bluuebunny/crossref_metadata_2025_split huggingface dataset:
An adaptive sampling scheme guided by BART—with an application to predict processor performance
Authors: Yu Qingzhao , Li Bin , Fang Zhide , Peng Lu 
Published: January 2010

AbstractThe evaluation of new processor designs is an important issue in electrical and computer engineering. Architects use simulations to evaluate designs and to understand trade‐offs and interactions among design parameters. However, due to the lengthy simulation time and limited resources, it is often practically impossible to simulate a full factorial design space. Effective sampling methods and predictive models are required. In this paper, the authors propose an automated performance predictive approach which employs an adaptive sampling scheme that interactively works with the predictive model to select samples for simulation. These samples are then used to build Bayesian additive regression trees, which in turn are used to predict the whole design space. Both real data analysis and simulation studies show that the method is effective in that, though sampling at very few design points, it generates highly accurate predictions on the unsampled points. Furthermore, the proposed model provides quantitative interpretation tools with which investigators can efficiently tune design parameters in order to improve processor performance. The Canadian Journal of Statistics 38: 136–152; 2010 © 2010 Statistical Society of Canada
Characteristic Analysis of Plants for the Removal of Nutrients from a Constructed Wetland using Reclaimed Water
Authors: Wang Lin , Gan Hong , Wang Fang , Sun Xiumin , Zhu Qilin 
Published: January 2010

AbstractOne of the main issues with the East Route (ER) of the South‐to‐North Water Transfer Project (SNWTP) in China is water pollution. The Pingyin wetland, situated near the SNWTP, collects reclaimed water discharging from a sewage treatment plant. Selected aquatic plants were cultivated in the constructed wetland and their biomass, total nitrogen (TN) and total phosphorus (TP) contents and accumulation were studied to assess whether the selected plants were suitable for cultivation in the reclaimed water environment and to determine their nutrient removal rates. Most of the introduced species showed high vitality after 60 days growth, and plant biomass increased greatly from the early to the middle part of the growing season. The TN content for different plant species during the growing season varied from 30–165 mg/g, while the TP contents varied from 5–35 mg/g. The TN and TP contents of the introduced species were significantly higher than those of the local species. The main TN absorption organ was the plant leaves. The nutrient accumulation by the local species was significantly higher than that of the main introduced species since accumulation is determined mainly by the species biomass. The TN and TP removal of plants contributed 9.66% and 49%, respectively, to total nutrient removal in the constructed wetland.
Electrochemical Coagulation for Chromium Removal: Process Optimization, Kinetics, Isotherms and Sludge Characterization
Authors: Vasudevan Subramanyan , Lakshmi Jothinathan , Vanathi Ramasamy 
Published: January 2010

AbstractThis study presents an electrochemical coagulation process for the removal of chromium from water using magnesium as the anode and galvanized iron as the cathode. The effects of pH, current density, concentration, temperature, adsorption kinetics and adsorption isotherms on chromium removal were investigated. The results showed that an optimum removal efficiency of 98.6% was achieved at a current density of 0.2 A/dm2 and a pH of 7.0. The adsorption kinetics showed that the first order rate expression fitted the adsorption kinetics. The equilibrium isotherm was measured experimentally. Results were analyzed by Langmuir, Freundlich, Dubinin‐Redushkevich and Frumkin isotherms using linearized correlation coefficients. The characteristic parameters for each isotherm were determined. The Langmuir adsorption isotherm was found to fit the equilibrium data best for chromium adsorption. Temperature studies showed that adsorption was endothermic and spontaneous in nature.
Toward a Consensus Model of the hERG Potassium Channel
Authors: Stary Anna , Wacker Sören J. , Boukharta Lars , Zachariae Ulrich , Karimi‐Nejad Yasmin , Åqvist Johan , Vriend Gert , de Groot Bert L. 
Published: January 2010

