bluuebunny/crossref_metadata_2025 huggingface dataset:
Biblical Gothic and the configurationality parameter
Authors: Berard Stephen A.
Published: December 2008

This article proposes a configurationality parameter based solely on the issue of criteriality for fulfillment of the fundamental function of syntax, which is the establishment of linkage between lexemes and their grammatical relations. The two alternative linking systems discussed here are structural and morphological (S-systems and M-systems). S-systems are found in all language, whereas M-systems are found only in certain languages, and there only in isolated pockets which co-occur with specificity gaps in the respective S-system. In the past, observations about the authenticity and idiomaticness of the language of the Gothic Bible have been based on the examination of very limited phenomena as well as on subjective impressions. A general methodology is suggested here for thorough comparison of the Gothic with the Greek original. Application of this methodology to four sample chapters reveals significant and consistent variation in certain areas, although very little variation is found in the area of word order. The latter fact, along with some other considerations, suggests that Gothic had an M-system somewhat comparable to that of Koine Greek.
The Old EnglishGenesis Bpoet: Bilingual or interlingual?
Authors: Rauch Irmengard
Published: December 2008

Although the celebrated 1875 conjecture of Sievers hypothesizing an Old SaxonGenesissource for the translation of the Old EnglishGenesisB (or Later Genesis) was confirmed by the 1894 find of Zangemeister, the question of the native language of the translator of the Old SaxonGenesisremains. TheGenesis Bevidence is reconsidered here from the viewpoint of contemporary empirical data to ascertain whether the translator was bilingual or interlingual, the former putatively associated with a native (Old Englishman in this case), the second with a second language learner (of Old English). The Old English data contrasted with the character of Old Saxon and configurated with extrapolations from differing cognitive strategies argue for an Anglo-Saxon provenance of theGenesis Bpoet.
Umlautless Residues in Germanic
Authors: Howell Robert B. , Salmons Joseph C.
Published: December 2008

Evidence suggests that Germanic languages resisted the spread of historical umlaut processes. We propose that examples of such superficially varied umlautless residues all yield to a single coherent phonological account. Specifically, these vocalic assimilations show strong preferences for reducing more extreme differences in place of articulation between trigger and target while failing to assimilate articulatorily closer vowels, so that triggering /i, j/ first and most consistently mutated /a/ and last and least consistently mutated /u(:)/. This vocalic cline interacts with the consonantal material intervening between trigger and target, so that obstruent clusters (especially velar or labial) are prone to inhibit umlaut. In both cases, the smaller the phonetic difference between target and trigger, the less likely umlaut is to occur. While umlaut failure has long been consigned to the margins of theories of umlaut, we argue that it is crucial, providing a snapshot of how umlaut unfolded across western and north Germanic.
The Future offor to
Authors: van Gelderen Elly
Published: December 2008

I examine the development offor to and forin several stages of English. I argue that as prepositions grammaticalize, they acquire certain intrinsic features and occupy special positions. In Old English,for tois a P, related to Case, and has some future sense (through an extension of the locative meaning). Verbs do not subcategorize for complements withfor(yet), however. In early Middle English,for tois used to introduce a complement with future meaning. Now,for (to)occupies C, which I assume is universally true for purpose/future indicators. In late Middle English, the situation solidifies, and more verbs select a complement withfor (to)indicating purpose and futurity. In Early Modern English,for todisappears, butforseparated fromtotakes over its function of introducing purposive adjuncts and future complements.
Studies in Runic Origins 1: Germanic *maþl-/*mahl- and Etruscanmeθlum
Authors: Markey Tom
Published: December 2008

Germanic *maþl- ‘council, court of law, tribunal, popular assembly, (public) speech, verbal (interpersonal) agreement’ is clearly a central piece of institutional vocabulary, but its etymology and, hence, its further cultural associations have long remained cryptic. It is argued that there is but one formally comparable and semantically contiguous form as a conceivable source for a Gmc. *maþl-, and that is Etruscanmeθlum.
Etymology of dialectal Swedishnårotandnargas reflected by Balto-Finnic loanwords: Finnishnaarmu‘scratch, scar’, Estoniannäru‘rag, tatter, frazzle’
Authors: Nilsson Torbjörn K.
Published: December 2008

The Swedish dialectal wordsnårot‘worn-out’ andnarg‘a piece of wornout cloth’ have not been etymologically treated so far. I here connect them with a family of Balto-Finnic words, likewise still lacking an etymology: Finn.naarmu˜narvas(<*narwa−), Est.näru(<*narwo-) andnarvas ˜ narmas, etc. In these Balto-Finnic words, the -v- has in most attested forms undergone a sound substitution to -m-, known to have taken place in some Germanic loan words in Balto-Finnic. I propose that the above dialectal Swedish words can be explained as oldwō/wa–stems, related to West Germanic words like Ger.Narbe, OEnearwian‘to constrain’, etc. Thus, it appears that Finn,narvas-, naarmu, Est.näru, etc. are Proto-Germanic loan words in Balto-Finnic, and that the words later died out in the Germanic languages, only to be retrievable through dialectal Norwegian and North Swedish data and reconstructable through comparison with the Balto-Finnic loan words.
Internal distribution of Li and B in serpentinites from the Feather River Ophiolite, California, based on laser ablation inductively coupled plasma mass spectrometry
Authors: Lee Cin‐Ty Aeolus , Oka Masaru , Luffi Peter , Agranier Arnaud
Published: December 2008

