bluuebunny/crossref_metadata_2025 huggingface dataset:
A snapshot of CO2 and CH4 evolution in a thermokarst pond near Igarka, northern Siberia
Authors: Blodau Christian , Rees Rainer , Flessa Heiner , Rodionov Andrej , Guggenberger Georg , Knorr Klaus‐Holger , Shibistova Olga , Zrazhevskaya Galina , Mikheeva Natalia , Kasansky Oleg A.
Published: August 2008

Thermokarst wetlands and ponds in the subarctic, which are located in land surface depressions resulting from permafrost melt, are strong sources of CH4, but little is known about respiration processes supporting these emissions. We determined CH4 fluxes and concentration profiles of dissolved gases and anions and some δ13C ratios of CO2 and CH4 in a thermokarst pond and adjacent smaller thermokarst depressions in the forest tundra near Igarka, northern Siberia in August 2006. Methane was emitted at 110–170 mg m−2 d−1 and produced mostly by CO2 reduction, which also provided high Gibbs free energies on the order of 50–70 KJ mol−1 H2 due to high H2 concentrations. The diffusive flux calculated from CH4 gradients in the floating mat contributed <2% to emissions. CH4 was apparently not oxidized deeper than 20 cm into the floating mat and the water body below. Anaerobic respiration required to reproduce nonsteady state CO2 concentration maxima in the floating mat above the water body was 30–80 nmol cm−3 d−1 or 250 mg m−2 d−1 and thus on a similar order of magnitude as CH4 fluxes. The results suggest that floating mat‐covered thermokarst ponds located in northern Siberian bogs effectively convert recently fixed carbon into CH4 and thus allow for emissions independently from the finite, bog‐derived carbon source. The relative contribution of recently fixed and old bog‐derived carbon to C fluxes requires further investigation, however.
Interlaboratory comparison study of calibration standards for foraminiferal Mg/Ca thermometry
Authors: Greaves M. , Caillon N. , Rebaubier H. , Bartoli G. , Bohaty S. , Cacho I. , Clarke L. , Cooper M. , Daunt C. , Delaney M. , deMenocal P. , Dutton A. , Eggins S. , Elderfield H. , Garbe‐Schoenberg D. , Goddard E. , Green D. , Groeneveld J. , Hastings D. , Hathorne E. , Kimoto K. , Klinkhammer G. , Labeyrie L. , Lea D. W. , Marchitto T. , Martínez‐Botí M. A. , Mortyn P. G. , Ni Y. , Nuernberg D. , Paradis G. , Pena L. , Quinn T. , Rosenthal Y. , Russell A. , Sagawa T. , Sosdian S. , Stott L. , Tachikawa K. , Tappa E. , Thunell R. , Wilson P. A.
Published: August 2008

An interlaboratory study of Mg/Ca and Sr/Ca ratios in three commercially available carbonate reference materials (BAM RS3, CMSI 1767, and ECRM 752‐1) was performed with the participation of 25 laboratories that determine foraminiferal Mg/Ca ratios worldwide. These reference materials containing Mg/Ca in the range of foraminiferal calcite (0.8 mmol/mol to 6 mmol/mol) were circulated with a dissolution protocol for analysis. Participants were asked to make replicate dissolutions of the powdered samples and to analyze them using the instruments and calibration standards routinely used in their laboratories. Statistical analysis was performed in accordance with the International Standardization Organization standard 5725, which is based on the analysis of variance (ANOVA) technique. Repeatability (RSDr%), an indicator of intralaboratory precision, for Mg/Ca determinations in solutions after centrifuging increased with decreasing Mg/Ca, ranging from 0.78% at Mg/Ca = 5.56 mmol/mol to 1.15% at Mg/Ca = 0.79 mmol/mol. Reproducibility (RSDR%), an indicator of the interlaboratory method precision, for Mg/Ca determinations in centrifuged solutions was noticeably worse than repeatability, ranging from 4.5% at Mg/Ca = 5.56 mmol/mol to 8.7% at Mg/Ca = 0.79 mmol/mol. Results of this study show that interlaboratory variability is dominated by inconsistencies among instrument calibrations and highlight the need to improve interlaboratory compatibility. Additionally, the study confirmed the suitability of these solid standards as reference materials for foraminiferal Mg/Ca (and Sr/Ca) determinations, provided that appropriate procedures are adopted to minimize and to monitor possible contamination from silicate mineral phases.
Synthetic aperture radar interferometry observations of theM= 6.0 Orta earthquake of 6 June 2000 (NW Turkey): Reactivation of a listric fault
Authors: Cakir Ziyadin , Akoglu Ahmet Murat
Published: August 2008

