bluuebunny/crossref_metadata_2025 huggingface dataset:
Visualizing Large-Scale Streaming Applications
Authors: De Pauw Wim , Andrade Henrique
Published: June 2009

Stream processing is a new and important computing paradigm. Innovative streaming applications are being developed in areas ranging from scientific applications (for example, environment monitoring), to business intelligence (for example, fraud detection and trend analysis), to financial markets (for example, algorithmic trading systems). In this paper we describe Streamsight, a new visualization tool built to examine, monitor and help understand the dynamic behavior of streaming applications. Streamsight can handle the complex, distributed and large-scale nature of stream processing applications by using hierarchical graphs, multi-perspective visualizations, and de-cluttering strategies. To address the dynamic and adaptive nature of these applications, Streamsight also provides real-time visualization as well as the capability to record and replay. All these features are used for debugging, for performance optimization, and for management of resources, including capacity planning. More than 100 developers, both inside and outside IBM, have been using Streamsight to help design and implement large-scale stream processing applications.
Design and Evaluation of Extensions to UML Sequence Diagrams for Modeling Multithreaded Interactions
Authors: Xie Shaohua , Kraemer Eileen , Stirewalt R. E. K. , Dillon Laura K , Fleming Scott D
Published: June 2009

Learning about concurrency and synchronization is difficult for novices. Our research seeks to support and improve the teaching and learning of concurrency concepts and to improve comprehension of the intricacies of multiple thread interactions. This paper describes a series of empirical studies in the first phase of our research. We began by conducting a comparative study to empirically evaluate the usability by novices of the existing variants of the UML sequence diagram notation in solving comprehension tasks involving multiple thread interactions. The results implied that a deliberately designed variant of this notation may provide better support for reasoning about concurrent behavior. We then investigated the factors that complicate learning, with the idea that the same complexities would also complicate comprehension tasks. In order to understand the practical difficulties novices encounter in learning about concurrency, we conducted an instructor interview and an observational study. These investigations guided us in determining the desirable properties of a new notation. We then designed synchronization-adorned UML (saUML) sequence diagrams, which extend UML sequence diagrams with those properties. Finally, we performed four empirical studies to evaluate the usability and efficacy of saUML. Through these empirical studies, we were able to validate the benefits of saUML in enhancing novices' understanding of programs with different levels of synchronization complexity.
Eclipse GEF3D: Bringing 3D to Existing 2D Editors
Authors: von Pilgrim Jens , Duske Kristian , McIntosh Paul
Published: June 2009

In this paper we present the Eclipse project GEF3D. It is a framework for three-dimensional (3D) editors and editors, based on the widely used two-dimensional (2D) graphical editing framework Eclipse Graphical Editing Framework (GEF). It enhances this framework, enabling programmers to easily implement 3D editors. As an Eclipse plugin GEF3D is seamlessly integrated into the Eclipse integrated development environment, allowing developers to work with one tool for developing and visualizing their software in 3D. The third dimension enables the visualization of more complex relationships than provided by existing two-dimensional representations. In this paper we explain the architecture and certain design patterns of GEF3D in order to give researchers and developers interested in 3D software visualization an overview of how to use GEF3D and the features provided by the framework. We present the results of a usability evaluation, show how GEF3D is applied to embed an existing 2D editor into a 3D editor, and discuss performance issues.
All Costs, No Benefits: How the US-Jordan Free Trade Agreement Affects Access to Medicines
Authors: Malpani Rohit
Published: June 2009

The US-Jordan free trade agreement and Jordan's terms of World Trade Organization accession introduced Trade-Related Aspects of Intellectual Property Rights (TRIPS)-plus rules to the country's intellectual property (IP) law. This paper examines the benefits and consequences of TRIPS-plus rules and reports numerous negative consequences. In particular, data exclusivity, a TRIPS-plus rule, delayed generic competition for 79 per cent of medicines launched by multinational pharmaceutical companies between 2002 and mid-2006, which otherwise would have been available in an inexpensive, generic form. The public health system and individuals, owing to a lack of generic competition, had to pay higher prices for new medicines. There have been no benefits from introducing strict IP rules in Jordan. There has been nearly no foreign direct investment by drug companies into Jordan between 2002 and mid-2006 to develop medicines with local companies. TRIPS-plus rules have not encouraged Jordanian generic companies to engage in research and development for medicines. Finally, new product launches in Jordan are only a fraction of total product launches in the United States and the European Union and are unaffordable for ordinary people. TRIPS-plus rules contributed to a 20 per cent increase in medicine prices between 2002 and 2006. Higher medicine prices will strain Jordan's public health system and require significant out-of-pocket expenditure that will harm the poorest.
Despite Global Downturn, Generics Makers Stand to Reap Great Rewards in China's Evolving Pharmaceutical Market
Authors: Chui Mandy
Published: June 2009

