bluuebunny/crossref_metadata_2025 huggingface dataset:
Radar target classification method with high accuracy and decision speed performance using MUSIC spectrum vectors and PCA projection
Authors: Secmen Mustafa
Published: August 2011

This paper introduces the performance of an electromagnetic target recognition method in resonance scattering region, which includes pseudo spectrum Multiple Signal Classification (MUSIC) algorithm and principal component analysis (PCA) technique. The aim of this method is to classify an “unknown” target as one of the “known” targets in an aspect‐independent manner. The suggested method initially collects the late‐time portion of noise‐free time‐scattered signals obtained from different reference aspect angles of known targets. Afterward, these signals are used to obtain MUSIC spectrums in real frequency domain having super‐resolution ability and noise resistant feature. In the final step, PCA technique is applied to these spectrums in order to reduce dimensionality and obtain only one feature vector per known target. In the decision stage, noise‐free or noisy scattered signal of an unknown (test) target from an unknown aspect angle is initially obtained. Subsequently, MUSIC algorithm is processed for this test signal and resulting test vector is compared with feature vectors of known targets one by one. Finally, the highest correlation gives the type of test target. The method is applied to wire models of airplane targets, and it is shown that it can tolerate considerable noise levels although it has a few different reference aspect angles. Besides, the runtime of the method for a test target is sufficiently low, which makes the method suitable for real‐time applications.
Validation of community models: 3. Tracing field lines in heliospheric models
Authors: MacNeice Peter , Elliott Brian , Acebal Ariel
Published: August 2011

Forecasting hazardous gradual solar energetic particle (SEP) bursts at Earth requires accurately modeling field line connections between Earth and the locations of coronal or interplanetary shocks that accelerate the particles. We test the accuracy of field lines reconstructed using four different models of the ambient coronal and inner heliospheric magnetic field, through which these shocks must propagate, including the coupled Wang‐Sheeley‐Arge (WSA)/ENLIL model. Evaluating the WSA/ENLIL model performance is important since it is the most sophisticated model currently available to space weather forecasters which can model interplanetary coronal mass ejections and, when coupled with particle acceleration and transport models, will provide a complete model for gradual SEP bursts. Previous studies using a simpler Archimedean spiral approach above 2.5 solar radii have reported poor performance. We test the accuracy of the model field lines connecting Earth to the Sun at the onset times of 15 impulsive SEP bursts, comparing the foot points of these field lines with the locations of surface events believed to be responsible for the SEP bursts. We find the WSA/ENLIL model performance is no better than the simplest spiral model, and the principal source of error is the model's inability to reproduce sufficient low‐latitude open flux. This may be due to the model's use of static synoptic magnetograms, which fail to account for transient activity in the low corona, during which reconnection events believed to initiate the SEP acceleration may contribute short‐lived open flux at low latitudes. Time‐dependent coronal models incorporating these transient events may be needed to significantly improve Earth/Sun field line forecasting.
A preliminary risk assessment of the Australian region power network to space weather
Authors: Marshall R. A. , Smith E. A. , Francis M. J. , Waters C. L. , Sciffer M. D.
Published: August 2011

It is well documented that power networks at high latitudes are vulnerable to the effects of space weather. In recent years the eastern Australia state power networks have been connected across state boundaries in order to improve robustness under increasing load demands and deliver power at competitive prices. However, this interconnectivity is likely to increase susceptibility of the network to space weather. Geomagnetically induced currents (GICs) flow in power transmission lines as the result of “geoelectric” fields and their associated geomagnetic field variations according to Faraday's Law. In this paper previously documented occurrences of GIC activity from regions around the world are investigated and categorized by their effects on nearby power networks. A frequency domain filter that produces an index representing GIC activity is applied to geomagnetic field data recorded at locations near the documented GIC activity to determine risk level “GIC index” thresholds. Geomagnetic field data from the Australian region are processed using the “GIC filter” to provide a preliminary risk assessment of space weather related GIC activity to the Australian power network. The analysis suggests lower limit threshold GICy indices of 50, 100, 250, and 600 corresponding to the risk levels of “low,” “moderate,” “high,” and “extreme,” respectively. Analysis of GICy indices derived from Australian magnetometer data shows that only southern Australian regions reached the “moderate” risk levels defined in this study with mainland southern Australia stations reaching this risk level twice over the previous two solar cycles. Southern Australian regions such as Tasmania reached moderate levels approximately 20 times during the previous solar cycle. Furthermore, elevated risk levels are typically only observed in Australia during solar maximum and its decline phase.
Dissolution and precipitation dynamics during dedolomitization
Authors: Edery Yaniv , Scher Harvey , Berkowitz Brian
Published: August 2011

