bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased cancer risk of heterozygotes with NBS1 germline mutations in poland
Authors: Steffen Jan , Varon Raymonda , Mosor Maria , Maneva Galina , Maurer Martin , Stumm Markus , Nowakowska Dorota , Rubach Maryna , Kosakowska Ewa , Ruka Włodzimierz , Nowecki Zbigniew , Rutkowski Piotr , Demkow Tomasz , Sadowska Małgorzata , Bidziński Mariusz , Gawrychowski Krzysztof , Sperling Karl 
Published: March 2004

AbstractIt has been suggested based on familial data that Nijmegen breakage syndrome (NBS) heterozygotes have an increased risk of malignant tumors. We found 15 carriers of the 657del5 mutation and 8 carriers of the R215W molecular variant of the NBS1 gene among 1,289 consecutive patients from Central Poland with various cancers and only 10 and 4 such carriers, respectively, in 1,620 controls from this region. Most of the 657del5 mutation carriers were found among patients with melanoma (4/105), non‐Hodgkin lymphoma (2/42) and breast cancer (4/224) and of the 234 patients with colorectal carcinoma 3 carried the 657del5 mutation and 3 others the R215W molecular variant. The frequencies of 657del5 mutation carriers among patients with melanoma and non‐Hodgkin lymphoma and of R215W carriers in patients with colorectal cancer were significantly higher than in controls (p < 0.01, < 0.05 and < 0.05 respectively). The pooled frequencies of 657del5 and R215W mutations in all cancer patients were also significantly higher than in controls (p < 0.05). Two carriers of the 657del5 mutation had second primary tumors. Malignant tumors among parents and siblings of 657del5 mutation carriers (14/77) were twice more frequent than in population controls. Three carriers of this mutation (2 probands with melanoma) reported melanoma in relatives. These results suggest strongly that NBS1 heterozygosity may be associated with elevated risk of some cancers. Larger studies are needed to evaluate the impact of the high frequency of germline NBS1 mutations on the cancer burden in the Slav populations. © 2004 Wiley‐Liss, Inc.
Colorectal cancer risk in adenoma patients: A nation‐wide study
Authors: Loeve F. , van Ballegooijen M. , Boer R. , Kuipers E.J. , Habbema J.D.F. 
Published: March 2004

AbstractColorectal cancer incidence after adenoma removal has been studied in selected populations of adenoma patients. Our study estimates the trend in colorectal cancer incidence after adenoma removal in actual clinical practice. From PALGA, a nationwide network and registry of histo‐ and cytopathology in the Netherlands, we extracted data of all patients diagnosed with colorectal adenomas between 1 January 1988 and 1 October 1998. The data were used to calculate population‐based colorectal cancer incidence rates after adenoma removal. A total of 78,473 adenoma patients were followed for a mean of 4.5 years after the first adenoma removal. The colorectal cancer incidence ratio compared with the general population matched by age and gender was 38.4 (37.3–39.5) in the first year after adenoma removal and 1.5 (95% confidence interval (CI): 1.4–1.6) after Year 1. The incidence ratio decreased from 2.8 (2.5–3.1) in Year 2 to 0.9 (0.6–1.2) in Years 9–11. This time trend is the opposite of the upward time trend that was expected after adenoma removal. Adenoma patients in the Netherlands are at increased risk for colorectal cancer compared to the general population. The high cancer incidence in Years 1–5 after polypectomy can be explained by a colonoscopic sensitivity for cancer of approximately 90%. © 2004 Wiley‐Liss, Inc.
Molecular responses of vascular smooth muscle cells to paclitaxel‐eluting bioresorbable stent materials
Authors: Nguyen Kytai Truong , Shaikh Nishat , Wawro Debra , Zhang Sheng , Schwade Nathan D. , Eberhart Robert C. , Tang Liping 
Published: April 2004

