bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression of TM4SF10, a Claudin/EMP/PMP22 family cell junction protein, during mouse kidney development and podocyte differentiation
Authors: Bruggeman Leslie A. , Martinka Scott , Simske Jeffrey S. 
Published: December 2006

AbstractCell junctions in the nephron are highly specialized to perform specific and distinct filtration and reabsorption functions. The mature kidney forms complex cell junctions including slit diaphragms that prevent the passage of serum proteins into the filtrate, and tubule cell junctions that regulate specific paracellular ion reuptake. We have investigated the expression of TM4SF10 (Trans‐Membrane tetra(4)‐Span Family 10) in mouse kidneys. TM4SF10 is the vertebrate orthologue of Caenorhabditis elegans VAB‐9, a tetraspan adherens junction protein in the PMP22/EMP/Claudin family of proteins. We found that TM4SF10 localizes at the basal‐most region of podocyte precursors before the capillary loop stage, at some tubule precursors, and at the ureteric bud junction with S‐shaped bodies. Overall expression of TM4SF10 peaked at postnatal day 4 and was virtually absent in adult kidneys. The very limited expression of TM4SF10 protein that persisted into adulthood was restricted to a few tubule segments but remained localized to the basal region of lateral membranes. In undifferentiated cultured podocytes, TM4SF10 localized to the perinuclear region and translocated to the cell membrane after Cadherin appearance at cell–cell contacts. TM4SF10 colocalized with ZO1 and p120ctn in undifferentiated confluent podocytes and also colocalized with the tips of actin filaments at cell contacts. Upon differentiation of cultured podocytes, TM4SF10 protein disappeared from cell contacts and expression ceased. These results suggest that TM4SF10 functions during differentiation of podocytes and may participate in the maturation of cell junctions from simple adherens junctions to elaborate slit diaphragms. TM4SF10 may define a new class of Claudin‐like proteins that function during junctional development. Developmental Dynamics 236:596–605, 2007. © 2006 Wiley‐Liss, Inc.
Rho kinase inhibitor Y27632 affects initial heart myofibrillogenesis in cultured chick blastoderm
Authors: Sakata Hirokazu , Sakabe Masahide , Matsui Hiroko , Kawada Norifumi , Nakatani Kazuki , Ikeda Kazuo , Yamagishi Toshiyuki , Nakajima Yuji 
Published: December 2006

AbstractDuring early vertebrate development, Rho‐associated kinases (ROCKs) are involved in various developmental processes. Here, we investigated spatiotemporal expression patterns of ROCK1 protein and examined the role of ROCK during initial heart myofibrillogenesis in cultured chick blastoderm. Immunohistochemistry showed that ROCK1 protein was distributed in migrating mesendoderm cells, visceral mesoderm of the pericardial coelom (from which cardiomyocytes will later develop), and cardiomyocytes of the primitive heart tube. Pharmacological inhibition of ROCK by Y27632 did not alter the myocardial specification process in cultured posterior blastoderm. However, Y27632 disturbed the formation of striated heart myofibrils in cultured posterior blastoderm. Furthermore, Y27632 affected the formation of costamere, a vinculin/integrin‐based rib‐like cell adhesion site. In such cardiomyocytes, cell–cell adhesion was disrupted and N‐cadherin was distributed in the perinuclear region. Pharmacological inactivation of myosin light chain kinase, a downstream of ROCK, by ML‐9 perturbed the formation of striated myofibrils as well as costameres, but not cell–cell adhesion. These results suggest that ROCK plays a role in the formation of initial heart myofibrillogenesis by means of actin–myosin assembly, and focal adhesion/costamere and cell–cell adhesion. Developmental Dynamics 236:461–472, 2007. © 2006 Wiley‐Liss, Inc.
Analysis of serine proteases from marine sponges by 2‐D zymography
Authors: Wilkesman Jeff G. , Schröder Heinz C. 
Published: December 2006