We simulate the processes of dedolomitization and calcium carbonate precipitation using particle tracking. The study is stimulated by the results of a laboratory experiment that examined reactive transport of injected CaCl2/HCl, into a column of sucrosic dolomite particles, with a constant flow field. The injected fluid supplies Ca2+ and H+. Dedolomitization is a protonation reaction yielding carbonic acid; a subsequent deprotonation reaction yields , and reaction with the abundant Ca2+ forms the precipitate CaCO3. The dedolomitization and precipitation processes involve multistep, multispecies chemical reactions, with both irreversible and reversible stages. The particle tracking is governed by spatial and temporal distributions within a continuous time random walk framework. This accounts for the effects of disorder of heterogeneous media (leading to non‐Fickian transport) and includes the option of treating purely advective‐dispersive (Fickian) transport. The dynamics of dedolomitization are examined for different flow conditions and reaction rates. The fluctuations in the local velocity distributions, due to porosity changes, create conditions for positive feedbacks leading to development of preferential pathways, large‐scale nonlinearity, and precipitation banding. These features have been observed in the laboratory experiments and are now accounted for by the simulation results at similar time frames, velocities, and pH levels.
Deriving multiple near‐optimal solutions to deterministic reservoir operation problems
Authors: Liu Pan , Cai Ximing , Guo Shenglian
Published: August 2011

Even deterministic reservoir operation problems with a single objective function may have multiple near‐optimal solutions (MNOS) whose objective values are equal or sufficiently close to the optimum. MNOS is valuable for practical reservoir operation decisions because having a set of alternatives from which to choose allows reservoir operators to explore multiple options whereas the traditional algorithm that produces a single optimum does not offer them this flexibility. This paper presents three methods: the near‐shortest paths (NSP) method, the genetic algorithm (GA) method, and the Markov chain Monte Carlo (MCMC) method, to explore the MNOS. These methods, all of which require a long computation time, find MNOS using different approaches. To reduce the computation time, a narrower subspace, namely a near‐optimal space (NOSP, described by the maximum and minimum bounds of MNOS) is derived. By confining the MNOS search within the NOSP, the computation time of the three methods is reduced. The proposed methods are validated with a test function before they are examined with case studies of both a single reservoir (the Three Gorges Reservoir in China) and a multireservoir system (the Qing River Cascade Reservoirs in China). It is found that MNOS exists for the deterministic reservoir operation problems. When comparing the three methods, the NSP method is unsuitable for large‐scale problems but provides a benchmark to which solutions of small‐ and medium‐scale problems can be compared. The GA method can produce some MNOS but is not very efficient in terms of the computation time. Finally, the MCMC method performs best in terms of goodness‐of‐fit to the benchmark and computation time, since it yields a wide variety of MNOS based on all retained intermediate results as potential MNOS. Two case studies demonstrate that the MNOS identified in this study are useful for real‐world reservoir operation, such as the identification of important operation time periods and tradeoffs among objectives in multipurpose reservoirs.
Determination of Isoflavone Contents for Selected Soybean Lines and Soy Foods by Fourier Transform Near Infrared Reflectance Spectroscopy
Authors: Baianu I. , You Tiefeng , Nelson Randall
Published: August 2011

Soybean isoflavones are of considerable interest in relation to their possible health effects in human diets. Rapid and economical determination of soybean isoflavone contents is essential for breeding and selection of soybean seeds with optimal isoflavone levels for food applications. Fourier Transform Near Infrared Spectroscopy (FT-NIR) calibrations were developed for rapid and reliable analysis of soybean isoflavone content. Our isoflavone calibrations are characterized by low standard errors (<0.02%) and high degrees of correlation (>99%).
Nuclear Medicine and Early Discovery of Disease
Authors: Baianu I.
Published: August 2011

There is an urgent need for the early detection of diseases such as Alzheimer’s (AD) and Cancers in order to enable their successful treatment. Cancer is the second major cause of death after Heart Disease, and AD is the third major cause of death with major consequences for the society.Three major Nuclear Medicine techniques that are established for diagnostic and research purposes are: Positron Emission Tomography (PET) CAT/CT and Nuclear Magnetic Resonance Imaging (NMRI/MRI). These nuclear medicine techniques are discussed together with their clinical and research applications to early diagnosis of Alzheimer's Disease (AD) and cancers. Novel approaches to early detection and modeling of AD and cancers are then proposed.
Anti-Stokes fluorescence imaging of microscale thermal fields in thin films
Authors: Kuzmin A. N. , Baev A. , Kachynski A. V. , Fisher T. S. , Shakouri A. , Prasad P. N.
Published: August 2011

We demonstrate that the in-plane thin film heat transport can be accurately mapped via confocal anti-Stokes fluorescence imaging using fluorescent dye probes and nanoheaters. We employ 3D finite elements analysis to evaluate the thermal conductivity of a control sample and to assess the validity of a point heat source approximation. We have found that this approximation is adequate with use of a tightly focused laser beam, providing a robust means for determining the thermal conductivity of a sample under investigation.
Frequency switching in a relativistic magnetron with diffraction output
Authors: Liu Meiqin , Liu Chun-Liang , Galbreath David , Michel Cedric , Prasad Sarita , Fuks Mikhail I. , Schamiloglu Edl
Published: August 2011

