bluuebunny/crossref_metadata_2025 huggingface dataset:
5-AZA-2′-deoxycytidine (5-AZA-CdR) leads to down-regulation of Dnmt1o and gene expression in preimplantation mouse embryos
Authors: Yu Jian-Ning , Xue Chun-Yang , Wang Xu-Guang , Lin Fei , Liu Chun-Yi , Lu Fu-Zeng , Liu Hong-Lin
Published: February 2009

5-AZA-2′-deoxycytidine (5-AZA-CdR) is a demethylating, teratogenic agent and a mutagen, which causes defects in the developing mouse and rat after implantation. Our previous data indicated that 5-AZA-CdR (0.2 and 1.0 μM) inhibited the development of mouse preimplantation embryos. Pronuclear embryos exposed to 5-AZA-CdR at the pronuclear stage were unable to form 8-cell embryos, while 2-cell-stage embryos exposed to 5-AZA-CdR only developed into uncompacted 8-cell-stage embryos. And there was no formation of blastocysts when 4-cell embryos cultured in 5-AZA-CdR. In our present study, we detected Dnmt1o protein and some developmental gene expression in order to find the reasons for the developmental arrest. Dnmt1o could not traffic to 8-cell nuclei as control when embryos were exposed to 5-AZA-CdR. Dnmt1o was in cytoplasm at 2-cell and 4-cell stages before and after treated with 5-AZA-CdR. Gene expression changes were also detected in this research. Our data indicated that connexin 31 (Cx31), connexin 43 (Cx43), connexin 45 (Cx45), E-cadherin (Cdh1) and β-catenin (Ctnnb1) were all downregulated by 5-AZA-CdR. Cx31, Cx43 and Cx45 are members of connexins family, which have a central role in gap junctions. Cdh1 and Ctnnb1 are necessary for the foundation of tight junctions. Therefore, developmental arrest induced by 5-AZA-CdR may be caused by the failure of Dnmt1o cytoplasmic–nuclear traffic and the down-regulation of developmental gene expression. Normal compaction and blastocoel cavitation need Dnmt1o traffic to 8-cell nuclei and the right gene expression, especially the correlative genes in gap junctions and tight junctions.
Logarithmic growth and Frobenius filtrations for solutions ofp-adic differential equations
Authors: Chiarellotto Bruno , Tsuzuki Nobuo
Published: February 2009

For a ∇-moduleMover the ringK[[x]]0of bounded functions over ap-adic local fieldKwe define the notion of special and generic log-growth filtrations on the base of the power series development of the solutions and horizontal sections. Moreover, ifMalso admits a Frobenius structure then it is endowed with generic and special Frobenius slope filtrations. We will show that in the case ofMa ϕ–∇-module of rank 2, the Frobenius polygon forMand the log-growth polygon for its dual,Mv, coincide, this is proved by showing explicit relationships between the filtrations. This will lead us to formulate some conjectural links between the behaviours of the filtrations arising from the log-growth and Frobenius structures of the differential module. This coincidence between the two polygons was only known for the hypergeometric cases by Dwork.
Arthedata – Aufbau und technische Realisierung einer wissenschaftlichen Datenbank für Kunsttherapie
Authors: Elbing Ulrich , Schulze Constanze , Zillmann Hartmut , Ostermann Thomas
Published: February 2009

Zusammenfassung. Hintergrund: Kunsttherapie ist eine vergleichsweise junge Disziplin, deren Methoden und Verfahren sich im Zusammenhang mit der Erschließung neuer Anwendungsbereiche in den letzten Jahrzehnten erweitert und ausdifferenziert haben. Die wissenschaftliche Situation der Kunsttherapie ist momentan dadurch gekennzeichnet, dass die vorliegende Wissens- und Forschungssubstanz kaum aufgearbeitet, systematisch gesammelt und somit nur mühevoll und lückenhaft zu recherchieren ist. Ziel des Arthedata-Projekts ist es, mittels web-basierter Anwendungen eine umfassende internationale Datenbank für die Kunsttherapieforschung zu etablieren. Material und Methoden: Die aktuelle Datenbank arthedata.de geht zurück auf die Datenbank kunthera, die als Gemeinschaftsprojekt von der Hochschule für Kunsttherapie Nürtingen (HKT) und vom Deutschen Fachverband für Kunst- und Gestaltungstherapie (DFKGT) getragen wurde. Diese Daten wurden mittels XML-basierter Protokolle (XML: eXtended Markup Language) in die Struktur von Arthedata importiert, indexiert und online unter www.arthedata.de verfügbar gemacht. Ergebnisse: Vor der Überführung in die neue Datenbank arthedata wurde kunthera pro Quartal von über 1500 externen Nutzern im Internet besucht. Die Datenbank umfasste am Ende ca. 3100 Titel kunsttherapeutischer Fachliteratur sowie relevanter Fachliteratur der Grund- und Bezugswissenschaften. Es konnten innovative Suchfunktionen realisiert werden: So wird es dem Benutzer durch sog. Trefferlandkarten ermöglicht, sequentiell vom zufälligen Bereich seiner möglicherweise unspezifischen oder unvollständigen Suchanfrage in einen kontrollierten Bereich des tatsächlich vorhandenen Datenbankvokabulars mit Sucherfolgsgarantie zu gelangen. Diskussion: In der Kunsttherapie wird die Systematisierung und empirische Untersuchung methodischer Konzepte und Ansätze der Kunsttherapie in den verschiedenen (klinischen) sozialen Praxisfeldern eine immer größere Rolle spielen. Daneben bedarf es des wissenschaftlichen Nachweises der therapeutischen Wirkungen des künstlerischen Arbeitens, die bisher vorwiegend durch einzelne Erfahrungen (wie z.B. in Fall- oder Praxisberichten) erfasst und dokumentiert sind. Mit arthedata.de wurde dafür ein Dokumentationsmedium geschaffen, das auf Basis innovativer technologischer Möglichkeiten eine solche wissenschaftlich fundierte Aufarbeitung der Hintergründe, Wurzeln und spezifischen Entwicklungslinien der Kunsttherapie ermöglicht.
Discrimination of sources of terrigenous sediment deposited in the central Arctic Ocean through the Cenozoic
Authors: Martinez Nahysa C. , Murray Richard W. , Dickens Gerald R. , Kölling Martin
Published: February 2009

