bluuebunny/crossref_metadata_2025_split huggingface dataset:
In situ synthesis of high molecular weight poly(L‐lactic acid) clay nanocomposites
Authors: Katiyar Vimal , Nanavati Hemant 
Published: September 2011

AbstractWe propose here a significantly improved process for the preparation of a lactide‐clay intercalated mixture, which yields a high molecular weight (MW, Mn ∼ 126,000 Da) poly(L‐lactic acid) (PLLA) clay nanocomposite (PLACN) in short times of in situ ring opening polymerization (ROP). In situ ROP using such a lactide‐clay mixture enables ROP in the “nano‐sized reactors” formed by the clay galleries. Cloisite®Na clays have been modified in‐house with two different surfactant modifiers, hexadecyltrimethylammonium bromide and dioctadecyl dimethyl ammonium bromide, and these modified clays are compared with Cloisite®20A and Cloisite®30B. Interlayer spacings of modified clays are correlated with the resulting PLACN morphology and polymer MW growth. The optical purity of PLACNs is found similar, whereas thermal stability is significantly superior to that of neat PLLA. XRD/SAXS and TEM analyses confirm that PLACN can be prepared either with intercalated or exfoliated morphology when using either nonfunctionalized or functionalized modified clay, respectively. POLYM. ENG. SCI., 2011. © 2011 Society of Plastics Engineers.
Alternating block copolymers based on polyamide‐12 and polycaprolactone
Authors: Gube Andrea , Jakisch Lothar , Häußler Liane , Schneider Konrad , Voit Brigitte , Böhme Frank 
Published: September 2011

AbstractA series of alternating polyester/polyamide block copolymers were prepared by sequential conversion of hydroxy‐terminated polycaprolactone and amino‐terminated polyamide‐12 with a selectively reacting coupling agent. The thermal properties of the block copolymers were investigated using differential scanning calorimetry and dynamic mechanical analysis. Mechanical properties were determined using tensile and impact tests. All polymers were phase‐separated, where the polyamide phase was semicrystalline in all compositions. Distinct crystallization of the polycaprolactone phase was observed only when the block length was greater than 2000 g mol−1. Mechanical testing showed that the polymers behave in a manner similar to that of thermoplastic elastomers. In particular, samples with a high content of polycaprolactone showed high strain and good impact behaviour. Copyright © 2011 Society of Chemical Industry
Photoresponsive soft materials: Synthesis and photophysical studies of a stilbene‐based diblock copolymer
Authors: Menon Sajith , Thekkayil Remyamol , Varghese Shinto , Das Suresh 
Published: September 2011

AbstractAn amphiphilic diblock copolymer composed of a photoresponsive dialkoxycyanostilbene polymethacrylate and poly(ethylene oxide) (PDACS‐b‐PEO) was synthesized and its photophysical and aggregation properties were investigated. The amphiphilic nature of the polymer caused it to self‐assemble in water, and dynamic light scattering studies indicated formation of spherical aggregates with an average size of 160 nm. Atomic force microscopy images of dried films cast from solutions containing the polymer aggregates revealed supramolecular aggregates with a spherical morphology. Photoisomerization of the stilbene chromophore in PDACS‐b‐PEO on UV irradiation resulted in the destruction of the self‐assembled superstructures which could be attributed both to change in shape of the chromophore from the linear trans isomer to the bent cis isomer which would hinder self‐aggregation of the molecules and the higher dipole moment of the cis isomer leading to a reduction of the hydrophobic nature of the stilbene containing block of PDACS‐b‐PEO. It was observed that hydrophobic dyes such as curcumin could be encapsulated within the hydrophobic interior of the spherical micellar aggregates from which the encapsulated dye could be released on UV irradiation. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Effects of an interactive tailored patient assessment on patient–clinician communication in cancer care
Authors: Heyn Lena , Finset Arnstein , Eide Hilde , Ruland Cornelia M. 
Published: September 2011

