bluuebunny/crossref_metadata_2025 huggingface dataset:
Theory of piezoelectricity, electrostriction, and pyroelectricity in molecular crystals
Authors: Munn R. W.
Published: March 2010

A microscopic theory is presented for piezoelectricity, electrostriction, and pyroelectricity in molecular crystals. The required coefficients are derived by combining a theoretical treatment of the dependence of molecular dipole moments on molecular displacement and a generalized elastic theory for internal strain.
Electron impact ionization of furanose alcohols
Authors: Milosavljević A. R. , Kočišek J. , Papp P. , Kubala D. , Marinković B. P. , Mach P. , Urban J. , Matejčík Š.
Published: March 2010

Electron impact ionization of the gas phase 3-furanol, tetrahydro (3-hydroxytetrahydrofuran, 3HTHF) and 2-furanmethanol, tetrahydro (α-tetrahydrofurfuryl alcohol, THFA) molecules has been studied both experimentally and theoretically. The electron induced positive ion formation has been investigated experimentally using a crossed electron/neutral beams technique in combination with a quadrupole mass spectrometry. The mass spectra of both molecules have been determined at the incident electron energy of 70 eV. The ionization efficiency curves for each parent cation and a number of fragment cations have been measured near the threshold, and the corresponding appearance energies have been derived using an iterative fitting procedure based on the Wannier threshold law, taking into account the incident electron energy resolution. The appearance energies of the parent cations were experimentally determined to be (9.620±0.058) eV for (C4H8O2+/3HTHF) and (9.43±0.12) eV for (C5H10O2+/THFA), which are in a good agreement with G3MP2 calculated results: 9.480 and 9.419 eV, respectively. The most abundant cations in the mass spectra were determined to be 57 amu for 3HTHF and 71 amu for THFA, with the corresponding experimentally determined appearance energies of (10.22±0.10) eV and (9.574±0.062) eV, respectively. With the help of the energies calculated at B3LYP and G3MP2 levels of theory, the possible fragmentation patterns were discussed.
Normal mode analysis of protein dynamics in a non-Eckart frame
Authors: Fuchigami Sotaro , Omori Satoshi , Ikeguchi Mitsunori , Kidera Akinori
Published: March 2010

Normal mode analysis, with the all-atom or coarse-grained elastic network model, represents the equilibrium fluctuation of protein molecule in the Eckart frame, where contributions from external motions (translation and rotation) of the entire protein molecule are eliminated. On the other hand, domain motion is frequently exhibited by the relative motion of one domain to the other. Such a representation of fluctuations in the non-Eckart frame cannot be achieved by conventional normal mode analysis. Here, we propose normal mode analysis in a non-Eckart frame, where the external degrees of freedom are fixed for any portion of the system. In this analysis, the covariance matrix in the Eckart frame is transformed into one in the non-Eckart frame. Using a molecular dynamics simulation, we have confirmed the validity of the transformation formula and discussed the physical implication of the formula.
Effect of gate dielectrics on the device performance of SnO2 nanowire field effect transistors
Authors: Park Hyun Hee , Kang Pil Soo , Kim Gyu Tae , Ha Jeong Sook
Published: March 2010

The effect of the gate dielectric materials on the device performance of SnO2 nanowire field effect transistors (FETs) was investigated. The usage of Al-doped TiO2 layer with a large dielectric constant, whose atomic layer deposition process was optimized based on a serially connected capacitor model, enhanced the device performance with lower operation voltages compared to those of SiO2 or Al2O3 film in an accumulated channel. The higher dielectric constant is attributed to give a lower threshold voltage and a smaller subthreshold slope, which will be useful for the low voltage operation of the nanowire FETs.
Electric field-modulated amplified spontaneous emission in waveguides based on poly [2-methoxy-5-(2′-ethylhexyloxy)-1, 4-phenylene vinylene]
Authors: Zhang Bo , Hou Yanbing , Teng Feng , Lou Zhidong , Liu Xiaojun , Wang Yongsheng
Published: March 2010

We report amplified spontaneous emission (ASE) in an optically pumped symmetric thin film waveguide based on poly [2-methoxy-5-(2′-ethylhexyloxy)-1, 4-phenylene vinylene] (MEH-PPV) and electric-field modulation of the ASE in the MEH-PPV thin film. The electric-field quenching of the ASE at 620 nm and the spontaneous emission (SE) at 580 nm was observed, which increased with the electric field. The ASE intensity was more effectively quenched than the SE intensity as the field increased. The field dependence of the ASE and the SE intensity can be attributed to field-induced dissociation of photogenerated excitons in the MEH-PPV thin film.
Unipolar and bipolar fatigue in antiferroelectric lead zirconate thin films and evidences for switching-induced charge injection inducing fatigue
Authors: Lou X. J. , Wang J.
Published: March 2010

We show that unipolar fatigue does occur in antiferroelectric capacitors, confirming the predictions of a previous work [Appl. Phys. Lett. 94, 072901 (2009)]. We also show that unipolar fatigue in antiferroelectrics is less severe than bipolar fatigue if the driving field is of the same magnitude. This phenomenon has been attributed to the switching-induced charge injection, the main cause for polarization fatigue in ferroelectric and antiferroelectric materials. Other evidences for polarization fatigue caused by the switching-induced charge injection from the nearby electrode rather than the charge injection during the stable/quasistable leakage current stage are also discussed.
Quintet electronic states of N2
Authors: Hochlaf M. , Ndome H. , Hammoutène D.
Published: March 2010