We analyzed a suite of sediment samples recovered in the central Arctic Ocean for major, trace, and rare earth elements in order to assess changes in terrigenous source material throughout the Cenozoic. The terrigenous component consists of two end‐members. Input from a shale‐like composition dominates bulk sediments, especially those deposited during the Paleocene and since the Miocene, and may represent sediment supply from the eastern Laptev Sea. Therefore, even though the environment and transport mechanisms may have varied from ice free to ice dominated, sequences of the early Paleogene and later Neogene appear to have been influenced by a single major terrigenous source. This suggests similar transport capabilities and trajectories for both ocean and drift currents through significant parts of the Cenozoic. Influence from a more mafic source appears to be more important through the early Eocene to the middle Miocene and most likely represents material from the western Laptev Sea or Kara Sea. Thus, Eocene major changes in surface water productivity appear broadly synchronous with those in terrigenous provenance. A combination of regional sea level variations, local shelf processes, and transport mechanisms are among the more probable causes for the observed source changes. Although the assignment of sources using chemistry presently is constrained by a lack of data from certain regions (e.g., eastern Siberian Sea) our results generally agree with inferences based on mineralogy or radiogenic isotopes and shed further light on long‐term reconstructions of the central Arctic Ocean.
A study on warning algorithms for Istanbul earthquake early warning system
Authors: Alcik Hakan , Ozel Oguz , Apaydin Nurdan , Erdik Mustafa
Published: February 2009

17 August (Mw 7.4) and 12 November 1999 (Mw 7.2) earthquakes have caused major concern about future earthquake occurrences in Istanbul and in the Marmara Region. Stress transfer studies and renewal model type probabilistic investigations indicate about 2% annual probability for a Mw = 7+ earthquake in the Marmara Sea. As part of the preparations for the expected earthquake in Istanbul, an early warning system has been established in 2002. A simple and robust algorithm, based on the exceedance of specified threshold time domain amplitude and the cumulative absolute velocity (CAV) levels, is implemented for this system. Rational threshold levels related to new bracketed CAV window approach (BCAV‐W) are determined, based on dataset of strong ground motion records with fault distances of less than 100 km, as 0.2 m/s, 0.4 m/s and 0.7 m/s related to three alarm levels which will be incorporated in the Istanbul earthquake early warning system.
A new framework for estimating englacial water content and pore geometry using combined radar and seismic wave velocities
Authors: Endres Anthony L. , Murray Tavi , Booth Adam D. , West L. Jared
Published: February 2009

Ice mechanical properties, and hence the response of glaciers to climate change, depend strongly on the presence of liquid water at ice‐grain boundaries. The propagation velocities of radar and seismic waves are also highly sensitive to this water. Mixing laws, typically the Looyenga and Riznichenko formulae, have traditionally been used to quantify liquid water content within glaciers from such velocity data; however, it has become apparent that these mixing laws are geometrically inconsistent. We present an inclusion‐based effective medium approximation in which we model water inclusions within solid ice. Two types of inclusions are used: spherical inclusions to represent water in the grain junction nodes, and high‐aspect ratio spheroidal inclusions to represent water in the grain boundary veins. We apply this model to radar and seismic data from a polythermal glacier in Svalbard to quantify both inclusion geometry and the unfrozen water content within the warm ice.
Evolution of the anemone AR NOAA 10798 and the related geo‐effective flares and CMEs
Authors: Asai Ayumi , Shibata Kazunari , Ishii Takako T. , Oka Mitsuo , Kataoka Ryuho , Fujiki Ken'ichi , Gopalswamy Nat
Published: February 2009

We present a detailed examination of the features of the active region (AR) NOAA 10798. This AR generated coronal mass ejections (CMEs) that caused a large geomagnetic storm on 24 August 2005 with the minimum Dst index of −216 nT. We examined the evolution of the AR and the features on/near the solar surface and in the interplanetary space. The AR emerged in the middle of a small coronal hole, and formed a sea anemone like configuration. Hα filaments were formed in the AR, which have southward axial field. Three M class flares were generated, and the first two that occurred on 22 August 2005 were followed by Halo‐type CMEs. The speeds of the CMEs were fast, and recorded about 1200 and 2400 km s−1, respectively. The second CME was especially fast, and caught up and interacted with the first (slower) CME during their travelings toward Earth. These acted synergically to generate an interplanetary disturbance with strong southward magnetic field of about −50 nT, which was followed by the large geomagnetic storm.
Cluster multispacecraft measurement of spatial scales of foreshock Langmuir waves
Authors: Soucek J. , Santolik O. , Dudok de Wit T. , Pickett J. S.
Published: February 2009