AbstractProteolytic activities isolated from the marine demosponges Geodia cydonium and Suberites domuncula were analyzed by 2‐D zymography, a technique that combines IEF and zymography. After purification, a 200 kDa proteolytically active protein band was obtained from G. cydonium when analyzed in gelatin copolymerized 1‐D zymograms. The enzymatic activity was quantified using α‐N‐benzoyl‐D‐arginine p‐nitroanilide (BAPNA) as a substrate and corresponded to a serine protease. The protease activity was resistant to urea and SDS. DTT and 2‐mercaptoethanol (2‐ME) did not significantly change the protease activity, but induced a shift in molecular mass of the proteolytic band to lower Mr values as detected by zymography. Under mild denaturing conditions, lower Mr bands (<200 kDa) were identified in 1‐D zymograms, suggesting that the protease is composed of subunits which retain the catalytic activity. After 2‐D zymography, the protease from G. cydonium revealed a pI of 8.0 and an Mr shift from 200 to 66 kDa. To contrast these results, a cytosolic sample from S. domuncula was analyzed. The proteolytic activity of this sponge after 2‐D zymography corresponded to an Mr of 40 kDa and a pI of 4.0. The biological function of both sponge proteases is not yet known. This study demonstrates that mild denaturing conditions required for IEF may alter the interpretation of the 2‐D zymography, and care must be taken during sample preparation.
Mapping of Malus domestica allergens by 2‐D electrophoresis and IgE‐reactivity
Authors: Herndl Anita , Marzban Gorji , Kolarich Daniel , Hahn Rainer , Boscia Donato , Hemmer Wolfgang , Maghuly Fatemeh , Stoyanova Elitza , Katinger Hermann , Laimer Margit 
Published: December 2006

AbstractThe importance of apple allergens has been repeatedly emphasized, and their presence has been confirmed both in pollen and in fruits. In the present study, a combination of proteomic tools have been used to build a complete allergen map of apple. The water‐soluble fraction of an apple extract was precipitated using a phenol‐based procedure and separated by 2‐DE. Initially four previously classified allergens, Mal d 1, Mal d 2, Mal d 3 and Mal d 4, could be identified in Western blots with polyclonal rabbit antibodies directed to the four respective allergens, and subsequently matched to the bands recognized by several patient sera. Further, all four known apple allergens were localized on a 2‐DE map and they were matched with spots recognized by sera of patients with different allergic patterns. Moreover, a new, putative allergen could be identified using MS. We evaluated the influence of post‐translational modifications and the immunoreactivity under different analytical conditions. The comparison of different visualization methods for 2‐DE gels and blots revealed that even very low concentrations of the intact epitopes are detectable by IgEs of patients, and therefore might be sufficient to trigger allergic symptoms in sensitized individuals.
Knowledge of dementia among South Asian (Indian) older people in Manchester, UK
Authors: Purandare Nitin , Luthra Vikram , Swarbrick Caroline , Burns Alistair 
Published: December 2006

AbstractObjectivesThe aim of this study was to examine knowledge of dementia in South Asian older people, as compared with Caucasian older people.MethodsAttendees, not known to suffer from dementia, of one South Asian and two predominantly Caucasian day centres for older people in Manchester (UK) were asked to complete the Dementia Knowledge Questionnaire (DKQ). The DKQ was translated into Gujarathi and Urdu by the professional translators.ResultsOne hundred and ninety‐one DKQs from Indian and 55 DKQs from Caucasian (white UK/Irish/European) older people were included in the analyses. Knowledge of dementia was poor in both Indian and Caucasian older people, especially so in the former. The median (25th–75th percentile) total DKQ scores were 3 (2–5) in Indians and 6 (3.5–9) in Caucasians (p < 0.001). Indian older people showed significantly less knowledge about basic aspects (p < 0.001) and epidemiology (p < 0.001) of dementia when compared to Caucasian older people. Both groups faired equally badly on questions about aetiology (p = 0.91) and symptomatology (p = 0.66). Indian older people were less aware of personality, reasoning, and speech being the affected in dementia (p < 0.001, p < 0.001 and p = 0.04, respectively).ConclusionIndian older people in Manchester (UK) do not seem to have sufficient knowledge about dementia, which may be one of the reasons for their relative absence in the local dementia treatment clinics. Copyright © 2006 John Wiley & Sons, Ltd.
Asymptomatic spontaneous cerebral emboli and cognitive decline in a cohort of older people: a prospective study
Authors: Voshaar Richard C. Oude , Purandare Nitin , Hardicre Jayne , McCollum Charles , Burns Alistair 
Published: December 2006