Laser ablation inductively coupled plasma mass spectrometry (LA‐ICP‐MS) analyses of B and Li in serpentinized peridotites from the Feather River Ophiolite (California) indicates that B is enriched in serpentine minerals compared to the whole‐rock and less altered olivine grains, while Li in serpentine is depleted or comparable to whole‐rock Li. The high B contents of serpentine minerals correlate with the relatively enriched whole‐rock B contents. The low Li contents of serpentine minerals are consistent with the relatively low Li whole‐rock contents and suggest that only small amounts of Li were added during serpentinization or that some Li was even leached out. A simple model of partial melting shows that Li/Yb increases with increasing melt depletion (and clinopyroxene depletion) in the peridotitic residue because Li is most compatible in olivine while Yb is most compatible in clinopyroxene. Thus, high Li/Yb ratios in peridotites by themselves do not indicate secondary enrichments in Li. However, Li/Yb and Yb contents of many of the Feather River Ophiolites plot above the melt depletion curve in Li/Yb versus Yb space, indicating that these serpentinites experienced subtle and preferential enrichments in Li during serpentinization. If serpentinized oceanic lithospheric mantle, as represented by the Feather River Ophiolite, is important in subduction recycling, then recycled mantle domains having a serpentinite protolith might be characterized by strong B enrichments but only small Li enrichments.
Extracting a climate signal from the skeletal geochemistry of the Caribbean coral Siderastrea siderea
Authors: Maupin Christopher R. , Quinn Terrence M. , Halley Robert B.
Published: December 2008

The first bimonthly time series of paired δ18O and Sr/Ca from the slow‐growing coral Siderastrea siderea, from the Dry Tortugas, Florida, has been generated that documents that robust proxy climate records of the tropical Atlantic and IntraAmerican Seas can be produced from this massive coral. The time series contain a 20‐year‐long calibration window (1973–1992) for both δ18O and Sr/Ca and a 73‐year‐long verification window (1900–1972) for Sr/Ca. These time series permit the quantification of the relationship between coral δ18O‐SST and Sr/Ca‐SST and the assessment of the stability of the proxy relationships over time. Both coral geochemical records are highly correlated with the augmented instrumental SST record through the calibration period, and Sr/Ca remains highly correlated through the verification period both at the bimonthly (r = −0.97) and annual average resolution (r = −0.72). Coral δ18O and Sr/Ca are highly reproducible within the same core, and Sr/Ca exhibits no extension‐related vital effects. This study sets the stage for generating multicentury scale climate records from the tropical Atlantic Ocean using the skeletal geochemistry of this massive, but slow growing coral.
Magma genesis by rifting of oceanic lithosphere above anomalous mantle: Terceira Rift, Azores
Authors: Beier Christoph , Haase Karsten M. , Abouchami Wafa , Krienitz Marc‐S. , Hauff Folkmar
Published: December 2008

The Terceira Rift formed relatively recently (∼1 Ma ago) by rifting of the old oceanic lithosphere of the Azores Plateau and is currently spreading at a rate of 2–4mm/a. Together with the Mid‐Atlantic Ridge, the Terceira Rift forms a triple junction that separates the Eurasian, African, and American Plates. Four volcanic systems (São Miguel, João de Castro, Terceira, Graciosa), three of which are islands, are distinguished along the axis and are separated by deep avolcanic basins similar to other ultraslow spreading centers. The major element, trace element and Sr‐Nd‐Pb isotope geochemistry of submarine and subaerial lavas display large along‐axis variations. Major and trace element modeling suggests melting in the garnet stability field at smaller degrees of partial melting at the easternmost volcanic system (São Miguel) compared to the central and western volcanoes, which appear to be characterized by slightly higher melting degrees in the spinel/garnet transition zone. The degrees of partial melting at the Terceira Rift are slightly lower than at other ultraslow mid‐ocean ridge spreading axes (Southwest Indian Ridge, Gakkel Ridge) and occur at greater depths as a result of the melting anomaly beneath the Azores. The combined interaction of a high obliquity, very slow spreading rates, and a thick preexisting lithosphere along the axis probably prevents the formation and eruption of larger amounts of melt along the Terceira Rift. However, the presence of ocean islands requires a relatively stable melting anomaly over relatively long periods of time. The trace element and Sr‐Nd‐Pb isotopes display individual binary mixing arrays for each volcanic system and thus provide additional evidence for focused magmatism with no (or very limited) melt or source interaction between the volcanic systems. The westernmost mantle sources beneath Graciosa and the most radiogenic lavas from the neighboring Mid‐Atlantic Ridge suggest a mantle flow from Graciosa toward the Mid‐Atlantic Ridge and hence a flux of mantle material from one spreading axis into the other. The Terceira Rift represents a unique oceanic rift system situated within the thickened, relatively old oceanic lithosphere and thus exhibits both oceanic and continental features.
Impact of clouds on atmospheric heating based on the R04 CloudSat fluxes and heating rates data set
Authors: L'Ecuyer Tristan S. , Wood Norman B. , Haladay Taryn , Stephens Graeme L. , Stackhouse Paul W.
Published: December 2008