In this article, we present the first multispacecraft study of spatial scales of Langmuir wave packets in the terrestrial foreshock. We used data from the Wideband Data (WBD) instrument on the Cluster satellites to identify simultaneous observations of the same wave packet on multiple spacecraft at very small separations. To overcome instrumental constraints, we developed a statistical technique for matching observations on different spacecraft by comparison of their Fourier spectra. In this article, we demonstrate an application of the technique on one multispacecraft foreshock event, and we afterward use it on a larger data set comprising several Cluster foreshock crossings. Our analysis shows that the typical scale of Langmuir wave packets in the direction transverse to the magnetic field falls between 40 and 100 km, and their size in the parallel direction is larger than 150 km. We also conclude that convection of wave packets may contribute to the large‐scale temporal modulation of Langmuir waves observed in previous spacecraft studies, but the small‐scale structure of the modulation must be attributed to other effects. Possible systematic errors and sources of uncertainty in our estimates are discussed in detail.
Spatial variations in lava flow field thermal structure and effusion rate derived from very high spatial resolution hyperspectral (MIVIS) data
Authors: Lombardo V. , Harris A. J. L. , Calvari S. , Buongiorno M. F.
Published: February 2009

High spatial resolution hyperspectral measurements of volcanic thermal anomalies allow for an unconstrained solution of a two‐component thermal model. This can be used for identification of lava flow emplacement style and the calculation of lava flow heat and volume flux. The multispectral infrared and visible imaging spectrometer (MIVIS) is an airborne sensor equipped with 72 bands in the short infrared range and 10 bands in the thermal infrared region of the spectrum. We used MIVIS acquired for Mount Etna (Italy) during the July–August 2001 eruption to solve the dual band equations in an unconstrained fashion using three bands of unsaturated data. Our results suggest a complex thermal structure for Etnean lava flows. This is characterized by a downflow transition from a lightly crusted active channel to a more heavily crusted distal section, both surrounded by zones of stagnant cooling flow where exposed molten material is absent and maximum temperatures are thus lower. The total flow field effusion rate obtained for 29 July 2001 (0700 local time) of 8–16 m3/s is in excellent agreement with that obtained from ground‐based measurements and Advanced Very High Resolution Radiometer data. Flow‐by‐flow effusion rates obtained from the MIVIS data vary depending on whether the vent is linked to the central conduit or the dyke that was injected from greater depth, as well as vent elevation, with lower elevation vents experiencing higher effusion rates.
Three‐dimensional joint inversion of traveltime and gravity data across the Chicxulub impact crater
Authors: Vermeesch P. M. , Morgan J. V. , Christeson G. L. , Barton P. J. , Surendra A.
Published: February 2009

In 2005 an extensive new seismic refraction data set was acquired over the central part of the Chicxulub impact crater, allowing us to image its structure with much better resolution than before. However, models derived from traveltime data are limited by the available ray coverage and the nonuniqueness that is inherent to all geophysical methods. Therefore, many different models can fit the data equally well. To address these issues, we have developed a new method to simultaneously invert traveltime and gravity data to obtain an integrated model. To convert velocity to density, we use a linear relationship derived from measurements on core from the Chicxulub impact basin, thus providing a reliable conversion equation that is typical for lithologies of the central part of this crater. Prior to utilizing the inversion on the observed data, we have run a suite of tests to establish the optimum weighting between traveltime and gravity constraints, using a synthetic model of central crater structure and the real experimental geometry. These synthetic tests indicate which inversion parameters lead to the best recovery of subsurface structure, as well as which parts of the model are well resolved. We applied the method to all existing gravity data and to seismic refraction data acquired in 1996 and the new, higher‐resolution seismic refraction data acquired in 2005. We favor the traveltime model wherever we have sufficient ray coverage and the joint model where we have no ray coverage.
Structural features and shear‐velocity structure of the “Pacific Anomaly”
Authors: He Yumei , Wen Lianxing
Published: February 2009

We constrain structural features and shear‐velocity structure of a low‐velocity anomaly in the lower mantle beneath the Pacific (we term it the “Pacific Anomaly”) on the basis of forward travel time and waveform modeling of the observed direct S, Sdiff, ScS, SKS, and SKKS phases sampling a great arc across the anomaly from eastern Eurasia to southern South America. After correction for the effects of earthquake mislocation and the seismic heterogeneities outside the Pacific Anomaly, seismic observations suggest that the Pacific Anomaly along the great arc consists of at least two separated portions with a 740‐km‐wide gap between them. The western portion of the anomaly is about 1050 km wide, extends at least 740 km above the core‐mantle boundary (CMB), and exhibits a trapezoidal shape with lateral dimensions increasing slightly with depth. The velocity structure of the western portion varies from −3.0% at the top (740 km above the CMB) to −3.5% at 100 km above the CMB and an average shear‐velocity reduction of −5% in the bottom 100 km of the mantle. The eastern portion of the anomaly reaches at least 340 km above the CMB beneath the mid‐Pacific with an 1800‐km‐wide base and has a uniform velocity reduction of −3%. Waveform modeling further suggests a very low velocity layer with a shear‐velocity reduction of −10% located at the edge of the western portion of the anomaly. Combining the latest results from others, we present a general picture of structural and velocity structures of the Pacific Anomaly. The structural and velocity features suggest that the anomaly represents a cluster of metastable thermo‐chemical piles.
Static stress drop associated with brittle slip events on exhumed faults
Authors: Griffith W. A. , Di Toro G. , Pennacchioni G. , Pollard D. D. , Nielsen S.
Published: February 2009

