bluuebunny/crossref_metadata_2025 huggingface dataset:
Contaminant sequestration in karstic aquifers: Experiments and quantification
Authors: Li Guangquan , Loper David E. , Kung Robin
Published: February 2008

A karstic aquifer typically has significant secondary porosity consisting of an interconnected system of caves or conduits. Conduit‐borne contaminants can enter the contiguous limestone matrix, remain inside for a longer time than in the conduit, and subsequently be flushed out. This retention or sequestration can significantly influence the fate of contaminants within the aquifer and alter the shape of the breakthrough curve. The mechanisms involved in sequestration have been identified and quantified by analysis of the breakthrough curves generated by a set of laboratory experiments in which a conduit, porous limestone matrix, and conservative contaminant were simulated by a porous‐walled pipe, chamber of closely packed glass beads, and salt, respectively. Experiments were conducted with both active and passive transfer of water between conduit and matrix, simulating differing hydrogeologic regimes. In active transfer the primary control parameter is the volume of water transferred; sequestration is primarily due to advection with the effects of diffusion and dispersion being minimal. In passive transfer the control parameters are the conduit Reynolds number and the duration that contaminant resides in the conduit; sequestration is caused by the combined effects of the conduit pressure drop, pressure variation due to bedform, and diffusion. Active and passive transfer can be unified by analyzing the ratio of the scale of pressure variation to the conduit length. In accordance with the resolved mechanisms a variety of models have been constructed to recover solute distributions in the matrix and to regenerate breakthrough curves. These analyses and models provide a potential approach to investigate contaminant migration in karstic aquifers.
Observations of the trade wind wakes of Kauai and Oahu
Authors: Yang Yang , Ma Jian , Xie Shang‐Ping
Published: February 2008

The Hawaiian islands of Kauai and Oahu stand in the path of the east‐northeasterly trade winds, creating wakes in the lee. For the first time, the structure of the wakes and their diurnal cycle were observed on a cruise during 18–20 December 2006. The dynamic wakes, characterized by reduced trades, extend about 1 km in height with strong wind shear at the top. Thermal forcing of these small islands also affects the wake circulations. Sea breezes develop in the afternoon turning the winds into westerly near the shore in the wakes. At night, land breezes advect cool air from the islands, creating a shallow cool layer between the sea surface and a capping inversion. The warming in the wake in the afternoon extends much deeper (1.4 km) than the cool layer (0.5 km) at night. The effect of diurnal changes on cloud formation in the wakes is discussed, and the sharp variations in wind velocity lee of the islands may affect ocean currents, waves and mixing.
The critical solar wind pressure for IMF penetration into the Venus ionosphere
Authors: Jin H. , Maezawa K. , Mukai T.
Published: February 2008

Early observations and simulations have revealed that the occurrence of IMF penetration into the Venus ionosphere depends on the upstream solar wind pressure, and that IMF is transported into the ionosphere by the downward convection when the solar wind dynamic pressure is relatively large. In this paper, we investigated the critical solar wind pressure for the IMF penetration, by using a two‐dimensional global MHD model. The simulations showed that variations in the upstream solar wind pressure (PSW) affect plasma dynamics and chemistry in the subsolar ionosphere. The chemical plasma loss rate increases as PSW increases, and the amount of plasma loss exceeds that of plasma production when PSW exceeds a certain critical level (Pcrtc). On this occasion, the plasma convection in the ionosphere connects to the solar wind flow, and as a result the connected downward convection transports IMF into the ionosphere. The simulations also showed that IMF penetration occurs only when PSW exceeds Pcrtc, even if the solar wind pressure changes abruptly. The critical pressure is not necessarily equal to the ionospheric peak thermal pressure (Ppeak). Our simulations suggested that Pcrtc is smaller than Ppeak.
Beryllium isotopes in central Arctic Ocean sediments over the past 12.3 million years: Stratigraphic and paleoclimatic implications
Authors: Frank Martin , Backman Jan , Jakobsson Martin , Moran Kate , O'Regan Matthew , King John , Haley Brian A. , Kubik Peter W. , Garbe‐Schönberg Dieter
Published: February 2008

The upper 200 m of the sediments recovered during IODP Leg 302, the Arctic Coring Expedition (ACEX), to the Lomonosov Ridge in the central Arctic Ocean consist almost exclusively of detrital material. The scarcity of biostratigraphic markers severely complicates the establishment of a reliable chronostratigraphic framework for these sediments, which contain the first continuous record of the Neogene environmental and climatic evolution of the Arctic region. Here we present profiles of cosmogenic 10Be together with the seawater‐derived fraction of stable 9Be obtained from the ACEX cores. The down‐core decrease of 10Be/9Be provides an average sedimentation rate of 14.5 ± 1 m/Ma for the uppermost 151 m of the ACEX record and allows the establishment of a chronostratigraphy for the past 12.3 Ma. The age‐corrected 10Be concentrations and 10Be/9Be ratios suggest the existence of an essentially continuous sea ice cover over the past 12.3 Ma.
Modeling biogeochemical processes in subterranean estuaries: Effect of flow dynamics and redox conditions on submarine groundwater discharge of nutrients
Authors: Spiteri Claudette , Slomp Caroline P. , Tuncay Kagan , Meile Christof
Published: February 2008