Among the largest uncertainties in quantifying the radiative impacts of clouds are those that arise from the inherent difficulty in precisely specifying the vertical distribution of cloud optical properties using passive satellite measurements. Motivated by the need to address this problem, CloudSat was launched in April 2006 carrying into orbit the first millimeter wavelength cloud radar to be flown in space. Retrieved profiles of liquid and ice cloud microphysical properties from this Cloud Profiling Radar form the basis of the CloudSat's fluxes and heating rates algorithm, 2B‐FLXHR, a standard product that provides high vertical resolution profiles of radiative fluxes and atmospheric heating rates on the global scale. This paper describes the physical basis of the 2B‐FLXHR algorithm and documents the first year of 2B‐FLXHR data in the context of assessing the radiative impact of clouds on global and regional scales. The analysis confirms that cloud contributions to atmospheric radiative heating are small on the global scale because of a cancelation of the much larger regional heating from high clouds in the tropics and cooling from low clouds at higher latitudes. Preliminary efforts to assess the accuracy of the 2B‐FLXHR product using coincident CERES data demonstrate that outgoing longwave fluxes are better represented than those in the shortwave but both exhibit good agreement with CERES on scales longer than 5 days and larger than 5°. Colocated CALIPSO observations of clouds that are undetected by CloudSat further indicate that while thin cirrus can introduce modest uncertainty in the products, low clouds that are obscured by ground clutter represent a far more important source of error in the current 2B‐FLXHR product that must be addressed in subsequent versions of the algorithm.
Analysis of the Summer 2004 ozone budget over the United States using Intercontinental Transport Experiment Ozonesonde Network Study (IONS) observations and Model of Ozone and Related Tracers (MOZART‐4) simulations
Authors: Pfister G. G. , Emmons L. K. , Hess P. G. , Lamarque J.‐F. , Thompson A. M. , Yorks J. E.
Published: December 2008

The origin of ozone over the summertime contiguous United States during summer 2004 was examined using the Intercontinental Transport Experiment (INTEX‐A) Ozonesonde Network Study (IONS‐04) over North America. We estimate the budget using the global chemistry transport Model of Ozone and Related Tracers version 4 (MOZART‐4) with synthetic tracers that keep track of the ozone produced from selected NOx sources (stratosphere, lightning, anthropogenic, and biomass burning sources in Eurasia and the contiguous United States, and North American boreal fires). This “model budget” is analyzed in conjunction with results from a “laminar identification method” (LID), a more empirical approach to extracting information about contributions from ozone transported down from the stratosphere, advection, and convection. Both methods give comparable results for the contribution from stratospheric ozone, an average over all sites of 20 ± 7% for the LID budget and of 26 ± 6% for the model budget (the standard deviation gives the variability over the IONS sites). These results point toward the important contribution of downward transport of ozone from the stratosphere in assessing tropospheric ozone. The contributions for the other tracers are 25 ± 9% for U.S. sources, 13 ± 5% for Eurasian sources, 3 ± 2% for boreal fires and 10 ± 2% from lightning. In the boundary layer the dominant contribution generally comes from local (U.S.) sources. Eurasian sources can add up to 8% on average for some sites, lightning up to 4%, and North American boreal fires up to 10%. Variations in the tracer contributions across the different sites can be large, but the budget estimated by the model for the entire United States is similar to the budget averaged over the IONS‐04 sites which lets us conclude that the sample of locations and launch days conveys a proper representation of the large‐scale picture.
Competition among thiols and inorganic sulfides and polysulfides for Hg and MeHg in wetland soils and sediments under suboxic conditions: Illumination of controversies and implications for MeHg net production
Authors: Skyllberg Ulf
Published: December 2008

Current research focus in mercury biogeochemistry is on the net production and accumulation of methyl mercury (MeHg) in organisms. The activity of iron‐ and sulfate‐reducing bacteria (FeRB and SRB) has been identified as important for MeHg production. There are indications of a passive uptake of neutral Hg‐sulfides by SRB, as well as of a facilitated bacterial uptake of Hg complexed by small organic molecules. In order to understand these processes, the chemical speciation of Hg and MeHg, and most important, the competition among organic thiols and inorganic sulfides and polysulfides, needs to be clarified under suboxic conditions (nM to low μM range of total sulfide concentrations) in wetland soils and sediments. In this paper the chemical speciation of Hg and MeHg is modeled at pH 4.0 and 7.0 in a conceptual wetland soil/sediment with typical concentrations of thiols, sulfides, Hg, and MeHg. Effects of precipitated HgS(s), the formation of Hg‐polysulfides, and the size of the controversial stability constant for the formation of HOHgSH0 (aq) are emphasized. The outcome of the modeling is discussed in light of chosen stability constants for Hg complexes with thiols, sulfides, and polysulfides. It is concluded that organic thiols are competitive with inorganic sulfides in the approximate total sulfide concentration range 0–1 μm. It is also concluded that increases in absolute aqueous concentrations of MeHg, or the molar ratio of dissolved MeHg/Hg, are not appropriate as indirect measures of MeHg net production, unless changes and differences in solubility of MeHg and Hg are corrected for.
Vestibular effects on cerebral blood flow
Authors: Serrador Jorge , Black F. Owen , Schlegel Todd , Wood Scott
Published: December 2008

Withdrawn.
Molecular cloning, expression profiling and functional analyses of a cDNA encoding isopentenyl diphosphate isomerase from Gossypium barbadense
Authors: Wang Yechun , Qiu Chengxiang , Zhang Fei , Guo Binhui , Miao Zhiqi , Sun Xiaofen , Tang Kexuan
Published: December 2008

