bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of ovarian cancer‐associated proteins in symptomatic women: A novel method for semi‐quantitative plasma proteomics
Authors: Shield‐Artin Kristy L. , Bailey Mark J. , Oliva Karen , Liovic Ana K. , Barker Gillian , Dellios Nicole L. , Reisman Simone , Ayhan Mustafa , Rice Gregory E.
Published: April 2012

Purpose

To evaluate the utility of an enhanced biomarker discovery approach in order to identify potential biomarkers relevant to ovarian cancer detection.

Experimental design

We combined immuno‐depletion, liquid‐phase IEF, 1D‐DIGE, MALDI‐TOF/MS and LC‐MS/MS to identify differentially expressed proteins in the plasma of symptomatic ovarian cancer patients, stratified by stage, compared to samples obtained from normal subjects.

Results

We demonstrate that this approach is a practical alternative to traditional 2D gel techniques and that it has some advantages, most notably increased protein capacity. Proteins were identified in all 76 bands excised from the gels in this project and confirmed the cancer‐associated expression of several well‐established biomarkers of ovarian cancer. These included C‐reactive protein (CRP), haptoglobin, alpha‐2 macroglobulin and A1A2. We also identified new ovarian cancer candidate biomarkers, Protein S100‐A9 (S100A9) and multimerin‐2. The cancer‐associated differential expression of CRP and S100A9 was further confirmed by Western blot and ELISA.

Conclusions

The methods developed in this study allow for the increased loading of plasma proteins into the analytical stream when compared to traditional 2D‐DIGE. This increased protein identification sensitivity allowed us to identify new putative ovarian cancer biomarkers.
Analysis of a membrane‐enriched proteome from postmortem human brain tissue in Alzheimer's disease
Authors: Donovan Laura E. , Higginbotham Lenora , Dammer Eric B. , Gearing Marla , Rees Howard D. , Xia Qiangwei , Duong Duc M. , Seyfried Nicholas T. , Lah James J. , Levey Allan I.
Published: April 2012

Purpose

The present study is a discovery mode proteomics analysis of the membrane‐enriched fraction of postmortem brain tissue from Alzheimer's disease (AD) and control cases. This study aims to validate a method to identify new proteins that could be involved in the pathogenesis of AD and potentially serve as disease biomarkers.

Experimental design

Liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) was used to analyze the membrane‐enriched fraction of human postmortem brain tissue from five AD and five control cases of similar age. Biochemical validation of specific targets was performed by immunoblotting.

Results

One thousand seven hundred and nine proteins were identified from the membrane‐enriched fraction of frontal cortex. Label‐free quantification by spectral counting and G‐test analysis identified 13 proteins that were significantly changed in disease. In addition to Tau (MAPT), two additional proteins found to be enriched in AD, ubiquitin carboxy‐terminal hydrolase 1 (UCHL1), and syntaxin‐binding protein 1 (Munc‐18), were validated through immunoblotting.

Discussion and clinical relevance

Proteomic analysis of the membrane‐enriched fraction of postmortem brain tissue identifies proteins biochemically altered in AD. Further analysis of this subproteome may help elucidate mechanisms behind AD pathogenesis and provide new sources of biomarkers.
Candidate biomarker verification: Critical examination of a serum protein pattern for human colorectal cancer
Authors: Albrethsen Jakob , Rikke Bøgebo  , Møller Christian H. , Olsen Jesper A. , Raskov Hans H. , Gammeltoft Steen
Published: April 2012

Purpose

We critically examine a candidate serum protein pattern for human colorectal cancer (CRC) with respect to reproducibility, sample handling, and disease specificity.

Experimental design

Serum samples from CRC patients, patients with benign colon tumors and healthy individuals, were obtained at two collection sites and analyzed by SELDI‐TOF MS on 8 days, over a period of 5 weeks. The spectra were subjected to multivariate analysis. Tissues from normal colon and CRC were analyzed by SELDI‐TOF MS. Selected mass peaks were identified.

Results

Using an elaborate experimental design we developed a multivariate classifier that correctly classified CRC and control serum measured on an independent day. The classifier did not discriminate between samples from CRC patients and patients with benign colon tumors, and, secondly, did not correctly classify serum from an independent collection site. All discriminatory mass peaks were identified as high abundant plasma proteins. Tissue profiling provided support of increased proteolytic activity in CRC tissue.

Conclusion and clinical relevance

Critical verification did not justify advancing the identified CRC serum protein pattern into clinical validation without improvement. We believe that proteomics biomarker research could benefit if the presented, or a similar, verification scheme was more commonly employed in explorative biomarker studies.
Effective mechanical properties of concentric cylindrical composites with auxetic phase
Authors: Strek Tomasz , Jopek Hubert
Published: April 2012

Materials with unusual mechanical properties can be potentially used as matrices to create high‐performance lightweight composites. The appearance of materials with negative Poisson's ratio (auxetics), has led to the evaluation of auxetic composites for possible engineering applications. Because the experimental evaluation of composites with specific properties is expensive and time consuming, computational modelling and simulation provide efficient alternatives to predict the parameters of the composites. In this paper a finite element method was used to find the engineering constants (Young's modulus and Poisson's ratio) of auxetic composites consisting of concentric cylindrical inclusions made of combinations of auxetic and classic (non‐auxetic) materials. It has been observed that not only the mechanical properties of the different composite phases influence the effective mechanical properties of the whole composite, but also the location of the same material phases do matter.
Extracts of Scutellaria baicalensis Reduced Body Weight and Blood Triglyceride in db/db Mice
Authors: Song Kwang Hoon , Lee Sun Hwa , Kim Bu‐Yeo , Park Ah Yeon , Kim Jong Yeol
Published: April 2012

Scutellaria baicalensis has been extensively employed for the clinical treatment of hyperlipidemia, atherosclerosis, hypertension, dysentery, inflammatory diseases, and the common cold. The present study was performed to investigate the anti‐obesity and anti‐dyslipidemia effect of Scutellaria baicalensis extracts (SBE) in type 2 diabetic db/db mice.

