness of 22 μm, volume doped with a varied concentration of Si (4.3% and 7.4%) and Ge (3.9%). The targets were imploded with 48 beams with a low-adiabat, triple-picket laser shape pulse with a peak intensity of 4×1014W/cm2, and a pulse duration of 2.5 ns. The shells were x-ray radiographed through a 400 -μm opening in the side of the target. The results show that volumetric impurity doping strongly reduces the shell density modulation and the instability growth rate. The amplitude of the initial imprint is reduced by a factor of 2.5 ± 0.5 for CH[4.3% Si] targets and by a factor of 3 ± 0.5 for CH[7.4% Si] and CH[3.9% Ge] targets. At the end of the acceleration phase, the reduction factor becomes 3 ± 0.5 and 5 ± 0.5, correspondingly. The RT instability growth rate in doped targets is reduced by a factor of 1.5 compared to undoped ones. Simulations using the two-dimensional, radiation-hydrodynamics code draco show good agreement with the measurements.
A method to integrate patterned electrospun fibers with microfluidic systems to generate complex microenvironments for cell culture applications
Authors: Wallin Patric , Zandén Carl , Carlberg Björn , Hellström Erkenstam Nina , Liu Johan , Gold Julie
Published: June 2012

The properties of a cell’s microenvironment are one of the main driving forces in cellular fate processes and phenotype expression invivo. The ability to create controlled cell microenvironments invitro becomes increasingly important for studying or controlling phenotype expression in tissue engineering and drug discovery applications. This includes the capability to modify material surface properties within well-defined liquid environments in cell culture systems. One successful approach to mimic extra cellular matrix is with porous electrospun polymer fiber scaffolds, while microfluidic networks have been shown to efficiently generate spatially and temporally defined liquid microenvironments. Here, a method to integrate electrospun fibers with microfluidic networks was developed in order to form complex cell microenvironments with the capability to vary relevant parameters. Spatially defined regions of electrospun fibers of both aligned and random orientation were patterned on glass substrates that were irreversibly bonded to microfluidic networks produced in poly-dimethyl-siloxane. Concentration gradients obtained in the fiber containing channels were characterized experimentally and compared with values obtained by computational fluid dynamic simulations. Velocity and shear stress profiles, as well as vortex formation, were calculated to evaluate the influence of fiber pads on fluidic properties. The suitability of the system to support cell attachment and growth was demonstrated with a fibroblast cell line. The potential of the platform was further verified by a functional investigation of neural stem cell alignment in response to orientation of electrospun fibers versus a microfluidic generated chemoattractant gradient of stromal cell-derived factor 1 alpha. The described method is a competitive strategy to create complex microenvironments invitro that allow detailed studies on the interplay of topography, substrate surface properties, and soluble microenvironment on cellular fate processes.
Design of acoustic beam aperture modifier using gradient-index phononic crystals
Authors: Lin Sz-Chin Steven , Tittmann Bernhard R. , Huang Tony Jun
Published: June 2012

This article reports the design concept of a novel acoustic beam aperture modifier using butt-jointed gradient-index phononic crystals (GRIN PCs) consisting of steel cylinders embedded in a homogeneous epoxy background. By gradually tuning the period of a GRIN PC, the propagating direction of acoustic waves can be continuously bent to follow a sinusoidal trajectory in the structure. The aperture of an acoustic beam can therefore be shrunk or expanded through change of the gradient refractive index profiles of the butt-jointed GRIN PCs. Our computational results elucidate the effectiveness of the proposed acoustic beam aperture modifier. Such an acoustic device can be fabricated through a simple process and will be valuable in applications, such as biomedical imaging and surgery, nondestructive evaluation, communication, and acoustic absorbers.
Millisecond annealing for advanced doping of dirty-silicon solar cells
Authors: Prucnal S. , Abendroth B. , Krockert K. , König K. , Henke D. , Kolitsch A. , Möller H. J. , Skorupa W.
Published: June 2012

Cost reduction is the overall goal in the further development of solar cell technologies. Multicrystalline silicon has attracted considerable attention because of its high stability against light soaking. In case of solar grade mc-Si, the rigorous control of metal impurities is desirable for solar cell fabrication. Although ion implantation doping got very recently distinct consideration for doping of monocrystalline solar material, efficient doping of multicrystalline solar material remains the main challenge to reduce costs. The influence of different annealing techniques on the optical and electrical properties of mc-Si solar cells was investigated. Flash lamp annealing (FLA) in the ms-range is demonstrated here as a very promising technique for the emitter formation at an overall low thermal budget. It could be presented that FLA at 1000 °C for 3 ms even without preheating is sufficient to recrystallize implanted silicon. The sheet resistance of FLA samples shows the values of about 50 Ω/sq. Especially, the minority carrier diffusion length for the FLA samples is in the range of 80 μm without surface passivation. This is up to one order of magnitude higher than that observed from rapid thermal annealing or furnace annealing samples. This technology shows great promise to replace the conventional POCl3-doping.
Electrical transport properties of (110)-oriented PrBa2(Cu0.8Ga0.2)3O7 thin films
Authors: Kandel Hom , Chen Tar-Pin , Bourdo Shawn , Iliev Milko N. , Watanabe Fumiya , Seo Hye-Won , Viswanathan Tito
Published: June 2012

