bluuebunny/crossref_metadata_2025 huggingface dataset:
Stochastic dynamics of complexation reaction in the limit of small numbers
Authors: Ghosh Kingshuk
Published: May 2011

We study stochastic dynamics of the non-linear bimolecular reaction A + B↔AB. These reactions are common in several bio-molecular systems such as binding, complexation, protein multimerization to name a few. We use master equation to compute the full distribution of several stochastic equilibrium properties such as number of complexes formed (Nc), equilibrium constant (K). We provide exact analytical and simpler approximate expression for equilibrium fluctuation quantities to quickly estimate the amount of noise as a function of reactant molecules and rates. We construct the phase diagram for a fluctuational quantity f, defined as the ratio of standard deviation to average (\documentclass[12pt]{minimal}\begin{document}$f = {\sqrt{\langle (\Delta N_{c})^2 \rangle } }/\langle N_c \rangle$\end{document}f=⟨(ΔNc)2⟩/⟨Nc⟩), as a function of different number of reactant molecules and reaction rates. One of the striking result is, it is possible to have f as high as 45% or higher in significant regions of the phase diagram even when number of reactants involved are around 20–40, typical in biology. Our finding indicates studying averages alone using mass action law needs careful scrutiny. We also outline possible application of our findings in gene expression. Furthermore, we compute average and fluctuation properties of time dependent quantities and derive equations of motion for different moments such as 〈Nc(t)〉 and 〈Nc(t)2〉. While mean-field mass action law fails to reproduce the exact time dependence, approximate solutions of coupled equations of motions for different moments, capturing fluctuation, is in good agreement with exact results. This may be a way to compute time development of averages and fluctuations in such non-linear systems where mass action law breaks down. Moreover, for this reaction, we outline connection to variational principle of maximum caliber and other more traditional approaches such as chemical Langevin equation. We derive noise statistics for the equivalent Langevin equation and show possible departure from Gaussian white noise. We believe quantitative estimates of phase diagrams for noise, time dependent quantities, and simple analytical expression for equilibrium quantities will be particularly useful to guide experiments involving such non-linear reactions with small numbers of reactants that are often encountered in biology.
An explicit expression for the relative entropy of entanglement in all dimensions
Authors: Friedland Shmuel , Gour Gilad
Published: May 2011

The relative entropy of entanglement is defined in terms of the relative entropy between an entangled state and its closest separable state (CSS). Given a multipartite-state on the boundary of the set of separable states, we find an explicit expression for all the entangled states for which this state is a CSS. Our formula holds for multipartite states in all dimensions. For the bipartite case of two qubits, our formula reduce to the one given by Miranowicz and Ishizaka [Phys. Rev. A 78, 032310 (2008)].
Controlling polarization anisotropy of site-controlled InAs/InP (100) quantum dots
Authors: Yuan Jiayue , Wang Hao , van Veldhoven René P. J. , Wang Jia , de Vries Tjibbe , Smalbrugge Barry , Jin C. Y. , Nouwens Peter , Geluk Erik Jan , Silov Andrei Yu. , Nötzel Richard
Published: May 2011

We report on the shape and polarization control of site-controlled multiple and single InAs quantum dots (QDs) on InP pyramids grown by selective-area metal-organic vapor phase epitaxy. With increasing growth temperature the QDs elongate causing strong linear polarization of the photoluminescence. With reduced pyramid base/pyramid top area/QD number, the degree of polarization decreases, attributed to the symmetric pyramid top, reaching zero for single QDs grown at lower temperature. This control of linear polarization is important for entangled photon sources operating in the 1.55 μm wavelength region.
Sterically stabilized lock and key colloids: A self-consistent field theory study
Authors: Egorov S. A.
Published: May 2011

A self-consistent field theory study of lock and key type interactions between sterically stabilized colloids in polymer solution is performed. Both the key particle and the lock cavity are assumed to have cylindrical shape and their surfaces are uniformly grafted with polymer chains. The lock-key potential of mean force is computed for various model parameters, such as length of free and grafted chains, lock and key size matching, free chain volume fraction, grafting density, and various enthalpic interactions present in the system. The lock-key interaction is found to be highly tunable, which is important in the rapidly developing field of particle self-assembly.
Photoinduced transparency of effective three-photon absorption coefficient for femtosecond laser pulses in Ge16As29Se55 thin films
Authors: Barik A. R. , Adarsh K. V. , Naik Ramakanta , Sandeep C. S. Suchand , Philip Reji , Zhao Donghui , Jain Himanshu
Published: May 2011

We report a dramatic change in effective three-photon absorption coefficient of amorphous Ge16As29Se55 thin films, when its optical band gap decreases by 10 meV with 532 nm light illumination. This large change provides valuable information on the higher excited states, which are otherwise inaccessible via normal optical absorption. The results also indicate that photodarkening in chalcogenide glasses can serve as an effective tool to tune the multiphoton absorption in a rather simple way.
Fractal nature of multiple shear bands in severely deformed metallic glass
Authors: Sun B. A. , Wang W. H.
Published: May 2011

We present an analysis of fractal geometry of extensive and complex shear band patterns in a severely deformed metallic glass. We show that the shear band patterns have fractal characteristics, and the fractal dimensions are determined by the stress noise induced by the interaction between shear bands. A theoretical model of the spatial evolution of multiple shear bands is proposed in which the collective shear bands slide is considered as a stochastic process far from thermodynamic equilibrium.
Electronic states and light absorption in quantum dot molecule
Authors: Dvoyan K. G. , Kazaryan E. M. , Tshantshapanyan A. A. , Wang Zh. M. , Salamo G. J.
Published: May 2011

