bluuebunny/crossref_metadata_2025 huggingface dataset:
Coherent diffraction tomography of nanoislands from grazing-incidence small-angle x-ray scattering
Authors: Yefanov O. M. , Zozulya A. V. , Vartanyants I. A. , Stangl J. , Mocuta C. , Metzger T. H. , Bauer G. , Boeck T. , Schmidbauer M.
Published: March 2009

The combination of grazing-incidence small-angle x-ray scattering with tomographic and phase retrieval methods is presented for the reconstruction of the three-dimensional (3D) electron density of nanometer sized objects. The measured 3D intensity distribution in reciprocal space is used for the phase retrieval and reconstruction of the shape and electron density of epitaxial SiGe islands with the shape of truncated pyramids with a 200 nm square base. A spatial resolution below 20 nm demonstrated in this work cannot be achieved by traditional tomographic methods.
Magnetically induced enhancement of shot noise in graphene-based structures
Authors: Gong Yiyang , Guo Yong
Published: March 2009

The authors have investigated resonant tunneling in nonuniform magnetically modulated graphene-based double-barrier structures, which can be realized experimentally by depositing successive ferromagnetic stripes on graphene monolayer. The effects of Klein tunneling, resonant tunneling, and magnetically induced wave vector filtering on the shot noise are taken into consideration. It is found that the shot noise is enormously enhanced in antiparallel magnetization alignment, and striking Poissonian value plateaus of the Fano factor can be formed, which is dramatically distinguishable from that in parallel alignment. The results indicate that the shot noise could be a sensitive probe to reveal mechanism of electronic transport in graphene.
Organic solar cells using few-walled carbon nanotubes electrode controlled by the balance between sheet resistance and the transparency
Authors: Feng Yiyu , Ju Xiaohui , Feng Wei , Zhang Hongbo , Cheng Yingwen , Liu Jie , Fujii Akihiko , Ozaki Masanori , Yoshino Katsumi
Published: March 2009

Organic photovoltaic devices (OPD) using high conductive transparent few-walled carbon nanotubes (FWNT) film prepared by spraying was fabricated as a selective hole collection. Photovoltaic response with different sheet resistance (Rs) and the transparency (T) of FWNT film was investigated. Maximum efficiency of OPD up to 0.61% with the structure of FWNT (T=70%, Rs=86 Ω/◻)/poly(3-hexylthiophene): [6-6]phenyl-C61-butyric acid methyl ester/Al demonstrates a promising alternative of ITO (0.68%) with almost identical operation. The performance improvement results from the optimal balance between sheet resistance and transparency with three-dimensional network interface between nanotubes and polymers.
Enhancement of synchronized vortex lattice motion in hybrid magnetic/amorphous superconducting nanostructures
Authors: Perez de Lara D. , Alija A. A. , Gonzalez E. M. , Martin J. I. , Velez M. , Colino J. M. , Anguita J. V. , Vicent J. L.
Published: March 2009

Superconducting a-Mo3Si and Nb films have been grown on arrays of Ni nanodots. We have studied the vortex lattice dynamics close to critical temperatures. Different vortex lattice configurations are obtained with the same array unit cell. These different vortex lattices occur at matching conditions between the vortex lattice and the array unit cell. The interplay between the random intrinsic pinning of the superconducting films and the periodic pinning of the array govern the vortex lattice configurations. Different vortex lattice configurations and enhancement of synchronized vortex lattice motion are obtained by increasing the periodic pinning strength and decreasing the random pinning strength.
Laser-induced atomic fragment fluorescence spectroscopy: A facile technique for molecular spectroscopy of spin-forbidden states
Authors: Zhang Qun , Chen Yang , Keil Mark
Published: March 2009

Spectra of spin-forbidden and spin-allowed transitions in the mixed b Π3u∼A Σ1u+ state of Na2 are measured separately by two-photon excitation using a single tunable dye laser. The two-photon excitation produces Na∗(3p) by photodissociation, which is easily and sensitively detected by atomic fluorescence. At low laser power, only the A Σ1u+ state is excited, completely free of triplet excitation. At high laser power, photodissociation via the intermediate b Π3u triplet state becomes much more likely, effectively “switching” the observations from singlet spectroscopy to triplet spectroscopy with only minor apparatus changes. This technique of perturbation-assisted laser-induced atomic fragment fluorescence may therefore be especially useful as a general vehicle for investigating perturbation-related physics pertinent to the spin-forbidden states, as well as for studying allowed and forbidden states of other molecules.
Introduction of molecular scale porosity into semicrystalline polymer thin films using supercritical carbon dioxide
Authors: Gin Peter , Asada Mitsunori , Endoh Maya K. , Gedelian Cynthia , Lu Toh-Ming , Koga Tadanori
Published: March 2009

We report supercritical carbon dioxide (scCO2) technology used for forming a large degree of molecular scale porosity in semicrystalline polymer thin films. The following three steps were integrated: (i) pre-exposure to an organic solvent which melted crystalline structures but did not cause a decrease in thickness, (ii) scCO2 exposure under the unique conditions where the anomalous absorption of CO2 occurred, and (iii) subsequent quick evaporation of CO2 to preserve the swollen structures. This unified process resulted in homogenous low-density polyphenylene vinylene films (a 15% reduction in density) with the sustained structure for at least 6 months at room temperature.
The conical shape filament growth model in unipolar resistance switching of TiO2 thin film
Authors: Kim Kyung Min , Hwang Cheol Seong
Published: March 2009