We study the coseismic surface displacement field due to the Orta earthquake of 6 June 2000, a moderate‐sized (Mw6.0) oblique‐slip event that took place on a previously unknown fault located about 70 km north of the capital, Ankara (Turkey), and about 35 km south of the North Anatolian Fault. We use European Space Agency ERS synthetic aperture radar (SAR) data to generate high‐resolution maps of the surface displacements by a two‐pass differential SAR interferometry method. The surface displacement field reaching up to 15 cm line of sight subsidence is captured in several coseismic interferograms from descending orbits and is inverted to determine the source parameters of the earthquake using elastic dislocations on rectangular fault surfaces with a nonlinear minimization procedure based on simulating annealing algorithm. Modeling of the coseismic interferograms indicates that the earthquake was associated with a shallow (<6 km) left‐lateral oblique normal displacement that occurred on a north‐south striking, eastward dipping, listric fault trending at a high angle to the plate boundary, right‐lateral strike‐slip North Anatolian fault. Careful analyses of multiple interferograms together with the field observations allow us to infer the rupture geometry in fine detail. Modeling shows that coseismic slip occurs nearly only on the lower portion of the listric fault at a centroid depth of about 5 km but partially reaches to the surface along the surface trace of the Dodurga fault, in agreement with the field observations. We show that in the absence of field observations, additional measurements, or multiple interferograms that capture the surface deformation from different look angles, SAR interferometry alone may not be sufficient to constrain earthquake rupture geometry if there is no clear surface faulting. The results suggest that the Dodurga fault developed most probably as a result of a restraining bend along the North Anatolian fault and its left‐lateral kinematics is consistent with the stress regime that favors the right‐lateral North Anatolian fault.
Assessment of Joule heating for the observed distributions of high‐latitude electric fields
Authors: Golovchanskaya I. V.
Published: August 2008

An assessment of Joule heating associated with electric field variability at high latitudes previously made by Codrescu et al. (1995) is refined with accounting for realistic probability density functions (PDFs) and root‐mean‐square (RMS) values of variable electric fields. It is shown that the observed PDFs constructed as functions of x ≡ Er/rms, Er being the amplitude and rms the root‐mean‐square amplitude of the residual field, which is left after subtracting the mean field Em from the data, can be fitted with a Castaing distribution. The parameter λ in this distribution that characterizes the degree of non‐Gaussianity of data appears ∼0.7. Joule heating patterns are demonstrated for the electric fields observed in two passes of the low‐altitude polar‐orbiting Dynamic Explorer 2 (DE2) satellite over the high‐latitude region in the Northern Hemisphere, one under positive IMF Bz in the presence of IMF By, and the other under negative IMF Bz. The relative contributions to Joule heating of the mean field, here considered as 1024 km running average of samples, and of the residual fields are estimated.
Future changes in snowmelt‐driven runoff timing over the western US
Authors: Rauscher Sara A. , Pal Jeremy S. , Diffenbaugh Noah S. , Benedetti Michael M.
Published: August 2008

We use a high‐resolution nested climate model to investigate future changes in snowmelt‐driven runoff (SDR) over the western US. Comparison of modeled and observed daily runoff data reveals that the regional model captures the present‐day timing and trends of SDR. Results from an A2 scenario simulation indicate that increases in seasonal temperature of approximately 3° to 5°C resulting from increasing greenhouse gas concentrations could cause SDR to occur as much as two months earlier than present. These large changes result from an amplified snow‐albedo feedback driven by the topographic complexity of the region, which is more accurately resolved in a high‐resolution nested climate model. Earlier SDR could affect water storage in reservoirs and hydroelectric generation, with serious consequences for land use, agriculture, and water management in the American West.
Clay mineral reactions caused by frictional heating during an earthquake: An example from the Taiwan Chelungpu fault
Authors: Hirono Tetsuro , Fujimoto Koichiro , Yokoyama Tadashi , Hamada Yohei , Tanikawa Wataru , Tadai Osamu , Mishima Toshiaki , Tanimizu Masaharu , Lin Weiren , Soh Wonn , Song Sheng‐Rong
Published: August 2008

To understand the chemical reactions of clay minerals in a fault zone during an earthquake, we analyzed the clay minerals in the Chelungpu fault, which slipped during the 1999 Chi‐Chi earthquake. X‐ray diffraction spectroscopy showed that kaolinite and smectite contents were lower in the black gouge zone than in the surrounding gray gouge, breccia, or fracture‐damaged zones. We applied a chemical kinetics approach to examine whether dehydroxylation of kaolinite and dehydration of interlayer water, dehydroxylation, and illitization of smectite occurred during coseismic frictional heating, and found that the first two reactions could complete under the temperature‐time profile of the Chi‐Chi earthquake, reconstructed by a previous study. Because dehydration of smectite interlayer water and dehydroxylation of kaolinite would have completed 3.6 and 8.2 s after the beginning of slip, the resulting release of water might have affected the frictional mechanism during the earthquake.
Thermospheric dark band structures at low latitudes in the Southern Hemisphere under different solar activity conditions: A study using OI 630 nm emission all‐sky images
Authors: Pimenta A. A. , Amorim D. C. M. , Candido C. M. N.
Published: August 2008

Using ground‐based measurements we investigate the occurrence of dark band structures in the OI 630 nm nightglow emission all‐sky images in the Brazilian low latitude region during the periods from January 1990 to December 1990 (high solar activity period‐HSA), May 1995 to July 1996 (low solar activity period‐LSA) and from January 1997 to December 1999 (ascending solar activity period‐ASA). Unfortunately we do not have all‐sky images for the descending phase of solar activity period. The OI 630 nm images obtained during these periods show thermospheric Dark Band Structures (DBS) in the low latitudes region propagating from southeast to northwest. These dark patches moved with average speed of about 50–200 m/s at an altitude of 220–300 km, which is the typical altitude range of the OI 630.0 nm airglow emission. Only during low solar activity period (LSA) and ascending solar activity period (ASA), the DBS occurrences were observed in the OI 630 nm nightglow emission all‐sky images. It should be pointed out that these thermospheric/ionospheric events are not related to geomagnetic disturbed conditions. In this paper, we present and discuss this phenomena in the Brazilian sector under different solar activity conditions. A possible mechanism for generation of these dark band structures is presented.
Aerosol optical depth over the Tibetan Plateau and its relation to aerosols over the Taklimakan Desert
Authors: Xia Xiangao , Wang Pucai , Wang Yuesi , Li Zhanqing , Xin Jinyuan , Liu Jing , Chen Hongbin
Published: August 2008

