bluuebunny/crossref_metadata_2025_split huggingface dataset:
The GD box: A widespread noncontiguous supersecondary structural element
Authors: Alva Vikram , Dunin‐Horkawicz Stanislaw , Habeck Michael , Coles Murray , Lupas Andrei N. 
Published: July 2009

AbstractIdentification and characterization of recurrent supersecondary structural elements is central to understanding the rules governing protein tertiary structure. Here, we describe the GD box, a widespread noncontiguous supersecondary element, which we initially found in a group of topologically distinct but homologous β‐barrels—the cradle‐loop barrels. The GD box is similar both in sequence and structure and comprises two short unpaired β‐strands connected by an orthogonal type‐II β‐turn and a noncontiguous β‐strand forming hydrogen bonds with the β‐turn. Using structure‐based analysis, we have detected 518 instances of the GD box in a nonredundant subset of the SCOP database comprising 3771 domains. Apart from the cradle‐loop barrels, this motif is also found in a diverse set of nonhomologous folds including other topologically related β‐barrels. Since nonlocal interactions are fundamental in the formation of protein structure, systematic identification and characterization of other noncontiguous supersecondary structural elements is likely to prove valuable to protein structure modeling, validation, and prediction.
Comparative surface geometry of the protein kinase family
Authors: Thompson Elaine E. , Kornev Alexandr P. , Kannan Natarajan , Kim Choel , Ten Eyck Lynn F. , Taylor Susan S. 
Published: July 2009

AbstractIdentifying conserved pockets on the surfaces of a family of proteins can provide insight into conserved geometric features and sites of protein–protein interaction. Here we describe mapping and comparison of the surfaces of aligned crystallographic structures, using the protein kinase family as a model. Pockets are rapidly computed using two computer programs, FADE and Crevasse. FADE uses gradients of atomic density to locate grooves and pockets on the molecular surface. Crevasse, a new piece of software, splits the FADE output into distinct pockets. The computation was run on 10 kinase catalytic cores aligned on the αF‐helix, and the resulting pockets spatially clustered. The active site cleft appears as a large, contiguous site that can be subdivided into nucleotide and substrate docking sites. Substrate specificity determinants in the active site cleft between serine/threonine and tyrosine kinases are visible and distinct. The active site clefts cluster tightly, showing a conserved spatial relationship between the active site and αF‐helix in the C‐lobe. When the αC‐helix is examined, there are multiple mechanisms for anchoring the helix using spatially conserved docking sites. A novel site at the top of the N‐lobe is present in all the kinases, and there is a large conserved pocket over the hinge and the αC‐β4 loop. Other pockets on the kinase core are strongly conserved but have not yet been mapped to a protein–protein interaction. Sites identified by this algorithm have revealed structural and spatially conserved features of the kinase family and potential conserved intermolecular and intramolecular binding sites.
A semiquantitative risk assessment methodology to prioritize recommendations
Authors: Bhimavarapu Kumar R. , Doerr William W. 
Published: July 2009

AbstractProcess safety engineers promote loss prevention by providing recommendations when deficiencies are observed. Deficiencies are undesirable conditions that aggravate the likelihood and/or the severity of loss events. Any improvement needs resources, and since the resources are always limited, process safety engineers have to establish priorities for loss prevention recommendations. One appropriate way to prioritize the recommendations is to evaluate and compare the cost of risk reduction associated with the improvements. While qualitative risk analysis techniques may not be able to provide the necessary resolution to differentiate the improvements, quantitative techniques need much expertise, time, and funds. A feasible approach would be a semiquantitative methodology with the simplifications necessary to make it easy to use, but at the same time providing the needed resolution for prioritization. This article presents such a methodology to prioritize loss prevention recommendations. The methodology uses the concept of engineered systems, which are simply hardware (equipment or facility), procedures, or a combination put in place to serve specific functional intents. The basis of the methodology is founded in the premise that deficiencies are always associated with engineered systems and deficiencies increase their failure likelihoods. A few examples are provided with the details of the methodology and the incorporated simplifications. © 2009 American Institute of Chemical Engineers Process Saf Prog, 2009
Core models of a‐edge threading dislocations in wurtzite III(Al,Ga,In)‐nitrides
Authors: Kioseoglou J. , Komninou Ph. , Karakostas Th. 
Published: July 2009