Male db/db mice were divided into three groups (n = 5) and orally administrated vehicle (control), SBE 10, and 100 mg/kg body weight/day for 4 weeks everyday. Administration of SBE improves weight gain, hypertriglyceridemia, and hyperinsulinemia in db/db mice. In obese db/db mice, SBE treatment also reduced plasma alanine aminotransferase levels. In the livers of db/db mice, SBE promoted 5' AMP‐activated protein kinase activity and restored metabolic process and insulin signaling pathways. Our data demonstrate that SBE exerts potent anti‐obesity and anti‐hypertriglyceride effects suggesting its useful potential function as adjuvant therapeutic agent for the treatment of weight gain and hypertriglyceridemia. Copyright © 2012 John Wiley & Sons, Ltd.
DEVELOPMENT OF A STOCHASTIC WATER TEMPERATURE MODEL AND PROJECTION OF FUTURE WATER TEMPERATURE AND EXTREME EVENTS IN THE OUELLE RIVER BASIN IN QUÉBEC, CANADA
Authors: Jeong D. I. , Daigle A. , St‐Hilaire A.
Published: April 2012

A stochastic model is proposed to reproduce daily water temperature at 18 observation sites (11 main stem and 7 tributary sites) in the Ouelle River basin located in southern Quebec, Canada, using meteorological variables as predictors. A random sampling procedure without replacement was adopted for the model calibration and validation to overcome the limited length of the observed water temperature series. The predicted water temperature series were then submitted to variance inflation to reproduce the observed variability of the water temperature series. Historical water temperature series were obtained from observed meteorological predictors, whereas reference and future water temperature series were obtained from stochastic water temperature model using five reference (1970–1999) and future (2046–2065) meteorological predictors simulated by five different climate model runs. The reference series reproduced summer mean water temperature and the number of consecutive days with water temperature higher than 21 °C or 25 °C fairly well. On the basis of the historical series, it can be assumed that the seven tributaries of the Ouelle River provided thermal refugia for native salmon between 1970 and 1999. Future water temperature series projected by the stochastic model show that the seven tributaries could still be used as refugia to prevent lethal stress, whereas the temperature in the main stem and in three tributaries will be high enough to constitute stressful conditions for feeding juvenile Atlantic salmon. Copyright © 2012 John Wiley & Sons, Ltd.
Surface characterization of plasma‐polymerized polyethylene glycol thin film modified by plasma treatment
Authors: Choi Changrok , Choi Kun Oh , Jung Donggeun , Moon Dae Won , Lee Tae Geol
Published: April 2012

Polyethylene glycol (PEG) is a well‐known non‐fouling material used for protein adsorption and cellular adhesion. Recently, we successfully fabricated plasma‐polymerized PEG (PP‐PEG) thin films on various substrates by using a plasma enhanced chemical vapor deposition method and PEG200 as a precursor. The structure of our PP‐PEG thin film was found to be very similar to the chemical structure of a PEG polymer and also bore a non‐fouling characteristic for numerous proteins and cells without in vitro or in vivo toxicity. In this study, we modified this PP‐PEG thin film with a simple H2/He plasma treatment to change the non‐fouling surface property to a fouling one for proteins and cells. To make the patterned surfaces for proteins or cells on the protein‐ or cell‐resistant areas, depositing a new fouling PP thin film was unnecessary since it was possible to perform a simple H2/He plasma treatment through a metal shadow mask on the PP‐PEG thin film. Various surface analysis techniques such as water contact angle, atomic force microscopy, X‐ray photoelectron spectroscopy and time‐of‐flight secondary ion mass spectrometry were used to confirm the drastic changes in the surface chemical properties resulting from the plasma treatment. These results show that a PP‐PEG film, together with its plasma treatment through a shadow mask, is a very simple and useful patterning technique for various biological applications. Copyright © 2012 John Wiley & Sons, Ltd.
Treatment of wx corn starch dispersions in a microwave reactor and their hydrodynamic properties determined using asymmetrical flow field‐flow fractionation
Authors: Juna Shazia , Damm Markus , Kappe C. Oliver , Huber Anton
Published: April 2012

Hydrodynamic properties of aqueous wx corn starch (native, un‐pregelatinised) dispersions treated in a dedicated single‐mode microwave reactor at temperatures ranging from 180 to 210°C were determined using asymmetrical flow field‐flow fractionation coupled with an RI detector. The dedicated microwave reactor enabled the fine control and monitoring of heating parameters (especially temperature) during the treatment. The translational diffusion co‐efficient and hydrodynamic radii (Rh) values determined for wx corn starch treated at 180 and 200°C indicate that the majority of the material (∼98%) consisted of highly mobile, small and compact molecules/particles, with Rh values ranging from 10 to 90 nm, while the remaining ∼2% of the material consisted of considerably larger molecules/particles Rh values ranging from ∼100 to ∼200 nm). Degradation of wx corn starch was observed at 210°C.
Distribution and derivation of white‐winged dove harvests in Texas
Authors: Collier Bret A. , Skow Kevin L. , Kremer Shelly R. , Mason Corey D. , Snelgrove Robert T. , Calhoun Kirby W.
Published: April 2012