The Multiangle Imaging SpectroRadiometer (MISR) aerosol optical depths (AODs) over the Tibetan Plateau (TP) are compared with ground‐based remote sensing data. The result shows that 27 out of 32 MISR AODs fall within the expected uncertainty, i.e., 0.05 or 20% × AOD. The mean bias and the root mean square error between ground and satellite AODs are 0.01 and 0.03, respectively. The 7‐year MISR AOD data are used to study seasonal and inter‐annual variations of AOD over the TP. The results show distinct seasonal variation, with seasonal AOD being 0.27, 0.25, 0.13 and 0.11 from spring to winter. AOD over the TP is closely related to that over the Taklimakan desert in summer; however poor correlation is observed in spring. Higher AOD in spring and summer over the TP merits further study, including its causes and implications for climate and environment.
Atlantic modulation of El Niño influence on summertime rainfall over southeastern South America
Authors: Barreiro Marcelo , Tippmann Andrés
Published: August 2008

This study addresses the effect of Atlantic sea surface temperature (SST) anomalies on rainfall over southeastern South America during January–February, particularly during El Niño years, using observations as well as model simulations. It is found that the state of the equatorial Atlantic during El Niño years can modulate its influence on rainfall over southeastern South America, such that when the equatorial Atlantic is warm, the El Niño influence is weaker. This Atlantic influence is shown to occur through the response of the low level winds to equatorial SST anomalies: the convergence of westerly anomalies onto the warm anomaly decreases the equatorial trades and moisture flow into the Amazon and, moreover, reduces the northerly flow that brings moisture to southeastern South America. The total rainfall response in this region can thus be thought as the combination of rainfall anomalies from the equatorial Pacific and Atlantic oceans.
Shoaling of nonlinear internal waves in Massachusetts Bay
Authors: Scotti A. , Beardsley R. C. , Butman B. , Pineda J.
Published: August 2008

The shoaling of the nonlinear internal tide in Massachusetts Bay is studied with a fully nonlinear and nonhydrostatic model. The results are compared with current and temperature observations obtained during the August 1998 Massachusetts Bay Internal Wave Experiment and observations from a shorter experiment which took place in September 2001. The model shows how the approaching nonlinear undular bore interacts strongly with a shoaling bottom, offshore of where KdV theory predicts polarity switching should occur. It is shown that the shoaling process is dominated by nonlinearity, and the model results are interpreted with the aid of a two‐layer nonlinear but hydrostatic model. After interacting with the shoaling bottom, the undular bore emerges on the shallow shelf inshore of the 30‐m isobath as a nonlinear internal tide with a range of possible shapes, all of which are found in the available observational record.
Simulating the effect of capillary flux on the soil water balance in a stochastic ecohydrological framework
Authors: Vervoort R. Willem , van der Zee Sjoerd E. A. T. M.
Published: August 2008

Groundwater uptake can play a major role in the survival of vegetation in semiarid areas, but this has not yet been included in an earlier developed ecohydrological stochastic framework. In this paper we provide a piecewise linear equation which includes capillary fluxes from shallow groundwater in the loss function of the ecohydrological stochastic model. The results indicate that this model is able to simulate the capillary fluxes, and the model also reflects the impact of the fluxes on the soil moisture balance. In addition, the results are analytically tractable and allow calculation of the probability density functions of soil water saturation and water stress for different groundwater depths below the root zone.
Edinger-Westphal Nucleus
Authors:   Allen Institute for Brain Science, Burnell Josh , Ng Lydia , Guillozet-Bongaarts Angela
Published: August 2008

This report contains a summary of expression patterns for genes that are enriched in the Edinger-Westphal nucleus (EW) of the midbrain. All data are derived from the Allen Brain Atlas (ABA) in situ hybridization mouse project. The structure's location and morphological characteristics in the mouse brain are described using the Nissl data found in the Allen Reference Atlas. Using an established algorithm, the expression values of the Edinger-Westphal nucleus were compared to the values of its larger parent structure, in this case the midbrain, for the purpose of extracting regionally selective gene expression data. The highest ranking genes were manually curated and verified. 50 genes were then selected and compiled for expression analysis. The experimental data for each gene may be accessed via the links provided; additional data in the sagittal plane may also be accessed using the ABA. Correlations between gene expression in the Edinger-Westphal nucleus and the rest of the brain, across all genes in the coronal dataset (~4300 genes), were derived computationally. A gene ontology table (derived from DAVID Bioinformatics Resources 2007) is also included, highlighting possible functions of the 50 genes selected for this report.
Facial Motor Nucleus
Authors:   Allen Institute for Brain Science, Dalley Rachel , Ng Lydia , Guillozet-Bongaarts Angela
Published: August 2008

This report contains a summary of expression patterns for genes that are enriched in the facial motor nucleus (VII) of the medulla. All data is derived from the Allen Brain Atlas (ABA) in situ hybridization mouse project. The structure's location and morphological characteristics in the mouse brain are described using the Nissl data found in the Allen Reference Atlas. Using an established algorithm, the expression values of the facial motor nucleus were compared to the values of its larger parent structure, in this case the medulla, for the purpose of extracting regionally selective gene expression data. The highest ranking genes were manually curated and verified. 50 genes were then selected and compiled for expression analysis. The experimental data for each gene may be accessed via the links provided; additional data in the sagittal plane may also be accessed using the ABA. Correlations between gene expression in the facial motor nucleus and the rest of the brain, across all genes in the coronal dataset (~4300 genes), were derived computationally. A gene ontology table (derived from DAVID Bioinformatics Resources 2007) is also included, highlighting possible functions of the 50 genes selected for this report.
Prediction of Functional Sites in SCOP Domains using Dynamics Perturbation Analysis
Authors: Cohn Judith , Ming Dengming , Wall Michael
Published: August 2008