AbstractBackgroundAsymptomatic spontaneous cerebral emboli (SCE) are common in dementia and are associated with cognitive decline in dementia. The significance of their presence in older people is unknown.MethodWe included 96 participants (mean (SD) age 76.8 (6.7) years, 46% female) who were the control group in a case‐control study to evaluate SCE in dementia. Cognitive functioning was assessed prospectively over 2.5 years, using the MMSE and CAMCOG.ResultsThe mean (SD) MMSE score was 28.7 (1.4) at baseline with an average (SD) drop of 0.79 (0.91) per year. The presence of SCE was not related to the annual drop in MMSE score, nor to the CAMCOG score at follow‐up (p = 0.88 and p = 0.41, respectively). Linear regression analyses identified higher age in years (β = 0.29, p = 0.003), history of stroke (β = 0.31, p = 0.001) and carotid stenosis (β = 0.28, p = 0.003) as independent predictors of cognitive decline.ConclusionWe found no association between the presence of SCE and subsequent cognitive decline in older people without dementia. Copyright © 2006 John Wiley & Sons, Ltd.
Utility of the Algase Wandering Scale in an outpatient Alzheimer's disease sample
Authors: Marcus Jacqueline F. , Cellar Janet S. , Ansari Farzaneh Pour , Bliwise Donald L. 
Published: December 2006

AbstractBackgroundWandering represents a major problem in the management of patients with Alzheimer's disease (AD). In this study we examined the utility of the Algase Wandering Scale (AWS), a newly developed psychometric instrument that asks caregivers to assess the likelihood of wandering behavior.MethodsThe AWS was administered to the caregivers of 40 AD patients and total and subscale scores were examined in relation to measures of mental and functional status, depressive symptoms and medication usage.ResultsAWS scores were comparable, though slightly lower, than those normative values previously published. Higher scores were associated with more severe dementia. The Negative Outcome subscale showed a significant increase in reported falls or injuries in association with anti‐depressant use.ConclusionsThese data provide some construct validation for the AWS as a potentially useful scale to assess wandering behaviors in AD. Copyright © 2006 John Wiley & Sons, Ltd.
Collisions of ideal gas molecules with a rough/fractal surface. A computational study
Authors: Panczyk Tomasz 
Published: December 2006

AbstractThe frequency of collisions of ideal gas molecules (argon) with a rough surface has been studied. The rough/fractal surface was created using random deposition technique. By applying various depositions, the roughness of the surface was controlled and, as a measure of the irregularity, the fractal dimensions of the surfaces were determined. The surfaces were next immersed in argon (under pressures 2 × 103 to 2 × 105 Pa) and the numbers of collisions with these surfaces were counted. The calculations were carried out using a simplified molecular dynamics simulation technique (only hard core repulsions were assumed). As a result, it was stated that the frequency of collisions is a linear function of pressure for all fractal dimensions studied (D = 2, …, 2.5). The frequency per unit pressure is quite complex function of the fractal dimension; however, the changes of that frequency with the fractal dimension are not strong. It was found that the frequency of collisions is controlled by the number of weakly folded sites on the surfaces and there is some mapping between the shape of adsorption energy distribution functions and this number of weakly folded sites. The results for the rough/fractal surfaces were compared with the prediction given by the Langmuir‐Hertz equation (valid for smooth surface), generally the departure from the Langmuir‐Hertz equation is not higher than 48% for the studied systems (i.e. for the surfaces created using the random deposition technique). © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 681–688, 2007
Neglect of four‐ and approximation of one‐, two‐, and three‐center two‐electron integrals in a symmetrically orthogonalized basis
Authors: Laikov Dimitri N. 
Published: December 2006