The electrical transport properties of (110)-oriented PrBa2(Cu0.8Ga0.2)3O7 (PBCGO) thin films have been investigated. The electrical resistivity, ρ(T), of (110)-oriented PBCGO thin films is 8.91 × 105 Ω-cm at 77 K, about five orders of magnitude higher than that of the (110)-oriented PrBa2Cu3O7 thin films and follows Mott’s T−1/4 law up to room temperature. Our experimental results suggest filling and localization of holes in Cu-O chains of (110)-oriented PBCGO thin films. We observed very less proximity effect on YBa2Cu3O7 (YBCO)/PBCGO multilayers indicating that the (110)-oriented PBCGO thin films may serve as effective insulators in YBCO SIS tunneling Josephson junction.
Few-layer graphene growth on 6H-SiC(0001) surface at low temperature via Ni-silicidation reactions
Authors: Kang C. Y. , Fan L. L. , Chen S. , Liu Z. L. , Xu P. S. , Zou C. W.
Published: June 2012

Few-layer graphene (FLG) has been prepared by thermal annealing of SiC crystal via the surface Ni-silicidation reactions. Results reveal that the temperature plays an important role for the final FLG quality and the optimized annealing temperature is about 800 °C. The investigation of surface morphology and microstructure for the FLG sample indicates that after the rapid cooling, the carbon atoms will segregate to form the FLG layer and the NiSix particles will congregate on the top surface. The mechanism of the FLG formation on SiC surface assisted by the Ni ultra-thin layer is briefly discussed based on the experimental results.
Phylogenetic assessment of the Caribbean weevil genus Lachnopus Schoenherr (Coleoptera:Curculionidae:Entiminae)
Authors: Girón Jennifer C. , Franz Nico M.
Published: June 2012

The genus Lachnopus Schoenherr (Coleoptera : Curculionidae : Entiminae : Geonemini Gistel), with 66 species described to date, is the largest and most widespread entimine weevil genus in the Caribbean region. The monophyly and internal phylogenetic composition of Lachnopus are tested, using a cladistic analysis of 61 adult morphological characters of 31 ingroup species and five outgroup taxa representing the genera Diaprepes Schoenherr, Exophthalmus Schoenherr, Pachnaeus Schoenherr (all Eustylini), Ischionoplus Chevrolat (Geonemini) and Apodrosus Marshall (Polydrusini). The analysis produced two most parsimonious cladograms with a length of 167 steps, a consistency index of 36 and a retention index of 73. According to the strict consensus and preferred character state optimisations, the examined species of Lachnopus do not form a monophyletic entity, even though most species are placed in a major L. coffeae–L. guerinii ingroup clade, which stands in sister relationship to Ischionoplus. This major clade is constituted by at least three well-recognisable subgroups, each associated with a particular geographic range in the Caribbean region: (1) a widely distributed L. coffeae–L. lineicollis ‘grade’; (2) the Hispaniolan L. proteus–L. mercator clade; (3) and the L. hispidus–L. guerinii clade with species from Cuba, Florida and Jamaica. This study provides a sound phylogenetic basis for future revisions of Lachnopus and related geonemine genera.
Cis
- and
trans
-membrane interactions of synaptotagmin-1
Authors: Vennekate Wensi , Schröder Sabrina , Lin Chao-Chen , van den Bogaart Geert , Grunwald Matthias , Jahn Reinhard , Walla Peter Jomo
Published: June 2012

In neurotransmission synaptotagmin-1 tethers synaptic vesicles to the presynaptic plasma membrane by binding to acidic membrane lipids and SNAREs and promotes rapid SNARE-mediated fusion upon Ca
2+
triggering. However, recent studies suggested that upon membrane contact synaptotagmin may not only bind
in trans
to the target membrane but also
in cis
to its own membrane. Using a sensitive membrane tethering assay we have now dissected the structural requirements and concentration ranges for Ca
2+
-dependent and -independent
cis
-binding and
trans
-tethering in the presence and absence of acidic phospholipids and SNAREs. Using variants of membrane-anchored synaptotagmin in which the Ca
2+
-binding sites in the C2 domains and a basic cluster involved in membrane binding were disrupted we show that Ca
2+
-dependent
cis
-binding prevents
trans
-interactions if the
cis
-membrane contains 12–20% anionic phospholipids. Similarly, no
trans
-interactions were observable using soluble C2AB-domain fragments at comparable concentrations. At saturating concentrations, however, tethering was observed with soluble C2AB domains, probably due to crowding on the vesicle surface and competition for binding sites. We conclude that
trans
-interactions of synaptotagmin considered to be essential for its function are controlled by a delicate balance between
cis
- and
trans
-binding, which may play an important modulatory role in synaptic transmission.
Cell crawling mediates collective cell migration to close undamaged epithelial gaps
Authors: Anon Ester , Serra-Picamal Xavier , Hersen Pascal , Gauthier Nils C. , Sheetz Michael P. , Trepat Xavier , Ladoux Benoît
Published: June 2012