A two‐dimensional density‐dependent reactive transport model, which couples groundwater flow and biogeochemical reactions, is used to investigate the fate of nutrients (NO3−, NH4+, and PO4) in idealized subterranean estuaries representing four end‐members of oxic/anoxic aquifer and seawater redox conditions. Results from the simplified model representations show that the prevalent flow characteristics and redox conditions in the freshwater‐seawater mixing zone determine the extent of nutrient removal and the input of nitrogen and phosphorus to coastal waters. At low to moderate groundwater velocities, simultaneous nitrification and denitrification can lead to a reversal in the depth of freshwater NO3− and NH4+‐PO4 plumes, compared to their original positions at the landward source. Model results suggest that autotrophic denitrification pathways with Fe2+ or FeS2 may provide an important, often overlooked link between nitrogen and phosphorus biogeochemistry through the precipitation of iron oxides and subsequent binding of phosphorus. Simulations also highlight that deviations of nutrient data from conservative mixing curves do not necessarily indicate nutrient removal.
Simulation assessment of the direct‐push permeameter for characterizing vertical variations in hydraulic conductivity
Authors: Liu Gaisheng , Bohling Geoffrey C. , Butler James J.
Published: February 2008

The direct‐push permeameter (DPP) is a tool for the in situ characterization of hydraulic conductivity (K) in shallow, unconsolidated formations. This device, which consists of a short screened section with a pair of pressure transducers near the screen, is advanced into the subsurface with direct‐push technology. K is determined through a series of injection tests conducted between advancements. Recent field work by Butler et al. (2007) has shown that the DPP holds great potential for describing vertical variations in K at an unprecedented level of detail, accuracy and speed. In this paper, the fundamental efficacy of the DPP is evaluated through a series of numerical simulations. These simulations demonstrate that the DPP can provide accurate K information under conditions commonly faced in the field. A single DPP test provides an effective K for the domain immediately surrounding the interval between the injection screen and the most distant pressure transducer. Features that are thinner than that interval can be quantified by reducing the vertical distance between successive tests and analyzing the data from all tests simultaneously. A particular advantage of the DPP is that, unlike most other single borehole techniques, a low‐K skin or a clogged screen has a minimal impact on the K estimate. In addition, the requirement that only steady‐shape conditions be attained allows for a dramatic reduction in the time required for each injection test.
The influence of climate on root depth: A carbon cost‐benefit analysis
Authors: Guswa A. J.
Published: February 2008

The depth of the active root zone identifies the portion of the subsurface that exchanges soil water with the atmosphere. The depth of this zone is determined by a number of factors, and this work focuses on the drivers related to water and climate. An analytical expression for a water‐optimal root depth is developed by equating the marginal carbon cost and benefit of deeper roots. Soil‐moisture dynamics are driven by stochastic rainfall, and the predicted root depth is a function climate, soil, and vegetation characteristics. Consistent with results from the field, deep roots coincide with environments for which precipitation and potential evapotranspiration are approximately equal. For water‐limited ecosystems, increases in the wetness of the climate produce deeper roots, and root depth is more sensitive to changes in the depth of rain events than to their frequency. In wet environments, the opposite is true; root depth generally decreases with increasing wetness and shows greater sensitivity to changes in rainfall frequency than intensity.
Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community
Authors: Jeans Chris , Singer Steven W , Chan Clara S , VerBerkmoes Nathan C , Shah Manesh , Hettich Robert L , Banfield Jillian F , Thelen Michael P
Published: February 2008

Recently, there has been intense interest in the role of electron transfer by microbial communities in biogeochemical systems. We examined the process of iron oxidation by microbial biofilms in one of the most extreme environments on earth, where the inhabited water is pH 0.5–1.2 and laden with toxic metals. To approach the mechanism of Fe(II) oxidation as a means of cellular energy acquisition, we isolated proteins from natural samples and found a conspicuous and novel cytochrome, Cyt572, which is unlike any known cytochrome. Both the character of its covalently bound prosthetic heme group and protein sequence are unusual. Extraction of proteins directly from environmental biofilm samples followed by membrane fractionation, detergent solubilization and gel filtration chromatography resulted in the purification of an abundant yellow-red protein. The purified protein has a cytochrome c-type heme binding motif, CxxCH, but a unique spectral signature at 572 nm, and thus is called Cyt572. It readily oxidizes Fe2+ in the physiologically relevant acidic regime, from pH 0.95–3.4. Other physical characteristics are indicative of a membrane-bound multimeric protein. Circular dichroism spectroscopy indicates that the protein is largely beta-stranded, and 2D Blue-Native polyacrylamide gel electrophoresis and chemical crosslinking independently point to a multi-subunit structure for Cyt572. By analyzing environmental genomic information from biofilms in several distinctly different mine locations, we found multiple genetic variants of Cyt572. MS proteomics of extracts from these biofilms substantiated the prevalence of these variants in the ecosystem. Due to its abundance, cellular location and Fe2+ oxidation activity at very low pH, we propose that Cyt572 provides a critical function for fitness within the ecological niche of these acidophilic microbial communities.
Self‐efficacy and Dietary Fat Reduction Behaviors in Obese African‐American and White Mothers
Authors: Chang Mei‐Wei , Brown Roger L. , Baumann Linda J. , Nitzke Susan A.
Published: February 2008