Gossypol, a type of plant defence sesquiterpenoid phytoalexin, is synthesized from the MEP (2C-methyl-D-erythritol 4-phosphate) and MVA (mevalonate) pathway in the isoprenoid biosynthetic system. The key step is the isomerization of IPP (isopentenyl diphosphate) to DMAPP (dimethylallyl diphosphate), which is catalysed by IPI (IPP isomerase; EC 5.3.3.2). A full-length cDNA encoding IPI (designated GbIPI) was cloned from Gossypium barbadense by RACE (rapid amplification of cDNA ends). The full-length cDNA of GbIPI was 1205 bp and contained a 906 bp ORF (open reading frame) encoding a protein of 302 amino acids, with a predicted molecular mass of 34.39 kDa and an isoelectric point of 6.07. Amino acid sequence analysis revealed that the GbIPI has a high level of similarity to other IPIs. Southern-blot analysis revealed that GbIPI belongs to a small gene family. Expression analysis indicated that GbIPI expression is highest in stems, followed by leaves, and is lowest in roots, and that the expression of GbIPI could be induced by Verticillium dahliae Kleb, MeJA (methyl jasmonate) and SA (salicylic acid). The functional colour assay indicated that GbIPI could accelerate the accumulation of β-carotene in Escherichia coli transformants. The cloning and functional analysis of GbIPI will be useful in increasing understanding of the role of IPI in isoprenoid biosynthesis at the molecular level.
Neuroscience of Swallowing: Strategies in Rehabilitation
Authors: Miller Arthur J.
Published: December 2008

The development of strategies to rehabilitate patients with dysphagia depends on an understanding of both the underlying neuroscientific principles that control normal swallowing and how a damaged central nervous system can respond. Strategies can incorporate the sensory and motor systems, as well as use the plasticity of the cortex and neuromuscular system. Treating dysphagia could involve stimulating the sensory system more often through the two primary nerves involved with swallowing, the glossopharyngeal and superior laryngeal nerves, as well as by enhancing the trigeminal sensory input. Enhancement of the motor system can occur by using muscles in special exercises or by electrically stimulating the target muscles directly. The cortex can be modified by increased sensory input, which will adapt the sensorimotor cortex. In addition, techniques of directly stimulating the cortex hold promise for rehabilitation.
Effective potentials and electrostatic interactions in self-assembled molecular bilayers II: The case of biological membranes
Authors: Gamba Z.
Published: December 2008

In order to study the electrostatic properties of a single biological membrane (not an stack of bilayers), we propose a very simple and effective external potential that simulates the interaction of the bilayer with the surrounding water and that takes into account the microscopic pair distribution functions of water. The electrostatic interactions are calculated using Ewald sums but, for the macroscopic electrostatic field, we use an approximation recently tested in simulations of Newton black films that essentially consists in a coarsed fit (perpendicular to the bilayer plane) of the molecular charge distributions with Gaussian distributions. The method of effective macroscopic and external potentials is extremely simple to implement in numerical simulations, and the spatial and temporal charge inhomogeneities are then roughly taken into account. As examples of their use, several molecular dynamics simulations of simple models of a single biological membrane, of neutral or charged polar amphiphilics, with or without water (using the TIP5P intermolecular potential for water) are included. The numerical simulations are performed using a simplified amphiphilic model which allows the inclusion of a large number of molecules in these simulations, but nevertheless taking into account molecular charge distributions, flexible amphiphilic molecules, and a reliable model of water. All these parameters are essential in a nanoscopic scale study of intermolecular and long range electrostatic interactions. This amphiphilic model was previously used by us to simulate a Newton black film, and, in this paper, we extend our investigation to bilayers of the biological membrane type.
Electronic-structure and quantum dynamical study of the photochromism of the aromatic Schiff base salicylideneaniline
Authors: Ortiz-Sánchez Juan Manuel , Gelabert Ricard , Moreno Miquel , Lluch José M.
Published: December 2008

The ultrafast proton transfer dynamics of salicylideneaniline has been theoretically analyzed in the ground and first singlet excited electronic states using density functional theory (DFT) and time-dependent DFT calculations, which predict a (π,π∗) barrierless excited state intramolecular proton transfer (ESIPT). In addition to this, the photochemistry of salicylideneaniline is experimentally known to present fast depopulation processes of the photoexcited species before and after the proton transfer reaction. Such processes are explained by means of conical intersections between the ground and first singlet (π,π∗) excited electronic states. The electronic energies obtained by the time-dependent density functional theory formalism have been fitted to a monodimensional potential energy surface in order to perform quantum dynamics study of the processes. Our results show that the proton transfer and deactivation of the photoexcited species before the ESIPT processes are completed within 49.6 and 37.7 fs, respectively, which is in remarkable good agreement with experiments.
The highly resolved electronic spectrum of the square planar CuCl42− ion
Authors: Dick Andrew , Rahemi Hedayat , Krausz Elmars R. , Hanson Graeme R. , Riley Mark J.
Published: December 2008