The electronic states and direct interband absorption of light in quantum dot molecule (QDM) consisting 4 or 5 QDs are investigated. The electron energy levels and wave functions are calculated. It is shown that the energy levels are split in azimuth direction. In the case of the presence of the central QD in QDM an additional splitting in the radial direction is revealed. The suggested method can be used to calculate the electronic states and light absorption of arbitrary number QDM. The results are useful for the application of the QDM to photoelectric devices.
A global ab initio potential energy surface for HNO (a3A″) and quantum mechanical studies of vibrational states and reaction dynamics
Authors: Li Anyang , Xie Changjian , Xie Daiqian , Guo Hua
Published: May 2011

A new global potential energy surface for the lowest triplet electronic state (a3A″) of HNO has been developed by a three-dimensional cubic spline interpolation of more than 13 000 ab initio points, which were calculated at the multireference configuration interaction level with Davidson correction using the augmented correlation-consistent polarized valence quintuple zeta basis set. Two minima and five saddle points were found on the potential energy surface. Low-lying vibrational states were obtained in this new potential using the Lanczos method and assigned. In addition, thermal rate constants for the N + OH → H + NO reactions were obtained using an exact wave packet method. Reasonably good agreement with experimental data was obtained.
Communication: Exploring the reorientation of benzene in an ionic liquid via molecular dynamics: Effect of temperature and solvent effective charge on the slow dynamics
Authors: Yasaka Yoshiro , Klein Michael L. , Nakahara Masaru , Matubayasi Nobuyuki
Published: May 2011

The rotational time correlation function (RTCF) of solute benzene molecules in the ionic liquid (1-butyl-3-methylimidazolium chloride) has been studied using classical molecular dynamics simulation. The effect of solvent charge on the functional form of RTCF was investigated by comparing four force fields for the solvent where the total charge on the anion and the cation was set to ±1e, ±0.7e, ±0.5e, and 0, respectively. For all three charged solvent models, the RTCF exhibits a long-time tail where the relaxation rate exhibits a significant slowdown. This feature is strengthened by higher solvent charges as well as lower temperatures, indicating the influence of the strong Coulombic fields arising from the solvent charges. The long-time tail is caused by the extraordinarily slow solvent structural relaxation of ionic liquids compared to the time scale of their local vibrational and librational dynamics.
Dynamic information for cardiotoxin protein desorption from a methyl-terminated self-assembled monolayer using steered molecular dynamics simulation
Authors: Hung Shih-Wei , Hsiao Pai-Yi , Chieng Ching-Chang
Published: May 2011

Dynamic information, such as force, structural change, interaction energy, and potential of mean force (PMF), about the desorption of a single cardiotoxin (CTX) protein from a methyl-terminated self-assembled monolayer (SAM) surface was investigated by means of steered molecular dynamics (SMD) simulations. The simulation results indicated that Loop I is the first loop to depart from the SAM surface, which is in good agreement with the results of the nuclear magnetic resonance spectroscopy experiment. The free energy landscape and the thermodynamic force of the CTX desorption process was represented by the PMF and by the derivative of PMF with respect to distance, respectively. By applying Jarzynski's equality, the PMF can be reconstructed from the SMD simulation. The PMFs, calculated by different estimators based upon Jarzynski's equality, were compared with the conventional umbrella sampling method. The best estimation was obtained by using the fluctuation-dissipation estimator with a pulling velocity of v = 0.25 nm/ns for the present study.
Power efficiency estimation of silicon nanocrystals based light emitting devices in alternating current regime
Authors: Marconi A. , Anopchenko A. , Pucker G. , Pavesi L.
Published: May 2011

The power efficiency of silicon nanocrystal light-emitting devices is studied in alternating current (ac) regime. An experimental method based on impedance spectroscopy is proposed. The power efficiency in ac regime is higher than the one measured in direct current before a threshold frequency and decreases significantly for higher frequencies. This decrease is attributed to an increase in electrical power injected at high frequencies and it is directly related to the disordered microscopic structure of the active material. The proposed method can be applied for any kind of device for which it is possible to measure the impedance characteristic.
Direct identification of interstitial Mn in heavily p-type doped GaAs and evidence of its high thermal stability
Authors: Pereira L. M. C. , Wahl U. , Decoster S. , Correia J. G. , da Silva M. R. , Vantomme A. , Araújo J. P.
Published: May 2011

We report on the lattice location of Mn in heavily p-type doped GaAs by means of β− emission channeling from the decay of M56n. The majority of the Mn atoms substitute for Ga and up to 31% occupy the tetrahedral interstitial site with As nearest neighbors. Contrary to the general belief, we find that interstitial Mn is immobile up to 400 °C, with an activation energy for diffusion of 1.7–2.3 eV. Such high thermal stability of interstitial Mn has significant implications on the strategies and prospects for achieving room temperature ferromagnetism in Ga1−xMnxAs.
High-performance metamorphic InGaAs resonant cavity enhanced photodetector grown on GaAs substrate
Authors: Liu S. Q. , Han Q. , Zhu B. , Yang X. H. , Ni H. Q. , He J. F. , Wang X. , Li M. F. , Zhu Y. , Wang J. , Wang X. P. , Niu Z. C.
Published: May 2011