For generics pharmaceutical makers, the decision to enter the Chinese market is almost a foregone conclusion. Despite a deepening global financial crisis, China remains a tempting target for the world's struggling drug companies. Thanks to aggressive government stimulus in the health-care sector, China will continue to enjoy double-digit growth. Given the strong demand for inexpensive drugs, generics makers can benefit significantly in this landscape. Yet, the challenges posed by increased local competition, growing government intervention and uncertainty around the health care reforms make the road to China far from smooth - worthy of intensive study and creative planning. For generic drug makers, a combination of carefully chosen portfolios, clearly defined target sectors and strategies, and cooperation between local companies and multinationals can pave the way to success in this promising market.
Patients must have Immediate Access to Affordable Generic Medicines at Day One After Patent Expiry: The EGA Response to the Public Consultation ‘DG Competition Pharmaceutical Sector Inquiry: Preliminary Report’
Authors: Grooten Elke ,   European Generic medicines Association (EGA)
Published: June 2009

In her speech launching DG Competition's preliminary report on the pharmaceutical sector inquiry on 28 November 2008, Commissioner Neelie Kroes clearly identified the Report's unspoken conclusion ‘competition in this industry does not work as well as it should’. Among others, the Report rightly identifies delays to generic entry as an important failure of the competitive process in the pharmaceutical sector. The result is that national health-care systems (and patients) pay unnecessarily high prices for pharmaceuticals and, ultimately, that patients are unable to obtain the medicines they need. The behaviour of originator companies is correctly stated to be a significant factor in delays to the entry of generic medicines. As set out in the Report, originator companies have a ‘tool box’ of strategies that they deploy to frustrate the entry of generic medicines. In the opinion of the European Generic Medicines Association (EGA), a number of strategies is the most significant in creating hurdles to generic competition. In highlighting these strategies, the Report confirms the experiences of generic companies operating in Europe. The EGA's members regularly encounter use of each of these strategies when seeking to launch new generic products in EU markets, and will frequently encounter the use of multiple strategies by an originator company in relation to a single medicine and across a range of Member States.
Temperature dependence of microwave-induced magnetoresistance oscillation in two-dimensional electron systems
Authors: Lei X. L. , Liu S. Y.
Published: June 2009

Microwave-induced magnetoresistance oscillations in two-dimensional electron systems are examined from a photon-assisted transport scheme with short-range impurity scatterings. Analytical results at high filling factors strongly support early considerations and the recent experimental observation that the temperature dependence of the oscillation amplitude is exponential and originates primarily from the single-particle lifetime.
Evolution of electroluminescence from multiple Si-implanted silicon nitride films with thermal annealing
Authors: Cen Z. H. , Chen T. P. , Ding L. , Liu Y. , Wong J. I. , Yang M. , Liu Z. , Goh W. P. , Zhu F. R. , Fung S.
Published: June 2009

Influence of thermal annealing on electroluminescence (EL) from multiple-Si-implanted silicon nitride films has been investigated. A reduced injection current and an enhanced EL intensity have been obtained simultaneously by increasing the annealing temperature, which results in a higher EL quantum efficiency. In addition, four emission bands are identified, and their peak energies, intensities, and full widths at half maxima are found to change with annealing temperature. A model is proposed to illustrate the carrier transport, the mechanisms of the four emission bands, and the evolution of the EL bands with annealing as well. The two major bands and the minor ultraviolet band are explained in terms of the recombination of the injected electrons in either the silicon dangling-bond (≡Si0) states or the nitride conduction band with the injected holes in either the band tail states above the nitride valence band or the valence band itself, while the minor near infrared band is attributed to the Si nanocrystals formed in the thin film.
Fluorescence emission enhanced by surface electromagnetic waves on one-dimensional photonic crystals
Authors: Soboleva I. V. , Descrovi E. , Summonte C. , Fedyanin A. A. , Giorgis F.
Published: June 2009

An appreciable increase in the fluorescence emission of an organic chromofore is obtained by exploiting the local field enhancement at the surface of one-dimensional photonic crystals after excitation of surface electromagnetic waves (SEW). Using a properly designed photonic crystal consisting of alternating a-Si1−xNx:H layers with different nitrogen content, efficient emission of R6G dye spun on the surface of the photonic crystal is detected and the intensity spatial distribution of the SEW is visualized by means of far-field fluorescence microscopy. Our results demonstrate potential applications in enhanced fluorescence microscopy with an increased sensitivity and spectral selectivity.
Liouville–von Neumann molecular dynamics
Authors: Jakowski Jacek , Morokuma Keiji
Published: June 2009

We present a novel first principles molecular dynamics scheme, called Liouville–von Neumann molecular dynamics, based on Liouville–von Neumann equation for density matrices propagation and Magnus expansion of the time-evolution operator. The scheme combines formally accurate quantum propagation of electrons represented via density matrices and a classical propagation of nuclei. The method requires a few iterations per each time step where the Fock operator is formed and von Neumann equation is integrated. The algorithm (a) is free of constraint and fictitious parameters, (b) avoids diagonalization of the Fock operator, and (c) can be used in the case of fractional occupation as in metallic systems. The algorithm is very stable, and has a very good conservation of energy even in cases when a good quality conventional Born–Oppenheimer molecular dynamics trajectories is difficult to obtain. Test simulations include initial phase of fullerene formation from gaseous C2 and retinal system.
Concept for support and cleavage of brittle crystals
Authors: Tröger L. , Schütte J. , Ostendorf F. , Kühnle A. , Reichling M.
Published: June 2009