AbstractAn empirical bond‐order many body interatomic Tersoff potential is used for atomistic calculations of the multiple atomic configurations (5/7, 8 and 4) of the a‐edge threading dislocations in III(Al,Ga,In)‐N compound semiconductors. Structural‐ and energy‐related conclusions are drawn which are attributed to the complexity of the III–III metal type and N–N interactions (bondGa–Ga < bondAl–Al < bondIn–In) in connection with the difference of the lattice parameters (aAlN < aGaN < aInN) and the elastic constants. The 5/7‐atomic core configuration is calculated as the most energetically and structurally favourable in all the three compounds. Taking the 5/7‐atom model as a reference, the 8‐atom core model becomes the next favourable one when the lattice parameter increases (aInN) while the 4‐atom core model is the second energetically favourable when the lattice parameter decreases (aAlN).
Polar AlN/GaN interfaces: Structures and energetics
Authors: Kioseoglou J. , Kalesaki E. , Lymperakis L. , Dimitrakopulos G. P. , Komninou Ph. , Karakostas Th. 
Published: July 2009

AbstractThe structures and energies of {0001} interfaces between GaN and AlN are studied by both ab initio methods and molecular dynamics using the Tersoff empirical inter‐atomic potential. Based on experimental observations, structural configurations depending on polarity and atomic stacking are considered. It is evidenced by both ab initio and empirical calculations that III‐polar interfaces are energetically favourable compared to the N‐polar. In addition, the ab initio analysis shows that the wurtzite interfacial stacking is energetically preferable compared to zinc blende. A linear dependence between the bandgap energy and the strain in AlN/GaN heterostructures is found. It is shown that the bandgap increases with increasing c/a ratio while an inverse proportionality relationship is observed in the case of lattice parameter a. However, biaxial strain is found to flatten this variation considerably. Empirical potential calculations yield the interfacial energies, taking into account the relaxation of the lattice mismatch due to arrays of misfit dislocations and in combination with ab initio methods estimate that the energetically favourable III polarity interface exhibits at least 18% larger critical thickness than the N polar.
Dislocation nucleation from surface step in silicon: The glide set versus the shuffle set
Authors: Godet Julien , Hirel Pierre , Brochard Sandrine , Pizzagalli Laurent 
Published: July 2009

AbstractWe have studied the mechanisms of dislocation nucleation from surface defects in silicon submitted to various stresses and temperatures. Molecular dynamics simulations with three classical potentials have shown the existence of two different plastic modes in silicon which can be activated from surfaces. At high temperatures and low stresses dislocations nucleation occurs in the {111} glide set planes, while at low temperatures and large stresses it occurs in the {111} shuffle set planes. The analysis of dislocation cores and kinks shows structures like those well known in bulk silicon. This study supports the idea that plasticity in crystalline Si structures could be governed by dislocation nucleation from surfaces.
Correctness of a particular solution of inverse problem in rocking curve imaging
Authors: Huber Isabella , Mikulík Petr , Baumbach Tilo 
Published: July 2009

AbstractLocal lattice misorientations on crystalline substrates can be visualized by rocking curve imaging. Local deviations from Bragg peak positions are extracted from a series of digital topographs recorded by a CCD detector under different azimuths. Bragg peaks from surface regions such as crystallites with a larger local misorientation overlap on the detector, which requires a back‐projection method in order to reconstruct the misorientation components on the sample surface from the measured angular position on the detector planes. From mathematical point of view, the reconstruction problem is an inverse problem. In this paper, we formulate the forward and back‐projection problems and we prove the correctness of a particular solution. The usability of the method is demonstrated on a phantom data set.
Two generations of phase‐change memory devices: Differences and common problems
Authors: Popov Anatoly 
Published: July 2009