AbstractBackgroundTo test the effect of Choice, an interactive tailored patient assessment (ITPA) tool on the number and types of symptoms addressed during consultations with cancer patients, cancer patients' active participation during consultation with clinicians, and clinicians' responses.MethodA total of 193 consultations were audio taped and coded with the task‐oriented part of Roter Interactive Assessment System. In addition, we recorded the initiator of each coded utterance (clinician or patient) as defined by Verona Coding Definitions of Emotional Sequences and indicated the symptoms addressed in a list of all symptoms within the Choice ITPA. Of the 193 consultations, 99 were standard consultations that served as a control group. In the 94 intervention group consultations, patients utilized the Choice ITPA prior to the consultation, and the assessment summary was available to both patients and clinicians. We compared the two groups in both multilevel and multivariate analyses.ResultsWe found significantly more symptoms addressed in the intervention group as compared with the control group. We also found that the patients asked more questions in the intervention group, indicating that they were more active participants when utilizing Choice. The clinicians also provided more information in the intervention group.ConclusionThe Choice ITPA was successful in making cancer patients more active participants in the consultation with their clinician. Copyright © 2011 John Wiley & Sons, Ltd.
pH replica‐exchange method based on discrete protonation states
Authors: Itoh Satoru G. , Damjanović Ana , Brooks Bernard R. 
Published: September 2011

AbstractWe propose a new algorithm for obtaining proton titration curves of ionizable residues. The algorithm is a pH replica‐exchange method (PHREM), which is based on the constant pH algorithm of Monganet al. (J Comput Chem 2004;25:2038–2048). In the original replica‐exchange method, simulations of different replicas are performed at different temperatures, and the temperatures are exchanged between the replicas. In our PHREM, simulations of different replicas are performed at different pH values, and the pHs are exchanged between the replicas. The PHREM was applied to a blocked amino acid and to two protein systems (snake cardiotoxin and turkey ovomucoid third domain), in conjunction with a generalized Born implicit solvent. The performance and accuracy of this algorithm and the original constant pH method (PHMD) were compared. For a single set of simulations at different pHs, the use of PHREM yields more accurate Hill coefficients of titratable residues. By performing multiple sets of constant pH simulations started with different initial states, the accuracy of predicted pKavalues and Hill coefficients obtained with PHREM and PHMD methods becomes comparable. However, the PHREM algorithm exhibits better samplings of the protonation states of titratable residues and less scatter of the titration points and thus better precision of measured pKavalues and Hill coefficients. In addition, PHREM exhibits faster convergence of individual simulations than the original constant pH algorithm. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Assessment of template based protein structure predictions in CASP9
Authors: Mariani Valerio , Kiefer Florian , Schmidt Tobias , Haas Juergen , Schwede Torsten 
Published: September 2011

AbstractIn the Ninth Edition of the Critical Assessment of Techniques for Protein Structure Prediction (CASP9), 61,665 models submitted by 176 groups were assessed for their accuracy in the template based modeling category. The models were evaluated numerically in comparison to their experimental control structures using two global measures (GDT and GDC), and a novel local score evaluating the correct modeling of local interactions (lDDT). Overall, the state of the art of template based modeling in CASP9 is high, with many groups performing well. Among the methods registered as prediction “servers”, six independent groups are performing on average better than the rest. The submissions by “human” groups are dominated by meta‐predictors, with one group performing noticeably better than the others. Most of the participating groups failed to assign realistic confidence estimates to their predictions, and only a very small fraction of the assessed methods have provided highly accurate models and realistic error estimates at the same time. Also, the accuracy of predictions for homo‐oligomeric assemblies was overall poor, and only one group performed better than a naïve control predictor. Here, we present the results of our assessment of the CASP9 predictions in the category of template based modeling, documenting the state of the art and highlighting areas for future developments. Proteins 2011; © 2011 Wiley‐Liss, Inc.
CASP9 assessment of free modeling target predictions
Authors: Kinch Lisa , Yong Shi Shuo , Cong Qian , Cheng Hua , Liao Yuxing , Grishin Nick V. 
Published: September 2011