We estimate the static stress drop on small exhumed strike‐slip faults in the Lake Edison granodiorite of the central Sierra Nevada (California). The subvertical strike‐slip faults were exhumed from 4 to 15 km depth and were chosen because they are exposed in outcrop along their entire tip‐to‐tip lengths of 8–12 m. Slip nucleated on joints and accumulated by crystal‐plastic shearing (forming quartz mylonites from early quartz vein filling in joints) and successive brittle faulting (forming epidote‐bearing cataclasites). The occurrence of thin, ≤300 μm wide, pseudotachylytes along some small faults throughout the study area suggests that some, if not all, of the brittle slip on the study area faults may have been seismic. We suggest that the contribution of brittle, cataclastic slip to the total slip along the studied cataclasite‐bearing small faults may be estimated by the length of epidote‐filled, rhombohedral dilatational jogs (rhombochasms) distributed quasi‐periodically along the length of the faults. The interpretation that slip recorded by rhombochasms occurred in single events is based on evidence that (1) epidote crystals are randomly oriented and undeformed within the rhombochasm; (2) cataclasite in principal slip zones does not include clasts of previous cataclasite, and (3) rhombochasm lengths vary systematically along the length of the faults with slip maximum occurring near the fault center, tapering to the fault tips. We thereby constrain both the rupture length and slip. On the basis of these measurements, we calculate stress drops ranging over 90–250 MPa, i.e., one to two orders of magnitude larger than typical seismological estimates for earthquakes, but similar in magnitude to seismological estimates of small (<M2) earthquakes from the San Andreas Fault Observatory at Depth (SAFOD). The slip events described in the present study occurred along small, deep‐seated faults, and, given the calculated stress drops and observations that brittle faults exploited joints sealed by quartz‐bearing mylonite, we conclude that these were “strong” faults.
On the shapes of natural sand grains
Authors: Barclay David R. , Buckingham Michael J.
Published: February 2009

Digitized outlines of sand grains from a dozen locations, including deserts, beaches, and seabeds, have been acquired using an optical microscope linked to a desktop computer. Fourier analysis of the outlines returns the normalized power spectrum of each sample, averaged over several hundred grains. Regardless of the origin of the samples, these power spectra all exhibit essentially the same inverse power law dependence on the harmonic number, n, varying as n−10/3 for 2 ≤ n ≤ 20. This “universal” spectrum provides the basis of a numerical technique for synthesizing the irregular outline of a sand grain: The outline is represented as a random pulse train in which identically shaped microasperities, with normally distributed amplitudes, are randomly superimposed on the perimeter of a circle. By identifying the spectrum of the microasperities with the observed inverse power law dependence derived from the optical images, the synthetic outlines are constrained to show the same statistical properties as the outlines of the real grains. The synthesized and real outlines are qualitatively similar in that visually, it is difficult to distinguish between them. The new numerical technique for synthesizing irregular outlines of sand grains has potential for investigating the random packing of realistically rough particles through computer simulation.
River basins as groundwater exporters and importers: Implications for water cycle and climate modeling
Authors: Schaller Morgan F. , Fan Ying
Published: February 2009

The groundwater reservoir and its interaction with surface water facilitate lateral transport of continental water and energy. Current climate models do not account for long‐distance groundwater flow between model cells but route the atmospheric surplus (precipitation (P) minus evapotranspiration (ET)) directly to stream discharge within a model grid cell. We ask how much water exits a river basin without ever passing through its surface outlet? What are the climatologic and geologic factors influencing this flux? To answer these questions, a separation of groundwater flow from river flow is necessary. We use the ratio of stream discharge (Qr) to basin recharge (R = P − ET) for this purpose; where Qr:R < 1, a basin is considered a groundwater exporter; and where Qr:R > 1, a basin is considered a groundwater importer. Here Qr is obtained from 39 years of U.S. Geological Survey Hydro‐Climatic Data Network observed stream discharge from 1555 basins across the continental United States, and R (P − ET) is derived from 50 years of hydrologic simulation by the Variable Infiltration Capacity model. It was found that the Qr:R ratio deviates significantly from 1 across the continent. Detailed investigations of individual basins suggest that the deviations are primarily a function of geology, while climate and basin scale influence the magnitude of these deviations. Further, a marked incongruity between the surface and groundwater flow directions is apparent, suggesting that surface drainage is only partially indicative of subsurface flow regimes. The apparent significance of this long‐distance groundwater flow component reinforces the need for inclusion of the groundwater reservoir in current water cycle and climate modeling efforts.
Ocean‐Atmosphere Interactions During Cyclone Nargis
Authors: McPhaden Michael J. , Foltz Gregory R. , Lee Tony , Murty V. S. N. , Ravichandran M. , Vecchi Gabriel A. , Vialard Jerome , Wiggert Jerry D. , Yu Lisan
Published: February 2009

Cyclone Nargis (Figure 1a) made landfall in Myanmar (formerly Burma) on 2 May 2008 with sustained winds of approximately 210 kilometers per hour, equivalent to a category 3–4 hurricane. In addition, Nargis brought approximately 600 millimeters of rain and a storm surge of 3–4 meters to the low‐lying and densely populated Irrawaddy River delta. In its wake, the storm left an estimated 130,000 dead or missing and more than $10 billion in economic losses. It was the worst natural disaster to strike the Indian Ocean region since the 26 December 2004 tsunami and the worst recorded natural disaster ever to affect Myanmar.
Illuminating Northern California's Active Faults
Authors: Prentice Carol S. , Crosby Christopher J. , Whitehill Caroline S. , Arrowsmith J. Ramón , Furlong Kevin P. , Phillips David A.
Published: February 2009

