bluuebunny/crossref_metadata_2025 huggingface dataset:
Geomorphology of the onset area of a paleo‐ice stream, Marguerite Bay, Antarctic Peninsula
Authors: Anderson John B. , Fretwell Lisa Oakes
Published: March 2008

Geomorphic features indicate that both glacial and melt‐water erosion characterize the onset area of the ancestral Marguerite Ice Stream. The large size of these features indicates that they formed over repeated glacial cycles, most recently during the Last Glacial Maximum. Ice drainage within the bay and on the inner continental shelf was strongly influenced by tectonic fabric.

Deep, isolated basins surrounded by rugged bedrock bathymetry characterize the innermost part of the bay. Drumlins and other streamlined features occur in the floors of these basins at depths of up to 900 m. The outer bay has three large interconnected basins. Drumlins and megaflutings within these basins indicate ice was grounded at water depths up to 1000 m. The orientations of these features show convergence of drainage from the northeast, east and south into the Marguerite paleo‐ice stream. On the inner continental shelf, the ice converged into a single, wide trough dominated by mega‐scale glacial lineations. This transition in geomorphic features from drumlins and megaflutings to mega‐scale glacial lineations occurs at the location on the continental shelf where sedimentary strata blanket bedrock, and marks a zone of acceleration of the ice stream.

The glacially sculptured geomorphic features within Marguerite Bay co‐exist with anastomosing, radial and relatively straight channels, which become increasingly focused in a seaward direction. This implies that a well organized subglacial drainage system existed within the bay at some point in the past. Copyright © 2008 John Wiley & Sons, Ltd.
Palaeo‐ice‐stream onsets: examples from the north‐eastern Laurentide Ice Sheet
Authors: Angelis Hernán De , Kleman Johan
Published: March 2008

In this paper we report on observations of glacial landscapes at the head of geomorphologically interpreted palaeo‐ice streams, i.e. palaeo‐ice‐stream onsets. Our work is based on the results of systematic palaeoglaciological mapping of the portion of north‐eastern Canada formerly covered by the Laurentide Ice Sheet. Four different cases are considered and analysed in detail: one is the Dubawnt Lake Ice Stream and the others are smaller (<70 km long) palaeo‐ice streams. We found that in this region onset zones are generally characterized by a heterogeneous landform record and are more easily recognized when landscapes typical of partially frozen beds are present. Based on publicly available topographical and geological data as well as theoretical developments, we discuss the conditions and controls on the location of these onset zones and their potential stability. Except for the Dubawnt Lake Ice Stream, we found that, although topography and geology are important conditioning factors, the geomorphological imprint of palaeo‐ice‐stream onsets cannot be explained without invoking the role of the basal thermal boundary between cold‐ and warm‐based ice. Finally, we observed that, except for the Dubawnt Lake Ice Stream, the onset zones of large ice streams are rarely preserved, and we suggest two possible explanations for this. We conclude that although the same qualitative processes are present under the majority of ice streams, conditions for the preservation of the onset zones are more likely to be met in the case of relatively small ice streams because these are more rapidly deglaciated. Copyright © 2008 John Wiley & Sons, Ltd.
Formation mechanisms for ice‐stream lateral shear margin moraines
Authors: Hindmarsh Richard C. A. , Stokes Chris R.
Published: March 2008

The lateral shear margins of palaeo‐ice stream beds are occasionally marked by large curvilinear moraines, but little work has addressed how they might form. In this paper we review the characteristics of ‘lateral shear margin moraines’ and present two quantitative models for their formation: (i) differential erosion rates related to lateral variations in the stream velocity and (ii) lateral incursion from inter‐stream ridges after the thinner stream retreats, where the shear margin moraine is consequently just a terminal moraine of the inter‐stream ridge. Other possible mechanisms of formation are addressed qualitatively. Both of our quantitative theories are, in principle, feasible, but the incursion model is less plausible and inconsistent with observations. The differential erosion model can predict moraines tens of metres thick and several kilometres wide, which can be formed in a thousand years. The width of the moraine depends on the competition between a term that varies across the ice stream because it is dependent on ice velocity and that always causes erosion, and a term related to the local accumulation rate, which causes erosion if is positive and deposition if negative. These terms combine to create the possibility of deposition at the shear margins of ice streams in ablation areas. The width of the moraine has a tendency to increase with the width of the stream. The conditions that permit shear margin moraines to form are quite constrained: too much ablation and deposition occurs everywhere rather than just near the lateral margins of the ice streams; too little ablation and there is erosion everywhere. This is consistent with the infrequent observations of lateral shear margin moraines. Copyright © 2008 John Wiley & Sons, Ltd.
The experimental basis for interpreting particle and magnetic fabrics of sheared till
Authors: Iverson Neal R. , Hooyer Thomas S. , Thomason Jason F. , Graesch Matt , Shumway Jacqueline R.
Published: March 2008