Symmetric axial extraction of radiation from a relativistic magnetron with diffraction output (MDO) facilitates the use of any eigenmode as the operating one. As a consequence, a relatively small input RF signal can be used for mode switching, unlike the case for asymmetric extraction when only non-degenerate modes (the π- mode or the 2π- mode) can be used as the operating one. Using the MAGIC particle-in-cell code we demonstrate that about 180 MW is required to switch these non-degenerate modes in the well-known 400 kV A6 magnetron with extraction of radiation from one of its cavities when driven by a solid cathode, and about 30 MW is required for the same device when driven by a transparent cathode. For the gigawatt A6 MDO with a transparent cathode, however, only 200–300 kW is sufficient for mode switching and the switched mode continues to be generated after elimination of the input short RF signal when the amplitude of the applied axial magnetic field is near the critical value corresponding to the boundary between synchronous regions for neighboring modes. In repetitively pulsed systems, in order to switch each subsequent pulse independent of the previous one, the time between voltage pulses must be chosen to be not less than 20–30 ns (the time for the stored electromagnetic energy to flow out of the cavity) so that decreasing the output power of the previous pulse cannot switch the subsequent pulse. Finally, using this mode switching technique, we demonstrate the possibility of generating short gigawatt microwave pulses with different frequency and polarization by using a short, weak, single frequency signal that is very attractive for radar applications.
Fourier transform infrared matrix and density functional theory study of the vibrational spectrum of the linear MgC3- anion
Authors: Bejjani Micheline , Rittby C. M. L. , Graham W. R. M.
Published: August 2011

The linear MgC3− anion has been identified in the products from the dual Nd:YAG laser ablation of carbon and magnesium rods trapped in solid Ar at ∼12 K. Measurements of 13C isotopic shifts confirm the identification of the ν1(σ) vibrational fundamental at 1797.5 cm−1. A second fundamental ν2(σ) has been tentatively identified at 1190.1 cm−1. The results are in good agreement with the predictions of density functional theory calculations using the B3LYP functional with the 6-311+G(d) basis set. This is the first optical detection of the linear isomer of MgC3−.
Boost of plasma current with active magnetic field shaping coils in rotamak discharges
Authors: Yang Xiaokang , Goss Jermain , Kalaria Dhara , Huang Tian Sen
Published: August 2011

A set of magnetic shaping coils is installed on the Prairie View (PV) rotamak for the study of active plasma shape control in the regimes with and without toroidal field (TF). In the spherical tokamak regime (with TF), plasma current Ip can be boosted by 200% when all five shaping coils (connected in series) are energized. The enhancement of current drive efficiency is mainly attributed to the radial compression and the substantially axial extension of the plasma column; this in turn improves the impedance matching and thus increases antenna input power. In the field-reversed configuration (without TF), plasma current can be boosted by 100% when one middle coil is used; the appearance of radial shift mode limits the achievable value of Ip. The experiments clearly demonstrate that the plasma shape control plays a role in effectively driving plasma current in rotamaks.
Increased carrier generation rate in Si nanocrystals in SiO2 investigated by induced absorption
Authors: de Boer W. D. A. M. , Trinh M. T. , Timmerman D. , Schins J. M. , Siebbeles L. D. A. , Gregorkiewicz T.
Published: August 2011

We report on investigations of optical generation of carriers in Si nanocrystals embedded in SiO2 matrix by time-resolved induced absorption technique. Results obtained for excitation below and above twice the bandgap energy hν < 2Eg and hν > 2Eg show very similar decay characteristics (within τresolution ≈ 100 fs). When intensity of the signal is correlated to number of generated excitons, it is found that for the high photon energy excitation, carrier generation rate is considerably enhanced. These results are discussed in terms of carrier multiplication reported previously for semiconductor nanocrystals and photoluminescence quantum yield measurements for similar materials.
MeV negative ion generation from ultra-intense laser interaction with a water spray
Authors: Ter-Avetisyan S. , Ramakrishna B. , Borghesi M. , Doria D. , Zepf M. , Sarri G. , Ehrentraut L. , Andreev A. , Nickles P. V. , Steinke S. , Sandner W. , Schnürer M. , Tikhonchuk V.
Published: August 2011

MeV negative oxygen ions are obtained from a water spray target irradiated by high intensity (5 × 1019 W/cm2) and ultrashort (50 fs) laser pulses. Generation of negative ions is ascribed to electron-capture processes that the laser-accelerated high-energy positive ion experiences when it interacts with atoms in the spray. This mechanism implies the existence of a large number of MeV neutral oxygen atoms, which is consistent with indirect experimental evidence.
Population dynamics and production effects of sheep lice (Bovicola ovis Schrank) in extensively grazed flocks
Authors: James P. J. , Horton B. J. , Campbell N. J. , Evans D. L. , Winkleman J. , McPhie R.
Published: August 2011