AbstractWe studied the influence of paclitaxel, eluted from poly(L‐lactic acid) (PLLA), on cultured vascular smooth muscle cell (VSMC) proliferation as a model of bioresorbable stent‐induced restenosis. We blended paclitaxel in cast PLLA films (P‐PLLA), demonstrating controlled release of the drug, then studied VSMC adhesion, proliferation, and gene expression profiles. No difference in cell adhesion was found between P‐PLLA and PLLA controls (105 ± 12% of PLLA controls). However, P‐PLLA significantly reduced VSMC proliferation (40 ± 15% of PLLA controls, p < 0.05). Using cDNA microarray technology, we identified major effects of P‐PLLA, including: upregulation of genes related to apoptosis, anti‐proliferation and antioxidation; and suppression of cell cycle regulators and cell survival markers. The expression patterns indicate that P‐PLLA regulates gene expression and cell functions via new pathways, including receptor tyrosine kinase (RTKs), mitogen‐activated protein kinase (MAPKs), and protein kinase (PKs, e.g., PKA) pathways, in addition to the stabilization of polymerized‐microtubules. © 2004 Wiley Periodicals, Inc. J Biomed Mater Res 69A: 513–524, 2004
Efficient approximate all‐atom solvent accessible surface area method parameterized for folded and denatured protein conformations
Authors: Guvench Olgun , Brooks Charles L. 
Published: March 2004

AbstractContinuing advances in computer hardware and software are permitting atomic‐resolution molecular simulations for longer time scales and on larger systems. Despite these advances, routinely performing atomistic simulations with explicit water for even small proteins, which reach the folding time of such proteins, remains intractable for the foreseeable future. An implicit approximation of the solvent environment using a solvent accessible surface area (SASA) term in a molecular mechanics potential function allows exclusion of the explicit water molecules in protein simulations. This reduces the number of particles by approximately an order of magnitude. We present a fast and acceptably accurate approximate all‐atom SASA method parameterized using a set of folded and heat‐denatured conformations of globular proteins. The parameters are shown to be transferable to folded and heat‐denatured conformations for another set of proteins. Calculation of the approximate SASA and the associated derivatives with respect to atomic positions for a 4644 atom protein requires only 1/11th the CPU time required for calculation of the nonbonded interactions for this system. On a per atom basis, this algorithm is three times faster than the fastest previously published approximate SASA method and achieves the same level of accuracy. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1005–1014, 2004
Stability issues of covalently and noncovalently bonded peptide subunits
Authors: Perczel András , Hudáky Péter , Füzéry Anna K. , Csizmadia Imre G. 
Published: March 2004

AbstractThe present study focuses on important questions associated with modeling of peptide and protein stability. Computing at different levels of theory (RHF, B3LYP) for a representative ensemble of conformers of di‐ and tripeptides of alanine, we found that the Gibbs Free Energy values correlate significantly with the total electronic energy of the molecules (0.922 ≤ R2). For noncovalently attached but interacting peptide subunits, such as [For‐NH2]2 or [For‐L‐Ala‐NH2]2, we have found, as expected, that the basis set superimposition error (BSSE) is large in magnitude for small basis set but significantly smaller when larger basis sets [e.g., B3LYP/6‐311++G(d,p)] are used. Stability of the two hydrogen bonds of antiparallel β‐pleated sheets were quantitatively determined as a function of the molecular structure, S10 and S14, computed as 4.0 ± 0.5 and 8.1 ± 1.1 kcal/mol, respectively. Finally, a suitable thermoneutral isodesmic reaction was introduced to scale both covalently and noncovalently attached peptide units onto a common stability scale. We found that a suitable isodesmic reaction can result in the total electronic energy as well as the Gibbs free energy of a molecule, from its “noninteracting” fragments, as accurate as a few tenths of a kcal per mol. The latter observation seems to hold for peptides regardless of their length (1 ≤ n ≤ 8) or the level of theory applied. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1084–1100, 2004
A semi‐implicit solvent model for the simulation of peptides and proteins
Authors: Basdevant Nathalie , Borgis Daniel , Ha‐Duong Tap 
Published: March 2004

AbstractWe present a new model of biomolecules hydration based on macroscopic electrostatic theory, that can both describe the microscopic details of solvent–solute interactions and allow for an efficient evaluation of the electrostatic hydration free energy. This semi‐implicit model considers the solvent as an ensemble of polarizable pseudoparticles whose induced dipole describe both the electronic and orientational solvent polarization. In the presented version of the model, there is no mutual dipolar interaction between the particles, and they only interact through short‐ranged Lennard–Jones interactions. The model has been integrated into a molecular dynamics code, and offers the possibility to simulate efficiently the conformational evolution of biomolecules. It is able to provide estimations of the electrostatic solvation free energy within short time windows during the simulation. It has been applied to the study of two small peptides, the octaalanine and the N‐terminal helix of ribonuclease A, and two proteins, the bovine pancreatic trypsin inhibitor and the B1 immunoglobin‐binding domain of streptococcal protein G. Molecular dynamics simulations of these biomolecules, using a slightly modified Amber force field, provide stable and meaningful trajectories in overall agreement with experiments and all‐atom simulations. Correlations with respect to Poisson–Boltzmann electrostatic solvation free energies are also presented to discuss the parameterization of the model and its consequences. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1015–1029, 2004
Diffusion–collision model algorithms for protein folding kinetics
Authors: Vasilkoski Zlatko , Weaver David L. 
Published: March 2004