Particle fabrics of basal tills may allow testing of the bed‐deformation model of glacier flow, which requires high bed shear strains (>100). Field studies, however, have not yielded a systematic relationship between shear‐strain magnitude and fabric development. To isolate this relationship four basal tills and viscous putty were sheared in a ring‐shear device to strains as high as 714. Fabric was characterized within a zone of shear deformation using the long‐axis orientations of fine‐gravel and sand particles and the anisotropy of magnetic susceptibility (AMS) of small (∼5·8 cm3) intact samples. Results indicate that till particles rotate toward the plane of shearing with long‐axis orientations that become tightly clustered in the direction of shear (0·78 < S1 < 0·94 for three‐dimensional data). These strong, steady‐state fabrics are attained at shear strains of 7–30, with no evidence of fabric weakening with further strain, regardless of the specific till or particle‐size fraction under consideration. These results do not support the Jeffery model of particle rotation, which correctly describes particle rotation in the viscous putty but not in the tills, owing to fluid‐mechanical assumptions of the model that are violated in till. The sensitivity of fabric development to shear‐strain magnitude indicates that, for most till units where shear‐strain magnitude is poorly known, attributing fabric variations to spatial differences in other variables, such as till thickness or water content, will be inherently speculative. Attributing fabric characteristics to particular basal till facies is uncertain because shear‐strain magnitude is unlikely to be closely correlated to till facies. Weak or spatially variable fabrics, in the absence of post‐depositional disturbance or major deviations from unidirectional simple shear, indicate that till has not been pervasively sheared to the high strains required by the bed‐deformation model. Strong flow‐parallel fabrics are a necessary but insufficient criterion for confirming the model. Copyright © 2008 John Wiley & Sons, Ltd.
Time‐transgressive tunnel valley formation indicated by infill sediment structure, North Sea – the role of glaciohydraulic supercooling
Authors: Kristensen Thomas Bojer , Piotrowski Jan A. , Huuse Mads , Clausen Ole R. , Hamberg Lars
Published: March 2008

Structure and lithology of the infill sediments from 16 subglacial buried tunnel valleys of Pleistocene age in the North Sea were analyzed using 3D seismic data and geophysical log data from five hydrocarbon exploration wells. The infill sediments are characterized by three seismic facies: Facies I, the volumetrically most important and structurally most distinct, is composed of clinoform reflections downlapping axially up‐valley (up‐ice), Facies II is composed of near‐horizontal, continuous and well layered reflections onlapping the clinoform reflections and the valley walls and Facies III is composed of clinoform reflections downlapping axially down‐valley (down‐ice). A model of formation of this sediment architecture is proposed, in which valley incision and infill are causally linked. It is proposed that Facies I is related to glaciohydraulic supercooling of subglacial meltwater in the distal parts of tunnel valleys. The valleys formed time‐transgressively during ice retreat, whereby sediment eroded further up‐ice was re‐deposited along adverse subglacial slopes of the valleys close to the ice margin. The formation of Facies II and III is related to the deposition in proglacial basins during final deglaciation. Copyright © 2008 John Wiley & Sons, Ltd.
Water entry into astrocytes during brain edema formation
Authors: Nase Gabriele , Helm P. Johannes , Enger Rune , Ottersen Ole P.
Published: March 2008

The process of brain edema formation has been studied extensively at the macroscopic level. In contrast, little is known about water fluxes and volume changes at the cellular level in the initial phase of brain edema. Insight in these “microscopic” events could pave the way for more efficient prevention and therapy. Here, we report measurements of brain cell volume responses recorded in vivo in a model of systemic hyponatremia. Transgenic mice expressing fluorescent proteins in astrocytes were subjected to hypo‐osmotic stress and two photon laser scanning microscopy. Volume measurements of glial cells in the cerebellum and the visual cortex indicate that individual astrocytes undergo a position‐dependent increase in cell volume by a factor of two or more during edema formation. Our data are the first to show that volume changes can be monitored at the cellular level in vivo and demonstrate that astrocytes are sites of water entry in the initial phase of brain edema formation. The uptake of water in astrocytes is likely to reflect the strong expression of aquaporin‐4 in these cells. © 2008 Wiley‐Liss, Inc.
Parents' emotion‐related beliefs and behaviours in relation to children's coping with the 11 September 2001 terrorist attacks
Authors: Halberstadt Amy G. , Thompson Julie A. , Parker Alison E. , Dunsmore Julie C.
Published: March 2008

To assess relationships between parental socialization of emotion and children's coping following an intensely emotional event, parents' beliefs and behaviours regarding emotion and children's coping strategies were investigated after a set of terrorist attacks. Parents (n=51) filled out the Parents' Beliefs about Negative Emotions questionnaire and were interviewed within two weeks of the attacks. Their elementary and middle school‐aged children were interviewed eight weeks later. First, parents' beliefs were related to two kinds of parental behaviours. Parents' beliefs about both the value of and the danger of children's emotions were positively related to their discussion with their children. Parents' belief about children's emotions as dangerous was also negatively related to parents' expressiveness with their children. Second, parents' beliefs were related to five kinds of coping strategies reported by their children. Parents' belief about children's emotions as valuable predicted children's problem‐solving, emotion‐oriented, and support‐seeking coping following the terrorist attacks. Parents' belief about children's emotions as dangerous predicted children's avoidance and distraction coping following the attacks. Parents' beliefs about the importance of children's emotions may foster a family atmosphere that facilitates children's coping with intensely emotional events. Results support differentiated, multi‐faceted analysis of the broader construct of parental beliefs. Copyright © 2008 John Wiley & Sons, Ltd.
Quantitative promoter methylation analysis of hepatocellular carcinoma, cirrhotic and normal liver
Authors: Harder Jan , Opitz Oliver G. , Brabender Jan , Olschewski Manfred , Blum Hubert E. , Nomoto Shuji , Usadel Henning
Published: March 2008

