bluuebunny/crossref_metadata_2025_split huggingface dataset:
Palaeo‐ice‐stream onsets: examples from the north‐eastern Laurentide Ice Sheet
Authors: Angelis Hernán De , Kleman Johan 
Published: March 2008

AbstractIn 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

AbstractThe 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

AbstractParticle 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

AbstractStructure 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

AbstractThe 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

AbstractTo 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

AbstractHepatocellular 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

AbstractApples 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

AbstractPlatycodin 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

AbstractLigands 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

AbstractNew 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

AbstractUnderstanding 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

AbstractCombinatorial 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