bluuebunny/crossref_metadata_2025 huggingface dataset:
A new algorithm for contact detection between spherical particle and triangulated mesh boundary in discrete element method simulations
Authors: Hu L. , Hu G.M. , Fang Z.Q. , Zhang Y.
Published: March 2013

In discrete element method (DEM) simulations of real scale, the spherical particles are commonly employed for increasing the computation speed, and the complex boundary models are represented by triangle meshes with controllable accuracy. A new contact detection algorithm has been developed to resolve the contacts between the spheres and the triangle mesh boundaries. The application of the barycentric coordinates makes this algorithm more efficient to identify contacts in the intersection test. As a particle probably collides with several triangles at the same time, the multiple contacts would be reported as face contacts, edge contacts, or vertex contacts. Moreover, the particle embedding in a triangle can be also contact with the edges or vertices of the next triangles. These contacts should be considered as invalid for updating contact forces in the DEM. To exclude invalid records from the multiple contacts, the algorithm gives attention to the mesh structure nearby contacts and analyzes all possible collision situations. Numerical experiments have been conducted to verify this algorithm by using the algorithm in the DEM simulation framework. The numerical results suggest that the algorithm can resolve all contacts precisely and stably when the spherical particles collide on the complex boundary circumstances. Copyright © 2013 John Wiley & Sons, Ltd.
Superconvergence of a full‐discrete combined mixed finite element and discontinuous Galerkin method for a compressible miscible displacement problem
Authors: Yang Jiming , Chen Yanping , Xiong Zhiguang
Published: March 2013

An efficient time‐stepping procedure is investigated for a two‐dimensional compressible miscible displacement problem in porous media in which the mixed finite element method with Raviart‐Thomas space is applied to the flow equation, and the transport one is solved by the symmetric interior penalty discontinuous Galerkin approximation on Cartesian meshes. Based on the projection interpolations and the induction hypotheses, a superconvergence error estimate is obtained. During the analysis, an extension of the Darcy velocity along the Gauss line is also used in the evaluation of the coefficients in the Galerkin procedure for the concentration. © 2013 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2013
Isotopically depleted carbon in the mid‐depth South Atlantic during the last deglaciation
Authors: Tessin A. C. , Lund D. C.
Published: March 2013

The initial rise in atmospheric CO2 during the last deglaciation was likely driven by input of carbon from a 13C‐depleted reservoir. Here we show that high resolution benthic foraminiferal records from the mid‐depth Brazil Margin display an abrupt drop in δ13C during Heinrich Stadial 1 (HS1) that is similar to but larger than in the atmosphere. Comparing the Brazil Margin results to published records from the North Atlantic, we are unable to account for the South Atlantic δ13C data with conservative mixing between northern and southern component water masses. Rapid input of abyssal water from the Southeast Atlantic could account for deglacial δ13C anomalies at the Brazil Margin but it would require a reversal in deep water flow direction compared to today. A new mid‐depth water mass may explain similar HS1 δ13C values in both the North and South Atlantic, but contrasting oxygen isotopic values between the two basins do not support such a scenario. Instead, it appears that δ13C behaved non‐conservatively during the deglaciation, possibly reflecting the input of carbon from an isotopically depleted source.
Preparation and characterization of polyimide/pure silica zeolite hybrid films
Authors: Huang Zhenxun , Zhao Jianqing , Yuan Yanchao , Yan Shijing , Liu Shumei , Zan Xingtao
Published: March 2013

In this study, amino derivative of pure silica zeolite nanocrystal (A‐PSZN) was dispersed into polyimide (PI) matrix to prepare PI/A‐PSZN hybrid films, and their thermal and mechanical properties, as well as hydrophobicity, were characterized scientifically. The test results show that PI/A‐PSZN hybrid films possess higher glass transition temperature, higher thermal stability and lower in‐plane coefficient of thermal expansion than pristine PI. The mechanical property data suggest that the incorporation of A‐PSZN results in an increase in Young's modulus and tensile strength of the hybrid films, but as its content exceeds the critical value (maybe 5 wt%), its enhancement effect on the hybrid's strength and toughness gets weaker. Furthermore, liquid dripping imaging analysis results indicate that the film's hydrophobicity is clearly improved by the introduction of A‐PSZN. As compared with PSZN, A‐PSZN exhibits better effect on enhancing the overall performance of pristine PI films. A comparison with other studies suggests that PI/A‐PSZN is a hybrid film with superior comprehensive properties. Copyright © 2013 John Wiley & Sons, Ltd.
A case study of personalized therapy for osteosarcoma
Authors: Davis Lara E. , Hofmann Nicolle E. , Li Guangheng , Huang Elaine T. , Loriaux Marc M. , Bracha Shay , Helfand Stuart C. , Mata John E. , Marley Kevin , Mansoor Atiya , Tyner Jeffrey W. , Abraham Jinu , Séguin Bernard , Keller Charles
Published: March 2013

Background

Effective targeted therapies are needed in sarcomas, but the biological heterogeneity of these tumors has presented a challenge to clinical integration of small molecule inhibitors in sarcoma treatment. Here we outline a process to personalize therapy for sarcomas through a case study of a canine with spontaneous osteosarcoma.

Procedure

Rapid establishment of a primary tumor cell culture is described, followed by efficient functional characterization of the tumor that identified the Src inhibitor dasatinib as the most effective targeted therapy for this individual dog.