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. Little is known about its molecular pathogenesis and the relevance of DNA methylation for disease initiation and progression. Nevertheless, promoter methylation of some genes has been implicated as potential marker for HCC. Thirty‐four HCC, 34 matching non‐malignant, cirrhotic livers and 16 normal livers were analyzed for the methylation status of the genes p16INK4a, GSTP1, MGMT, DAP‐K and APC by quantitative methylation‐specific PCR. DNA promoter methylation frequencies in HCC and matching non‐malignant cirrhotic liver, respectively, were as follows: p16INK4a (76% vs. 24%), GSTP1 (53% vs. 32%), MGMT (6 vs. 12%), DAP‐K (68 vs. 100%) and APC (100 vs. 100%). GSTP1 and/or p16INK4a promoter methylation was observed in 88% of the HCC samples. In normal liver tissue, the p16INK4a, GSTP1 and MGMT promoter were not methylated. DAP‐K was methylated in 31% and APC even in 100% of normal liver samples. Quantitative levels of methylated promoter DNA of all genes were significantly different in the various tissue types except for MGMT. Our results suggest that promoter methylation of tumor‐associated genes is a common event in hepatocarcinogenesis. Significantly, higher levels and frequencies of promoter methylation in HCC were found for p16INK4a and GSTP1 compared to non‐malignant cirrhotic liver. This indicates that these epigenetic events may serve as a good marker for HCC. These data also demonstrate the importance of the quantification of methylated promoter DNA within a given sample and the use of normal tissue as controls. Quantitative analyses of methylated GSTP1 and p16INK4a promoter may serve as a powerful molecular marker in detecting HCC in biopsies. © 2008 Wiley‐Liss, Inc.
Apple polyphenols modulate expression of selected genes related to toxicological defence and stress response in human colon adenoma cells
Authors: Veeriah Selvaraju , Miene Claudia , Habermann Nina , Hofmann Thomas , Klenow Stefanie , Sauer Julia , Böhmer Frank , Wölfl Stefan , Pool‐Zobel Beatrice Louise
Published: March 2008

Apples contain significant amounts of flavonoids that are potentially cancer risk reducing by acting antioxidative or antiproliferative and by favorably modulating gene expression. The purpose of this study was to investigate whether polyphenols from apples modulate expression of genes related to colon cancer prevention in preneoplastic cells derived from colon adenoma (LT97). For this, LT97 cells were treated with effective concentrations of apple extracts (AEs). RNA was isolated and used for synthesis and labeling of cDNA that was hybridized to cDNA‐arrays. Gene expression studies were performed using a commercial cDNA‐array from Superarray® that contains a limited number of genes (96 genes) related to drug metabolism, and a custom‐made cDNA microarray that contains a higher number of genes (300 genes, including some genes from Superarray) related to mechanisms of carcinogenesis or chemoprevention. Real‐time PCR and enzyme activity assays were additionally performed to confirm selected array results. Treatment of cells with AE resulted in 30 and 46 genes expressed over cut‐off values (≥1.5‐ or ≤0.7‐fold) in Superarray and custom array, respectively. Of 87 genes spotted on both arrays, 4 genes (CYP3A7, CYP4F3, CHST7, GSTT2) were regulated with similar directional changes. Expression of selected phase II genes (GSTP1, GSTT2, GSTA4, UGT1A1, UGT2B7), regulated on either array, was confirmed by real‐time PCR. The enzyme activities of glutathione S‐transferases and UDP‐glucuronosyltransferases were altered by treatment of LT97 cells with AE. The observed altered gene expression patterns in LT97 cells, resulting from AE treatment, points to a possible protection of the cells against some toxicological insults. © 2008 Wiley‐Liss, Inc.
Platycodin D induces mitotic arrest in vitro, leading to endoreduplication, inhibition of proliferation and apoptosis in leukemia cells
Authors: Kim Mun‐Ock , Moon Dong‐Oh , Choi Yung Hyun , Lee Jae‐Dong , Kim Nam Deuk , Kim Gi‐Young
Published: March 2008

Platycodin D (PD), a major constituent of triterpene saponins in Platycodon grandiflorum, has also become an interesting candidate for cancer chemotherapy; however, little is known about apoptotic mechanisms on cancer cells. We herein investigated the mechanisms that are related to PD‐induced antiproliferation and cell death in human leukemia cells (U937, THP‐1 and K562 cells). Cell growth was assessed with proliferation assays, cell counting, flow cytometry, phase contrast microscopy and Western blot assay. Microtubule (MT) formation was measured with immunofluorescent staining and in vitro tubulin polymerization assay. Apoptotic effect was analyzed by assessing increase in annexin V‐staining and caspase‐3 activity. Treatment of synchronized leukemia cells with varying concentrations of PD resulted in significant mitotic arrest and endoreduplication (END) via downregulation of Cdc2/cyclin B1 and upregulation of wee1 expression, and elevated the Cdk2 protein via downregulation of p21 within 48 hr. We also researched PD's induction of polyploidy through the MT polymerization. Immunofluorescent microscopy and Western blot analysis revealed that PD significantly caused MT polymerization in leukemia cells. We also found that very high concentrations of PD (>200 μM) were required to directly induce MT polymerization in vitro. Finally, PD exposure induced apoptosis in U937 cells through caspase‐3‐dependent PARP and lamin A cleavage. We conclude that the primary antileukemia activity of PD is induction of endoreduplication and mitotic arrest, as a consequence of suppressing spindle MT dynamics and in promoting apoptosis in human leukemia cells. © 2008 Wiley‐Liss, Inc.
Loss of XIAP sensitizes rosiglitazone‐induced growth inhibition of colon cancer in vivo
Authors: Dai Yun , Qiao Liang , Chan Kwok Wah , Zou Bing , Ma Juan , Lan Hui Y. , Gu Qing , Li Zesong , Wang Yan , Wong Benny L.W. , Wong Benjamin C.Y.
Published: March 2008

