bluuebunny/crossref_metadata_2025 huggingface dataset:
Creativity of Chinese and American Cultures: A Synthetic Analysis
Authors: Niu Weihua , Kaufman James C.
Published: February 2013

The article integrates the seven papers of the two special issues with a special focus on discussing the differences in people's beliefs about creativity between the Chinese and American cultures: How it is conceived, evaluated, and nurtured. It uses three metaphors to capture major differences in these aspects, and highlights areas with profound cultural variations in conceptions and creative education for future research.
Boron behavior in apple plants in acidic and limed soil
Authors: Antoniadis Vasileios , Chatzissavvidis Christos , Paparnakis Asterios
Published: February 2013

In dry Mediterranean‐type climates boron (B) levels may naturally be high and even toxic to plants. Although liming of an acidic soil is expected to decrease B levels, it is not known what the effects would be in such areas of high‐B soils, especially in B‐sensitive crops such as apple trees. Thus, our aim was to study the behavior of added B in newly planted apple rootstocks in an acidic soil which was limed to pH 6.5 in an outdoor pot experiment. Added B increased significantly B extractability from soil, and B levels were lower in the limed compared to the acidic soils. Plant B concentrations also increased with added B but differences between limed and unlimed soils were not evident, because plant B did not seem to reflect changes in B behavior in soil. However, B uptake was significantly increased with added B, and was further increased with liming, contrary to what the soil extractions indicated, due to improved growth conditions. Our results show that although liming decreased soil B levels, at the same time it did not affect plant B concentration and accelerated the uptake of added B, indicating a possibility for increased soil‐to‐plant mobility of B.
Effects of model Maillard compounds on bone characteristics and functionality
Authors: Roncero‐Ramos Irene , Delgado‐Andrade Cristina , Rufián‐Henares José Ángel , Carballo José , Navarro M Pilar
Published: February 2013

Background

Physical and biomechanical properties of bone can be affected by non‐enzymatic crosslinks, which are implicated in bone pathologies such as osteoporosis. The purpose of this study was to analyse the effects of the consumption of model Maillard reaction product (MRP) from glucose–lysine heated for 90 min at 150 °C (GL90) on bone composition and features. Rats were fed either a control diet or a diet containing 30 g kg−1 GL90 for 88 days. Food consumption and the animals' body weights were monitored. After sacrifice, the femur, pelvic bone and tibia were removed for analysis of their composition and physical and biomechanical properties.

Results

The organic matrix of the femur and the density of the pelvic bone decreased after MRP intake, whereas pentosidine content increased greatly with respect to the control group (41.7 ± 9.9 vs 171.4 ± 3.3 mmol mol−1 collagen). The rising level of C‐telopeptide degradation products from type I collagen (β‐CTX) suggested a possible situation of increased bone resorption and/or higher turnover.

Conclusion

In conjunction, the detrimental effect on the organic matrix, the situation of higher resorption and/or bone turnover indicated by the β‐CTX values and the high pentosidine content in bone provoked negative consequences on certain mechanical properties such as the ability to withstand force and absorb energy without failure. © 2013 Society of Chemical Industry
Initial experience with seven tesla magnetic resonance spectroscopy of hypothalamic GABA during hyperinsulinemic euglycemia and hypoglycemia in healthy humans
Authors: Moheet A. , Emir U. E. , Terpstra M. , Kumar A. , Eberly L. E. , Seaquist E. R. , Öz G.
Published: February 2013

Purpose

Hypothalamic GABA signaling has been shown to regulate the hormonal response to hypoglycemia in animals. The hypothalamus is a challenging brain region for magnetic resonance spectroscopy (MRS) due to its small size and central location. To investigate the feasibility of measuring GABA in the hypothalamus in humans, ultra‐high field MRS was used.

Methods

GABA levels in the hypothalamus and occipital cortex (control region) were measured in healthy volunteers during euglycemia and hypoglycemia at 7 tesla using short‐echo STEAM (TE = 8 ms, TR = 5 s).

Results

Hypothalamic GABA levels were quantified with a mean within‐session test–retest coefficient of variance of 9%. Relatively high GABA levels were observed in the hypothalamus compared with other brain regions. Hypothalamic GABA levels were 3.5 ± 0.3 µmol/g during euglycemia (glucose 89 ± 6 mg/dL) vs. 3.0 ± 0.4 µmol/g during hypoglycemia (glucose 61 ± 3 mg/dL) (P = 0.06, N = 7). In the occipital cortex, GABA levels remained constant at 1.4 ± 0.4 vs.1.4 ± 0.3 µmol/g (P = 0.3, N = 5) as glucose fell from 91 ± 4 to 61 ± 4 mg/dL.

Conclusion

GABA concentration can be quantified in the human hypothalamus and shows a trend toward decrease in response to an acute fall in blood glucose. These methods can be used to further investigate role of GABA signaling in the counterregulatory response to hypoglycemia in humans. Magn Reson Med 71:12–18, 2014. © 2013 Wiley Periodicals, Inc.
Retracted: Role of STAT3 and vitamin D receptor in EZH2‐mediated invasion of human colorectal cancer
Authors: Lin Yan‐Wei , Ren Lin‐Lin , Xiong Hua , Du Wan , Yu Ya‐Nan , Sun Tian‐Tian , Weng Yu‐Rong , Wang Zhen‐hua , Wang Ji‐Lin , Wang Ying‐Chao , Cui Yun , Sun Dan‐Feng , Han Ze‐Guang , Shen Nan , Zou Weiping , Xu Jie , Chen Hao‐yan , Cao Weibiao , Hong Jie , Fang Jing‐Yuan
Published: February 2013