Results

Adjuvant dasatinib was administered for a total of 26 weeks following treatment with chemotherapy. Pharmacokinetic studies confirm that a therapeutic serum concentration was achieved at a tolerable dose of 0.75 mg/kg/day. The canine patient remains without evidence of recurrent disease 24 months following initial diagnosis.

Conclusions

The approach described through this illustrative case study is broadly applicable and might be used for other solid tumors in canines as well as in humans. Pediatr Blood Cancer 2013;60:1313–1319. © 2013 Wiley Periodicals, Inc.
RASSF1A in maternal plasma as a molecular marker of preeclampsia
Authors: Papantoniou Nikolas , Bagiokos Vassilis , Agiannitopoulos Kostantinos , Kolialexi Aggeliki , Destouni Aspasia , Tounta Georgia , Kanavakis Emmanuel , Antsaklis Aris , Mavrou Ariadni
Published: March 2013

Objectives

This study aimed to quantitate cell free (cf) and cell free fetal (cff) DNA in maternal plasma by determining RASSF1A levels before and after enzyme digestion in women who subsequently developed preeclampsia (PE) and compare them with uncomplicated pregnancies.

Methods

Twenty‐four samples from pregnant women who developed PE and 48 samples from women with uncomplicated pregnancies were analysed. Blood samples were obtained at 11–13 weeks. cfDNA was determined by quantifying RASSF1A using qRT‐PCR. A second qRT‐PCR was performed following methylation‐sensitive enzyme digestion by BstUI, to quantitate hypermethylated RASSF1A sequences of fetal origin. ACTB gene was used as control to confirm complete enzyme digestion.

Results

cfDNA and cffDNA levels were significantly increased in women who developed PE as compared with uncomplicated pregnancies (median cfDNA: 9402 vs 2698, median cffDNA: 934.5 vs 62, respectively). Following operating characteristic curve analysis, cut‐off values of 7486 Εq/mL for cfDNA and 512 Εq/mL for cffDNA were chosen, which provided a sensitivity of 75% and 100% and specificity of 98% and 100%, respectively, to identify women at risk for PE.

Conclusions

The study demonstrates potential use of cfDNA and cffDNA in maternal plasma as markers for the early prediction of women at risk for PE. © 2013 John Wiley & Sons, Ltd.
Statins of high versus low cholesterol‐lowering efficacy and the development of severe renal failure
Authors: Chung Yu‐Heng , Lee Yen‐Chieh , Chang Chia‐Hsuin , Lin Min‐Shung , Lin Jou‐Wei , Lai Mei‐Shu
Published: March 2013

Background

The objective of this nationwide retrospective cohort study was to examine the renal outcomes of HMG‐CoA reductase inhibitor (statin) initiators.

Methods

The patients who started to take statins with high cholesterol‐lowering efficacy (atorvastatin and rosuvastatin) and low efficacy (lovastatin, simvastatin, pravastatin, and fluvastatin) between 1 January 2001 and 31 December 2008 were identified from the Taiwan National Health Insurance claims database. The outcome of interest was severe renal failure, defined as the composite endpoint of hemodialysis, peritoneal dialysis, and kidney transplantation. A proportional hazard regression model was applied to estimate the incidence ratio between the two groups, adjusted for the propensity scores based upon baseline characteristics.

Results

Among of the 26 007 and 42 249 statin initiators, the crude incidence rate for developing severe renal failure was 0.65 and 0.46 per 100 person‐years for the high‐efficacy and low‐efficacy groups, respectively. Despite that these two groups had comparable risk for myocardial infarction (hazard ratio: 1.06, 95%CI: 0.92–1.21), there was a 13% increased hazard for developing severe renal failure in the rosuvastatin and atorvastatin initiators (hazard ratio: 1.13, 95%CI: 1.02–1.26). The increased risk associated with these two statins was consistent across different risk groups (diabetes, chronic kidney disease, and ischemic heart disease).

Conclusions

Statins with high cholesterol‐lowering efficacy might increase the risk for developing severe renal failure. An alternative explanation is that the renal risk cannot be ameliorated as much as cardiovascular risk. Further follow‐up studies or meta‐analyses are needed to solve the controversy. Copyright © 2013 John Wiley & Sons, Ltd.
Use of Preoperative CHA2DS2‐VASc Score to Predict the Risk of Atrial Fibrillation After Cardiothoracic Surgery: A Nested Case–Control Study from the Atrial Fibrillation Suppression Trials (AFIST) I, II, and III
Authors: Baker William L , Coleman Craig I. , White C. Michael , Kluger Jeffrey
Published: March 2013

Study Objective

To evaluate whether the preoperative CHA2DS2‐VASc score predicts the risk of atrial fibrillation (AF) after cardiothoracic surgery (CTS).

Design

Retrospective, nested case–control study.

Patients

A total of 560 patients undergoing coronary artery bypass grafting and/or valvular surgery from the Atrial Fibrillation Suppression Trials I, II, and III.

Measurements and Main Results

All variables showing a univariate association (p≤0.20) with AF occurrence were entered into a backward stepwise multivariate logistic regression analysis to control for potential confounders and to calculate adjusted odds ratios (AORs) with 95% confidence intervals (CIs). The population was age 67.8 ± 8.6 (mean ± SD) years and 77.1% male, with CHA2DS2‐VASc scores of 0–1 (low) in 34 patients (6.1%), 2–3 (medium) in 261 patients (46.6%), and more than 3 (high) in 265 patients (47.3%). Post‐CTS AF occurred in 177 patients (31.6%), with 27%, 23%, and 41% in the low–, medium–, and high–CHA2DS2‐VASc score groups, respectively. The high‐score group had a 2.3‐fold increased odds of developing AF versus the medium‐score group (p<0.0001). The differences between the high‐ and medium‐score groups when each group was compared with the low‐score group were not statistically significant. On the multivariate logistic regression analysis, CHA2DS2‐VASc score was associated with development of AF (AOR 1.20, 95% CI 1.06–1.36).