Dynamics perturbation analysis (DPA) finds regions in a protein structure where proteins are "ticklish", i.e., where interactions cause a large change in protein dynamics. Previously, such regions were shown to predict the location of native binding sites in a docking test set, but the more general applicability of DPA to the prediction of functional sites in proteins was not shown. Here we describe the results of applying an accelerated algorithm, called Fast DPA, to predict functional sites in over 50,000 SCOP domains.
A Pilot of a Video Game (DDR) to Promote Physical Activity and Decrease Sedentary Screen Time
Authors: Maloney Ann E. , Bethea T. Carter , Kelsey Kristine S. , Marks Julie T. , Paez Sadye , Rosenberg Angela M. , Catellier Diane J. , Hamer Robert M. , Sikich Linmarie
Published: August 2008

Objective: We examined the feasibility of Dance Dance Revolution (DDR), a dance video game, in participants' homes, to increase physical activity (PA) and to decrease sedentary screen time (SST).

Methods And Procedures: Sixty children (7.5 ± 0.5 years) were randomized in a 2:1 ratio to DDR or to wait‐list control (10‐week delay). DDR use was logged, PA was measured objectively by accelerometry. SST was self‐reported at weeks 0 and 10. At week 28, after both groups had access to DDR, accelerometry and SST were repeated.

Results: Mean use of DDR was 89 ± 82 (range 0–660min) min per week (mpw). The DDR group showed increased vigorous PA and a reduction in light PA; the control group showed no increase in moderate and/or vigorous PA (MVPA) although they also had a reduction in light PA. Differences between the groups were not observed. The DDR group also reported a decrease in SST of −1.2 ± 3.7 h per week (hpw) (P < 0.05), whereas the controls reported an increase of +3.0 ± 7.7 hpw (nonsignificant). The difference in SST between the groups was significant, with less SST in the DDR group. Between weeks 10 and 28, numeric reductions in SST were reported in both groups. In the DDR group, SST at week 28 (8.8 ± 6.0 hpw) was lower than baseline (10.5 ± 5.5 hpw; P < 0.03).

Discussion: This pilot study suggests that DDR reduces SST and may facilitate slight increases in vigorous PA. Further study is needed to better characterize children and contexts in which DDR may promote a healthy lifestyle.
Bingeing, Self‐restriction, and Increased Body Weight in Rats With Limited Access to a Sweet‐fat Diet
Authors: Berner Laura A. , Avena Nicole M. , Hoebel Bartley G.
Published: August 2008

Objective: Prior research has shown that fasting alternated with a diet of standard rodent chow and a 10% sucrose solution produces bingeing on the sucrose, but animals remain at normal body weight. The present study investigated whether restricted access to a highly palatable combination of sugar and fat, without food deprivation, would instigate binge eating and also increase body weight.

Methods and Procedures: Male rats were maintained for 25 days on one of four diets: (i) sweet‐fat chow for 2 h/day followed by ad libitum standard chow, (ii) 2‐h sweet‐fat chow only 3 days/week and access to standard chow the rest of the time, (iii) ad libitum sweet‐fat chow, or (iv) ad libitum standard chow.

Results: Both groups with 2‐h access to the sweet‐fat chow exhibited bingeing behavior, as defined by excessively large meals. The body weight of these animals increased due to large meals and then decreased between binges as a result of self‐restricted intake of standard chow following binges. However, despite these fluctuations in body weight, the group with 2‐h access to sweet‐fat chow every day gained significantly more weight than the control group with standard chow available ad libitum.

Discussion: These findings may have implications for the body weight fluctuations associated with binge‐eating disorder, as well as the relationship between binge eating and the obesity epidemic.
Application of SCAR (sequence characterized amplified region) analysis to authenticate Lycium barbarum (wolfberry) and its adulterants
Authors: Sze Stephen Cho‐Wing , Song Ju‐Xian , Wong Ricky Ngok‐Shun , Feng Yi‐Bin , Ng Tzi‐Bun , Tong Yao , Zhang Kalin Yan‐Bo
Published: August 2008

Fructus Lycii (Gouqizi) is well known in Chinese herbal medicine for its restorative function of benefiting the liver and kidney, replenishing vital essence and improving eyesight. However, ten species and varieties of Lycium have benn found to be substitutes or adulterants of Lycium barbarum (wolfberry) in commercial markets in the Hong Kong Special Administrative Region and in China generally. L. barbarum cv. ‘Tianjinense’ and Lycium chinense var. potaninii are the most common examples. It is difficult to differentiate among the Lycium species by traditional morphological and histological analyses. An easy and reliable approach based on SCAR (sequence characterized amplified region) analysis was developed in the present study to differentiate L. barbarum from other Lycium species. Two characteristic bands of approx. 700 and 650 bp were detected on the RAPD (random amplification of polymorphic DNA) profiles generated from samples of L. barbarum and L. chinense var. potaninii using the primer OPC‐7. They were isolated and sequenced. Two primer sets, based on the sequences, could amplify a single specific band in samples of L. barbarum respectively, whereas no bands were detected in samples of L. chinense var. potaninii. The results confirmed that the SCAR technique can be employed for authenticating L. barbarum and its adulterants.
Detection and identification of Dehalococcoides species responsible for in situ dechlorination of trichloroethene to ethene enhanced by hydrogen‐releasing compounds
Authors: Nishimura Minoru , Ebisawa Maiko , Sakihara Sakari , Kobayashi Ai , Nakama Tetsushi , Okochi Mina , Yohda Masafumi
Published: August 2008