We report on sample holders for crystals to be cleaved for the preparation of surfaces with large atomically flat terraces. The concept for mounting sample crystals is based on a vicelike clamping mechanism to securely hold the crystal in position while reducing the risk of fragmentation. Sample holders based on this concept and made of suitable materials allow preparation and cleavage of crystals in the ultrahigh vacuum at high or low temperatures. To cleave the crystal, we employ a scalpel blade mounted on a wobble stick to generate a highly localized stress field initiating the cleavage process. The sample holders are used for experiments of highest resolution scanning force microscopy, however, the concept can be transferred to any other system where cleavage faces of crystals are of interest. Exemplarily, scanning force microscopy results demonstrate that (111) cleavage faces of CaF2 crystals can be prepared with steps only a few F–Ca–F triple-layers high and atomically flat terraces extending over areas of several μm2.
Infrared spectra of the OCS-CO2 complex: Observation of two distinct slipped near-parallel isomers
Authors: Dehghany M. , Oliaee J. Norooz , Afshari Mahin , Moazzen-Ahmadi N. , McKellar A. R. W.
Published: June 2009

Infrared spectra of OCS-CO2 complexes are studied in a pulsed supersonic slit-jet expansion using a tunable diode laser probe in the 2060 cm−1 region of the C–O stretching fundamental of OCS. Two bands are observed and analyzed, corresponding to two distinct isomers of the complex. Isomer a is the known form which has been previously studied in the microwave region. Isomer b is a new form, expected theoretically but first observed here. Structures are determined with the help of isotopic substitution. Both isomers are planar, with slipped near-parallel geometries. In isomer a, the intermolecular (center of mass) separation is 3.55 Å and the C atom of the CO2 is closer to the S atom of the OCS. In isomer b, the C atom of CO2 slides closer to the O atom of OCS and the center of mass separation increases to 3.99 Å. Isomer a is the lowest energy form, but paradoxically isomer b appears to be stronger in our infrared spectra. Predicted pure rotational transition frequencies are given to help in a search for the microwave spectrum of isomer b.
A new potential energy surface and predicted infrared spectra of the Ar–CO2 van der Waals complex
Authors: Cui Yali , Ran Hong , Xie Daiqian
Published: June 2009

A new potential energy surface for Ar–CO2 is constructed at the coupled-cluster singles and doubles with noniterative inclusion of connected triple [CCSD(T)] level with augmented correlation-consistent triple-zeta (aug-cc-pVTZ) basis set plus midpoint bond functions. The Q3 normal mode for the v3 antisymmetric stretching vibration of CO2 is involved in the construction of the potential. Effective two-dimensional potentials with CO2 in the ground and first excited v3 vibrational states are obtained by averaging a three-dimensional potential for each case over the Q3 asymmetric stretch vibrational coordinate. Both potentials have only a T-shaped minimum with a well depth of 200.97 and 201.37 cm−1, respectively. No linear local minima are detected. The radial discrete variable representation/angular finite basis representation method and the Lanczos algorithm are employed to calculate the related rovibrational energy levels. The calculated band origin shift of the complex agrees very well with the observed one (−0.474 versus −0.470 cm−1). In addition, the predicted infrared spectra based on the two averaged potentials are in excellent agreement with the available experimental data, which again testifies the accuracy of the new potentials.
Dielectric response of AlSb from 0.7 to 5.0 eV determined by in situ ellipsometry
Authors: Jung Y. W. , Ghong T. H. , Byun J. S. , Kim Y. D. , Kim H. J. , Chang Y. C. , Shin S. H. , Song J. D.
Published: June 2009

We present pseudodielectric function data ⟨ε⟩=⟨ε1⟩+i⟨ε2⟩ from 0.7 to 5.0 eV of oxide-free AlSb that are the closest representation to date of the intrinsic bulk dielectric response ε of the material. Measurements were done on a 1.5 μm thick film grown on (001) GaAs by molecular beam epitaxy. Data were obtained with the film in situ to avoid oxidation artifacts. Overlapping critical-point (CP) structures in the E2 energy region were identified by means of band-structure calculations done with the linear augmented Slater-type orbital method. Calculated CP energies agree well with those obtained from data, confirming the validity of the calculations.
Effect of electron blocking layer on efficiency droop in InGaN/GaN multiple quantum well light-emitting diodes
Authors: Han Sang-Heon , Lee Dong-Yul , Lee Sang-Jun , Cho Chu-Young , Kwon Min-Ki , Lee S. P. , Noh D. Y. , Kim Dong-Joon , Kim Yong Chun , Park Seong-Ju
Published: June 2009

The effect of an electron blocking layer (EBL) on the efficiency droop in InGaN/GaN multiple quantum well light-emitting diodes (LEDs) is investigated. At low current density, the LEDs with a p-AlGaN EBL show a higher external quantum efficiency (EQE) than LEDs without an EBL. However, the EQE of LEDs without an EBL is higher than LEDs with an EBL as injection current density is increased. The improved EQE of LEDs without an EBL at high current density is attributed to the increased hole injection efficiency.
Theoretical spectroscopy of trans-HNNH+ and isotopomers
Authors: Lauvergnat D. , Hochlaf M.
Published: June 2009