An experiment was conducted to characterise population dynamics of lice and associated production loss in extensively grazed flocks infested at different times after shearing. Merino wethers were allocated to six groups of 31 sheep. In the first year (Y1), one sheep in each of two groups was infested with 2500 lice at 6 weeks after shearing (September), sheep in two groups were infested at 4 months (December) and two groups remained uninfested. In year 2 (Y2), infestations carried over from Y1, but a lousy sheep was added to each 6-week infestation mob. In year 3 (Y3), the infested mobs were treated and remained lice free, while lousy donor sheep were added to the two previously uninfested mobs. In Y1, lice appeared to die out in one 6-week-infestation group and were found on only two sheep before next shearing in the other. Lice persisted and spread in the two 4-month-infestation flocks, reaching mean counts (±s.e.) of 0.5 (±0.2) and 0.2 (±0.1) per part before shearing. In Y2 and Y3, lice persisted and increased in all infested flocks, reaching mean counts of 2.3 (±0.6), 8.5 (±1.5), 3.6 (±0.6) and 2.8 (±0.7) per part in Y2 and 1.0 (±0.2) and 1.2 (±0.4) per part in Y3. The count of 8.5 was in the flock with both a carry-over infestation and an infestor sheep. Exponential and logistic models were fitted to describe lice increase; differences in fleece derangement reflected louse numbers. Clean fleece weight was higher in flocks without lice in all years (0.12 kg/head in Y1; 0.22 kg/head in Y2 and Y3; P < 0.05). Classer-assigned colour scores (although not measured colour), cott score and line into which the wool was classed also differed significantly (P < 0.05) between infested and non-infested flocks and there was an indication that staple length was reduced in more heavily infested flocks. In spring-shorn flocks in environments with high solar radiation and no lice present at shearing, even if lice subsequently enter the mob, it appears unlikely that they will increase to levels where serious economic loss will be experienced before next shearing. The study also indicated that lice could persist in flocks at levels unlikely to be detected by most commercial wool producers for extended periods, possibly through one season, which may help to explain reports of new infestations with no apparent source.
The
D
-dopachrome tautomerase (
DDT
) gene product is a cytokine and functional homolog of macrophage migration inhibitory factor (MIF)
Authors: Merk Melanie , Zierow Swen , Leng Lin , Das Rituparna , Du Xin , Schulte Wibke , Fan Juan , Lue Hongqi , Chen Yibang , Xiong Huabao , Chagnon Frederic , Bernhagen Jürgen , Lolis Elias , Mor Gil , Lesur Olivier , Bucala Richard
Published: August 2011

Macrophage migration inhibitory factor (MIF) is a pivotal regulator of the immune response. Neutralization or genetic deletion of MIF does not completely abrogate activation responses, however, and deletion of the MIF receptor, CD74, produces a more pronounced phenotype than MIF deficiency. We hypothesized that these observations may be explained by a second MIF-like ligand, and we considered a probable candidate to be the protein encoded by the homologous,
D
-dopachrome tautomerase (D-DT) gene. We show that recombinant D-DT protein binds CD74 with high affinity, leading to activation of ERK1/2 MAP kinase and downstream proinflammatory pathways. Circulating D-DT levels correlate with disease severity in sepsis or malignancy, and the specific immunoneutralization of D-DT protects mice from lethal endotoxemia by reducing the expression of downstream effector cytokines. These data indicate that D-DT is a MIF-like cytokine with an overlapping spectrum of activities that are important for our understanding of MIF-dependent physiology and pathology.
Phosphatidylinositol monophosphate-binding interface in the oomycete RXLR effector AVR3a is required for its stability in host cells to modulate plant immunity
Authors: Yaeno Takashi , Li Hua , Chaparro-Garcia Angela , Schornack Sebastian , Koshiba Seizo , Watanabe Satoru , Kigawa Takanori , Kamoun Sophien , Shirasu Ken
Published: August 2011

The oomycete pathogen
Phytophthora infestans
causes potato late blight, one of the most economically damaging plant diseases worldwide.
P. infestans
produces AVR3a, an essential modular virulence effector with an N-terminal RXLR domain that is required for host-cell entry. In host cells, AVR3a stabilizes and inhibits the function of the E3 ubiquitin ligase CMPG1, a key factor in host immune responses including cell death triggered by the pathogen-derived elicitor protein INF1 elicitin. To elucidate the molecular basis of AVR3a effector function, we determined the structure of
Phytophthora capsici
AVR3a4, a close homolog of
P. infestans
AVR3a. Our structural and functional analyses reveal that the effector domain of AVR3a contains a conserved, positively charged patch and that this region, rather than the RXLR domain, is required for binding to phosphatidylinositol monophosphates (PIPs) in vitro. Mutations affecting PIP binding do not abolish AVR3a recognition by the resistance protein R3a but reduce its ability to suppress INF1-triggered cell death
in planta
. Similarly, stabilization of CMPG1
in planta
is diminished by these mutations. The steady-state levels of non–PIP-binding mutant proteins
in planta
are reduced greatly, although these proteins are stable in vitro. Furthermore, overexpression of a phosphatidylinositol phosphate 5-kinase results in reduction of AVR3a levels
in planta
. Our results suggest that the PIP-binding ability of the AVR3a effector domain is essential for its accumulation inside host cells to suppress CMPG1-dependent immunity.
The nature of variable sensitivity to agreement violations in L2 English
Authors: Bannai Masanori
Published: August 2011