In this letter, we demonstrated a top illuminated 1.55 μm metamorphic InGaAs resonant-cavity-enhanced p-i-n photodetector grown on GaAs substrate. The photodetectors were grown by a solid-source molecular beam epitaxy system. The high quality linearly graded InxAl0.4Ga1−x−0.4As metamorphic buffer layer enabled photodiodes to achieve ultralow dark current densities of 2.3×10−6 A/cm2 at 0 V and 4.2×10−5 A/cm2 at a reverse bias of 5 V. A high quantum efficiency of 84.4% at resonant wavelength of 1542 nm, a full width at half maximum about 14 nm, and a −3 dB bandwidth up to 13 GHz were also obtained.
Wave mixing in nonlinear magnetic metacrystal
Authors: Huang Da , Rose Alec , Poutrina Ekaterina , Larouche Stéphane , Smith David R.
Published: May 2011

We present experimental measurements of three- and four-wave mixing phenomena in an artificially structured nonlinear magnetic metacrystal at microwave frequencies. The sum frequency generation signal for the varactor-loaded split-ring resonator (VLSRR) metamaterial agrees quantitatively with that predicted using an analytical effective medium model describing the VLSRR medium. A resonant enhancement of the nonlinear response is observed near the metamaterial resonance.
Solution processed Ni-doped TiO2 p-type channel in field effect transistor assembly with <10 nm thin Ba0.5Sr0.5TiO3 dielectric layer
Authors: Das Soumen , Kim Jin-Hwan , Park Yong-Kyu , Hahn Yoon-Bong
Published: May 2011

Solution processed field effect transistor structures were fabricated by inserting a Ba0.5Sr0.5TiO3 layer to form Ag/ZnO/Ba0.5Sr0.5TiO3/Ni2+:TiO2/n-Si assembly. Such assembly registered an on-to-off current ratio as large as 103 with very low off-state current ∼10−12 A. The low leakage current is attributed to the appreciably higher values of valence/conduction band off-set of Ba0.5Sr0.5TiO3/semiconductor heterojunction. The device response was studied as a function of temperature in the range of 25–175 °C. The hole diffusion coefficient and mobility of p-TiO2 was calculated ∼10−3 cm2/s and ∼0.13–0.15 cm−2 V−1 s−1, respectively.
Interference of surface plasmon polaritons from a “point” source
Authors: Ren Xifeng , Liu Aiping , Zou Changling , Wang Lulu , Cai Yongjing , Sun Fangwen , Guo Guangcan , Guo Guoping
Published: May 2011

The interference patterns of the surface plasmon polaritons (SPPs) on the metal surface from a “point” source are observed. Innovation to the previous works, a point SPPs source with diameter of 100 nm is generated at the freely chosen positions on Au/air interface using near field excitation method. Such a point source provides good enough coherence to generate obvious interference phenomenon. This point SPPs source may be useful in the investigation of plasmonics for its high coherence, deterministic position, and minimum requirement for the initial light source.
Anisotropic thermopower and magnetothermopower in a misfit-layered calcium cobaltite
Authors: Tang G. D. , Guo H. H. , Yang T. , Zhang D. W. , Xu X. N. , Wang L. Y. , Wang Z. H. , Wen H. H. , Zhang Z. D. , Du Y. W.
Published: May 2011

An unusual anisotropy of thermopower and magnetothermopower has been observed in the powerful thermoelectric Ca3Co4O9+δ single crystal. The in-plane thermopower is about twice as big as the out-of-plane thermopower. Combining ab initio band structure calculation with semiclassical model analysis, we understand this anisotropy with band structure effects and especially with anisotropic Fermi surface. We find that a strong anisotropy in the topology of Fermi surface leads to the anisotropy of (magneto)thermopower. This study may also shed light on anisotropic properties of other layered cobalt oxides.
Lasing in Thue–Morse structures with optimized aperiodicity
Authors: Noh Heeso , Yang Jin-Kyu , Boriskina Svetlana V. , Rooks Michael J. , Solomon Glenn S. , Dal Negro Luca , Cao Hui
Published: May 2011

We demonstrate lasing in two-dimensional Thue–Morse structures fabricated in a semiconductor membrane. By changing the relative size of two scatterers that correspond to the building blocks A and B, we gradually vary structural aperiodicity and find an optimal degree of aperiodicity where light confinement is maximal and lasing is the strongest. At various degrees of aperiodicity, different types of modes acquire the highest quality factors and may be selected for lasing. This work opens a way of controlling lasing characteristic via structural aperiodicity.
Do droplets always move following the wettability gradient?
Authors: Wu Jun , Ma Ruiyuan , Wang Zuankai , Yao Shuhuai
Published: May 2011

Impacting droplets on rough surfaces with a wettability gradient have been reported to rebound obliquely or migrate following the wettability gradient due to the unbalanced interfacial forces created by such heterogeneous architectures. Here we demonstrate under certain conditions, droplets can be self-propelled against the wettability gradient. We show that the local Cassie-to-Wenzel transition in the droplet is critical for such a counter-intuitive phenomenon. We believe that our letter extends our conventional understanding of wettability dynamics to heterogeneous surfaces and provides important insight for the design of micro/nanotextured surfaces for controlled droplet manipulation.
Experimental verification of the bending of electromagnetic waves using metamaterials
Authors: He Xiao-Yang , Yang Chun , Li Biao , Chen Qi , Zhou Bang-Hua , Tang Chuan-Xiang
Published: May 2011

