bluuebunny/crossref_metadata_2025_split huggingface dataset:
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 ObjectiveTo evaluate whether the preoperative CHA2DS2‐VASc score predicts the risk of atrial fibrillation (AF) after cardiothoracic surgery (CTS).DesignRetrospective, nested case–control study.PatientsA 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 ResultsAll 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).ConclusionIncreasing 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.
Sequence‐specific determination of protein and peptide concentrations by absorbance at 205 nm
Authors: Anthis Nicholas J. , Clore G. Marius 
Published: March 2013

AbstractQuantitative 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

AbstractExpression 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

AbstractThe 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

ABSTRACTToxoplasma 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

ABSTRACTThe 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.
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

AbstractThe 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

AbstractLineshape‐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

Abstractmagnified imageReduction 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 imageEffect 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).
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

AbstractBackgroundLaparoscopic 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.MethodsForty 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.ResultsThe 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)ConclusionsDespite 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

AbstractAnalysis 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

AbstractThe 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

AbstractAn 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

AbstractThe 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

AbstractThe 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

SummaryVascular 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.