We use large scale ab initio calculations to investigate the valence and valence-Rydberg quintet states of N2, their transition moments and their spin-orbit couplings to the close lying triplet electronic states. In addition to the A′ ∑5g+ and the C″ Π5ui states already known, we identify two weakly bound states (2 ∑5g+ and 2 Π5u) at ∼95 300 and 106 200 cm−1 above N2(X ∑1g+,  v=0). The other quintets are viewed to be repulsive in nature. Our potentials and couplings are used later to derive a set of accurate spectroscopic data for these quintets, their spin-orbit constants, and to elucidate the quintet-triplet dynamics and the role of these newly identified quintets for the production of cold atomic nitrogen.
A photoresponsive single electron transistor prepared from oligothiophene molecules and gold nanoparticles in a nanogap electrode
Authors: Yamaguchi Hidehiro , Terui Toshifumi , Noguchi Yutaka , Ueda Rieko , Nasu Keiro , Otomo Akira , Matsuda Kenji
Published: March 2010

Gold nanoparticle-oligothiophene pentamer networks were prepared in a nanogap electrode and their photoresponsive and conductive properties were measured. Coulomb diamond appeared in the differential conductance map of the device at cryogenic temperatures, indicating that the device worked as a single electron transistor. Upon irradiation with UV light, the current showed discontinuous changes. The I-VSD curve and differential conductance mapping before and after irradiation showed that the abrupt changes in current can be explained by a shift in the potential of the Coulomb island.
Near-ultraviolet light emitting diodes using strained ultrathin InN/GaN quantum well grown by metal organic vapor phase epitaxy
Authors: Lin Wei , Li Shuping , Kang Junyong
Published: March 2010

The near-ultraviolet (UV) light emitting diodes (LED) using ultrathin InN/GaN quantum well (QW) are fabricated by metal organic vapor phase epitaxy. The x-ray diffraction measurement shows well-defined satellite peaks, which implies abrupt interfaces and good layer periodicity of the QWs. The electroluminescence only exhibits a near-UV emission centered at approximately 3.14–3.18 eV without other emission peaks even the common yellow luminescence, which further confirms the advantages of the near-UV LED especially the minimization of phase separation, interdiffusion, and defects in the QWs. The near-UV emission is found to be stable even under high pulsed injection-current in contrast to the conventional InGaN based LED. This behavior indicates effective avoidance of the redshift related to the many body effect as well as the blueshift induced by band filling effect, localized states in the barrier, and the quantum confined stark effect. The realization of the near-UV LED using the ultrathin InN/GaN QW would facilitate the application of near-UV solid-state lighting source.
A Survey of IUE Spectra of the Active Binary System UX Arietis
Authors: Ekmekçi Fehmi
Published: March 2010

To investigate the ultraviolet (UV) activity of the bright, non-eclipsing, double-lined spectroscopic binary system UX Ari, IUE spectra (194 images) were taken from the IUE archive. The spectra, obtained during the period 1978–1996, show emission lines originating in the chromosphere and transition region. The long-wavelength low dispersion spectra were examined for ultraviolet excess by comparing the UV continuum level of UX Ari with the levels of k Cet and η Cep in the spectral range 2100–3200 Å. The individual Mgiih and k emission-line fluxes of component stars show that the contributions to the activity of the system for G5 V and K0 IV are about 20% and 80%, respectively. Apart from the flare event observed on 1979 Jan 1, there are some flux enhancements in the years 1987, 1991 and 1994 which may suggest existence of a periodicity of about 7–9 years. Examination of the ultraviolet excess in the system showed that there is some UV excess in UX Ari, which varies from 1% up to 24% with the exception of two images which showed no UV excess. The results revealed that there was an agreement on the source of emission regions which could be attributed to magnetic activity. The contribution of G5 V and K0 IV components to the Mgii activity of the system suggests a need to take into consideration the spot distribution not only on the surface of the K0 IV but also on the surface of the G5 V component of UX Ari.
Stellar Over-Densities in the Outer Halo of the Milky Way
Authors: Keller Stefan C.
Published: March 2010

This study presents a tomographic survey of a subset of the outer halo (10–40 kpc) drawn from the Sloan Digital Sky Survey Data Release 6. Halo substructure on spatial scales of >3 degrees is revealed as an excess in the local density of sub-giant stars. With an appropriate assumption of a model stellar isochrone it is possible for us to then derive distances to the sub-giant population. We describe three new candidate halo substructures; the 160- and 180-degree over-densities (at distances of 17 and 19 kpc respectively and radii of 1.3 and 1.5 kpc respectively) and an extended feature at 28 kpc that covers at least 162 deg2, the Virgo Equatorial Stream. In addition, we recover the Sagittarius dwarf galaxy (Sgr) leading-arm material and the Virgo Over-Density.