AbstractTwo generations of phase‐change memory (PCM) devices are analyzed from the point of view of material requirements. The first generation of PCM devices was based on chalcogenide glasses. The lack of sufficient information on the physical and chemical processes within the material that occur during operation of the devices led to poor reliability of the first‐generation PCM integrated circuits (ICs). The second generation of PCM devices uses memory switches based on crystalline chalcogenide alloys. The basic operating mechanisms of the first‐ and second‐generation nonvolatile PCM devices are largely the same. The PCM ICs designers of either generation face the same problems: contradictory requirements toward the phase‐change material, where both low SET and RESET power and high reliability of cells retention are important, the problem of the dispersions of cell characteristics in the SET and RESET states, the problem of the forming process of PCM elements and others. The analysis of the results allows the problems that need solving to be looked at to avoid making the same mistake twice and to create highly reliable PCM devices with acceptable power and geometrical characteristics.
Photoinduced effects in AsSP glasses
Authors: Santagneli Silvia Helena , Messaddeq Sandra Helena , Ribeiro Sidney José Lima , Messaddeq Younès 
Published: July 2009

AbstractWe report the photoinduced effects on the glass composition As2S3 and As29.6P7.4S63 when exposed to UV light. The morphology of the glass surface irradiated at different power densities was investigated by use of optical microscopy and scanning electron microscopy (SEM). A power density dependence on the photoexpansion (PE) and photoablation (PA) is observed. Raman measurement after irradiation shows the formation of AsO bonds in As29.6P7.4S63. Also, the appearance of PO bonds indicate the incorporation of oxygen at the glass surface during the irradiation process.
Leveraging prior quantitative knowledge in guiding pediatric drug development: a case study
Authors: Jadhav Pravin R. , Zhang Jialu , Gobburu Jogarao V. S. 
Published: July 2009

AbstractThe manuscript presents the FDA's focus on leveraging prior knowledge in designing informative pediatric trial through this case study. In developing written request for Drug X, an anti‐hypertensive for immediate blood pressure (BP) control, the sponsor and FDA conducted clinical trial simulations (CTS) to design trial with proper sample size and support the choice of dose range. The objective was to effectively use prior knowledge from adult patients for drug X, pediatric data from Corlopam (approved for a similar indication) trial and general experience in developing anti‐hypertensive agents. Different scenarios governing the exposure response relationship in the pediatric population were simulated to perturb model assumptions. The choice of scenarios was based on the past observation that pediatric population is less responsive and sensitive compared with adults. The conceptual framework presented here should serve as an example on how the industry and FDA scientists can collaborate in designing the pediatric exclusivity trial. Using CTS, inter‐disciplinary scientists with the sponsor and FDA can objectively discuss the choice of dose range, sample size, endpoints and other design elements. These efforts are believed to yield plausible trial design, qrational dosing recommendations and useful labeling information in pediatrics. Published in 2009 by John Wiley & Sons, Ltd.
Evaluation of the antiprotozoal activity of neo‐clerodane type diterpenes from Salvia polystachya against Entamoeba histolytica and Giardia lamblia
Authors: Calzada Fernando , Yepez‐Mulia Lilian , Tapia‐Contreras Amparo , Bautista Elihú , Maldonado Emma , Ortega Alfredo 
Published: July 2009

AbstractChia (Salvia polystachya Ort., Lamiaceae) is frequently used in Mexican traditional medicine to treat dysentery. In this study the main neo‐clerodane diterpenes (polystachynes A, B and D, as well as linearolactone) were isolated from the aerial parts of chia, and their antiprotozoal activities toward Entamoeba histolytica and Giardia lamblia trophozoites were evaluated in vitro. Linearolactone was the most potent antiamoebic and antigiardial compound with IC50 values of 22.9 μM for E. histolytica and 28.2 μM for G. lamblia. Polystachynes A, B and D, showed moderate antiprotozoal activity against both protozoans with IC50 values ranging from 117.0 to 160.6 μM for E. histolytica and from 107.5 to 134.7 μM for G. lamblia. These data suggest that linearolactone may play an important role in the antidiarrhoeal activity of S. polystachya. Copyright © 2009 John Wiley & Sons, Ltd.
Screening of binding activity of Streptococcus pneumoniae, Streptococcus agalactiae and Streptococcus suis to berries and juices
Authors: Toivanen Marko , Huttunen Sanna , Duricová Jana , Soininen Pasi , Laatikainen Reino , Loimaranta Vuokko , Haataja Sauli , Finne Jukka , Lapinjoki Seppo , Tikkanen‐Kaukanen Carina 
Published: July 2009