AbstractWe present an overview of the ninth round of Critical Assessment of Protein Structure Prediction (CASP9) “Template free modeling” category (FM). Prediction models were evaluated using a combination of established structural and sequence comparison measures and a novel automated method designed to mimic manual inspection by capturing both global and local structural features. These scores were compared to those assigned manually over a diverse subset of target domains. Scores were combined to compare overall performance of participating groups and to estimate rank significance. Moreover, we discuss a few examples of free modeling targets to highlight the progress and bottlenecks of current prediction methods. Notably, a server prediction model for a single target (T0581) improved significantly over the closest structure template (44% GDT increase). This accomplishment represents the “winner” of the CASP9 FM category. A number of human expert groups submitted slight variations of this model, highlighting a trend for human experts to act as “meta predictors” by correctly selecting among models produced by the top‐performing automated servers. The details of evaluation are available at http://prodata.swmed.edu/CASP9/. © Proteins 2011; © 2011 Wiley‐Liss, Inc.
CASP9 results compared to those of previous casp experiments
Authors: Kryshtafovych Andriy , Fidelis Krzysztof , Moult John 
Published: September 2011

AbstractThe quality of structure models submitted to CASP9 is analyzed in the context of previous CASPs. Comparison methods are similar to those used in previous articles in this series, with the addition of new methods looking at model quality in regions not covered by a single best structural template, alignment accuracy, and progress for template‐free models. Progress in this CASP was again modest and statistically hard to validate. Nevertheless, there are several positive trends. There is an indication of improvement in overall model quality for the midrange of template‐based modeling difficulty, methods for identifying the best model from a set generated have improved, and there are strong indications of progress in the quality of template‐free models of short proteins. In addition, the new examination of a model quality in regions of model not covered by the best available template reveals better performance than had previously been apparent. © Proteins 2011; © 2011 Wiley‐Liss, Inc.
Molecular dynamics simulation of conformational heterogeneity in transportin 1
Authors: Wang Xia , Xu Xue , Zhu Shanna , Xiao Zhengtao , Ma Zhi , Li Yan , Wang Yonghua 
Published: September 2011

AbstractTransportin 1 (Trn1), as a typical transport receptor of the karyopherin‐β family, mediates numerous RNA binding proteins into the nucleus by recognizing proline‐tyrosine nuclear localization signals (PY‐NLSs). Such process is regulated by RanGTP through its nucleotide cycle, which is associated with ligand dissociation. Yet a proper description including dynamic properties of Trn1 and its response on ligand/Ran binding has not been accessible so far. Here, we use molecular dynamics simulations to probe the conformational dynamics of the apo‐Trn1 and Trn1 in complex with ligand and Ran. The results reveal a strikingly intrinsic flexibility and conformational heterogeneity of Trn1, identified as generally segmental architecture. The segments rotate relative to each other about a flexible hinge and thereby force Trn1 to adopt a conformation compatible with the binding of Ran or substrates. Such binding significantly suppresses the flexibility and conformational heterogeneity of Trn1 and results in a disorder‐to‐order transition of HR8 loop, which facilitates this loop to allosterically communicate with the C‐terminal arch of Trn1. These results give insights into the disassembly and recycling of the Trn1, which has important implications for the regulation of the nuclear transport cycle and for the ligand selectivity. Proteins 2012. © 2011 Wiley Periodicals, Inc.
Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics
Authors: Arthur Evan J. , Yesselman Joseph D. , Brooks Charles L. 
Published: September 2011