This study examined the relationship between the conducting filament resistance and reset voltage during the resistance switching of TiO2 thin films assuming a filament with a conical shape. There was a critical resistance (∼20 Ω) of the set state above and below which the filament responded differently in response to the current. Maintaining a higher set state resistance was more beneficial in achieving a more uniform reset voltage. This filament model coincides well with the localized switching behavior and the recently microscopically observed filament shape.
Domain growth dynamics in single-domain-like BiFeO3 thin films
Authors: Chen Y. C. , Lin Q. R. , Chu Y. H.
Published: March 2009

We present a quantitative study of 180° domain wall motion in epitaxial BiFeO3 (111) films, which can be treated as a nearly ideal single-domain environment. The domains were dynamically written by applying voltage pulses and examined by the piezoresponse force microscope technique. A transition of domain growth behaviors from the activated type to the nonactivated type was observed when increasing the pulse voltages. The obtained activation field was close to the ideally thermodynamic switching field of BiFeO3. The asymmetry of activated fields showed the preference of the downward polarization in the BiFeO3/SrRuO3 films.
Room-temperature stability of Pt nanogaps formed by self-breaking
Authors: Prins F. , Hayashi T. , de Vos van Steenwijk B. J. A. , Gao B. , Osorio E. A. , Muraki K. , van der Zant H. S. J.
Published: March 2009

We present a method to make Pt nanometer-spaced electrodes that are free of metallic particles and stable at ambient conditions. The nanogaps are fabricated using feedback-controlled electromigration to form few-atom contacts. When performing this procedure at elevated temperatures (>420 K), the Pt contacts undergo self-breaking so that nanometer separated electrode pairs are formed. Once cooled down to lower temperatures, the nanogaps stabilize and can be characterized in detail. We find that current-voltage characteristics can be well fitted to a Simmons model for tunneling and gap-size fluctuations at room temperature determined from these fits stay within 0.6 Å for at least 50 h.
Dielectric breakdown of MgO magnetic tunnel junctions
Authors: Dimitrov D. V. , Gao Zheng , Wang Xiaobin , Jung Wonjoon , Lou Xiaohua , Heinonen Olle G.
Published: March 2009

We have investigated high-quality MgO tunnel junctions with a range of barrier thickness in order to identify the underlying physical mechanism responsible for dielectric breakdown. Two types of dielectric breakdown (“soft” and “hard”) were observed. Soft breakdown was observed in a few percent of the devices. This breakdown mode is not intrinsic and is attributed to tunnel junction imperfections. The hard breakdown occurs because a critical electric field is reached across the tunnel barrier. Other possible breakdown mechanisms, such as thermally driven mass diffusion or charge trapping, were not consistent with the hard dielectric breakdown data and were ruled out.
Mid-infrared tunable two-dimensional Talbot array illuminator
Authors: Maddaloni P. , Paturzo M. , Ferraro P. , Malara P. , De Natale P. , Gioffrè M. , Coppola G. , Iodice M.
Published: March 2009

We report the realization and characterization of a tunable, two-dimensional Talbot array illuminator for mid-infrared (MIR) wavelengths. A phase array, prepared by deposing tin-doped indium oxide electrodes on a square-lattice-geometry poled LiNbO3 sample, is illuminated by a difference-frequency generator emitting at 3 μm. Then, combining the electro-optic with the Talbot effect allows generation of a variety of light patterns under different values of distance and external electric field. Several potential applications with great relevance to the MIR spectral region are discussed.
Off on the Wrong Foot: Local Features in Biological Motion
Authors: Saunders Daniel R , Suchan Julia , Troje Nikolaus F
Published: March 2009

Biological-motion perception consists of a number of different phenomena. They include global mechanisms that support the retrieval of the coherent shape of a walker, but also mechanisms which derive information from the local motion of its parts about facing direction and animacy, independent of the particular shape of the display. A large body of the literature on biological-motion perception is based on a synthetic stimulus generated by an algorithm published by James Cutting in 1978 ( Perception7 393–405). Here we show that this particular stimulus lacks a visual invariant inherent to the local motion of the feet of a natural walker, which in more realistic motion patterns indicates the facing direction of a walker independent of its shape. Comparing Cutting's walker to a walker derived from motion-captured data of real human walkers, we find no difference between the two displays in a detection task designed such that observers had to rely on global shape. In a direction discrimination task, however, in which only local motion was accessible to the observer, performance on Cutting's walker was at chance, while direction could still be retrieved from the stimuli derived from the real walker.
Impact of secondary salinisation on freshwater ecosystems: effect of experimentally increased salinity on an intermittent floodplain wetland
Authors: James Kimberley R. , Hart Barry T. , Bailey Paul C. E. , Blinn Dean W.
Published: March 2009

Intermittent wetlands are particularly at risk from secondary salinisation because salts are concentrated during drawdown. We conducted a field experiment to examine the effect of adding salt at two different concentrations (to achieve nominal conductivities of 1000 μS cm–1 (low salt) and 3000 μS cm–1 (high salt)) on water quality, freshwater plants and epiphytic diatoms in an intermittent wetland during a 3.3-month drawdown. Conductivity increased to 3000 and 8500 μS cm–1 in low-salt and high-salt treatments respectively. Salt was apparently lost to the sediments, causing protons to be released from the sediments and reducing water column pH from 6.9 to 5.5 in the low-salt treatment and to 4.0 in the high-salt treatments. Forty days after adding the salt, biomass, %cover and flower production in Potamogeton cheesmanii were significantly reduced, whereas Amphibromus fluitans was not significantly affected. The salt effect on Triglochin procera was intermediate between the other two macrophytes. Significant reductions in the density, species richness and diversity of epiphytic diatoms occurred in the high-salt, but not in the low-salt, treatments. Our work shows that increases in salinity, and thus conductivity (up to 8500 μS cm–1), in low-alkalinity intermittent wetlands can change water quality, with significant adverse effects on some macrophyte and diatom communities.
Ontogeny of behaviour relevant to dispersal and connectivity in the larvae of two non-reef demersal, tropical fish species
Authors: Leis Jeffrey M. , Piola Richard F. , Hay Amanda C. , Wen Colin , Kan Kun-Ping
Published: March 2009