Ligands for peroxisome proliferator‐activated receptor gamma (PPARγ) possess anticancer properties. However, the efficacy of PPARγ ligands varies in different cancers. In colon cancer, the role of PPARγ and its ligands is controversial. We recently showed that downregulation of X‐linked inhibitor of apoptosis protein (XIAP) could sensitize colon cancer cells to troglitazone, and 15‐deoxy‐D12,14‐prostaglandin J2 (15‐PGJ2) induced cell killing. In our study, we aimed to examine whether rosiglitazone, another more clinically relevant PPARγ ligand, has any synergistic anticancer effect with XIAP downregulation in colon cancer. Human colon cancer cell lines HCT116‐XIAP+/+ cells and HCT116‐XIAP−/− cells were treated with various concentrations of rosiglitazone. The effects of rosiglitazone on cell proliferation, apoptosis and growth of xenograft colon cancers were studied. Rosiglitazone barely suppressed the growth and only very weakly induced apoptosis in HCT116 cells in vitro. Loss of XIAP did not sensitize HCT116 cells to rosiglitazone‐induced growth inhibition or apoptosis. In vivo studies revealed that rosiglitazone strongly suppressed the growth of xenograft colon cancer, especially tumors derived from HCT116‐XIAP−/− cells. The rosiglitazone‐treated tumor had reduced expression of ki‐67 and lowered mitotic rate. Downregulation of XIAP was associated with an impaired activation of PPARγ by its ligand. Rosiglitazone induced marked upregulation of PTEN in HCT116‐XIAP−/− cells, as well as in xenograft tumors derived from HCT116‐XIAP−/− cells. We concluded that rosiglitazone significantly suppresses the growth of xenograft colon cancer, and downregulation of XIAP sensitizes the xenograft tumors to rosiglitazone‐induced tumor suppression in vivo via upregulation of PTEN. © 2008 Wiley‐Liss, Inc.
Energy minimizations with a combination of two knowledge‐based potentials for protein folding
Authors: de Sancho David , Rey Antonio
Published: March 2008

New force fields that are both simple and accurate are needed for computationally efficient molecular simulation studies to give insight into the actual features of the protein folding process. In this work, we assess a force field based on a new combination of two coarse‐grained potentials taken from the bibliography. These potentials have already been proved efficient in representing different types of interactions, namely the side‐chain interactions and the backbone hydrogen bonds. Now we combine them weighing their contribution to the global energy with a very simplified parameterization. To assess this combination of potentials, we use our evolutionary method to carry out energy minimization experiments for a set of all‐α, all‐β, and (α + β) protein structures. Our results, based on the assembly of short rigid native fragments, suggest that this combination of potentials can be successfully employed in coarse‐grained folding simulations. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Analysis and prediction of protein folding rates using quadratic response surface models
Authors: Huang Liang‐Tsung , Gromiha M. Michael
Published: March 2008

Understanding the relationship between amino acid sequences and folding rates of proteins is an important task in computational and molecular biology. In this work, we have systematically analyzed the composition of amino acid residues for proteins with different ranges of folding rates. We observed that the polar residues, Asn, Gln, Ser, and Lys, are dominant in fast folding proteins whereas the hydrophobic residues, Ala, Cys, Gly, and Leu, prefer to be in slow folding proteins. Further, we have developed a method based on quadratic response surface models for predicting the folding rates of 77 two‐ and three‐state proteins. Our method showed a correlation of 0.90 between experimental and predicted protein folding rates using leave‐one‐out cross‐validation method. The classification of proteins based on structural class improved the correlation to 0.98 and it is 0.99, 0.98, and 0.96, respectively, for all‐α, all‐β, and mixed class proteins. In addition, we have utilized Baysean classification theory for discriminating two‐ and three‐state proteins, which showed an accuracy of 90%. We have developed a web server for predicting protein folding rates and it is available at http://bioinformatics.myweb.hinet.net/foldrate.htm. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces
Authors: Iori F. , Corni S.
Published: March 2008