The six-dimensional potential energy surface of the electronic ground state of trans-HNNH+ (X̃ A2g) is mapped at the RCCSD(T)/aug-cc-pV5Z level of theory. This potential energy surface is incorporated later into perturbative and variational treatments to solve the nuclear motion and to derive a set of spectroscopic data for trans-HNNH+, trans-HNND+, and trans-DNND+. Our vibrational spectra are compared with those deduced from the earlier photoelectron spectra by Frost et al. [J. Chem. Phys. 64, 4719 (1976)], for which a good agreement between the theoretical and experimental results is found. Our calculations reveal the presence of strong anharmonic resonances between the vibrational levels of these cations even at low energies, thus complicating even more their assignment by vibrational quantum numbers. These resonances should participate in the transfer of intensities between the active modes during the direct photoionization of the neutral molecule and the combination modes and overtones of the inactive modes belonging to the totally symmetric irreducible representation.
Study of hole accumulation in individual germanium quantum dots in p-type silicon by off-axis electron holography
Authors: Li Luying , Ketharanathan Sutharsan , Drucker Jeff , McCartney Martha R.
Published: June 2009

Epitaxial germanium quantum dots (QDs) embedded in boron-doped silicon have been studied using off-axis electron holography to estimate the number of holes associated with a single QD. Holes were confined near the base of the pyramidal, 25-nm-wide Ge QDs. The resulting estimate of charge density was 0.03 holes/nm3 which corresponded to about 30 holes localized to the investigated dot. For comparison, the average number of holes confined to each Ge dot was found to be about 40, using a capacitance-voltage measurement. The difference emphasizes the value of measuring charges confined to individual nm-scale regions of a heterogeneous sample.
Dielectric properties and electric breakdown strength of a subpercolative composite of carbon black in thermoplastic copolymer
Authors: Stoyanov Hristiyan , Mc Carthy Denis , Kollosche Matthias , Kofod Guggi
Published: June 2009

We investigate the dielectric properties and electric breakdown strength of subpercolative composites of conductive carbon black particles in a rubber insulating matrix. A significant increase in the permittivity in the vicinity of the insulator to conductor transition was observed, with relatively low increases in dielectric loss; however, a rapid decrease in electric breakdown strength was inevitable. A steplike feature was ascribed to agglomeration effects. The low ultimate values of the electric field strength of such composites appear to prohibit practical use.
Orientation dependent nonlinear optical effects in ZnSe nanowires
Authors: Spencer T. L. , Cisek R. , Barzda V. , Philipose U. , Ruda H. E. , Shik A.
Published: June 2009

Three nonlinear optical phenomena, two-photon induced luminescence, second-harmonic generation, and third-harmonic generation, were studied experimentally in ZnSe nanowires. All three effects demonstrate a strong dependence on the orientation of linearly polarized excitation, being maximal for the polarization parallel to the nanowire axis. The phenomenon is caused by the anisotropic nanowire depolarization due to the difference in dielectric constants between the nanowires and the environment and has different amplitude for nanowires embedded in different dielectrics. The amplitude depends also on nanowire bending and nonuniformity.
Kinaesthetic and Visual Perceptions of Orientations
Authors: Lejeune Laure , Thouvarecq Régis , Anderson David J , Caston Jean , Jouen François
Published: June 2009

In the present study we compare the kinaesthetic and visual perception of the vertical and horizontal orientations (subjective vertical and subjective horizontal) to determine whether the perception of cardinal orientations is amodal or modality-specific. The influence of methodological factors on the accuracy of perception is also investigated by varying the stimulus position as a function of its initial tilt (clockwise or counterclockwise) and its angle (22°, 45°, 67°, and 90°) in respect to its physical orientation. Ten participants estimated the vertical and horizontal orientations by repositioning a rod in the kinaesthetic condition or two luminous points, forming a ‘virtual line’ in the visual condition. Results within the visual modality replicated previous findings by showing that estimation of the physical orientations is very accurate regardless of the initial position of the virtual line. In contrast, the perception of orientation with the kinaesthetic modality was less accurate and systematically influenced by the angle between the initial position of the rod and the required orientation. The findings question the assumption that the subjective vertical is derived from an internal representation of gravity and highlight the necessity of taking into account methodological factors in studies on subjective orientations.
Row spacing and planting density effects on the growth and yield of sugarcane. 1. Responses in fumigated and non-fumigated soil
Authors: Garside A. L. , Bell M. J.
Published: June 2009