In demersal marine fishes, the dispersal of larvae determines the geographical scale of population connectivity, and larval behaviour may influence dispersal. Yet, little is known of the ontogeny of behaviours that can influence dispersal. The present study examined the development of these behaviours in pelagic larvae of tropical marine fishes (4–21 mm) that occupy non-reef habitats as adults: Eleutheronema tetradactylum (Polynemidae) and Leiognathus equulus (Leiognathidae). In the laboratory, critical speed (Ucrit) increased from 3 to 34 cm s–1 at 1.3–1.7 cm s–1 per mm of size, with the fastest larvae up to 50% faster. In situ speed increased from 4 to 25 cm s–1 at 0.7–2.2 cm s–1 per mm, and was 10–14 body length s–1 (60–90% of Ucrit). Endurance increased from 0 to >40 km at 2.4–4.7 km per mm. In the sea, orientation precision did not change ontogenetically, both species tended to swim in loops, and neither significant overall directionality nor ontogenetic change in orientation was present. Larval orientation of these non-reef species was less precise than that of reef fishes. The two species differed in depth distribution, and one ascended ontogenetically. These behaviours can potentially influence dispersal outcomes over the full size range of these larvae.
A dedicated thioesterase of the Hotdog-fold family is required for the biosynthesis of the naphthoquinone ring of vitamin K
1
Authors: Widhalm Joshua R. , van Oostende Chloë , Furt Fabienne , Basset Gilles J. C.
Published: March 2009

Phylloquinone (vitamin K
1
) is a bipartite molecule that consists of a naphthoquinone ring attached to a phytyl side chain. The coupling of these 2 moieties depends on the hydrolysis of the CoA thioester of 1,4-dihydroxy-2-naphthoate (DHNA), which forms the naphthalenoid backbone. It is not known whether such a hydrolysis is enzymatic or chemical. In this study, comparative genomic analyses identified orthologous genes of unknown function that in most species of cyanobacteria cluster with predicted phylloquinone biosynthetic genes. The encoded approximately 16-kDa proteins display homology with some Hotdog domain-containing CoA thioesterases that are involved in the catabolism of 4-hydroxybenzoyl-CoA and gentisyl-CoA (2,5-dihydroxybenzoyl-CoA) in certain soil-dwelling bacteria. The
Synechocystis
ortholog, encoded by gene slr0204, was expressed as a recombinant protein and was found to form DHNA as reaction product. Unlike its homologs in the Hotdog domain family, Slr0204 showed strict substrate specificity. The
Synechocystis slr0204
knockout was devoid of DHNA-CoA thioesterease activity and accumulated DHNA-CoA. As a result, knockout cells contained 13-fold less phylloquinone than their wild-type counterparts and displayed the typical photosensitivity to high light associated to phylloquinone deficiency in cyanobacteria.
A barley
cellulose synthase-like CSLH
gene mediates (1,3;1,4)-β-
d
-glucan synthesis in transgenic
Arabidopsis
Authors: Doblin Monika S. , Pettolino Filomena A. , Wilson Sarah M. , Campbell Rebecca , Burton Rachel A. , Fincher Geoffrey B. , Newbigin Ed , Bacic Antony
Published: March 2009

The walls of grasses and related members of the Poales are characterized by the presence of the polysaccharide (
1
,
3
,
1
,
4
)-β-D-glucan (β-glucan). To date, only members of the grass-specific
cellulose synthase-like F
(
CSLF
) gene family have been implicated in its synthesis. Assuming that other grass-specific
CSL
genes also might encode synthases for this polysaccharide, we cloned
HvCSLH1
, a
CSLH
gene from barley (
Hordeum vulgare
L.), and expressed an epitope-tagged version of the cDNA in
Arabidopsis
, a species with no
CSLH
genes and no β-glucan in its walls. Transgenic
Arabidopsis
lines that had detectable amounts of the epitope-tagged HvCSLH1 protein accumulated β-glucan in their walls. The presence of β-glucan was confirmed by immunoelectron microscopy (immuno-EM) of sectioned tissues and chemical analysis of wall extracts. In the chemical analysis, characteristic tri- and tetra-saccharides were identified by high-performance anion-exchange chromatography and MALDI-TOF MS following their release from transgenic
Arabidopsis
walls by a specific β-glucan hydrolase. Immuno-EM also was used to show that the epitope-tagged HvCSLH1 protein was in the endoplasmic reticulum and Golgi-associated vesicles, but not in the plasma membrane. In barley,
HvCSLH1
was expressed at very low levels in leaf, floral tissues, and the developing grain. In leaf, expression was highest in xylem and interfascicular fiber cells that have walls with secondary thickenings containing β-glucan. Thus both the
CSLH
and
CSLF
families contribute to β-glucan synthesis in grasses and probably do so independently of each other, because there is no significant transcriptional correlation between these genes in the barley tissues surveyed.
𝑧-classes of isometries of the hyperbolic space
Authors: Gongopadhyay Krishnendu , Kulkarni Ravi
Published: March 2009

LetGGbe a group. Two elementsx,yx, yare said to bezz-equivalentif their centralizers are conjugate inGG. The class equation ofGGis the partition ofGGinto conjugacy classes. Further decomposition of conjugacy classes intozz-classes provides important information about the internal structure of the group; cf. J. Ramanujan Math. Soc. 22 (2007), 35-56, for the elaboration of this theme.

