bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonparametric One‐way Analysis of Variance of Replicated Bivariate Spatial Point Patterns
Authors: Landau Sabine , Rabe‐Hesketh Sophia , Everall Ian P. 
Published: February 2004

AbstractA common problem in neuropathological studies is to assess the spatial patterning of cells on tissue sections and to compare spatial patterning between disorder groups. For a single cell type, the cell positions constitute a univariate point process and interest focuses on the degree of spatial aggregation. For two different cell types, the cell positions constitute a bivariate point process and the degree of spatial interaction between the cell types is of interest. We discuss the problem of analysing univariate and bivariate spatial point patterns in the one‐way design where cell patterns have been obtained for groups of subjects. A bootstrapping procedure to perform a nonparametric one‐way analysis of variance of the spatial aggregation of a univariate point process has been suggested by Diggle, Lange and Beneš (1991). We extend their replication‐based approach to allow the comparison of the spatial interaction of two cell types between groups, to include planned comparisons (contrasts) and to assess whole groups against complete spatial randomness and spatial independence. We also accommodate several replicate tissue sections per subject. An advantage of our approach is that it can be applied when processes are not stationary, a common problem in brain tissue sections since neurons are arranged in cortical layers. We illustrate our methods by applying them to a neuropathological study to investigate abnormalities in the functional relationship between neurons and astrocytes in HIV associated dementia. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the Online Detection of Monotonic Trends in Time Series
Authors: Fried R. , Imhoff M. 
Published: February 2004

AbstractThe online detection of a monotonic trend in a time series with a time‐varying mean is an important task in medical applications like intensive care monitoring, that is rendered difficult by autocorrelations. Statistical control charts designed for industrial processes are not adequate as they typically rely on a fixed target value, and many detection rules assume a trend to be linear or neglect autocorrelations. We report our experience with the online detection of slow monotonic trends. Our approach is based on a moving time window, and time‐varying autocorrelations are estimated online using parametric assumptions. The performance of versions of this approach is investigated in a simulation study. We find that shrinkage estimation of the time‐varying mean improves the results. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A Comparison of Nonparametric Error Rate Estimation Methods in Classification Problems
Authors: Wehberg Sonja , Schumacher Martin 
Published: February 2004

AbstractAssessment of the misclassification error rate is of high practical relevance in many biomedical applications. As it is a complex problem, theoretical results on estimator performance are few. The origin of most findings are Monte Carlo simulations, which take place in the “normal setting”: The covariables of two groups have a multivariate normal distribution; The groups differ in location, but have the same covariance matrix and the linear discriminant function LDF is used for prediction.We perform a new simulation to compare existing nonparametric estimators in a more complex situation. The underlying distribution is based on a logistic model with six binary as well as continuous covariables. To study estimator performance for varying true error rates, three prediction rules including nonparametric classification trees and parametric logistic regression and sample sizes ranging from 100‐1,000 are considered. In contrast to most published papers we turn our attention to estimator performance based on simple, even inappropriate prediction rules and relatively large training sets.For the major part, results are in agreement with usual findings. The most strikingly behavior was seen in applying (simple) classification trees for prediction: Since the apparent error rate Êrr.app is biased, linear combinations incorporating Êrr.app underestimate the true error rate even for large sample sizes. The .632+ estimator, which was designed to correct for the overoptimism of Efron's .632 estimator for nonparametric prediction rules, performs best of all such linear combinations. The bootstrap estimator Êrr.B0 and the crossvalidation estimator Êrr.cv, which do not depend on Êrr.app, seem to track the true error rate. Although the disadvantages of both estimators – pessimism of Êrr.B0 and high variability of Êrr.cv – shrink with increased sample sizes, they are still visible.We conclude that for the choice of a particular estimator the asymptotic behavior of the apparent error rate is important. For the assessment of estimator performance the variance of the true error rate is crucial, where in general the stability of prediction procedures is essential for the application of estimators based on resampling methods. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Implication of mitochondrial involvement in apoptotic activity of fragile histidine triad gene: Application of synchronous luminescence spectroscopy
Authors: Askari Minoo D. F. , Vo‐Dinh Tuan 
Published: February 2004