Previous studies have shown that Dehalococcoides species are responsible for the anaerobic bioremediation of chloroethene pollution. It has been thought that co‐operation of several species is required for complete dechlorination to ethene. In the present study, we used quantitative PCR of 16 S rRNA and RDase (reductive dehalogenase) genes to examine species changes and the population of Dehalococcoides species in ground water in which the dechlorination of TCE (trichloroethene) to ethene was enhanced by delivery of hydrogen‐releasing compounds. The results have shown that at least two different Dehalococcoides species co‐operate in the dechlorination of TCE to ethene. Initially, the number of strains equipped with TCE RDase increased approx. 105‐fold. This was followed by a decrease to the original level, according to the exhaustion of TCE. Subsequently, another strain appeared, which had a VC (vinyl chloride) RDase gene similar to bvcA of Dehalococcoides sp. BAV1 and is probably responsible for the dechlorination of VC to ethene. Analysis of several genes has suggested that the former strain is like Dehalococcoides sp. FMC‐TCE, and the latter strain is similar to the Dehalococcoides sp. strain that exists in the Dehalococcoides‐containing mixed culture KB1. These results support the notion that monitoring Dehalococcoides species by the presence of RDase genes as genetic markers provides detailed information on the progress of bioremediation of chloroethenes, which will be useful to improve the efficiency of bioremediation.
Purification and properties of the alkaline lipase from Burkholderia cepacia A.T.C.C. 25609
Authors: Dalal Sohel , Singh Pradeep Kumar , Raghava Smita , Rawat Seema , Gupta Munishwar Nath
Published: August 2008

A Burkholderia cepacia (bacteria) strain, A.T.C.C. 25609, which had been isolated from the bronchial washings of a cystic fibrosis patient, was used to produce lipase. The presence of sodium alginate at an optimal concentration of 8 mg·ml−1 in the growth medium nearly doubled the production of extracellular lipase activity. The enzyme could be purified with 38‐fold purification and 96% activity recovery using a two‐step purification protocol. The molecular mass of the purified lipase determined by SDS/PAGE was shown to be 28 kDa. The pH optimum of the purified enzyme was 9 and it was stable up to 12 h at pH 9 and 10. The enzyme has a temperature optimum of 40 °C and its half‐life (t1/2) values were 54 and 46 min at 50 and 60 °C respectively. The lipase was found to be stable in the presence of the detergents Tween 20 and Triton X‐100. The secondary‐structure analysis of lipase by CD spectroscopy showed 52% α‐helix, 7.7% β‐sheet, 12.6% β‐turn and 27.8% random structure. The lipase was cloned and overexpressed in Escherichia coli. The gene sequence of the cloned lipase was determined and compared with other lipases.
Novel preparation protocol for the expression and purification of recombinant staphylokinase
Authors: Ren Dongsheng , Li Dehua , Yang Weihua , Li Yun , Gou Xinghua , Liang Bo , Li Bogang , Wu Qiaqing
Published: August 2008

Staphylokinase (Sak), produced by lysogenic strains of Staphylococcus aureus, can convert plasminogen into its proteolytic form, plasmin, and thus is widely used to dissolve pathological clots in clinical applications. In the present paper, we report a novel approach to produce r‐Sak (recombinant Sak) using an engineered Escherichia coli expression system. The expression plasmid was constructed by placing the Sak gene into the expression vector pET32(a), resulting in the expression of 35% fusion protein. Subsequently, a rapid and simple chromatographic procedure was developed for the large‐scale purification of therapeutic‐grade r‐Sak from E. coli, which includes Ni2+‐affinity chromatography, ultrafiltration and Q‐Sepharose Fast Flow chroma‐tography. This method led to the production of highly pure r‐Sak (>99%), according to SDS/PAGE and HPLC analysis.
Ajuba: a new microtubule‐associated protein that interacts with BUBR1 and Aurora B at kinetochores in metaphase
Authors: Ferrand Alexia , Chevrier Véronique , Chauvin Jean‐Paul , Birnbaum Daniel
Published: August 2008

Background information. The role of the LIM‐domain‐containing protein Ajuba was initially described in cell adhesion and migration processes and recently in mitosis as an activator of the Aurora A kinase.

Results. In the present study, we show that Ajuba localizes to centrosomes and kinetochores during mitosis. This localization is microtubule‐dependent and Ajuba binds microtubules in vitro. A microtubule regrowth assay showed that Ajuba follows nascent microtubules from centrosomes to kinetochores. Owing to its contribution to mitotic commitment and its microtubule‐dependent localization, Ajuba could also play a role during the metaphase—anaphase transition. We show that Ajuba interacts with Aurora B and BUBR1 [BUB (budding uninhibited by benomyl)‐related 1], two major components of the mitotic checkpoint. Inhibition of BUBR1 by siRNA (small interfering RNA) disrupts chromosome alignment at the metaphase plate and modifies Ajuba localization due to premature mitotic exit.