AbstractMalfunction of hERG potassium channels, due to inherited mutations or inhibition by drugs, can cause long QT syndrome, which can lead to life‐threatening arrhythmias. A three‐dimensional structure of hERG is a prerequisite to understand the molecular basis of hERG malfunction. To achieve a consensus model, we carried out an extensive analysis of hERG models based on various alignments of helix S5. We analyzed seven models using a combination of conventional geometry/packing/normality validation methods as well as molecular dynamics simulations and molecular docking. A synthetic test set with the X‐ray crystal structure of Kv1.2 with artificially shifted S5 sequences modeled into the structure served as a reference case. We docked the known hERG inhibitors (+)‐cisapride, (S)‐terfenadine, and MK‐499 into the hERG models and simulation snapshots. None of the single analyses unambiguously identified a preferred model, but the combination of all three revealed that there is only one model that fulfils all quality criteria. This model is confirmed by a recent mutation scanning experiment (P. Ju, G. Pages, R. P. Riek, P. C. Chen, A. M. Torres, P. S. Bansal, S. Kuyucak, P. W. Kuchel, J. I. Vandenberg, J. Biol. Chem. 2009, 284, 1000–1008).1 We expect the modeled structure to be useful as a basis both for computational studies of channel function and kinetics as well as the design of experiments.
Pharmacokinetics of contrast agents targeted to the tumor vasculature in molecular magnetic resonance imaging
Authors: Oostendorp Marlies , Douma Kim , Hackeng Tilman M. , van Zandvoort Marc A. M. J. , Post Mark J. , Backes Walter H. 
Published: January 2010

AbstractMolecular magnetic resonance imaging (MRI) is increasingly used to investigate tumor angiogenic activity non‐invasively. However, the pharmacokinetic behavior and tumor penetration of the often large contrast agent particles is thus far unknown. Here, pharmacokinetic analysis of cyclic asparagine–glycine–arginine (cNGR) labeled paramagnetic quantum dots (pQDs) was developed to quantify the contrast agent's homing efficacy to activated endothelial cells of angiogenic tumor vessels using dynamic contrast‐enhanced (DCE) MRI. cNGR homes to CD13, an overexpressed aminopeptidase on angiogenic tumor endothelial cells. First, a two‐compartment pharmacokinetic model, comprising the blood space and endothelial cell surface, was compared with a three‐compartment model additionally including the extravascular–extracellular component. The resulting extravasation parameter was irrelevantly small and was therefore neglected. Next, the association constant Ka, the dissociation constant kd and the fractional plasma volume vP were determined from the time‐series data using the two‐compartment model. Magnitude and spatial distribution of the parameters were compared for cNGR‐labeled and unlabeled pQDs. The tumor area with significant Ka values was approximately twice as large for cNGR‐pQDs compared with unlabeled pQDs (p < 0.05), indicating more contrast agent binding for cNGR‐pQDs. Using cNGR‐pQDs, a two‐fold larger area with significant Ka was also found for the angiogenic tumor rim compared with tumor core (p < 0.05). It was furthermore found that both contrast agents perfused the tumor at all depths, thereby providing unequivocal evidence that rim/core differences can indeed be ascribed to stronger angiogenic activity in the rim. Summarizing, molecular DCE‐MRI with pharmacokinetic modeling provides unique information on contrast agent delivery and angiogenic activity in tumors. Copyright © 2010 John Wiley & Sons, Ltd.
Nonendosomal cellular uptake of ligand‐free, positively charged gold nanoparticles
Authors: Taylor Ulrike , Klein Sabine , Petersen Svea , Kues Wilfried , Barcikowski Stephan , Rath Detlef 
Published: January 2010