Combinatorial bio‐techniques have demonstrated that proteins can be good and even selective binders for several inorganic surfaces, including metals. However, the understanding of the basic physical mechanisms that govern such interactions did not keep up with the success in these experiments. The comprehension of such mechanisms would greatly benefit from the computational investigation of the problem. Because of the complexity of the system, classical molecular dynamics simulations based on an atomistic description appear to be the best compromise between reliability and feasibility. For proteins interacting with metal surfaces, however, methodological improvements with respect to standard Molecular Dynamics (MD) of proteins are needed, since the polarization of the metal induced by the protein (and the surrounding water) is not generally negligible. In this article, we present a simple approach to introduce metal polarization effects (often termed image effects) in MD simulations by exploiting standard features of bio‐oriented MD codes such as the widely used GROMACS and NAMD. Tests to show the reliability of the proposed methods are presented, and the results for a model application showing the importance of image effects are also discussed. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Computational modeling of tetrahydroimidazo‐[4,5,1‐jk][1,4]‐benzodiazepinone derivatives: An atomistic drug design approach using Kier‐Hall electrotopological state (E‐state) indices
Authors: Sapre Nitin S. , Pancholi Nilanjana , Gupta Swagata , Sapre Neelima
Published: March 2008

Quantitative structure‐activity relationships (QSAR), based on E‐state indices have been developed for a series of tetrahydroimidazo‐[4,5,1‐jk]‐benzodiazepinone derivatives against HIV‐1 reverse transcriptase (HIV‐1 RT). Statistical modeling using multiple linear regression technique in predicting the anti‐HIV activity yielded a good correlation for the training set (R2 = 0.913, R = 0.897, Q2 = 0.849, MSE = 0.190, F‐ratio = 59.97, PRESS = 18.05, SSE = 0.926, and p value = 0.00). Leave‐one‐out cross‐validation also reaffirmed the predictions (R2 = 0.850, R = 0.824, Q2 = 0.849, MSE = 0.328, and PRESS = 18.05). The predictive ability of the training set was also cross‐validated by a test set (R2 = 0.812, R = 0.799, Q2 = 0.765, MSE = 0.347, F‐ratio = 64.69, PRESS = 7.37, SSE = 0.975, and p value = 0.00), which ascertained a satisfactory quality of fit. The results reflect the substitution pattern and suggest that the presence of a bulky and electropositive group in the five‐member ring and electron withdrawing groups in the seven‐member ring will have a positive impact on the antiviral activity of the derivatives. Bulky groups in the six‐member ring do not show an activity‐enhancing impact. Outlier analysis too reconfirms our findings. The E‐state descriptors indicate their importance in quantifying the electronic characteristics of a molecule and thus can be used in chemical interpretation of electronic and steric factors affecting the biological activity of compounds. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Reference energy extremal optimization: A stochastic search algorithm applied to computational protein design
Authors: Zhang Naigong , Zeng Chen
Published: March 2008

We adapt a combinatorial optimization algorithm, extremal optimization (EO), for the search problem in computational protein design. This algorithm takes advantage of the knowledge of local energy information and systematically improves on the residues that have high local energies. Power‐law probability distributions are used to select the backbone sites to be improved on and the rotamer choices to be changed to. We compare this method with simulated annealing (SA) and motivate and present an improved method, which we call reference energy extremal optimization (REEO). REEO uses reference energies to convert a problem with a structured local‐energy profile to one with more random profile, and extremal optimization proves to be extremely efficient for the latter problem. We show in detail the large improvement we have achieved using REEO as compared to simulated annealing and discuss a number of other heuristics we have attempted to date. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
A dynamic lattice searching method with interior operation for unbiased optimization of large Lennard‐Jones clusters
Authors: Shao Xueguang , Yang Xiaoli , Cai Wensheng
Published: March 2008

For improving the efficiency of dynamic lattice searching (DLS) method for unbiased optimization of large Lennard‐Jones (LJ) clusters, a variant of the interior operation (IO) proposed by Takeuchi was combined with DLS. The method is named as DLS‐IO. In the method, the IO moves outer atoms with higher energy toward the coordinates center, i.e., (0, 0, 0), of a cluster and a local minimization (LM) follows each IO. This makes the interior atoms more compact and the outer atoms more uniformly distributed with lower potential energy. Therefore, the starting structure for DLS operations is closer to the global optimum compared with the randomly generated structures. On the other hand, a method to identify the central atom is proposed for the central vacancy problem. Optimizations of LJ500, LJ561, LJ660, LJ665, and LJ670 were investigated with the DLS‐IO, and the structural transition during the optimization was analyzed. It was found that the method is efficient and unbiased for optimization of large LJ clusters, and it may be a promising approach to be universally used for structural optimizations. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
The equivalent potential of water for electronic structure of aspartic acid
Authors: Zhang Tian , Zheng Haoping , Yan Shu
Published: March 2008

The equivalent potential of water for the electronic structure of aspartic acid (Asp−) in solution is constructed by the first‐principles, all‐electrons, ab initio calculations. Aspartic acid is a hydrophilic amino acid which is negatively charged in neutral water solution. The main process of calculation consists of three steps. Firstly, the geometric structure of the cluster containing Asp− and water molecules is calculated by the free cluster calculation. Then, based on the obtained geometric structure, the electronic structure of Asp− with the potential of water molecules is calculated using the self‐consistent cluster‐embedding method. Finally, the electronic structure of Asp− with the potential of dipoles is calculated. The results show that the major effect of water on Asp−'s electronic structure is lowering the occupied molecular orbitals by about 0.02 Ry on average, and narrowing energy gap by 10.8%. The effect of water on the electronic structure of Asp− can be simulated by dipoles potential. © 2008 Wiley Periodicals, Inc.J Comput Chem, 2008.
Prediction of densities for solid energetic molecules with molecular surface electrostatic potentials
Authors: Kim Chan Kyung , Cho Soo Gyeong , Kim Chang Kon , Park Hyung‐Yeon , Zhang Hui , Lee Hai Whang
Published: March 2008