Conclusion

Increasing CHA2DS2‐VASc score was an independent predictor for the development of post‐CTS AF, with patients in the high‐score group having the highest overall incidence.
VIOLENT AND PROSOCIAL BEHAVIOR BY ADOLESCENTS TOWARD PARENTS AND TEACHERS IN A COMMUNITY SAMPLE
Authors: Jaureguizar Joana , Ibabe Izaskun , Straus Murray A.
Published: March 2013

This study focused on violent and prosocial behaviors by adolescents toward parents and teachers, and the relation between such behaviors and adolescents’ perceptions about the family and school environment. Gender differences in child‐to‐parent violence and student‐to‐teacher violence were also studied. The sample comprised 687 adolescents from secondary schools in the province of Gipuzkoa, Spain, aged between 12 and 16 years. Participants responded to the relationship domains of the Family Environment Scale and the Classroom Environment Scale, among other instruments. A positive family relationship was related to less violent and more prosocial behavior toward parents. However, a positive classroom relationship was associated only with more prosocial behavior toward teachers. The results show that criminal and antisocial behaviors had a mediating influence on the relation between family and school relationships and violence against authority. The implications for intervention and prevention programs are discussed.
ARTICLES PUBLISHED IN SIX SCHOOL PSYCHOLOGY JOURNALS FROM 2005–2009: WHERE'S THE INTERVENTION RESEARCH?
Authors: Villarreal Victor , Gonzalez Jorge E. , McCormick Anita S. , Simek Amber , Yoon Hyunhee
Published: March 2013

This article reports on a content analysis of six school psychology journals spanning the years 2005–2009, with a particular focus on published intervention research. The analysis showed that (a) research articles were the most frequently published, with the largest category being descriptive research; (b) the percentage of intervention studies was higher (9.3%) than previously reported but lower than reported in special education journals (15.9%); (c) of the published interventions, the most frequent design was quasi‐experimental, followed by single‐subject research; (d) most intervention studies were conducted in school settings utilizing children in kindergarten through Grade 5, followed as a distant second by middle school settings; (e) the preponderance of intervention studies were academic or social/behavioral, with emotional interventions being the least represented; and (f) of the academic interventions, the most widely studied dimension was reading, followed as a distant second by math. The findings are discussed in terms of their relevance for addressing the research‐to‐practice gap as well as their implications for school psychology research and practice.
PROSPECTIVE TEACHERS' AWARENESS AND EXPRESSION OF EMOTIONS: ASSOCIATIONS WITH PROPOSED STRATEGIES FOR BEHAVIORAL MANAGEMENT IN THE CLASSROOM
Authors: Garner Pamela W. , Moses Laurence K. , Waajid Badiyyah
Published: March 2013

This research examined whether prospective teachers’ emotion regulation styles, dispositional empathy, and conceptions of competent student emotion and behavior were predictive of their attitudes about bullying and proposed responses to peer conflict. Overall, participants perceived physical bullying as more serious than verbal and relational bullying. Prospective teachers also expressed higher levels of sympathy for victims and a greater likelihood of intervention in response to physical bullying. Regression analyses demonstrated that valuing emotional competence and the role of teachers in supporting its development were meaningfully associated with expressed support for victims and with proposed responses to the perpetrators of this type of classroom aggression. Interestingly, those respondents who reported higher levels of situationally specific sympathy for victims (and not dispositional empathy) also reported that they would be more likely than their counterparts to intervene on their behalf. The emotional reactivity component of dispositional empathy was, however, positively associated with regulated responses to peer conflict involving a difficult child. The emotion regulation variables, although associated with the outcome measures in correlational analyses, were not unique predictors of prospective teachers’ bullying attitudes.
An Improved Method for Site‐Specific End Modification of Zeolite L for the Formation of Zeolite L and Gold Nanoparticle Self‐Assembled Structures
Authors: Beierle John M. , Roswanda Robby , Erne Petra M. , Coleman Anthony C. , Browne Wesley R. , Feringa Ben L.
Published: March 2013

The ability to site‐selectively modify micro‐ and nanosized particles has allowed for directed self‐assembly in two and three dimensions. Site‐selective modification of particles can be a complicated task requiring the pre‐organization of particles or enhanced particle fabrication methods. The aluminum silicate, zeolite L has been reported to undergo site‐specific modification at the zeolite channel entrances, post‐fabrication in a solution‐based method. The process by which the channel entrances are site selectively modified is explored here. The preliminary step of charging the zeolite channels with aqueous acid allows for catalysis of covalent bond formation at the channel entrances. Three new end‐specific modification reagents are described based on silanol and silyl ether functional groups. These reagents are purified by column chromatography and characterized by1H NMR spectroscopy and high resolution mass spectrometry (HRMS); they provide for reliable end modification of zeolites L. Preferential reactivity at the channel entrances is also observed. The utility of the approach is demonstrated by modifying zeolite L with adamantane at the channel entrances. Site‐specific self‐assembly with β‐cyclodextrin coated gold nanoparticles can be triggered with a chemical stimulus. The resulting multivalent host‐guest interactions give gold clustered nanoparticles at the ends of the micrometer‐sized zeolites.
Response to boguslaw stec's letter to the editor of protein science
Authors: Celeste Lesa , Lovelace Leslie , Lebioda Lukasz
Published: March 2013

