bluuebunny/crossref_metadata_2025_split huggingface dataset:
A near‐annual palaeohydrological study based on testate amoebae from a sub‐alpine mire: surface wetness and the role of climate during the instrumental period
Authors: Lamentowicz Mariusz , Van Der Knaap Willem , Lamentowicz Łukasz , Van Leeuwen Jacqueline F. N. , Mitchell Edward A. D. , Goslar Tomasz , Kamenik Christian 
Published: July 2009

AbstractWe present the first testate amoeba‐based palaeohydrological reconstruction from the Swiss Alps, and the first depth to the water table (DWT) calibration dataset for this region. Compared to existing models, our new calibration dataset performs well (RMSEP = 4.88), despite the length of the water table gradient covered (53 cm). The present‐day topography and vegetation of the study mire Mauntschas suggest that it is partly ombrotrophic (large Sphagnum fuscum hummocks, one of which was the coring site) but mostly under the minerotrophic influence of springs in the mire and runoff from the surrounding area. Ombrotrophic Sphagnum fuscum hummocks developed at the sampling site only during the last 50 years, when testate amoebae indicate a shift towards dry and/or acid conditions. Prior to AD 1950 the water table was much higher, suggesting that the influence of the mineral‐rich water prevented the development of ombrotrophic hummocks. The reconstructed DWT correlated with Pinus cembra pollen accumulation rates, suggesting that testate amoebae living on the mire and P. cembra growing outside of it partly respond to the same factor(s). Finally, temperature trends from the nearby meteorological station paralleled trends in reconstructed DWT. However, contrary to other studies made on raised bogs of northwestern Europe, the highest correlation was observed for winter temperature, despite the fact that testate amoebae would more logically respond to moisture conditions during the growing season. The observed correlation with winter temperature might reflect a control of winter severity on surface moisture during at least the first part of the growing season, through snow melt and soil frost phenomena influencing run‐off. More ecohydrological work on sub‐alpine mires is needed to understand the relationships between climate, testate amoebae and peatland development. Copyright © 2009 John Wiley & Sons, Ltd.
Generalized finite differences using fundamental solutions
Authors: Leitão V. M. A. 
Published: July 2009

AbstractIt is well known that solutions for linear partial differential equations may be given in terms of fundamental solutions. The fundamental solutions solve the homogeneous equation exactly and are obtained from the solution of the inhomogeneous equation where the inhomogeneous term is described by a Dirac delta distribution. Fundamental solutions are the building blocks of the boundary element method and of the method of fundamental solutions and are traditionally used to build boundary‐only global approximations in the domain of interest. In this work the same characteristic of the fundamental solutions, that of solving the homogeneous equation exactly, is used but not to build a global approximation. On the contrary, local approximations are built in such a manner that it is possible to construct finite difference operators that are free from any form of structured grid. Copyright © 2009 John Wiley & Sons, Ltd.
Epitaxial crystallization and oriented structure of linear low‐density polyethylene/isotactic polypropylene blends obtained via dynamic packing injection molding
Authors: Su Run , Wang Ke , Zhang Qin , Chen Feng , Fu Qiang , Hu Nan , Chen Erqiang 
Published: July 2009

AbstractIn this work, as a part of a long‐term project aimed at controlling of crystal structure and phase morphology for a injection molded product, we investigated the oriented structure and possible epitaxial growth of polyolefin blend (low‐density polyethylene (LLDPE)/isotatic polypropylene (iPP)), achieved by dynamic packing injection molding, which introduced strong oscillatory shear on the gradually‐cooled melt during the packing process. The crystalline and oriented structures of the prepared blends with different compositions were estimated in detail through 2D X‐ray diffraction, calorimetry, and optical microscopy. As iPP was the dominant phase (its content was more than 50 wt%), our results indicated that it could be highly oriented in the blends. In such case, it was interesting to find that LLDPE epitaxially crystallized on the oriented iPP through a crystallographic matching between (100)LLDPE and (010)iPP, resulting in an inclination of LLDPE chains, about 50° to the iPP chain axis. On the other hand, as iPP was the minor phase, iPP was less oriented and no epitaxial growth between iPP and LLDPE was observed; even LLDPE remained oriented. The composition‐dependent epitaxial growth of LLDPE on oriented iPP could be understood as due to: (1) the effect of crystallization sequence, it was found that iPP always crystallized before LLDPE for all compositions; (2) the dependence of oriented iPP structure on the blend composition; (3) the “mutual nucleation” between LLDPE and iPP due to their partial miscibility. Copyright © 2009 John Wiley & Sons, Ltd.
Methodological variability in detecting prescribing errors and consequences for the evaluation of interventions
Authors: Franklin Bryony Dean , Birch Sylvia , Savage Imogen , Wong Ian , Woloshynowych Maria , Jacklin Ann , Barber Nick 
Published: July 2009