In this study, the bending of electromagnetic waves using metamaterials in free space was demonstrated. The optical transformation approach was utilized to design the bend, and the required metamaterials are inhomogeneous and anisotropic. The corresponding parameter-reduced metamaterials were realized using nonresonant cut-wire structures, which worked over an ultrabroad bandwidth with uniform permittivities and permeabilities. A microwave horn antenna focused the electromagnetic wave into the bend. The radiation patterns of the horn with and without bend were compared. The experimental and full-wave simulation results showed that the electromagnetic waves were bent in the desired direction.
Highly efficient blue phosphorescent polymer light-emitting diodes by using interfacial modification
Authors: Li Lu , Liu Jun , Yu Zhibin , Pei Qibing
Published: May 2011

Solution processed highly efficient blue electrophosphorescent polymer light-emitting diodes have been fabricated containing an oligo(ethylene oxide) (PEO-DME) additive to enhance the electroluminescence efficiency. The addition of PEO-DME at 5–10 wt % effectively lowers both the electron and hole injection barriers. The maximum current efficiency obtained was 26.5 cd/A at an emission brightness of 2500 cd/m2. The high performance is due to (i) improved charge carrier injection at the interface resulting from specific interfacial interactions between PEO-DME and aluminum and (ii) improved charge carrier transporting ability and high electric field resulting from PEO-DME doping.
Canonical hedgehog signaling augments tumor angiogenesis by induction of VEGF-A in stromal perivascular cells
Authors: Chen Weiwei , Tang Tracy , Eastham-Anderson Jeff , Dunlap Debra , Alicke Bruno , Nannini Michelle , Gould Stephen , Yauch Robert , Modrusan Zora , DuPree Kelly J. , Darbonne Walter C. , Plowman Greg , de Sauvage Frederic J. , Callahan Christopher A.
Published: May 2011

Hedgehog (Hh) signaling is critical to the patterning and development of a variety of organ systems, and both ligand-dependent and ligand-independent Hh pathway activation are known to promote tumorigenesis. Recent studies have shown that in tumors promoted by Hh ligands, activation occurs within the stromal microenvironment. Testing whether ligand-driven Hh signaling promotes tumor angiogenesis, we found that Hh antagonism reduced the vascular density of Hh-producing LS180 and SW480 xenografts. In addition, ectopic expression of sonic hedgehog in low-Hh–expressing DLD-1 xenografts increased tumor vascular density, augmented angiogenesis, and was associated with canonical Hh signaling within perivascular tumor stromal cells. To better understand the molecular mechanisms underlying Hh-mediated tumor angiogenesis, we established an Hh-sensitive angiogenesis coculture assay and found that fibroblast cell lines derived from a variety of human tissues were Hh responsive and promoted angiogenesis in vitro through a secreted paracrine signal(s). Affymetrix array analyses of cultured fibroblasts identified VEGF-A, hepatocyte growth factor, and PDGF-C as candidate secreted proangiogenic factors induced by Hh stimulation. Expression studies of xenografts and angiogenesis assays using combinations of Hh and VEGF-A inhibitors showed that it is primarily Hh-induced VEGF-A that promotes angiogenesis in vitro and augments tumor-derived VEGF to promote angiogenesis in vivo.
Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome
Authors: Colaneri Alejandro , Staffa Nickolas , Fargo David C. , Gao Yuan , Wang Tianyuan , Peddada Shyamal D. , Birnbaumer Lutz
Published: May 2011

Methyl-sensitive cut counting (MSCC) with the HpaII methylation-sensitive restriction enzyme is a cost-effective method to pinpoint unmethylated CpGs at single base-pair resolution. However, it has the drawback of addressing only CpGs in the context of the CCGG site, leaving out the remainder of the possible 16 XCGX tetranucleotides in which CpGs are found. We expanded MSCC to include three additional enzymes to address a total of 5 of the 16 XCGX combinations. This allowed us to survey methylation at about one-third of all a mammalian genome's CpGs. Applied to mouse liver DNA, we correctly confirmed data reported with other methods showing hypomethylation to be concentrated at promoters and in CpG islands (CGIs), with gene bodies and intergenic regions being mostly methylated. Grouping unmethylated CpGs, characterized by high MSCC scores (7% false discovery rate), we found a large number of unmethylated regions not qualifying as CGIs located in intergenic and intronic regions, which are highly enriched in functional DNA sequences (open regulatory annotation database) as well as in noncoding yet highly conserved mammalian sequences thought to be important but with as yet unknown function. About 50% of MSCC-defined unmethylated regions do not overlap algorithm-defined CGIs and offer a novel search space in which new functionalities of DNA may be found in health and disease.
Elitocide in Bosnia and Herzegovina and its impact on the contemporary understanding of the crime of genocide
Authors: Gratz Dennis
Published: May 2011