The derived distances, together with the number of sub-giant stars associated with each substructure, enables us to derive the integrated luminosity for the features. The tenuous, low surface brightness of the features strongly suggests an origin from the tidal disruption of an accreted galaxy or galaxies. Given the dominance of the tidal debris of Sgr in this region of the sky we investigate if our observations can be accommodated by tidal disruption models for Sgr. The clear discordance between observations and model predictions for known Sgr features means it is difficult to tell unambiguously if the new substructures are related to Sgr or not. Radial velocities in the stellar over-densities will be critical in establishing their origins.
The Adventures of the Rocketeer: Accelerated Motion Under the Influence of Expanding Space
Authors: Kwan Juliana , Lewis Geraint F. , James J. Berian
Published: March 2010

It is well known that interstellar travel is bounded by the finite speed of light, but on very large scales any rocketeer would also need to consider the influence of cosmological expansion on their journey. This paper examines accelerated journeys within the framework of Friedmann–Lemaître–Robertson–Walker universes, illustrating how the duration of a fixed acceleration sharply divides exploration over interstellar and intergalactic distances. Furthermore, we show how the universal expansion increases the difficulty of intergalactic navigation, with small uncertainties in cosmological parameters resulting in significantly large deviations. This paper also shows that, contrary to simplistic ideas, the motion of any rocketeer is indistinguishable from Newtonian gravity if the acceleration is kept small.
Balmer-Dominated Shocks: A Concise Review
Authors: Heng Kevin
Published: March 2010

A concise and critical review of Balmer-dominated shocks (BDSs) is presented, summarizing the state of theory and observations, including models with/without shock precursors and their synergy with atomic physics. Observations of BDSs in supernova remnants are reviewed on an object-by-object basis. The relevance of BDSs towards understanding the acceleration of cosmic rays in shocks is emphasized. Probable and possible detections of BDSs in astrophysical objects other than supernova remnants, including pulsar wind nebulae and high-redshift galaxies, are described. The case for the continued future of studying BDSs in astrophysics is made, including their relevance towards understanding electron–ion temperature equilibration in collisionless shocks.
psrchive and psrfits: Definition of the Stokes Parameters and Instrumental Basis Conventions
Authors: van Straten W. , Manchester R. N. , Johnston S. , Reynolds J. E.
Published: March 2010

This paper defines the mathematical convention adopted to describe an electromagnetic wave and its polarisation state, as implemented in the psrchive software and represented in the psrfits definition. Contrast is made between the convention that has been widely accepted by pulsar astronomers and the IAU/IEEE definitions of the Stokes parameters. The former is adopted as the PSR/IEEE convention, and a set of useful parameters are presented for describing the differences between the PSR/IEEE standard and the conventions (either implicit or explicit) that form part of the design of observatory instrumentation. To aid in the empirical determination of instrumental convention parameters, well-calibrated average polarisation profiles of PSR J0304+1932 and PSR J0742–2822 are presented at radio wavelengths of approximately 10, 20, and 40 cm.
Chromosome and morphological studies in the Mimosa debilis complex (Mimosoideae, Leguminosae) from southern South America
Authors: Morales Matías , Wulff Arturo F. , Fortunato Renée H. , Poggio Lidia
Published: March 2010

Mimosa debilis Humb. & Bonpl. ex Willd. and M. nuda Benth. were grouped in specific and infraspecific complexes. Both taxa showed exomorphological similarities, with conflicts in their taxonomic circumscription and present different ploidy levels. The objective of the present contribution was to analyse chromosome numbers of different populations and to evaluate morphological characters of specimens from Paraguay, Argentina and boundary regions. Chromosome numbers of M. debilis var. debilis (2n = 2x = 26 and 2n = 4x = 52) confirmed previous reports, whereas those of M. nuda var. glaberrima (2x = 26, 4x = 52), M. nuda var. gracilipes (2x = 26, 4x = 52) and M. nuda var. nuda (4x = 52) are presented for the first time. Variation was observed in habit, foliar and floral morphology and was correlated with the chromosome number and the geographical distribution of the taxa. Groups with stable morphological characters and restricted geographic distribution were identified. Also, the results showed a pattern of hybrid swarms and polyploids of different origin that may explain the existence of taxonomic conflicts in the M. debilis–M. nuda species complex. On the basis of these results, M. nuda should be included in the synonymy of M. debilis.
Polyploidy and possible implications for the evolutionary history of some Australian Danthonieae
Authors: Waters C. , Murray B. G. , Melville G. , Coates D. , Young A. , Virgona J.
Published: March 2010