This study examined the influence of weight management and education on five types of fat reduction behaviors mediated through three task‐specific domains of self‐efficacy among young, low‐income obese African‐American and white mothers. It also investigated interaction of race with the relationships between weight management, education, self‐efficacy, and fat reduction behaviors. A sample of obese African‐American and white mothers was recruited from the Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) in Wisconsin. Participants reported their weight management status, education, self‐efficacy for eating low‐fat food, and fat reduction behaviors. For both racial groups, weight management status predicted low‐fat food substitution and meat modification behaviors; education predicted meat modification behavior. Three task‐specific domains of self‐efficacy (negative mood, positive mood, and food availability) predicted different types of fat reduction behaviors and differed by race. Weight management influenced behaviors of low‐fat food substitution, meat modification, and fried‐food avoidance, mediated partially through self‐efficacies of negative mood (African Americans), positive mood (African Americans, whites), and food availability (African Americans). Race affected the relationships between weight management, education, three task‐specific domains of self‐efficacy, and five types of fat reduction behaviors. Self‐efficacies operated differentially for African Americans and whites. Thus, strategies to address specific fat reduction behaviors have the potential to be more effective when tailored to specific individual characteristics such as racial background, history of weightmanagement strategies and task‐specific domains of self‐efficacy.
Herpesvirus saimiri transformation may help disclose inherent functional defects of mucosal T lymphocytes in patients with gastric adenocarcinoma
Authors: Valeri Anna P , Aguilera‐Montilla Noemí , López‐Santalla Mercedes , Mencía Ángeles , Rodríguez‐Juan Cristina , Gutiérrez‐Calvo Alberto , Martín Javer , Lasa Inmaculada , García‐Sancho Luis , Granell Javier , Pérez‐Blas Mercedes , Martín‐Villa José M
Published: February 2008

To dissect the phenotypic and functional features of mucosal T lymphocytes in patients with gastric adenocarcinoma, we have used the Herpesvirus saimiri transformation procedure to achieve T‐cell lines from gastric origin. Once achieved, cell function was assessed by in vitro stimulation with mitogens. CD2‐specific monoclonal antibodies (α‐CD2), alone or in combination with interleukin (IL)‐2, rendered fewer counts in patients (34 408±3965 and 52 157±6473 c.p.m., respectively) than in controls (67 471±11 755 c.p.m., P<0.01 and 77 864±12 545 c.p.m., P<0.05, respectively). Likewise, CD3‐based responses were defective in cancer cell lines: α‐CD3 (54 794±9269 vs 86 104±10 341 c.p.m., P<0.01), α‐CD3+IL‐2 (57 789±8590 vs 88855±8516 c.p.m., P<0.01) and α‐CD3+α‐CD2 (52 130±7559 vs 120 852±16 552 c.p.m., P<0.01). Finally, IL‐2 failed to adequately stimulate patient cell lines (39 310±4023 vs 60 945±9463 c.p.m., P<0.05). These results suggest that mucosal T lymphocytes in cancer patients are inherently impaired in their proliferative ability. This may be crucial in the control of tumour growth.
Shh and forebrain evolution in the blind cavefish Astyanax mexicanus
Authors: Rétaux Sylvie , Pottin Karen , Alunni Alessandro
Published: February 2008

The blind cavefish and its surface counterpart of the teleost species Astyanax mexicanus constitute an excellent model to study the evolution of morphological features. During adaptation to their lives in perpetual darkness, the cave population has lost eyes (and pigmentation), but has gained several constructive traits. Recently, the demonstration that an increase in Shh (Sonic Hedgehog) midline signalling was indirectly responsible for the loss of eyes in cavefish led to new ways to search for possible modifications in the forebrain of these cavefish, as this anterior‐most region of the vertebrate central nervous system develops under close control of the powerful Shh morphogen. In this review, we summarize the recent progress in the understanding of forebrain and eye modifications in cavefish. These include major changes in cell death, cell proliferation and cell migration in various parts of the forebrain when compared with their surface counterparts with eyes. The outcome of these modifications, in terms of neuronal circuitry, morphological and behavioral adaptations are discussed.
Presence of aquaporin and V‐ATPase on the contractile vacuole of Amoeba proteus
Authors: Nishihara Eri , Yokota Etsuo , Tazaki Akira , Orii Hidefumi , Katsuhara Maki , Kataoka Kensuke , Igarashi Hisako , Moriyama Yoshinori , Shimmen Teruo , Sonobe Seiji
Published: February 2008

Background information. The results of water permeability measurements suggest the presence of an AQP (aquaporin) in the membrane of the CV (contractile vacuole) in Amoeba proteus [Nishihara, Shimmen and Sonobe (2004) Cell Struct. Funct. 29, 85–90].

Results. In the present study, we cloned an AQP gene from A. proteus [ApAQP (A. proteus AQP)] that encodes a 295‐amino‐acid protein. The protein has six putative TMs (transmembrane domains) and two NPA (Asn‐Pro‐Ala) motifs, which are conserved among various AQPs and are thought to be involved in the formation of water channels that span the lipid bilayer. Using Xenopus oocytes, we have demonstrated that the ApAQP protein product can function as a water channel. Immunofluorescence microscopy with anti‐ApAQP antibody revealed that ApAQP is detected on the CV membrane and on the vesicles around the CV. The presence of V‐ATPase (vacuolar H+‐ATPase) on the vesicle membrane around the CV was also detected.

