bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reliability of the reported ingested dose of acetaminophen for predicting the risk of toxicity in acetaminophen overdose patients
Authors: Zyoud Sa'ed H. , Awang Rahmat , Sulaiman Syed Azhar Syed 
Published: August 2011

ABSTRACTPurposeThe present study examines the relationship between the dose of acetaminophen reported to have been ingested by patients and the occurrence of serum acetaminophen levels above the ‘possible toxicity’ line in patients presenting at the hospital after acetaminophen overdose. The prognostic value of patient‐reported dosage cut‐offs of 8, 10 and 12 g was determined.MethodsThis retrospective cohort study included patients admitted to the emergency department or hospital within 24 hours of acetaminophen ingestion. Serum acetaminophen concentrations were considered to be the gold standard, and specificity, sensitivity and positive/negative predictive values were calculated from the reported ingested dose, to predict toxicity using the Rumack–Matthew nomogram (i.e. the ‘possible toxicity’ treatment line) and standard equations.ResultsOf 305 patients identified, 291 met the study inclusion criteria, and 121 (41.6%) had serum acetaminophen concentrations above the ‘possible toxicity’ treatment line. The range of patient‐reported acetaminophen ingested was 1–75 g, with 185 patients (63.6%) reporting ≥8 g. One hundred eighteen patients (97.5%) who reported ingesting ≥8 g had serum acetaminophen concentrations above the ‘150‐line’, compared with only three patients (2.5%) who reported ingesting <8 g (p < 0.001). The positive predictive value of a patient‐reported dose ≥8 g for predicting serum acetaminophen concentrations above the ‘possible toxicity’ treatment line was 63.78%, with a negative predictive value of 97.17%. The sensitivity of patient‐reported doses ≥8 g was high (97.52%) but with low specificity (60.59%). The sensitivity of patient‐reported doses ≥10 g also was high (89.26%) with low specificity (65.29%), whereas the sensitivity of ≥12 g dose was low (61.16%) with high specificity (86.47%).ConclusionsPatient‐reported doses of acetaminophen are good risk indicators for acetaminophen overdose patients in Malaysia. Patient‐reported ingestion of ≥8 g (as a cut‐off dose) had a higher sensitivity than ≥10 g or ≥12 g. The results of this study have important implications for toxicity risk evaluations in areas with poor serum acetaminophen assay availability. Copyright © 2011 John Wiley & Sons, Ltd.
Speed improvements of peptide–spectrum matching using Single‐Instruction Multiple‐Data instructions
Authors: Zhang Jian , McQuillan Ian , Wu Fang‐Xiang 
Published: August 2011

AbstractPeptide–spectrum matching is one of the most time‐consuming portion of the database search method for assignment of tandem mass spectra to peptides. In this study, we develop a parallel algorithm for peptide–spectrum matching using Single‐Instruction Multiple Data (SIMD) instructions. Unlike other parallel algorithms in peptide–spectrum matching, our algorithm parallelizes the computation of matches between a single spectrum and a given peptide sequence from the database. It also significantly reduces the number of comparison operations. Extra improvements are obtained by using SIMD instructions to avoid conditional branches and unnecessary memory access within the algorithm. The implementation of the developed algorithm is based on the Streaming SIMD Extensions technology that is embedded in most Intel microprocessors. Similar technology also exists in other modern microprocessors. A simulation shows that the developed algorithm achieves an 18‐fold speedup over the previous version of Real‐Time Peptide–Spectrum Matching algorithm [F. X. Wu et al., Rapid Commun. Mass Sepctrom. 2006, 20, 1199–1208]. Therefore, the developed algorithm can be employed to develop real‐time control methods for MS/MS.
Holomorphic couplings in non‐perturbative string compactifications
Authors: Klevers D. 
Published: August 2011