Newly acquired light detection and ranging (lidar) topographic data provide a powerful community resource for the study of landforms associated with the plate boundary faults of northern California (Figure 1). In the spring of 2007, GeoEarthScope, a component of the EarthScope Facility construction project funded by the U.S. National Science Foundation, acquired approximately 2000 square kilometers of airborne lidar topographic data along major active fault zones of northern California. These data are now freely available in point cloud (x, y, z coordinate data for every laser return), digital elevation model (DEM), and KMZ (zipped Keyhole Markup Language, for use in Google EarthTM and other similar software) formats through the GEON OpenTopography Portal (http://www.OpenTopography.org/data). Importantly, vegetation can be digitally removed from lidar data, producing high‐resolution images (0.5‐ or 1.0‐meter DEMs) of the ground surface beneath forested regions that reveal landforms typically obscured by vegetation canopy (Figure 2).
Kastner Receives 2008 Maurice Ewing Medal
Authors: Elderfield Henry , Kastner Miriam
Published: February 2009

Miriam Kastner was awarded the 2008 Maurice Ewing Medal at the AGU Fall Meeting Honors Ceremony, held 17 December 2008 in San Francisco, Calif. The medal is “for significant original contributions to the scientific understanding of the processes in the ocean; for the advancement of oceanographic engineering technology, and instrumentation; or outstanding service to marine science.”
Data, Databases, and Communities
Authors: Day Matthew
Published: February 2009

Overview* Publishing landscape and challenges* Nature gateways and databases* NCI-Nature Pathway Interaction Database* A few other communication tools
Stabilization of naked and condensed plasmid DNA against degradation induced by ultrasounds and high‐shear vortices
Authors: Wu Ming L. , Freitas Sindélia S. , Monteiro Gabriel A. , Prazeres Duarte M. F. , Santos José A. L.
Published: February 2009

Micrometre‐sized aggregates of a 6050‐bp plasmid obtained by the addition of 1.5–3.0 mM CaCl2 and 20% (v/v) t‐butanol or 0.3–1.0% (v/v) APG (aluminium phosphate gel) were subjected to degradation induced by sonication or vortex flows. Dynamic light scattering revealed that the plasmid hydrodynamic radius increases from 116 nm to >1300 nm and approx. 1000 nm, when formulated with CaCl2/t‐butanol and APG respectively. CD showed that addition of CaCl2/t‐butanol leads to transition in plasmid structure from B‐DNA to a ψ‐DNA negative form, whereas no detectable transitions were observed for APG formulations. The ability of the condensing agents to stabilize supercoiled plasmid isoforms subjected to sonication or turbulent Taylor vortices was assessed by agarose‐gel electrophoresis. Although naked plasmid was completely fragmented after 5 s of sonication, condensing agents increased the plasmid stability dramatically [e.g. up to 80% after 30 s with 1.5 mM CaCl2+20% (v/v) t‐butanol]. In the case of the vorticular flow system, the extent of degradation correlated well with the shear stress associated with flow of the solutions being processed. Overall, the results from the present study demonstrate that condensing agents such as CaCl2/t‐butanol and APG can effectively stabilize plasmids against shear‐induced degradation; the extent of protection, however, depends on both the condensing agents and the shear‐inducing system used.
Identification and characterization of the lipid-binding property of GrlR, a locus of enterocyte effacement regulator
Authors: Jobichen Chacko , Fernandis Aaron Z. , Velazquez-Campoy Adrian , Leung Ka Yin , Mok Yu-Keung , Wenk Markus R. , Sivaraman J.
Published: February 2009

Lipocalins are a broad family of proteins identified initially in eukaryotes and more recently in Gram-negative bacteria. The functions of lipocalin or lipid-binding proteins are often elusive and very diverse. Recently, we have determined the structure of GrlR (global regulator of LEE repressor), which plays a key role in the regulation of LEE (locus of enterocyte effacement) proteins. GrlR adopts a lipocalin-like fold that is composed of an eight-stranded β-barrel followed by an α-helix at the C-terminus. GrlR has a highly hydrophobic cavity region and could be a potential transporter of lipophilic molecules. To verify this hypothesis, we carried out structure-based analysis of GrlR, determined the structure of the lipid–GrlR complex and measured the binding of lipid to recombinant GrlR by ITC (isothermal titration calorimetry). In addition, we identified phosphatidylglycerol and phosphatidylethanolamine as the endogenously bound lipid species of GrlR using electrospray-ionization MS. Furthermore, we have shown that the lipid-binding property of GrlR is similar to that of its closest lipocalin structural homologue, β-lactoglobulin. Our studies demonstrate the hitherto unknown lipid-binding property of GrlR.
Modular regulation analysis of integrative effects of hypoxia on the energetics of contracting skeletal muscle in vivo
Authors: Beuste Christophe , Miraux Sylvain , Deschodt-Arsac Véronique J. , Thiaudiere Eric , Franconi Jean-Michel , Diolez Philippe , Arsac Laurent M.
Published: February 2009