In my paper I will present and discuss the theoretical concept of elitocide (a systematic elimination of leading figures of a society or a group) and its impact on the crime of genocide on the example of the war in Bosnia and Herzegovina 1992-1995. A systematization and scientific classification of elitocide as a sociological phenomenon bears great importance to the field of study on genocide, mass murder and human rights abuses. The scientific elaboration of new or hitherto neglected occurrences of organized violence has a significant impact on the understanding of the phenomenon of systematic war crimes and mass atrocities in modern war conflicts. In order to better understand how genocide or potentially genocidal mass murders emerge and how they can be prevented, it is necessary to modify and redevelop their conventional theoretical framework. Since the premises of modern war have changed, the science is obliged to adapt its approach to this new reality. This paper is a contribution to making the causes and consequences of mass atrocities practically cognizable and theoretically comprehensive.
Belarus: an emerging civic nation?
Authors: Buhr Renee L. , Shadurski Victor , Hoffman Steven
Published: May 2011

Early commentators on the newly independent Belarusian state of the 1990s indicated that there was something lacking in Belarusian identity. The people did not seem to respond powerfully to the new symbols of the state, use of the national language intermingled with Russian, and economic concerns appeared to trump popular concerns with promoting Belarusian language or culture. Other former Soviet states were embracing ethnic national ideals, and as such, many assumed that Belarus should follow a similar path. However, as an examination of the history of the Belarusian territory demonstrates, a national ideal based on ethnicity was problematic in Belarusian society, and as such, the ethnic notions of Belarusian identity forwarded by some Belarusian elites failed to appeal to the masses. Instead, Belarus seems better suited to a more inclusive civic identity than an exclusive ethnic one. This research examines the nature of contemporary Belarusian identity, with particular attention to the civic versus ethnic aspects of that identity. We argue that although Belarusian identity is obviously in flux and subject to heavy debate, it is currently demonstrating more civic aspects than ethnic ones. This finding is based on original survey data obtained in Belarus in 2009 and 2010.
Foes of our rebirth: Ukrainian nationalist discussions about Jews, 1929-1947
Authors: Carynnyk Marco
Published: May 2011

The Organization of Ukrainian Nationalists, or OUN, came into being in 1929 as an “integral nationalist” movement that set itself the goal of driving Polish landowners and officials out of eastern Galicia and Volhynia, joining hands with Ukrainians in other countries, and establishing an independent state. The OUN defined Jews, along with Russians and Poles, as aliens and enemies. There was no need, wrote an OUN ideologist in 1929, to list all the injuries that Jews caused Ukrainians. “In addition to a number of external enemies Ukraine also has an internal enemy … Jewry and its negative consequences for our liberation cause can be liquidated only by an organized collective effort”. The article examines archival documents, publications by OUN members, and recent scholarly literature to trace the evolution of OUN thinking about Jews from 1929 through the war years, when the German occupation of Ukraine gave the OUN an opportunity to stage pogroms and persecute Jews, and the prime minister of the state that the OUN proclaimed wrote that he supported “the destruction of the Jews and the expedience of bringing German methods of exterminating Jewry to Ukraine”.
Conclusion: Ukrainians, Jews and the Holocaust
Authors: Abramson Henry
Published: May 2011

In December 2009 I had the privilege of participating in an unique gathering of scholars at Ditchley Park, near Oxford sponsored by the Ukrainian Jewish Encounter project. As is usual with such conclaves, the formal discussion of papers in panel sessions was useful, but the exchanges between sessions - over breakfast, or late into the night sitting in the common areas - were often far more revealing. Looking back on the conference as a whole, including both formal and informal discourse, I would like to make two broad assertions about the current state of the academic debate, which are well reflected in the papers published in this symposium. First, the Holocaust looms larger than ever as the great challenge for historians of Ukraine. Although the program of the conference was dedicated to the interwar period, the topic was unavoidable and was engaged directly in virtually every session. Arcane yet heated debate over, for example, specific anti-Semitic statements of the Organization of Ukrainian Nationalists (OUN) during the 1930s was only cut short when a participant reminded the group that the OUN was numerically insignificant at the time these statements were made - yet limited attention was paid to the far more mainstream Ukrainian political movements such as the Ukrainian National Democratic Organization (UNDO). The trajectory of academic focus was pulled into a distorted orbit around the Holocaust, and that gravitational pull is increasing as the field matures.
Bounding the first Hilbert coefficient
Authors: Hanumanthu Krishna , Huneke Craig
Published: May 2011

This paper gives new bounds on the first Hilbert coefficient of an ideal of finite colength in a Cohen-Macaulay local ring. The bound given is quadratic in the multiplicity of the ideal. We compare our bound to previously known bounds and give examples to show that at least in some cases it is sharp. The techniques come largely from work of Elias, Rossi, Valla, and Vasconcelos.
On the integrability of Tonelli Hamiltonians
Authors: Sorrentino Alfonso
Published: May 2011

In this article we discuss a weaker version of Liouville’s Theorem on the integrability of Hamiltonian systems. We show that in the case of Tonelli Hamiltonians the involution hypothesis on the integrals of motion can be completely dropped and still interesting information on the dynamics of the system can be deduced. Moreover, we prove that on the

n
n

-dimensional torus this weaker condition implies classical integrability in the sense of Liouville. The main idea of the proof consists in relating the existence of independent integrals of motion of a Tonelli Hamiltonian to the “size” of its Mather and Aubry sets. As a byproduct we point out the existence of “non-trivial” common invariant sets for all Hamiltonians that Poisson-commute with a Tonelli Hamiltonian.
The Winners' Choice: Sustainable Economic Strategies for Successful 21st‐Century Regions
Authors: Partridge Mark D. , Olfert M. Rose
Published: May 2011