Fundamental biological processes such as morphogenesis and wound healing involve the closure of epithelial gaps. Epithelial gap closure is commonly attributed either to the purse-string contraction of an intercellular actomyosin cable or to active cell migration, but the relative contribution of these two mechanisms remains unknown. Here we present a model experiment to systematically study epithelial closure in the absence of cell injury. We developed a pillar stencil approach to create well-defined gaps in terms of size and shape within an epithelial cell monolayer. Upon pillar removal, cells actively respond to the newly accessible free space by extending lamellipodia and migrating into the gap. The decrease of gap area over time is strikingly linear and shows two different regimes depending on the size of the gap. In large gaps, closure is dominated by lamellipodium-mediated cell migration. By contrast, closure of gaps smaller than 20 μm was affected by cell density and progressed independently of Rac, myosin light chain kinase, and Rho kinase, suggesting a passive physical mechanism. By changing the shape of the gap, we observed that low-curvature areas favored the appearance of lamellipodia, promoting faster closure. Altogether, our results reveal that the closure of epithelial gaps in the absence of cell injury is governed by the collective migration of cells through the activation of lamellipodium protrusion.
Cold-inducible RNA-binding protein (Cirp) interacts with Dyrk1b/Mirk and promotes proliferation of immature male germ cells in mice
Authors: Masuda Tomoko , Itoh Katsuhiko , Higashitsuji Hiroaki , Higashitsuji Hisako , Nakazawa Noa , Sakurai Toshiharu , Liu Yu , Tokuchi Hiromu , Fujita Takanori , Zhao Yan , Nishiyama Hiroyuki , Tanaka Takashi , Fukumoto Manabu , Ikawa Masahito , Okabe Masaru , Fujita Jun
Published: June 2012

Cold-inducible RNA-binding protein (Cirp) was the first cold-shock protein identified in mammals. It is structurally quite different from bacterial cold-shock proteins and is induced in response to mild, but not severe, hypothermia. To clarify the physiological function of Cirp in vivo, we producedcirp-knockout mice. They showed neither gross abnormality nor defect in fertility, but the number of undifferentiated spermatogonia was significantly reduced and the recovery of spermatogenesis was delayed after treatment with a cytotoxic agent, busulfan. Cirp accelerated cell-cycle progression from G0 to G1 as well as from G1 to S phase in cultured mouse embryonic fibroblasts. Cirp directly bound to dual-specificity tyrosine-phosphorylation–regulated kinase 1B (Dyrk1b, also called Mirk) and inhibited its binding to p27, resulting in decreased phosphorylation and destabilization of p27. Cirp did not affect binding of Dyrk1b to cyclin D1 but inhibited phosphorylation of cyclin D1 by Dyrk1b, resulting in cyclin D1 stabilization. In the spermatogonial cell line GC-1spg, suppression of Cirp expression increased the protein level of p27, decreased that of cyclin D1, and decreased the growth rate, which depended on Dyrk1b. Consistent changes in the protein levels of p27 and cyclin D1 as well as the percentage of cells in G0 phase were observed in undifferentiated spermatogonia ofcirp-knockout mice. In undifferentiated spermatogonia of wild-type mice, Cirp and Dyrk1b colocalized in the nucleus. Thus, our study demonstrates that Cirp functions to fine-tune the proliferation of undifferentiated spermatogonia by interacting with Dyrk1b.
Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species
Authors: Stukenbrock Eva Holtgrewe , Christiansen Freddy Bugge , Hansen Troels Toftebjerg , Dutheil Julien Yann , Schierup Mikkel Heide
Published: June 2012

In a genome alignment of five individuals of the ascomycete fungus
Zymoseptoria pseudotritici
, a close relative of the wheat pathogen
Z. tritici
(synonym
Mycosphaerella graminicola
), we observed peculiar diversity patterns. Long regions up to 100 kb without variation alternate with similarly long regions of high variability. The variable segments in the genome alignment are organized into two main haplotype groups that have diverged ∼3% from each other. The genome patterns in
Z. pseudotritici
are consistent with a hybrid speciation event resulting from a cross between two divergent haploid individuals. The resulting hybrids formed the new species without backcrossing to the parents. We observe no variation in 54% of the genome in the five individuals and estimate a complete loss of variation for at least 30% of the genome in the entire species. A strong population bottleneck following the hybridization event caused this loss of variation. Variable segments in the
Z. pseudotritici
genome exhibit the two haplotypes contributed by the parental individuals. From our previously estimated recombination map of
Z. tritici
and the size distribution of variable chromosome blocks untouched by recombination we estimate that the hybridization occurred ∼380 sexual generations ago. We show that the amount of lost variation is explained by genetic drift during the bottleneck and by natural selection, as evidenced by the correlation of presence/absence of variation with gene density and recombination rate. The successful spread of this unique reproductively isolated pathogen highlights the strong potential of hybridization in the emergence of pathogen species with sexual reproduction.
Regulation of RAS oncogenicity by acetylation
Authors: Yang Moon Hee , Nickerson Seth , Kim Eric T. , Liot Caroline , Laurent Gaelle , Spang Robert , Philips Mark R. , Shan Yibing , Shaw David E. , Bar-Sagi Dafna , Haigis Marcia C. , Haigis Kevin M.
Published: June 2012