It has been reported that high-density planting of sugarcane can improve cane and sugar yield through promoting rapid canopy closure and increasing radiation interception earlier in crop growth. It is widely known that the control of adverse soil biota through fumigation (removes soil biological constraints and improves soil health) can improve cane and sugar yield. Whether the responses to high-density planting and improved soil health are additive or interactive has important implications for the sugarcane production system.
Field experiments established at Bundaberg and Mackay, Queensland, Australia, involved all combinations of 2-row spacings (0.5 and 1.5 m), two planting densities (27 000 and 81 000 two-eyed setts/ha), and two soil fumigation treatments (fumigated and non-fumigated). The Bundaberg experiment had two cultivars (Q124, Q155), was fully irrigated, and harvested 15 months after planting. The Mackay experiment had one cultivar (Q117), was grown under rainfed conditions, and harvested 10 months after planting.
High-density planting (81 000 setts/ha in 0.5-m rows) did not produce any more cane or sugar yield at harvest than low-density planting (27 000 setts/ha in 1.5-m rows) regardless of location, crop duration (15 v. 10 months), water supply (irrigated v. rainfed), or soil health (fumigated v. non-fumigated). Conversely, soil fumigation generally increased cane and sugar yields regardless of site, row spacing, and planting density. In the Bundaberg experiment there was a large fumigation × cultivar × density interaction (P < 0.01). Cultivar Q155 responded positively to higher planting density in non-fumigated soil but not in fumigated soil, while Q124 showed a negative response to higher planting density in non-fumigated soil but no response in fumigated soil. In the Mackay experiment, Q117 showed a non-significant trend of increasing yield in response to increasing planting density in non-fumigated soil, similar to the Q155 response in non-fumigated soil at Bundaberg.
The similarity in yield across the range of row spacings and planting densities within experiments was largely due to compensation between stalk number and stalk weight, particularly when fumigation was used to address soil health. Further, the different cultivars (Q124 and Q155 at Bundaberg and Q117 at Mackay) exhibited differing physiological responses to the fumigation, row spacing, and planting density treatments. These included the rate of tiller initiation and subsequent loss, changes in stalk weight, and propensity to lodging. These responses suggest that there may be potential for selecting cultivars suited to different planting configurations.
Row spacing and planting density effects on the growth and yield of sugarcane. 3. Responses with different cultivars
Authors: Garside A. L. , Bell M. J.
Published: June 2009

The promotion of controlled traffic (matching wheel and row spacing) in the Australian sugar industry is necessitating a widening of row spacing beyond the standard 1.5 m. As all cultivars grown in the Australian industry have been selected under the standard row spacing there are concerns that at least some cultivars may not be suitable for wider rows. To address this issue, experiments were established in northern and southern Queensland in which cultivars, with different growth characteristics, recommended for each region, were grown under a range of different row configurations. In the northern Queensland experiment at Gordonvale, cultivars Q187, Q200, Q201, and Q218 were grown in 1.5-m single rows, 1.8-m single rows, 1.8-m dual rows (50 cm between duals), and 2.3-m dual rows (80 cm between duals). In the southern Queensland experiment at Farnsfield, cvv. Q138, Q205, Q222 and Q188 were also grown in 1.5-m single rows, 1.8-m single rows, 1.8-m dual rows (50 cm between duals), while 1.8-m-wide throat planted single row and 2.0-m dual row (80 cm between duals) configurations were also included.
There was no difference in yield between the different row configurations at Farnsfield but there was a significant row configuration × cultivar interaction at Gordonvale due to good yields in 1.8-m single and dual rows with Q201 and poor yields with Q200 at the same row spacings. There was no significant difference between the two cultivars in 1.5-m single and 2.3-m dual rows.
The experiments once again demonstrated the compensatory capacity that exists in sugarcane to manipulate stalk number and individual stalk weight as a means of producing similar yields across a range of row configurations and planting densities.
There was evidence of different growth patterns between cultivars in response to different row configurations (viz. propensity to tiller, susceptibility to lodging, ability to compensate between stalk number and stalk weight), suggesting that there may be genetic differences in response to row configuration. It is argued that there is a need to evaluate potential cultivars under a wider range of row configurations than the standard 1.5-m single rows. Cultivars that perform well in row configurations ranging from 1.8 to 2.0 m are essential if the adverse effects of soil compaction are to be managed through the adoption of controlled traffic.
Chilling tolerance in maize: agronomic and physiological approaches
Authors: Farooq Muhammad , Aziz Tariq , Wahid Abdul , Lee Dong-Jin , Siddique Kadambot H. M.
Published: June 2009

Maize is a C4 plant species with higher temperature optima than C3 plant species. Growth and productivity of maize are severely constrained by chilling stress. Here, we review the effects of chilling stress on growth, phenology, water and nutrient relations, anatomy, and photosynthesis in maize. Several management strategies to cope with chilling stress are also proposed. In maize, chilling stress is known to reduce leaf size, stem extension and root proliferation, disturb plant water relations, and impede nutrient uptake. Chilling stress in maize is a complex phenomenon with physiological and biochemical responses at both cellular and whole-organ level. CO2 assimilation by leaves is reduced mainly due to membrane damage, photoinhibition, and disturbed activity of various enzymes. Enhanced metabolite flux through the photorespiratory pathway increases the oxidative load on tissues as both processes generate reactive oxygen species (ROS). Injury caused by ROS to macromolecules under chilling stress is one of the major deterrents to growth. Low-molecular-weight osmolytes, including glycinebetaine, proline, and organic acids, are crucial in sustaining cellular function under chilling stress. Plant growth substances such as salicylic acid, gibberellic acid, and abscisic acid modulate the response of maize to chilling stress. Polyamines and several enzymes act as antioxidants and reduce the adverse effects of chilling stress. Chilling tolerance in maize can be managed through the development and selection of chilling-tolerant genotypes by breeding and genomic approaches. Agronomic approaches such as exogenous application of growth hormones and osmoprotectants to seeds or plants, and early vigour, can also aid in chilling tolerance.
Dicer-regulated microRNAs 222 and 339 promote resistance of cancer cells to cytotoxic T-lymphocytes by down-regulation of ICAM-1
Authors: Ueda Ryo , Kohanbash Gary , Sasaki Kotaro , Fujita Mitsugu , Zhu Xinmei , Kastenhuber Edward R. , McDonald Heather A. , Potter Douglas M. , Hamilton Ronald L. , Lotze Michael T. , Khan Saleem A. , Sobol Robert W. , Okada Hideho
Published: June 2009