Band recoveries provide requisite data for evaluating the spatial distribution of harvest relative to the distribution of breeding stocks for a wide variety of migratory species. We used direct and indirect band‐recovery data to evaluate the distribution and derivation of harvest of white‐winged doves (Zenaida asiatica) banded before hunting season in 3 distinct strata in Texas, USA, during 2007–2010. We banded 60,742 white‐winged doves during 2007–2010, and based on 2,458 harvest recoveries, the majority (>95%) of white‐winged dove harvest occurred during the first 2 months of the hunting season (Sep–Oct). Juvenile white‐winged doves represented a greater percentage of the direct recoveries than adults across all strata (north = 80%, central = 69%, south = 82%) and the majority of direct band recoveries (north = 75%, central = 90%, south = 78%) occurred within the original banding strata. Age‐specific weighting factors and harvest derivation indicated that both juvenile and adult harvest were highest within the strata of original banding. Harvest distribution data corrected for band‐reporting rates indicated high fidelity of white‐winged doves to specific geographic strata, with little interplay between strata. Our results suggest that population vital‐rate estimates for survival and harvest for use in future Adaptive Harvest Management should focus on stock‐specific levels. © 2012 The Wildlife Society.
Environmental determinants of food‐chain length: a meta‐analysis
Authors: Takimoto Gaku , Post David M.
Published: April 2012

Food‐chain length is an important character of ecological communities that affects many of their functional aspects. Recently, an increasing number of studies have tested the effects of productivity, disturbance, or ecosystem size on food‐chain length in a variety of natural systems. Here we conduct a formal meta‐analysis to summarize findings from these empirical studies. We found significant positive mean effects of productivity and ecosystem size but no significant mean effect of disturbance on food‐chain length. The strength of mean effect sizes was not significantly different between productivity and ecosystem size. These results lend general support to previous theories predicting the effect of productivity and ecosystem size, but fail to support the prediction that disturbance shortens food chains. In addition, our meta‐analysis found that the effect sizes of primary studies were significantly heterogeneous for ecosystem size and disturbance, but not for productivity. This pattern might reflect that ecosystem size and disturbance can affect food‐chain length through multiple different mechanisms, while productivity influences food‐chain length in a simple manner through energy limitation.
Rhombomys opimus contribution to the “fertile island” effect of tamarisk mounds in Junggar Basin
Authors: Xu Wenxuan , Liu Wei , Yang Weikang , Tang Chaowen , Blank David
Published: April 2012

Fertile islands are created and maintained by a combination of physical and biologically mediated processes. Plants have been shown to be very important in the formation of fertile islands, and recent research indicates that the activities of burrowing animals have a significant influence on the physiochemical properties of soil that can promote the development of fertile islands. In this paper, we chose tamarisk (Tamarix spp.)—a constructive species that grows in the oasis‐desert ecotone, and the great gerbil (Rhombomys opimus)—a widely distributed rodent in Central Asia to study the influence of great gerbils on soil nutrient dynamics in tamarisk mounds. Results indicate that fertile islands exist in tamarisk mounds without burrows of the great gerbil. However, the great gerbil's burrowing activities promote the fertile island effect in tamarisk mounds: soil nutrients under shrubs with great gerbil activity were significantly higher than inter‐mound areas in both surface soil and deep soil from 15 to 50 cm. Available nitrogen in mounds with rodent burrows was over twice as high as in tamarisk mounds without burrows at the same depth. The great gerbil's burrowing activities promote the concentration of soil nutrients in the tamarisk mounds.
Beyond Patchwork Precaution in the Dual-Use Governance of Synthetic Biology
Authors: Kelle Alexander
Published: April 2012

The emergence of synthetic biology holds the potential of a major breakthrough in the life sciences by transforming biology into a predictive science. The dual-use characteristics of similar breakthroughs during the twentieth century have led to the application of benignly intended research in e.g. virology, bacteriology and aerobiology in offensive biological weapons programmes. Against this background the article raises the question whether the precautionary governance of synthetic biology can aid in preventing this techno-science witnessing the same fate? In order to address this question, this paper proceeds in four steps: it firstly introduces the emerging techno-science of synthetic biology and presents some of its potential beneficial applications. It secondly analyses contributions to the bioethical discourse on synthetic biology as well as precautionary reasoning and its application to life science research in general and synthetic biology more specifically. The paper then identifies manifestations of a moderate precautionary principle in the emerging synthetic biology dual-use governance discourse. Using a dual-use governance matrix as heuristic device to analyse some of the proposed measures, it concludes that the identified measures can best be described as “patchwork precaution” and that a more systematic approach to construct a web of dual-use precaution for synthetic biology is needed in order to guard more effectively against the field’s future misuse for harmful applications.
How context shapes category inferences and attribute preference for new ambiguous products
Authors: Noseworthy Theodore J. , Wang Juan , Islam Towhidul
Published: April 2012