Members of the RAS small GTPase family regulate cellular responses to extracellular stimuli by mediating the flux through downstream signal transduction cascades. RAS activity is strongly dependent on its subcellular localization and its nucleotide-binding status, both of which are modulated by posttranslational modification. We have determined that RAS is posttranslationally acetylated on lysine 104. Molecular dynamics simulations suggested that this modification affects the conformational stability of the Switch II domain, which is critical for the ability of RAS to interact with guanine nucleotide exchange factors. Consistent with this model, an acetylation-mimetic mutation in K-RAS4B suppressed guanine nucleotide exchange factor-induced nucleotide exchange and inhibited in vitro transforming activity. These data suggest that lysine acetylation is a negative regulatory modification on RAS. Because mutations in RAS family members are extremely common in cancer, modulation of RAS acetylation may constitute a therapeutic approach.
Crown ether–electrolyte interactions permit nanopore detection of individual DNA abasic sites in single molecules
Authors: An Na , Fleming Aaron M. , White Henry S. , Burrows Cynthia J.
Published: June 2012

DNA abasic (AP) sites are one of the most frequent lesions in the genome and have a high mutagenic potential if unrepaired. After selective attachment of 2-aminomethyl-18-crown-6 (18c6), individual AP lesions are detected during electrophoretic translocation through the bacterial protein ion channel α-hemolysin (α-HL) embedded in a lipid bilayer. Interactions between 18c6 and Na
+
produce characteristic pulse-like current amplitude signatures that allow the identification of individual AP sites in single molecules of homopolymeric or heteropolymeric DNA sequences. The bulky 18c6-cation complexes also dramatically slow the DNA motion to more easily recordable levels. Further, the behaviors of the AP-18c6 adduct are different with respect to the directionalities of DNA entering the protein channel, and they can be precisely manipulated by altering the cation (Li
+
, Na
+
or K
+
) of the electrolyte. This method permits detection of multiple AP lesions per strand, which is unprecedented in other work. Additionally, insights into the thermodynamics and kinetics of 18c6-cation interactions at a single-molecule level are provided by the nanopore measurement.
High-cost, high-capacity backbone for global brain communication
Authors: van den Heuvel Martijn P. , Kahn René S. , Goñi Joaquín , Sporns Olaf
Published: June 2012

Network studies of human brain structural connectivity have identified a specific set of brain regions that are both highly connected and highly central. Recent analyses have shown that these putative hub regions are mutually and densely interconnected, forming a “rich club” within the human brain. Here we show that the set of pathways linking rich club regions forms a central high-cost, high-capacity backbone for global brain communication. Diffusion tensor imaging (DTI) data of two sets of 40 healthy subjects were used to map structural brain networks. The contributions to network cost and communication capacity of global cortico-cortical connections were assessed through measures of their topology and spatial embedding. Rich club connections were found to be more costly than predicted by their density alone and accounted for 40% of the total communication cost. Furthermore, 69% of all minimally short paths between node pairs were found to travel through the rich club and a large proportion of these communication paths consisted of ordered sequences of edges (“path motifs”) that first fed into, then traversed, and finally exited the rich club, while passing through nodes of increasing and then decreasing degree. The prevalence of short paths that follow such ordered degree sequences suggests that neural communication might take advantage of strategies for dynamic routing of information between brain regions, with an important role for a highly central rich club. Taken together, our results show that rich club connections make an important contribution to interregional signal traffic, forming a central high-cost, high-capacity backbone for global brain communication.
Widely accessible method for superresolution fluorescence imaging of living systems
Authors: Dedecker Peter , Mo Gary C. H. , Dertinger Thomas , Zhang Jin
Published: June 2012