The RNase III endonuclease Dicer plays a key role in generation of microRNAs (miRs). We hypothesized that Dicer regulates cancer cell susceptibility to immune surveillance through miR processing. Indeed,
Dicer
disruption up-regulated intercellular cell adhesion molecule (ICAM)-1 and enhanced the susceptibility of tumor cells to antigen-specific lysis by cytotoxic T-lymphocytes (CTLs), while expression of other immunoregulatory proteins examined was not affected. Blockade of ICAM-1 inhibited the specific lysis of CTLs against
Dicer
-disrupted cells, indicating a pivotal role of ICAM-1 in the interaction between tumor cells and CTL. Both miR-222 and -339 are down-regulated in
Dicer
-disrupted cells and directly interacted with the 3′ untranslated region (UTR) of ICAM-1 mRNA. Modulation of
Dicer
or these miRs inversely correlated with ICAM-1 protein expression and susceptibility of U87 glioma cells to CTL-mediated cytolysis while ICAM-1 mRNA levels remained stable. Immunohistochemical and in situ hybridization analyses of 30 primary glioblastoma tissues demonstrated that expression of Dicer, miR-222, or miR-339 was inversely associated with ICAM-1 expression. Taken together, Dicer is responsible for the generation of the mature miR-222 and -339, which suppress ICAM-1 expression on tumor cells, thereby down-regulating the susceptibility of tumor cells to CTL-mediated cytolysis. This study suggests development of novel miR-targeted therapy to promote cytolysis of tumor cells.
Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs
Authors: Kosugi Shunichi , Hasebe Masako , Tomita Masaru , Yanagawa Hiroshi
Published: June 2009

The cell cycle-dependent nucleocytoplasmic transport of proteins is predominantly regulated by CDK kinase activities; however, it is currently difficult to predict the proteins thus regulated, largely because of the low prediction efficiency of the motifs involved. Here, we report the successful prediction of CDK1-regulated nucleocytoplasmic shuttling proteins using a prediction system for nuclear localization signals (NLSs). By systematic amino acid replacement analyses in budding yeast, we created activity-based profiles for different classes of importin-α-dependent NLSs that represent the functional contributions of different amino acids at each position within an NLS class. We then developed a computer program for prediction of the classical importin-α/β pathway-specific NLSs (cNLS Mapper, available at
http//nls-mapper.iab.keio.ac.jp/
) that calculates NLS activities by using these profiles and an additivity-based motif scoring algorithm. This calculation method achieved significantly higher prediction accuracy in terms of both sensitivity and specificity than did current methods. The search for NLSs that overlap the consensus CDK1 phosphorylation site by using cNLS Mapper identified all previously reported and 5 previously uncharacterized yeast proteins (Yen1, Psy4, Pds1, Msa1, and Dna2) displaying CDK1- and cell cycle-regulated nuclear transport. CDK1 activated or repressed their nuclear import activity, depending on the position of CDK1-phosphorylation sites within NLSs. The application of this strategy to other functional linear motifs should be useful in systematic studies of protein–protein networks.
Sexual selection and mating systems
Authors: Shuster Stephen M.
Published: June 2009

Sexual selection is among the most powerful of all evolutionary forces. It occurs when individuals within one sex secure mates and produce offspring at the expense of other individuals within the same sex. Darwin was first to recognize the power of sexual selection to change male and female phenotypes, and, in noting that sexual selection is nonubiquitous, Darwin was also first to recognize the importance of mating system—the “special circumstances” in which reproduction occurs within species. Analyses of mating systems since Darwin have emphasized either the genetic relationships between male and female mating elements, usually among plants, or the numbers of mates males and females may obtain, usually among animals. Combining these schemes yields a quantitative methodology that emphasizes measurement of the sex difference in the variance in relative fitness, as well as phenotypic and genetic correlations underlying reproductive traits that may arise among breeding pairs. Such information predicts the degree and direction of sexual dimorphism within species, it allows the classification of mating systems using existing genetic and life history data, and with information on the spatial and temporal distributions of fertilizations, it may also predict floral morphology in plants. Because this empirical framework identifies selective forces and genetic architectures responsible for observed male-female differences, it compliments discoveries of nucleotide sequence variation and the expression of quantitative traits. Moreover, because this methodology emphasizes the process of evolutionary change, it is easier to test and interpret than frameworks emphasizing parental investment in offspring and its presumed evolutionary outcomes.
Synchrony through twice-frequency forcing for sensitive and selective auditory processing
Authors: Jackson Joseph C. , Windmill James F. C. , Pook Victoria G. , Robert Daniel
Published: June 2009