Polyploidy is a widespread feature of some plants that allows for rapid speciation and occurs widely in Poaceae. However, there have been few studies of Australian native grasses reporting the distribution patterns of cytotypes and examining the potential role of different cytotypes in adaptation. We determined chromosome number for 48, 113, 8, 43 and 33 plants of Austrodanthonia bipartita (Link) H.P.Linder, A. caespitosa (Gaudich.) H.P.Linder, A. eriantha (Lindl.) H.P.Linder, A. fulva (Vickery) H.P.Linder and A. setacea (R.Br.) H.P.Linder, respectively, representing 28 wild populations collected in central western New South Wales. A widespread distribution is reported for tetraploids (2n = 48), whereas diploids (2n = 24) and a limited number of hexaploids (2n = 72) appear to be associated with northern and western populations. In all populations, coexistent cytotypes were found, although tetraploids were the most widespread cytotype for the most commonly occurring species, A. caespitosa. The occurrence of low frequencies of putative intermediate cytotypes, particularly triploids, in all five species provides evidence for inter-specific hybridisation and/or intra-specific crossing between cytotypes. The lack of common ecological factors (climate, edaphic or micro-site) that clearly distinguish diploid from tetraploid A. caespitosa plants provides further evidence for hybridisation between cytological races of this species.
Pollination ecology of the rare desert species Eremosparton songoricum (Fabaceae)
Authors: Shi X. , Wang J. C. , Zhang D. Y. , Gaskin J. F. , Pan B. R.
Published: March 2010

The pollination ecology of Eremosparton songoricum (Litv.) Vass., a rare desert species endemic to central Asia, was examined by a series of observational studies and manipulative experiments in two natural populations during 2007–2008. Results showed that the duration of flowering lasted 21 and 23 days, respectively, in Populations A and B from late May to late June in 2008. Anthesis of a single flower often lasted for 3 days. However, if pollinators were excluded, both the anthesis and stigma receptivity lasted 2 days longer. Mating-system experiment showed that E. songoricum was self-compatible and pollination success relied on pollinators. Fruit set after bagging without emasculation was 0.02 ± 0.01%. This suggested that spontaneous autogamy rarely happened. E. songoricum primarily relies on a combination of large floral display, secretion of nectar and a yellow ‘nectar guide’ on the standard to further attract pollinators, which may be the result of adaptation to a habitat with unreliable access to pollinators. A single flower produced ~0.18 μL and 0.50 μL of nectar during 2 days in Populations A and B, respectively. The peak secretion occurred at 1300–1500 hours, which overlapped with the climax of visitation of the effective pollinators at 1300–1400 hours. There were four effective pollinators in both populations, namely Colletes popovi Nosk., Megachile terminate Morawitz, Coelioxys sp. and Bembix planifrons F.Mor. The most frequent one, Colletes popovi Nosk., was observed pollinating many flowers of the same individual plant (65.8 ± 1.1%) in Population A, suggesting that geitonogamous self-pollination is unavoidable. Inbreeding depression played a role during the period from fertilisation to fruit maturation.
Spectral tuning in photoactive yellow protein by modulation of the shape of the excited state energy surface
Authors: Philip Andrew F. , Nome Rene A. , Papadantonakis George A. , Scherer Norbert F. , Hoff Wouter D.
Published: March 2010

Protein-chromophore interactions in photoreceptors often shift the chromophore absorbance maximum to a biologically relevant spectral region. A fundamental question regarding such spectral tuning effects is how the electronic ground state
S
0
and excited state
S
1
are modified by the protein. It is widely assumed that changes in energy gap between
S
0
and
S
1
are the main factor in biological spectral tuning. We report a generally applicable approach to determine if a specific residue modulates the energy gap, or if it alters the equilibrium nuclear geometry or width of the energy surfaces. This approach uses the effects that changes in these three parameters have on the absorbance and fluorescence emission spectra of mutants. We apply this strategy to a set of mutants of photoactive yellow protein (PYP) containing all 20 side chains at active site residue 46. While the mutants exhibit significant variation in both the position and width of their absorbance spectra, the fluorescence emission spectra are largely unchanged. This provides strong evidence against a major role for changes in energy gap in the spectral tuning of these mutants and reveals a change in the width of the
S
1
energy surface. We determined the excited state lifetime of selected mutants and the observed correlation between the fluorescence quantum yield and lifetime shows that the fluorescence spectra are representative of the energy surfaces of the mutants. These results reveal that residue 46 tunes the absorbance spectrum of PYP largely by modulating the width of the
S
1
energy surface.
Molecular cloning ofSdr4, a regulator involved in seed dormancy and domestication of rice
Authors: Sugimoto Kazuhiko , Takeuchi Yoshinobu , Ebana Kaworu , Miyao Akio , Hirochika Hirohiko , Hara Naho , Ishiyama Kanako , Kobayashi Masatomo , Ban Yoshinori , Hattori Tsukaho , Yano Masahiro
Published: March 2010

Seed dormancy provides a strategy for flowering plants to survive adverse natural conditions. It is also an important agronomic trait affecting grain yield, quality, and processing performance. We cloned a rice quantitative trait locus,Sdr4, which contributes substantially to differences in seed dormancy betweenjaponica(Nipponbare) andindica(Kasalath) cultivars.Sdr4expression is positively regulated byOsVP1, a global regulator of seed maturation, and in turn positively regulates potential regulators of seed dormancy and represses the expression of postgerminative genes, suggesting thatSdr4acts as an intermediate regulator of dormancy in the seed maturation program.Japonicacultivars have only the Nipponbare allele (Sdr4-n), which endows reduced dormancy, whereas both the Kasalath allele (Srd4-k) andSdr4-nare widely distributed in theindicagroup, indicating prevalent introgression.Srd4-kalso is found in the wild ancestorOryza rufipogon, whereasSdr4-nappears to have been produced through at least two mutation events from the closestO. rufipogonallele among the accessions examined. These results are discussed with respect to possible selection of the allele during the domestication process.
Modularity map of the network of human cell differentiation
Authors: Galvão Viviane , Miranda José G. V. , Andrade Roberto F. S. , Andrade José S. , Gallos Lazaros K. , Makse Hernán A.
Published: March 2010