LetI(Hn)I(\mathbb {H}^n)denote the group of isometries of the hyperbolicnn-space, and letIo(Hn)I_o(\mathbb {H}^n)be the identity component ofI(Hn)I(\mathbb {H}^n). We show that the number ofzz-classes inI(Hn)I(\mathbb {H}^n)is finite. We actually compute their number; cf. theorem 1.3. We interpret the finiteness ofzz-classes as accounting for the finiteness of “dynamical types” inI(Hn)I(\mathbb {H}^n). Along the way we also parametrize conjugacy classes. We mainly use the linear model of the hyperbolic space for this purpose. This description of parametrizing conjugacy classes appears to be new; cf. Academic Press, New York, 1974, 49–87 and Conformal geometry (Bonn, 1985/1986), 41–64, Aspects Math., E12, Vieweg, Braunschweig, 1988, for previous attempts. Ahlfors (Differential Geometry and Complex Analysis (Springer, 1985), 65–73) suggested the use of Clifford algebras to deal with higher dimensional hyperbolic geometry; cf. Ann. Acad. Sci. Fenn. Ser. A I Math. 10 (1985), 15–27, Quasiconformal Mappings and Analysis (Springer, 1998), 109–139, Complex Variables Theory Appl. 15 (1990), 125–133, and Adv. Math. 101 (1993), 87–113. These works may be compared to the approach suggested in this paper.

In dimensions22and33, by remarkable Lie-theoretic isomorphisms,Io(H2)I_o(\mathbb {H}^2)andIo(H3)I_o(\mathbb {H}^3)can be lifted toGLo(2,R)GL_o(2, \mathbb {R}), andGL(2,C)GL(2, \mathbb {C})respectively. For orientation-reversing isometries there are some modifications of these liftings. Using these liftings, in the appendix A, we have introduced a single numerical invariantc(A)c(A), to classify the elements ofI(H2)I(\mathbb {H}^2)andI(H3)I(\mathbb {H}^3), and explained the classical terminology.

Using the “Iwasawa decomposition” ofIo(Hn)I_o(\mathbb {H}^n), it is possible to equipHn\mathbb {H}^nwith a group structure. In the appendix B, we visualize the stratification of the groupHn\mathbb {H}^ninto its conjugacy andzz-classes.
DrosophilaBld10 Is a Centriolar Protein That Regulates Centriole, Basal Body, and Motile Cilium Assembly
Authors: Mottier-Pavie Violaine , Megraw Timothy L.
Published: March 2009

Cilia and flagella play multiple essential roles in animal development and cell physiology. Defective cilium assembly or motility represents the etiological basis for a growing number of human diseases. Therefore, how cilia and flagella assemble and the processes that drive motility are essential for understanding these diseases. Here we show that Drosophila Bld10, the ortholog of Chlamydomonas reinhardtii Bld10p and human Cep135, is a ubiquitous centriolar protein that also localizes to the spermatid basal body. Mutants that lack Bld10 assemble centrioles and form functional centrosomes, but centrioles and spermatid basal bodies are short in length. bld10 mutant flies are viable but male sterile, producing immotile sperm whose axonemes are deficient in the central pair of microtubules. These results show that Drosophila Bld10 is required for centriole and axoneme assembly to confer cilium motility.
Interaction between Connexin50 and Mitogen-activated Protein Kinase Signaling in Lens Homeostasis
Authors: Shakespeare Teresa I. , Sellitto Caterina , Li Leping , Rubinos Clio , Gong Xiaohua , Srinivas Miduturu , White Thomas W.
Published: March 2009

Both connexins and signal transduction pathways have been independently shown to play critical roles in lens homeostasis, but little is known about potential cooperation between these two intercellular communication systems. To investigate whether growth factor signaling and gap junctional communication interact during the development of lens homeostasis, we examined the effect of mitogen-activated protein kinase (MAPK) signaling on coupling mediated by specific lens connexins by using a combination of in vitro and in vivo assays. Activation of MAPK signaling pathways significantly increased coupling provided by Cx50, but not Cx46, in paired Xenopus laevis oocytes in vitro, as well as between freshly isolated lens cells in vivo. Constitutively active MAPK signaling caused macrophthalmia, cataract, glucose accumulation, vacuole formation in differentiating fibers, and lens rupture in vivo. The specific removal or replacement of Cx50, but not Cx46, ameliorated all five pathological conditions in transgenic mice. These results indicate that MAPK signaling specifically modulates coupling mediated by Cx50 and that gap junctional communication and signal transduction pathways may interact in osmotic regulation during postnatal fiber development.
Modeling Macro-Political Dynamics
Authors: Brandt Patrick T. , Freeman John R.
Published: March 2009