Male mosquitoes detect flying females using antennal hearing organs sensitive to nanoscale mechanical displacements and that harbor motile mechanosensory neurons. The mechanisms supporting neuronal motility, and their function in peripheral sensory processing, remain, however, puzzling. The mechanical and neural responses reveal a transition that unmasks the onset of synchronization between sensory neurons. This synchronization constitutes an unconventional, mechanically driven, process of communication between sensory neurons. Enhancing auditory sensitivity and selectivity, synchronization between mechanosensors in the mosquito arises from entrainment to twice-frequency forcing and is formally analogous to injection-locking in high-power laser technology. This discovery opens up the enticing possibility that other sensory systems, even nonsensory cell ensembles, coordinate their actions through mechanical signaling.
Mre11-Rad50-Nbs complex is required to cap telomeres during
Drosophila
embryogenesis
Authors: Gao Guanjun , Bi Xiaolin , Chen Jie , Srikanta Deepa , Rong Yikang S.
Published: June 2009

Using
Drosophila
as a model system, we identified here a stringent requirement for Mre11-Rad50-Nbs (MRN) function in telomere protection during early embryonic development. Animals homozygous for hypomorphic mutations in either
mre11
or
nbs
develop normally with minimal telomere dysfunction. However, they produce inviable embryos that succumb to failure of mitosis caused by covalent fusion of telomeric DNA. Interestingly, the molecular defect is not the absence of MRN interaction or of Mre11 nuclease activities, but the depletion of the maternal pool of Nbs protein in these embryos. Because of Nbs depletion, Mre11 and Rad50 (MR) are excluded from chromatin. This maternal effect lethality in
Drosophila
is similar to that seen in mice carrying hypomorphic
mrn
mutations found in human patients, suggesting a common defect in telomere maintenance because of the loss of MRN integrity.
Structural study of X-ray induced activation of carbonic anhydrase
Authors: Sjöblom Björn , Polentarutti Maurizio , Djinović-Carugo Kristina
Published: June 2009

Carbonic anhydrase, a zinc metalloenzyme, catalyzes the reversible hydration of carbon dioxide to bicarbonate. It is involved in processes connected with acid–base homeostasis, respiration, and photosynthesis. More than 100 distinct human carbonic anhydrase II (HCAII) 3D structures have been generated in last 3 decades [Liljas A, et al. (1972)
Nat New Biol
235:131–137], but a structure of an HCAII in complex with CO
2
or HCO
3
−
has remained elusive. Here, we report previously undescribed structures of HCAII:CO
2
and HCAII:HCO
3
−
complexes, together with a 3D molecular film of the enzymatic reaction observed successively in the same crystal after extended exposure to X-ray. We demonstrate that the unexpected enzyme activation was caused in an X-ray dose-dependent manner. Although X-ray damage to macromolecular samples has long been recognized [Ravelli RB, Garman EF (2006)
Curr Opin Struct Biol
16:624–629], the detailed structural analysis reports on X-ray-driven reactions have been very rare in literature to date. Here, we report on enzyme activation and the associated chemical reaction in a crystal at 100 K. We propose mechanisms based on water photoradiolysis and/or electron radiolysis as the main cause of enzyme activation.
Effect of B–B impact ionization on GRPVC output: a semiconductor–nuclear physics interface
Authors: Liakos John K
Published: June 2009

We present calculations of efficiency, η, and open circuit voltage,Voc, of gamma ray photovoltaic cell (GRPVCs), in which impact ionization processes initiated by electrons in the conduction band (C-B) are taken into account. The contributions made to η andVocby multiple e–h-pair production, caused by high energy γ-photons, are incorporated by summing up all possible higher order processes for given γ-photon energy. The discussion is divided into two types of impact ionization: (i) in type-I, pair creation by γ-photons and by subsequent photons due to electron impact are treated on an equal footing; (ii) in type-II the probability for impact ionization by electrons is a function of the γ-photon energy, and the latter is subject to constraints set by the energy threshold parameter Θe. We find that for a GRPVC energy gapEg= 3.5 eV, and single e–h pair creation probabilityPe–h=0.8, driven by Th-229m1(Eγ= variable,T1/2= 45 h)-like nuclear isomers,Vocreaches the maximumVocmax= 2.7 V at ηmax≈ 95% whenEγ= 25 eV. In type-II processes the higher orders of e–h production do not make as high a contribution to η andVocbecause of higher energy losses. Output power is also calculated for both types of processes and comparisons are made.
Gene Disruption of an Arabinofuranosidase/β-Xylosidase Precursor DecreasesSclerotinia sclerotiorumVirulence on Canola Tissue
Authors: Yajima William , Liang Yue , Kav Nat N. V.
Published: June 2009

Although Sclerotinia sclerotiorum (Lib.) de Bary has been studied extensively, there are still aspects of this important phytopathogen's ability to cause disease in susceptible plants that remain unclear. A recent comprehensive proteome-level investigation of this fungus identified a number of proteins whose functions in disease initiation and progression have not been clearly established. Included among these proteins was an arabinofuranosidase/β-xylosidase precursor whose role as a potential virulence factor had not been investigated previously. This article describes the generation of gene-disrupted mutant S. sclerotiorum unable to produce this arabinofuranosidase/β-xylosidase precursor as well as the comparison of the virulence of this mutant with that of wild-type mycelia on susceptible canola leaves and stems. At all time points tested, the degree of necrosis was observed to be significantly greater on the plant tissue inoculated with wild-type mycelia. To our knowledge, this is the first report that clearly demonstrates that this arabinofuranosidase/β-xylosidase precursor is a virulence factor for S. sclerotiorum.
The Putative Secreted Serine Protease Chp-7 Is Required for Full Virulence and Induction of a Nonhost Hypersensitive Response by Clavibacter michiganensis subsp. sepedonicus
Authors: Nissinen Riitta , Xia Yunjian , Mattinen Laura , Ishimaru Carol A. , Knudson Dennis L. , Knudson Susan E. , Metzler Mary , Pirhonen Minna
Published: June 2009