Throughout the second half of the 20th century, urbanization, new technologies, rapid labor‐saving productivity growth in primary industries, and improved highways combined to create large‐scale regions which are now functionally integrated at the rural‐urban level. These forces have raised the stakes for regions in their pursuit of economic development and growth, making successful regional policy even more important. Changes to the governance structures consistent with the increased interdependence within broad rural‐urban regions will improve the region's competitiveness; adopting fad‐based approaches and policies aimed at “picking winners” will be less fruitful. Going forward, continuing globalization and environmental sustainability have the potential to reshape fundamentally the relative attractiveness of regions.
rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks
Authors: Thorleifsson Stefan Gretar , Thiele Ines
Published: May 2011

Motivation: Genome-scale metabolic networks are widely used in systems biology. However, to date no freely available tool exists that ensures quality control during the reconstruction process.

Results: Here, we present a COBRA toolbox extension, rBioNet, enabling the construction of publication-level biochemical networks while enforcing necessary quality control measures. rBioNet has an intuitive user interface facilitating the reconstruction process for novices and experts.

Availability: The rBioNet is freely available from http://opencobra.sourceforge.net.

Contact:  ithiele@hi.is
Unamplified cap analysis of gene expression on a single-molecule sequencer
Authors: Kanamori-Katayama Mutsumi , Itoh Masayoshi , Kawaji Hideya , Lassmann Timo , Katayama Shintaro , Kojima Miki , Bertin Nicolas , Kaiho Ai , Ninomiya Noriko , Daub Carsten O. , Carninci Piero , Forrest Alistair R.R. , Hayashizaki Yoshihide
Published: May 2011

We report the development of a simplified cap analysis of gene expression (CAGE) protocol adapted for single-molecule sequencers that avoids second strand synthesis, ligation, digestion, and PCR. HeliScopeCAGE directly sequences the 3′ end of cap trapped first-strand cDNAs. As with previous versions of CAGE, we better define transcription start sites (TSS) than known models, identify novel regions of transcription and alternative promoters, and find two major classes of TSS signal, sharp peaks and broad regions. However, using this protocol, we observe reproducible evidence of regulation at the much finer level of individual TSS positions. The libraries are quantitative over 5 orders of magnitude and highly reproducible (Pearson's correlation coefficient of 0.987). We have also scaled down the sample requirement to 5 μg of total RNA for a standard HeliScopeCAGE library and 100 ng for a low-quantity version. When the same RNA was run as 5-μg and 100-ng versions, the 100 ng was still able to detect expression for ∼60% of the 13,468 loci detected by a 5-μg library using the same threshold, allowing comparative analysis of even rare cell populations. Testing the protocol for differential gene expression measurements on triplicate HeLa and THP-1 samples, we find that the log fold change compared to Illumina microarray measurements is highly correlated (0.871). In addition, HeliScopeCAGE finds differential expression for thousands more loci including those with probes on the array. Finally, although the majority of tags are 5′ associated, we also observe a low level of signal on exons that is useful for defining gene structures.
Development of Cellulosic Secondary Walls in Flax Fibers Requires β-Galactosidase
Authors: Roach Melissa J. , Mokshina Natalia Y. , Badhan Ajay , Snegireva Anastasiya V. , Hobson Neil , Deyholos Michael K. , Gorshkova Tatyana A.
Published: May 2011

Bast (phloem) fibers, tension wood fibers, and other cells with gelatinous-type secondary walls are rich in crystalline cellulose. In developing bast fibers of flax (Linum usitatissimum), a galactan-enriched matrix (Gn-layer) is gradually modified into a mature cellulosic gelatinous-layer (G-layer), which ultimately comprises most of the secondary cell wall. Previous studies have correlated this maturation process with expression of a putative β-galactosidase. Here, we demonstrate that β-galactosidase activity is in fact necessary for the dynamic remodeling of polysaccharides that occurs during normal secondary wall development in flax fibers. We found that developing stems of transgenic (LuBGAL-RNAi) flax with reduced β-galactosidase activity had lower concentrations of free Gal and had significant reductions in the thickness of mature cellulosic G-layers compared with controls. Conversely, Gn-layers, labeled intensively by the galactan-specific LM5 antibody, were greatly expanded in LuBGAL-RNAi transgenic plants. Gross morphology and stem anatomy, including the thickness of bast fiber walls, were otherwise unaffected by silencing of β-galactosidase transcripts. These results demonstrate a specific requirement for β-galactosidase in hydrolysis of galactans during formation of cellulosic G-layers. Transgenic lines with reduced β-galactosidase activity also had biochemical and spectroscopic properties consistent with a reduction in cellulose crystallinity. We further demonstrated that the tensile strength of normal flax stems is dependent on β-galactosidase-mediated development of the phloem fiber G-layer. Thus, the mechanical strength that typifies flax stems is dependent on a thick, cellulosic G-layer, which itself depends on β-galactosidase activity within the precursor Gn-layer. These observations demonstrate a novel role for matrix polysaccharides in cellulose deposition; the relevance of these observations to the development of cell walls in other species is also discussed.
Guideline on the investigation, management and prevention of venous thrombosis in children*
Authors: Chalmers Elizabeth , Ganesen Vijeya , Liesner Ri , Maroo Sanjay , Nokes Timothy , Saunders D. , Williams Michael
Published: May 2011