Superresolution fluorescence microscopy overcomes the diffraction resolution barrier and allows the molecular intricacies of life to be revealed with greatly enhanced detail. However, many current superresolution techniques still face limitations and their implementation is typically associated with a steep learning curve. Patterned illumination-based superresolution techniques [e.g., stimulated emission depletion (STED), reversible optically-linear fluorescence transitions (RESOLFT), and saturated structured illumination microscopy (SSIM)] require specialized equipment, whereas single-molecule–based approaches [e.g., stochastic optical reconstruction microscopy (STORM), photo-activation localization microscopy (PALM), and fluorescence-PALM (F-PALM)] involve repetitive single-molecule localization, which requires its own set of expertise and is also temporally demanding. Here we present a superresolution fluorescence imaging method, photochromic stochastic optical fluctuation imaging (pcSOFI). In this method, irradiating a reversibly photoswitching fluorescent protein at an appropriate wavelength produces robust single-molecule intensity fluctuations, from which a superresolution picture can be extracted by a statistical analysis of the fluctuations in each pixel as a function of time, as previously demonstrated in SOFI. This method, which uses off-the-shelf equipment, genetically encodable labels, and simple and rapid data acquisition, is capable of providing two- to threefold-enhanced spatial resolution, significant background rejection, markedly improved contrast, and favorable temporal resolution in living cells. Furthermore, both 3D and multicolor imaging are readily achievable. Because of its ease of use and high performance, we anticipate that pcSOFI will prove an attractive approach for superresolution imaging.
A secreted protein is an endogenous chemorepellant in
Dictyostelium discoideum
Authors: Phillips Jonathan E. , Gomer Richard H.
Published: June 2012

Chemorepellants may play multiple roles in physiological and pathological processes. However, few endogenous chemorepellants have been identified, and how they function is unclear. We found that the autocrine signal AprA, which is produced by growing
Dictyostelium discoideum
cells and inhibits their proliferation, also functions as a chemorepellant. Wild-type cells at the edge of a colony show directed movement outward from the colony, whereas cells lacking AprA do not. Cells show directed movement away from a source of recombinant AprA and dialyzed conditioned media from wild-type cells, but not dialyzed conditioned media from
aprA
−
cells. The secreted protein CfaD, the G protein Gα8, and the kinase QkgA are necessary for the chemorepellant activity of AprA as well as its proliferation-inhibiting activity, whereas the putative transcription factor BzpN is dispensable for the chemorepellant activity of AprA but necessary for inhibition of proliferation. Phospholipase C and PI3 kinases 1 and 2, which are necessary for the activity of at least one other chemorepellant in
Dictyostelium
, are not necessary for recombinant AprA chemorepellant activity. Starved cells are not repelled by recombinant AprA, suggesting that aggregation-phase cells are not sensitive to the chemorepellant effect. Cell tracking indicates that AprA affects the directional bias of cell movement, but not cell velocity or the persistence of cell movement. Together, our data indicate that the endogenous signal AprA acts as an autocrine chemorepellant for
Dictyostelium
cells.
Dissociating effects of stimulus identity and load on working memory attentional guidance: Lengthening encoding time eliminates the effect of load but not identity
Authors: Tsvetanov Kamen A. , Arvanitis Theodoros N. , Humphreys Glyn W.
Published: June 2012

Effects of the identity and load of items in working memory (WM) on visual attention were examined. With a short interval between the WM item and a subsequent search task, there were effects of both load (slowed overall reaction times, RTs, in a WM condition relative to a mere repetition baseline) and identity (search RTs were affected by re-presentation of the item in WM in the search display). As the time to encode the initial display increased, the effects of load decreased while the effect of identity remained. The data indicate that the identity of stimuli in WM can affect the subsequent deployment of attention even when time is allowed for consolidation of the stimuli in WM, and that the WM effects are not causally related to the presence of cognitive load. The results are consistent with the identity of stimuli in WM modulating attention post the memory consolidation stage.
Bicarbonate and functional CFTR channel are required for proper mucin secretion and link cystic fibrosis with its mucus phenotype
Authors: Gustafsson Jenny K. , Ermund Anna , Ambort Daniel , Johansson Malin E.V. , Nilsson Harriet E. , Thorell Kaisa , Hebert Hans , Sjövall Henrik , Hansson Gunnar C.
Published: June 2012

Cystic fibrosis (CF) is caused by a nonfunctional chloride and bicarbonate ion channel (CF transmembrane regulator [CFTR]), but the link to the phenomenon of stagnant mucus is not well understood. Mice lacking functional CFTR (CftrΔ508) have no lung phenotype but show similar ileal problems to humans. We show that the ileal mucosa in CF have a mucus that adhered to the epithelium, was denser, and was less penetrable than that of wild-type mice. The properties of the ileal mucus of CF mice were normalized by secretion into a high concentration sodium bicarbonate buffer (∼100 mM). In addition, bicarbonate added to already formed CF mucus almost completely restored the mucus properties. This knowledge may provide novel therapeutic options for CF.
Push the Button
Authors: Ahmed Arif
Published: June 2012

The article discusses a well-known type of counterexample to Causal Decision Theory (CDT), in which CDT recommends an option that probably causes the best outcome while itself being evidence that it causes the worst. Intuition disagrees. Many philosophers accept that this justifies either modifying CDT or dropping it altogether. I argue to the contrary that (a) if intuition is right about this case, then transitivity of preference must be violated in another, but (b) this violation is untenable. I conclude that CDT stands.
Do Counterfactuals Ground the Laws of Nature? A Critique of Lange
Authors: Demarest Heather
Published: June 2012