AbstractThe diffusion–collision model (DCM) of protein folding is described qualitatively and quantitatively. The input parameters required to perform a calculation are explained, and the output data are outlined. Three examples are given of calculating DCM folding kinetics: the Engrailed Homeodomain (a three‐helix bundle with three helical microdomains, pdb code 1ENH), protein G (with three microdomains having a β‐hairpin‐α‐helix‐β‐hairpin motif, pdb code 1PGA), and apomyoglobin (with eight helices and seven strong microdomain–microdomain pairings). © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1101–1107, 2004
Evaluation of the protein solvent‐accessible surface using reduced representations in terms of critical points of the electron density
Authors: Becue A. , Meurice N. , Leherte L. , Vercauteren D.P. 
Published: March 2004

AbstractThe aim of our study is the development of a method for calculating the interface of dimerization of protein–protein complexes based on simplified medium‐resolution structures. In particular, we wished to evaluate if the existing concepts for the computation of the Solvent‐Accessible Surface Area (SASA) of macromolecules could be applied to medium‐resolution models. Therefore, we selected a set of 140 protein chains and computed their reduced representations by topological analysis of their electron density maps at 2.85 Å crystallographic resolution. This procedure leads to a limited number of critical points (CPs) that can be identified and associated to backbone and side‐chain parts. To evaluate the SASA and interfaces of dimerization of the reduced representations, we chose and modified two existing programs that calculate the SASA of atomic representations, and tested (1) several radii tables of amino acids, (2) the influence of the backbone and side‐chain points, and (3) the radius of the solvent molecule, which rolls over the surface. The results are shown in terms of relative error compared to the values calculated on the corresponding atomic representations of the proteins. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1117–1126, 2004
Geometry optimization in density functional methods
Authors: Reveles J. Ulises , Köster Andreas M. 
Published: March 2004

AbstractThe geometry optimization in delocalized internal coordinates is discussed within the framework of the density functional theory program deMon. A new algorithm for the selection of primitive coordinates according to their contribution to the nonredundant coordinate space is presented. With this new selection algorithm the excessive increase in computational time and the deterioration of the performance of the geometry optimization for floppy molecules and systems with high average coordination numbers is avoided. A new step selection based on the Cartesian geometry change is introduced. It combines the trust radius and line search method. The structure of the new geometry optimizer is described. The influence of the SCF convergence criteria and the grid accuracy on the geometry optimization are discussed. A performance analysis of the new geometry optimizer using different start Hessian matrices, basis sets and grid accuracies is given. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1109–1116, 2004
A method to obtain a near‐minimal‐volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints
Authors: Bekker Henk , Van Den Berg Jur P. , Wassenaar Tsjerk A. 
Published: March 2004

AbstractIf the rotational motion of a single macromolecule is constrained during a molecular dynamics simulation with periodic boundary conditions it is possible to perform such simulations in a computational box with a minimal amount of solvent. In this article we describe a method to construct such a box, and test the approach on a number of macromolecules, randomly chosen from the protein databank. The essence of the method is that the molecule is first dilated with a layer of at least half the cut‐off radius. For the enlarged molecule a near‐densest lattice packing is calculated. From this packing the simulation box is derived. On average, the volume of the resulting box proves to be about 50% of the volume of standard boxes. In test simulations this yields on average a factor of about two in simulation speed. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1037–1046, 2004
Weaving hadamard matrices with maximum excess and classes with small excess
Authors: Craigen R. , Kharaghani H. 
Published: April 2004