This study focuses on the nature of variable sensitivity to violations of subject-verb number agreement in L2 English by examining Japanese-speaking learners’ performance in a self-paced reading task. The results of the experiment indicated that the learners were insensitive to agreement violations deriving from omission of 3rd person singular (3sg)-s, but were highly sensitive to violations deriving from overuse of 3sg-s. Their sensitivity to this type of violation, however, turned out to be non-categorical in that it was adversely affected by an adverb intervening between the subject and the verb. These results are interpreted to indicate that intermediate learners’ implementation of subject-verb agreement is not based on Agree operations, but on the Vocabulary entry for /s/ which is sensitive to the condition of the string of co-occurring terminal nodes as proposed by Hawkins and Casillas (2008).
Named entity recognition in Bengali and Hindi using support vector machine
Authors: Ekbal Asif , Bandyopadhyay Sivaji
Published: August 2011

Named Entity Recognition (NER) aims to classify each word of a document into predefined target named entity (NE) classes and is nowadays considered to be fundamental for many Natural Language Processing (NLP) tasks such as information retrieval, machine translation, information extraction, question answering systems and others. This paper reports about the development of a NER system for Bengali and Hindi using Support Vector Machine (SVM). We have used the annotated corpora of 122,467 tokens of Bengali and 502,974 tokens of Hindi tagged with the twelve different NE classes, defined as part of the IJCNLP-08 NER Shared Task for South and South East Asian Languages (SSEAL). An appropriate tag conversion routine has been developed in order to convert the data into the forms tagged with the four NE tags, namely Person name, Location name, Organization name and Miscellaneous name. The system makes use of the different contextual information of the words along with the variety of orthographic word-level features that are helpful in predicting the different NE classes. The system has been tested with the gold standard test sets of 35K, and 38K tokens for Bengali, and Hindi, respectively. Evaluation results have demonstrated the overall recall, precision, and f-score values of 85.11%, 81.74%, and 83.39%, respectively, for Bengali and 82.76%, 77.81%, and 80.21%, respectively, for Hindi. Statistical analysis, ANOVA is performed to show that the improvement in the performance with the use of language dependent features is statistically significant over the language independent features for Bengali and Hindi both.
Ratings gathered online vs. in person
Authors: Wurm Lee H. , Cano Annmarie , Barenboym Diana A.
Published: August 2011

Barenboym, Wurm, and Cano (2010) recently showed that significant differences emerged for ratings gathered online and in person. They also showed that researchers could reach different statistical conclusions in a regression analysis, depending on whether the norms were gathered online or in person. In the current study that research was extended. Familiarity ratings gathered online were significantly higher than those gathered in the lab, for a set of 300 potential stimuli. The in-person ratings correlated significantly better with an existing database of familiarity values. It is also shown that under three different grouping methods, online and in-person familiarity ratings produce different sets of stimuli. Finally, it is demonstrated that in each case, different conclusions are reached about variables that have a significant relationship with familiarity. Simulations show that the effects are driven disproportionately by higher intra-item variability in the online ratings. Studies in which stimuli are grouped on the basis of ratings can be affected by the choice of rating methodology.
Mirror quintics, discrete symmetries and Shioda maps
Authors: Bini Gilberto , van Geemen Bert , Kelly Tyler
Published: August 2011

In a recent paper, Doran, Greene and Judes considered one parameter families of quintic threefolds with finite symmetry groups. A surprising result was that each of these six families has the same Picard–Fuchs equation associated to the holomorphic

3
3

-form. In this paper we give an easy argument, involving the family of Mirror Quintics, which implies this result. Using a construction due to Shioda, we also relate certain quotients of these one-parameter families to the family of Mirror Quintics. Our constructions generalize to degree

n
n

Calabi–Yau varieties in

(
n
−
1
)

(n-1)

-dimensional projective space.
Hasse-Arf filtrations in 𝑝-adic analytic geometry
Authors: Ramero Lorenzo
Published: August 2011

We develop a theory of local Fourier transforms for abelian sheaves on the étale site of a

p
p

-adic punctured disc, and we prove a principle of stationary phase linking these local Fourier transforms to the global Fourier transform that was introduced in one of our earlier works. We use this theory to study the local monodromy of abelian sheaves on the étale site of a

p
p

-adic punctured disc, and in particular we exhibit a natural slope decomposition for (germs of) such sheaves, with properties that are wholly analogous to those of the slope decomposition for representation of the Galois group of a local field. We conclude with an application to the study of the so-called cohomological epsilon factor of a locally constant abelian sheaf on the étale site of an affine curve defined over a

p
p

-adic field: namely, we exhibit a decomposition of such factor as a tensor product of “local epsilon factors” that depend only on the local monodromies of the abelian sheaf.
NeuroPedia: neuropeptide database and spectral library
Authors: Kim Yoona , Bark Steven , Hook Vivian , Bandeira Nuno
Published: August 2011