The above article from The Journal of Pathology, published online on 7 June 2013 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the authors, the journal Editor‐in‐Chief, Prof. C. Simon Herrington, and John Wiley & Sons Limited. Some sequences in Figure 6C were mistakenly identified, with consequent errors in the description of this figure and in the Materials and Methods section. Additionally, in Figures 5C, 5F and 7 some images were duplicated and erroneously presented as unique. The authors apologise to readers of the journal.
Elementarteilchen
Authors: Futscher Klaus
Published: February 2013

Eine Übersicht über die sogenannten Elementarteilchen und ihre einfachsten Kombinationen kann, sofern sie noch einigermaßen übersichtlich sein soll, nicht entfernt den Anspruch auf Vollständigkeit erheben, sondern nur mehr oder minder pauschal die wichtigsten Ergebnisse bringen. Ein ‘Literaturführer zur Physik der Elementarteilchen und der kosmischen Strahlung’, von J. Tiomno und J. A. Wheeler zusammengestellt, erscheint gegenwärtig in der Zeitschrift AMERICAN SCIENTIST 37, (April u. Juli 49) No. 1 u. 2, worin die Veröffentlichungen bis Ende 1943, jedoch ohne Anspruch auf Vollständigkeit, nach Sachgebieten und 217 Untertiteln geordnet sind.
X‐Ray Lithography and X‐Ray Microscopy
Authors: Spiller E. , Feder R. , Topalian J.
Published: February 2013

Plenarvortrag 40. Physikertagung 1976 in Bonn: Experimental system, Wavelength selection, Resist sensitivity and resolution, Subsequent Processing, Specific Advantages of X‐rays, Biological applications, Future work.
Neue spurgeführte Transportmittel (Teil II)
Authors: Albrecht C. , Bohn G.
Published: February 2013

Im Anschluß an Teil I in Phys. Bl. 32 (1976) Nr. 7, S. 309–326, in dem nach einer allgemeinen Einführung die elektromagnetische Schwebetechnik (EMS) behandelt wurde, folgt jetzt eine Beschreibung des elektrodynamischen Verfahrens: Aufgaben und Kennzeichen — Elektrodynamische Trag‐Führ‐Systeme (Prinzip, Plattensysteme, Diskrete Schienenschleifen, Entwicklungsschwerpunkte) — Antriebe für elektrodynamische Schwebefahrzeuge (Auswahl, Synchroner Langständermotor, Entwicklungsschwerpunkte) — Entwicklungen im Ausland.
Chemie und Physik der Festkörperoberfläche
Authors: Ibach H.
Published: February 2013

Die Festkörperoberfläche ist der Schauplatz einer Vielzahl von chemischen Prozessen: erwünschten, wie in der heterogenen Katalyse, und unerwünschten, wie bei Korrosionsvorgängen. Elektronische Eigenschaften der Oberfläche sind in der Halbleitertechnologie von großer Bedeutung. Praktischen Bezügen solcher Art verdankt die Oberflächenforschung einen Teil ihrer Attraktivität. Viele interessante, ungelöste Fragen zielen aber auch auf das grundlegende Verständnis.
Das EPR‐Paradoxon und die Unbestimmtheit der Realität
Authors: Mückenheim W.
Published: February 2013

Wie neuere Experimente unter sehr allgemeinen Voraussetzungen beweisen, betreffen die Unbestimmtheitsrelationen nicht nur unsere Kenntnis der Realität, sondern deren Existenz. Räumlich separierte Systeme zeigen ein Korrelationsverhalten, dessen Ursache nicht in ihnen enthalten sein kann. Dieser Sachverhalt — sofern man ihn nicht als unerklärbar hinnehmen will — zwingt dazu, fundamentale Prinzipien der Physik aufzugeben. In jedem Falle führt sowohl der Versuch einer Erklärung als auch der Verzicht darauf zu einer drastischen Revision der gewöhnlichen Realitätsvorstellung.
Chemical Characterization of the Long‐Term Ageing of Nitrogen‐Rich Plasma Polymer Films under Various Ambient Conditions
Authors: Girard‐Lauriault Pierre‐Luc , Dietrich Paul M. , Gross Thomas , Wirth Thomas , Unger Wolfgang E. S.
Published: February 2013

Nitrogen rich plasma polymer films (L‐PPE:N) were prepared by low‐pressure RF plasma using a 1:1 mixture of ethylene and ammonia and aged for 345 d in four different ambient conditions: (i) at room temperature (RT) in air; (ii) at RT in nitrogen; (iii) at −20 °C in air and; (iv) at −20 °C in nitrogen. The films were analyzed by X‐ray photoelectron spectroscopy (XPS) and by time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) at various intervals over the duration of the experiment. The ageing of primary amines, NH2, was followed by chemical derivatization with 4‐trifluoromethyl benzaldehyde. Storage at −20 °C, mostly independently of ambient atmosphere, slowed down ageing to almost undetectable levels as evaluated by the analytical methods used for this study.