PDB Code(s): 4JIM, 4JJZ, 4JJK, 4JKI
Sequence‐specific determination of protein and peptide concentrations by absorbance at 205 nm
Authors: Anthis Nicholas J. , Clore G. Marius
Published: March 2013

Quantitative studies in molecular and structural biology generally require accurate and precise determination of protein concentrations, preferably via a method that is both quick and straightforward to perform. The measurement of ultraviolet absorbance at 280 nm has proven especially useful, since the molar absorptivity (extinction coefficient) at 280 nm can be predicted directly from a protein sequence. This method, however, is only applicable to proteins that contain tryptophan or tyrosine residues. Absorbance at 205 nm, among other wavelengths, has been used as an alternative, although generally using absorptivity values that have to be uniquely calibrated for each protein, or otherwise only roughly estimated. Here, we propose and validate a method for predicting the molar absorptivity of a protein or peptide at 205 nm directly from its amino acid sequence, allowing one to accurately determine the concentrations of proteins that do not contain tyrosine or tryptophan residues. This method is simple to implement, requires no calibration, and should be suitable for a wide range of proteins and peptides.
A multipurpose fusion tag derived from an unstructured and hyperacidic region of the amyloid precursor protein
Authors: Sangawa Takeshi , Tabata Sanae , Suzuki Kei , Saheki Yasushi , Tanaka Keiji , Takagi Junichi
Published: March 2013

Expression and purification of aggregation‐prone and disulfide‐containing proteins in Escherichia coli remains as a major hurdle for structural and functional analyses of high‐value target proteins. Here, we present a novel gene‐fusion strategy that greatly simplifies purification and refolding procedure at very low cost using a unique hyperacidic module derived from the human amyloid precursor protein. Fusion with this polypeptide (dubbed FATT for Flag‐Acidic‐Target Tag) results in near‐complete soluble expression of variety of extracellular proteins, which can be directly refolded in the crude bacterial lysate and purified in one‐step by anion exchange chromatography. Application of this system enabled preparation of functionally active extracellular enzymes and antibody fragments without the need for condition optimization.
Analyses of the general rule on residue pair frequencies in local amino acid sequences of soluble, ordered proteins
Authors: Shirota Matsuyuki , Kinoshita Kengo
Published: March 2013

The amino acid sequences of soluble, ordered proteins with stable structures have evolved due to biological and physical requirements, thus distinguishing them from random sequences. Previous analyses have focused on extracting the features that frequently appear in protein substructures, such as α‐helix and β‐sheet, but the universal features of protein sequences have not been addressed. To clarify the differences between native protein sequences and random sequences, we analyzed 7368 soluble, ordered protein sequences, by inspecting the observed and expected occurrences of 400 amino acid pairs in local proximity, up to 10 residues along the sequence in comparison with their expected occurrence in random sequence. We found the trend that the hydrophobic residue pairs and the polar residue pairs are significantly decreased, whereas the pairs between a hydrophobic residue and a polar residue are increased. This trend was universally observed regardless of the secondary structure content but was not observed in protein sequences that include intrinsically disordered regions, indicating that it can be a general rule of protein foldability. The possible benefits of this rule are discussed from the viewpoints of protein aggregation and disorder, which are both caused by low‐complexity regions of hydrophobic or polar residues.
The crystal structure of Toxoplasma gondii nucleoside triphosphate diphosphohydrolase 1 represents a conformational intermediate in the reductive activation mechanism of the tetrameric enzyme
Authors: Krug Ulrike , Totzauer Robert , Sträter Norbert
Published: March 2013

Toxoplasma gondii nucleoside triphosphate diphosphohydrolase (NTPDase) 1 was crystallized in an intermediate tetrameric conformation. The crystal structure is similar to that of T. gondii NTPDase3 and represents an inactive conformation as the activating disulfide bridge is not reduced and the active site cleft between the two domains of each monomer is open. However, the arrangement of the monomers within the tetramer differs from that of the inactive form of NTPDase3 and may represent an intermediate conformation on the path of the closure motion of the tetramer induced upon activation. Proteins 2013; 81:1271–1276. © 2013 Wiley Periodicals, Inc.
Crystal structure of SsfS6, the putative C‐glycosyltransferase involved in SF2575 biosynthesis
Authors: Wang Fengbin , Zhou Maoquan , Singh Shanteri , Yennamalli Ragothaman M. , Bingman Craig A. , Thorson Jon S. , Phillips George N.
Published: March 2013

The molecule known as SF2575 from Streptomyces sp. is a tetracycline polyketide natural product that displays antitumor activity against murine leukemia P388 in vivo. In the SF2575 biosynthetic pathway, SsfS6 has been implicated as the crucial C‐glycosyltransferase (C‐GT) that forms the C‐C glycosidic bond between the sugar and the SF2575 tetracycline‐like scaffold. Here, we report the crystal structure of SsfS6 in the free form and in complex with TDP, both at 2.4 Å resolution. The structures reveal SsfS6 to adopt a GT‐B fold wherein the TDP and docked putative aglycon are consistent with the overall C‐glycosylation reaction. As one of only a few existing structures for C‐glycosyltransferases, the structures described herein may serve as a guide to better understand and engineer C‐glycosylation. Proteins 2013; 81:1277–1282. © 2013 Wiley Periodicals, Inc.
A convenient method for europium‐labeling of a recombinant chimeric relaxin family peptide R3/I5 for receptor‐binding assays
Authors: Zhang Wei‐Jie , Jiang Qian , Wang Xin‐Yi , Song Ge , Shao Xiao‐Xia , Guo Zhan‐Yun
Published: March 2013