Conclusions. Ajuba is a microtubule‐associated protein that collaborates with Aurora B and BUBR1 at the metaphase—anaphase transition and this may be important to ensure proper chromosome segregation.
Human D-Tyr-tRNATyr deacylase contributes to the resistance of the cell to D-amino acids
Authors: Zheng Gen , Liu Wei , Gong Yanhua , Yang Hongbo , Yin Bin , Zhu JingXi , Xie Yi , Peng Xiaozhong , Qiang Boqin , Yuan Jiangang
Published: August 2008

DTD (D-Tyr-tRNATyr deacylase) is known to be able to deacylate D-aminoacyl-tRNAs into free D-amino acids and tRNAs and therefore contributes to cellular resistance against D-amino acids in Escherichia coli and yeast. We have found that h-DTD (human DTD) is enriched in the nuclear envelope region of mammalian cells. Treatment of HeLa cells with D-Tyr resulted in nuclear accumulation of tRNATyr. D-Tyr treatment and h-DTD silencing caused tRNATyr downregulation. Furthermore, inhibition of protein synthesis by D-Tyr treatment and h-DTD silencing were also observed. D-Tyr, D-Asp and D-Ser treatment inhibited mammalian cell viability in a dose-dependent manner; overexpression of h-DTD decreased the inhibition rate, while h-DTD-silenced cells became more sensitive to the D-amino acid treatment. Our results suggest that h-DTD may play an important role in cellular resistance against D-amino acids by deacylating D-aminoacyl tRNAs at the nuclear pore. We have also found that m-DTD (mouse DTD) is specifically enriched in central nervous system neurons, its nuclear envelope localization indicates that D-aminoacyl-tRNA editing may be vital for the survival of neurons under high concentration of D-amino acids.
Prolonged L-alanine exposure induces changes in metabolism, Ca2+ handling and desensitization of insulin secretion in clonal pancreatic β-cells
Authors: McClenaghan Neville H. , Scullion Siobhan M. , Mion Brian , Hewage Chandralal , Malthouse J. Paul G. , Flatt Peter R. , Newsholme Philip , Brennan Lorraine
Published: August 2008

Acute insulin-releasing actions of amino acids have been studied in detail, but comparatively little is known about the β-cell effects of long-term exposure to amino acids. The present study examined the effects of prolonged exposure of β-cells to the metabolizable amino acid L-alanine. Basal insulin release or cellular insulin content were not significantly altered by alanine culture, but acute alanine-induced insulin secretion was suppressed by 74% (P<0.001). Acute stimulation of insulin secretion with glucose, KCl or KIC (2-oxoisocaproic acid) following alanine culture was not affected. Acute alanine exposure evoked strong cellular depolarization after control culture, whereas AUC (area under the curve) analysis revealed significant (P<0.01) suppression of this action after culture with alanine. Compared with control cells, prior exposure to alanine also markedly decreased (P<0.01) the acute elevation of [Ca2+]i (intracellular [Ca2+]) induced by acute alanine exposure. These diminished stimulatory responses were partially restored after 18 h of culture in the absence of alanine, indicating reversible amino-acid-induced desensitization. 13C NMR spectra revealed that alanine culture increased glutamate labelling at position C4 (by 60%; P<0.01), as a result of an increase in the singlet peak, indicating increased flux through pyruvate dehydrogenase. Consistent with this, protein expression of the pyruvate dehydrogenase kinases PDK2 and PDK4 was significantly reduced. This was accompanied by a decrease in cellular ATP (P<0.05), consistent with diminished insulin-releasing actions of this amino acid. Collectively, these results illustrate the phenomenon of β-cell desensitization by amino acids, indicating that prolonged exposure to alanine can induce reversible alterations to metabolic flux, Ca2+ handling and insulin secretion.
Detailed arsenic concentration profiles at Si/SiO2 interfaces
Authors: Pei Lirong , Duscher Gerd , Steen Christian , Pichler Peter , Ryssel Heiner , Napolitani Enrico , De Salvador Davide , Piro Alberto Maria , Terrasi Antonio , Severac Fabrice , Cristiano Filadelfo , Ravichandran Karthik , Gupta Naveen , Windl Wolfgang
Published: August 2008

The pile-up of arsenic at the Si/SiO2 interface after As implantation and annealing was investigated by high resolution Z-contrast imaging, electron energy-loss spectroscopy (EELS), grazing incidence x-ray fluorescence spectroscopy (GI-XRF), secondary ion mass spectrometry, x-ray photoelectron spectroscopy, Rutherford backscattering spectrometry, as well as Hall mobility and four-point probe resistivity measurements. After properly taking into account their respective artifacts, the results of all methods are compatible with each other, with EELS and GI-XRF combined with etching providing similar spatial resolution on the nanometer scale for the dopant profile. The sheet concentration of the piled-up As at the interface was found to be ∼1×1015 cm−2 for an implanted dose of 1×1016 cm−2 with a maximum concentration of ∼10 at. %. The strain observed in the Z-contrast images also suggests a significant concentration of local distortions within 3 nm from the interface, which, however, do not seem to involve intrinsic point defects.
Energy calibration of a high-resolution inelastic x-ray scattering spectrometer
Authors: Verbeni Roberto , D’Astuto Matteo , Krisch Michael , Lorenzen Maren , Mermet Alain , Monaco Giulio , Requardt Herwig , Sette Francesco
Published: August 2008