Venous thrombo‐embolism (VTE) is increasingly recognized in paediatric practice. Few clinical trials have been performed in this area in children and management is largely extrapolated from adult practice where there is a considerable evidence base. This is likely to be unsatisfactory for a number of reasons. Firstly, there are significant differences in epidemiology and potential differences in the mechanisms for VTE in this age group. Secondly, many aspects of haemostasis are age‐dependant, which has implications for the use of anticoagulants in the paediatric population. Thirdly, there are very limited data available on the safety and efficacy of anticoagulants to manage specific indications in paediatric practice, often with limited paediatric formulations available. In addition, children may survive for a prolonged period following these events so that long‐term consequences may be highly significant in this age group. The aim of this guideline is to provide a rational basis for the investigation and management of children aged 1 month–16 years with VTE, including cerebral venous thrombosis (CVT). The guideline is targeted at healthcare professionals involved in the management of children and adolescents with VTE, particularly paediatric haematologists.
Awareness of coeliac disease and the gluten status of ‘gluten‐free’ food obtained on request in catering outlets in Ireland
Authors: McIntosh James , Flanagan Andrew , Madden Nora , Mulcahy Maurice , Dargan Lawrence , Walker Michael , Burns Duncan Thorburn
Published: May 2011

The only current effective treatment for coeliac disease (CD) is a lifelong diet that is as free from gluten as possible. This study provides baseline evidence to inform future interventions of benefit to CD sufferers by examining awareness of CD issues by food servers and preparation staff, assessing their claims to provide gluten‐free foods by analysis of a meal concurrently sampled. While the majority of attempts to purchase a ‘gluten‐free’ meal on request in restaurants were successful, some 10% of all samples contained gluten, 2.7% between 21 and 100 mg kg−1, and 7.7% >100 mg kg−1 and two unsatisfactory samples were purchased from so‐called coeliac‐friendly restaurants. These findings were consistent with those obtained previously by Collin et al. [Alimentary Pharmacology & Therapeutics 19 (2004) 1277], Størsrud et al. [European Food Research & Technology 217 (2003) 481], Gélinas et al. [International Journal of Food Science & Technology 43 (2008) 1245] for cross contamination with gluten. Staff confidence, ‘gluten‐free’ notices, signs and menu choices were no guarantee of risk‐free dining for CD sufferers. Based on our findings we suggest the need for further training, specifically for chefs and managers.
Surface charge and conformational properties of phaseolin, the major globulin in red kidney bean (Phaseolus vulgaris L): effect of pH
Authors: Yin Shou‐Wei , huang Ke‐Li , Tang Chuan‐He , Yang Xiao‐Quan , Wen Qi‐Biao , Qi Jun‐Ru
Published: May 2011

The aim of this investigation was to explore the pH‐induced conformational changes of phaseolin using differential scanning calorimetry (DSC), fluorescence and circular dichroism (CD) spectra. The surface charges at the varying pH and ionic strength were also determined to probe the possible relationship between the surface charges of phaseolin and its conformation. The ζ‐potential of phaseolin decreased from 27.9 mV at pH 3.0 to –44 mV at pH 9.4, and the isoelectric point (iep) occurred at pH 4.21, which were comparable with the theoretical estimations derived from amino acid composition and pK values. The iep of phaseolin was independent of ionic strength, while the magnitude of ζ‐potential decreased as the ionic strength increased. The near‐UV CD, DSC and fluorescence spectra analyses indicated highly acidic and alkaline pH conditions induced the loss of tertiary conformation of phaseolin. The far‐UV CD spectra analysis confirmed pH‐shift led to the decreases in ordered secondary structure compositions. The present results suggested the loss of secondary and/or tertiary conformation of phaseolin as a result of the varying pattern in electrostatic interactions as pH shifted from 7.0 to acidic or alkalic pH.
Effects of potassium alum addition on physicochemical, pasting, thermal and gel texture properties of potato starch
Authors: Li Wenhao , Bai Yunfei , Zhang Qing , Hu Xiaosong , Shen Qun
Published: May 2011

The study investigated the effects of the addition of different concentrations of potassium alum (PA, 0, 0.1, 0.3, 0.5, and 0.7 g 100 g−1; w/w, on a starch weight basis) on the pasting, thermal, gel texture and other physicochemical properties of potato starch. The addition of PA resulted in a significant increase in solubility and a decrease in swelling power and light transmittance of stored pastes. Differential scanning calorimeter analysis demonstrated an increase in gelatinisation temperatures and gelatinisation enthalpy and a decrease in phase transition temperature range (ΔTr) with increasing PA concentration. Results of rapid visco‐analysis indicated that addition of PA decreased the peak, trough, breakdown, final and setback viscosities, but increased in peak time. Textural tests showed that the addition of PA retarded gel strength development during refrigerated storage. The high ionic strength and water‐binding capacities of Al3+, K+ and SO42− point to being the key factors for these observed changes.
Extraction of inulin from Burdock root (Arctium lappa) using high intensity ultrasound
Authors: Milani Elnaz , Koocheki Arash , Golimovahhed Q. Ali.
Published: May 2011