AbstractGold nanoparticles (GNPs) have interesting optical properties, such as exceptionally high quantum yields and virtually limitless photostability. Therefore, they show the potential for applications as biomarkers especially suitable for in vivo and long‐term studies. The generation of GNPs using pulsed laser light rather than chemical means provides nanoparticles, which are remarkably stable in a variety of media without the need of stabilizing agents or ligands. This stabilization is achieved by partial oxidation of the gold surface resulting in positively charged GNPs. However, little is known about cellular uptake of such ligand‐free nanoparticles, their intracellular fate, or cell viability after nanoparticle contact. The current work is aimed to explore the response of a bovine cell line to GNP exposure mainly using laser scanning confocal microscopy (LSCM) supported by other techniques. Cultured bovine immortalized cells (GM7373) were coincubated with GNP (average diameter 15 nm, 50 μM Au) for 2, 24, and 48 h. The detection of GNP‐associated light scattering by the LSCM facilitated a clear distinction between GNP‐containing cells and the negative controls. After 48 h, 75% of cells had visibly incorporated nanoparticles. No colocalization was detected with either Rab5a or Lamp1‐positive structures, i.e., endosomes or lysosomes, respectivley. However, transmission electron microscope analysis of GNP‐coincubated cells indicated the nanoparticles to be positioned within electron‐dense structures. Coincubation at 4°C did not inhibit nanoparticle uptake, suggesting diffusion as possible entrance mechanism. Although the assessment of cell morphology, membrane integrity, and apoptosis revealed no GNP‐related loss of cell viability at a gold concentration of 25 μM or below, a cytotoxic effect was observed in a proliferation assay after exposing low cell numbers to 50 μM Au and above. In conclusion, this study confirmed the cellular uptake of ligand‐free gold nanoparticles during coincubation apparently without using endocytic pathways. © 2010 International Society for Advancement of Cytometry
Translocation of histone H1 subtypes between chromatin and cytoplasm during mitosis in normal human fibroblasts
Authors: Gréen Anna , Lönn Anita , Peterson Kajsa Holmgren , Öllinger Karin , Rundquist Ingemar 
Published: January 2010

AbstractHistone H1 is an important constituent of chromatin, which undergoes major structural rearrangements during mitosis. However, the role of H1, multiple H1 subtypes, and H1 phosphorylation is still unclear. In normal human fibroblasts, phosphorylated H1 was found located in nuclei during prophase and in both cytoplasm and condensed chromosomes during metaphase, anaphase, and telophase as detected by immunocytochemistry. Moreover, we detected remarkable differences in the distribution of the histone H1 subtypes H1.2, H1.3, and H1.5 during mitosis. H1.2 was found in chromatin during prophase and almost solely in the cytoplasm of metaphase and early anaphase cells. In late anaphase, it appeared in both chromatin and cytoplasm and again in chromatin during telophase. H1.5 distribution pattern resembled that of H1.2, but H1.5 was partitioned between chromatin and cytoplasm during metaphase and early anaphase. H1.3 was detected in chromatin in all cell cycle phases. We propose therefore, that H1 subtype translocation during mitosis is controlled by phosphorylation, in combination with H1 subtype inherent affinity. We conclude that H1 subtypes, or theirphosphorylated forms, may leave chromatin in a regulated way to give access for chromatin condensing factors or transcriptional regulators during mitosis. © 2010 International Society for Advancement of Cytometry
A generative model of microtubule distributions, and indirect estimation of its parameters from fluorescence microscopy images
Authors: Shariff Aabid , Murphy Robert F. , Rohde Gustavo K. 
Published: January 2010

AbstractThe microtubule network plays critical roles in many cellular processes, and quantitative models of how its organization varies across cell types and conditions are required for understanding those roles and as input to cell simulations. High‐throughput image acquisition technologies are potentially valuable for this purpose, but do not provide sufficient resolution for current analysis methods that rely on tracing of individual microtubules. We describe a parametric conditional model of microtubule distribution that can generate a microtubule network in intact cells using a persistent random walk approach. The model parameters are physically meaningful as they directly describe the spatial distribution of microtubules and include the number of microtubules as well as the mean of the length distribution. We also present an indirect method for estimating the parameters of the model from three‐dimensional fluorescence microscope images of cells that relies on comparing acquired images with simulated images generated from the model. Our results show that our method can reasonably recover parameters for a given query image, and we present the distributions of parameters estimated by our method for a collection of HeLa cell images. © 2010 International Society for Advancement of Cytometry
Lineage‐specific transcription factors in unexpected places
Authors: Munn David H. 
Published: January 2010

AbstractFoxp3 is a transcription factor closely associated with the Treg lineage in humans and mice. In the immune system, Foxp3 appears highly specific for Treg, and is not known to be expressed by other immune cell types. In this issue of the European Journal of Immunology, an article reports that human DC transfected with ectopic Foxp3 unexpectedly acquire an immunosuppressive phenotype. Foxp3‐transfected DC suppressed proliferation of naive T cells, and biased the differentiation of CD4+ cells into Treg‐like cells that themselves expressed Foxp3. The molecular mechanism of these effects required functional activity of the immunoregulatory enzyme IDO. Thus, a transcription factor not native to DC nevertheless conferred elements of a regulatory phenotype following ectopic expression.
Comparison of two derivatisation methods for conjugated linoleic acid isomer analysis by Ag+‐HPLC/DAD in beef fat
Authors: Dance Lyndsey J. E. , Doran Olena , Hallett Kathy , Dannenberger Dirk , Nuernberg Gerd , Nuernberg Karin 
Published: January 2010