AbstractWeaving is a matrix construction developed in 1990 for the purpose of obtaining new weighing matrices. Hadamard matrices obtained by weaving have the same orders as those obtained using the Kronecker product, but weaving affords greater control over the internal structure of matrices constructed, leading to many new Hadamard equivalence classes among these known orders. It is known that different classes of Hadamard matrices may have different maximum excess. We explain why those classes with smaller excess may be of interest, apply the method of weaving to explore this question, and obtain constructions for new Hadamard matrices with maximum excess in their respective classes. With this method, we are also able to construct Hadamard matrices of near‐maximal excess with ease, in orders too large for other by‐hand constructions to be of much value. We obtain new lower bounds for the maximum excess among Hadamard matrices in some orders by constructing candidates for the largest excess. For example, we construct a Hadamard matrix with excess 1408 in order 128, larger than all previously known values. We obtain classes of Hadamard matrices of order 96 with maximum excess 912 and 920, which demonstrates that the maximum excess for classes of that order may assume at least three different values. Since the excess of a woven Hadamard matrix is determined by the row sums of the matrices used to weave it, we also investigate the properties of row sums of Hadamard matrices and give lists of them in small orders. © 2004 Wiley Periodicals, Inc. J Combin Designs 12: 233–255, 2004.
Hepatocyte growth factor/scatter factor stimulates migration of muscle precursors in developing mouse tongue
Authors: Bandow Kenjiro , Ohnishi Tomokazu , Tamura Masato , Semba Ichiro , Daikuhara Yasushi 
Published: March 2004

AbstractHepatocyte growth factor (HGF) stimulates the migration of myogenic cells during the development of skeletal muscles. The inactivation of HGF genes or that of its receptor, c‐met, in mice causes hypoplasia of skeletal muscle organs, such as the tongue. Basic fibroblast growth factor (FGF‐2) also induces migration of skeletal myoblasts. A comparison of the functions of HGF and FGF‐2 in myogenesis revealed the crucial effect of HGF in the development of skeletal muscles. Unlike FGF‐2, HGF induced migration of myoblasts from the developing mouse tongue. The differences between the activities of HGF and FGF‐2 were determined by comparing their effects on the expression of matrix metalloproteinase‐9 (MMP‐9) in myoblasts, C2C12 cells, cultured in collagen‐coated dishes. The results showed that HGF, but not FGF‐2, stimulated MMP‐9 expression, and that the stimulation was mediated through the activation of phosphoinositide 3‐kinase (PI3K) which was not associated with FGF‐2 signal transduction. Nevertheless, both growth factors exerted almost the same effect on the reduction of myogenin expression in, and on the proliferation of, C2C12 cells, suggesting that HGF, rather than FGF‐2, plays a crucial role in the generation of skeletal muscles, including the tongue. Moreover, the specific role of HGF through the PI3K signal pathway is the induction of MMP‐9 expression in, and the migration of, myoblasts. © 2004 Wiley‐Liss, Inc.
Effect of recombinant porcine IGFBP‐3 on IGF‐I and long‐R3‐IGF‐I‐stimulated proliferation and differentiation of L6 myogenic cells
Authors: Xi G. , Kamanga‐Sollo E. , Pampusch M.S. , White M.E. , Hathaway M.R. , Dayton William R. 
Published: March 2004

AbstractInsulin‐like growth factor (IGF)‐I stimulates both proliferation and differentiation of myogenic precursor cells. In vivo, IGFs are bound to one of the members of a family of six high‐affinity IGF binding proteins (IGFBP 1–6) that regulate their biological activity. One of these binding proteins, IGFBP‐3, affects cell proliferation via both IGF‐dependent and IGF‐independent mechanisms and it has generally been shown to suppress proliferation of cultured cells; however, it also may stimulate proliferation depending upon the cell type and the assay conditions. Cultured porcine embryonic myogenic cells (PEMCs) produce IGFBP‐3 and its level drops significantly immediately prior to differentiation. Additionally, IGFBP‐3 suppresses both IGF‐I and Long‐R3‐IGF‐I‐stimulated proliferation of embryonic porcine myogenic cells. In this study, we have examined the effects of recombinant porcine IGFBP‐3 (rpIGFBP‐3) on IGF‐I‐ and Long‐R3‐IGF‐I‐stimulated proliferation and differentiation of the L6 myogenic cell line. L6 cells potentially provide a good model for studying the actions of IGFBP‐3 on muscle because they contain no non‐muscle cells and they do not produce detectable levels of IGFBP‐3. RpIGFBP‐3 suppresses both IGF‐I and Long‐R3‐IGF‐I‐stimualted proliferation of L6 cells, indicating that it suppresses proliferation via both IGF‐dependent and IGF‐independent mechanisms. Our data also show that rpIGFBP‐3 causes IGF‐independent suppression of proliferation without increasing the level of phosphosmad‐2 in L6 cultures. Additionally, rpIGFBP‐3 suppresses IGF‐I‐stimulated differentiation of L6 cells. In contrast, however, rpIGFBP‐3 does not suppress Long‐R3‐IGF‐I‐stimulated differentiation. This suggests that rpIGFBP‐3 does not have IGF‐independent effects on L6 cell differentiation. © 2004 Wiley‐Liss, Inc.
Characterization of the biological activities of uridine diphosphate in human dendritic cells: Influence on chemotaxis and CXCL8 release
Authors: Idzko Marco , Panther Elisabeth , Sorichter Stephan , Herouy Yared , Berod Luciana , Geissler Michael , Mockenhaupt Maja , Elsner Peter , Girolomoni Giampiero , Norgauer Johannes 
Published: March 2004