AbstractPurposeTo compare four methods of detecting prescribing errors (PE) in the same patient cohorts before and after an intervention (computerised physician order entry; CPOE) and to determine whether the impact of CPOE is identified consistently by all methods.MethodsPEs were identified using (1) prospective detection by ward pharmacist; (2) retrospective health record review; (3) retrospective use of a trigger tool and (4) spontaneous reporting over two separate 4‐week periods on one surgical ward in a UK teaching hospital.ResultsWe reviewed 93 patients pre‐ and 114 post‐CPOE. Using all four methods, we identified 135 PE (10.7% of all medication orders) pre‐CPOE, and 127 (7.9%) post‐CPOE. There was little overlap in PE detected by the different methods: prospective detection identified 48 (36% of all PE) pre‐ and 30 (24%) post‐CPOE; retrospective review (RR) revealed 93 (69%) pre‐ and 105 (83%) post‐CPOE, trigger tool 0 pre‐ and 2 (2%) post‐CPOE and spontaneous reporting 1 (1%) pre‐ and 1 (1%) post‐CPOE. The calculated relative reduction in risk of PE was 50% using prospective data, 12% with RR and 26% using data from all four methods.ConclusionsIn this study, each method predominantly identified different PE. A combination of methods may be required to understand the true effectiveness of different interventions. Copyright © 2009 John Wiley & Sons, Ltd.
Anti‐Stokes cooling in semiconductor nanocrystal quantum dots: A feasibility study
Authors: Rakovich Yury P. , Donegan John F. , Vasilevskiy Mikhail I. , Rogach Andrey L. 
Published: July 2009

AbstractIn this review, we discuss the feasibility of laser cooling of semiconductor nanocrystal quantum dots by phonon‐assisted anti‐Stokes photoluminescence. Taking into account recent experimental advances, in particular, the development of semiconductor nanocrystals with very high quantum yield, we analyze in detail how the various physical processes in nanocrystals might help or hinder the cooling process. Possible experimental approaches to achieve efficient optical cooling are also discussed.
Initial molecular orientation of phthalocyanines on oxide substrates
Authors: Biswas Indro , Peisert Heiko , Casu Maria Benedetta , Schuster Britt‐Elfriede , Nagel Peter , Merz Michael , Schuppler Stefan , Chassé Thomas 
Published: July 2009

AbstractThe molecular orientation of ultra‐thin films of copper phthalocyanine and perfluoro‐copper phthalocyanine (F16PcCu) on various oxide substrates is examined with polarisation dependent NEXAFS spectroscopy. The focus is on the adsorption geometry of the first adsorbed layers, which can strongly vary from the observed orientation in thin‐films above the few nanometre regime. Native silicon dioxide, indium tin oxide and titanium dioxide are chosen for their relevance to technical applications. On chemically and thermally cleaned oxide surfaces a predominantly standing initial orientation is preferred, while on ion bombarded activated surfaces the molecules prefer a lying orientation.
Influence of the gas medium on the nonlinear electrical characteristics of semi‐insulating GaAs
Authors: Inalöz A. , Kurt H. Y. , Koç E. , Salamov B. G. 
Published: July 2009

AbstractElectrical instability in semi‐insulating (SI) GaAs plates of the semiconductor gas‐discharge structure (SGDS) is studied experimentally in air and neon as a function of pressure, interelectrode distance, and cathode area diameter. While being driven with a stationary voltage, it generates current and discharge light‐emission instabilities with different amplitudes of the oscillation in Ne up to atmospheric pressure. The presence of the deep electronic levels of defects, give rise to the N‐shaped negative differential resistance (NDR) of the material, and as a consequence, to oscillations in the discharge light emission when a dc voltage of a high enough magnitude is applied to the GaAs cathode. A SGDS with an N‐shaped current–voltage characteristic (CVC) has been analyzed using both the current and discharge light emission data showing the electrical instability in the GaAs cathode. It is observed that application of high feeding voltage to the cathode gives rise to a nonuniform spatial distribution of the discharge light emission, which disturbed the operation of the system. The experiment also presents a new method to study and visualization of the electrical instabilities in the high‐resistivity GaAs plates of large diameter.
Determination of levitation force and pinning properties of (Sm123)1−x(Yb211)x bulk superconductor depending on Yb211 doping ratio
Authors: Ozturk K. , Celik S. , Cansiz A. 
Published: July 2009