AbstractIn this review article we present an analysis of several aspects of four‐dimensional, non‐perturbative 𝒩 = 1 compactifications of string theory. Our study focuses on brane dynamics and their effective physics as encoded in the holomorphic couplings of the low‐energy 𝒩 = 1 effective action, most prominently the superpotential W. This article is divided into three parts. In part one we derive the effective action of a spacetime‐filling D5‐brane in generic Type IIB Calabi‐Yau orientifold compactifications. In the second part we invoke tools from string dualities, namely from F‐theory, heterotic/F‐theory duality and mirror symmetry, for a more elaborate study of the dynamics of (p,q) 7‐branes and heterotic five‐branes. In this context we perform exact computations of the complete perturbative effective superpotential, both due to branes and background fluxes. Finally, in the third part we present a novel geometric description of five‐branes in Type IIB and heterotic M‐theory Calabi‐Yau compactifications via a non‐Calabi‐Yau threefold $\hat {Z}_3$, that is canonically constructed from the original five‐brane and the Calabi‐Yau threefold Z3 via a blow‐up. We use the blow‐up threefold $\hat {Z}_3$ to derive open‐closed Picard‐Fuchs differential equations, that govern the complete effective brane and flux superpotential. In addition, we present first evidence to interpret $\hat {Z}_3$ as a flux compactification geometrically dual to the original five‐brane by defining an SU(3)‐structure on $\hat {Z}_3$, that is generated dynamically by the five‐brane backreaction.
Docking and free energy simulations to predict conformational domains involved in hCG–LH receptor interactions using recombinant antibodies
Authors: Majumdar Ritankar , Railkar Reema , Dighe Rajan R. 
Published: August 2011

AbstractSingle chain fragment variables (ScFvs) have been extensively employed in studying the protein–protein interactions. ScFvs derived from phage display libraries have an additional advantage of being generated against a native antigen, circumventing loss of information on conformational epitopes. In the present study, an attempt has been made to elucidate human chorionic gonadotropin (hCG)–luteinizing hormone (LH) receptor interactions by using a neutral and two inhibitory ScFvs against hCG. The objective was to dock a computationally derived model of these ScFvs onto the crystal structure of hCG and understand the differential roles of the mapped epitopes in hCG–LH receptor interactions. An anti‐hCG ScFv, whose epitope was mapped previously using biochemical tools, served as the positive control for assessing the quality of docking analysis. To evaluate the role of specific side chains at the hCG–ScFv interface, binding free energy as well as residue interaction energies of complexes in solution were calculated using molecular mechanics Poisson–Boltzmann/surface area method after performing the molecular dynamic simulations on the selected hCG–ScFv models and validated using biochemical and SPR analysis. The robustness of these calculations was demonstrated by comparing the theoretically determined binding energies with the experimentally obtained kinetic parameters for hCG–ScFv complexes. Superimposition of hCG–ScFv model onto a model of hCG complexed with the 51–266 residues of LH receptor revealed importance of the residues previously thought to be unimportant for hormone binding and response. This analysis provides an alternate tool for understanding the structure–function analysis of ligand–receptor interactions. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Role of different β‐turns in β‐hairpin conformation and stability studied by optical spectroscopy
Authors: Wu Ling , McElheny Dan , Setnicka Vladimír , Hilario Jovencio , Keiderling Timothy A. 
Published: August 2011

AbstractModel β‐hairpin peptides based on variations in the turn sequence of Cochran's tryptophan zipper peptide, SWTWENGKWTWK, were studied using electronic circular dichroism (ECD), fluorescence, and infrared (IR) spectroscopies. The trpzip2 Asn–Gly turn sequence was substituted with Thr–Gly, Aib–Gly, DPro–Gly, and Gly–Asn (trpzip1) to study the impact of turn stability on β‐hairpin formation. Stability and conformational changes of these hairpins were monitored by thermodynamic analyses of the temperature variation of both FTIR (amide I′) and ECD spectral intensities. These changes were fit to a two‐state model which yielded different Tm values, representing the folding/unfolding process, for hairpins with different β‐turns. Different β‐turns show systematic contributions to hairpin structure formation, and their inclusion in hairpin design can modify the folding pathways. Aib–Gly or DPro–Gly sequences stabilize the turn resulting in residual Trp–Trp interaction at high temperatures, but at the same time the β‐structure (cross strand H‐bonds) can become less stable due to constraints of the turn, as seen for DPro–Gly. The structure of the Aib–Gly turn containing hairpin was determined by NMR and was shown to be like trpzip2 (Asn–Gly turn) as regards turn and strand geometries, but to differ from trpzip1 (Gly–Asn turn). The Munoz and Eaton statistical mechanically derived multistate model, tested as an alternate point of view, represented contributions from H‐bonds and hydrophobic interactions as well as conformational change as interdependent. Use of different spectral methods that vary in dependence on these physical interactions along with the structural variations provided insight to the complex folding pathways of these small, well‐folded peptides. Proteins 2012. © 2011 Wiley Periodicals, Inc.
Structure‐based, biophysical annotation of molecular coevolution of acetylcholinesterase
Authors: Weißgraeber Stephanie , Hoffgaard Franziska , Hamacher Kay 
Published: August 2011