The low temperature magnetic circular dichroism (MCD) and electron paramagnetic resonance (EPR) spectra of Cu(II) doped Cs2ZrCl6 are reported. The Cu(II) ion is incorporated as the square planar copper tetrachloride ion, CuCl42−, which substitutes at the Zr(IV) site in the Cs2ZrCl6 lattice, with a complete absence of axial coordination. Both the EPR and MCD show highly resolved spectra from which it is possible to determine the superhyperfine coupling constants and excited state geometries respectively. The Franck–Condon intensity patterns suggest that there is a substantial relaxation of the host lattice about the impurity ion. For the lowest energy B21g(x2-y2)→B22g(xy) transition, both the magnetic dipole allowed electronic origin as well as vibronic false origins are observed. The high resolution of the spectra allowed the accurate determination of the odd parity vibrations that are active in the spectra. The opposite sign of the MCD of the two components of the E2g(xz,yz) excited state allows this splitting to be determined for the first time. Accurate and unambiguous spectral parameters for the CuCl42− ion are important as it has become a benchmark transition metal complex for theoretical electronic structure calculations.
Exchange bias effect in a granular system of NiFe2O4 nanoparticles embedded in an antiferromagnetic NiO matrix
Authors: Tian Z. M. , Yuan S. L. , Yin S. Y. , Liu L. , He J. H. , Duan H. N. , Li P. , Wang C. H.
Published: December 2008

A granular system composed of ferrimagnetic NiFe2O4 nanoparticles, about 8 nm in size, embedded in an antiferromagnetic NiO matrix has been synthesized by a high-temperature phase precipitation method from Fe-doped NiO matrix. Both the exchange bias field and vertical magnetization shift can be observed in this system below 250 K after field cooling, above which the exchange bias disappears. Furthermore, the exchange bias field shows a linear dependence on the magnetization shift. This observed exchange bias effect is explained in terms of the exchange interaction between the ferrimagnetic phase and the spin-glass-like phase at the interface.
All-optical routing by light storage in a Pr3+:Y2SiO5 crystal
Authors: Wang Hai-Hua , Li Ai-Jun , Du Dun-Mao , Fan Yun-Fei , Wang Lei , Kang Zhi-Hui , Jiang Yun , Wu Jin-Hui , Gao Jin-Yue
Published: December 2008

We experimentally demonstrate an all-optical routing based on light storage in a Pr3+:Y2SiO5 crystal. Under electromagnetically induced transparency, the optical information of the probe light pulse can be stored in the crystal. By simultaneously switching on two retrieve control fields in the release process, the stored optical information from one light channel can be distributed into two light channels. Such an all-optical routing in solids may have practical applications in quantum information and all-optical network.
High-temperature dielectric properties and enhanced temperature-response attenuation of β-MnO2 nanorods
Authors: Shi Xiao-Ling , Cao Mao-Sheng , Fang Xiao-Yong , Yuan Jie , Kang Yu-Qing , Song Wei-Li
Published: December 2008

Large-scale β-MnO2 nanorods were synthesized by the hydrothermal method. In X band, the microwave attenuation of the β-MnO2 nanorods is evidently enhanced with increasing temperature from 293 to 773 K. The enhanced temperature-response attenuation of β-MnO2 nanorods is mainly attributed to the decrease in the real permittivity and the increase in the imaginary permittivity at high temperature. The decrease in real permittivity would be mainly ascribed to the increase in the disorder degree of orientational alignment of the intrinsic polar moment in the β-MnO2 nanorods with temperature increasing. The increase in imaginary permittivity may result from the lower resistivity with rising temperature.
Effect of dopants on grain boundary decohesion of Ni: A first-principles study
Authors: Sanyal Suchismita , Waghmare Umesh V. , Subramanian P. R. , Gigliotti Michael F. X.
Published: December 2008

First-principles density functional theory (DFT) calculations were used to determine decohesion properties of Σ5(012) grain boundary of Ni with dopants B, C, S, Cr, and Hf. The relative stability of sites was evaluated and cleavage energies were calculated. Electronic structure was used to understand these properties in terms of changes in bonding with addition of dopants. It was found that strengthening of the Ni grain boundary results from Hf, B, and Cr doping. In contrast, the grain boundary weakens with S and C doping. These results should be useful in the design of next-generation nanostructured Ni-based alloys with improved mechanical behavior.
Quantum resistance metrology in graphene
Authors: Giesbers A. J. M. , Rietveld G. , Houtzager E. , Zeitler U. , Yang R. , Novoselov K. S. , Geim A. K. , Maan J. C.
Published: December 2008

We performed a metrological characterization of the quantum Hall resistance in a 1 μm wide graphene Hall bar. The longitudinal resistivity in the center of the ν=±2 quantum Hall plateaus vanishes within the measurement noise of 20 mΩ up to 2 μA. Our results show that the quantization of these plateaus is within the experimental uncertainty (15 ppm for 1.5 μA current) equal to that in conventional semiconductors. The principal limitation of the present experiments is the relatively high contact resistances in the quantum Hall regime, leading to a significantly increased noise across the voltage contacts and a heating of the sample when a high current is applied.
Charging dynamics of discrete gold nanoparticle arrays self-assembled within a poly(styrene-b-4-vinylpyridine) diblock copolymer template
Authors: Leong W. L. , Mathews N. , Mhaisalkar S. G. , Chen T. P. , Lee P. S.
Published: December 2008

The kinetics of charging and discharging of charge carriers in a memory device based on gold nanoparticles in self-assembled block copolymer of poly(styrene-b-4-vinylpyridine) (PS-b-P4VP) has been studied. Hole trapping is observed to be more efficient than electron trapping and is attributed to a lower electron injection current (due to presence of Schottky barrier between the gold electrode and P4VP layer). At higher electric fields (>0.4 MV/cm), quasi-two-dimensional charge transport through the arrays of gold nanoparticles in P4VP nanodomains is observed. The contribution of electrode work function was demonstrated with improved electron charging by the replacement of gold electrode with aluminum.
Driving frequency effects on the characteristics of atmospheric pressure capacitive helium discharge
Authors: Moon Se Youn , Kim D. B. , Gweon B. , Choe W.
Published: December 2008