Extant research suggests that when marketers introduce products with functions that span multiple categories, consumers tend to generate beliefs in line with only a single category. This has been regarded as a major marketing challenge because it leads consumers to ignore key attributes from the product's supplementary category. Contrary to this prediction, the authors find that because consumers tend to classify new hybrid products by contrasting them against the competitive context, attributes from the supplementary category become more salient and thus contribute greater utility in choice. The authors pit the strength of this effect against several of the most dominant and favored category cues. The results confirm that classification inferences and attribute preference for new hybrid products are highly contextual, and as such, single category inferences need not translate directly into attribute preference.
Diagnostic Accuracy of Bedside Swallow Evaluation Versus Videofluoroscopy to Assess Dysphagia in Individuals With Tetraplegia
Authors: Shem Kazuko L. , Castillo Kathleen , Wong Sandra Lynn , Chang James , Kao Ming‐Chih , Kolakowsky‐Hayner Stephanie A.
Published: April 2012

Objective

To assess the accuracy of bedside swallow evaluation (BSE) compared with videofluorosopic swallow study (VFSS) in diagnosing dysphagia in individuals with tetraplegia due to spinal cord injury (SCI).

Design

A prospective diagnostic accuracy study according to STAndards for the Reporting of Diagnostic accuracy studies (STARD) criteria.

Setting

A county hospital with acute inpatient SCI unit.

Patients

Thirty‐nine subjects with SCI and tetraplegia were enrolled. All of the subjects underwent BSE, and 26 subjects completed the VFSS.

Methods

Individuals with SCI underwent a BSE followed by a VFSS within 72 hours of the BSE. The subjects were diagnosed as having dysphagia if they had positive findings in either BSE or VFSS.

Main Outcome Measures

Sensitivity, specificity, and positive and negative predictive values were calculated by using VFSS as the criterion standard.

Results

Fifteen subjects (38%) were diagnosed as having dysphagia based on the BSE results. Among the subjects who completed the VFSS, 11 were diagnosed with dysphagia (42%) and 4 were diagnosed with aspiration (10%). Of the 26 subjects who completed both BSE and VFSS, only 1 subject was diagnosed differently compared with BSE (3.8%). Different diet recommendations were made in 4 cases after VFSS versus BSE. Different liquid recommendations were made in 8 cases after VFSS versus BSE. Sensitivity of BSE was 100% (95% confidence interval [CI], 71.5%‐100%), specificity was 93.3% (95% CI, 68.1%‐99.8%). A positive predictive value of BSE was 91.7% (95% CI, 61.5%‐100%), and the negative predictive value was 100% (95% CI, 76.8%‐100%).

Conclusions

Dysphagia is present in approximately 38% of individuals with acute tetraplegia. Because only one of the 21 subjects was diagnosed differently based on VFSS, we believe that BSE is an appropriate screening tool for dysphagia for individuals with cervical SCI. However, VFSS provided additional information on diet and liquid recommendations, so there appears to be an important clinical role for the VFSS.
Feeding the next billion: hunger and conservation
Authors: Adams William M.
Published: April 2012

Sometime in October 2011 the human population reached seven billion. The date is uncertain—nobody knows exactly how many people there are as national censuses are intermittent and many inaccurate (Bloom, 2011). But the exact date does not matter: this was a political not demographic event. The seven billionth child was deemed by the UN to have been a girl, born in Manila, Philippines.
Estimation of significance levels and confidence intervals for first‐order reversal curve distributions
Authors: Heslop David , Roberts Andrew P.
Published: April 2012

First‐order reversal curve (FORC) distributions provide a means with which to describe a magnetic mineral assemblage in terms of coercivities and interaction fields. In recent years the use of experimentally derived FORC distributions has increased dramatically and they are being placed in an increasingly quantitative interpretational framework. An outstanding issue for calculation and interpretation of FORC data sets is the statistical significance that can be assigned to structures in experimentally determined distributions. Without this knowledge, the selection and characterization of structures that can be deemed interpretable within a FORC distribution is a subjective process. We demonstrate how FORC processing algorithms can be adapted to provide a measure of statistical significance and a confidence interval for each point in a FORC distribution. This information can guide measurement protocols and provides a more quantitative framework for interpretation of FORC distributions.
Retrievals of sea surface temperature fronts from SAR imagery
Authors: Kuang Hai‐lan , Perrie William , Xie Tao , Zhang Biao , Chen Wei
Published: April 2012

We present a new methodology to identify SST fronts of the Gulf Stream, using linear relationships between sea surface temperature (SST) gradients, and curl and divergence of wind stress fields, derived from high resolution (1 km) SAR data. The new approach uses a composite metric determined from the wind stress divergence and curl fields from individual SAR images. Multi‐stage spatial filtering, Wiener and Gaussian low‐pass filters, and a statistically‐based high pass spatial filter are applied to the derived wind stress curl and divergence fields. Results are significantly improved by restricting SAR imagery to cases where wind speed is less than 12 m/s, thus removing strong wind shear fronts. The method is demonstrated with SAR images of the Gulf Stream and has potential to be applied in near real time operations. The advantages of SAR imagery over optical sensors are its independence of cloud or night‐time conditions and high accuracy.
TheCandida albicansplasma membrane protein Rch1p, a member of the vertebrate SLC10 carrier family, is a novel regulator of cytosolic Ca2+ homoeostasis
Authors: Jiang Linghuo , Alber Joerg , Wang Jihong , Du Wei , Yang Xuexue , Li Xichuan , Sanglard Dominique , Geyer Joachim
Published: April 2012