AbstractTwo different procedures for the methylation of conjugated linoleic acid isomers (CLA) were compared by silver ion (Ag+)‐HPLC. The base‐catalysed method followed by an acid‐catalysed method (NaOCH3/BF3), and base hydrolysis followed by methylation with diazomethane in diethyl ether (diazomethane) were used to prepare fatty acid methyl esters from lipids present in subcutaneous adipose tissue from beef steers. The repeatability θ of the two derivatisation methods was high (>0.9) for the major CLA isomers cis‐9,trans‐11 and trans‐11,cis‐13. A significant difference between the methods was found for the four isomers trans‐11,trans‐13, trans‐10,trans‐12, trans‐9,trans‐11, and trans‐8,trans‐10 and for the sum of total trans/trans isomers for both absolute (mg/100 g) and relative (%), which were higher with the NaOCH3/BF3 method. For the main isomer cis‐9,trans‐11 and the sum of total CLA isomers, a higher concentration was identified with the diazomethane method (781.2 mg/100 g vs. 749.3 mg/100 g and 991.59 vs. 962.99, respectively).
Frying performance of the hull oil unsaponifiable matter of Pistacia atlantica subsp. mutica
Authors: Farhoosh Reza , Kafrani Mohammad Hossein Tavassoli 
Published: January 2010

AbstractThe anti‐rancidity effect of the hull oil unsaponifiable matter (USM, 100 ppm) of Pistacia atlantica subsp. mutica (Bene) on sunflower oil (SFO) during frying at 180 °C was investigated and compared to that of tert‐butylhydroquinone (TBHQ, 100 ppm). The unsaponifiable constituents of the Bene hull oil (BHO) were separated into hydrocarbons (3.7%), carotenes (3.6%), tocopherols and tocotrienols (24.7%), linear and triterpenic alcohols (0.9%), methylsterols (5.7%), sterols (3.2%), triterpenic dialcohols (4.7%), and triterpenic dialcohol methylesters (4.5%), by means of silica gel TLC. The results obtained from the measurements of total polar compounds, conjugated diene value, carbonyl value, and acid value during 32 h of frying showed that the frying stability of SFO improves more in the presence of the USM of BHO than in the presence of TBHQ. Moreover, compared to TBHQ, the USM had a better protective effect on the indigenous tocopherols of SFO during frying.
Palladium‐Catalyzed Direct Arylation of 4‐Chromanones: Selective Synthesis of Racemic Isoflavanones and 3,3‐Diaryl‐4‐chromanones
Authors: Bellina Fabio , Masini Tiziana , Rossi Renzo 
Published: January 2010

AbstractFor the first time, the synthesis of racemic isoflavanones has been achieved in satisfactory to good yields and with high selectivity by Pd‐catalyzed direct C‐3 arylation of 3‐unsubstituted 4‐chromanones with aryl bromides with the aid of a Pd2(dba)3/tBu3PHBF4 catalyst system in the presence of KHCO3 as the base in a dioxane/water mixture (4:1). This catalyst system has also been employed in an unprecedented synthesis of 3,3‐diaryl‐4‐chromanones through direct arylation of 4‐chromanones in water.
Morphodynamics of the exit of a cutoff meander: experimental findings from field and laboratory studies
Authors: Coz J. Le , Michalková M. , Hauet A. , C̆omaj M. , Dramais G. , Holubová K. , Piégay H. , Paquier A. 
Published: January 2010