Burdock root could be a source of inulin, but scarce studies about its extraction exist. To optimise conventional and ultrasound‐assisted extraction of inulin, various combinations were used. The independent variables for ultrasound extraction were sonication amplitude (20–100%), sonication temperature (20–60 °C) and sonication time (5–25 min) while for conventional extraction the following variables were water to solid ratio (5–15 v/w), temperature (40–90 °C) and time (5–40 min). For each response, a second‐order polynomial model was developed using multiple linear regression analysis. The use of high intensity ultrasound significantly improves the extraction of inulin contained within the body of Burdock root. It was shown that increasing the amplitude (from 20% to 85%) and extraction time increased the extraction yield; however, the effect of temperature was minor. Optimum extraction condition was found to be sonication time: 25 min, sonication amplitude 83.22% and temperature: 36.76 °C.
Microstructures of starch granule, starch digestibilities and predicted glycaemic index of common bean mutants in Taiwan
Authors: Chiou Shiow Ying , Chen Huei Juan , Jeng Toong Long , Sung Jih Min
Published: May 2011

In this study, the microstructure of starch granule and in vitro starch digestibility were compared in de‐coated seeds of common bean variety Hwachia and its NaN3‐induced mutants. Significant differences in starch granule size (between 17.92 and 27.00 μm), total starch content (between 436.5 and 456.8 mg per seed) and resistant starch content (between 51.6 and 203.3 mg per seed) were found among mutants. Both boiling and autoclaving decreased resistant starch content in processed common beans. Significant difference in predicted gylcaemic index (pGI) (between 48.82 and 64.55%) for processed beans also existed among mutants. However, 96 h of 4 °C storage increased resistant starch content in processed common beans, possibly resulted from starch retrogradation during storage. Mutants SA‐05, SA‐08 and SA‐31, which have smaller seed weight and lower pGI (average of 50.08%) compared to Hwachia (pGI of 57.05%), can be used to produce common bean based low GI dietary carbohydrate.
Cell division blockage: but this time by a surprisingly conserved protein
Authors: Hamoen Leendert W.
Published: May 2011

Activation of DNA repair proteins is often accompanied by an arrest in cell division. Several proteins have been identified that regulate the division blockage associated with the SOS response. When Bacillus subtilis cells become genetically competent they also activate DNA repair proteins and stop dividing. In this issue of Molecular Microbiology, Briley et al., 2011 describe a new protein involved in this process. This protein, Maf, does not prevent FtsZ polymerization, but it inhibits synthesis of the division septum. What is fascinating about Maf is that it is conserved and can be found in all kingdoms of life.
Orthoglymma wangapeka gen.n., sp.n. (Coleoptera: Carabidae: Broscini): a newly discovered relict from the Buller Terrane, north‐western South Island, New Zealand, corroborates a general pattern of Gondwanan endemism
Authors: LIEBHERR JAMES K. , MARRIS JOHN W. M. , EMBERSON ROWAN M. , SYRETT PAULINE , ROIG‐JUÑENT SERGIO
Published: May 2011

Orthoglymma Liebherr, Marris, Emberson, Syrett & Roig‐Juñent gen.n. (Coleoptera: Carabidae: Broscini) is described to accommodate the single type species Orthoglymma wangapeka Liebherr, Marris, Emberson, Syrett & Roig‐Juñent sp.n., known from the Wangapeka Track, Kahurangi National Park, north‐western South Island, New Zealand. Orthoglymma wangapekasp.n. is analysed cladistically along with a comprehensive array of 42 other broscine generic terminals and four out‐group taxa, using information obtained from 73 morphological characters, and placed as adelphotaxon to the remainder of subtribe Nothobroscina, a clade distributed in New Zealand, southern South America and Australia. Based on fossil evidence for Carabidae, the occurrence of Orthoglymma wangapekasp.n. on the Buller Terrane, a geological feature once situated on the eastern margin of Gondwana, and early cladistic divergence of Orthoglymma from the remaining Nothobroscina, Orthoglymma wangapekasp.n. is interpreted as a Gondwanan relict. The New Zealand arthropod fauna is reviewed to identify other taxa in existence at the time of Cretaceous vicariance of New Zealand and Australia. These candidate Gondwanan taxa, all of which are specified using fossil data or molecular divergence‐based estimates, are analysed biogeographically. Where phylogenetic hypotheses are available, primordial distributions are optimized using event‐based, dispersal‐vicariance (DIVA) analysis. The hypothesized Gondwanan‐aged taxa demonstrate inordinate fidelity to the Gondwanan‐aged geological terranes that constitute the western portions of New Zealand, especially in the South Island. Persistence of these relicts through a hypothesized ‘Oligocene drowning’ event is the most parsimonious explanation for the concentration of Gondwanan relicts in the Nelson, Buller and Fiordland districts of the South Island. Geographic patterns of Gondwanan‐aged taxa are compared with distributions of taxa hypothesized to have colonized New Zealand across the Tasman Sea from Australia and New Caledonia, subsequent to Cretaceous vicariance. These post‐Gondwanan taxa exhibit very different patterns of distribution and diversification in New Zealand, including: (i) abundant endemism in Northland, and the islands and peninsulas of the North Island; (ii) species geographically restricted to areas underlain by the youngest Rakaia and Pahau geological terranes; and (iii) species exhibiting exceedingly widespread geographic distributions spanning geological terranes of disparate ages.

In relation to the world fauna the austral disjunct insect groups…form a very small fraction, and the pertinent species are, moreover, predominantly very small and inconspicuous creatures which makes it still more easy to overlook their great biogeographic importance.

(Brundin, 1966: 458)