AbstractAcetylcholinesterase (AChE) is an important enzyme in the nervous system. It terminates signal transmission at chemical synapses by degrading the neurotransmitter acetylcholine and was found to play a role in plaque formation in Alzheimer's disease. Several functional parts of its structure have been identified in the past. Here, we use a coarse‐grained anisotropic network model approach based on structure data to analyze protein mechanics of AChE. Single contacts in the protein are “switched off” and the change in the intrinsic dynamics is measured. We correlate the gained insight with information about coevolution within the molecule derived from multiple sequence alignments. More than 300 AChE sequences were aligned and the mutual information of the positions was calculated. From these structural, biophysical, and evolutionary data we could reveal sites of coevolutionary signatures in AChE, annotate them by the selective pressure induced for biophysical reasons, and further pave the way for a more detailed understanding of evolutionary boundary conditions for AChE. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Analysis of electrostatic interactions in the denatured state ensemble of the N‐terminal domain of L9 under native conditions
Authors: Meng Wenli , Raleigh Daniel P. 
Published: August 2011

AbstractThe pH dependence of protein stability is defined by the difference in the number of protons bound to the folded state and to the denatured state ensemble (DSE) as a function of pH. In many cases, the protonation behavior can be described as the sum of a set of independently titrating residues; in this case, the pH dependence of stability reflects differences in folded and DSE pKa's. pH dependent stability studies have shown that there are energetically important interactions involving charged residues in the DSE of the N‐terminal domain of L9 (NTL9), which affect significantly the stability of the protein. The DSE of wild type NTL9 cannot be directly characterized under native conditions because of its high stability. A destabilized double mutant of NTL9, V3AI4A, significantly populates the folded state and the DSE in the absence of denaturant. The two states are in slow exchange on the nuclear magnetic resonance time scale, and diffusion measurements indicate that the DSE is compact. The DSE pKa's of all of the acidic residues were directly determined. The DSE pKa of Asp8 and Asp23 are depressed relative to model compounds values. Use of the mutant DSE pKa's together with known native state pKa's leads to a significantly improved agreement between the measured pH dependent stability and that predicted by the Tanford‐Wyman linkage relationship. An analysis of the literature suggests that DSE interactions involving charged residues are relatively common and should be considered in discussions of protein stability. Proteins 2011; © 2011 Wiley‐Liss, Inc.
New risk acceptance criteria for process safety
Authors: Moseman James 
Published: August 2011

AbstractA new risk acceptable criteria (RAC) is derived and compared to those previously reported. The derived RAC is based on previously published industrial and social mortality rates. The derived RAC in this article include acceptable risks (1 × 10−7), where no actions are recommended, compared to unacceptable or marginally acceptable levels (1 × 10−5), where mitigation actions are recommended. Justifications for these results are included. © 2011 American Institute of Chemical Engineers Process Saf Prog, 2012
Basis of safety: A concise communication method for critical process safety information
Authors: Wincek John C. 
Published: August 2011