Summary: Neuropeptides are essential for cell–cell communication in neurological and endocrine physiological processes in health and disease. While many neuropeptides have been identified in previous studies, the resulting data has not been structured to facilitate further analysis by tandem mass spectrometry (MS/MS), the main technology for high-throughput neuropeptide identification. Many neuropeptides are difficult to identify when searching MS/MS spectra against large protein databases because of their atypical lengths (e.g. shorter/longer than common tryptic peptides) and lack of tryptic residues to facilitate peptide ionization/fragmentation. NeuroPedia is a neuropeptide encyclopedia of peptide sequences (including genomic and taxonomic information) and spectral libraries of identified MS/MS spectra of homolog neuropeptides from multiple species. Searching neuropeptide MS/MS data against known NeuroPedia sequences will improve the sensitivity of database search tools. Moreover, the availability of neuropeptide spectral libraries will also enable the utilization of spectral library search tools, which are known to further improve the sensitivity of peptide identification. These will also reinforce the confidence in peptide identifications by enabling visual comparisons between new and previously identified neuropeptide MS/MS spectra.

Availability:  http://proteomics.ucsd.edu/Software/NeuroPedia.html

Contact:  bandeira@ucsd.edu

Supplementary information:  Supplementary materials are available at Bioinformatics online.
Pelosinus defluvii sp. nov., isolated from chlorinated solvent-contaminated groundwater, emended description of the genus Pelosinus and transfer of Sporotalea propionica to Pelosinus propionicus comb. nov.
Authors: Moe William M. , Stebbing Rachael E. , Rao Jyoti U. , Bowman Kimberly S. , Nobre M. Fernanda , da Costa Milton S. , Rainey Fred A.
Published: August 2011

Two anaerobic bacterial strains, designated SHI-1Tand SHI-2, were isolated from chlorinated solvent-contaminated groundwater. They were found to be identical in phenotypic properties and shared high (98.5–99.8 %) pairwise 16S rRNA gene sequence similarity. Multiple 16S rRNA genes were found to be present in the isolates as well asPelosinus fermentansDSM 17108TandSporotalea propionicaDSM 13327T. Strains SHI-1Tand SHI-2 could be differentiated from their closest phylogenetic relatives,P. fermentansDSM 17108TandS. propionicaDSM 13327T, on the basis of their phenotypic and phylogenetic properties. The isolates were Gram-negative, spore-forming, motile rods with peritrichous flagella. Growth occurred at 10–42 °C and pH 5.5–8.5. Fermentative growth was observed on Casamino acids, fructose, fumarate, glucose, glycerol, pyruvate and yeast extract. The major organic acids produced from glucose and glycerol fermentation were propionate and acetate. The major organic acids produced from fermentation of fumarate were propionate, acetate and succinate. The major cellular fatty acids were summed feature 4 (consisting of C15 : 1ω8cand/or C15 : 2), summed feature 8 (consisting of C17 : 1ω8cand/or C17 : 2) and C14 : 0dimethyl aldehyde. The polar lipids comprised aminophospholipids, including phosphatidylethanolamine and phosphatidylserine, and an unknown phospholipid. The genomic DNA G+C content was 39.2 mol%. We propose that strains SHI-1Tand SHI-2 are assigned to a novel species of the genusPelosinus, with the namePelosinusdefluviisp. nov. (type strain SHI-1T = NRRL Y-59407T = LMG 25549T). The description of the genusPelosinusis emended. We also propose the transfer ofS. propionicato the genusPelosinusasPelosinuspropionicuscomb. nov. (type strain TmPN3T = DSM 13327T = ATCC BAA-626T), on the basis of phylogenetic, chemotaxonomic and phenotypic properties.
miR-17∼92 cooperates with RB pathway mutations to promote retinoblastoma
Authors: Conkrite Karina , Sundby Maggie , Mukai Shizuo , Thomson J. Michael , Mu David , Hammond Scott M. , MacPherson David
Published: August 2011