Conclusions. Our data on ApAQP allow us to provide the first informed explanation of the high water permeability of the CV membrane in amoeba. Moreover, the results suggest that vesicles possessing V‐ATPase are involved in generating an osmotic gradient. Based on our findings, we propose a new hypothesis for the mechanism of CV function.
Identification and characterization of theArabidopsisgene encoding the tetrapyrrole biosynthesis enzyme uroporphyrinogen III synthase
Authors: Tan Fui-Ching , Cheng Qi , Saha Kaushik , Heinemann Ilka U. , Jahn Martina , Jahn Dieter , Smith Alison G.
Published: February 2008

UROS (uroporphyrinogen III synthase; EC 4.2.1.75) is the enzyme responsible for the formation of uroporphyrinogen III, the precursor of all cellular tetrapyrroles including haem, chlorophyll and bilins. Although UROS genes have been cloned from many organisms, the level of sequence conservation between them is low, making sequence similarity searches difficult. As an alternative approach to identify the UROS gene from plants, we used functional complementation, since this does not require conservation of primary sequence. A mutant of Saccharomyces cerevisiae was constructed in which the HEM4 gene encoding UROS was deleted. This mutant was transformed with an Arabidopsis thaliana cDNA library in a yeast expression vector and two colonies were obtained that could grow in the absence of haem. The rescuing plasmids encoded an ORF (open reading frame) of 321 amino acids which, when subcloned into an Escherichia coli expression vector, was able to complement an E. coli hemD mutant defective in UROS. Final proof that the ORF encoded UROS came from the fact that the recombinant protein expressed with an N-terminal histidine-tag was found to have UROS activity. Comparison of the sequence of AtUROS (A. thaliana UROS) with the human enzyme found that the seven invariant residues previously identified were conserved, including three shown to be important for enzyme activity. Furthermore, a structure-based homology search of the protein database with AtUROS identified the human crystal structure. AtUROS has an N-terminal extension compared with orthologues from other organisms, suggesting that this might act as a targeting sequence. The precursor protein of 34 kDa translated in vitro was imported into isolated chloroplasts and processed to the mature size of 29 kDa. Confocal microscopy of plant cells transiently expressing a fusion protein of AtUROS with GFP (green fluorescent protein) confirmed that AtUROS was targeted exclusively to chloroplasts in vivo.
The C-terminus of the transmembrane mucin MUC17 binds to the scaffold protein PDZK1 that stably localizes it to the enterocyte apical membrane in the small intestine
Authors: Malmberg Emily K. , Pelaseyed Thaher , Petersson Åsa C. , Seidler Ursula E. , De Jonge Hugo , Riordan John R. , Hansson Gunnar C.
Published: February 2008

The membrane-bound mucins have a heavily O-glycosylated extracellular domain, a single-pass membrane domain and a short cytoplasmic tail. Three of the membrane-bound mucins, MUC3, MUC12 and MUC17, are clustered on chromosome 7 and found in the gastrointestinal tract. These mucins have C-terminal sequences typical of PDZ-domain-binding proteins. To identify PDZ proteins that are able to interact with the mucins, we screened PDZ domain arrays using YFP (yellow fluorescent protein)-tagged proteins. MUC17 exhibited a strong binding to PDZK1 (PDZ domain containing 1), whereas the binding to NHERF1 (Na+/H+-exchanger regulatory factor 1) was weak. Furthermore, we showed weak binding of MUC12 to PDZK1, NHERF1 and NHERF2. GST (glutathione transferase) pull-down experiments confirmed that the C-terminal tail of MUC17 co-precipitates with the scaffold protein PDZK1 as identified by MS. This was mediated through the C-terminal PDZ-interaction site in MUC17, which was capable of binding to three of the four PDZ domains in PDZK1. Immunostaining of wild-type or Pdzk1−/− mouse jejunum with an antiserum against Muc3(17), the mouse orthologue of human MUC17, revealed strong brush-border membrane staining in the wild-type mice compared with an intracellular Muc3(17) staining in the Pdzk1−/− mice. This suggests that Pdzk1 plays a specific role in stabilizing Muc3(17) in the apical membrane of small intestinal enterocytes.
Functional asymmetry in cohesin binding belies inherent symmetry of the dockerin module: insight into cellulosome assembly revealed by systematic mutagenesis
Authors: Karpol Alon , Barak Yoav , Lamed Raphael , Shoham Yuval , Bayer Edward A.
Published: February 2008

The cellulosome is an intricate multi-enzyme complex, known for its efficient degradation of recalcitrant cellulosic substrates. Its supramolecular architecture is determined by the high-affinity intermodular cohesin–dockerin interaction. The dockerin module comprises a calcium-binding, duplicated ‘F-hand’ loop–helix motif that bears striking similarity to the EF-hand loop–helix–loop motif of eukaryotic calcium-binding proteins. In the present study, we demonstrate by progressive truncation and alanine scanning of a representative type-I dockerin module from Clostridium thermocellum, that only one of the repeated motifs is critical for high-affinity cohesin binding. The results suggest that the near-symmetry in sequence and structure of the repeated elements of the dockerin is not essential to cohesin binding. The first calcium-binding loop can be deleted entirely, with almost full retention of binding. Likewise, significant deletion of the second repeated segment can be achieved, provided that its calcium-binding loop remains intact. Essentially the same conclusion was verified by systematically mutating the highly conserved residues in the calcium-binding loop. Mutations in one of the calcium-binding loops failed to disrupt cohesin recognition and binding, whereas a single mutation in both loops served to reduce the affinity significantly. The results are mutually compatible with recent crystal structures of the type-I cohesin–dockerin heterodimer, which demonstrate that the dockerin can bind in an equivalent manner to its cohesin counterpart through either its first or second repeated motif. The observed plasticity in cohesin–dockerin binding may facilitate cellulosome assembly in vivo or, alternatively, provide a conformational switch that promotes access of the tethered cellulosomal enzymes to their polysaccharide substrates.
Localization of PKA phosphorylation site, Ser2030, in the three-dimensional structure of cardiac ryanodine receptor
Authors: Jones Peter P. , Meng Xing , Xiao Bailong , Cai Shitian , Bolstad Jeff , Wagenknecht Terence , Liu Zheng , Chen S. R. Wayne
Published: February 2008