AbstractAccurate computational methods of determining protein and nucleic acid pKa values are vital to understanding pH‐dependent processes in biological systems. In this article, we use the recently developed method constant pH molecular dynamics (CPHMD) to explore the calculation of highly perturbed pKa values in variants of staphylococcal nuclease (SNase). Simulations were performed using the replica exchange (REX) protocol for improved conformational sampling with eight temperature windows, and yielded converged proton populations in a total sampling time of 4 ns. Our REX‐CPHMD simulations resulted in calculated pKa values with an average unsigned error (AUE) of 0.75 pK units for the acidic residues in Δ + PHS, a hyperstable variant of SNase. For highly pKa‐perturbed SNase mutants with known crystal structures, our calculations yielded an AUE of 1.5 pK units and for those mutants based on modeled structures an AUE of 1.4 pK units was found. Although a systematic underestimate of pK shifts was observed in most of the cases for the highly perturbed pK mutants, correlations between conformational rearrangement and plasticity associated with the mutation and error in pKa prediction was not evident in the data. This study further extends the scope of electrostatic environments explored using the REX‐CPHMD methodology and suggests that it is a reliable tool for rapidly characterizing ionizable amino acids within proteins even when modeled structures are employed. Proteins 2011; © 2011 Wiley‐Liss, Inc.
High resolution TEM study of WS2 nanotubes
Authors: Krause Matthias , Mücklich Arndt , Zak Alla , Seifert Gotthard , Gemming Sibylle 
Published: September 2011

AbstractClosed capped WS2 nanotubes with diameters from 30 to 110 nm are studied by high resolution transmission electron microscopy (HRTEM). The tubes exhibit preferentially a hexagonal stacking order. Atomic resolution images of a 30 nm diameter tube reveal a zigzag chirality. A lattice expansion in c‐axis direction of ≤11% is found within the outermost triple layers. The tube caps often display regular polygon angles. Structural defects like grain boundaries, non‐planar triple layers, dislocations, platelet‐like fragments, terraces, and amorphous precipitates are identified.
Editor's perspective‐‐‐Shale gas development: Environmental issues and opportunities
Authors: Simon John A. , Fleming Martha E. 
Published: September 2011

AbstractMany professionals in the environmental industry have questioned whether the rapid expansion in shale gas development, particularly in the Marcellus Shale Play, is providing business opportunities. While gas production is a routine practice, the development of shale gas requires a process (fracturing, or, more commonly, “fracing'') that uses chemicals and is far more intrusive to the subsurface environment than traditional gas production. In this Editor's Perspective, we evaluate the environmental issues surrounding shale gas development, with a specific focus on the Marcellus Shale Play because it is currently the most active play in the United States, from both the drilling and political perspectives. In addition, we examine where the business opportunities are likely to be for environmental professionals relative to shale gas development. © 2011 Wiley Periodicals, Inc.
Sustainable remediation: Quo vadis?
Authors: Nathanail Paul 
Published: September 2011

AbstractSustainable remediation is at a crossroads. In a few short years it has become a mainstream topic while simultaneously maintaining its chimeral status. Sustainable remediation is a term claimed by many yet a concept apparently understood by few. Its characterization has necessitated the development of a plethora of metrics and tools yet its essence readily emerges. U.S.‐led initiatives have been adopted around the globe. Relative sustainability appraisal is easy to carry out and potentially sufficient for most site circumstances. The need to adequately protect human health and the environment has been recognized. Now the industry needs to focus our attention on protection and restoration that itself has a reasonably maximized net benefit. © 2011 Wiley Periodicals, Inc.
Two‐dimensional transport of lactate‐modified nanoscale iron particles in porous media
Authors: Darko‐Kagya Kenneth , Reddy Krishna R. 
Published: September 2011