Cell differentiation in multicellular organisms is a complex process whose mechanism can be understood by a reductionist approach, in which the individual processes that control the generation of different cell types are identified. Alternatively, a large-scale approach in search of different organizational features of the growth stages promises to reveal its modular global structure with the goal of discovering previously unknown relations between cell types. Here, we sort and analyze a large set of scattered data to construct the network of human cell differentiation (NHCD) based on cell types (nodes) and differentiation steps (links) from the fertilized egg to a developed human. We discover a dynamical law of critical branching that reveals a self-similar regularity in the modular organization of the network, and allows us to observe the network at different scales. The emerging picture clearly identifies clusters of cell types following a hierarchical organization, ranging from sub-modules to super-modules of specialized tissues and organs on varying scales. This discovery will allow one to treat the development of a particular cell function in the context of the complex network of human development as a whole. Our results point to an integrated large-scale view of the network of cell types systematically revealing ties between previously unrelated domains in organ functions.
Recruitment of lateral rostral prefrontal cortex in spontaneous and task-related thoughts
Authors: Dumontheil Iroise , Gilbert Sam J. , Frith Christopher D. , Burgess Paul W.
Published: March 2010

Behavioural and neuroimaging studies suggest that spontaneous and task-related thought processes share common cognitive mechanisms and neural bases. Lateral rostral prefrontal cortex (RPFC) is a brain region that has been implicated both in spontaneous thought and in high-level cognitive control processes, such as goal/subgoal integration and the manipulation of self-generated thoughts. We therefore propose that the recruitment of lateral RPFC may follow a U-shaped function of cognitive demand: relatively high in low-demand situations conducive to the emergence of spontaneous thought, and in high-demand situations depending on processes supported by this brain region. We used functional magnetic resonance imaging to investigate brain activity while healthy participants performed two tasks, each with three levels of cognitive demands, in a block design. The frequency of task-unrelated thoughts, measured by questionnaire, was highest in the low cognitive demand condition. Low and high cognitive demand conditions were each compared to the intermediate level. Lateral RPFC and superior parietal cortex were recruited in both comparisons, with additional activations specific to each contrast. These results suggest that RPFC is involved both when (a) task demands are low, and the mind wanders, and (b) the task requires goal/subgoal integration and manipulation of self-generated thoughts.
Interaction of the Double-Strand Break Repair Kinase DNA-PK and Estrogen Receptor-α
Authors: Medunjanin Senad , Weinert Sönke , Schmeisser Alexander , Mayer Doris , Braun-Dullaeus Ruediger C.
Published: March 2010

Estrogens are suggested to play a role in the development and progression of proliferative diseases such as breast cancer. Like other steroid hormone receptors, the estrogen receptor-α (ERα) is a substrate of protein kinases, and phosphorylation has profound effects on its function and activity. Given the importance of DNA-dependent protein kinase (DNA-PK) for DNA repair, cell cycle progression, and survival, we hypothesized that it modulates ERα signaling. Here we show that, upon estrogen stimulation, DNA-PK forms a complex with ERα in a breast cancer cell line (MELN). DNA-PK phosphorylates ERα at Ser-118. Phosphorylation resulted in stabilization of ERα protein as inhibition of DNA-PK resulted in its proteasomal degradation. Activation of DNA-PK by double-strand breaks or its inhibition by siRNA technology demonstrated that estrogen-induced ERα activation and cell cycle progression is, at least, partially dependent on DNA-PK.
PanCGHweb: a web tool for genotype calling in pangenome CGH data
Authors: Bayjanov Jumamurat R. , Siezen Roland J. , van Hijum Sacha A. F. T.
Published: March 2010

Summary: A pangenome is the total of genes present in strains of the same species. Pangenome microarrays allow determining the genomic content of bacterial strains more accurately than conventional comparative genome hybridization microarrays. PanCGHweb is the first tool that effectively calls genotype based on pangenome microarray data.

Availability: PanCGHweb, the web tool is accessible from: http://bamics2.cmbi.ru.nl/websoftware/pancgh/

Contact:  sacha.vanhijum@nizo.nl
Identification of Quantitative Trait Loci Affecting Grain Fat Content in Rice (Oryza sativa L.)
Authors: Shen Yingyue , Liu Linglong , Jiang Ling , Zhang Yingxing , Liu Xiaolu , Zhai Huqu , Wan Jianmin
Published: March 2010