PKA (protein kinase A)-dependent phosphorylation of the cardiac Ca2+-release channel/RyR2 (type 2 ryanodine receptor) is believed to directly dissociate FKBP12.6 (12.6 kDa FK506-binding protein) from the channel, causing abnormal channel activation and Ca2+ release. To gain insight into the structural basis of the regulation of RyR2 by PKA, we determined the three-dimensional location of the PKA site Ser2030. GFP (green fluorescent protein) was inserted into RyR2-wt (wild-type RyR2) and RyR2 mutant, A4860G, after Thr2023. The resultant GFP–RyR2 fusion proteins, RyR2T2023-GFP and RyR2(A4860G)T2023-GFP, were expressed in HEK-293 (human embryonic kidney) cells and functionally characterized. Ca2+-release assays revealed that both GFP–RyR2 fusion proteins formed caffeine- and ryanodine-sensitive Ca2+-release channels. Further analyses using [3H]ryanodine binding demonstrated that the insertion of GFP into RyR2-wt after Thr2023 reduced the sensitivity of the channel to activation by Ca2+ or caffeine. RyR2(A4860G)T2023-GFP was found to be structurally more stable than RyR2T2023-GFP and was subsequently used as a basis for three-dimensional reconstruction. Cryo-electron microscopy and single particle image processing of the purified RyR2(A4860G)T2023-GFP protein revealed the location of the inserted GFP, and hence the Ser2030 PKA site in domain 4, a region that may be involved in signal transduction between the transmembrane and cytoplasmic domains. Like the Ser2808 PKA site reported previously, the Ser2030 site is not located close to the FKBP12.6-binding site mapped previously, indicating that neither of these PKA sites is directly involved in FKBP12.6 binding. On the basis of the three-dimensional localizations of a number of residues or regions, a model for the subunit organization in the structure of RyR2 is proposed.
EmbR2, a structural homologue of EmbR, inhibits theMycobacterium tuberculosiskinase/substrate pair PknH/EmbR
Authors: Molle Virginie , Reynolds Robert C. , Alderwick Luke J. , Besra Gurdyal S. , Cozzone Alain J. , Fütterer Klaus , Kremer Laurent
Published: February 2008

EmbR is a transcriptional regulator that is phosphorylated by the cognate mycobacterial STPK (serine/threonine protein kinase) PknH. Recent studies demonstrated that PknH-dependent phosphorylation of EmbR enhances its DNA-binding activity and activates the transcription of the embCAB genes encoding arabinosyltransferases, which participate in arabinan biosynthesis. In the present study, we identified a genomic region of 4425 bp, which is present in Mycobacterium tuberculosis CDC1551, but absent from M. tuberculosis H37Rv, comprising the MT3428 gene, which is homologous with embR. Homology modelling of the MT3428 gene product illustrated its close relationship (56% identity) to EmbR, and it was hence termed EmbR2. In marked contrast with EmbR, EmbR2 was not phosphorylated by PknH, although it is a substrate of other M. tuberculosis kinases, including PknE and PknF. Tryptophan fluorescence emission of EmbR2 was monitored in the presence of three different PknH-derived phosphopeptides and demonstrated that EmbR2 binds to at least two of the threonine sites known to undergo autophosphorylation in PknH. We observed that the capacity of EmbR2 to interact physically with PknH without being phosphorylated was a result of EmbR2-mediated inhibition of kinase activity: incubation of PknH with increasing concentrations of EmbR2 led to a dose–response inhibition of the autokinase activity, similarly to O6-cyclohexylmethylguanine, a known inhibitor of eukaryotic cyclin-dependent kinases. Moreover, EmbR2 inhibited PknH-dependent phosphorylation of EmbR in a dose-dependent manner. Together, these results suggest that EmbR2 is a regulator of PknH activation, thus directly participating in the control of the PknH/EmbR pair and potentially in mycobacterial physiology/virulence of M. tuberculosis CDC1551.
Spatial structure of electric potential near the extraction region in Cs-seeded H− ion sources
Authors: Fukano A. , Hanatani J. , Matsumiya T. , Hatayama A.
Published: February 2008

Structure of electric potential near the extraction region in a negative ion source is investigated analytically with the effect of strong surface H− production. The potential profile is analyzed one dimensional by solving the plasma-sheath equation, which gives the electric potential in the plasma region and the sheath region near the wall self-consistently. The potential profile depends on the production rate and the temperature of negative ions. As the production rate becomes large and the negative ion energy becomes small, the potential near the extraction region decreases. The negative potential peak is formed near the plasma grid (PG) surface for the case of large amount and low energy surface production. As a result, negative ions are reflected by this negative potential peak near the PG and returned to the PG surface. This reflection mechanism by the negative potential peak possibly affects the negative ion extraction.
Status of the heavy ion beam probe system in the Large Helical Device
Authors: Nishiura M. , Ido T. , Shimizu A. , Nakano H. , Kato T. , Kato S. , Hamada Y. ,   LHD Experimental Group, Shevelko V. P. , Janev R. K. , Wada M.
Published: February 2008