The densities of high energetic molecules in the solid state were calculated with a simplified scheme based on molecular surface electrostatic potentials (MSEP). The MSEP scheme for density estimation, originally developed by Politzer et al., was further modified to calculate electrostatic potential on a simpler van der Waals surface. Forty‐one energetic molecules containing at least one nitro group were selected from among a variety of molecular types and density values, and were used to test the suitability of the MSEP scheme for predicting the densities of solid energetic molecules. For comparison purposes, we utilized the group additivity method (GAM) incorporating the parameter sets developed by Stine (Stine‐81) and by Ammon (Ammon‐98 and ‐00). The absolute average error in densities from our MSEP scheme was 0.039 g/cc. The results based on our MSEP scheme were slightly better than the GAM results. In addition, the errors in densities generated by the MSEP scheme were almost the same for various molecule types, while those predicted by GAM were somewhat dependent upon the molecule types. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
CHARMM‐GUI: A web‐based graphical user interface for CHARMM
Authors: Jo Sunhwan , Kim Taehoon , Iyer Vidyashankara G. , Im Wonpil
Published: March 2008

CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM‐GUI, http://www.charmm‐gui.org, has been developed to provide a web‐based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM‐GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM‐GUI development project are also discussed briefly together with other features in the CHARMM‐GUI website, such as Archive and Movie Gallery. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Time‐dependent density functional theory study on hydrogen‐bonded intramolecular charge‐transfer excited state of 4‐dimethylamino‐benzonitrile in methanol
Authors: Zhao Guang‐Jiu , Han Ke‐Li
Published: March 2008

The time‐dependent density functional theory (TDDFT) method was carried out to investigate the hydrogen‐bonded intramolecular charge‐transfer (ICT) excited state of 4‐dimethylaminobenzonitrile (DMABN) in methanol (MeOH) solvent. We demonstrated that the intermolecular hydrogen bond C≡N···HO formed between DMABN and MeOH can induce the C≡N stretching mode shift to the blue in both the ground state and the twisted intramolecular charge‐transfer (TICT) state of DMABN. Therefore, the two components at 2091 and 2109 cm−1 observed in the time‐resolved infrared (TRIR) absorption spectra of DMABN in MeOH solvent were reassigned in this work. The hydrogen‐bonded TICT state should correspond to the blue‐side component at 2109 cm−1, whereas not the red‐side component at 2091 cm−1 designated in the previous study. It was also demonstrated that the intermolecular hydrogen bond C≡N···HO is significantly strengthened in the TICT state. The intermolecular hydrogen bond strengthening in the TICT state can facilitate the deactivation of the excited state via internal conversion (IC), and thus account for the fluorescence quenching of DMABN in protic solvents. Furthermore, the dynamic equilibrium of these electronically excited states is explained by the hydrogen bond strengthening in the TICT state. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Structures and stability of lithium monosilicide clusters SiLin (n = 4–16): What is the maximum number, magic number, and core number for lithium coordination to silicon?
Authors: He Ning , Xie Hong‐Bin , Ding Yi‐Hong
Published: March 2008

In the coordination, hypervalent and cluster chemistry, three important characteristic properties are the maximum coordination number, magic number, and core coordination number. Yet, few studies have considered these three numbers at the same time for an MLn cluster with n larger than 8. In this article, we systematically studied the three properties of SiLin (n = 4–16) clusters at the B3LYP/6‐31G(d), B3LYP/6‐311++G(2d), and CCSD(T)/6‐311++G(3df)//B3LYP/6‐311++G(2d) (for energy only) levels. Various isomeric forms with different symmetries were calculated. For each SiLin (n = 4–9), silicon cohesive energy (cE) from SiLin → Si + Lin reaction, vertical ionization potential (vIP), and vertical electron affinity (vEA) were obtained for the lowest‐energy isomer. We found that the maximum Li‐coordination number of Si is 9, which is the largest number among the known MLin clusters. All cE, vIP, and vEA values predicted that 6 is the magic Li‐coordination number of Si. For small SiLin (n ≤ 6) clusters, Li atoms favor direct coordination to Si, whereas for larger SiLin (n ≥ 7) clusters, there is a core cluster that is surrounded by excessive Li atoms. The core Li‐coordination number is 6 for SiLin (n = 7,8), 7 for SiLin (n = 9,10), 8 for SiLin (n = 11–15) and 9 for SiLin (n ≥ 16). Through the calculations, we verified the relationship between the structure and stability of SiLin with the maximum coordination number, magic number, and core coordination number. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Role of structural water molecule in HIV protease‐inhibitor complexes: A QM/MM study
Authors: Suresh Cherumuttathu H. , Vargheese Aswathy Mary , Vijayalakshmi K. Periya , Mohan Neetha , Koga Nobuaki
Published: March 2008