Fat content (FC) partially determines rice grain quality. The objective of this study was to identify stably expressed quantitative trait loci (QTL) for FC. A total of 85 inbred lines derived from the backcross between Sasanishiki (japonica, as the recurrent parent) and Habataki (indica) were used to detect QTLs for rice fat content. Seven QTLs (denoted as qFC‐1, qFC‐2, qFC‐3, qFC‐6, qFC‐10, qFC‐11, and qFC‐12) were detected on chromosomes 1, 2, 3, 6 10, 11, and 12, respectively, using inclusive composite interval mapping (ICIM) method. Among them, three major QTLs (qFC‐3, qFC‐6, and qFC‐11) with large effect were further confirmed across two different environments using some chromosome segment substitution lines (CSSLs), where Habataki was used as the donor parent and Sasanishiki as the recurrent parent. Further experiments showed that one of the major QTLs (qFC‐11) could increase fat content, fat index, and grain yield together. To our knowledge, qFC‐11 is a newly detected stable QTL that will provide new opportunities for improving rice fat content through marker‐assisted selection.
Thermal vibration of carbon nanotubes predicted by beam models and molecular dynamics
Authors: Wang Lifeng , Hu Haiyan , Guo Wanlin
Published: March 2010

The paper presents a detailed study on the thermal vibration of a single-walled carbon nanotube by using different beam models of continuum mechanics, together with the law of energy equipartition, and the molecular dynamics simulations. The basic finding of the study is the relation, derived by using the Timoshenko beam model and the law of energy equipartition, between the temperature and the root-of-mean-squared (RMS) amplitude of thermal vibration at any cross section of the carbon nanotube. The molecular dynamics simulations show that both the Euler beam model and the Timoshenko beam model can roughly predict the thermal vibration of lower order modes for a relatively long carbon nanotube. However, the Timoshenko beam model, compared with the Euler beam model, offers a much better prediction of the RMS amplitude of the thermal vibration near the fixed end of the carbon nanotube. For the thermal vibration of a relatively short carbon nanotube or higher order models of a relatively long carbon nanotube, the difference between the Timoshenko beam and the Euler beam in dynamic prediction becomes obvious, and the Timoshenko beam model works much better than the Euler beam model.
On the inverse problem of calculus of variations for fourth-order equations
Authors: Nucci M. C. , Arthurs A. M.
Published: March 2010

Fels’ conditions (Fels, M. E. 1996Trans. Amer. Math. Soc.348, 5007–5029. (doi:10.1090/S0002-9947-96-01720-5)) ensure the existence and uniqueness of the Lagrangian in the case of a fourth-order equation. We show that when Fels’ conditions are satisfied, the Lagrangian can be derived from the Jacobi last multiplier, as in the case of a second-order equation. Indeed, we prove that if a Lagrangian exists for an equation of any even order, then it can be derived from the Jacobi last multiplier. Two equations from a Number Theory paper by Hall (Hall, R. R. 2002J. Number Theory93, 235–245. (doi:10.1006/jnth.2001.2719)), one of the second and one of the fourth order, will be used to exemplify the method. The known link between Jacobi last multiplier and Lie symmetries is also exploited. Finally, the Lagrangians of two fourth-order equations drawn from Physics are determined with the same method.
Stochastically forced water waves in a circular basin
Authors: Onu Kristjan , Sri Namachchivaya N.
Published: March 2010

An analysis of wave motion under stochastic excitation is presented. The starting point is a Hamiltonian model of surface wave motion. This model is augmented with linear damping and stochastic forcing terms. An asymptotic scaling parameter is then introduced to show that the problem has three time scales. Integrability of the system is established for the case of two wave modes near 1:1 resonance. Stochastic averaging is used to reduce the dimensions of the system from four to two and the evolution of surface waves is now described, over long time scales and small amplitude stochastic forcing, by the evolution of the integrals of motion, as a random process. The domain of the generator of this random process is characterized and it includes a ‘gluing’ boundary condition. The adjoint of the generator yields the Fokker–Planck partial-differential equation (FPE). This equation governs the time evolution of the joint probability density of the two integrals of motion. The coefficients of the FPE are calculated numerically and the steady-state solution is found using the finite-element method. Results of the analysis show a distinct peak in the probability density along one edge of the reduced domain.
The instability theory of drumlin formation applied to Newtonian viscous ice of finite depth
Authors: Fowler A. C.
Published: March 2010

The Hindmarsh instability theory of drumlin formation is applied to the study of interfacial instabilities, which may arise when ice flows viscously over deformable sediments. Here, the analytic form of this theory is extended to the case where the ice is Newtonian viscous and of finite depth, and where the basal till can be both sheared by the ice and squeezed by basal effective pressure gradients: previous authors assumed infinitely deep ice, based on the assumption that the developing waveforms had wavelength much less than ice depth.