Atmospheric pressure helium discharge characteristics were investigated for varying driving radio frequencies in the range between 1.86 and 27.1 MHz. As the driving frequency is raised, both gas breakdown and α-γ transition voltages decrease due to the reduction in the electron drift loss. In addition, different discharge features such as normal, abnormal, α, and γ modes show certain dependences on the frequency. Using a simple circuit model, the changes in sheath thickness from 2.35 to 0.11 mm, electron density from 0.26 to 15.6×1011 cm−3 was obtained by raising the frequency from 1.86 to 27.1 MHz.
Sulfiredoxin is an AP-1 target gene that is required for transformation and shows elevated expression in human skin malignancies
Authors: Wei Qiou , Jiang Hong , Matthews Connie P. , Colburn Nancy H.
Published: December 2008

Previous studies have shown that a dominant negative form of c-Jun (TAM67) suppresses mouse skin carcinogenesis both
in vitro
and
in vivo
. The current study identifies Sulfiredoxin (Srx) as a unique target of activator protein-1 (AP-1) activation and TAM67 inhibition. Manipulation of Srx levels by ShRNA or over-expression demonstrates that Srx is critical for redox homeostasis through reducing hyperoxidized peroxiredoxins. In JB6 cells, knockdown of Srx abolishes tumor promoter-induced transformation and enhances cell sensitivity to oxidative stress. Knockdown of Srx also impairs c-Jun phosphorylation, implicating a role for Srx in the feedback regulation of AP-1 activity. Screening of patient tissues by tissue microarray reveals elevated Srx expression in several types of human skin cancers. Our study indicates that Srx is a functionally significant target of AP-1 blockade that may have value in cancer prevention or treatment.
Using fMRI to Test Models of Complex Cognition
Authors: Anderson John R. , Carter Cameron S. , Fincham Jon M. , Qin Yulin , Ravizza Susan M. , Rosenberg‐Lee Miriam
Published: December 2008

This article investigates the potential of fMRI to test assumptions about different components in models of complex cognitive tasks. If the components of a model can be associated with specific brain regions, one can make predictions for the temporal course of the BOLD response in these regions. An event‐locked procedure is described for dealing with temporal variability and bringing model runs and individual data trials into alignment. Statistical methods for testing the model are described that deal with the scan‐to‐scan correlations in the errors of measurement of the BOLD signal. This approach is illustrated using a “sacrificial” ACT‐R model that involves mapping 6 modules onto 6 brain regions in an experiment from concerned with equation solving. The model's visual encoding predicted the BOLD response in the fusiform gyrus, its controlled retrieval predicted the BOLD response in the lateral inferior prefrontal cortex, and its subgoal setting predicted the BOLD response in the anterior cingulate cortex. On the other hand, its motor programming failed to predict anticipatory activation in the motor cortex, its representational changes failed to predicted the pattern of activity in the posterior parietal cortex, and its procedural component failed to predict an initial spike in caudate. The results illustrate the power of such data to direct the development of a theory of complex problem solving, both at the level of a specific task model as well as at the level of the cognitive architecture.
Parameters, Predictions, and Evidence in Computational Modeling: A Statistical View Informed by ACT–R
Authors: Weaver Rhiannon
Published: December 2008

Model validation in computational cognitive psychology often relies on methods drawn from the testing of theories in experimental physics. However, applications of these methods to computational models in typical cognitive experiments can hide multiple, plausible sources of variation arising from human participants and from stochastic cognitive theories, encouraging a “model fixed, data variable” paradigm that makes it difficult to interpret model predictions and to account for individual differences. This article proposes a likelihood‐based, “data fixed, model variable” paradigm in which models are treated as stochastic processes in experiments with participant‐to‐participant variation that can be applied to a broad range of mechanistic cognitive architectures. This article discusses the implementation and implications of this view in model validation, with a concrete focus on a simple class of ACT‐R models of cognition. This article is not intended as a recipe for broad application of these preliminary, proof‐of‐concept methods, but as a framework for communication between statisticians searching for interesting problems in the cognitive modeling sphere, and cognitive modelers interested in generalizing from deterministic to stochastic model validation, in the face of random variation in human experimental data.
Measuring Model Flexibility With Parameter Space Partitioning: An Introduction and Application Example
Authors: Pitt Mark A. , Myung Jay I. , Montenegro Maximiliano , Pooley James
Published: December 2008

A primary criterion on which models of cognition are evaluated is their ability to fit empirical data. To understand the reason why a model yields a good or poor fit, it is necessary to determine the data‐fitting potential (i.e., flexibility) of the model. In the first part of this article, methods for comparing models and studying their flexibility are reviewed, with a focus on parameter space partitioning (PSP), a general‐purpose method for analyzing and comparing all classes of cognitive models. PSP is then demonstrated in the second part of the article in which two connectionist models of speech perception (TRACE and ARTphone) are compared to learn how design differences affect model flexibility.
Hydroacoustic measures of Mysis relicta abundance and distribution in Lake Ontario
Authors: Rudstam Lars G. , Schaner Ted , Gal Gideon , Boscarino Brent T. , O'Gorman Robert , Warner David M. , Johannsson Ora E. , Bowen Kelly L.
Published: December 2008