The miR-17∼92 cluster is a potent microRNA-encoding oncogene. Here, we show that miR-17∼92 synergizes with loss of Rb family members to promote retinoblastoma. We observed miR-17∼92 genomic amplifications in murine retinoblastoma and high expression of miR-17∼92 in human retinoblastoma. While miR-17∼92 was dispensable for mouse retinal development, miR-17∼92 overexpression, together with deletion of Rb and p107, led to rapid emergence of retinoblastoma with frequent metastasis to the brain. miR-17∼92 oncogenic function in retinoblastoma was not mediated by a miR-19/PTEN axis toward apoptosis suppression, as found in lymphoma/leukemia models. Instead, miR-17∼92 increased the proliferative capacity of Rb/p107-deficient retinal cells. We found that deletion of Rb family members led to compensatory up-regulation of the cyclin-dependent kinase inhibitor p21Cip1. miR-17∼92 overexpression counteracted p21Cip1 up-regulation, promoted proliferation, and drove retinoblastoma formation. These results demonstrate that the oncogenic determinants of miR-17∼92 are context-specific and provide new insights into miR-17∼92 function as an RB-collaborating gene in cancer.
Medicago truncatula CYP716A12 Is a Multifunctional Oxidase Involved in the Biosynthesis of Hemolytic Saponins
Authors: Carelli Maria , Biazzi Elisa , Panara Francesco , Tava Aldo , Scaramelli Laura , Porceddu Andrea , Graham Neil , Odoardi Miriam , Piano Efisio , Arcioni Sergio , May Sean , Scotti Carla , Calderini Ornella
Published: August 2011

Saponins, a group of glycosidic compounds present in several plant species, have aglycone moieties that are formed using triterpenoid or steroidal skeletons. In spite of their importance as antimicrobial compounds and their possible benefits for human health, knowledge of the genetic control of saponin biosynthesis is still poorly understood. In the Medicago genus, the hemolytic activity of saponins is related to the nature of their aglycone moieties. We have identified a cytochrome P450 gene (CYP716A12) involved in saponin synthesis in Medicago truncatula using a combined genetic and biochemical approach. Genetic loss-of-function analysis and complementation studies showed that CYP716A12 is responsible for an early step in the saponin biosynthetic pathway. Mutants in CYP716A12 were unable to produce hemolytic saponins and only synthetized soyasaponins, and were thus named lacking hemolytic activity (lha). In vitro enzymatic activity assays indicate that CYP716A12 catalyzes the oxidation of β-amyrin and erythrodiol at the C-28 position, yielding oleanolic acid. Transcriptome changes in the lha mutant showed a modulation in the main steps of triterpenic saponin biosynthetic pathway: squalene cyclization, β-amyrin oxidation, and glycosylation. The analysis of CYP716A12 expression in planta is reported together with the sapogenin content in different tissues and stages. This article provides evidence for CYP716A12 being a key gene in hemolytic saponin biosynthesis.
Efficiency in agricultural commodity futures markets in India
Authors: Ali Jabir , Bardhan Gupta Kriti
Published: August 2011

Purpose

In line with the ongoing global and domestic reforms in agriculture and allied sectors, the Indian Government is reducing its direct market intervention and encouraging private participation based on market forces. This has led to increased exposure of agricultural produce to price and other market risks, which consequently emphasize the importance of futures markets for price discovery and price risk management. The purpose of this paper is to analyze the efficiency of agricultural commodity markets by assessing the relationships between futures prices and spot market prices of major agricultural commodities in India.

Design/methodology/approach

The efficiency of the futures market for 12 agricultural commodities, traded at one of the largest commodity exchanges of India, i.e. National Commodity & Derivatives Exchange Ltd, has been explored by using Johansen's cointegration analysis and Granger causality tests. Unit root test procedures such as Augmented Dickey‐Fuller and non‐parametric Phillips‐Perron were initially applied to examine whether futures and spot prices are stationary or not. The hypothesis, that futures prices are unbiased predictors of spot prices has been tested using econometric software package.

Findings

Results show that cointegration exists significantly in futures and spot prices for all the selected agricultural commodities except for wheat and rice. This suggest that there is a long‐term relationship between futures and spot prices for most of the agricultural commodities like maize, chickpea, black lentil, pepper, castor seed, soybean and sugar. The causality test further distinguishes and categorizes the commodities based on direction of relationship between futures and spot prices. The analysis of short‐term relationship by causality test indicates that futures markets have stronger ability to predict subsequent spot prices for chickpea, castor seed, soybean and sugar as compared to maize, black lentil and pepper, where bi‐directional relationships exist in the short run.

Practical implications

The results of this study are useful for various stakeholders active in agricultural commodities markets such as producers, traders, commission agents, commodity exchange participants, regulators and policy makers.

Originality/value

There are very few studies that have explored the efficiency of the commodity futures market in India in a detailed manner, especially at individual commodity level.
Regulation and the financial performance of Canadian agribusinesses
Authors: Schaufele Brandon , Sparling David
Published: August 2011

Purpose

The purpose of this paper is to investigate the relationships between regulatory changes, returns on equity and stock market valuations for Canadian food and non‐food agribusinesses.

Design/methodology/approach

Two empirical approaches are employed. First, an event study is used to evaluate the impact of official regulatory announcements on the stock market valuations of selected Canadian agribusinesses. Next, an approach introduced by Mishra et al. using the Du Pont expansion is applied to investigate the effect of regulations on firms' accounting profits. Data on Canadian food and non‐food agribusinesses are collected from Bloomberg, Thompson One Banker and SEDAR.

Findings

The event study demonstrates that official regulatory announcement dates do not correspond with abnormal stock market returns for Canadian firms, while the Du Pont model yields mixed evidence with respect to their accounting profits.