Analyzing macro-political processes is complicated by four interrelated problems: model scale, endogeneity, persistence, and specification uncertainty. These problems are endemic in the study of political economy, public opinion, international relations, and other kinds of macro-political research. We show how a Bayesian structural time series approach addresses them. Our illustration is a structurally identified, nine-equation model of the U.S. political-economic system. It combines key features of the model of Erikson, MacKuen, and Stimson (2002) of the American macropolity with those of a leading macroeconomic model of the United States (Sims and Zha, 1998; Leeper, Sims, and Zha, 1996). This Bayesian structural model, with a loosely informed prior, yields the best performance in terms of model fit and dynamics. This model 1) confirms existing results about the countercyclical nature of monetary policy (Williams 1990); 2) reveals informational sources of approval dynamics: innovations in information variables affect consumer sentiment and approval and the impacts on consumer sentiment feed-forward into subsequent approval changes; 3) finds that the real economy does not have any major impacts on key macropolity variables; and 4) concludes, contrary to Erikson, MacKuen, and Stimson (2002), that macropartisanship does not depend on the evolution of the real economy in the short or medium term and only very weakly on informational variables in the long term.
Landscape modelling spatial bottlenecks: implications for raccoon rabies disease spread
Authors: Rees Erin E. , Pond Bruce A. , Cullingham Catherine I. , Tinline Rowland R. , Ball David , Kyle Christopher J. , White Bradley N.
Published: March 2009

A landscape genetic simulation modelling approach is used to understand factors affecting raccoon rabies disease spread in southern Ontario, Canada. Using the Ontario Rabies Model, we test the hypothesis that landscape configuration (shape of available habitat) affects dispersal, as indicated by genetic structuring. We simulated range expansions of raccoons from New York into vacant landscapes in Ontario, in two areas that differed by the presence or absence of a landscape constriction. Our results provide theoretical evidence that landscape constriction acts as a vicariant bottleneck. We discuss implications for raccoon rabies spread.
A quantitative comparison of bird and bat wakes
Authors: Johansson L. Christoffer , Wolf Marta , Hedenström Anders
Published: March 2009

Qualitative comparison of bird and bat wakes has demonstrated significant differences in the structure of the far wake. Birds have been found to have a unified vortex wake of the two wings, while bats have a more complex wake with gradients in the circulation along the wingspan, and with each wing generating its own vortex structure. Here, we compare quantitative measures of the circulation in the far wake of three bird and one bat species. We find that bats have a significantly stronger normalized circulation of the start vortex than birds. We also find differences in how the circulation develops during the wingbeat as demonstrated by the ratio of the circulation of the dominant start vortex and the total circulation of the same sense. Birds show a more prominent change with changing flight speed and a relatively weaker start vortex at minimum power speed than bats. We also find that bats have a higher normalized wake loading based on the start vortex, indicating higher relative induced drag and therefore less efficient lift generation than birds. Our results thus indicate fundamental differences in the aerodynamics of bird and bat flight that will further our understanding of the evolution of vertebrate flight.
Broad-scale determinants of non-native fish species richness are context-dependent
Authors: Blanchet Simon , Leprieur Fabien , Beauchard Olivier , Staes Jan , Oberdorff Thierry , Brosse Sébastien
Published: March 2009

Identifying the factors determining the non-native species richness (NNSR) in a given area is essential for preventing species invasions. The relative importance of human-related and natural factors considered for explaining NNSR might depend upon both the spatial scale (i.e. the extent of the gradients sampled) and the historical context of the area surveyed. Here, using a worldwide database of freshwater fish occurrences, we tested whether the relative influence of human and ecological determinants of non-native fish species establishment at the scale of the biogeographic realm was consistent (i) with that observed worldwide, and (ii) among the different biogeographical realms. The prominent role of human activity in shaping the global (i.e. worldwide) pattern of NNSR cannot be directly extrapolated to the biogeographic realms. Furthermore, the relationships between human and ecological determinants and NNSR vary strikingly across biogeographic realms, revealing a strong context dependency of the determinants of NNSR. In particular, the human-related factors play a predominant role in explaining the establishment of non-native species in economically developed realms, while in the other realms environmental characteristics of the river basins best explained geographical patterns of NNSR. In the face of future biological invasions, considering both the spatial scale and the historical context of the surveyed area is crucial to adopt effective conservation strategies.
Flight speeds of swifts (Apus apus): seasonal differences smaller than expected
Authors: Henningsson P. , Karlsson H. , Bäckman J. , Alerstam T. , Hedenström A.
Published: March 2009

We have studied the nocturnal flight behaviour of the common swift (Apus apusL.), by the use of a tracking radar. Birds were tracked from Lund University in southern Sweden during spring migration, summer roosting flights and autumn migration. Flight speeds were compared with predictions from flight mechanical and optimal migration theories. During spring, flight speeds were predicted to be higher than during both summer and autumn due to time restriction. In such cases, birds fly at a flight speed that maximizes the overall speed of migration. For summer roosting flights, speeds were predicted to be lower than during both spring and autumn since the predicted flight speed is the minimum power speed that involves the lowest energy consumption per unit time. During autumn, we expected flight speeds to be higher than during summer but lower than during spring since the expected flight speed is the maximum range speed, which involves the lowest energy consumption per unit distance. Flight speeds during spring were indeed higher than during both summer and autumn, which indicates time-selected spring migration. Speeds during autumn migration were very similar to those recorded during summer roosting flights. The general result shows that swifts change their flight speed between different flight behaviours to a smaller extent than expected. Furthermore, the difference between flight speeds during migration and roosting among swifts was found to be less pronounced than previously recorded.
Loss of 26S Proteasome Function Leads to Increased Cell Size and Decreased Cell Number in Arabidopsis Shoot Organs
Authors: Kurepa Jasmina , Wang Songhu , Li Yan , Zaitlin David , Pierce Andrew J. , Smalle Jan A.
Published: March 2009