Candida albicans RCH1 (regulator of Ca2+ homoeostasis 1) encodes a protein of ten TM (transmembrane) domains, homologous with human SLC10A7 (solute carrier family 10 member 7), and Rch1p localizes in the plasma membrane. Deletion of RCH1 confers hypersensitivity to high concentrations of extracellular Ca2+ and tolerance to azoles and Li+, which phenocopies the deletion of CaPMC1 (C. albicans PMC1) encoding the vacuolar Ca2+ pump. Additive to CaPMC1 mutation, lack of RCH1 alone shows an increase in Ca2+ sensitivity, Ca2+ uptake and cytosolic Ca2+ level. The Ca2+ hypersensitivity is abolished by cyclosporin A and magnesium. In addition, deletion of RCH1 elevates the expression of CaUTR2 (C. albicans UTR2), a downstream target of the Ca2+/calcineurin signalling. Mutational and functional analysis indicates that the Rch1p TM8 domain, but not the TM9 and TM10 domains, are required for its protein stability, cellular functions and subcellular localization. Therefore Rch1p is a novel regulator of cytosolic Ca2+ homoeostasis, which expands the functional spectrum of the vertebrate SLC10 family.
Mechanotransduction and focal adhesions
Authors: Goldmann Wolfgang H.
Published: April 2012

Cellular FAs (focal adhesions) respond to internal and external mechanical stresses which make them prime candidates for mechanotransduction. Recent observations showed that the FA proteins including vinculin, FAK (FA kinase) and p130Cas are crucial for the ability of cells to transmit forces and to generate cytoskeletal tension. When mechanically stimulated, cells respond by modulating the spreading area, remodel the actin cytoskeleton, activate actomyosin interactions, recruit integrins and reinforce FAs and cytoskeletal structures. These complex cellular responses are orchestrated such that mechanical stresses within the FA complex remained within a narrow range.
Analysis of electron-positron wavefunctions in the nuclear-electronic orbital framework
Authors: Swalina Chet , Pak Michael V. , Hammes-Schiffer Sharon
Published: April 2012

The nuclear-electronic orbital explicitly correlated Hartree-Fock (NEO-XCHF) approach is extended and applied to the positronic systems PsH, LiPs, and e+LiH. In this implementation, all electrons and positrons are treated quantum mechanically, and all nuclei are treated classically. This approach utilizes molecular orbital techniques with Gaussian basis sets for the electrons and positrons and includes electron-positron correlation with explicitly correlated Gaussian-type geminal functions. An efficient strategy is developed to reduce the number of variational parameters in the NEO-XCHF calculations. The annihilation rates, electron and positron densities, and electron-positron contact densities are compared to available results from higher-level calculations. Our analysis illustrates that the NEO-XCHF method produces qualitative to semi-quantitative results for these properties at a relatively low computational cost by treating only the essential electron-positron correlation explicitly. The NEO-HF method, which does not include explicit correlation and therefore is extremely efficient, is found to provide qualitatively accurate electron-positron contact densities for the e+LiH system but not for the LiPs system. Thus, the utility of the NEO-HF method for determining where annihilation occurs is system dependent and not generally reliable. The NEO-XCHF method, however, provides a computationally practical and reliable approach for determining where annihilation will occur in positronic systems.
A method to provide rapid in situ determination of tip radius in dynamic atomic force microscopy
Authors: Santos Sergio , Guang Li , Souier Tewfik , Gadelrab Karim , Chiesa Matteo , Thomson Neil H.
Published: April 2012

We provide a method to characterize the tip radius of an atomic force microscopy in situ by monitoring the dynamics of the cantilever in ambient conditions. The key concept is that the value of free amplitude for which transitions from the attractive to repulsive force regimes are observed, strongly depends on the curvature of the tip. In practice, the smaller the value of free amplitude required to observe a transition, the sharper the tip. This general behavior is remarkably independent of the properties of the sample and cantilever characteristics and shows the strong dependence of the transitions on the tip radius. The main advantage of this method is rapid in situ characterization. Rapid in situ characterization enables one to continuously monitor the tip size during experiments. Further, we show how to reproducibly shape the tip from a given initial size to any chosen larger size. This approach combined with the in situ tip size monitoring enables quantitative comparison of materials measurements between samples. These methods are set to allow quantitative data acquisition and make direct data comparison readily available in the community.
Basal plane dislocation multiplication via the Hopping Frank-Read source mechanism in 4H-SiC
Authors: Wang H. , Wu F. , Byrappa S. , Sun S. , Raghothamachar B. , Dudley M. , Sanchez E. K. , Hansen D. , Drachev R. , Mueller S. G. , Loboda M. J.
Published: April 2012

Synchrotron white beam x-ray topography (SWBXT) observations are reported of single-ended Frank-Read sources in 4H-SiC. These result from inter-conversion between basal plane dislocations (BPDs) and threading edge dislocations (TEDs) brought about by step interactions on the growth interface resulting in a dislocation comprising several glissile BPD segments on parallel basal planes interconnected by relatively sessile TED segments. Under stress, the BPD segments become pinned by the TED segments producing single ended Frank-Read sources. Since the BPDs appear to “hop” between basal planes, this apparently dominant multiplication mechanism for BPDs in 4H-SiC is referred to as the “Hopping” Frank-Read source mechanism.
On the consistency of the solutions of the space fractional Schrödinger equation
Authors: Bayın Selçuk Ş.
Published: April 2012