Relaxin family peptides have important biological functions, and so far, four G‐protein‐coupled receptors have been identified as their receptors (RXFP1–4). A chimeric relaxin family peptide R3/I5, containing the B‐chain of relaxin‐3 and the A‐chain of INSL5, is a selective agonist for both RXFP3 and RXFP4. In a previous study, europium‐labeled R3/I5, as a nonradioactive and low‐background receptor‐binding tracer, was prepared through a chemical synthesis approach. In the present study, we established a convenient alternative approach for preparing the europium‐labeled R3/I5 tracer based on a recombinant R3/I5 designed to carry a solubilizing tag at the A‐chain N‐terminus and a pyroglutamate residue at the B‐chain N‐terminus. Because of the presence of a single primary amine moiety, the recombinant R3/I5 peptide was site‐specifically mono‐labeled at the A‐chain N‐terminus by a diethylenetriaminepentaacetic acid/europium moiety through a convenient one‐step procedure. The diethylenetriaminepentaacetic acid/Eu3+‐labeled R3/I5 bound both receptors RXFP3 and RXFP4 with high binding affinities and low nonspecific binding. Thus, we have presented a valuable nonradioactive tracer for future interaction studies on RXFP3 and RXFP4 with various natural or designed ligands. The present approach could also be adapted for preparing and labeling of other chimeric relaxin family peptides. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.
Water adsorption on r‐TiO2(110): Presence of a well‐defined (1 × 1)‐structure as evidenced by He‐atom scattering
Authors: Osterloh Niklas , Silber David , Traeger Franziska , Wöll Christof
Published: March 2013

The adsorption of water on r‐TiO2(110) has been investigated with thermal desorption spectroscopy (TDS) and helium atom scattering. Conventional TDS using a mass spectrometer and He‐TDS monitoring reflected He beam intensity consistently show the existence of a structurally well‐defined monolayer as well as a highly ordered second layer of water and a disordered multilayer phase. He diffraction patterns recorded along the high symmetry [001], $[1{\bar {1}}0]$, and $[1{\bar {1}}1]$ directions reveal a well‐ordered superstructure with (1 × 1) symmetry, providing strong evidence for the absence of a partially dissociated monolayer on the perfect parts of the substrate. No changes in the diffraction patterns are observed after irradiation with UV‐light.
Effects of valence band tails on the blue and red spectral shifts observed in the temperature‐dependent photoluminescence of InN
Authors: Seetoh Ian P. , Soh Chew Beng , Fitzgerald Eugene A. , Chua Soo Jin
Published: March 2013

Lineshape‐fitting, using a model that takes into account of band tails, was performed on the photoluminescence spectra measured from InN samples at temperatures varying from 5 to 300 K. By analyzing how the fitted parameters varied with temperature, it was found that the previously observed blue and then red shift of emission peak position with increasing temperature is related to valence band tails. The initial blue‐shift at low temperature is due to filling of valence band tails while the subsequent Varshni red‐shift is due to lattice expansion. In a series of samples grown using increasing trimethylindium flow rates during metal organic chemical vapor deposition, the impurity potential that describes the width of the valence band tail increased from 18 to 26 meV, possibly due to more nitrogen vacancies being created in the material.
Structural insights into the formation and evolution of amorphous phase‐change materials
Authors: Skelton J. M. , Loke D. , Lee T. H. , Elliott S. R.
Published: March 2013

magnified image

Reduction of programming current is a major research goal in the development of phase‐change random‐access memory devices. The power‐limiting step is the amorphization of the phase‐change material (PCM), where a significant energy input is required to induce melting prior to amorphization. To address the challenge of reducing power consumption while retaining switching speed, a detailed understanding of the physics underpinning the amorphization process is required. As yet, little has been done to study the dynamics of the melt‐quench process at the atomic level. In this article, we report a detailed study of the melting mechanism and kinetics, and the effect of quench rate on the amorphization process in the prototypical PCM Ge2Sb2Te5, using ab initio molecular‐dynamics simulations. We also study the evolution of the amorphous phase under low‐temperature annealing, shedding light on the structural changes, which may occur after amorphization at device operating temperatures. Our results give microscopic insight into the amorphization of PCMs, and should inform future work to understand and resolve important issues in device engineering.

magnified image

Effect of quench rate on the structure of Ge2Sb2Te5: While quenching at −5 K ps−1 leads to successful amorphization (left), quenching at a slower −1 K ps−1 leads to crystallization as the temperature is lowered (right).
Multiple Phytoestrogens Inhibit Cell Growth and Confer Cytoprotection By Inducing Manganese Superoxide Dismutase Expression
Authors: Robb Ellen L. , Stuart Jeffrey A.
Published: March 2013