The previous infinite depth theory only allowed transverse instabilities to occur, and these have been associated with the formation of ribbed moraine; one of the purposes of extending the analysis to finite depth is to see whether three-dimensional instabilities, which might be associated with the formation of drumlins or mega-scale glacial lineations, can occur: we find that they do not. A second purpose is to calculate under what circumstances the infinite depth theory provides accurate prediction of bedform development in ice of finite depth
d
i
. We find that this is the case if the waveforms have a wavelength less than approximately 1.2
d
i
. Finally, the finite depth theory allows us to compute, for the first time, the response of the ice surface to the developing unstable bedforms. We find that this response is rapid, and we give explicit recipes for the surface perturbation transfer functions in terms of the perturbations to the basal stress and the basal topography.
The evolution of phototransduction from an ancestral cyclic nucleotide gated pathway
Authors: Plachetzki David C. , Fong Caitlin R. , Oakley Todd H.
Published: March 2010

The evolutionary histories of complex traits are complicated because such traits are comprised of multiple integrated and interacting components, which may have different individual histories. Phylogenetic studies of complex trait evolution often do not take this into account, instead focusing only on the history of whole, integrated traits; for example, mapping eyes as simply present or absent through history. Using the biochemistry of animal vision as a model, we demonstrate how investigating the individual components of complex systems can aid in elucidating both the origins and diversification of such systems. Opsin-based phototransduction underlies all visual phenotypes in animals, using complex protein cascades that translate light information into changes in cyclic nucleotide gated (CNG) or canonical transient receptor potential (TRPC) ion-channel activity. Here we show that CNG ion channels play a role in cnidarian phototransduction. Transcripts of a CNG ion channel co-localize with opsin in specific cell types of the eyeless cnidarianHydra magnipapillata. Further, the CNG inhibitorcis-diltiazem ablates a stereotypical photoresponse in the hydra. Our findings in the Cnidaria, the only non-bilaterian lineage to possess functional opsins, allow us to trace the history of CNG-based photosensitivity to the very origin of animal phototransduction. Our general analytical approach, based on explicit phylogenetic analysis of individual components, contrasts the deep evolutionary history of CNG-based phototransduction, today used in vertebrate vision, with the more recent assembly of TRPC-based systems that are common to protostome (e.g. fly and mollusc) vision.
Fossil avian eggshell preserves ancient DNA
Authors: Oskam Charlotte L. , Haile James , McLay Emma , Rigby Paul , Allentoft Morten E. , Olsen Maia E. , Bengtsson Camilla , Miller Gifford H. , Schwenninger Jean-Luc , Jacomb Chris , Walter Richard , Baynes Alexander , Dortch Joe , Parker-Pearson Michael , Gilbert M. Thomas P. , Holdaway Richard N. , Willerslev Eske , Bunce Michael
Published: March 2010

Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful isolation and amplification of DNA from fossil eggshell up to 19 ka old. aDNA was successfully characterized from eggshell obtained from New Zealand (extinct moa and ducks), Madagascar (extinct elephant birds) and Australia (emu and owl). Our data demonstrate excellent preservation of the nucleic acids, evidenced by retrieval of both mitochondrial and nuclear DNA from many of the samples. Using confocal microscopy and quantitative PCR, this study critically evaluates approaches to maximize DNA recovery from powdered eggshell. Our quantitative PCR experiments also demonstrate that moa eggshell has approximately 125 times lower bacterial load than bone, making it a highly suitable substrate for high-throughput sequencing approaches. Importantly, the preservation of DNA in Pleistocene eggshell from Australia and Holocene deposits from Madagascar indicates that eggshell is an excellent substrate for the long-term preservation of DNA in warmer climates. The successful recovery of DNA from this substrate has implications in a number of scientific disciplines; most notably archaeology and palaeontology, where genotypes and/or DNA-based species identifications can add significantly to our understanding of diets, environments, past biodiversity and evolutionary processes.
Dispersal capacity and diet breadth modify the response of wild bees to habitat loss
Authors: Bommarco Riccardo , Biesmeijer Jacobus C. , Meyer Birgit , Potts Simon G. , Pöyry Juha , Roberts Stuart P. M. , Steffan-Dewenter Ingolf , Öckinger Erik
Published: March 2010

Habitat loss poses a major threat to biodiversity, and species-specific extinction risks are inextricably linked to life-history characteristics. This relationship is still poorly documented for many functionally important taxa, and at larger continental scales. With data from five replicated field studies from three countries, we examined how species richness of wild bees varies with habitat patch size. We hypothesized that the form of this relationship is affected by body size, degree of host plant specialization and sociality. Across all species, we found a positive species–area slope (
z
= 0.19), and species traits modified this relationship. Large-bodied generalists had a lower
z
value than small generalists. Contrary to predictions, small specialists had similar or slightly lower
z
value compared with large specialists, and small generalists also tended to be more strongly affected by habitat loss as compared with small specialists. Social bees were negatively affected by habitat loss (
z
= 0.11) irrespective of body size. We conclude that habitat loss leads to clear shifts in the species composition of wild bee communities.
A developmental perspective on the evolution of sexual size dimorphism of a moth
Authors: Stillwell R. Craig , Davidowitz Goggy
Published: March 2010

Males and females of almost all organisms exhibit sexual differences in body size, a phenomenon called sexual size dimorphism (SSD). How the sexes evolve to be different sizes, despite sharing the same genes that control growth and development, and hence a common genetic architecture, has remained elusive. Here, we show that the genetic architecture (heritabilities and genetic correlations) of the physiological mechanism that regulates size during the last stage of larval development of a moth, differs between the sexes, and thus probably facilitates, rather than hinders, the evolution of SSD. We further show that the endocrine system plays a critical role in generating SSD. Our results demonstrate that knowledge of the genetic architecture underlying the physiological process during development that ultimately produces SSD in adults can elucidate how males and females of organisms evolve to be of different sizes.
Atmospheric oxygen level and the evolution of insect body size
Authors: Harrison Jon F. , Kaiser Alexander , VandenBrooks John M.
Published: March 2010