Most philosophers of science hold that the laws of nature play an important role in determining which counterfactuals are true. Marc Lange reverses this dependence, arguing that it is the truth of certain counterfactuals that determines which statements are laws. I argue that the context sensitivity of counterfactual sentences makes it impossible for them to determine the laws. Next, I argue that Lange's view cannot avoid additional counterexamples concerning nested counterfactuals. Finally, I argue that Lange's counterfacts, posited as the ultimate ontological ground for the laws of nature, are unsuited to the role he demands of them.
Fourier analysis and expanding phenomena in finite fields
Authors: Hart Derrick , Li Liangpan , Shen Chun-Yen
Published: June 2012

In this paper we study set expansion in finite fields. Fourier analytic proofs are given for several results recently obtained by other authors using spectral graph theory. In addition, several generalizations of these results are given.

In the case thatAAis a subset of a prime fieldFp\mathbb F_pof size less thanp1/2p^{1/2}it is shown that|{a2+b:a,b∈A}|≥C1|A|147/146|\{a^2+b:a,b \in A\}|\geq C_1 |A|^{147/146}and<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="StartAbsoluteValue left-brace StartFraction b plus 1 Over a EndFraction colon a comma b element-of upper A right-brace EndAbsoluteValue greater-than-or-equal-to upper C 2 StartAbsoluteValue upper A EndAbsoluteValue Superscript 110 slash 109">|{b+1a:a,b∈A}|≥C2|A|110/109|\{\frac {b+1}{a}:a,b \in A\}|\geq C_2 |A|^{110/109}, where|⋅||\cdot |denotes the cardinality of a set andC1C_1andC2C_2are absolute constants.
MolClass: a web portal to interrogate diverse small molecule screen datasets with different computational models
Authors: Wildenhain Jan , FitzGerald Nicholas , Tyers Mike
Published: June 2012

Summary: The MolClass toolkit and data portal generate computational models from user-defined small molecule datasets based on structural features identified in hit and non-hit molecules in different screens. Each new model is applied to all datasets in the database to classify compound specificity. MolClass thus defines a likelihood value for each compound entry and creates an activity fingerprint across diverse sets of screens. MolClass uses a variety of machine-learning methods to find molecular patterns and can therefore also assign a priori predictions of bioactivities for previously untested molecules. The power of the MolClass resource will grow as a function of the number of screens deposited in the database.

Availability and implementation: The MolClass webportal, software package and source code are freely available for non-commercial use at http://tyerslab.bio.ed.ac.uk/molclass. A MolClass tutorial and a guide on how to build models from datasets can also be found on the web site. MolClass uses the chemistry development kit (CDK), WEKA and MySQL for its core functionality. A REST service is available at http://tyerslab.bio.ed.ac.uk/molclass/api based on the OpenTox API 1.2.

Contact:  jan.wildenhain@ed.ac.uk or md.tyers@umontreal.ca
Structural study of TTR-52 reveals the mechanism by which a bridging molecule mediates apoptotic cell engulfment
Authors: Kang Yanyong , Zhao Dongfeng , Liang Huanhuan , Liu Bin , Zhang Yan , Liu Qinwen , Wang Xiaochen , Liu Yingfang
Published: June 2012

During apoptosis, apoptotic cells are removed by professional phagocytes or neighboring engulfing cells either directly through phagocytic receptors or indirectly through bridging molecules that cross-link dying cells to phagocytes. However, how bridging molecules recognize “eat me” signals and phagocytic receptors to mediate engulfment remains unclear. Here, we report the structural and functional studies of Caenorhabditis elegans TTR-52, a recently identified bridging molecule that cross-links surface-exposed phosphatidylserine (PtdSer) on apoptotic cells to the CED-1 receptor on phagocytes. Crystal structure studies show that TTR-52 has an open β-barrel-like structure with some similarities to the PKCα-C2 domain. TTR-52 is proposed to bind PtdSer via an “ion-mediating” PtdSer-binding mode. Intensive functional studies show that CED-1 binds TTR-52 through its N-terminal EMI domain and that the hydrophobic region of the TTR-52 C terminus is involved in this interaction. In addition, unlike other PtdSer-binding domains, TTR-52 forms dimers, and its dimerization is important for its function in vivo. Our results reveal the first full-length structure of a bridging molecule and the mechanism underlying bridging molecule-mediated apoptotic cell recognition.
Tumor-derived microvesicles: shedding light on novel microenvironment modulators and prospective cancer biomarkers
Authors: D'Souza-Schorey Crislyn , Clancy James W.
Published: June 2012