AbstractProcess safety information (PSI) typically describes the process equipment, process chemicals, and how the process is intended to be operated. Lack of operator familiarity with this information can lead to process upsets, resulting in release of hazardous materials. The most critical of the PSI is that which pertains to the prevention of catastrophic incidents. By prioritizing PSI, emphasis can be placed on critical PSI during training, development of reference documents and assessment of operator competency. A Basis of Safety (BoS) document is described as a method to facilitate communication, learning and referencing of critical PSI by and for operators, engineers and managers. This BoS document for a process lists the worst‐case incident consequences, the safety objectives that must be achieved, the control measures that implement these safety objectives, and the safe operating envelope for the process. By limiting the BoS contents to only that which pertains to catastrophic incident prevention, the highest emphasis on learning can be placed where it is most critical. © 2011 American Institute of Chemical Engineers Process Saf Prog, 2011
Improving transmission calculations for the Edwards–Slingo radiation scheme using a correlated‐k distribution method
Authors: Sun Zhian 
Published: August 2011

AbstractA new version of the Edwards–Slingo (ES) radiation scheme is developed using the correlated‐k distribution (CKD) method. The work is conducted based on the line‐by‐line radiative transfer scheme GENLN2. A dataset of new ozone absorption cross‐section in the ultraviolet spectrum and new oxygen collision‐induced continuum data have been implemented in both the GENLN2 and new ES schemes. In order to improve the efficiency of the ES scheme, a new technique is proposed in this work to optimize the k distribution and a new method is used to deal with the gaseous overlapping absorption in a spectral band. The accuracy of the scheme is improved by replacing the scaling function used in the ES scheme with a pre‐determined look‐up table for consideration of the pressure and temperature dependency of the absorption oefficients. The number of spectral bands and number of absorbing species are both increased in the new scheme for better resolution of the spectral variation of absorbing species, aerosols and clouds. However, this does not increase the computational cost. Instead, it is reduced substantially compared with the previous version of the code. The treatment of transmission in the short‐wave spectrum is improved by implementing the absorbing species of CH4, N2O and O2 collision‐induced continuum absorption which are not included in the ES scheme. New O3 absorption cross‐section data in the ultraviolet spectrum measured by the European Space Agency are used to generate the CKD spectral data in the short‐wave spectral bands. These data have a temperature dependency and better spectral resolution. The irradiance and heating rate determined by the new scheme are tested against the same variables determined by GENLN2. It has been shown that the new scheme produces results more accurate than the ES scheme. Copyright © 2011 Royal Meteorological Society
A new small‐gain theorem with an application to the stabilization of the chemostat
Authors: Karafyllis Iasson , Jiang Zhong‐Ping 
Published: August 2011

SUMMARYNew small‐gain results are obtained for nonlinear feedback systems under relaxed assumptions. Specifically, during a transient period, the solutions of the feedback system may not satisfy some key inequalities that previous small‐gain results usually utilize to prove stability properties. The results allow the application of the small‐gain perspective to various systems that satisfy less‐demanding stability notions than the input‐to‐output stability property. The robust global feedback stabilization problem of an uncertain time‐delayed chemostat model is solved by means of the new small‐gain results. Copyright © 2011 John Wiley & Sons, Ltd.
One‐Pot Synthesis of Near‐Infrared Fluorescent Gold Clusters for Cellular Fluorescence Lifetime Imaging
Authors: Shang Li , Azadfar Naghmeh , Stockmar Florian , Send Winfried , Trouillet Vanessa , Bruns Michael , Gerthsen Dagmar , Nienhaus G. Ulrich 
Published: August 2011

AbstractA facile strategy to synthesize water‐soluble fluorescent gold nanoclusters (Au NCs) stabilized with the bidentate ligand dihydrolipoic acid (DHLA) is reported. The DHLA‐capped Au NCs are characterized by UV–vis absorption spectroscopy, fluorescence spectroscopy, transmission electron microscopy, and X‐ray photoelectron spectroscopy. The Au NCs possess many attractive features including ultrasmall size, bright near‐infrared luminescence, high colloidal stability, and good biocompatibility, making them promising imaging agents for biomedical and cellular imaging applications. Moreover, their long fluorescence lifetime (>100 ns) makes them attractive as labels in fluorescence lifetime imaging (FLIM) applications. As an example, the internalization of Au NCs by live HeLa cells is visualized using the FLIM technique.
Layer‐by‐Layer Assembly of Chitosan and Recombinant Biopolymers into Biomimetic Coatings with Multiple Stimuli‐Responsive Properties
Authors: Costa Rui R. , Custódio Catarina A. , Arias Francisco J. , Rodríguez‐Cabello José C. , Mano João F. 
Published: August 2011