Insects are small relative to vertebrates, possibly owing to limitations or costs associated with their blind-ended tracheal respiratory system. The giant insects of the late Palaeozoic occurred when atmospheric PO2(aPO2) was hyperoxic, supporting a role for oxygen in the evolution of insect body size. The paucity of the insect fossil record and the complex interactions between atmospheric oxygen level, organisms and their communities makes it impossible to definitively accept or reject the historical oxygen-size link, and multiple alternative hypotheses exist. However, a variety of recent empirical findings support a link between oxygen and insect size, including: (i) most insects develop smaller body sizes in hypoxia, and some develop and evolve larger sizes in hyperoxia; (ii) insects developmentally and evolutionarily reduce their proportional investment in the tracheal system when living in higher aPO2, suggesting that there are significant costs associated with tracheal system structure and function; and (iii) larger insects invest more of their body in the tracheal system, potentially leading to greater effects of aPO2on larger insects. Together, these provide a wealth of plausible mechanisms by which tracheal oxygen delivery may be centrally involved in setting the relatively small size of insects and for hyperoxia-enabled Palaeozoic gigantism.
An immunological cost of begging in house sparrow nestlings
Authors: Moreno-Rueda Gregorio
Published: March 2010

Parent–offspring conflict predicts that offspring should demand a greater parental investment than is optimal for their parents to deliver. This would escalate the level of offspring demandad infinitum, but most of the models on the evolution of parent–offspring communication predict that begging must be costly, such costs limiting the escalation and defining an optimal level of begging. However, empirical evidence on this issue is mixed. A potential begging cost that remains to be accurately explored is a decrease in immunocompetence for offspring begging fiercely. This study experimentally analyses this cost in house sparrow (Passer domesticus) nestlings. A group of nestlings was forced to beg fiercely for a prolonged time while a control group begged at low levels, both groups receiving the same quantity of food. At the same time, the nestling response to an antigen (phytohaemagglutinin) was measured. Nestlings forced to beg fiercely showed a reduction in immunocompetence with respect to control chicks, but the two groups showed no difference in growth rate. The largest and the smallest nestlings in each brood showed a similar response to the treatment. These results strongly suggest a trade-off between begging and immunocompetence in this species. This trade-off may be a consequence either of resources from the immune system being reallocated to begging behaviour, or of adaptive immunosuppression in order to avoid oxidative stress. Steroid hormones are proposed as mediators of such a trade-off.
Histone demethylase KDM5A is an integral part of the core Notch–RBP-J repressor complex
Authors: Liefke Robert , Oswald Franz , Alvarado Cristobal , Ferres-Marco Dolores , Mittler Gerhard , Rodriguez Patrick , Dominguez Maria , Borggrefe Tilman
Published: March 2010

Timely acquisition of cell fates and the elaborate control of growth in numerous organs depend on Notch signaling. Upon ligand binding, the core transcription factor RBP-J activates transcription of Notch target genes. In the absence of signaling, RBP-J switches off target gene expression, assuring the tight spatiotemporal control of the response by a mechanism incompletely understood. Here we show that the histone demethylase KDM5A is an integral, conserved component of Notch/RBP-J gene silencing. Methylation of histone H3 Lys 4 is dynamically erased and re-established at RBP-J sites upon inhibition and reactivation of Notch signaling. KDM5A interacts physically with RBP-J; this interaction is conserved in Drosophila and is crucial for Notch-induced growth and tumorigenesis responses.
A CTCF-independent role for cohesin in tissue-specific transcription
Authors: Schmidt Dominic , Schwalie Petra C. , Ross-Innes Caryn S. , Hurtado Antoni , Brown Gordon D. , Carroll Jason S. , Flicek Paul , Odom Duncan T.
Published: March 2010

The cohesin protein complex holds sister chromatids in dividing cells together and is essential for chromosome segregation. Recently, cohesin has been implicated in mediating transcriptional insulation, via its interactions with CTCF. Here, we show in different cell types that cohesin functionally behaves as a tissue-specific transcriptional regulator, independent of CTCF binding. By performing matched genome-wide binding assays (ChIP-seq) in human breast cancer cells (MCF-7), we discovered thousands of genomic sites that share cohesin and estrogen receptor alpha (ER) yet lack CTCF binding. By use of human hepatocellular carcinoma cells (HepG2), we found that liver-specific transcription factors colocalize with cohesin independently of CTCF at liver-specific targets that are distinct from those found in breast cancer cells. Furthermore, estrogen-regulated genes are preferentially bound by both ER and cohesin, and functionally, the silencing of cohesin caused aberrant re-entry of breast cancer cells into cell cycle after hormone treatment. We combined chromosomal interaction data in MCF-7 cells with our cohesin binding data to show that cohesin is highly enriched at ER-bound regions that capture inter-chromosomal loop anchors. Together, our data show that cohesin cobinds across the genome with transcription factors independently of CTCF, plays a functional role in estrogen-regulated transcription, and may help to mediate tissue-specific transcriptional responses via long-range chromosomal interactions.