Recent advances in the study of tumor-derived microvesicles reveal new insights into the cellular basis of disease progression and the potential to translate this knowledge into innovative approaches for cancer diagnostics and personalized therapy. Tumor-derived microvesicles are heterogeneous membrane-bound sacs that are shed from the surfaces of tumor cells into the extracellular environment. They have been thought to deposit paracrine information and create paths of least resistance, as well as be taken up by cells in the tumor microenvironment to modulate the molecular makeup and behavior of recipient cells. The complexity of their bioactive cargo—which includes proteins, RNA, microRNA, and DNA—suggests multipronged mechanisms by which microvesicles can condition the extracellular milieu to facilitate disease progression. The formation of these shed vesicles likely involves both a redistribution of surface lipids and the vertical trafficking of cargo to sites of microvesicle biogenesis at the cell surface. Current research also suggests that molecular profiling of these structures could unleash their potential as circulating biomarkers as well as platforms for personalized medicine. Thus, new and improved strategies for microvesicle identification, isolation, and capture will have marked implications in point-of-care diagnostics for cancer patients.
Three-dimensional Bragg coherent diffraction imaging of an extended ZnO crystal
Authors: Huang Xiaojing , Harder Ross , Leake Steven , Clark Jesse , Robinson Ian
Published: June 2012

A complex three-dimensional quantitative image of an extended zinc oxide (ZnO) crystal has been obtained using Bragg coherent diffraction imaging integrated with ptychography. By scanning a 2.5 µm-long arm of a ZnO tetrapod across a 1.3 µm X-ray beam with fine step sizes while measuring a three-dimensional diffraction pattern at each scan spot, the three-dimensional electron density and projected displacement field of the entire crystal were recovered. The simultaneously reconstructed complex wavefront of the illumination combined with its coherence properties determined by a partial coherence analysis implemented in the reconstruction process provide a comprehensive characterization of the incident X-ray beam.
Trends in populations of elephant and other large herbivores in Gonarezhou National Park, Zimbabwe, as revealed by sample aerial surveys
Authors: Dunham Kevin M.
Published: June 2012

For 30 years, regular aerial surveys in Zimbabwean protected areas were funded, designed and executed primarily to estimate elephant numbers. Other large herbivores were recorded, even though some species were not easily seen from the air in savannah woodlands. Population estimates for species other than elephant provided indices of abundance that could be used to determine temporal trends in population size. This study tests for significant trends in the abundance of large herbivores in Gonarezhou National Park, assuming that data from aerial sample surveys designed for elephant also provide accurate estimates of real trends in the populations of other herbivores. For each species, the exponential rate of population change was calculated using weighted regression, with the variance of this rate based on the sampling variances of the population estimates. Significant population trends were detected for eight species. Before the 1992 drought, elephant number was held approximately constant by frequent culls, but afterwards, it increased at a mean annual rate of 6.2% (confidence limits 4.0% and 8.6%). Elephants in cow herds increased at 7.3%, significantly faster than elephants in bull herds (−0.5%). Buffalo, eland, kudu, nyala, waterbuck, wildebeest and zebra all increased in number, after population declines during the drought.
Randomised clinical trial: pre‐dosing with taribavirin before starting pegylated interferon vs. standard combination regimen in treatment‐naïve patients with chronic hepatitis C genotype 1
Authors: Palmer M. , Rubin R. , Rustgi V. ,   Taribavirin Viral Kinetic Study Group
Published: June 2012

Background

Combination therapy with the ribavirin (RBV) prodrug taribavirin (TBV) and pegylated interferon (PIFN) has produced lower rates of anaemia than with RBV and PIFN. Studies have demonstrated that the sharpest decline in viral load during TBV therapy occurs at Weeks 4 through 6, when TBV reaches steady‐state blood levels.

Aim

The current proof‐of‐concept study was conducted to examine whether first‐order viral kinetics could be influenced by pre‐dosing TBV to steady state before introducing PIFN.

Methods

Therapy‐naïve patients with chronic hepatitis C virus (HCV) genotype 1 (G1) were randomised to receive (i) TBV 600 mg BID monotherapy for 4 weeks followed by combination therapy with PIFN [pre‐dosing arm (n = 23)] or (ii) TBV administered concurrently with PIFN [standard dosing arm (n = 19)].

Results

More patients achieved undetectable virus or a ≥2‐log10 reduction of HCV RNA at Week 4 in the pre‐dosing vs. the standard dosing arm [33% vs. 22% (P = 0.497)]. There was also a trend towards greater reduction in mean log10 change in HCV RNA in the pre‐dosing vs. the standard dosing arm, which was statistically significant at Day 1 [−0.34 ± 0.46 vs. 0.09 ± 0.32 (P < 0.003)] but not at other time points up to Week 24. No significant difference was observed in the rates of anaemia (haemoglobin <10 g/dL) between study arms (4.5% vs. 5.3%).