Although the final size of plant organs is influenced by environmental cues, it is generally accepted that the primary size determinants are intrinsic factors that regulate and coordinate cell proliferation and cell expansion. Here, we show that optimal proteasome function is required to maintain final shoot organ size in Arabidopsis (Arabidopsis thaliana). Loss of function of the subunit regulatory particle AAA ATPase (RPT2a) causes a weak defect in 26S proteasome activity and leads to an enlargement of leaves, stems, flowers, fruits, seeds, and embryos. These size increases are a result of increased cell expansion that compensates for a reduction in cell number. Increased ploidy levels were found in some but not all enlarged organs, indicating that the cell size increases are not caused by a higher nuclear DNA content. Partial loss of function of the regulatory particle non-ATPase (RPN) subunits RPN10 and RPN12a causes a stronger defect in proteasome function and also results in cell enlargement and decreased cell proliferation. However, the increased cell volumes in rpn10-1 and rpn12a-1 mutants translated into the enlargement of only some, but not all, shoot organs. Collectively, these data show that during Arabidopsis shoot development, the maintenance of optimal proteasome activity levels is important for balancing cell expansion with cell proliferation rates.
Aberrant DNA methylation profile of hepatocellular carcinoma and surgically resected margin
Authors: Lou Cheng , Du Zhi , Yang Bin , Gao YingTang , Wang YiJun , Fang ShuChang
Published: March 2009

Field cancerization currently described the theory of tumorigenesis and, until now, has been described in almost all organ systems except in liver. For this reason, we explore the presence of field cancerization in liver and its underlying clinical implication in hepatocellular carcinoma (HCC). In our study, methylation profile of HCC and surgically resected margin (SRM) were established by methylation‐specific PCR. Liver cirrhosis (LC), chronic hepatitis and normal liver were treated in the same way as the background control. The correlation analysis among the methylation profile of HCC, SRM and clinicopathological data of HCC patients was made respectively. Our results showed that methylation abnormities related to HCC, but not background disease existed in histologically negative SRM. Monoclonal and polyclonal models may coexist in field cancerization in liver. Patients with RIZ1 methylation in SRM had a shorter disease free survival. The local recurrence trend of early and later recurrence in HCC is potentially related to a second field tumor. From these results, we can suggest that field cancerization exists in liver. The study of field cancerization in liver plays an important role in hepatocarcinogenesis. Second field tumor derived form field cancerization may have important implications in HCC prognosis assessment that is worthy of further study. (Cancer Sci 2009; 100: 996–1004)
Antibodies to Helicobacter pylori and CagA protein are associated with the response to antibacterial therapy in patients with H. pylori‐positive API2–MALT1‐negative gastric MALT lymphoma
Authors: Sumida Tomonori , Kitadai Yasuhiko , Hiyama Toru , Shinagawa Kei , Tanaka Miwako , Kodama Michiyo , Masuda Hiroshi , Ito Masanori , Tanaka Shinji , Yoshihara Masaharu , Chayama Kazuaki
Published: March 2009

The aim of this study was to clarify predictive factors for response to eradication therapy in cases of Helicobacter pylori (H. pylori)‐positive API2–MALT1‐negative gastric mucosa‐associated lymphoid tissue (MALT) lymphoma. Sixty‐six patients who were examined for H. pylori infection and the presence of the API2–MALT1 chimeric transcript and who underwent H. pylori eradication therapy as first‐line therapy, were enrolled in this study. Immunohistochemical markers (p53, Ki‐67, and BCL10), microsatellite instability, loss of heterozygosity, serum levels of antibodies (anti‐H. pylori and anti‐CagA), and markers for gastritis (gastrin and pepsinogens) were examined, and the results were compared between patients whose tumors regressed completely after eradication therapy (responders) and patients whose tumors did not regress (non‐responders). Of the 66 patients with localized gastric MALT lymphoma, 47 (71.2%) showed complete remission after eradication therapy. None of the H. pylori‐negative (n = 9) and/or API2–MALT1‐positive (n = 7) patients responded to antibacterial treatment. Of 44 patients with H. pylori‐positive API2–MALT1‐negative gastric MALT lymphoma, 38 (86.4%) showed complete remission after eradication therapy. Titers of antibodies against H. pylori and CagA protein were significantly higher in the responders than in the non‐responders (P = 0.0235 and 0.0089, respectively). No significant difference between the groups was observed for the other factors. In conclusion, measurement of titers of serum antibodies to H. pylori and CagA protein may be useful for predicting the response to eradication therapy in patients with H. pylori‐positive API2–MALT1‐negative gastric MALT lymphoma. (Cancer Sci 2009; 100: 1075–1081)
Deficiency of regulatory T cells in children with autoimmune neutropenia
Authors: Nakamura Kazuhiro , Miki Mizuka , Mizoguchi Yoko , Karakawa Syuhei , Sato Takashi , Kobayashi Masao
Published: March 2009

CD4+ 25+ regulatory T cells (Tregs) play a role in controlling the development and progression of autoimmunity. The transcription factors Foxp3 and NFATC2 (NFAT1) play key roles in regulating the development and function of Tregs. The present study examined the involvement of Tregs in the pathophysiology of autoimmune neutropenia in children. Tregs were analysed by flow cytometry, based on the expressions of CD4, CD25, and intracellular Foxp3. The expressions of FOXP3 and NFATC2 mRNA in the CD4+ 25+ cells were determined by quantitative real‐time polymerase chain reaction. The percentage of CD4+ 25high Tregs in patients with autoimmune neutropenia was significantly lower than that in age‐matched healthy subjects. The intracellular expression of Foxp3 of CD4+ 25+ cells in patients similarly decreased in comparison to that in healthy subjects. The expression of FOXP3 and NFATC2 mRNA of CD4+ 25+ cells in patients also significantly decreased in comparison to that in healthy subjects. These results suggest that the deficiency of Tregs might thus play an important role in the immunopathophysiology of autoimmune neutropenia in children.
Oct‐4A isoform is expressed in human cord blood‐derived CD133 stem cells and differentiated progeny
Authors: Howe M.  , Zhao J.  , Bodenburg Y. , McGuckin C. P.  , Forraz N.  , Tilton R. G.  , Urban R. J.  , Denner L. 
Published: March 2009

Objectives: This study aims to establish whether the pluripotent embryonic stem cell marker and nuclear transcription factor Oct‐4A isoform is expressed in human umbilical cord blood CD133 stem cells (CD133 cells) and their differentiated progeny.