The energy scale of a triple-axis x-ray spectrometer with meV energy resolution based on perfect silicon crystal optics is calibrated, utilizing the most recent determination of the silicon lattice parameter and its thermal expansion coefficient and recording the dispersion of longitudinal acoustic and optical phonons in a diamond single crystal and the molecular vibration mode in liquid nitrogen. Comparison of the x-ray results with previous inelastic neutron and Raman scattering results as well as with ab initio phonon dispersion calculations yields an overall agreement better than 2%.
Microprobe photoluminescence assessment of the wall-plug efficiency in interband cascade lasers
Authors: Vitiello Miriam S. , Scamarcio Gaetano , Spagnolo Vincenzo , Bewley William W. , Kim Mijin , Kim Chul-Soo , Vurgaftman Igor , Meyer Jerry R. , Lops Antonia
Published: August 2008

We employ a microprobe photoluminescence (PL) technique to determine the thermal resistance and wall-plug efficiency of narrow-ridge interband cascade lasers emitting at 3.8 μm. Using two different semiconductor epilayers as integrated thermometers, the local lattice temperature is extracted from the PL spectra and the wall-plug efficiency (ηw) derived from the slope of the temperature increase versus electrical power. The maximum ηw at 78 K is found to be 8.1±0.5%, and a fit to the lattice temperature gradient implies cross-plane thermal conductivities of 4.5–6.5 W/m K for the short-period InAs/AlSb superlattice cladding and of ≈1.5–4 W/m K for the active region.
Silicon nanocluster crystallization in SiOx films studied by Raman scattering
Authors: Hernández S. , Martínez A. , Pellegrino P. , Lebour Y. , Garrido B. , Jordana E. , Fedeli J. M.
Published: August 2008

Precipitation and crystallization of Si nanocrystals have been monitored by means of Raman spectroscopy. SiOx films with different compositions have been deposited by low-pressure chemical-vapor deposition technique onto silica substrates and treated to temperatures exceeding 800 °C. The evolution of the Raman signal with the thermal budget reveals that the silicon transition from amorphous to crystalline state shifts to higher temperatures as the Si content in the layers is lowered. A rather complete crystallization of the nanoparticles is achieved after annealing at 1250 °C for a Si excess lower than 20%, while for higher excesses the crystalline fraction reaches only 40%, suggesting the formation of a crystalline core surrounded by an amorphous shell. The Raman spectra have been analyzed by a phonon confinement model that takes into account stress effects. An increasing nanocrystal size, from 2.5 to 3.4 nm, has been estimated when the Si excess varies from 16 to 29 at. %. For small Si nanocrystals a strong hydrostatic stress has been observed, induced by a very abrupt transition with the surrounding SiO2. Its magnitude correlates with the increase in thermal budget required for the crystallization of the amorphous clusters. This study underlines the fundamental role of hydrostatic stress in retarding the crystallization of Si nanoclusters.
Changing adsorption mode of FePc on TiO2(110) by surface modification with bipyridine
Authors: Palmgren P. , Yu S. , Hennies F. , Nilson K. , Åkermark B. , Göthelid M.
Published: August 2008

Surface modification of reactive oxide substrates to obtain a less strongly interacting template for dye adsorption may be a way to enhance performance in dye-sensitized solar cells. In this work, we have investigated the electronic and structural properties of 4,4′-bipyridine (bipy) as modifier adsorbed on the TiO2(110) surface. The modified surface is then coated with iron phthalocyanine (FePc) and the properties of this heterostructure are investigated with synchrotron based photoelectron spectroscopy, x-ray absorption spectroscopy, and scanning tunneling microscopy. We find that a saturated monolayer consisting of standing bipy molecules with one nitrogen atom pointing outward is formed on the oxide surface. FePc adsorb in molecular chains along the [001] direction on top of bipy and ordered in a tilted arrangement with adjacent molecules partially overlapping. Already from the first layer, the electronic properties of FePc resemble those of multilayer films. FePc alone is oxidized on the TiO2(110) surface, but preadsorbed bipy prevents this reaction. The energy level lineup at the interface is clarified.
Protein aggregation probed by two-photon fluorescence correlation spectroscopy of native tryptophan
Authors: Sahoo Bankanidhi , Balaji J. , Nag Suman , Kaushalya Sanjeev Kumar , Maiti Sudipta
Published: August 2008

Fluorescence correlation spectroscopy (FCS) has proven to be a powerful tool for the study of a range of biophysical problems including protein aggregation. However, the requirement of fluorescent labeling has been a major drawback of this approach. Here we show that the intrinsic tryptophan fluorescence, excited via a two-photon mechanism, can be effectively used to study the aggregation of tryptophan containing proteins by FCS. This method can also yield the tryptophan fluorescence lifetime in parallel, which provides a complementary parameter to understand the aggregation process. We demonstrate that the formation of soluble aggregates of barstar at pH 3.5 shows clear signatures both in the two-photon tryptophan FCS data and in the tryptophan lifetime analysis. The ability to probe the soluble aggregates of unmodified proteins is significant, given the major role played by this species in amyloid toxicity.
1,8-octanedithiol as a processing additive for bulk heterojunction materials: Enhanced photoconductive response
Authors: Coates Nelson E. , Hwang In-Wook , Peet Jeffrey , Bazan Guillermo C. , Moses Daniel , Heeger Alan J.
Published: August 2008