Mysis relicta can be observed on echograms as a sound scattering layer when they migrate into the water column at night to feed on zooplankton. However, quantitative measures of mysid abundance with hydroacoustics requires knowledge of mysid target strength (TS), a method of removing fish echoes and contribution from noise, and an understanding of the effect of range on the ability of hydroacoustics to detect mysids (the detection limit). Comparisons of paired net data and acoustics data from July 7, 2005 yielded a mysid TS of −86.3 dB (9 mm animal) and a biomass TS of −58.4 dB (g dry wt)−1. With ambient noise levels (Sv of −125 dB at 1 m depth) and this TS, we can detect a mysid density of 1 m−3 at 60 m depth with a signal to noise ratio of 3 dB. We present a method to remove backscattering from both noise and fish and apply this method and the new TS data to whole lake acoustic data from Lake Ontario collected in July 25–31, 2005 with a 120 kHz echosounder as part of the annual standard fish survey in that lake. Mysis abundance was strongly depth dependent, with highest densities in areas with bottom depth > 100 m, and few mysids in areas with bottom depth < 50 m. With the data stratified in five bottom depth strata (> 100 m, 100-75 m, 75–50 m, 50–30 m, < 30 m), the whole-lake average mysid density was 118 m−2 (CV 21%) and the whole-lake average mysid biomass was 0.19 g dry wt m−2 (CV 22%) in July 2005. The CVs of these densities also account for uncertainty in the TS estimates. This is comparable to whole-lake density estimates using vertical net tows in November, 2005 (93 m−2, CV 16%).
Identification of microRNA regulatory modules inArabidopsisvia a probabilistic graphical model
Authors: Joung Je-Gun , Fei Zhangjun
Published: December 2008

Motivation: MicroRNAs miRNAs play important roles in gene regulation and are regarded as key components in gene regulatory pathways. Systematically understanding functional roles of miRNAs is essential to define core transcriptional units regulating key biological processes. Here, we propose a method based on the probabilistic graphical model to identify the regulatory modules of miRNAs and the core regulatory motifs involved in their ability to regulate gene expression.

Results: We applied our method to datasets of different sources from Arabidopsis consisting of miRNA-target pair information, upstream sequences of miRNAs, transcriptional regulatory motifs and gene expression profiles. The graphical model used in this study can efficiently capture the relationship between miRNAs and diverse conditions such as various developmental processes, thus allowing us to detect functionally correlated miRNA regulatory modules involved in specific biological processes. Furthermore, this approach can reveal core transcriptional elements associated with their miRNAs. The proposed method found clusters of miRNAs, as well as putative regulators controlling the expression of miRNAs, which were highly related to diverse developmental processes of Arabidopsis. Consequently, our method can provide hypothetical miRNA regulatory circuits for functional testing that represent transcriptional events of miRNAs and transcriptional factors involved in gene regulatory pathways.

Contact:  zf25@cornell.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment
Authors: Paten Benedict , Herrero Javier , Beal Kathryn , Birney Ewan
Published: December 2008

Motivation: Multiple sequence alignment is a cornerstone of comparative genomics. Much work has been done to improve methods for this task, particularly for the alignment of small sequences, and especially for amino acid sequences. However, less work has been done in making promising methods that work on the small-scale practically for the alignment of much larger genomic sequences.

Results: We take the method of probabilistic consistency alignment and make it practical for the alignment of large genomic sequences. In so doing we develop a set of new technical methods, combined in a framework we term ‘sequence progressive alignment’, because it allows us to iteratively compute an alignment by passing over the input sequences from left to right. The result is that we massively decrease the memory consumption of the program relative to a naive implementation. The general engineering of the challenges faced in scaling such a computationally intensive process offer valuable lessons for planning related large-scale sequence analysis algorithms. We also further show the strong performance of Pecan using an extended analysis of ancient repeat alignments. Pecan is now one of the default alignment programs that has and is being used by a number of whole-genome comparative genomic projects.

Availability: The Pecan program is freely available at http://www.ebi.ac.uk/∼bjp/pecan/ Pecan whole genome alignments can be found in the Ensembl genome browser.

Contact:  benedict@soe.ucsc.edu

supplementary information:  Supplementary data are available at Bioinformatics online.
GmRAR1 and GmSGT1 Are Required for Basal, R Gene–Mediated and Systemic Acquired Resistance in Soybean
Authors: Fu Da-Qi , Ghabrial Said , Kachroo Aardra
Published: December 2008

RAR1, SGT1, and HSP90 are important components of effector-triggered immunity (ETI) in diverse plants, where RAR1 and SGT1 are thought to serve as HSP90 co-chaperones. We show that ETI in soybean requires RAR1 and SGT1 but not HSP90. Rsv1-mediated extreme resistance to Soybean mosaic virus (SMV) and Rpg-1b-mediated resistance to Pseudomonas syringae were compromised in plants silenced for GmRAR1 and GmSGT1-2 but not GmHSP90. This suggests that RAR1- or SGT1-dependant signaling is not always associated with a dependence on HSP90. Unlike in Arabidopsis, SGT1 in soybean also mediates ETI against the bacterial pathogen P. syringae. Similar to Arabidopsis, soybean RAR1 and SGT1 proteins interact with each other and two related HSP90 proteins. Plants silenced for GmHSP90 genes or GmRAR1 exhibited altered morphology, suggesting that these proteins also contribute to developmental processes. Silencing GmRAR1 and GmSGT1-2 impaired resistance to virulent bacteria and systemic acquired resistance (SAR) in soybean as well. Because the Arabidopsis rar1 mutant also showed a defect in SAR, we conclude that RAR1 and SGT1 serve as a point of convergence for basal resistance, ETI, and SAR. We demonstrate that, although soybean defense signaling pathways recruit structurally conserved components, they have distinct requirements for specific proteins.
Identification of the H2‐Kd‐restricted cytotoxic T lymphocyte epitopes of a tumor‐associated antigen, SPARC, which can stimulate antitumor immunity without causing autoimmune disease in mice
Authors: Ikuta Yoshiaki , Hayashida Yuki , Hirata Shinya , Irie Atsushi , Senju Satoru , Kubo Tatsuko , Nakatsura Tetsuya , Monji Mikio , Sasaki Yutaka , Baba Hideo , Nishimura Yasuharu
Published: December 2008