Structural water molecule 301 found at the interface of HIV protease‐inhibitor complexes function as a hydrogen bond (H‐bond) donor to carbonyl groups of the inhibitor as well as H‐bond acceptor to amide/amine groups of the flap region of the protease. In this study, six systems of HIV protease‐inhibitor complexes were analyzed, which have the presence of this “conserved” structural water molecule using a two‐layer QM/MM ONIOM method. The combination of QM/MM and QM method enabled the calculation of strain energies of the bound ligands as well as the determination of their binding energies in the ligand–water and ligand–water–protease complexes. Although the ligand experiences considerable strain in the protein bound structure, the H‐bond interactions through the structural water overcomes this strain effect to give a net stability in the range of 16–24 kcal/mol. For instance, in 1HIV system, the strain energy of the ligand was 12.2 kcal/mol, whereas the binding energy associated with the structural water molecule was 20.8 kcal/mol. In most of the cases, the calculated binding energy of structural water molecule showed the same trend as that of the experimental binding free energy values. Further, the classical MD simulations carried out on 1HVL system with and without structural water 301 showed that this conserved water molecule enhances the H‐bond dynamics occurring at the Asp‐bound active site region of the protease‐inhibitor system, and therefore it will have a direct influence on the mechanism of drug action. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
The amphioxus Hox cluster: characterization, comparative genomics, and evolution
Authors: Amemiya Chris T. , Prohaska Sonja J. , Hill‐Force Alicia , Cook April , Wasserscheid Jessica , Ferrier David E.K. , Pascual‐Anaya Juan , Garcia‐Fernàndez Jordi , Dewar Ken , Stadler Peter F.
Published: March 2008

The amphioxus Hox cluster is often viewed as “archetypal” for the chordate lineage. Here, we present a descriptive account of the 448 kb region spanning the Hox cluster of the amphioxus Branchiostoma floridae from Hox14 to Hox1. We provide complete coding sequences of all 14 previously described amphioxus sequences and give a detailed analysis of the conserved noncoding regulatory sequence elements. We find that the posterior part of the Hox cluster is so highly derived that even the complete genomic sequence is insufficient to decide whether the posterior Hox genes arose by independent duplications or whether they are true orthologs of the corresponding gnathostome paralog groups. In contrast, the anterior region is much better conserved. The amphioxus Hox cluster strongly excludes repetitive elements with the exception of two repeat islands in the posterior region. Repeat exclusion is also observed in gnathostomes, but not protostome Hox clusters. We thus hypothesize that the much shorter vertebrate Hox clusters are the result of extensive resolution of the redundancy of regulatory DNA after the genome duplications rather than the consequence of a selection pressure to remove nonfunctional sequence from the Hox cluster. J. Exp. Zool. (Mol. Dev. Evol.) 310B:465–477, 2008. © 2008 Wiley‐Liss, Inc.
Sensitivity of the regional climate of East/Southeast Asia to convective parameterizations in the RegCM3 modelling system. Part 1: Focus on the Korean peninsula
Authors: Im Eun‐Soon , Ahn Joong‐Bae , Remedio Armelle Reca , Kwon Won‐Tae
Published: March 2008

This study investigates the capability of the regional climate model, RegCM3, to simulate fine‐scale regional climate over a narrow peninsula or archipelago. The model is run in one‐way double‐nested mode with one mother domain and two nested domains. The mother domain encompasses the eastern and southern regions of Asia and adjacent oceans with a grid spacing of 60 km. The first nested domain focuses on the Korean peninsula and the second one covers the Philippine archipelago with a grid spacing of 20 km. The simulation spans a period of 5 years and 1 month, from November 2000 to December 2004. The sensitivity of the two convection schemes, namely, the Grell scheme (Grell) and the MIT‐Emanuel scheme (EMU), is studied.

Model results obtained with both the Grell and EMU show reasonable performance in capturing the seasonal variation and the spatial characteristics of the East Asian monsoon. However, the Grell simulation appears to have persistent cold and dry biases in the summer season. There is a definite improvement in these model deficiencies by the implementation of EMU. Although the temperature fields in the Grell and EMU simulations are essentially the same in terms of the spatial distribution, the EMU simulation is quantitatively in better agreement with the observed estimates, indicating a substantial reduction in the cold bias. Further, in comparison with the Grell simulation, the EMU simulation shows an improvement in the timing and amplitude of the rain band propagating northward. The spatial distributions of precipitation also have good quality, capturing the localized maxima over Korea. The frequency distributions of daily temperature and precipitation simulated by EMU are closer to observations than those of the Grell simulation. It is found that the convective precipitation derived from different convection parameterizations is a major contributor to the performance of the model in summer. Copyright © 2008 Royal Meteorological Society
Investigating the climatic impact of urban planning strategies through the use of regional climate modelling: a case study for Melbourne, Australia
Authors: Coutts Andrew M. , Beringer Jason , Tapper Nigel J.
Published: March 2008