AbstractAntiadhesion therapy is a promising approach to the fight against pathogens. Antibiotic resistance and the lack of effective vaccines have increased the search for new methods to prevent infectious diseases. Previous studies have shown the antiadhesion activity of juice from cultivated cranberries (Vaccinium macrocarpon Ait.) against bacteria, especially E. coli. In this study, the binding of two streptococcal strains, Streptococcus pneumoniae and Streptococcus agalactiae, to molecular size fractions (FI, FII and FIII, <10 kDa, 10–100 kDa, and >100 kDa, respectively) of berries and berry and fruit juices from 12 plant species were studied using a microtiter well assay. For Streptococcus suis a hemagglutination inhibition assay was used. In general, binding activity was detected especially to wild cranberry (Vaccinium oxycoccos L.) and to other Vaccinium species. S. pneumoniae cells bound most to cranberry juice fraction FI and S. agalactiae cells to cranberry fraction FIII. Hemagglutination induced by S. suis was most effectively inhibited by cranberry fraction FII. NMR spectra of some characteristic active and non‐active fractions were also measured. They indicate that fractions FII and FIII contained proanthocyanidins and/or other phenolic compounds. The results suggest Vaccinium berries as possible sources of antiadhesives against bacterial infections. Copyright © 2009 John Wiley & Sons, Ltd.
Danshen (Salvia miltiorrhiza) extract inhibits proliferation of breast cancer cells via modulation of Akt activity and p27 level
Authors: Yang Wonseok , Ju Ji‐hyun , Jeon Min Jeong , Han Xiangzi , Shin Incheol 
Published: July 2009

AbstractDanshen is widely used in traditional Chinese medicine, often in combination with other herbs. To check the effect of Danshen on the proliferation of breast cancer cells, Danshen extract was used to treat MCF‐7 and MCF‐7 HER2 cells, the latter of which overexpresses HER2. HER2 is a receptor tyrosine kinase, and is involved in signal transduction pathways leading to tumor cell proliferation. MTT and cell proliferation assays revealed that Danshen strongly inhibited the proliferation of both MCF‐7 vec cells and MCF‐7 HER2 cells. Flow cytometry analyses indicated that Danshen induced cell cycle delay in the G1 phase. HER2 expression was shown to confer resistance to Danshen‐induced inhibition of proliferation and cell cycle delay, suggesting that HER2 is responsible for the resistance to Danshen. Danshen treatment induced the down‐regulation of Akt phosphorylation and an increase in p27 in MCF‐7 vec and MCF‐7 HER2 cells. Nevertheless, MCF‐7 HER2 cells were more resistant to the Danshen‐induced inhibition of Akt phosphorylation and p27 up‐regulation. Copyright © 2009 John Wiley & Sons, Ltd.
Cytotoxic effect of mistletoe (Viscum album L.) extract on Jurkat cells and its interaction with doxorubicin
Authors: Sabová Lucia , Pilátová Martina , Szilagyi Katarína , Sabo Rastislav , Mojžiš Ján 
Published: July 2009

AbstractMistletoe preparations are frequently used by cancer patients because of their ability to stimulate the immunity and to improve the quality of life. Moreover mistletoe and its active substances (especially lectins) possess cytotoxic effect on various cancer cell lines. However, only little is known about its interaction with anticancer drugs. Therefore the cytotoxic and apoptosis‐inducing effects of aqueous mistletoe extract (VA) and its interaction with doxorubicin (DOXO) were investigated in Jurkat cells.The results show that VA extract as well as DOXO exert cytotoxic effects on Jurkat cells in a dose‐dependent manner. Cytotoxicity of DOXO was much stronger (LC50 = 11.68 ng/mL) than that of VA extract (LC50 = 35.67 μg/mL). Their combination led to synergism only at those concentrations that were highly cytotoxic alone. Both substances (alone and in combination) induced DNA fragmentation in Jurkat cells. In conclusion, an aqueous extract prepared from mistletoe tops exerted cytotoxic and apoptosis‐inducing effects on Jurkat cells alone as well as in combination with DOXO. Copyright © 2009 John Wiley & Sons, Ltd.
Theoretical electronic studies of aluminum monobromide and aluminum monoiodide
Authors: Hamade Y. , Taher F. , Monteil Y. 
Published: July 2009