Materials and methods: CD133 cells were examined for expression of the embryonic stem cell marker Oct‐4A by reverse transcription–polymerase chain reaction using primers specific for the coding region of the Oct‐4A isoform. Immunocytochemistry and flow cytometry were performed using an antibody raised to a peptide from the unique amino‐terminal domain of the Oct‐4A isoform, that does not exist in the Oct‐4B isoform. Furthermore, specificity was confirmed by pre‐adsorption of the antibody with the peptide immunogen. Differentiation was determined before and after expansion in culture, by flow cytometry for haematopoietic stem cell and differentiation markers. For many studies, after 7 days of culture CD133‐positive and CD133‐negative cells were separated by flow cytometry for additional analyses. Multilineage haematopoietic proliferative potential was determined using colony‐forming assays.

Results: Freshly isolated CD133 cells expressed Oct‐4A mRNA and protein. The cells proliferated rapidly in culture producing only a small proportion of CD133‐positive cells and a much larger proportion of non‐self‐renewing CD133‐negative cells. Proliferation was also associated with loss of other adult stem cell markers, gain of differentiated haematopoietic markers, and maintenance of potential to generate haematopoietic lineages. Oct‐4A mRNA and protein were expressed throughout these changes.

Conclusions: Oct‐4A, which is associated with self‐renewal in embryonic stem cells, neither defines nor confers self‐renewal to CD133 stem cells.
Long‐term repeatability of winter basal metabolic rate and mass in a wild passerine
Authors: Broggi Juli , Hohtola Esa , Koivula Kari , Orell Markku , Nilsson Jan‐Åke
Published: March 2009

Basal metabolic rate (BMR) is an important trait in the study of energy management of an individual, especially in small wintering passerines from the north which have one of the highest energy turnover rates in vertebrates. Laboratory studies have shown the trait to be repeatable and heritable, despite its plastic nature. However there is currently a lack of empirical data from wild passerine populations.

We studied within‐ and between‐year repeatability of BMR, body mass and mass‐independent BMR from two populations of wintering great tits (Parus major) at the northern range of their distribution.

We found body mass, BMR and mass‐independent BMR to be highly repeatable both within and between years.

Our results provide the first evidence from a wild small passerine that, despite a large environmentally induced variation in metabolic rate, individuals show consistent metabolic strategies over periods even longer than a year.

Homeotherm species exposed to new or changing environmental conditions may be able to evolve specific energetic strategies in the wild, as previously found in captive species.
Effect of simulated environmental change on alpine soil arthropods
Authors: HÅGVAR SIGMUND , KLANDERUD KARI
Published: March 2009

The effects of environmental change on soil animal communities are poorly known. Norwegian mountains are subject to both atmospheric nitrogen deposition and increased temperature. In a nutrient poor alpineDryasheath in south Norway, soil arthropods were studied after 4 years of simulated environmental change by warming and/or nutrient addition. Warming alone only affected three low‐density Collembola species, while nutrient addition, with or without warming, greatly changed the dominance hierarchy of the microarthropod community. Certain Collembola species with a short (1 year) life cycle and predatory Gamasina mites increased markedly in density. These groups may have been favored by increased litter production, as plant biomass and litter producing graminoids and forbs increased significantly in plots with nutrient addition and nutrient addition combined with warming. Microarthropods with a longer life cycle, such as Oribatida and certain Collembola, were generally unaffected by nutrient addition and probably need more time to respond. The number of Oribatida taxa was, however, reduced in plots with nutrient addition, both with and without warming. A ground‐living species of Coccoidea (Homoptera) declined in plots with nutrient addition and warming compared with only warming, probably due to reduced cover of its host plantDryas. The density of Diptera larvae (Sciaridae and Chironomidae) was unaffected by the treatments. Our results show that increased nutrient availability in nutrient poor alpine soils may have large but different effects on different taxa of soil animals. Species with short life cycles reacted first. Nutrient addition and nutrient addition combined with warming resulted in several effects below ground on microarthropods as previously shown above ground on plants: Increased biomass, high dominance of a few rapid‐growing species, contrasting responses of closely related species, and a reduction in species numbers. These short‐term responses may have profound long‐term effects in this alpine ecosystem.
Annual emissions of dissolved CO2, CH4, and N2O in the subsurface drainage from three cropping systems
Authors: MINAMIKAWA KAZUNORI , NISHIMURA SEIICHI , SAWAMOTO TAKUJI , NAKAJIMA YASUHIRO , YAGI KAZUYUKI
Published: March 2009

Indirect emission of nitrous oxide (N2O), associated with nitrogen (N) leaching and runoff from agricultural lands is a major source of atmospheric N2O. Recent studies have shown that carbon dioxide (CO2) and methane (CH4) are also emitted via these pathways. We measured the concentrations of three dissolved greenhouse gases (GHGs) in the subsurface drainage from field lysimeter that had a shallow groundwater table. Aboveground fluxes of CH4 and N2O were monitored using an automated closed‐chamber system. The annual total emissions of dissolved and aboveground GHGs were compared among three cropping systems; paddy rice, soybean and wheat, and upland rice.