We previously reported that the secreted protein acidic and rich in cystein (SPARC) was overexpressed in melanoma in humans, and the serum SPARC level was useful as a novel tumor marker for melanoma. SPARC was also reported to be overexpressed in various human cancers. In this study, we asked whether SPARC‐specific cytotoxic T lymphocytes (CTL) could induce antitumor immunity to SPARC‐expressing tumor in mice or not as a preclinical study of SPARC‐directed anticancer immunotherapy. Because of similarities in the structural motifs of major histocompatibility complex‐binding peptides between H2‐Kd and HLA‐A24 (A*2402), the most common human leukocyte antigen class I allele in the Japanese population, we attempted to identify the H2‐Kd‐restricted SPARC epitope for CTL in BALB/c mice and we found that the mouse SPARC143–151 (DYIGPCKYI) and SPARC225–234 (MYIFPVHWQF) peptides could induce peptide‐reactive CTL in BALB/c mice without causing autoimmune diseases. The immunization of mice with SPARC225–234 peptide‐pulsed bone marrow‐derived dendritic cells (BMDC) inhibited the growth of s.c. inoculated mouse mammary cancer cell line, N2C, expressing SPARC and these mice lived longer than the mice immunized with peptide‐unpulsed BMDC. In conclusion, our study indicated that SPARC peptide‐based cancer immunotherapy was effective and safe at least in a mouse tumor prevention model. (Cancer Sci 2009; 100: 132–137)
Preventing the unfolded protein response via aberrant activation of 4E‐binding protein 1 by versipelostatin
Authors: Matsuo Junichi , Tsukumo Yoshinori , Sakurai Junko , Tsukahara Satomi , Park Hae‐Ryong , Shin‐ya Kazuo , Watanabe Toshiki , Tsuruo Takashi , Tomida Akihiro
Published: December 2008

We recently isolated a macrocyclic compound, versipelostatin (VST), that exerts in vivo antitumor activity. VST shows unique, selective cytotoxicity to glucose‐deprived tumor cells by preventing the unfolded protein response (UPR). Here we show that eukaryotic initiation factor 4E‐binding protein 1 (4E‐BP1), a negative regulator of eukaryotic initiation factor 4E‐mediated protein translation, plays a role in the UPR‐inhibitory action of VST. Indeed, 4E‐BP1 is aberrantly activated by VST. This activation occurs specifically during glucose deprivation and results in profound translation repression and prevents induction of the typical UPR markers glucose‐regulated protein (GRP) 78 and activating transcription factor (ATF) 4. Our overexpression and knockdown experiments showed that 4E‐BP1 can regulate GRP78 and ATF4 expression. These mechanisms appear to be specific for VST. By contrast, rapamycin, which activates 4E‐BP1 regardless of cellular glucose availability, has only marginal effects on the expression of GRP78 and ATF4. Our present findings demonstrate that aberrant 4E‐BP1 activation can contribute to UPR preventing by VST, possibly through a mechanism that does not operate in rapamycin‐treated cells. (Cancer Sci 2009; 100: 327–333)
Combination of all‐trans retinoic acid and a human papillomavirus therapeutic vaccine suppresses the number and function of immature myeloid cells and enhances antitumor immunity
Authors: Song Xinxin , Ye Dongxia , Liu Bo , Cui Jianfeng , Zhao Xinhua , Yi Linan , Liang Jianming , Song Jietao , Zhang Zhiyuan , Zhao Qingzheng
Published: December 2008

Despite advances in the development of human papillomavirus (HPV) prophylactic vaccines, little progress has been made in the field of therapeutic vaccines in recent years. In the present study, we found a significant accumulation of immature myeloid cells (ImC) in large TC‐1 tumors and demonstrated that a HPV therapeutic vaccine restored antitumor immune responses with the correction of aberrant myeloid cell differentiation by all‐trans retinoic acid (ATRA). Our study demonstrated that combining ATRA with vaccination not only decreased the number of Gr‐1+ CD11b+ ImC, but for the first time also suppressed the function of Gr‐1+ CD11b+ ImC with decreased expression of CD80. Furthermore, large numbers of CD11c+ CD80+, CD11c+ CD86+, and CD11c+ MHCII+ mature dendritic cells were recruited. The combination therapy generated significantly increased numbers of functional E7‐specific T cells with elevated interferon‐γ secretion and enhanced cytotoxic T‐cell activity. These findings suggest potential clinical benefits for the combined use of ATRA and HPV therapeutic vaccines. (Cancer Sci 2009; 100: 334–340)