A heavy ion beam probe (HIBP) system has been installed into the Large Helical Device (LHD) to measure the spatial profile of the plasma potential and density fluctuations. The optimization of the HIBP system, especially the beam injector, is described. The negative ion beam is required for the MeV beam production in a tandem accelerator. A sputter-type heavy negative ion source has been developed as an intense Au− beam source to produce Au+ beams with energy in the MeV range. The extraction electrodes and the Einzel lens system of the ion source have been designed taking into account the beam optics, and installed into the real machine. Throughout the plasma diagnostics on LHD experiments, the consumptions of vaporized caesium and gold target are being characterized for practical operations. In addition, the experimental charge fractions are compared with the theoretical fractions for understanding the charge-changing behavior of Au− ions and optimizing the fraction of Au+ ions at the exit of the tandem accelerator of the HIBP system.
Laser generation of Au ions with charge states above 50+
Authors: Láska L. , Jungwirth K. , Krása J. , Krouský E. , Rohlena K. , Skála J. , Velyhan A. , Margarone D. , Torrisi L. , Ryć L. , Ullschmied J.
Published: February 2008

Results of recent studies on highly charged Au ion generation, using the intense long pulses of the PALS high power iodine laser (λ=1.315μm, EL=800J∕400ps), operating under variable experimental conditions (1ω, 3ω, varying target thickness and changing focus positions), are presented. Both the ion collectors and the ion electrostatic analyzers were applied for the identification of ions in a large distance from the target. The time-of-flight collector signals were treated by a means of peak deconvolution assuming a shifted Maxwell-Boltzmann form of the constituent ion current peaks. Attention was paid to the influence of pulse precursor, which becomes evident, especially, if using thinner targets and 1ω. The results for 3ω point to the presence of several groups of ions with the highest recorded charge state Au53+.
Generation of space charge compensated low energy ion flux
Authors: Vizir A. V. , Shandrikov M. V. , Oks E. M.
Published: February 2008

The results of an experimental study of low-energy (<200eV) ion flux generation with space charge neutralization are presented. Argon was used as a working gas. The working gas pressure in the vacuum chamber was 2–4×10−2Pa. Ion beam was extracted from the hollow cathode of main discharge plasma by a single mesh extractor with subsequent deceleration of ions to a required energy in a layer between the mesh and the beam plasma. The ion beam current was measured on the collector located on the distance of 30–60cm from the discharge system. The penetration of electron component from the main discharge plasma through the mesh into the region of the ion beam drift space was realized by potential barrier reduction, in conditions of the optimal extractor potential with respect to the hollow cathode. The space charge neutralization of low-energy ion beam resulted in drift space plasma potential reduction and ion beam current growth. At the main discharge current of 1A and main discharge voltage of 300V, the ion beam current of up to 100mA with the ion energy of 50–150eV was obtained.
Electrode structures in diode-type cadmium telluride detectors: Field emission scanning electron microscopy and energy-dispersive x-ray microanalysis
Authors: Okada Kyoko , Yasufuku Hideyuki , Yoshikawa Hideki , Sakurai Yoshiharu
Published: February 2008

The structures of the interface regions between CdTe crystal and electrodes in diode-type CdTe x-ray detectors with a layout of In(anode)∕CdTe∕Pt(cathode) are reported. The structures have been investigated by field emission scanning electron microscopy and energy-dispersive x-ray microanalysis. The investigation has revealed that the structures are complicated. The anode-side interface is a contact between In1−xTex alloys and CdTe crystal. The cathode side is a structure of Pt∕(Te-richphase)∕CdTe. These findings suggest that the complicated structures in the interface regions are a possible cause for the polarization phenomenon observed in the diode-type CdTe detectors.
Density matrix purification with rigorous error control
Authors: Rubensson Emanuel H. , Rudberg Elias , Sałek Paweł
Published: February 2008

Density matrix purification, although being a powerful tool for linear scaling construction of the density matrix in electronic structure calculations, has been limited by uncontrolled error accumulation. In this article, a strategy for the removal of small matrix elements in density matrix purification is proposed with which the forward error can be rigorously controlled. The total forward error is separated into two parts, the error in eigenvalues and the error in the occupied invariant subspace. We use the concept of canonical angles to measure and control differences between exact and approximate occupied subspaces. We also analyze the conditioning of the density matrix construction problem and propose a method for calculation of interior eigenvalues to be used together with density matrix purification.
Fast electron correlation methods for molecular clusters without basis set superposition errors
Authors: Kamiya Muneaki , Hirata So , Valiev Marat
Published: February 2008

Two critical extensions to our fast, accurate, and easy-to-implement binary or ternary interaction method for weakly interacting molecular clusters [S. Hirata et al., Mol. Phys. 103, 2255 (2005)] have been proposed, implemented, and applied to water hexamers, hydrogen fluoride chains and rings, and neutral and zwitterionic glycine-water clusters with an excellent initial performance assessment result. Our original method included up to two- or three-body Coulomb, exchange, and correlation energies exactly and higher-order Coulomb energies in the dipole-dipole interaction approximation. In this work, the dipole moments are replaced by atom-centered point charges determined so that they reproduce the electrostatic potentials of the cluster subunits accurately and also self-consistently with one another in the cluster environment. They have been shown to lead to a dramatic improvement in the description of short-range electrostatic potentials not only of large, charge-separated subunits such as zwitterionic glycine but also of small subunits. Furthermore, basis set superposition errors (BSSEs) have been eliminated by combining the Valiron–Mayer function counterpoise (VMFC) correction with our binary or ternary interaction method. A new BSSE-correction scheme has been proposed on this basis, wherein three-body and all higher-order Coulomb effects on BSSE are also estimated. The BSSE-corrected ternary interaction method with atom-centered point charges reproduces the VMFC-corrected results within 0.1kcal∕mol. The proposed method is not only more efficient but also significantly more accurate than conventional correlation methods uncorrected of BSSE.
Electronic and magnetic properties of endohedrally doped fullerene Mn@C60: A total energy study
Authors: Li Guangping , Sabirianov R. F. , Lu Jing , Zeng X. C. , Mei W. N.
Published: February 2008