AbstractThe vertical force density curves of (Sm123)1−x(Yb211)x high temperature superconductor (HTS) samples prepared by a melt‐powder‐melt‐growth technique were measured during vertical and lateral traverses in zero field cooling (ZFC) regime for various doping levels (x). It was determined that the maximum vertical force density of the samples increases when the doping level increases and after certain level of the doping the force saturates. The pinning properties, which create attractive force, were enhanced up to a certain Yb211 doping level by introducing locally suppressed superconducting regions. These results indicate that the optimization fabrication conditions and Yb211 doping level should be further investigated for larger dimensional samples to enhance technological applicability. The frozen image model was used to predict the experimentally measured levitation force between a permanent magnet (PM) and the superconductor samples. Various configurations of the PM/HTS force interaction were tested according to the magnet and superconductor size. The doped HTS samples do not show very strong diamagnetic behavior as the frozen image model predicts. The levitation force behavior regarding the dimensions of the PM and HTS indicates an illustration how the diamagnetic behavior of the superconductor transforms into the flux pinning.
The spin‐3/2 Ising model on a two‐layer Bethe lattice with AFM/AFM interactions
Authors: Albayrak Erhan , Yigit Ali 
Published: July 2009

AbstractThe spin‐3/2 Ising model is studied on a two‐layer Bethe lattice with antiferromagnetic/antiferromagnetic (AFM/AFM) intralayer and either FM or AFM type of interlayer interactions by using the pairwise approach for the coordination numbers q = 3, 4, and 6. In the guidance of the ground‐state phase diagrams, the thermal variations of the magnetizations, susceptibility and specific heat are examined in detail to obtain the critical behaviors of the model. Thus, it was found that the model presents second‐ and first‐order phase transitions; where their lines are combined is a tricritical point. In addition, the model also presents two Néel temperatures, the existence of which leads to the re‐entrant behavior.
Towards Ideal Magnetofluorescent Nanoparticles for Bimodal Detection of Breast‐Cancer Cells
Authors: Corsi Fabio , De Palma Clara , Colombo Miriam , Allevi Raffaele , Nebuloni Manuela , Ronchi Silvia , Rizzi Giuseppina , Tosoni Antonella , Trabucchi Emilio , Clementi Emilio , Prosperi Davide 
Published: July 2009

AbstractAn increasing number of novel molecular markers based on nanomaterials for tumor diagnostics have been developed in recent years. Many efforts have focused on the achievement of site‐targeted bioconjugated nanoparticles. In contrast, the mechanisms of toxicity, endocytosis, and degradation pathways are still poorly understood, despite their primary importance for clinical translation. In this study, three different model nanoscale magnetofluorescent particle systems (MFNs) are designed and fabricated. These nanoparticles are evaluated in terms of size, morphology, zeta potential, fluorescence efficiency, capability of enhancing T2 relaxivity of water protons, and stability. Accordingly, two are developed and the mechanism of internalization, the intracellular fate, and the toxicity in MCF‐7 adenocarcinoma cells are studied. Besides the well‐documented size effect, the anionic charge seems to be a crucial factor for particle internalization, as MFN penetration through the cell membrane could be modulated by surface charge. Ultrastructural analysis of transmission electron micrographs combined with evidence from confocal microscopy reveals that MFNs are internalized by clathrin‐mediated endocytosis and macropinocytosis. Moreover, MFNs are found in EEA1‐positive endosomes and in lysosomes, indicating that they follow a physiological pathway of endocytosis. Magnetorelaxometric analysis demonstrates that MFNs enable the detection of 5 × 105 cells mL−1 after treatment with particle dosages as low as 30 µg mL−1. Hence, MFNs appear to be a valuable and safe bimodal contrast agent that can be developed for the noninvasive diagnosis of breast cancer.
Wind effect on milad tower using computational fluid dynamics
Authors: Yahyai Mahmoud , Daryan Amir Saedi , Ziaei Masoud , Mirtaheri Seyed Masoud 
Published: July 2009