AbstractThis study investigates the two‐dimensional transport of nanoscale iron particles (NIP) and lactate‐modified NIP (LMNIP) in homogeneous and heterogeneous porous media under typical pressurized groundwater flow conditions. A two‐dimensional bench‐scale test setup was developed and a series of experiments was conducted simulating homogeneous sand profile and two‐layer profile with two different sands. NIP and LMNIP at a concentration of 4 g/L were prepared in electrolyte simulating groundwater conditions and were injected at the inlet of the test setup under different pressure gradients (0.5. 0.8, 1, and 2 pounds per square inch). During the testing, effluent was collected and its volume and nanoiron concentrations were measured. At the end of the testing, soil cores were obtained at different distances from the inlet and were used to measure nanoiron concentrations and magnetic susceptibility values. Results showed that the transport of NIP and LMNIP was enhanced by increased pressure gradient. LMNIP transport occurred more uniformly as compared to bare NIP. The iron concentrations decreased with distance from the inlet to the outlet and increased from the top to the bottom of the test cell. The data indicate that, as the particles were transported, they underwent aggregation and sedimentation, which resulted in the observed non‐uniform spatial distribution of iron. The NIP and LMNIP transported through the high‐porosity and high‐permeability soil layer in the heterogeneous soil profile, implying that the transport occurred predominantly along the path of least resistance for the flow. Magnetic susceptibility values are found to have good correlation with the iron content in the soil and are helpful to characterize the transport of NIP and LMNIP. Overall, this study shows that the non‐uniform distribution of NIP and LMNIP occurs under two‐dimensional transport conditions and the soil heterogeneities can significantly impact the transport of NIP and LMNIP. The design of field delivery systems should consider such conditions and optimize the pressurized injection systems. © 2011 Wiley Periodicals, Inc.
Physical impact of waterjet‐based sediment remediation on benthic organisms
Authors: Harper Grace , Elmore Andrew Curtis , Redell Christopher , Risley Gavin , Burken Joel G. 
Published: September 2011

AbstractAdding activated carbon to sediments has been shown to be an effective means of reducing the bioavailability of certain contaminants. The current state of the practice is to mechanically mix activated carbon to a target concentration of 3 percent at depths of approximately 30 cm using a rotovator or similar construction equipment. Waterjets have been used to cut hard material using a mixture of water and an abrasive. If activated carbon is substituted for the abrasive, waterjets have the potential to use surface injection as a replacement for mechanical mixing during sediment remediation. A perceived benefit of waterjet‐based sediment remediation is that there may be a reduced potential for benthic organism mortality related to amendment delivery. A set of waterjet parameters were identified that have the potential to achieve amendment placement goals, and a series of waterjet tests were conducted to evaluate the potential impact on the benthic community. The tests included mortality testing using a swimming macroinvertebrate and a burrowing invertebrate, benthic artifacts such as shells, and craft foam as a surrogate for living organisms. The results indicated that the immediate survivability was typically greater than 50 percent, and that empirical relationships between two variables (waterjet nozzle diameter and the water column height between the nozzle and the target) and the depth of cut in the foam could be established. Data are not available in the literature for direct comparison of organism survivability immediately after mechanical mixing, but the results of this study provide motivation for the further evaluation of waterjets on the basis of the low observed mortality rates. Future waterjet work may address field‐scale characterization of mixing effectiveness, resuspension potential, technical feasibility, and cost. © 2011 Wiley Periodicals, Inc.
Designing funnel‐and‐gate groundwater remediation systems near property corners
Authors: Hudak Paul F. 
Published: September 2011

AbstractNumerical models were used to simulate alternative funnel‐and‐gate groundwater remediation structures near property corners in hypothetical homogeneous and heterogeneous unconfined aquifers. Each structure comprised a highly permeable central gate (hydraulic conductivity = 25 m/d) and soil‐bentonite slurry walls (hydraulic conductivity = 0.00009 m/d). Gates were perpendicular to regional groundwater flow and approximately 5 m from a contaminant plume's leading tip. Funnel segments collinear to the central gate reached property boundaries; additional funnel segments followed property boundaries in the most hydraulically upgradient direction. Structures were 1 m thick and anchored into the base of the aquifer. Two structures were simulated for each aquifer: one with a 3.0‐m‐long central gate and funnels on either side; and a second with a 1.5‐m‐long central gate, funnels on either side, and 0.75‐m‐long end gates. Funnels were lengthened in successive simulations, until a structure contained a contaminant plume. Results suggest that, for the same total gate length, one‐gate structures may facilitate more rapid remediation, up to 44 percent less time in trials conducted in this study, than multiple‐gate structures constructed near property corners. However, in order to effectively contain a plume, one‐gate structures were up to 46 percent larger than multiple‐gate structures. © 2011 Wiley Periodicals, Inc.