The annual drainage in the paddy rice, the soybean and wheat, and the upland rice plots was 1435, 782, and 1010 mm yr−1, respectively. Dissolved CO2 emissions were highest in the paddy rice plots, and were equivalent to 1.05–1.16% of the carbon storage in the topsoil. Dissolved CH4 emissions were also higher in the paddy rice plots, but were only 0.03–0.05% of the aboveground emissions. Dissolved N2O emissions were highest in the upland rice plots, where leached N was greatest due to small crop biomass. In the soybean and wheat plots, large crop biomass, due to double cropping, decreased the drainage volume, and thus decreased dissolved GHG emissions. Dissolved N2O emissions from both the soybean and wheat plots and the upland rice plots were equivalent to 50.3–67.3% of the aboveground emissions. The results indicate that crop type and rotation are important factors in determining dissolved GHG emissions in the drainage from a crop field.
Impact of human immunodeficiency virus 1 infection and inflammation on the composition and yield of cervical mononuclear cells in the female genital tract
Authors: Nkwanyana Nonhlanhla N. , Gumbi Pamela P. , Roberts Lindi , Denny Lynette , Hanekom Willem , Soares Andreia , Allan Bruce , Williamson Anna‐Lise , Coetzee David , Olivier Abraham J. , Burgers Wendy A. , Passmore Jo‐Ann
Published: March 2009

Cervical cytobrush sampling is a relatively non‐invasive method for obtaining mucosal cells from the female genital tract. To define mucosal immune cells sampled by cervical cytobrushing and to validate this approach for local immunity studies, we investigated the impact of human immunodeficiency virus (HIV) status and inflammation on the yield and composition of cervical cytobrush specimens. Cervical cytobrush samples were obtained from 89 chronically HIV‐infected and 46 HIV‐negative women. The HIV‐infected women had significantly higher yields of CD3+, CD45+, CD19+, CD14+, Langerin+ and CD24+ cells than the uninfected women. While cytobrush‐derived T cells from uninfected women were predominantly CD4+ (4·2 CD4 : 1 CD8), CD8+ T cells were predominant in HIV‐infected women (0·6 CD4 : 1 CD8). The majority of CD4+ and CD8+ T cells from HIV‐infected and uninfected women were of the effector memory (CD45RA− CCR7− CD27−) phenotype. HIV‐infected women had significantly elevated levels of interleukin (IL)‐1β, IL‐6 and IL‐8 in cervical supernatants compared with uninfected women. We observed a significant positive correlation between T‐cell counts and IL‐1β, tumour necrosis factor (TNF)‐α and IL‐12 concentrations. Neutrophil counts correlated significantly with cervical concentrations of IL‐1β, TNF‐α, IL‐8, IL‐6 and IL‐10. Antigen‐presenting cell numbers correlated significantly with TNF‐α and IL‐12 concentrations. HIV‐infected women on antiretroviral therapy had similar levels of cervical lymphocyte infiltration and inflammation to women naïve to therapy. In conclusion, we suggest that inflammation at the cervix and HIV infection are likely to be key determinants in the absolute number of mucosal immune cells recovered by cervical cytobrushing.
Peptidoglycan from lactobacilli inhibits interleukin‐12 production by macrophages induced by Lactobacillus casei through Toll‐like receptor 2‐dependent and independent mechanisms
Authors: Shida Kan , Kiyoshima‐Shibata Junko , Kaji Rumi , Nagaoka Masato , Nanno Masanobu
Published: March 2009

We previously showed that Lactobacillus strains having a rigid cell wall resistant to intracellular digestion can stimulate macrophages to induce large a quantity of interleukin‐12 (IL‐12). In this study, we examined the influence of lactobacilli and bacterial cell wall components on IL‐12 production by macrophages that was induced by Lactobacillus casei, which has a rigid cell wall. Easily digestible lactobacilli such as Lactobacillus johnsonii and Lactobacillus plantarum or their intact cell walls (ICWs) weakly or very weakly induced IL‐12 production by macrophages, and inhibitedL. casei‐induced IL‐12 production. While the ICW of L. casei was resistant to intracellular digestion and did not inhibit L. casei‐induced IL‐12 production, its polysaccharide‐depleted ICW, i.e. intact peptidoglycan, was sensitive to intracellular digestion and inhibited L. casei‐induced IL‐12 production. Furthermore, the peptidoglycans of L. johnsonii, L. plantarum and Staphylococcus aureus also inhibited L. casei‐induced IL‐12 production. Peptidoglycans from lactobacilli suppressed L. casei‐induced expression of IL‐12p40 but not IL‐12p35 mRNA. Inhibition of IL‐12 production by peptidoglycan was mitigated in Toll‐like receptor 2 (TLR2)‐deficient macrophages compared with the inhibition in wild‐type macrophages. A derivative of the minimal structural unit of peptidoglycan (6‐O‐stearoyl‐muramyl dipeptide) recognized by nucleotide‐binding oligomerization domain 2 (NOD2) could also suppress L. casei‐induced IL‐12 production. These findings demonstrate that easily digestible bacteria and peptidoglycan suppress IL‐12 production through pattern recognition receptors such as TLR2 and NOD2. IL‐12 production in the gut may be negatively regulated by the simultaneous inhibitory actions of various resident bacteria that are susceptible to intracellular digestion.