AbstractMilad tower is located in Tehran, Iran, and is a 436‐m telecommunication tower ranked as the fourth tallest structure in the world. Because of its specific use and also because of highly sensitive communication devices installed on the tower, nonlinear deformations under future severe winds and earthquakes should be studied. In this paper, a comprehensive study is carried out to investigate the effect of wind on this tower. The techniques of computational fluid dynamics, such as large eddy simulation (LES), Reynolds Averaged Navier–Stokes Equations (RANS) model and so on, were adopted in this study to predict wind loads on and wind flows around the building. The calculated results are compared with those of wind tunnel test. It was found through the comparison that the LES with a dynamic subgrid‐scale model can give satisfactory predictions for mean and dynamic wind loads on the specific structure of Milad tower, while the RANS model with modifications can yield encouraging results in most cases and has the advantage of providing rapid solutions. Furthermore, it was observed that typical features of the flow fields around such a surface‐mounted bluff body standing in atmospheric boundary layers can be captured numerically. Copyright © 2009 John Wiley & Sons, Ltd.
The “114” Cobaltites and Ferrites: New Routes to Ferrimagnetism and Magnetic Frustration
Authors: Raveau Bernard , Caignaert Vincent , Pralong Valérie , Maignan Antoine 
Published: July 2009

AbstractAn overview of the magnetic properties of the “114” cobaltites and ferrites in connection with their crystal structure, built up of triangular and kagomé layers of CoO4 tetrahedra is presented. These oxides can be classified into three different structural types according to their room temperature structure: the trigonal P31c phases LnBaCo4O7 and CaBaFe4O7, the orthorhombic Pbn21 CaBaCo4O7 phase, and the cubic LnBaFe4O7 oxides. The magnetic properties show complex transitions for LnBaCo4O7 oxides, whereas spin glass like behavior is observed for LnBaFe4O7 and ferrimagnetic like properties are observed for CaBaFe4O7 and CaBaCo4O7. The topotactic oxidation of those oxides is also discussed.
A modified LOESS normalization applied to microRNA arrays: a comparative evaluation
Authors: Risso Davide , Massa Maria Sofia , Chiogna Monica , Romualdi Chiara 
Published: July 2009

AbstractMotivation: Microarray normalization is a fundamental step in removing systematic bias and noise variability caused by technical and experimental artefacts. Several approaches, suitable for large-scale genome arrays, have been proposed and shown to be effective in the reduction of systematic errors. Most of these methodologies are based on specific assumptions that are reasonable for whole-genome arrays, but possibly unsuitable for small microRNA (miRNA) platforms. In this work, we propose a novel normalization (loessM), and we investigate, through simulated and real datasets, the influence that normalizations for two-colour miRNA arrays have on the identification of differentially expressed genes.Results: We show that normalizations usually applied to large-scale arrays, in several cases, modify the actual structure of miRNA data, leading to large portions of false positives and false negatives. Nevertheless, loessM is able to outperform other techniques in most experimental scenarios. Moreover, when usual assumptions on differential expression distribution are missed, channel effect has a strikingly negative influence on small arrays, bias that cannot be removed by normalizations but rather by an appropriate experimental design. We find that the combination of loessM with eCADS, an experimental design based on biological replicates dye-swap recently proposed for channel-effect reduction, gives better results in most of the experimental conditions in terms of specificity/sensitivity both on simulated and real data.Availability: LoessM R function is freely available at http://gefu.cribi.unipd.it/papers/miRNA-simulation/Contact: chiara.romualdi@unipd.itSupplementary information: Supplementary data are available at Bioinformatics online.
Modified variational Bayes EM estimation of hidden Markov tree model of cell lineages
Authors: Olariu Victor , Coca Daniel , Billings Stephen A. , Tonge Peter , Gokhale Paul , Andrews Peter W. , Kadirkamanathan Visakan 
Published: July 2009