AbstractIn this work, biomimetic smart thin coatings using chitosan and a recombinant elastin‐like recombinamer (ELR) containing the cell attachment sequence arginine–glycine–(aspartic acid) (RGD) are fabricated through a layer‐by‐layer approach. The synthetic polymer is characterized for its molecular mass and composition using mass spectroscopy and peptide sequencing. The adsorption of each polymeric layer is followed in situ at room temperature and pH 5.5 using a quartz‐crystal microbalance with dissipation monitoring, showing that both polymers can be successfully combined to conceive nanostructured, multilayered coatings. The smart properties of the coatings are tested for their wettability by contact angle (CA) measurements as a function of external stimuli, namely temperature, pH, and ionic strength. Wettability transitions are observed from a moderate hydrophobic surface (CAs approximately from 62° to 71°) to an extremely wettable one (CA considered as 0°) as the temperature, pH, and ionic strength are raised above 50 °C, 11, and 1.25 M, respectively. Atomic force microscopy is performed at pH 7.4 and pH 11 to assess the coating topography. In the latter, the results reveal the formation of large and compact structures upon the aggregation of ELRs at the surface, which increase water affinity. Cell adhesion tests are conducted using a SaOs‐2 cell line. Enhanced cell adhesion is observed in the coatings, as compared to a coating with a chitosan‐ending film and a scrambled arginine–(aspartic acid)–glycine (RDG) biopolymer. The results suggest that such films could be used in the future as smart biomimetic coatings of biomaterials for different biomedical applications, including those in tissue engineering or in controlled delivery systems.
Air‐Water Mist and Homogeneity Degree of Spray Cooling Zones for Improving Quality in Continuous Casting of Steel
Authors: El‐Bealy Mostafa O. 
Published: August 2011

AbstractA theoretical investigation used previous experimental works for validation of model predications and for studying the effect of different nozzle designs on the quality of continuously cast steel slabs has been undertaken. This is by optimizing the homogeneity degree of cooling pattern “HDCP” between a pair of rolls. The idea behind this technique is to maximize the solid shell resistance against thermo‐metallurgical and mechanical stresses and therefore minimizes the defects generated in different cooling zones. A 2‐D mathematical model of thermal, solidification, solid shell resistance and cooling conditions has been developed. The model determines the temperature distributions, the different phases associated with the solidification and three phase peritectic reaction L + δ → γ of Fe−0.12%C steel alloy as well as isotherms. The effect of different cooling patterns for various spray cooling systems on the homogeneity degree and solid shell resistance are examined. In additional to traditional water and air‐water (AWM) nozzles, a new design of air‐water mist nozzle has been proposed to improve the homogeneity degree of spray cooling system. The results indicate generally that the increasing in the homogeneity degree of cooling conditions is proportional to the increasing in the solid shell resistance and therefore to the improving of slab quality. Model predications of different effects of different nozzle designs on the surface and inner quality levels are compared and discussed in the mold and secondary spray cooling zones.
Microstructural Aspects and Wear Behavior of Sinter Hardened Distaloy HP
Authors: Sheikhi Moghaddam K. , Ghambari M. , Farhangi H. , Solimanjad N. , Bergmark A. , Khorsand H. 
Published: August 2011

AbstractEffect of cooling rate during sinter hardening on the microstructure and wear behavior of sintered steel grade Distaloy HP has been studied. Wear performances are closely related to macro and micro hardness of the materials. Dry sliding wear tests have been conducted using a reciprocating pin on flat wear testing machine under normal loads of 25, 35 and 45N and at a constant speed of 0.3 m/s. The samples were sinter hardened at different cooling rates 0.5–3 °C/s in order to investigate the influence of microstructure and hardness on wear behavior. It has been shown that, sintering process and cooling rate change the microstructure and hence the hardness and wear behavior of the material. The best wear resistance was detected at a cooling rate of 3 °C/s. At this cooling rate the material had an almost martensitic microstructure and the wear rate was some how independent of the applied load.