In the exercising muscle, acute reduction in ambient oxygen impairs muscle contraction because of the effects of hypoxia on mitochondrial ATP supply. The less marked impairment reported after long-term exposure to hypoxia points to changes in the regulation of the energetic system of contraction in HC (hypoxic conditioned) animals. This energetic system is conceptually defined here as two modules: the ATP/PCr (phosphocreatine)-producer and the ATP/PCr-consumer connected by energetic intermediates. Modular control analysis that combines top-down control analysis with non-invasive 31P-NMR spectroscopy was used to describe the effects of hypoxia on each module and their adaptation. Modulations of steady levels of ATP turnover (indirectly assessed as force output) and muscle PCr were obtained in HC rats (6 weeks at 10.5% O2) compared with N (normoxic) rats. Modular control and regulation analyses quantified the elasticity to PCr of each module in N and HC rats as well as the direct effect of acute hypoxia on the ATP/PCr-producer module. Similar elasticities in N and HC rats indicate the absence of response to long-term hypoxia in internal regulations of the ATP supply and demand pathways. The less marked impairment of contraction by acute hypoxia in HC rats (−9±6% versus −17±14% in N rats, P<0.05) was therefore fully explained by a lower direct effect (HC −31±13% versus N −44±23%, P<0.05) of acute hypoxia on mitochondrial ATP supply. This points to a positive adaptation to chronic hypoxia. Modular control analysis in vivo may provide powerful tools to find out improved function (alternatively dysfunction) at the system level in conditioned animals.
In vivo regulatory phosphorylation of the phosphoenolpyruvate carboxylase AtPPC1 in phosphate-starved Arabidopsis thaliana
Authors: Gregory Allison L. , Hurley Brenden A. , Tran Hue T. , Valentine Alexander J. , She Yi-Min , Knowles Vicki L. , Plaxton William C.
Published: February 2009

PEPC [PEP(phosphoenolpyruvate) carboxylase] is a tightly controlled cytosolic enzyme situated at a major branchpoint in plant metabolism. Accumulating evidence indicates important functions for PEPC and PPCK (PEPC kinase) in plant acclimation to nutritional Pi deprivation. However, little is known about the genetic origin or phosphorylation status of native PEPCs from −Pi (Pi-deficient) plants. The transfer of Arabidopsis suspension cells or seedlings to −Pi growth media resulted in: (i) the marked transcriptional upregulation of genes encoding the PEPC isoenzyme AtPPC1 (Arabidopsis thaliana PEPC1), and PPCK isoenzymes AtPPCK1 and AtPPCK2; (ii) >2-fold increases in PEPC specific activity and in the amount of an immunoreactive 107-kDa PEPC polypeptide (p107); and (iii) In vivo p107 phosphorylation as revealed by immunoblotting of clarified extracts with phosphosite-specific antibodies to Ser-11 (which could be reversed following Pi resupply). Approx. 1.3 mg of PEPC was purified 660-fold from −Pi suspension cells to apparent homogeneity with a specific activity of 22.3 units · mg−1 of protein. Gel filtration, SDS/PAGE and immunoblotting demonstrated that purified PEPC exists as a 440-kDa homotetramer composed of identical p107 subunits. Sequencing of p107 tryptic and Asp-N peptides by tandem MS established that this PEPC is encoded by AtPPC1. Pi-affinity PAGE coupled with immunoblotting indicated stoichiometric phosphorylation of the p107 subunits of AtPPC1 at its conserved Ser-11 phosphorylation site. Phosphorylation activated AtPPC1 at pH 7.3 by lowering its Km(PEP) and its sensitivity to inhibition by L-malate and L-aspartate, while enhancing activation by glucose 6-phosphate. Our results indicate that the simultaneous induction and In vivo phosphorylation activation of AtPPC1 contribute to the metabolic adaptations of −PiArabidopsis.
Effective screening length and quasiuniversality for the restricted primitive model of an electrolyte solution
Authors: Janeček Jiří , Netz Roland R.
Published: February 2009

Monte Carlo simulations for the restricted primitive model of an electrolyte solution above the critical temperature are performed at a wide range of concentrations and temperatures. Thermodynamic properties such as internal energy, osmotic coefficient, activity coefficient, as well as spatial correlation functions are determined. These observables are used to investigate whether quasiuniversality in terms of an effective screening length exists, similar to the role played by the effective electron mass in solid-state physics. To that end, an effective screening length is extracted from the asymptotic behavior of the Fourier-transformed charge-correlation function and plugged into the Debye–Hückel limiting expressions for various thermodynamic properties. Comparison with numerical results is favorable, suggesting that correlation and other effects not captured on the Debye–Hückel limiting level can be successfully incorporated by a single effective parameter while keeping the functional form of Debye–Hückel expressions. We also compare different methods to determine mean ionic activity coefficient in molecular simulations and check the internal consistency of the numerical data.
Disturbance of visual search by stimulating to posterior parietal cortex in the brain using transcranial magnetic stimulation
Authors: Iramina Keiji , Ge Sheng , Hyodo Akira , Hayami Takehito , Ueno Shoogo
Published: February 2009

In this study, we applied a transcranial magnetic stimulation (TMS) to investigate the temporal aspect for the functional processing of visual attention. Although it has been known that right posterior parietal cortex (PPC) in the brain has a role in certain visual search tasks, there is little knowledge about the temporal aspect of this area. Three visual search tasks that have different difficulties of task execution individually were carried out. These three visual search tasks are the “easy feature task,” the “hard feature task,” and the “conjunction task.” To investigate the temporal aspect of the PPC involved in the visual search, we applied various stimulus onset asynchronies (SOAs) and measured the reaction time of the visual search. The magnetic stimulation was applied on the right PPC or the left PPC by the figure-eight coil. The results show that the reaction times of the hard feature task are longer than those of the easy feature task. When SOA=150 ms, compared with no-TMS condition, there was a significant increase in target-present reaction time when TMS pulses were applied. We considered that the right PPC was involved in the visual search at about SOA=150 ms after visual stimulus presentation. The magnetic stimulation to the right PPC disturbed the processing of the visual search. However, the magnetic stimulation to the left PPC gives no effect on the processing of the visual search.
Evidence for correlation between spin and charge dynamics in La2Cu1−xLixO4
Authors: Park Eunsung , Park Tuson , Sarrao J. L. , Thompson J. D.
Published: February 2009