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Structural investigation of the VEGF receptor interaction with a helical antagonist peptide
Authors: Diana Donatella , Di Stasi Rossella , De Rosa Lucia , Isernia Carla , D'Andrea Luca D. , Fattorusso Roberto
Published: February 2013

Angiogenesis is mainly regulated by the vascular endothelial growth factor (VEGF), a mitogen specific for endothelial cells, which binds two tyrosine kinase receptors, VEGFR1 and VEGFR2, on the surface of endothelial cells. Molecules targeting VEGF receptors are attractive to pharmacologically treat diseases associated with angiogenesis or to be used as probes in angiogenesis imaging. Recently, we reported a designed peptide targeting VEGF receptors and able to inhibit the VEGF‐angiogenic response in vitro and in vivo. In this study, we employed NMR and molecular modeling methodology to investigate the molecular determinants of the interaction peptide‐receptor. In particular, the peptide binding site on VEGFR1 domain 2 and the residues involved in receptor recognition have been determined. These results provide significant information to develop a new class of molecules able to recognize the VEGF receptors overexpressed in pathological angiogenesis. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.
Influence of Mg‐doping on the optical properties of ZnO thin films prepared via electrochemical deposition
Authors: Shi Hongtao , Alfaro Cristhyan F. , Barrera Kalie R. , Hessong Timothy L. , Halbert Stephanie R.
Published: February 2013

Polycrystalline ZnO thin films were deposited on pure Al foils at 80 °C using electrochemical deposition (ECD) in solutions containing zinc nitrate hexahydrate and hexamethylenetetramine. Photoluminescence (PL) spectra between 20 and 200 K showed intense UV emissions near the band edge along with weak broad bands due to defects. When the source solution was slightly doped with Mg2+ ions, the defect‐induced band was suppressed along with a redshift, whereas the UV peak position and intensity remained the same. Surprisingly, Auger electron spectroscopy (AES) revealed no Mg contents in the films within the detection limit. Based on the solubility products of Mg(OH)2 and Zn(OH)2, we put forward a mechanism to describe how metal impurities could be incorporated into ZnO in such an aqueous process, which was strongly supported by samples grown in Ca‐ or Cu‐doped solutions. To further corroborate, we also fabricated, for the first time via ECD, MgZnO alloys in Mg‐doped solutions with very high nitrate concentrations. Blue shift of the UV emission peak was clearly observed from as‐prepared samples on Al. MgZnO films, deposited on Si substrates under similar supersaturated conditions and annealed in ambient air at 350 °C for 30 min, showed a similar peak shift. This electrochemical route could therefore be used as an effective approach to enhance the optical properties of compound semiconductors, demonstrating its potential for deep UV applications as well.
Mid‐infrared (IR) – A hot topic: The potential for using mid‐IR light for non‐invasive early detection of skin cancer in vivo
Authors: Seddon Angela B.
Published: February 2013

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After an introduction to the mid‐infrared (IR) spectral region, the tremendous significance of mid‐IR spectroscopic sensing is highlighted. The remarkable progress made towards mid‐IR spectral in vitro mapping of tissue and cancer detection is reviewed, with emphasis on diagnosis of skin cancer. The status quo of chalcogenide glass mid‐IR fibre optics and photonics for meeting opportunities for remote mid‐IR sensing in general, and in in vivo cancer detection in particular, is assessed. Raman spectroscopy is a sister technique to mid‐IR spectroscopy. The current success of Raman spectroscopy in medical diagnosis is appraised, with particular emphasis on Raman spectral imaging of tissue towards skin cancer diagnosis in vivo, based on a silica‐glass fibreoptic sensor‐head. The challenges to be met in chalcogenide glass science and technology towards facilitating analogous fibreoptic diagnostics based on mid‐IR spectroscopy are addressed.
Effects of organic matter on carbonate stable isotope ratios (δ13C, δ18O values) – implications for analyses of bulk sediments
Authors: Oehlerich Markus , Baumer Marlene , Lücke Andreas , Mayr Christoph
Published: February 2013

RATIONALE

Stable isotope ratio (δ13C, δ18O values) analyses of carbonates can be biased by CO2 release from organic impurities. This is most critical for carbonate isotope analyses from bulk sediments containing comparably high amounts of organic matter (OM). Several methods have been developed to remove OM prior to analyses, but none of them can be universally applied. Moreover, pretreatment methods cause isotopic bias in themselves and should probably best be avoided. Thus, it is essential to have indicators for reliable isotope values of untreated carbonate‐OM mixtures.

METHODS

Artificial mixtures of organic compounds with a standard carbonate were analyzed to investigate the bias on carbonate isotope ratios caused by OM in the sample. The total‐inorganic‐carbon to total‐organic‐carbon ratio (TIC/TOC) was used as a measure for the " organic impurity" of the sample. The target was to evaluate TIC/TOC as a measure for sample quality and to define TIC/TOC thresholds for reliable isotope measurements of mixtures between calcium carbonate and organic compounds.

RESULTS

The effect of organic impurities on carbonate stable isotope values depended on the specific OM compound and the respective TIC/TOC ratio. Different CO2 release rates were determined for the pure OM compounds. A sample TIC/TOC ratio ≥0.3 was found to be a threshold for reliable measurements of the isotope composition of calcium carbonate.

CONCLUSIONS

Bulk carbonate analyses from carbonate‐OM mixtures are reliable only if the TIC/TOC values do not fall below certain thresholds. This has implications for carbonate isotope studies from bulk sediments for which the TIC/TOC ratios should be considered as an easy‐to‐determine measure for sample‐quality assessment. Copyright © 2013 John Wiley & Sons, Ltd.
Otolith oxygen isotopes measured by high‐precision secondary ion mass spectrometry reflect life history of a yellowfin sole (Limanda aspera)
Authors: Matta Mary Elizabeth , Orland Ian J. , Ushikubo Takayuki , Helser Thomas E. , Black Bryan A. , Valley John W.
Published: February 2013

RATIONALE

The oxygen isotope ratio (δ18O value) of aragonite fish otoliths is dependent on the temperature and the δ18O value of the ambient water and can thus reflect the environmental history of a fish. Secondary ion mass spectrometry (SIMS) offers a spatial‐resolution advantage over conventional acid‐digestion techniques for stable isotope analysis of otoliths, especially given their compact nature.