Conclusions

Pre‐dosing TBV prior to starting PIFN produces a trend towards improved efficacy although statistical significance was not reached in this small patient population. These results warrant larger clinical trials of TBV pre‐dosing.
Role of granulocyte/neutrophil transfusions for haematology/oncology patients in the modern era
Authors: Strauss Ronald G.
Published: June 2012

Infections continue to be a serious problem for severely neutropenic oncology and haematopoietic progenitor cell (HPC) transplant patients. Although it is now possible to collect much larger numbers of neutrophils (PMNs) from donors stimulated with granulocyte colony‐stimulating factor + corticosteroids, the efficacy of these ‘modern’ granulocyte/PMN transfusions, with higher doses of PMNs, has not been established by convincing randomized control trials. Accordingly, they cannot be recommended for standard therapy at this time.
Self‐esteem of children and adolescents with chronic illness: a meta‐analysis
Authors: Pinquart M.
Published: June 2012

Chronic illness may be a risk factor for low self‐esteem; however, previous meta‐analyses are inconclusive whether children with a chronic illness have lower self‐esteem than their healthy peers. The goal of the present study was to summarize available research in order to compare the self‐esteem of children and adolescents with a chronic illness with that of healthy children. Random‐effects meta‐analysis was used to integrate the results of 621 empirical studies that compare levels of self‐esteem of children with a chronic physical illness with healthy peers or general test norms. Studies were identified via the electronic databases Adolesc, Embase, Google Scholar, MEDLINE, PSNYDEX, PSYCINFO, and cross‐referencing. Children with chronic illnesses have lower self‐esteem than healthy peers or test norms (g=−0.18 standard deviation units). The lowest levels of self‐esteem were observed in children with chronic fatigue syndrome and chronic headaches. Lower levels of self‐esteem in children with a chronic illness were found in girls than in boys, in adolescents than in children, in children from developing or threshold countries, when results were collected from observer ratings rather than child reports, in studies published in the 1990s, and when children with chronic illnesses were directly compared with healthy children instead of test norms. Paediatricians, parents, and teachers should promote experiences of success and positive peer‐relations, which are important sources of self‐esteem. In addition, psychosocial interventions for children with chronic illnesses should be offered for children with reduced self‐esteem.
Does biological maturity actually confound gender‐related differences in physical activity in preadolescence?
Authors: Guinhouya B. C. , Fairclough S. J. , Zitouni D. , Samouda H. , Vilhelm C. , Zgaya H. , de Beaufort C. , Lemdani M. , Hubert H.
Published: June 2012

Aim

To examine: (i) if maturity‐related gender differences in moderate‐to‐vigorous physical activity (MVPA) depend on how maturity status is defined and measured; and (ii) the influence of maturity level on compliance with PA recommendations.

Methods

The study involved 253 children (139 boys) aged 9.9 ± 0.9 years, with mean stature and weight of 1.39 ± 0.08 m and 35.8 ± 8.8 kg respectively. Their PA was evaluated using an Actigraph accelerometer (Model 7164). Maturity was assessed using the estimated age at peak height velocity (APHV) and a standardized APHV by gender (i.e. centred APHV).

Results

Boys engaged in significantly more MVPA than girls (P < 0.0001). There was a significant correlation between the centred APHV and MVPA in boys (r = 0.20; P = 0.016), but not in girls (r = 0.13; P = 0.155). An ancova controlling for the estimated APHV showed no significant interactions between gender and APHV, and the main effect of gender on MVPA was negated. Conversely, there was a significant main effect of APHV on MVPA (F
1,249 = 6.12; P = 0.014; η
p
2 = 0.024). Only 9.1% of children met the PA recommendations, including 14.4% of boys and 2.6% of girls (P < 0.01). This observation also applies in both pre‐APHV (12.7% of boys vs. 2.4% of girls, P < 0.001) and post‐APHV children (23.8% of boys vs. 3.4% of girls, P < 0.0001). No differences in PA guidelines were observed between pre‐APHV and post‐APHV children.

Conclusions

Among prepubescent children, the influence of biological maturity on gender differences in PA may be a function of how maturity status is determined. The most physically active prepubescent children were those who were on time according to APHV.
A proline repeat polymorphism of the Frost gene of Drosophila melanogaster showing clinal variation but not associated with cold resistance
Authors: Hoffmann A. A. , Blacket M. J. , McKechnie S. W. , Rako L. , Schiffer M. , Rane R. V. , Good R. T. , Robin C. , Lee S. F.
Published: June 2012

Genetic polymorphisms underlying adaptive shifts in thermal responses are poorly known even though studies are providing a detailed understanding of these responses at the cellular and physiological levels. The Frost gene of Drosophila melanogaster is a prime candidate for thermal adaptation; it is up‐regulated under cold stress and knockdown of this gene influences cold resistance. Here we describe an amino‐acid INDEL polymorphism in proline repeat number in the structural component of this gene. The two main repeats, accounting for more than 90% of alleles in eastern Australia, show a strong clinal pattern; the 6P allele was at a high frequency in tropical locations, and the 10P allele was common in temperate populations. However, the frequency of these alleles was not associated with three different assays of cold resistance. Adult transcription level of Frost was also unrelated to cold resistance as measured through post chill coma mobility. The functional significance of the proline repeat polymorphism therefore remains unclear despite its clinal pattern. The data also demonstrate the feasibility of using Roche/454 sequencing for establishing clinal patterns.