Recently, it was pointed out that the solutions found in the literature for the space fractional Schrödinger equation in a piecewise manner are wrong, except the case with the delta potential. We re-analyze this problem and show that an exact and a proper treatment of the relevant integral prove otherwise. We also discuss effective potential approach and present a free particle solution for the space and time fractional Schrödinger equation in general coordinates in terms of Fox's H-functions.
A nanoimprinted, optically tuneable organic laser
Authors: Wallikewitz Bodo H. , Nikiforov Gueorgui O. , Sirringhaus Henning , Friend Richard H.
Published: April 2012

We present a means to optically tune the emission of an organic laser reversibly over a range of 14 nm. This is enabled by incorporating a photochromic spiropyran (10,30-dihydro-10,30,30-trimethyl-6-nitrospiro[2H-1-benzopyran-2,20-(2H)-indole]) into the gain medium formed by the laser dye Rhodamine 700 in poly(methyl methacrylate). This is structured by nanoimprinting to form a distributed feedback resonator. Exposure of the device to ultraviolet and visible light leads to a reversible refractive index change of the photochromic additive and the gain medium, which enables the continuous shift of the laser wavelength. This is possible without compromising the optical gain properties of the device.
Stability and magnetism of tetracyanoethylene adsorbed on substitutionally doped graphene
Authors: Yong Yongliang , Song Bin , Liu Kai , He Pimo
Published: April 2012

The stability and magnetism of tetracyanoethylene (TCNE) adsorbed on Si-, B-, and N-doped graphenes are investigated using the spin-polarized density functional theory. TCNE molecules energetically prefer chemisorption on Si-doped graphene, whereas they favor physisorption on B- and N-doped graphenes. The interaction between TCNE molecules and graphene can be improved by doping, which induces a remarkable change in the electronic properties of graphene. The magnetic moment due to the adsorption depends on the adsorption orientation of TCNE and the substitutionally doped atoms. Furthermore, spin density analysis shows that the magnetic moment is located mainly on the TCNE molecule.
Dimensional transition and carrier dynamics in CdxZn1−xTe/ZnTe nanostructures on Si substrates
Authors: Park K.-D. , Yim S.-Y. , Lee H. S.
Published: April 2012

We investigate the dimensional transition and carrier dynamics in CdxZn1−xTe/ZnTe nanostructures with various Cd mole fractions, grown on Si substrates. Atomic force microscopy images show that the dimensional transition from quantum dots (QDs) to quantum wires occurs with increasing Cd mole fraction. The activation energy of the electrons confined in CdxZn1−xTe QDs with a Cd mole fraction of 0.6 is higher than that of electrons confined in CdxZn1−xTe nanostructures. In addition, the radiative recombination rate shows a linear dependence on the length of the CdxZn1−xTe nanostructures, which is well explained in terms of the “coherence volume” of the bound excitons.
Large and stable piezoelectric response in Bi0.97Nd0.03FeO3 thin film
Authors: Jiang Bo , Li Xiaolong , Zhang Hongyan , Sun Wen , Liu Jingjing , Hu Guangda
Published: April 2012

Bi1−xNdxFeO3 (BNFO) (x = 0.01 ∼ 0.045) films were epitaxially prepared on LaNiO3 [100]/Si substrates via a metal organic decomposition method. Well-saturated and rectangular P-E hysteresis loop can be observed in BNFOx=0.03 film. Additionally, the domains in all BNFO films can be fully switched using a piezoelectric-mode atomic force microscope. More importantly, the BNFOx=0.03 film exhibits a large and stable piezoresponse (∼160 pm/V). These phenomena can be ascribed to the lowest leakage current and redistribution of VO•• in this film.
Electrical and reliability characteristics of polycrystalline silicon thin-film transistors with high-κ Eu2O3 gate dielectrics
Authors: Yen Li-Chen , Hu Chia-Wei , Chiang Tsung-Yu , Chao Tien-Sheng , Pan Tung-Ming
Published: April 2012

In this study, we developed a high-performance low-temperature polycrystalline silicon thin-film transistor (LTPS-TFT) incorporating an ultra thin Eu2O3 gate dielectric. High-κ Eu2O3 LTPS-TFT annealed at 500 °C exhibits a low threshold voltage of 0.16 V, a high effective carrier mobility of 44 cm2/V-s, a small subthreshold swing of 142 mV/decade, and a high Ion/Ioff current ratio of 1.34 × 107. These significant improvements are attributed to the high gate-capacitance density due to the adequate quality of Eu2O3 gate dielectric with small interfacial layer of effective oxide thickness of 2.5 nm. Furthermore, the degradation mechanism of positive bias temperature instability was studied for a high-k Eu2O3 LTPS-TFT device.
Direct evidence of current blocking by ZnSe in Cu2ZnSnSe4 solar cells
Authors: Timo Wätjen Jörn , Engman Jessica , Edoff Marika , Platzer-Björkman Charlotte
Published: April 2012