METHODS

High‐precision otolith δ18O analysis was conducted with an IMS‐1280 ion microprobe to investigate the life history of a yellowfin sole (Limanda aspera), a Bering Sea species known to migrate ontogenetically. The otolith was cut transversely through its core and one half was roasted to eliminate organic contaminants. Values of δ18O were measured in 10‐µm spots along three transects (two in the roasted half, one in the unroasted half) from the core toward the edge. Otolith annual growth zones were dated using the dendrochronology technique of crossdating.

RESULTS

Measured values of δ18O ranged from 29.0 to 34.1‰ (relative to Vienna Standard Mean Ocean Water). Ontogenetic migration from shallow to deeper waters was reflected in generally increasing δ18O values from age‐0 to approximately age‐7 and subsequent stabilization after the expected onset of maturity at age‐7. Cyclical variations of δ18O values within juvenile otolith growth zones, up to 3.9‰ in magnitude, were caused by a combination of seasonal changes in the temperature and the δ18O value of the ambient water.

CONCLUSIONS

The ion microprobe produced a high‐precision and high‐resolution record of the relative environmental conditions experienced by a yellowfin sole that was consistent with population‐level studies of ontogeny. Furthermore, this study represents the first time that crossdating has been used to ensure the dating accuracy of δ18O measurements in otoliths. Copyright © 2013 John Wiley & Sons, Ltd.
Mitigating colluding injected attack using monitoring verification in mobile ad‐hoc networks
Authors: Kandah Farah , Singh Yashaswi , Zhang Weiyi , Wang Chonggang
Published: February 2013

Mobile ad‐hoc networks (MANETs) have attracted significant research attention recently because of the fast growth of laptops, personal digital assistant, and 802.11/Wi‐Fi wireless networking. However, the flexible deployment nature and the lack of fixed infrastructure make MANETs suffer from a variety of security attacks. In this paper, we show how an adversary can utilize a colluding injected attack (CIA) in MANET by injecting malicious nodes in the network, while hiding their identities from other legitimate nodes. These injected nodes will work together (colluding) to create a collision at an arbitrary node, thus preventing it from receiving or relaying any packet. Because of this collision, a legitimate node could be reported as malicious nodes by monitoring nodes in the neighborhood. In this work, we propose a monitoring verification scheme to mitigate the effect of the CIA attack. Our proposed scheme is able to accurately detect malicious nodes in the network compared with previous detection schemes. Through simulations, we show that our proposed scheme outperforms previous detection schemes in terms of true/false detection of any malicious behavior in the network caused by the CIA attack. Copyright © 2013 John Wiley & Sons, Ltd.
Nano‐SAR Development for Bioactivity of Nanoparticles with Considerations of Decision Boundaries
Authors: Liu Rong , Rallo Robert , Weissleder Ralph , Tassa Carlos , Shaw Stanley , Cohen Yoram
Published: February 2013

The development of classification nano‐structure–activity Relationships (nano‐SARs) of nanoparticle (NP) bioactivity is presented with the aim of demonstrating the integration of multiparametric toxicity/bioactivity assays to arrive at statistically meaningful class definitions (i.e., bioactivity/inactivity endpoints), as well as the implications of nano‐SAR applicability domains and decision boundaries. Nano‐SARs are constructed based on a dataset of 44 iron oxide core nanoparticles (NPs), used in molecular imaging and nano‐sensing, containing bioactivity profiles for four cell types and four different assays. Class definitions are developed on the basis of ‘hit’ (i.e., significant bioactivity) identification analysis and self‐organizing map based consensus clustering; these class definitions enable construction of nano‐SARs of a high classification accuracy (>78%) with different NP descriptor combinations that include primary size, spin‐lattice and spin‐spin relaxivities, and zeta potentials. Analysis of the nano‐SAR performance for different class definitions suggests that H4 (i.e., class with at least four hits) is a reasonable endpoint (from a ‘regulatory’ viewpoint) for keeping the level of false negatives (i.e., incorrect labeling of bioactive NPs as inactive) low. The establishment of a quantitative nano‐SAR applicability domain is demonstrated, making use of a probability density with the H4 class definition and naive Bayesian classifier (NBC) model (with spin‐lattice relaxivity and zeta potential as descriptors). Decision boundaries are determined for the above H4/NBC nano‐SAR for different acceptance levels of false negative to false positive predictions, illustrating a practical approach that may assist in regulatory decision making with a consideration of reducing the likelihood of identifying bioactive NPs as being inactive.
Membrane Perturbation by Carbon Nanotube Insertion: Pathways to Internalization
Authors: Lelimousin Mickaël , Sansom Mark S. P.
Published: February 2013

Carbon nanotubes (CNTs) can penetrate the membranes of cells, offering prospects for nanomedicine but problems for nanotoxicity. Molecular simulations are used to provide a systematic analysis of the interactions of single‐walled and multi‐walled CNTs of different radii with a model lipid bilayer membrane. The simulations allow characterization of the mechanism of spontaneous exothermic insertion of CNTs into lipid bilayer membranes. The size and type of CNT determine the nature and extent of the local perturbation of the bilayer. Single‐walled CNTs are shown to insert via a two‐step mechanism with initial transient formation of a water filled pore followed by full insertion of the CNT into the bilayer. The latter stage is associated with formation of a persistent inverted micelle arrangement of lipid molecules trapped inside the CNT. This suggests a possible vehicle for nano‐encapsulation of drugs, enabling their entry into and subsequent release within cells following endocytosis of CNT‐containing membranes.
Viscosity of Fluoride‐Free Mold Fluxes Containing B2O3 and TiO2
Authors: Wang Zhen , Shu Qifeng , Chou Kuochih
Published: February 2013