We present measurements of steady state and transient (τ<70ps) photoconductivity of the low bandgap polymer poly[2,6-(4,4-bis-(2-ethylhexyl)-4H-cyclopenta[2,1-b;3,4-b′]-dithiophene)-alt-4,7-(2,1,3-benzothiadiazole)] mixed with [6,6]-phenyl C71-butyric acid methyl ester films processed with and without the 1,8-octanedithiol additive. The data demonstrate enhanced photoconductive response in the bulk heterojunction material processed with the additive. The increase results primarily from enhanced carrier mobility and to a lesser extent from a more efficient photogeneration of mobile carriers and longer mobile carrier lifetimes. The enhanced photoresponse is consistent with the increase in power conversion efficiency obtained from solar cells in which the bulk heterojunction film is processed using 1,8-octanedithiol.
Stabilization of tetra- and pentavalent Fe ions in Fe-substituted Li2MnO3 with layered rock-salt structure
Authors: Tabuchi Mitsuharu , Tatsumi Kuniaki , Morimoto Shotaro , Nasu Saburo , Saito Tadashi , Ikeda Yasuhiro
Published: August 2008

Origins of various valence states of various Fe ions above the 3+ state for 30% Fe-substituted Li2MnO3 [Li1+x(Fe0.3Mn0.7)1−xO2] with a layered rock-salt structure (R3¯m) have been investigated using magnetization measurement and Fe57 Mössbauer spectroscopy at less than 300K. The temperature dependence of magnetization data revealed that small spontaneous magnetization [1.26(9)Gcm3∕g at 5K] appeared at less than 81K and cusps were observed at 24K under both zero field and field cooling runs. Analyses of Fe57 Mössbauer spectra showed that all samples contained tetravalent (Fe4+) and pentavalent (Fe(5−δ)+) iron ions (20%–40%) along with trivalent ones. High-valence (Fe(5−δ)+) iron might be the result of Fe(3+δ)+∕Fe(5−δ)+ charge disproportionation from tetravalent iron, as in SrMn0.5Fe0.5O3. Small paramagnetic iron doublets (2%–5%) with highly negative isomer shift values (−0.5to−0.6mm∕s) were detected at less than 10K. They might be pentavalent Fe(5+δ)+ ion. The Fe(5+δ)+ ion can be stabilized under high excess lithium content x (>0.28) according to the chemical formula Li1+x(Fe0.3Mn0.7)1−xO2 close to Li2MO3 composition and by suppressing 3d cation disordering to the Li layer. The unique valence state of Fe ions (>4+ state) might be stabilized in the Mn–Li layer of the Li2MnO3 structure. These results mean that Fe ions at 5+ states are stable ions in oxides not only in a perovskite-related structure but also in a rock-salt-related one.
Nonequilibrium molecular dynamics calculation of the thermal conductivity based on an improved relaxation scheme
Authors: Cao Bing-Yang
Published: August 2008

A nonequilibrium molecular dynamics (NEMD) method using stochastic energy injection and removal as uniform heat sources and sinks is developed to calculate the thermal conductivity. The stochastic energy is generated by a Maxwell function generator and is imposed on only a few individual molecules each time step. The relaxation of the thermal perturbation is improved compared to other NEMD algorithms because there are no localized heat source and sink slab regions in the system. The heat sources are uniformly distributed in the right half of the system while the sinks are in the left half, which leads to a periodically quadratic temperature distribution that is almost sinusoidal. The thermal conductivity is then easily calculated from the mean temperatures of the right and left half systems rather than by fitting the temperature profiles. This improved relaxation NEMD scheme is used to calculate the thermal conductivities of liquid and solid argons. It shows that the present algorithm gives accurate results with fast convergence and small size effects. Other stochastic energy perturbation, e.g., thermal noise, can be used to replace the Maxwell-type perturbation used in this paper to make the improved relaxation scheme more effective.
Multifractality in plasma edge electrostatic turbulence
Authors: Neto C. Rodrigues , Guimarães-Filho Z. O. , Caldas I. L. , Nascimento I. C. , Kuznetsov Yu. K.
Published: August 2008

Plasma edge turbulence in Tokamak Chauffage Alfvén Brésilien (TCABR) [R. M. O. Galvão et al., Plasma Phys. Contr. Fusion 43, 1181 (2001)] is investigated for multifractal properties of the fluctuating floating electrostatic potential measured by Langmuir probes. The multifractality in this signal is characterized by the full multifractal spectra determined by applying the wavelet transform modulus maxima. In this work, the dependence of the multifractal spectrum with the radial position is presented. The multifractality degree inside the plasma increases with the radial position reaching a maximum near the plasma edge and becoming almost constant in the scrape-off layer. Comparisons between these results with those obtained for random test time series with the same Hurst exponents and data length statistically confirm the reported multifractal behavior. Moreover, the persistence of these signals, characterized by their Hurst exponent, present radial profile similar to the deterministic component estimated from analysis based on dynamical recurrences.
Intramolecular vibrational frequencies of water clusters (H2O)n (n=2–5): Anharmonic analyses using potential functions based on the scaled hypersphere search method
Authors: Watanabe Yu , Maeda Satoshi , Ohno Koichi
Published: August 2008

Potential energy functions (PEFs) in the form of the sixth-order polynomial concerned with intramolecular motions of (H2O)n (n=2–5) were constructed by the scaled hypersphere search (SHS) based polynomial fitting (SHS-PF) method, in which the numbers of ab initio calculations can be considerably reduced via the selection of sampling directions by the SHS method. Concerning fundamental frequencies of the dimer cluster, the root mean square error from gas-phase experiments was only 10 cm−1. For the trimer, tetramer, and pentamer, computed anharmonic frequencies reproduced available gas-phase experimental frequencies of HOH bending, donor-OH stretching, and free-OH stretching excellently with errors of approximately 10–20cm−1 on average. It follows that the SHS-PF method is promising for highly accurate anharmonic vibrational analyses of intramolecular modes of H-bond clusters.