Abstract
Motivation: Human pluripotent stem cell lines persist in culture as a heterogeneous population of SSEA3 positive and SSEA3 negative cells. Tracking individual stem cells in real time can elucidate the kinetics of cells switching between the SSEA3 positive and negative substates. However, identifying a cell's substate at all time points within a cell lineage tree is technically difficult.
Results: A variational Bayesian Expectation Maximization (EM) with smoothed probabilities (VBEMS) algorithm for hidden Markov trees (HMT) is proposed for incomplete tree structured data. The full posterior of the HMT parameters is determined and the underflow problems associated with previous algorithms are eliminated. Example results for the prediction of the types of cells in synthetic and real stem cell lineage trees are presented.
Availability:The Matlab code for the VBEMS algorithm is freely available at http://www.acse.dept.shef.ac.uk/repository/vbems_lineage_tree/VBEMS.ZIP
Contact: visakan@sheffield.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Plasma soluble tumour necrosis factor‐α receptor 2 is elevated in obesity: specific contribution of visceral adiposity
Authors: Cartier Amélie , Côté Mélanie , Bergeron Jean , Alméras Natalie , Tremblay Angelo , Lemieux Isabelle , Després Jean‐Pierre 
Published: July 2009

SummaryObjective  We examined the obesity phenotype most strongly associated with increased plasma concentrations of sTNFR2, and compared which of the two markers, TNF‐α or sTNFR2, better predicts indices of plasma glucose‐insulin homeostasis.Design, patients and measurements  Plasma sTNFR2 levels were measured in a sample of 287 healthy nondiabetic men [age: 43·9 ± 8·0 years (mean ± SD)], covering a wide range of adiposity values (BMI: 29·0 ± 4·4 kg/m2; waist girth: 100·0 ± 11·7 cm).Results  Plasma sTNFR2 levels correlated positively and significantly with BMI (r = 0·36; P < 0·0001), fat mass (r = 0·42; P < 0·0001), waist girth (r = 0·38; P < 0·0001) as well as with visceral (r = 0·37; P < 0·0001) and subcutaneous adipose tissue (AT) (r = 0·40; P < 0·0001) areas measured by computed tomography. Two subgroups (n = 27 in each group) of overweight men (BMI ≥25 kg/m2) were individually matched for similar BMI values, but with markedly different levels of visceral AT (< or ≥130 cm2) and then compared with a control group of 46 lean subjects (with both BMI <25 kg/m2 and visceral AT <130 cm2). This analysis revealed that men characterized by high levels of visceral AT had significantly higher concentrations of sTNFR2 compared with obese men with low visceral AT (1861 ± 457 pg/ml vs. 1722 ± 400; P < 0·05) and with lean controls (1570 ± 291 pg/ml; P < 0·001). Whereas subjects classified across tertiles of TNF‐α levels showed no difference in glucose tolerance and insulin levels, subjects in the upper tertile of plasma sTNFR2 levels were characterized with the highest plasma insulin concentrations during the OGTT and had the highest area under the curve of insulin concentrations.Conclusions  These results indicate that sTNFR2 levels are more closely related to abdominal AT accumulation than to total adiposity. Furthermore, plasma concentrations of sTNFR2 are independently related to plasma glucose‐insulin homeostasis beyond the known contribution of visceral adiposity.
Targeting energy expenditure in muscle as a means of combating obesity
Authors: Clarke Iain J , Henry Belinda A 
Published: July 2009

Summary1. To date, an effective therapeutic agent that induces weight loss in obese subjects remains elusive. In order to establish a successful means to combat obesity, it is imperative that we identify novel targets that regulate energy balance.2. Exciting new data have created resurgence in interest in the role of thermogenesis in energy balance. Recently, it has been demonstrated that functional brown adipocytes are present in adult humans and that brown adipocytes and myocytes are derived from a similar cell lineage and are thus likely to have similar physiological functions.3. Recent work in the sheep has demonstrated that diffuse fat beds and skeletal muscle exhibit thermogenic properties. Furthermore, in sheep, central administration of leptin markedly increases postprandial thermogenesis in both fat and muscle tissues. This demonstrates that thermogenic processes in skeletal muscle can be manipulated in a similar way to thermogenesis in brown fat.4. Given that skeletal muscle comprises a significant portion of bodyweight, approximately 30–40% of total body mass, we predict that energy expended by this tissue is likely to have significant ramifications for the regulation of bodyweight.5. We propose that manipulation of skeletal muscle thermogenesis may provide a novel avenue for the development of anti‐obesity therapies.