Phytoestrogens are of interest because of their reported beneficial effects on many human maladies including cancer, neurodegeneration, cardiovascular disease and diabetes. As data on phytoestrogens continues to accumulate, it is clear that there is significant overlap in the cellular effects elicited by these various compounds. Here, we show that one mechanism by which a number of phytoestrogens achieve their growth inhibitory and cytoprotective effects is via induction of the mitochondrial manganese superoxide dismutase (MnSOD). Eight phytoestrogens, including resveratrol, coumestrol, kaempferol, genistein, daidzein, apigenin, isoliquirtigenin and glycitin, were tested for their ability to induce MnSOD expression in mouse C2C12 and primary myoblasts. Five of these, resveratrol, coumestrol, kaempferol, genistein and daidzein, significantly increased MnSOD expression, slowed proliferative growth and enhanced stress resistance (hydrogen peroxide LD50). When siRNA was used to prevent the MnSOD induction by genistein, coumestrol or daidzein, none of these compounds exerted any effect on proliferative growth, and only the effect of coumestrol on stress resistance persisted. The estrogen antagonist ICI182780 prevented the increased MnSOD expression and also the changes in cell growth and stress resistance, indicating that these effects are mediated by estrogen receptors (ER). The absence of effects of resveratrol or coumestrol, but not genistein, in ERβ‐null cells further indicated that this ER in particular is important in mediating these effects. Thus, an ER‐mediated induction of MnSOD expression appears to underlie the growth inhibitory and cytoprotective activities of multiple phytoestrogens. Copyright © 2013 John Wiley & Sons, Ltd.
Robot assistance in liver surgery: a real advantage over a fully laparoscopic approach? Results of a comparative bi‐institutional analysis
Authors: Troisi Roberto I. , Patriti Alberto , Montalti Roberto , Casciola Luciano
Published: March 2013

Background

Laparoscopic liver resection (LAPR) is safe and feasible with a better postoperative course as compared to open resections. Robot‐assisted liver surgery (ROBR) is a potential alternative to LAPR. In this study we compare outcomes between ROBR and LAPR.

Methods

Forty patients underwent ROBR and 223 LAPR for various indications. The surgical outcomes of two institutions, each with a specific advanced experience in laparoscopic and robotic surgery, were reviewed.

Results

The major hepatectomy rate was significantly higher in LAPR (16.6% vs 0%, p = 0.011) while a parenchyma‐preserving approach was favoured in ROBR (55% vs 34.1%, p = 0.019). More nodules were resected in the ROBR group (1.97 ± 1.4 vs 1.57 ± 1.1, p = 0.04). Overall conversion rate was 8/40 (20%) in the ROBR and 17/223 (7.6%) in the LAPR group (p = 0.034). Mean blood loss was 330 ± 303 ml and 174 ± 133 ml for the ROBR and LAPR groups, respectively (p = 0.001)

Conclusions

Despite higher conversion rates and blood loss, robot‐assisted surgery may allow the resection of more liver lesions, especially those located in the postero‐superior segments, facilitating parenchyma‐saving surgery with a comparable complication rate with respect to LAPR. Copyright © 2013 John Wiley & Sons, Ltd.
Spatial Distribution of Geobacteraceae and Sulfate‐Reducing Bacteria During In Situ Bioremediation of Uranium‐Contaminated Groundwater
Authors: Dar Shabir A. , Tan Hui , Peacock Aaron D. , Jaffe Peter , N'Guessan Lucie , Williams Kenneth H. , Strycharz‐Glaven Sarah
Published: March 2013

Analysis of the physiological status of subsurface microbial communities generally relies on the study of unattached microorganisms in the groundwater. These approaches have been employed in studies on bioremediation of uranium‐contaminated groundwater at a study site in Rifle, Colorado, in which Geobacter species typically account for over 90 percent of the microbial community in the groundwater during active uranium reduction. However, to develop efficient in situ bioremediation strategies it is necessary to know the status of sediment‐associated microorganisms as well. In order to evaluate the distribution of the natural community of Geobacter during bioremediation of uranium, subsurface sediments were packed into either passive flux meters (PFMs) or sediment columns deployed in groundwater monitoring wells prior to acetate injection during in situ biostimulation field trials. The trials were performed at the Department of Energy's (DOE's) Rifle Integrated Field Research Challenge site. Sediment samples were removed either during the peak of Fe(III) reduction or the peak of sulfate reduction over the course of two separate field experiments and preserved for microscopy. Direct cell counts using fluorescence in situ hybridization (FISH) probes targeting Geobacter species indicated that the majority of Geobacter cells were unattached during Fe(III) reduction, which typically tracks with elevated rates of uranium reduction. Similar measurements conducted during the sulfate‐reducing phase revealed the majority of Geobacter to be attached following exhaustion of more readily bioavailable forms of iron minerals. Laboratory sediment column studies confirmed observations made with sediment samples collected during field trials and indicated that during Fe(III) reduction, Geobacter species are primarily unattached (90 percent), whereas the majority of sulfate‐reducing bacteria and Geobacter species are attached to sediment surfaces when sulfate reduction is the predominant form of metabolism (75 percent and 77 percent, respectively). In addition, artificial sediment experiments showed that pure cultures of Geobacter uraniireducens, isolated from the Rifle site, were primarily unattached once Fe(III) became scarce. These results demonstrate that, although Geobacter species must directly contact Fe(III) oxides in order to reduce them, cells do not firmly attach to the sediments, which is likely an adaptive response to sparsely and heterogeneously dispersed Fe(III) minerals in the subsurface. © 2013 Wiley Periodicals, Inc.
Matrix Diffusion Modeling Applied to Long‐Term Pump‐and‐Treat Data: 2. Results From Three Sites
Authors: Seyedabbasi M. Ahmad , Kulkarni Poonam R. , McDade James M. , Newell Charles J. , Gandhi Deepa , Gallinatti John D. , Cocianni Virgilio , Ferguson DúBois J.
Published: March 2013