Thin films of polycrystalline Cu2ZnSnSe4 were made by selenization of co-sputtered metallic precursors and processed to solar cells. Electron beam induced current (EBIC) in combination with microscopic scale IV characterization is used to investigate lateral inhomogeneities in electrical performance across the solar cell area. Transmission electron microscopy relates areas with low EBIC response to the formation of a ZnSe phase at the absorber surface resulting in a current blocking behavior and a reduced short-circuit current density for the solar cells. Areas without ZnSe have a high EBIC response and result in high quality diodes well suited for solar cells.
Long range surface plasmon resonance and enhanced fluorescence near the ultra-violet vacuum cutoff limit
Authors: Crosbie Stephen , Zerulla Dominic
Published: April 2012

Reported is the observation of surface plasmon resonance (SPR), long range SPR and surface plasmon enhanced fluorescence at 204 nm, close to the vacuum cut-off limit. The development of deep ultra-violet plasmonics is challenging as it requires alternative materials and design considerations compared to traditional visible devices. However, it offers inherent advantages, including improved sensitivity to local refractive index changes and applicability to bio-sensing. In this wavelength region the amplified near fields enhance the absorption and fluorescence of electronic transitions. In particular, this is demonstrated by the measurement of intrinsic fluorescence from low concentration organic impurities in reagent grade water.
Magnetic-field-induced reverse martensitic transformation and large magnetoresistance in Ni50−xCoxMn32Al18 Heusler alloys
Authors: Xuan H. C. , Shen L. J. , Tang T. , Cao Q. Q. , Wang D. H. , Du Y. W.
Published: April 2012

We have studied the magnetic and magnetoresistance properties in polycrystalline Ni50−xCoxMn32Al18 Heusler alloys. A unique martensitic transformation (MT) from the ferromagnetic austenite to the weak-magnetic martensite phase was obtained and magnetic-field-induced reverse MT was confirmed in these alloys. A magnetic difference up to 45 emu/g was measured across the MT for Ni42Co8Mn32Al18 alloy. In the same quaternary alloy, the large magnetoresistance effect of 67% at 225 K was observed through this field-induced magnetic phase transition.
In-line Si1-xGex epitaxial process monitoring and diagnostics using multiwavelength high resolution micro-Raman spectroscopy
Authors: Chang Chun-Wei , Hong Min-Hao , Lee Wei-Fan , Lee Kuan-Ching , Yang Shen-Min , Tsai Ming-Shan , Chuang Yen , Fan Yu-Ta , Hasuike Noriyuki , Harima Hiroshi , Ueda Takeshi , Ishigaki Toshikazu , Kang Kitaek , Yoo Woo Sik
Published: April 2012

Multiwavelength, high resolution micro-Raman spectroscopy was applied to in-line process monitoring and diagnostics of undoped and B-doped Si1-xGex epitaxy on Si(100) device wafers. This noncontact technique was used to monitor the Ge content, B concentration and thickness of single and double Si1-xGex epitaxial layers. Epitaxial process problems were diagnosed nondestructively. Raman peak positions and full-width-at-half-maximum of the Si-Si peak(s) from the Si1-xGex epitaxial layer(s) and Si substrates, in the wavenumber range of 475 ∼ 535 cm-1, were monitored under ultraviolet and visible excitation wavelengths. The Ge content, B concentration and Si1-xGex epitaxial film structures were verified by secondary ion mass spectroscopy (SIMS) depth profiling results. In-line monitoring of Si-Si and Si Raman peaks is very effective in noncontact material property characterization, epitaxial process optimization, and quality control applications.
The Ingenious Mr Hughes: Combining Forced, Fat, and Reverse Perspective All in One Art Piece to Pit Objects against Surfaces
Authors: Papathomas Thomas V , Baker Nicholas , Yeshua Arielle S , Zhuang Xiaohua , Ng Andrew
Published: April 2012

The artist Patrick Hughes has ingeniously painted rows of stacked Brillo boxes in Forced into Reverse Perspective. The geometry is in reverse perspective, predicting only one type of illusory motion for each planar surface for moving viewers. He “broke” these surfaces into objects by painting the boxes in three types of perspective (planar, forced, and reverse). Our experiments confirmed that he succeeded in eliciting different types of illusory motion, including “differential motion” between boxes for most viewers. In some sense, this illustrates the superiority of secondary (painted) over primary (physical) cues.
Space-Time Disarray and Visual Awareness
Authors: Koenderink Jan , Richards Whitman , van Doorn Andrea J
Published: April 2012

Local space-time scrambling of optical data leads to violent jerks and dislocations. On masking these, visual awareness of the scene becomes cohesive, with dislocations discounted as amodally occluding foreground. Such cohesive space-time of awareness is technically illusory because ground truth is jumbled whereas awareness is coherent. Apparently the visual field is a construction rather than a (veridical) perception.
The Same Old New Look: Publication Bias in a Study of Wishful Seeing
Authors: Francis Gregory
Published: April 2012

A recent study reported evidence of “wishful seeing,” where observers reported seeing a desired object as being closer than other objects. A statistical analysis of the experimental findings reveals evidence of publication bias in the study, so the existence of wishful seeing remains unproven.
NuST: analysis of the interplay between nucleoid organization and gene expression
Authors: Scolari Vittore F. , Zarei Mina , Osella Matteo , Cosentino Lagomarsino Marco
Published: April 2012

Summary: Different experimental results suggest the presence of an interplay between global transcriptional regulation and chromosome spatial organization in bacteria. The identification and clear visualization of spatial clusters of contiguous genes targeted by specific DNA-binding proteins or sensitive to nucleoid perturbations can elucidate links between nucleoid structure and gene expression patterns. Similarly, statistical analysis to assess correlations between results from independent experiments can provide the integrated analysis needed in this line of research. NuST (Nucleoid Survey tools), based on the Escherichia coli genome, gives the non-expert the possibility to analyze the aggregation of genes or loci sets along the genome coordinate, at different scales of observation. It is useful to discover correlations between different sources of data (e.g. expression, binding or genomic data) and genome organization. A user can use it on datasets in the form of gene lists coming from his/her own experiments or bioinformatic analyses, but also make use of the internal database, which collects data from many published studies.