We perform total energy calculations on a manganese atom encapsulated inside a C60 cage using density functional theory with the generalized gradient approximation through three optimization schemes and along four paths inside the cage. We find that when Mn is located in the central region, its electronic and magnetic properties are not exactly the same as those of a free Mn atom due to weak coupling between Mn and the cage. As Mn is shifted toward to the edge, the total energy and spin start to change significantly when Mn is situated about one-third of the way between the cage center and edge, and the total energy reaches a local minimum. Finally the interaction between Mn and the cage turns repulsive as Mn approaches the edge. We also find that, along the lowest energy path, there exist three consecutive local energy minima and each of these has a different spin M. The ground state has the lowest M=3, Mn is located about 1.6Å away from the cage center, and the binding energy is 0.08eV. We attribute the decrease in total energy and spin to Mn and C hybridization.
Conformational and phase transformations of chlorocyclohexane at high pressures by Raman spectroscopy
Authors: Dong Zhaohui , Beilby Nicholas G. , Huang Yining , Song Yang
Published: February 2008

Pressure induced conformational and phase transformations of chlorocyclohexane (CCH) were investigated in a diamond anvil cell by Raman spectroscopy at room temperature. Pure CCH was compressed up to 20GPa and then decompressed to ambient pressure. The conformational equilibrium was shifted by pressure from equatorial to axial conformers in the fluid phase below 0.7GPa, consistent with previous observations. Upon further compression, several solid-to-solid phase transitions were identified by the observation of markedly different Raman patterns as well as different pressure dependences of characteristic Raman modes. The possible structures of these phases were analyzed in correlation with previously observed solid phases at low temperatures. Finally, CCH exhibits pressure hysteresis and partial reversibility upon decompression which result in the formation of the phases with different Raman patterns from those obtained upon compression. The difference can be interpreted as conformational contribution as well as the intrinsic plasticity of CCH crystals.
Production of U beam from RIKEN 18GHz electron cyclotron resonance ion source
Authors: Higurashi Y. , Nakagawa T. , Kidera M. , Haba H. , Aihara T. , Kase M. , Goto A. , Yano Y.
Published: February 2008

For the RIKEN radio isotope factory (RIBF) project, we produced the multicharged uranium beam with two methods. To produce lower charge state U ion beams (14+–20+) we used the UF6 gas as an ionized gas. The typical beam intensity of U14+–20+ was 2–1particleμA at the extraction voltage of 14kV. To produce higher charge state U ion beam (U35+), we chose the sputtering method. The beam intensity was 70particlenA at the extraction voltage of 5.4kV. Using this method, we successfully produced multicharged U beam continuously for one month without break for RIBF commissioning.
Beam formation by ion optical system with slit finite length apertures
Authors: Davydenko V. I. , Ivanov A. A. , Shikhovtsev I. V. , Sorokin A. V. , Uhlemann R.
Published: February 2008

Ion beam formation by four-electrode ion optical system with slit finite length apertures is considered. Results of numerical simulations by two and three dimensional codes shown that accurate ion beam formation in slit aperture with semicircular ends can be provided. In experimental studies of beam formation in single slit ion optical system angular beam divergences of 0.53° across the slit and 0.35° along it were measured. Studied slit ion optical system will be used for ion beam formation in diagnostic neutral injector for large W-7X stellarator.
Ferromagnetic resonance study of polycrystalline Fe1−xVx alloy thin films
Authors: Beaujour J.-M. L. , Kent A. D. , Abraham D. W. , Sun J. Z.
Published: February 2008

Ferromagnetic resonance has been used to study the magnetic properties and magnetization dynamics of polycrystalline Fe1−xVx alloy films with 0⩽x<0.7. Films were produced by cosputtering from separate Fe and V targets, leading to a composition gradient across a Si substrate. Ferromagnetic resonance studies were conducted at room temperature with a broadband coplanar waveguide at frequencies up to 50GHz using the flip-chip method. The effective demagnetization field 4πMeff and the Gilbert damping parameter α have been determined as a function of V concentration. The results are compared to those of epitaxial FeV films.
Tunneling spectroscopy in Fe∕ZnSe∕Ga1−xMnxAs magnetic tunnel diodes
Authors: Saito H. , Yamamoto A. , Yuasa S. , Ando K.
Published: February 2008

We performed tunneling spectroscopy in Fe∕ZnSe∕Ga1−xMnxAs magnetic tunnel diodes with a metal-insulator-semiconductor (MIS) structure. A GaAs-like longitudinal optical phonon mode was observed for the first time in M∕I∕Ga1−xMnxAs junctions. This implies a better quality with fewer defect states in a ZnSe barrier as compared to other barrier materials, such as AlAs and GaAs. The normalized conductance spectra reflect the density of states of Ga1−xMnxAs in MIS tunnel diodes, suggesting that direct tunneling is a major transport mechanism due to high-quality ZnSe barrier.
Magnetic and photomagnetic studies in nanocrystalline Ni0.5Zn0.5Fe1.7Co0.3O4
Authors: Bahadur D. , Desplanches C. , Rajakumar S. , Létard J.-F.
Published: February 2008