AbstractBy using CASSCF/MRCI methods, theoretical molecular calculations have been performed for 12 electronic states for AlBr molecule and 12 electronic states for AlI molecule in the representation 2s+1Λ (neglecting spin‐orbit effects). Calculated potential energy curves are displayed. Spectroscopic constants including the harmonic vibrational wave number ωe, the electronic energy Te referred to the ground state and the equilibrium internuclear distance Re are predicted for these singlet and triplet electronic states for both AlBr and AlI molecules. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Dynamical properties and thermal rate coefficients for the Na + HF reaction using genetic algorithm
Authors: Antunes Adoniel W. S. , Ferreira Da Cunha Wiliam , Magela E Silva Geraldo , Martins João B. L. , Gargano Ricardo 
Published: July 2009

AbstractThe genetic algorithm optimization technique (GAOT) was used to build a new potential energy surface (PES) to the Na + HF → NaF + H reaction. Quasi‐Classical Trajectories and Transition State Theory methods were used to obtain the dynamical properties and thermal rate coefficients (TRCs), respectively, of this new PES. These features were compared with the dynamical properties and TRCs available in the literature. It was found that the GAOT PES agrees very well with other PESs, in which the maximum difference found is smaller than 1.0 Å2 for the cross‐sections. These results endow the GAOT approach as a method to build PESs of reactive scattering processes. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Theoretical study on the influence of ancillary ligand on the spectroscopic properties and electronic structures of phosphorescent Pt(II) complexes
Authors: Zhang Min , Li Yan , Li Ze‐Sheng , Sun Jia‐Zhong 
Published: July 2009

AbstractThe geometries, energies, and electronic properties of a series of phosphorescent Pt(II) complexes including FPt, CFPt, COFPt, and NFPt have been characterized within density functional theory DFT calculations which can reproduce and rationalize experimental results. The properties of excited‐states of the Pt(II) complexes were characterized by configuration interaction with singles (CIS) method. The ground‐ and excited‐state geometries were optimized at the B3LYP/LANL2DZ and CIS/LANL2DZ levels, respectively. In addition, we also have performed a triplet UB3LYP optimization for complex FPt and compared it with CIS method in the emission properties. The datum (562.52 nm) of emission wavelength for complex FPt, which were computed based on the triplet UB3LYP optimization excited‐state geometry, is not agreement with the experiment value (500 nm). The absorption and phosphorescence wavelengths were computed based on the optimized ground‐ and excited‐state geometries, respectively, by the time‐dependent density functional theory (TD‐DFT) methods. The results revealed that the nature of the substituent at the phenylpyridine ligand can influence the distributions of HOMO and LUMO and their energies. Moreover, the auxiliary ligand pyridyltetrazole can make the molecular structure present a solid geometry. In addition, the charge transport quality has been estimated approximately by the predicted reorganization energy (λ). Our result also indicates that the substitute groups and different auxiliary ligand not only change the nature of transition but also affect the rate and balance of charge transfer. By summarizing the results, we can conclude that the NFPt is good OLED materials with a solid geometry and a balanced charge transfer rate. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
A linear three‐center four electron bonding identity nucleophilic substitution at carbon, boron, and phosphorus. A theoretical study in combination with van't Hoff modeling
Authors: Buck Henk M. 
Published: July 2009

AbstractWe studied various identity nucleophilic substitution reactions based on an SN2 reaction profile. With calculations and experimental geometries concerning the nature of the various complexes indicated as stable, intermediate, and transition state we were able to show the additional value of van't Hoff 's tetrahedron by changing its geometry via a trigonal pyramid into a trigonal bipyramid. The ratio of the apical and the corresponding tetrahedral bond distance is then 1.333. This value has been used in general as a calibration point for the understanding of the (in)stabilities of the complex formation on the SN2 reaction coordinate. The relevance of this approach has been also proved for enzymatic reactions focused on carbon and phosphorus substrates. Furthermore, it could be established that identity proton‐in‐line displacements are fully comparable with the relocation of carbon in a nucleophilic substitution reaction as Cl− + CH3Cl. The significance of this information will afford new insight in the dynamics of a linear three‐center four‐electron complex. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010