AbstractThe morphological evolution of the entrances and exits of abandoned river channels governs their hydrological connectivity. The study focusses on flow and sediment dynamics in the exit of a cutoff meander where the downstream entrance is still connected to the main channel, but the upstream entrance is closed. Two similar field and laboratory cases were investigated using innovative velocimetry techniques (acoustic Doppler profiling, image analysis). Laboratory experiments were conducted with a mobile‐bed physical model of the Morava River (Slovakia). Field measurements were performed in the exit of the Port‐Galland cutoff meander, Ain River (France). Both cases yielded consistent and complementary results from which a generic scheme for flow patterns and morphological evolution was derived. A simple analogy with flows in rectangular side cavities was used to explain the recirculating flow patterns which developed in the exit. A decelerating inflow deposits bedload in the downstream part of the cavity, while the upstream part is eroded by an accelerating outflow, leading to the retreat of the upstream bank. In the field, strong secondary currents were observed, especially in the inflow, which may enhance the scouring of the downstream corner of the cavity. Also, fine sediment deposits constituted a silt layer in a transitional zone, located between the mouth of the abandoned channel and the oxbow‐lake within the cutoff meander. Attempts at morphological prediction should consider not only the flow and sediment conditions in the cavity, but also the dynamics of the main channel. Copyright © 2010 John Wiley & Sons, Ltd
Impact of ambient bright light on agitation in dementia
Authors: Barrick Ann Louise , Sloane Philip D. , Williams Christianna S. , Mitchell C. Madeline , Connell Bettye Rose , Wood Wendy , Hickman Susan E. , Preisser John S. , Zimmerman Sheryl 
Published: January 2010

AbstractObjectiveTo evaluate the effect of ambient bright light therapy (BLT) on agitation among institutionalized persons with dementia.MethodsHigh intensity, low glare ambient lighting was installed in activity and dining areas of a state psychiatric hospital unit in North Carolina and a dementia‐specific residential care facility in Oregon. The study employed a cluster‐unit crossover design involving four ambient lighting conditions: AM bright light, PM bright light, All Day bright light, and Standard light. Sixty‐six older persons with dementia participated. Outcome measures included direct observation by research personnel and completion by staff caregivers of the 14‐item, short form of the Cohen‐Mansfield Agitation Inventory (CMAI).ResultsAnalyses of observational data revealed that for participants with mild/moderate dementia, agitation was higher under AM light (p = 0.003), PM light (p < 0.001), and All Day light (p = 0.001) than Standard light. There was also a trend toward severely demented participants being more agitated during AM light than Standard light (p = 0.053). Analysis of CMAI data identified differing responses by site: the North Carolina site significantly increased agitation under AM light (p = 0.002) and PM light (p = 0.013) compared with All Day light while in Oregon, agitation was higher for All Day light compared to AM light (p = 0.030). In no comparison was agitation significantly lower under any therapeutic condition, in comparison to Standard lighting.ConclusionsAmbient bright light is not effective in reducing agitation in dementia and may exacerbate this behavioral symptom. Copyright © 2010 John Wiley & Sons, Ltd.
The assessment of surface water resources for the semi‐arid Yongding River Basin from 1956 to 2000 and the impact of land use change
Authors: Wang Lei , Wang Zhongjing , Koike Toshio , Yin Hang , Yang Dawen , He Shan 
Published: January 2010

AbstractThe assessment of surface water resources (SWRs) in the semi‐arid Yongding River Basin is vital as the basin has been in a continuous state of serious water shortage over the last 20 years. In this study, the first version of the geomorphology‐based hydrological model (GBHM) has been applied to the basin over a long period of time (1956–2000) as part of an SWR assessment. This was done by simulating the natural hydrological processes in the basin. The model was first evaluated at 18 stream gauges during the period from 1990 to 1992 to evaluate both the daily streamflows and the annual SWRs using the land use data for 1990. The model was further validated in 2000 with the annual SWRs at seven major stream gauges. Second, the verified model was used in a 45‐year simulation to estimate the annual SWRs for the basin from 1956 to 2000 using the 1990 land use data. An empirical correlation between the annual precipitation and the annual SWRs was developed for the basin. Spatial distribution of the long‐term mean runoff coefficients for all 177 sub‐basins was also achieved. Third, an additional 10‐year (1991–2000) simulation was performed with the 2000 land use data to investigate the impact of land use changes from 1990 to 2000 on the long‐term annual SWRs. The results suggest that the 10‐year land use changes have led to a decrease of 8·3 × 107 m3 (7·9% of total) for the 10‐year mean annual SWRs in the simulation. To our knowledge, this work is the first attempt to assess the long‐term SWRs and the impact of land use change in the semi‐arid Yongding River Basin using a semi‐distributed hillslope hydrological model. Copyright © 2010 John Wiley & Sons, Ltd.