AbstractA new integral approximation for use in molecular electronic structure calculations is proposed as an alternative to the traditional neglect of diatomic differential overlap models. The similarity between the symmetrically orthogonalized and the original basis functions (assumed orthonormal within each atomic set but nonorthogonal between different centers) is used to construct a robust approximation for the two‐electron integrals, with the error being quadratic in the deviation between the products of the functions. Invariance properties of this procedure are rigorously proved. Numerical studies on a representative set of molecules at valence‐only minimal basis Hartree–Fock level show that the approximation introduces relatively small errors, encouraging its future application in the semiempirical field. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 698–702, 2007
Modifying the OPLS‐AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off‐plane charge model for aromatic residues
Authors: Xu Zhitao , Luo Harry H. , Tieleman D. Peter 
Published: December 2006

AbstractThe hydration free energies of amino acid side chains are an important determinant of processes that involve partitioning between different environments, including protein folding, protein complex formation, and protein–membrane interactions. Several recent papers have shown that calculated hydration free energies for polar and aromatic residues (Trp, His, Tyr, Asn, Gln, Asp, Glu) in several common molecular dynamics force fields differ significantly from experimentally measured values. We have attempted to improve the hydration energies for these residues by modifying the partial charges of the OPLS‐AA force field based on natural population analysis of density functional theory calculations. The resulting differences between calculated hydration free energies and experimental results for the seven side chain analogs are less than 0.1 kcal/mol. Simulations of the synthetic Trp‐rich peptide Trpzip2 show that the new charges lead to significantly improved geometries for interacting Trp‐side chains. We also investigated an off‐plane charge model for aromatic rings that more closely mimics their electronic configuration. This model results in an improved free energy of hydration for Trp and a somewhat altered benzene–sodium potential of mean force with a more favorable energy for direct benzene–sodium contact. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 689–697, 2007
Computational alanine scanning mutagenesis—An improved methodological approach
Authors: Moreira Irina S. , Fernandes Pedro A. , Ramos Maria J. 
Published: December 2006

AbstractAlanine scanning mutagenesis of protein–protein interfacial residues can be applied to a wide variety of protein complexes to understand the structural and energetic characteristics of the hot‐spots. Binding free energies have been estimated with reasonable accuracy with empirical methods, such as Molecular Mechanics/Poisson‐Boltzmann surface area (MM‐PBSA), and with more rigorous computational approaches like Free Energy Perturbation (FEP) and Thermodynamic Integration (TI). The main objective of this work is the development of an improved methodological approach, with less computational cost, that predicts accurately differences in binding free energies between the wild‐type and alanine mutated complexes (ΔΔGbinding). The method was applied to three complexes, and a mean unsigned error of 0.80 kcal/mol was obtained in a set of 46 mutations. The computational method presented here achieved an overall success rate of 80% and an 82% success rate in residues for which alanine mutation causes an increase in the binding free energy > 2.0 kcal/mol (warm‐ and hot‐spots). This fully atomistic computational methodological approach consists in a computational Molecular Dynamics simulation protocol performed in a continuum medium using the Generalized Born model. A set of three different internal dielectric constants, to mimic the different degree of relaxation of the interface when different types of amino acids are mutated for alanine, have to be used for the proteins, depending on the type of amino acid that is mutated. This method permits a systematic scanning mutagenesis of protein–protein interfaces and it is capable of anticipating the experimental results of mutagenesis, thus guiding new experimental investigations. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 644–654, 2007
Nearest‐neighbor nonparametric method for estimating the configurational entropy of complex molecules
Authors: Hnizdo Vladimir , Darian Eva , Fedorowicz Adam , Demchuk Eugene , Li Shengqiao , Singh Harshinder 
Published: December 2006