AbstractUridine nucleotides are endogenous nucleotides which are released into the extracellular space from mechanical stressed endothelial and epithelial cells as well as lipopolysaccharide (lps)‐stimulated monocytes. Here, we studied the biological activity of the selective purinoreceptor P2Y6 (P2YR6) agonist Uridine 5′diphosphate (UDP) as well as the P2YR2‐ and P2YR4‐activating uridine 5′triphosphate (UTP) on human dendritic cells (DC). These cells in their immature state have the ability to migrate from blood to peripheral target sites where they sense dangerous signals and capture potential antigens. Moreover, mature DC induce innate immune responses and migrate from peripheral tissues to secondary lymphoid organs in order to activate naive T cells and initiate adaptive immunity. Here, we were able to show that uridine nucleotides stimulated Ca2+ transients, actin polymerization, and chemotaxis in immature DC. Experiments with pertussis toxin, the stable pyrimidine agonist uridine 5′‐O‐(2‐thiodiphosphate) (UDPγS) and receptor antagonists, as well as desensitization studies suggested that these uridine nucleotides activities were mediated by different Gi protein‐coupled receptors. During lps‐induced maturation, DC lost their ability to respond towards uridine nucleotides with these activities. Instead, UDP, but not UTP, stimulated the release of the CXC‐chemokine 8 (CXCL8) from mature DC in a reactive blue sensitive manner. Moreover, our study indicates that UDP stimulates different signaling pathways in immature and mature DC in order to favor the accumulation of immature DC and to augment the capacity to secrete CXCL8 in mature DC. © 2004 Wiley‐Liss, Inc.
Optimized procedures for microarray analysis of histological specimens processed by laser capture microdissection
Authors: Upson John J. , Stoyanova Radka , Cooper Harry S. , Patriotis Christos , Ross Eric A. , Boman Bruce , Clapper Margie L. , Knudson Alfred G. , Bellacosa Alfonso 
Published: March 2004

AbstractAnalysis of cell‐specific gene expression patterns using microarrays can reveal genes that are differentially expressed in diseased and normal tissue, as well as identify genes associated with specialized cellular functions. However, the cellular heterogeneity of the tissues precludes the resolution of expression profiles of specific cell types. While laser capture microdissection (LCM) can be used to obtain purified cell populations, the limited quantity of RNA isolated makes it necessary to perform an RNA amplification step prior to microarray analysis. The linearity and reproducibility of two RNA amplification protocols—the Baugh protocol (Baugh et al., 2001, Nucleic Acids Res 29:E29) and an in‐house protocol have been assessed by conducting microarray analyses. Cy3‐labeled total RNA from the colorectal cell line Colo‐205 was compared to Cy5‐labeled Colo‐205 amplified RNA (aRNA) generated with each of the two protocols, using a human 10K cDNA array. The correlation of the gene intensities between amplified and total RNA measured in the two channels of each microarray was 0.72 and 0.61 for the Baugh protocol and the in‐house protocol, respectively. The two protocols were further evaluated using aRNA obtained from normal colonic crypt cross‐sections isolated via LCM. In both cases a microarray profile representative of colonic mucosa was obtained; statistically, the Baugh protocol was superior. Furthermore, a substantial overlap between highly expressed genes in the Colo‐205 cells and colonic crypts underscores the reliability of the microarray analysis of LCM‐derived material. Taken together, these results demonstrate that LCM‐derived tissue from histological specimens can generate abundant amounts of high‐quality aRNA for subsequent microarray analysis. J. Cell. Physiol. 201: 366–373, 2004. © 2004 Wiley‐Liss, Inc.