The data mining/groundwater modeling methodology developed in McDade et al. (2013) was performed to determine if matrix diffusion is a plausible explanation for the lower‐concentration but persistent chlorinated solvent plumes in the groundwater‐bearing units at three different pump‐and‐treat systems. Capture‐zone maps were evaluated, and eight wells were identified that did not draw water from any of the historical source areas but captured water from the sides of the plume. Two groundwater models were applied to study the persistence of the plumes in the absence of contributions from the historical source zones. In the wells modeled, the observed mass discharge generally decreased by about one order of magnitude or less over 4 to 10 years of pumping, and 1.8 to 17 pore volumes were extracted. In five of the eight wells, the matrix diffusion model fit the data much better than the advection dispersion retardation model, indicating that matrix diffusion better explains the persistent plume. In the three other wells, confounding factors, such as a changing capture zone over time (caused by changes in pumping rates in adjacent extraction wells); potential interference from a high‐concentration unremediated source zone; and limited number of pore volumes removed made it difficult to confirm that matrix diffusion processes were active in these areas. Overall, the results from the five wells indicate that mass discharge rates from the pumping wells will continue to show a characteristic “long tail'' of mass removal from zones affected by active matrix diffusion processes. Future site management activities should include matrix diffusion processes in the conceptual site models for these three sites. © 2013 Wiley Periodicals, Inc.
Chlorinated Hydrocarbon–Contaminated Site Investigation With Optimized 3D‐CSIA Approach
Authors: Wang Yi
Published: March 2013

An optimized “Three‐Dimensional Compound Specific Isotope Analysis (3D‐CSIA)'' investigation was conducted at a chlorinated hydrocarbon–contaminated site in order to (1) determine if multiple onsite sources of groundwater contamination existed and (2) demonstrate the cost‐effectiveness of applying isotope fingerprinting at such a complex contaminated site. Previous groundwater investigations identified chlorinated hydrocarbons at levels that significantly exceed drinking‐water standards but failed to determine the source(s) of contamination due to the lack of vadose‐zone contamination and the absence of groundwater contaminants in shallow portions of the surficial aquifer. To better understand the contaminant source(s), groundwater samples were taken and tested for both the presence of chlorinated hydrocarbons and their isotopic signatures of 13C/12C, 37Cl/35Cl, and 2H/1H. A site investigation with an optimized 3D‐CSIA approach revealed multiple chlorinated hydrocarbon releases from different sources, which was also cost‐effective considering the new lines of evidence of target contaminants obtained with the 3D‐CSIA approach instead of any traditional fingerprinting approaches. In addition, the 3D‐CSIA results inferred in situ bioremediation of chlorinated hydrocarbons would be feasible at the site. © 2013 Wiley Periodicals, Inc.
NYSDEC's DER‐31/Green Remediation Policy Influences Tool Development and Global Program
Authors: McDonough Scott T. , Woodward David S. , Doherty Michael J. , Underhill Scott A.
Published: March 2013

The New York State Department of Environmental Conservation (NYSDEC) Division of Environmental Remediation (DER) issued a program policy focused on the overall sustainability of hazardous waste site cleanups on August 11, 2010. This DER‐31/Green Remediation program policy (DER‐31) was issued in accordance with 6 New York Codes, Rules and Regulations (NYCRR) Part 375 Environmental Remediation Programs. DER‐31 represents one of the first government‐issued green and sustainable remediation (GSR) policies in the United States. Consistent with other DER policies, DER‐31's provisions are broadly considered to be an expectation/requirement. GSR experts from within AECOM's Remediation Services (RS) Practice Area developed and implemented a GSR program designed to comply with DER‐31 provisions and have now broadly incorporated GSR into our New York remediation projects. Lessons learned from this experience in New York have influenced AECOM's global GSR program and implementation procedures and prompted the development of a new GSR tool (GSRxTM) for identifying and assessing GSR best management practices (BMPs), which has also been employed globally. © 2013 Wiley Periodicals, Inc.
Biosorption of Hg(II) Ions From Aqueous Solution Using the Aquatic Weed Water Hyacinth With Equilibrium and Kinetic Modeling
Authors: Padmapriya G. , Murugesan A. G.
Published: March 2013

The potential for biosorption of Hg(II) ions from aqueous solutions using water hyacinth was studied. The effect of the retention period (0, 1, 3, 7, and 15 days), pH (3, 5, 7, and 9), initial concentration of Hg(II) ions (5, 10, and 15 mg/L), and organic loading rate (25, 50, and 75 percent) on biosorption were investigated. The physicochemical parameters were also analyzed at various concentrations of Hg(II) ions before and after treatment. The maximum biosorption rate was obtained at 15 days with the initial concentration of 10 mg/L at a pH of 7 and organic loading rate of 50 percent. The maximum biosorption capacity of both water hyacinth roots and shoots were 5.5 mg/L and 3.8 mg/L, respectively. The Hg(II) biosorption data were analyzed using the first‐ and second‐order kinetic models. Pseudo second‐order kinetics was considered the most appropriate model for predicting the biosorption capacity of both water hyacinth roots and shoots, and the modeled results were compared to the experimental results. Langmuir and Freundlich isotherms were used to evaluate the experimental data, and their constants were derived. Biosorption equilibrium data were best described by the Langmuir isotherm model followed by the Freundlich model. © 2013 Wiley Periodicals, Inc.
The biophysical property of A549 cells transferred by VEGF‐D
Authors: Wang Zhen , Wu Xiu‐Li , Wang Xu , Tian Hong‐Xia , Chen Zhi‐Hong , Li Yang‐Qiu
Published: March 2013