Molecular biological studies on Clavibacter michiganensis subsp. sepedonicus, the causal agent of bacterial ring rot of potato, have gained greater feasibility due to the recent availability of whole genomic sequences and genetic tools for related taxa. Here, we describe the first report of construction and characterization of a transposon (Tn) mutant library of C. michiganensis subsp. sepedonicus sp. strain R10. Since virulence of R10 in potato has been shown previously to be associated with elicitation of a nonhost hypersensitive response (HR), the mutant library was screened initially for loss of HR in tobacco. The screen identified two HR-negative mutants containing Tn insertions within the same gene, CMS2989 (chp-7), although at distinct locations. chp-7 is one of 11 pat-1 homologs in C. michiganensis subsp. sepedonicus. HR-negative mutants of R10 multiplied to the same extent as wild type in planta but were less virulent in potato. Complementation with chp-7 restored virulence as well as the HR phenotype. Together, these findings demonstrate a role for chp-7 in C. michiganensis subsp. sepedonicus–plant interactions.
Suppression of the Rice Fatty-Acid Desaturase GeneOsSSI2Enhances Resistance to Blast and Leaf Blight Diseases in Rice
Authors: Jiang Chang-Jie , Shimono Masaki , Maeda Satoru , Inoue Haruhiko , Mori Masaki , Hasegawa Morifumi , Sugano Shoji , Takatsuji Hiroshi
Published: June 2009

Fatty acids and their derivatives play important signaling roles in plant defense responses. It has been shown that suppressing a gene for stearoyl acyl carrier protein fatty-acid desaturase (SACPD) enhances the resistance of Arabidopsis (SSI2) and soybean to multiple pathogens. In this study, we present functional analyses of a rice homolog of SSI2 (OsSSI2) in disease resistance of rice plants. A transposon insertion mutation (Osssi2-Tos17) and RNAi-mediated knockdown of OsSSI2 (OsSSI2-kd) reduced the oleic acid (18:1) level and increased that of stearic acid (18:0), indicating that OsSSI2 is responsible for fatty-acid desaturase activity. These plants displayed spontaneous lesion formation in leaf blades, retarded growth, slight increase in endogenous free salicylic acid (SA) levels, and SA/benzothiadiazole (BTH)-specific inducible genes, including WRKY45, a key regulator of SA/BTH-induced resistance, in rice. Moreover, the OsSSI2-kd plants showed markedly enhanced resistance to the blast fungus Magnaporthe grisea and leaf-blight bacteria Xanthomonas oryzae pv. oryzae. These results suggest that OsSSI2 is involved in the negative regulation of defense responses in rice, as are its Arabidopsis and soybean counterparts. Microarray analyses identified 406 genes that were differentially expressed (≥2-fold) in OsSSI2-kd rice plants compared with wild-type rice and, of these, approximately 39% were BTH responsive. Taken together, our results suggest that induction of SA-responsive genes, including WRKY45, is likely responsible for enhanced disease resistance in OsSSI2-kd rice plants.
Bacterial Growth Restriction During Host Resistance toPseudomonas syringaeIs Associated with Leaf Water Loss and Localized Cessation of Vascular Activity inArabidopsis thaliana
Authors: Freeman Brian C. , Beattie Gwyn A.
Published: June 2009

The physiological mechanisms by which plants limit the growth of bacterial pathogens during gene-for-gene resistance are poorly understood. We characterized early events in the Arabidopsis thaliana–Pseudomonas syringae pathosystem to identify physiological changes for which the kinetics are consistent with bacterial growth restriction. Using a safranine-O dye solution to detect vascular activity, we demonstrated that A. thaliana Col-0 resistance to P. syringae pv. tomato DC3000 cells expressing avrRpm1 involved virtually complete cessation of vascular water movement into the infection site within only 3 h postinoculation (hpi), under the conditions tested. This vascular restriction preceded or was simultaneous with precipitous decreases in photosynthesis, stomatal conductance, and leaf transpiration, with the latter two remaining at detectable levels. Microscopic plant cell death was detected as early as 2 hpi. Interestingly, suppression of bacterial growth during AvrRpm1-mediated resistance was eliminated by physically blocking leaf water loss through the stomata without altering plant cell death and was nearly eliminated by incubating plants at high relative humidity. The majority of the population growth benefit from blocking leaf water loss occurred early after inoculation, i.e., between 4 and 8 hpi. Collectively, these results support a model in which A. thaliana suppresses P. syringae growth during gene-for-gene resistance, at least in part, by coupling restricted vascular flow to the infection site with water loss through partially open stomata; that is, the plants effectively starve the invading bacteria for water.