Viscosities of B2O3 and TiO2‐bearing fluoride‐free mold fluxes have been measured by the rotating cylinder method in this work. Effects of different B2O3, TiO2 content, and basicities on the viscosity characteristics have been examined. Viscosity of fluoride‐free mold fluxes containing B2O3 and TiO2 was found to decrease with the increase of B2O3, TiO2 content, and basicity. The values of apparent activation energy for viscous flow of slags decrease with additions of B2O3 and TiO2 and the increase of basicity. Two parameters A and B in Riboud model were re‐evaluated based on the present experimental data, and the modified Riboud model was used to estimate the viscosity of fluoride‐free slag system investigated in present work. The viscosity values obtained by the experimental measurement were in good agreement with those calculated by the modified Riboud model.
Cardiac outflow tract anomalies
Authors: Neeb Zachary , Lajiness Jacquelyn D. , Bolanis Esther , Conway Simon J
Published: February 2013

The mature outflow tract (OFT) is, in basic terms, a short conduit. It is a simple, although vital, connection situated between contracting muscular heart chambers and a vast embryonic vascular network. Unfortunately, it is also a focal point underlying many multifactorial congenital heart defects (CHDs). Through the use of various animal models combined with human genetic investigations, we are beginning to comprehend the molecular and cellular framework that controls OFT morphogenesis. Clear roles of neural crest cells (NCC) and second heart field (SHF) derivatives have been established during OFT formation and remodeling. The challenge now is to determine how the SHF and cardiac NCC interact, the complex reciprocal signaling that appears to be occurring at various stages of OFT morphogenesis, and finally how endocardial progenitors and primary heart field (PHF) communicate with both these colonizing extra‐cardiac lineages. Although we are beginning to understand that this dance of progenitor populations is wonderfully intricate, the underlying pathogenesis and the spatiotemporal cell lineage interactions remain to be fully elucidated. What is now clear is that OFT alignment and septation are independent processes, invested via separate SHF and cardiac neural crest (CNC) lineages. This review will focus on our current understanding of the respective contributions of the SHF and CNC lineage during OFT development and pathogenesis. WIREs Dev Biol 2013, 2:499–530. doi: 10.1002/wdev.98

This article is categorized under:

Birth Defects > Organ Anomalies
Specifying a hierarchical mixture of experts for hydrologic modeling: Gating function variable selection
Authors: Jeremiah Erwin , Marshall Lucy , Sisson Scott A , Sharma Ashish
Published: February 2013

Key Points

Addressing model parameter and structural uncertainties in a Bayesian setting

Specifying catchment predictors for better model mixing and simulation

Predicting streamflow for ungauged basin by regionalising predictor coefficients
Use of NMR logging to obtain estimates of hydraulic conductivity in the High Plains aquifer, Nebraska, USA
Authors: Dlubac Katherine , Knight Rosemary , Song Yi‐Qiao , Bachman Nate , Grau Ben , Cannia Jim , Williams John
Published: February 2013

Key Points

NMR-logging provides reliable estimates of hydraulic conductivity in aquifers

Provided equations to predict hydraulic conductivity in unconsolidated materials

Problems acquiring advanced geophysical logging data in unconsolidated materials
Saturation‐dependent solute dispersivity in porous media: Pore‐scale processes
Authors: Raoof A. , Hassanizadeh S. M.
Published: February 2013

Key Points

Solute dispersion is a function of soil saturation

The relation between solute dispersivity and saturation is non‐monotonic.

Solute dispersivity is maximum at intermediate saturations.
The Tetrakis‐(trifluoromethanesulfonato)‐aurate Anion: Syntheses and Properties of M[Au(CF3SO3)4] (M = Li – Rb, Ag)
Authors: Logemann Christian , Klüner Thorsten , Wickleder Mathias S.
Published: February 2013

The reaction of Au(OH)3 and trifluoromethanesulfonic acid (triflic acid) in the presence of M2CO3 (M = Li, Na, K, Rb) and Ag(CF3SO3), respectively, yielded yellow single crystals of M[Au(CF3SO3)4] (M = Li, Na, K, Rb, Ag). They exhibit the [Au(CF3SO3)4]– anion with the gold atom in a square‐planar coordination of four monodentate triflate ions. The structural characteristics of the anion are well reproduced by theoretical calculations that allowed also for a reliable assignment of observed IR energies. Charge compensation for the anions is achieved by different M+ counter cations. According to their coordination requirements different crystal structures are adopted. For M = Li, Na, the compounds are triclinic [M = Li/Na: triclinic, P$\bar{1}$, Z = 1, a = 509.92(2)/525.43(2), b = 854.08(3)/902.08(4), c = 1044.67(4)/1080.28(5) pm, α = 94.006(2)/104.367(2)°, β = 92.935(2)/93.602(3)°, γ = 93.841(2)/90.706(2)°, V = 452.12(3)/494.83(4) Å3] and octahedral coordination of the cations is observed. The monoclinic Ag[Au(CF3SO3)4] [C2/c, Z = 4, a = 2218.83(5), b = 499.19(1), c = 1751.73(4) pm, β = 104.736(1)°, V = 1876.43(7) Å3] shows the Ag+ ion in trigonal prismatic surrounding of oxygen atoms. A coordination number of eight is found for K[Au(CF3SO3)4] [orthorhombic, Pbcn, Z = 4, a = 904.32(4), b = 1050.64(4), c = 2120.71(9) pm, V = 2014.92(15) Å3] and also for Rb[Au(CF3SO3)4] [monoclinic, P21/n, Z = 4, a = 919.80(3), b = 2121.77(6), c = 1083.40(3) pm, β = 90.120(2)°, V = 2114.36(11) Å3]. In both cases the [MO8] polyhedra have dodecahedral shape. The thermal decomposition of selected compounds was monitored up to 1050 °C and shows that a mixture of elemental gold and the respective alkaline metal sulfate is the residue. For M = Ag elemental silver is formed instead of a sulfate.
Akt kinase targets the association of CBP with histone H3 to regulate the acetylation of lysine K18
Authors: Liu Yan , Xing Zhao-bin , Zhang Jing-hua , Fang Yue
Published: February 2013