AbstractA method for estimating the configurational (i.e., non‐kinetic) part of the entropy of internal motion in complex molecules is introduced that does not assume any particular parametric form for the underlying probability density function. It is based on the nearest‐neighbor (NN) distances of the points of a sample of internal molecular coordinates obtained by a computer simulation of a given molecule. As the method does not make any assumptions about the underlying potential energy function, it accounts fully for any anharmonicity of internal molecular motion. It provides an asymptotically unbiased and consistent estimate of the configurational part of the entropy of the internal degrees of freedom of the molecule. The NN method is illustrated by estimating the configurational entropy of internal rotation of capsaicin and two stereoisomers of tartaric acid, and by providing a much closer upper bound on the configurational entropy of internal rotation of a pentapeptide molecule than that obtained by the standard quasi‐harmonic method. As a measure of dependence between any two internal molecular coordinates, a general coefficient of association based on the information‐theoretic quantity of mutual information is proposed. Using NN estimates of this measure, statistical clustering procedures can be employed to group the coordinates into clusters of manageable dimensions and characterized by minimal dependence between coordinates belonging to different clusters. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 655–668, 2007
Efficient combination of Wang–Landau and transition matrix Monte Carlo methods for protein simulations
Authors: Ghulghazaryan Ruben G. , Hayryan Shura , Hu Chin‐Kun 
Published: December 2006

AbstractAn efficient combination of the Wang‐Landau and transition matrix Monte Carlo methods for protein and peptide simulations is described. At the initial stage of simulation the algorithm behaves like the Wang‐Landau algorithm, allowing to sample the entire interval of energies, and at the later stages, it behaves like transition matrix Monte Carlo method and has significantly lower statistical errors. This combination allows to achieve fast convergence to the correct values of density of states. We propose that the violation of TTT identities may serve as a qualitative criterion to check the convergence of density of states. The simulation process can be parallelized by cutting the entire interval of simulation into subintervals. The violation of ergodicity in this case is discussed. We test the algorithm on a set of peptides of different lengths and observe good statistical convergent properties for the density of states. We believe that the method is of general nature and can be used for simulations of other systems with either discrete or continuous energy spectrum. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 715–726, 2007
Effects of entropy on the gas‐phase pyrolysis of ethyl N,N‐dimethylcarbamate
Authors: Kim Chang K. , Kim Dong J. , Hsieh Y. , Lee Hai W. , Lee Bon‐Su , Kim Chan K. 
Published: December 2006

AbstractIn this study, we examined the gas‐phase pyrolysis of ethyl N,N‐dimethylcarbamate theoretically at various theoretical levels. The reaction consists of a two‐step mechanism, with N,N‐dimethylcarbamic acid and ethylene as reaction intermediates. In the first step, the reaction proceeds via a six‐membered cyclic transition state (TS), which is more favorable than that via a four‐membered cyclic TS. Here, the contribution of entropy to the overall potential energy surface was found to play an important role in determining the rate‐limiting step, which was found to be the second step when viewed in terms of the enthalpy of activation (ΔH≠), but the first step when entropy changes (−TΔS≠) were considered. These results are consistent with experimental findings. Moreover, the experimental activation entropy can be reproduced by using the hindered rotor approximation, which converts some low vibration frequencies that correspond to internal rotational modes into hindered rotors. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 625–631, 2007
Electronic structures and chemical bonding in diatomic ScX to ZnX (X = S, Se, Te)
Authors: Wu Z. J. , Wang M. Y. , Su Z. M. 
Published: December 2006

AbstractBond distances, vibrational frequencies, electron affinities, ionization potentials, dissociation energies, and dipole moments of the title molecules in neutral, positively, and negatively charged ions were studied using density functional method. Ground electronic state was assigned for each molecule. The bonding patterns were analyzed and compared with both the available data and across the series. It was found that, besides ionic component, covalent bonds are formed between the metal s, d orbitals, and the p orbital of S, Se, and Te. For neutral and cationic molecules, the covalent character increases from ScX to CrX and from FeX to CuX with an exception of decrease at MnX and ZnX, while for anionic molecules, the trend is not obvious. For both neutral and charged molecules, the sulfides have the shortest bond distance and largest vibrational frequency, while tellurides have the largest bond distance and smallest vibrational frequency. For neutral and anionic molecules, the dissociation energy of sulfides is the largest, that of tellurides is the smallest, while this only remains true for cationic molecules from ScX+ to FeX+. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 703–714, 2007