From ac magnetic susceptibility measurements on Li-doped La2CuO4, with Hac parallel and perpendicular to the CuO plane, we find frequency-dependent behavior below a spin-glass temperature (TSG). TSG obtained from magnetic susceptibility is higher than the charge-glass temperature TCG obtained from dielectric constant measurements, indicating that spin freezes first and drives charge freezing at a lower temperature. Similar frequency dependence of the two characteristic freezing temperatures underlines that charge and spin dynamics are strongly correlated in this cuprate compound.
Magneto- and electroresistance of La0.7Sr0.3MnO3/Nb(1.0%):SrTiO3 junctions
Authors: Chen Y. F. , Ziese M.
Published: February 2009

The current-voltage characteristics and magnetotransport properties of La0.7Sr0.3MnO3/Nb(1.0%):SrTiO3 junctions under various currents ranging from 10−6 to 10−3 A and different temperatures ranging from 10 to 300 K were investigated. The current-voltage curves exhibit rectifying behavior. The resistance, magnetoresistance, and electroresistance of the junctions are strongly dependent on bias-current direction, current, temperature, and magnetic field. A detailed analysis of the conductance-voltage curves showed that quantum mechanical tunneling was the dominating transport mechanism.
Magnetoimpedance of a glass-coated amorphous microwire
Authors: Sinha S. , Das B. , Mandal K.
Published: February 2009

A maximum magnetoimpedance (∼66%) was observed at 5.2 MHz in a positive magnetostrictive glass-coated amorphous Co83.2Mn7.6Si5.8B3.3 microwire. Giant magnetoimpedance in this microwire was increased to 129% on short-duration heat treatment by passing four current pulses of amplitude of 100 mA and each of 12 s duration. Magnetoimpedance of the as-quenched and heat treated microwires was investigated as a function of a dc magnetic field Hdc within ±120 Oe and frequency f up to 12.85 MHz. The magnetization measurements of the samples indicated that the increase in giant magnetoimpedance on short-duration annealing is due to the increase in outer shell volume of the domain structure.
High coercivity Sm–Fe melt-spun ribbon
Authors: Saito Tetsuji , Furutani Tomokazu
Published: February 2009

The results of an investigation of the synthesis of the Sm5Fe17 phase and its magnetic properties are presented. It was found that the Sm5Fe17 phase can be produced by the annealing of a Sm–Fe melt-spun ribbon with a Sm content of 15–27.5 at. %. The coercivity of the annealed melt-spun ribbon was highly dependent on both the annealing temperature and the Sm content of the Sm–Fe alloy. The Sm22.5Fe77.5 melt-spun ribbon annealed at 973 K consisted of the Sm5Fe17 phase and exhibited a large coercivity of over 40 kOe.
Spin-polarized tunneling through a ferromagnetic insulator
Authors: Kok M. , Beukers J. N. , Brinkman A.
Published: February 2009

The polarization of the tunnel conductance of spin-selective ferromagnetic insulators is modeled, providing a generalized concept of polarization including both the effects of electrode and barrier polarization. The polarization model is extended to take additional non-spin-polarizing insulating layers into account. These additional tunnel barriers are found to have a large effect on the tunneling polarization, both positively and negatively, depending on the material parameters. The model is applied to spin-filter devices containing the promising spin filter material EuO.
Magnetic force microscopy and spinstand testing of multi-row-per-track discrete bit patterned media fabricated by focused ion beam
Authors: Chen Y. J. , Huang T. L. , Leong S. H. , Hu S. B. , Ng K. W. , Yuan Z. M. , Zong B. Y. , Shi J. Z. , Hendra S. K. , Liu B. , Ng V.
Published: February 2009

Multi-row-per-track discrete bit patterned media with interleaved bits have been fabricated on granular perpendicular media disks by focused ion beam and tested by magnetic force microscopy and spinstand tester. It was found that sub-100 nm patterned magnetic islands showed single domain behavior and narrowed switching field distribution. We further demonstrate from captured spinstand readback waveforms the concept of recording two rows of interleaved dot bits as one track. In addition to overcoming the down track patterning resolution limit, the proposed concept patterned media provide many other advantages including higher data rate for read/write, a flexible bit aspect ratio (BAR)≥2 design for better integration with head design and servo control, as well as allowing the use of wider write pole to improve writing efficiency for high density recording.
First-principles calculation of the 6.1 Å family bowing parameters and band offsets
Authors: Wang Fei , Jia Yu , Li Shun-Fang , Sun Qiang
Published: February 2009

Using the first-principles band-structure method and the special quasirandom structure approach, we have studied the electronic band structure of 6.1 Å family binary antimonide compounds and their ternary alloys. The direct and indirect optical bowing parameters for the AlxGa1−xSb and AlxIn1−xSb ternary alloys have been calculated. The direct to indirect crossover point of ternary alloy is given. Furthermore we calculated the important band offsets between InAs and antimonide compounds, which determine both transport and quantum confinement in the interface of a heterostructure.
Exciton localization on basal stacking faults in a-plane epitaxial lateral overgrown GaN grown by hydride vapor phase epitaxy
Authors: Corfdir P. , Lefebvre P. , Levrat J. , Dussaigne A. , Ganière J.-D. , Martin D , Ristić J. , Zhu T. , Grandjean N. , Deveaud-Plédran B.
Published: February 2009