CBP
physically interacts
with
AKT1
by
anti tag coimmunoprecipitation
(View interaction)
Sugar consumption and global prevalence of obesity and hypertension: an ecological analysis
Authors: Siervo Mario , Montagnese Concetta , Mathers John C , Soroka Katrina R , Stephan Blossom CM , Wells Jonathan CK
Published: February 2013

Objective

The nutrition transition model provides an integrated approach to analyse global changes in food consumption and lifestyle patterns. Whether variability in food availability for consumption, lifestyle and sociodemographic factors is associated with the worldwide prevalence distribution of overweight, obesity and hypertension is unclear.

Design

Ecological analysis.

Setting

Country-specific prevalence estimates of overweight, obesity and hypertension were obtained. Prevalence estimates were then matched to year- and country-specific food and energy availability for consumption of cereals, sugar, sweeteners and honey, vegetable oils, fruits, starchy roots, pulses, total vegetables, alcoholic beverages, total meat, animal fat, eggs, milk, and fish and seafood. The per capita Gross Domestic Product (GDP), urbanization rates and prevalence of physical inactivity for each country were also obtained.

Subjects

The overweight, obesity and hypertension databases included information from 128, 123 and seventy-nine countries, respectively.

Results

Consumption of sugar and animal products were directly associated with GDP and urbanization rates. In a multivariate regression model, physical inactivity (B = 0·01, se = 0·005, P = 0·003), cereal consumption (B = −0·02, se = 0·006, P < 0·001) and sugar consumption (B = 0·03, se = 0·01, P = 0·03) were significant predictors of obesity prevalence. Midpoint age (B = 0·21, se = 0·10, P = 0·02), prevalence of overweight (B = 0·18, se = 0·08, P = 0·02) and consumption of cereals (B = −0·22, se = 0·10, P = 0·02) were significant predictors of hypertension. Women appeared to have a significant obesity excess compared with men.

Conclusions

High sugar consumption and sedentary lifestyle are associated with increased obesity prevalence. The non-linear association of sugar consumption with prevalence of obesity suggests that effective strategies to reduce its consumption may have differential effects in countries at different stages of the nutrition transition.
Autonomy, vulnerability and capacity: a philosophical appraisal of the Mental Capacity Act
Authors: Mackenzie Catriona , Rogers Wendy
Published: February 2013

The UK Mental Capacity Act provides an important legislative framework for protecting persons who are vulnerable, by virtue of partial or total lack of capacity, from abuse, coercion, exploitation, disrespect or unwarranted intrusions on their privacy and liberty. In this article we argue, however, that in order to effectively implement the Act's governing principles and promote the autonomy of persons whose capacities are impaired, health and social welfare professionals must go beyond a primarily cognitive approach to capacity assessment and refer to a range of more demanding autonomy conditions relating to authenticity, diachronic coherence and consistency, accountability to others, and affective attitudes towards oneself. We suggest that these conditions are in fact implicit in the guidelines, scenarios and practical advice contained in the Act's accompanyingCode of Practice. To ground our analysis, we discuss two cases of end-of-life decision-making, and consider how these cases might have been assessed had the Mental Capacity Act been applied. We also address the question of whether the conditions for autonomy we identify raise the bar too high to be met by persons who are vulnerable because their capacity is partially compromised.
Understanding and resolving the discrepancy between differential and actual minority carrier lifetime
Authors: Giesecke J. A. , Glunz S. W. , Warta W.
Published: February 2013

Differential light-biased dynamic measurements of charge carrier recombination properties in semiconductors have long been known to yield only differential rather than actual recombination properties. Therefore, the determination of injection-dependent recombination properties from such measurements was previously found to require integration over the entire injection range. Recent investigations of the phase shift between a time-modulated irradiation of silicon samples and excess carrier density reveal a striking analogy to the above findings: the phase shift is greater than the actual effective carrier lifetime in the case of a positive derivative of lifetime with respect to excess carrier density, and vice versa. This work attempts to rearrange the mentioned previous findings in a quantitative theoretical description of light-biased dynamic measurements of effective carrier lifetime. Both light-biased differential lifetime measurements as well as harmonically time-modulated methods without additional bias light are shown to represent a limiting case in a general treatment of light-biased dynamic lifetime measurements derived here. Finally, we sketch a way to obtain actual recombination properties from differential measurements—referred to as a differential-to-actual (d2a) lifetime analysis, which does not require integration over the entire injection range.
ACKS2: Atom-condensed Kohn-Sham DFT approximated to second order
Authors: Verstraelen T. , Ayers P. W. , Van Speybroeck V. , Waroquier M.
Published: February 2013