Availability and Implementation: NuST is a web server (available at http://www.lgm.upmc.fr/nust/). The website is implemented in PHP, SQLite and Ajax, with all major browsers supported, while the core algorithms are optimized and implemented in C. NuST has an extensive help page and provides a direct visualization of results as well as different downloadable file formats. A template Perl code for automated access to the web server can be downloaded at http://www.lgm.upmc.fr/nust/downloads/, in order to allow the users to use NuST in systematic bioinformatic analyses.

Contact:  vittore.scolari@upmc.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
IL-17 contributes to cardiac fibrosis following experimental autoimmune myocarditis by a PKCβ/Erk1/2/NF-κB-dependent signaling pathway
Authors: Liu Yanfang , Zhu Haitao , Su Zhaoliang , Sun Caixia , Yin Jingping , Yuan Hongyan , Sandoghchian Siamak , Jiao Zhijun , Wang Shengjun , Xu Huaxi
Published: April 2012

Myocarditis is a common clinical cardiovascular disease, and some patients progress to dilated cardiomyopathy (DCM) with chronic heart failure. Common viral infections are the most frequent cause of myocarditis, but other pathogens and autoimmune diseases have also been implicated. Th17 cells are novel IL-17-producing effector T helper cells that play an important role in the development of autoimmune myocarditis. Furthermore, IL-17 is also important in post-myocarditis cardiac remodeling and progression to DCM. However, the mechanisms whereby IL-17 and IL-17-producing cells promote the progression of cardiac fibrosis remain unclear. We therefore investigated whether IL-17 directly induced cardiac fibrosis in experimental autoimmune myocarditis (EAM) and explored the possible molecular mechanisms. The EAM model was induced and serum IL-17 level was detected by ELISA; western blot, immunofluorescence and sirius red staining were used to analyze the collagen expression. PCR was used to assay the IL-17RA and IL-17RC. The results indicated that IL-17 induced cardiac fibrosis both in vitro and in vivo. The protein kinase C (PKC)β/Erk1/2/NF-κB (Nuclear Factor κappa B) pathway was involved in the development of myocardial fibrosis and IL-17 contributed to cardiac fibrosis following EAM via this pathway. These results provide the first direct evidence for the involvement of the PKCβ/Erk1/2/NF-κB signaling pathway in IL-17-induced myocardial fibrosis.
Association of Spring Pruning Practices with Severity of Powdery Mildew and Downy Mildew on Hop
Authors: Gent David H. , Nelson Mark E. , Grove Gary G. , Mahaffee Walter F. , Turechek William W. , Woods Joanna L.
Published: April 2012

Downy mildew (caused by Pseudoperonospora humuli) and powdery mildew (caused by Podosphaera macularis) are important diseases of hop in the Pacific Northwest United States, and cultural practices may affect the severity of both diseases. The association of spring pruning quality and timing with severity of downy mildew and powdery mildew was assessed through analysis of survey data collected from commercial hop yards in Oregon and Washington. Among 149 hop yards surveyed, the most common pruning method was chemical desiccation (48% of yards), mechanical pruning (23%), or a combination of these practices (15%). The quality of pruning was assessed using a three-category ordinal scale (“excellent”, “moderate”, or “poor”) based on the amount of foliage remaining on plants following pruning. Excellent pruning quality was attained more often in yards pruned twice (74.6 to 82.1% of yards) versus once (33.8% of yards), independent of pruning method. Seasonal severity of downy mildew in Oregon increased approximately twofold with reduction in pruning quality from excellent to moderate to poor. Pruning quality was not significantly related to levels of powdery mildew on leaves or cones in Oregon. Under more severe disease pressure in Washington, however, seasonal severity of powdery mildew on leaves and the incidence of cones with powdery mildew were significantly greater in yards that had poor pruning compared with excellent pruning. Moreover, yards that had excellent pruning quality received, on average, 1.1 to 1.5 fewer fungicide applications per season for downy mildew or powdery mildew compared with yards that had moderate or poor pruning quality. This savings was associated with delayed initiation of the first application by 7.5 to 14.2 days in yards with excellent pruning quality. Replicated experiments in commercial yards in Oregon quantified the effect of delaying pruning timing 5 to 21 days compared with growers' standard practices on the diseases and yield. Downy mildew suppression by delayed pruning was dependent on cultivar and year of sampling, being significantly reduced fivefold only in ‘Willamette’ in 2007. Severity of powdery mildew and cone yield was similar between plots that received the delayed or standard pruning timing treatments. Collectively, these studies emphasize that early spring sanitation measures are associated with reduced primary inoculum and are critically important for managing both downy mildew and powdery mildew. A savings of at least one fungicide application per year appears achievable when spring pruning is conducted thoroughly and slightly delayed compared with growers' current practices.