We present a detailed study of the luminescence at 3.42 eV usually observed in a-plane epitaxial lateral overgrowth (ELO) GaN grown by hydride vapor phase epitaxy on r-plane sapphire. This band is related to radiative recombination of excitons in a commonly encountered extended defect of a-plane GaN: I1 basal stacking fault. Cathodoluminescence measurements show that these stacking faults are essentially located in the windows and the N-face wings of the ELO-GaN and that they can appear isolated as well as organized into bundles. Time-integrated and time-resolved photoluminescence, supported by a qualitative model, evidence not only the efficient trapping of free excitons (FXs) by basal plane stacking faults but also some localization inside I1 stacking faults themselves. Measurements at room temperature show that FXs recombine efficiently with rather long luminescence decay times (360 ps), comparable to those encountered in high-quality GaN epilayers. We discuss the possible role of I1 stacking faults in the overall recombination mechanism of excitons.
Volatile electrical switching in a functional polyimide containing electron-donor and -acceptor moieties
Authors: Liu Yi-Liang , Ling Qi-Dan , Kang En-Tang , Neoh Koon-Gee , Liaw Der-Jang , Wang Kun-Li , Liou Wun-Tai , Zhu Chun-Xiang , Chan Daniel Siu-Hung
Published: February 2009

A solution-processable functional polyimide (PYTPA-PI), containing triphenylamine-substituted diphenylpyridine moieties (PYTPA, electron donors) and phthalimide moieties (PI, electron acceptors), was synthesized. The copolymer exhibits a high glass transition temperature of 342 °C. A switching device, based on a solution-cast thin film of PYTPA-PI sandwiched between an indium-tin oxide (ITO) bottom electrode and an Al top electrode, exhibits two accessible conductivity states and can be switched from the low-conductivity (OFF) state to the high-conductivity (ON) state, with an ON/OFF current ratio of more than 103, at the threshold voltage of about 2.7 V. The ON state is volatile and relaxes readily to the OFF state. However, it can be electrically sustained by a refreshing voltage pulse of 2 V. The ON state can also be reset to the initial OFF state by a reverse bias of −0.9 V. The ability to write, erase, read, and refresh the electrical states fulfills the functionality of a dynamic random access memory. The electronic transitions and transport mechanisms associated with the memory effect were elucidated from molecular simulation. In comparison with that of other functional polyimides, the electrical switching performance in PYTPA-PI illustrates the possibility of tuning memory properties in imide polymers via molecular design and synthesis.
Critical turbulent energy reductions in plasmas using weak magnetic fields
Authors: Raynor Chavis T. , Mezonlin Ephrem D. , Johnson Joseph A.
Published: February 2009

With an arc-driven shock tube, laser induced fluorescence, and a multipoint density diagnostic technique, we study the turbulence behind an ionizing shock wave in the presence of a magnetic field. The magnetic field is directed either parallel to or antiparallel to the direction of the shock wave’s propagation, and is configured in such a way as to couple with turbulent velocity fluctuations in the plane perpendicular to the direction of flow. We find that the magnetic field can be used to reduce the turbulent energy in a plasma system. Further, when the evolution to turbulence is treated as a second-order phase transformation, the critical turbulent energy decreases with increasing magnetic field.
Determination of the mobility gap of intrinsic μc-Si:H in p-i-n solar cells
Authors: Pieters B. E. , Stiebig H. , Zeman M. , van Swaaij R. A. C. M. M.
Published: February 2009

Microcrystalline silicon (μc-Si:H) is a promising material for application in multijunction thin-film solar cells. A detailed analysis of the optoelectronic properties is impeded by its complex microstructural properties. In this work we will focus on determining the mobility gap of μc-Si:H material. Commonly a value of 1.1eV is found, similar to the bandgap of crystalline silicon. However, in other studies mobility gap values have been reported to be in the range of 1.48–1.59eV, depending on crystalline volume fraction. Indeed, for the accurate modeling of μc-Si:H solar cells, it is paramount that key parameters such as the mobility gap are accurately determined. A method is presented to determine the mobility gap of the intrinsic layer in a p-i-n device from the voltage-dependent dark current activation energy. We thus determined a value of 1.19eV for the mobility gap of the intrinsic layer of an μc-Si:H p-i-n device. We analyze the obtained results in detail through numerical simulations of the μc-Si:H p-i-n device. The applicability of the method for other than the investigated devices is discussed with the aid of numerical simulations.
Ultrafast optical probes of polaron dynamics in La0.7Ca0.3MnO3 thin films
Authors: Wu K. H. , Hsu T. Y. , Shih H. C. , Chen Y. J. , Luo C. W. , Uen T. M. , Lin J.-Y. , Juang J. Y. , Kobayashi T.
Published: February 2009

In this work, we use ultrafast optical pump-optical probe spectroscopy to probe the polaron dynamics in La0.7Ca0.3MnO3 (LCMO) thin films. The temporal evolution in transient reflectivity change ΔR/R exhibits two relaxing components: a fast component with a time constant of subpicosecond and a slow component with time constant ranging from tens of picoseconds to hundreds of picoseconds. The amplitude of the fast component, though has been seldom discussed before, exhibits the similar temperature dependence with that of the resistivity and the neutron scattering intensity due to nanoscale correlated polarons. The results strongly suggest that the fast photoinduced reflectivity change may have been due to the photoexcitation and trapping process of correlated Jahn–Teller polarons in the paramagnetic and ferromagnetic phases and, thus, implies the presence of electronic inhomogeneity in LCMO manganites.