A new polarizable force field (PFF), namely atom-condensed Kohn-Sham density functional theory approximated to second order (ACKS2), is proposed for the efficient computation of atomic charges and linear response properties of extended molecular systems. It is derived from Kohn-Sham density functional theory (KS-DFT), making use of two novel ingredients in the context of PFFs: (i) constrained atomic populations and (ii) the Legendre transform of the Kohn-Sham kinetic energy. ACKS2 is essentially an extension of the Electronegativity Equalization Method (EEM) [W. J. Mortier, S. K. Ghosh, and S. Shankar, J. Am. Chem. Soc. 108, 4315 (1986)]10.1021/ja00275a013 in which two major EEM shortcomings are fixed: ACKS2 predicts a linear size-dependence of the dipole polarizability in the macroscopic limit and correctly describes the charge distribution when a molecule dissociates. All ACKS2 parameters are defined as atoms-in-molecules expectation values. The implementation of ACKS2 is very similar to that of EEM, with only a small increase in computational cost.
On the squared eigenfunction symmetry of the Toda lattice hierarchy
Authors: Cheng Jipeng , He Jingsong
Published: February 2013

The squared eigenfunction symmetry for the Toda lattice hierarchy is explicitly constructed in the form of the Kronecker product of the vector eigenfunction and the vector adjoint eigenfunction, which can be viewed as the generating function for the additional symmetries when the eigenfunction and the adjoint eigenfunction are the wave function and the adjoint wave function, respectively. Then after the Fay-like identities and some important relations about the wave functions are investigated, the action of the squared eigenfunction related to the additional symmetry on the tau function is derived, which is equivalent to the Adler-Shiota-van Moerbeke formulas.
Communication: Origin of the contributions to DNA structure in phages
Authors: Myers Christopher G. , Pettitt B. Montgomery
Published: February 2013

Cryo electron microscopy (cryo-EM) data of the interior of phages show ordering of the interior DNA that has been interpreted as a nearly perfectly ordered polymer. We show surface-induced correlations, excluded volume, and electrostatic forces are sufficient to predict most of the major features of the current structural data for DNA packaged within viral capsids without additional ordering due to elastic bending forces for the polymer. Current models assume highly-ordered, even spooled, hexagonally packed conformations based on interpretation of cryo-EM density maps. We show herein that the surface induced packing of short (6mer), unconnected DNA polymer segments is the only necessary ingredient in creating ringed densities consistent with experimental density maps. This implies the ensemble of possible conformations of polymeric DNA within the capsid that are consistent with cryo-EM data may be much larger than implied by traditional interpretations where such rings can only result from highly-ordered spool-like conformations. This opens the possibility of a more disordered, entropically-driven view of phage packaging thermodynamics. We also show the electrostatics of the DNA contributes a large portion of the internal hydrostatic and osmotic pressures of a phage virion, suggesting that nonlinear elastic anomalies might reduce the overall elastic bending enthalpy of more disordered conformations to have allowable free energies.
Effect of local structures on structural evolution during crystallization in undercooled metallic glass-forming liquids
Authors: Wu Z. W. , Li M. Z. , Wang W. H. , Song W. J. , Liu K. X.
Published: February 2013

The effect of local structures on structural evolution during the crystallization of undercooled ZrCu metallic glass-forming liquid was studied via molecular dynamics simulations. It is found that body-centered-cubic (bcc)-like clusters play a key role in structural evolution during crystallization. In contrast to previous speculations, the number of bcc-like crystal nuclei does not change much before the onset of crystallization. Instead, the development of a bcc-like critical nucleus during annealing leads to a strong spatial correlation with other nuclei in its surroundings, forming a crystalline structure template. It is also found that the size distribution of bcc-like nuclei follows a power-law form with an exponential cutoff in the early stage of annealing, but changes to a pure power-law behavior just before the onset of crystallization. This implies that the crystalline structure template has fractal feature and the undercooled liquids evolve to a self-organized critical state before the onset of crystallization, which might trigger the subsequent rapid crystallization. According to the graph theory analysis, it is also found that the observed large scatter of the onset time of crystallization in different liquid samples results from the connectivity of the bcc-like clusters.
Achieving direct band gap in germanium through integration of Sn alloying and external strain
Authors: Gupta Suyog , Magyari-Köpe Blanka , Nishi Yoshio , Saraswat Krishna C.
Published: February 2013

GeSn is predicted to exhibit an indirect to direct band gap transition at alloy Sn composition of 6.5% and biaxial strain effects are investigated in order to further optimize GeSn band structure for optoelectronics and high speed electronic devices. A theoretical model has been developed based on the nonlocal empirical pseudopotential method to determine the electronic band structure of germanium tin (GeSn) alloys. Modifications to the virtual crystal potential accounting for disorder induced potential fluctuations are incorporated to reproduce the large direct band gap bowing observed in GeSn alloys.
Dependence of the switching current density on the junction sizes in spin transfer torque
Authors: You Chun-Yeol , Jung Myung-Hwa
Published: February 2013

We investigate the dependence of switching current density on the junction sizes in the in-plane spin transfer torque nanopillar structures by using micromagnetic simulations. While the macrospin model predicts weak dependence of switching current density on the junction sizes, we find that the switching current density is a sensitive function of the junction sizes. It can be explained with the complicated spin configurations and dynamics during the switching process. The detail spin configurations and dynamics are determined by spin wave excitation with the finite wave vector, which is related with the exchange coupling energy and junction shape.
Temperature dependent polarization switching properties of ferroelectric Pb0.92La0.08Zr0.52Ti0.48Oδ films grown on nickel foils
Authors: Ma Beihai , Hu Zhongqiang , Liu Shanshan , Narayanan Manoj , (Balu) Balachandran U.
Published: February 2013