Urban planning is a useful method for improving local climate and human health in cities through purposefully modifying urban land surface characteristics. This can reduce the potential risks of elevated city temperatures due to the urban heat island (UHI). Unfortunately, simple tools are not readily available for urban planners to assess the climatological impacts of various urban development scenarios. Urban modelling could be developed into such a tool to achieve this. This study attempts to design and evaluate a suitable tool for application in Melbourne, Australia. The Air Pollution Model (TAPM) was chosen to assess the impact of a long‐term urban planning strategy on local climate and the above canopy UHI in Melbourne. Improvements were made to TAPM by increasing the number of urban land‐use classes in the model and creating a higher resolution land cover database focused on housing density. This modified version of TAPM showed a good performance in replicating the surface energy balance compared with an observational flux tower site in suburban Melbourne during summer. TAPM simulated a mean maximum UHI intensity of 3–4 °C at 2 a.m. in January. A future UHI scenario was then examined (year 2030) using an urban land cover database derived from plans in the Melbourne 2030 urban planning strategy. Results highlighted specific areas where planning intervention would be particularly useful to improve local climates, namely activity centres and growth areas. The appropriateness of the use of TAPM and climate models as a tool in urban planning is also discussed. Copyright © 2008 Royal Meteorological Society
Keeping it real: anticounterfeiting strategies in the pharmaceutical industry
Authors: Lybecker Kristina M.
Published: March 2008

Although pharmaceutical counterfeiting incidents can be traced back thousands of years, it has been downplayed and even dismissed by pharmaceutical manufacturers in the past. That has changed. Pharmaceutical firms are newly dedicated to eradicate counterfeits globally and spending more money on anticounterfeiting efforts than ever before. The confluence of three factors seems to have drastically changed the existing paradigm for the pharmaceutical industry: increasing globalization, advancing technology, and the controversies surrounding the WTO Trade‐related Aspects of Intellectual Property Rights Agreement and access to medicines. Given that counterfeit pharmaceuticals slip into the supply chain at every link, multinational pharmaceutical firms are searching for global solutions through increased interfirm cooperation along the supply chain. This research presents a theoretical model for characterizing the implications of these interventions on the motivations driving counterfeiters. The interventions are shown to increase the share of real pharmaceuticals and decrease the welfare losses attributable to counterfeiting. In practice, it is too early to evaluate the success of these new measures, but this research reflects on the extent of cooperation both across the supply chain and national boundaries and examines the likely long‐run implications of these measures. Copyright © 2008 John Wiley & Sons, Ltd.
The entry and exit decisions of foreign banks in Hong Kong
Authors: Leung Man K. , Young Trevor , Fung Michael K.
Published: March 2008

This paper presents a theoretical framework for explaining the entry and exit decisions of a firm, motivated by the differential returns in its home and a host market. Within this framework, the factors underpinning the entry and exit decisions of foreign banks in Hong Kong are examined, using a duration (accelerated failure time) model. It can be seen that a foreign bank, with international experience from having more overseas markets will take a shorter (longer) time to enter (exit) the Hong Kong market. Faster (slower) growth both in home trade with Hong Kong and in the Hong Kong banking sector itself will increase the likelihood of entry (exit). Ceteris paribus, Asian banks enter at a faster rate and survive longer in the Hong Kong market. Copyright © 2008 John Wiley & Sons, Ltd.
Measurement of turbulence intensity profile by a mini‐sodar
Authors: Chan P. W.
Published: March 2008

Low‐level turbulence can bring about rapid bumps and jolts to an aircraft. In severe turbulence, the aircraft may suffer momentary loss of control. In accordance with the practice of the International Civil Aviation Organization (ICAO), turbulence intensity is expressed in terms of the cube root of the eddy dissipation rate (EDR). Measurement of the EDR is an important component in the provision of turbulence alerting services for arriving and departing aircraft at an airport. This article describes a method to calculate the EDR profile using the wind measurements from a ground‐based mini‐sodar located near the Hong Kong International Airport (HKIA). The method makes use of the vertical wind data at 0.25 or 0.5 Hz provided by the mini‐sodar (depending on the maximum measurement range) and searches for the inertial sub‐range in the frequency spectrum of the vertical wind. The accuracy of the wind and EDR measurements of the mini‐sodar is first established by comparison with meteorological tower data in a field experiment. The potential application of the EDR profiles in terrain‐disrupted airflow at HKIA is then demonstrated through two case studies. The EDR profiles obtained from the mini‐sodar are found to be of good quality and could be useful in the monitoring of low‐level turbulence for aviation applications. Copyright © 2008 Royal Meteorological Society
Shape measures of rain shields as indicators of changing environmental conditions in a landfalling tropical storm
Authors: Matyas Corene
Published: March 2008

The atmosphere and land surface can alter the structure of a landfalling tropical cyclone (TC), resulting in complex spatial patterns of rainfall. Rather than average observations from many TCs, this study utilizes a Geographic Information System (GIS) to spatially analyse radar reflectivity data that define the rain shield of TC Dennis (1999). The effects of the atmosphere and land surface upon the rain shield are quantified through the calculation of six shape metrics: areal coverage, elongation, compactness, fragmentation, orientation, and distance and bearing of the polygon centroid from the storm circulation centre. Analysis of the data in hourly intervals reveals the extent to which the landfall process, vertical wind shear, dry air intrusion, interaction with mountains, and extratropical transition (ET) affect the location, size, and shape of the rain shield. Results illustrate the influences that multiple forcings can have upon TC structure and demonstrate that the calculation of the shape metrics can provide a method to evaluate the effects of environmental conditions upon multiple TCs. Copyright © 2008 Royal Meteorological Society