Vascular endothelial growth factor‐D (VEGF‐D) together with VEGF‐C is considered to be associated with lymphangiogenesis and angiogenesis and involve in tumorization. This study aims to investigate the influence of exogenous VEGF‐D gene on the biophysical property of cell surface of lung adenocarcinoma cell line. A panel of lung adenocarcinoma cell lines were examined the expression of VEGF‐D and VEGF‐C by real‐time PCR. The VEGF‐D recombinant plasmid containing enhanced green fluorescence protein (EGFP) was constructed and transfected to the cell line with no expression of VEGF‐D and confirmed by real‐time PCR and Western blot analysis. Topographic images of cells were obtained by using atomic force microscope (AFM) in contact mode. Unlike VEGF‐C, VEGF‐D was found to have a very low expression or undetectable expression in lung adenocarcinoma cell lines. The VEGF‐D recombinant plasmid had been constructed successfully and was transferred into the human lung adenocarcinoma cell line A549 cells which had no endogenous expression of VEGF‐D, and exogenous VEGF‐D could be detected in mRNA and protein expression levels in the gene modified cells, while the VEGF‐C gene expression had no change after VEGF‐D transfection. After transfection, the irregular microspikes or nano clusters could observe on the surface of A549 cells, and VEGF‐D transfected A549 cells became more rigid. The exogenous VEGF‐D gene might cause the remarkable biophysical architectural changes in the A549 cells, which might as a novel biomarker for evaluation of its biological function. SCANNING 36:202–208, 2014. © 2013 Wiley Periodicals, Inc.
Structurized grammar‐based fuzz testing for programs with highly structured inputs
Authors: Yan Jingbo , Zhang Yuqing , Yang Dingning
Published: March 2013

Fuzz testing, also known as fuzzing, has long been recognized as an effective technique to detect software vulnerabilities. Unfortunately, this approach is demonstrated noneffective when applied to test programs with highly structured inputs, such as interpreters and compilers. These programs usually process inputs in several stages as lexing and parsing, where the test input will be rejected if its structure does not obey the grammar. In this paper, we present a novel approach for fuzzing highly structured input programs. By disassembling the existing test cases into multiple grammatical fragments and inferring their grammar structures, we build a new series of test cases that can pass the validation and reach the previously unexplored places in the target program. We have implemented this approach in our general fuzzing framework BlendFuzz. Experiments have shown that BlendFuzz achieves higher code coverage compared with other blackbox fuzzing tools. BlendFuzz has also detected over two dozens of previously unreported vulnerabilities in real‐world applications, with seven of them being considered high risky. Copyright © 2013 John Wiley & Sons, Ltd.
Anomaly detection in big data from UWB radars
Authors: Wang Wei , Zhou Xin , Zhang Baoju , Mu Jiasong
Published: March 2013

The definitions of big data and anomaly detection are presented. The theory of ultra‐wideband radar and the through‐wall detection of a human model based on ultra‐wideband radar are briefly introduced. The target criterion with wavelet packet transform is deduced, and the procedure for the through‐wall human detection with statistical process control is constructed. The radar echo signals are collected at stationary and moving statuses of a human being for three types of walls. The experimental results demonstrate the effective of through‐wall target detection based on the proposed algorithm. Copyright © 2013 John Wiley & Sons, Ltd.
Interplay between parameter variation and oxide structure of a modified PAA process
Authors: Schneider M. , Kremmer K. , Weidmann S. K. , Fürbeth W.
Published: March 2013

In the present work, the robustness of an anodizing process was tested. Important anodizing parameters such as the anodizing potential, the dwell time at the anodizing potential, and the bath temperature were varied. The influence of the parameter variation on the microstructure of the oxide layers was investigated by SEM. It could be shown that the pore diameter as well as the layer thickness reacts very sensitively on the alternating parameters. The barrier layer thickness clearly depends on the anodizing voltage but is independent on the dwell time. Copyright © 2013 John Wiley & Sons, Ltd.
Imaging, work function, and compositional changes of thiols on gold via shadow mask ozonolysis
Authors: Brumbach Michael T. , Jaye Cherno , Ohlhausen James T. , Fischer Daniel
Published: March 2013

Self‐assembled monolayers (SAMs) of alkyl and fluorinated thiols were investigated after ozonolysis shadow mask treatments with varying areal domains and after exposure to displacing thiols. Imaging near edge X‐ray absorption fine structure (NEXAFS) spectroscopy was used as a novel method for investigating the resulting heterogeneous SAM films. Composition and work function were characterized via X‐ray and ultraviolet photoelectron spectroscopy, respectively. Imaging NEXAFS characterization of these heterogeneous films clearly shows the displacement of oxidized thiols after ozonolysis patterning. Changes in the SAM after patterning, and after displacement from back‐filling thiols, can be inferred from changes in the effective work function. Larger changes in work function were observed for cases where thiols were deposited after ozonolysis suggesting that the displacing SAM was denser and/or more ordered than as‐deposited films. These results highlight one of the first demonstrations of imaging NEXAFS and present measurements of effective work function on intentionally heterogeneous SAM films. Copyright © 2013 John Wiley & Sons, Ltd.