Ferroelectric Pb0.92La0.08Zr0.52Ti0.48Oδ films (≈2-μm thickness) were grown on LaNiO3-buffered nickel foils by chemical solution deposition. Their ferroelectric and dielectric properties were measured as a function of temperature. With increasing temperature from room temperature to 200 °C, back-switching polarization increased while spontaneous polarization, remanent polarization, and coercive field decreased. The domain wall energy barrier was determined from the temperature-dependent back-switching polarization. Decreased irreversible/extrinsic and reversible/intrinsic dielectric responses were observed with increasing frequency. The ratio of irreversible to reversible contributions to dielectric nonlinearity was analyzed by the Rayleigh law. This ratio decreased with increasing frequency from 500 Hz to 500 kHz.
Rbfox3-regulated alternative splicing of Numb promotes neuronal differentiation during development
Authors: Kim Kee K. , Nam Joseph , Mukouyama Yoh-suke , Kawamoto Sachiyo
Published: February 2013

Alternative premRNA splicing is a major mechanism to generate diversity of gene products. However, the biological roles of alternative splicing during development remain elusive. Here, we focus on a neuron-specific RNA-binding protein, Rbfox3, recently identified as the antigen of the widely used anti-NeuN antibody. siRNA-mediated loss-of-function studies using the developing chicken spinal cord revealed that Rbfox3 is required to promote neuronal differentiation of postmitotic neurons. Numb premRNA encoding a signaling adaptor protein was found to be a target of Rbfox3 action, and Rbfox3 repressed the inclusion of an alternative exon via binding to the conserved UGCAUG element in the upstream intron. Depleting a specific Numb splice isoform reproduced similar neuronal differentiation defects. Forced expression of the relevant Numb splice isoform was sufficient to rescue, in an isoform-specific manner, postmitotic neurons from defects in differentiation caused by Rbfox3 depletion. Thus, Rbfox3-dependent Numb alternative splicing plays an important role in the progression of neuronal differentiation during vertebrate development.
Germinal center B cells govern their own fate via antibody feedback
Authors: Zhang Yang , Meyer-Hermann Michael , George Laura A. , Figge Marc Thilo , Khan Mahmood , Goodall Margaret , Young Stephen P. , Reynolds Adam , Falciani Francesco , Waisman Ari , Notley Clare A. , Ehrenstein Michael R. , Kosco-Vilbois Marie , Toellner Kai-Michael
Published: February 2013

Affinity maturation of B cells in germinal centers (GCs) is a process of evolution, involving random mutation of immunoglobulin genes followed by natural selection by T cells. Only B cells that have acquired antigen are able to interact with T cells. Antigen acquisition is dependent on the interaction of B cells with immune complexes inside GCs. It is not clear how efficient selection of B cells is maintained while their affinity matures. Here we show that the B cells’ own secreted products, antibodies, regulate GC selection by limiting antigen access. By manipulating the GC response with monoclonal antibodies of defined affinities, we show that antibodies in GCs are in affinity-dependent equilibrium with antibodies produced outside and that restriction of antigen access influences B cell selection, seen as variations in apoptosis, plasma cell output, T cell interaction, and antibody affinity. Feedback through antibodies produced by GC-derived plasma cells can explain how GCs maintain an adequate directional selection pressure over a large range of affinities throughout the course of an immune response, accelerating the emergence of B cells of highest affinities. Furthermore, this mechanism may explain how spatially separated GCs communicate and how the GC reaction terminates.
Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry
Authors: Chung Clement , Emili Andrew , Frey Brendan J.
Published: February 2013

Motivation: Tandem mass spectrometry (MS/MS) is a dominant approach for large-scale high-throughput post-translational modification (PTM) profiling. Although current state-of-the-art blind PTM spectral analysis algorithms can predict thousands of modified peptides (PTM predictions) in an MS/MS experiment, a significant percentage of these predictions have inaccurate modification mass estimates and false modification site assignments. This problem can be addressed by post-processing the PTM predictions with a PTM refinement algorithm. We developed a novel PTM refinement algorithm, iPTMClust, which extends a recently introduced PTM refinement algorithm PTMClust and uses a non-parametric Bayesian model to better account for uncertainties in the quantity and identity of PTMs in the input data. The use of this new modeling approach enables iPTMClust to provide a confidence score per modification site that allows fine-tuning and interpreting resulting PTM predictions.

Results: The primary goal behind iPTMClust is to improve the quality of the PTM predictions. First, to demonstrate that iPTMClust produces sensible and accurate cluster assignments, we compare it with k-means clustering, mixtures of Gaussians (MOG) and PTMClust on a synthetically generated PTM dataset. Second, in two separate benchmark experiments using PTM data taken from a phosphopeptide and a yeast proteome study, we show that iPTMClust outperforms state-of-the-art PTM prediction and refinement algorithms, including PTMClust. Finally, we illustrate the general applicability of our new approach on a set of human chromatin protein complex data, where we are able to identify putative novel modified peptides and modification sites that may be involved in the formation and regulation of protein complexes. Our method facilitates accurate PTM profiling, which is an important step in understanding the mechanisms behind many biological processes and should be an integral part of any proteomic study.

Availability: Our algorithm is implemented in Java and is freely available for academic use from http://genes.toronto.edu.

Contact:  frey@psi.utoronto.ca

Supplementary information:  Supplementary data are available at Bioinformatics online