Research limitations/implications

This paper only considers publicly traded companies. As a result, survivorship bias may exist. Future research should include privately held and cooperative firms.

Social implications

Food regulations can influence firm profits and shareholder wealth, so understanding how government actions influence agribusiness is important when considering the total costs of current and future food policy.

Originality/value

The interaction between policy and the financial performance of Canada's publicly traded agribusinesses is an under‐researched area and no studies have examined Canadian data. The results of this study are valuable to both policy makers and researchers.
Farmer demand for financial record‐keeping system attributes
Authors: Wolf Christopher A. , Lupi Frank , Harsh Stephen
Published: August 2011

Purpose

The purpose of this paper is to determine which financial record‐keeping system farmers use, as well as what system attributes farmers value and to what degree.

Design/methodology/approach

This research uses a choice experiment to examine farmer's demand for attributes of financial record‐keeping systems. A sample from the general Michigan farm population is compared to samples from university and agribusiness record system clients.

Findings

Results reveal that university and agribusiness clients are willing to pay considerably more for a farm‐specific record system to backstop their farm management decisions.

Practical implications

The results provide an understanding of farmer demands for farm financial record systems and can be used to position record‐keeping systems to meet those demands.

Originality/value

This paper describes and analyzes farm financial accounting system use and preferences by type.
Which mode is better for knowledge creation?
Authors: Kao Shu‐Chen , Wu ChienHsing , Su Ping‐Chieh
Published: August 2011

Purpose

The purpose of this paper is to examine the impact of knowledge creation mode (e.g. goal‐driven and goal‐free) and organizational culture on knowledge creation performance in the context of high‐tech manufacturing companies having received at least 20 patents.

Design/methodology/approach

This paper uses an empirical study to examine the research model.

Findings

Both goal‐free and goal‐framed creation modes are more likely to support knowledge creation, while the goal‐driven mode is not likely to be favorable for knowledge creation. Manufacturing companies who are frequently looking for new ideas for product design and manufacturing technologies are more likely to adopt the goal‐free creation mode. Adhocracy culture is more likely to be a predicator of product and manufacturing creation.

Practical implications

This work provides policy implications for government and high‐tech industry associations. A company whose cohesion comes mainly from the task achievements is likely to emphasize manufacturing creation. Companies who would like to emphasize goal achievement with respect to creation in manufacturing should form an organizational culture with a characteristic of market competition. Also, a company with both goal‐free and/or goal‐framed creation modes is more likely to be willing to frame its strategic decisions (or goals) and then freely look for creative ways to reach the goals.

Originality/value

Manufacturing creation‐based companies are becoming increasingly knowledge‐sensitive as the competition becomes more intense, and thus may try multiple modes of knowledge creation to strengthen their creation capability in some areas. The research findings are quite remarkable because the impacts of culture and creation mode on creation performance are statistically examined.
Intellectual capital disclosure payback
Authors: Curado Carla , Henriques Lopes , Bontis Nick
Published: August 2011

Purpose

The purpose of this paper is to propose an integrated framework for intellectual capital disclosure.

Design/methodology/approach

The measure, manage and report intellectual capital (MMRIC) methodology is a six‐step process that will enable firms to more accurately describe their intangible assets.

Findings

The proposed step‐by‐step process also complements the exploration‐exploitation tension that is highlighted in the knowledge management literature.

Research limitations/implications

This paper provides academic researchers with a comprehensive framework that can be utilized for future empirical studies related to intellectual capital disclosure.

Practical implications

The MMRIC process is a very useful tool for practitioners in that it provides a sequential system that can be followed for intellectual capital disclosure.

Social implications

Society at large benefits when corporate entities help to reduce risk and volatile market fluctuations by reducing information asymmetry with more comprehensive reporting.

Originality/value

This paper provides an initial theoretical framework that has been developed by integrating the extant literature on intellectual capital disclosure.
Variations in evaluative repertoires
Authors: Pernkopf‐Konhäusner Katharina , Brandl Julia
Published: August 2011

Purpose

While it is acknowledged that societal context matters for employee expectations on training and development, the complexity of this relationship is still little explored. This paper aims to study which higher‐order principles employees of a German and Russian company use to justify their views on beneficial training and development in order to identify how evaluative repertoires differ between the two settings.

Design/methodology/approach

Building on interviews conducted in two professional services firms in Germany and Russia, the paper identifies patterns in the repertoire that employees use for evaluating training and development activities at each research site.

Findings

The findings reveal that employees working for the German company predominantly use the industrial principle for justifying their views on training and development. In contrast, employees in the Russian company apply market, industrial and domestic principles with a tendency for long‐term employees more often to justify their views using the market principle.

Research limitations/implications

The case comparison points to variations in the evaluative repertoire that the paper explains with the societal context of Germany and Russia. By examining evaluative repertoires, companies learn what employees expect from training and development.

Originality/value

Applying convention theory, the paper introduces a promising, but so far neglected approach for linking employee expectations with societal context and for comparing boundaries between people across different settings.