This work presents magnetic and photomagnetic studies on the nanocrystalline form of the spinel Ni0.5Zn0.5Fe1.7Co0.3O4. Field cooled, zero field cooled, and hysteresis have been recorded for this compound with and without irradiation. Kinetics of relaxation of the magnetization in the dark and after irradiation has also been studied. An explanation of these results is given in the framework of freezing/melting of cluster glass behavior.
First principle study of AlX (X=3d,4d,5d elements and Lu) dimer
Authors: Ouyang Yifang , Wang Jianchuan , Hou Yuhua , Zhong Xiaping , Du Yong , Feng Yuanping
Published: February 2008

The ground state equilibrium bond length, harmonic vibrational frequency, and dissociation energy of AlX (X=3d,4d,5d elements and Lu) dimers are investigated by density functional method B3LYP. The present results are in good agreement with the available experimental and other theoretical values except the dissociation energy of AlCr. The present calculations show that the late transition metal can combine strongly with aluminum compared with the former transition metal. The present calculation also indicates that it is more reasonable to replace La with Lu in the Periodic Table and that the bonding strengths of zinc, cadmium, and mercury with aluminum are very weak.
Self-assembly of rod-coil-rod ABA-type triblock copolymers
Authors: Chen Ji-Zhong , Sun Zhao-Yan , Zhang Cheng-Xiang , An Li-Jia , Tong Zhen
Published: February 2008

Self-assembled behavior of symmetric ABA rod-coil-rod triblock copolymer melts is studied by applying self-consistent-field lattice techniques in three-dimensional space. The phase diagram is constructed to understand the effects of the chain architecture on the self-assembled behavior. Four stable structures are observed for the ABA rod-coil-rod triblock, i.e., spherelike, lamellar, gyroidlike, and cylindrical structures. Different from AB rod-coil diblock and BAB coil-rod-coil triblock copolymers, the lamellar structure observed in ABA rod-coil-rod triblock copolymer melts is not stable for high volume fraction of the rod component (frod=0.8), which is attributed to the intramolecular interactions between the two rod blocks of the polymer chain. When 0.3<frod<0.7, the intramolecular interactions between the two rigid blocks of the polymer chain are decrease, which results in the occurrence of some interesting metastable mixed structures. These structures have not been observed in polymers containing only one rod block, such as a lamellar-alt-lamellar structure. The results are expected to provide guidance for the design of microstructures in experiments.
Ferromagnetic and half-metallic behaviors of fullerene-cobalt polymer chains
Authors: Xu Xiang , Kang Hong Seok
Published: February 2008

We present the results of first-principles calculations for polymers (C60–Co)n and (C70–Co)n, which consist of alternating chains of fullerenes and cobalt. Both of them favor a ferromagnetic ground state. The latter one is a half-metal which will give rise to 100% spin polarization in the electronic transport, while the former is a semiconductor. Polymers (N@C60–Co)n and (N@C70–Co)n, which encapsulate a nitrogen atom in each fullerene have magnetic moments four times larger than those without encapsulated nitrogen atoms. All these results can be explained in terms of π(fullerene)-d(Co) and π(fullerene)-p(N) hybridizations.
Study of γ-ray irradiation effect on permanent magnets
Authors: Gao R. S. , Zhen L. , Shao W. Z. , Hao X. P. , Sun X. Y. , Yang L. , Wang B. Y.
Published: February 2008

Irradiation damage of FeCrCo, AlNiCo, SmCo, and NdFeB permanent magnets was investigated by using γ-ray irradiation. Results of magnetic property measurement show that FeCrCo and NdFeB have more demagnetization than AlNiCo and SmCo. X-ray diffraction analysis shows that γ-ray irradiation leads to the increase of FeCrCo crystal mismatch and decrease of AlNiCo ordering degree. The investigations by positron annihilation spectroscopy technique show that the defects in AlNiCo and SmCo increase after γ-ray irradiation. The defects induced by γ-ray irradiation in NdFeB magnets are not the main source that leads to partial demagnetization. The irradiation resistances of these magnets are discussed in detail considering the thermal stability, coercivity mechanisms, and defect damage.
High-resolution multiwire proportional soft x-ray diagnostic measurements on TCV
Authors: Sushkov A. , Andreev V. , Camenen Y. , Pochelon A. , Klimanov I. , Scarabosio A. , Weisen H.
Published: February 2008

A multiwire proportional x-ray (MPX) detector is used on the TCV tokamak (Tokamak à configuration variable) as a high spatial and temporal resolution soft x-ray emissivity imaging diagnostic. The MPX system consists of 64 vertically viewing channels and has been designed to complement the existing TCV soft x-ray tomography system by enhancing the spatial resolution. The MPX detector is suitable for the measurement of fast and localized phenomena and can be used, for instance, for the observation of magnetohydrodynamic activity, for the characterization of transport barriers or for an improved determination of the electron cyclotron heating power deposition profile. The MPX detector operates in continuous-current mode and measures the plasma soft x-ray emission in the 3–30keV range with a radial resolution of about 5mm—1% of plasma diameter—and a frequency bandwidth of 50kHz. A detailed description of the MPX detector construction and the principle of its operation are given. The properties of the detector in photon-counting and continuous-current operation modes are studied. The implementation of the system on TCV and experimental results illustrating the potential of the diagnostic are also presented.