AbstractThe fragile histidine triad (FHIT) tumor suppressor gene incorporates the common human chromosomal fragile site at 3p14.2. The structure and expression of the FHIT gene are frequently altered in many cancers. The tumor suppressor activity of the FHIT gene has been previously demonstrated as potentially involving apoptotic induction. Here, mitochondria are implicated as being involved in the apoptotic activity of the FHIT gene. A number of morphological and biochemical events, including the disruption of the inner mitochondrial transmembrane potential (ΔΨm) and the release of apoptogenic cytochrome c protein into the cytoplasm, are characteristic features of the apoptotic program. The proapoptotic activity of the FHIT gene is studied by investigating the loss of ΔΨm in mitochondria and translocation of cytochrome c. Synchronous luminescence (SL) spectroscopy is applied to measure mitochondrial incorporation of rhodamine 123 for direct analysis of alterations in the mitochondrial ΔΨm. The SL methodology is based on synchronous excitation in which the excitation and emission wavelengths are scanned simultaneously while a constant wavelength interval is maintained between the excitation and emission monochromators. An enhanced collapse of ΔΨm in apoptotically induced FHIT expressing cells compared to FHIT negative cells is observed. The loss of ΔΨm is greatly restricted in the presence of the apoptotic inhibitor, cyclosporin A. Cytoplasmic translocation of cytochrome c in the FHIT expressing cells as an early event in apoptosis is also demonstrated. It is concluded that Fhit protein expression maintained apoptotic function by altering the ΔΨm and by enhancing cytochrome c efflux from the mitochondria. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Spectroscopic evidence revealing polyproline II structure in hydrophobic, putatively elastomeric sequences encoded by specific exons of human tropoelastin
Authors: Bochicchio Brigida , Aït‐Ali Amina , Tamburro Antonio M. , Alix Alain J. P. 
Published: February 2004

AbstractElastin, the protein responsible for tissue elasticity, is contained in arterial walls, lungs, and skin. Given the cassettelike organization of the human tropoelastin gene, giving rise to alternating exons encoding for crosslink domains and elastomeric domains, it is tempting to suggest that polypeptides encoded by different exons could adopt structures independent of the other exons. The results obtained with the polypeptide sequences encoded by exons 3, 7, and 30 of human tropoelastin are described. It is shown that these hydrophobic exons may partly assume the polyproline II (PPII) structure, as found by circular dichroism studies in aqueous solution. Classical Raman spectroscopy evidences a specific sharp band at 1314 cm−1, which is assigned to the PPII structure adopted by these exons in the solid state. As these sequences are among those putatively responsible for elastomeric properties, these findings are of particular interest in relation to the current models of the elasticity of elastin. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Schiff base of gossypol with 3,6,9‐trioxa‐decylamine complexes with monovalent cations studied by mass spectrometry, 1H‐NMR, FTIR, and PM5 semiempirical methods
Authors: Przybylski Piotr , Ilkevych Nataliya , Schroeder Grzegorz , Brzezinski Bogumil , Bartl Franz 
Published: February 2004

AbstractA new Schiff base of gossypol with 3,6,9‐trioxa‐decylamine (GSTB) forms stable complexes with monovalent cations. This process of complex formation was studied by electrospray ionization mass spectrometry, 1H‐NMR and FTIR spectroscopy, and the PM5 (parametric method 5) semiempirical method. It is found that GSTB forms 1 : 1 and 1 : 2 complexes with Li+ and Na+ and 1 : 1 complexes with K+, Rb+, or Cs+ cations and exists in all these complexes in the enamine–enamine tautomeric form. Moreover, within these complexes only Li+ cations can fluctuate between the oxygen atoms of trioxaalkyl chains. All other cations are strongly localized. In the complex of GSTB with two protons localized on the N atoms of the Schiff base, the imine–imine tautomeric form is realized. The complexes of the Schiff base with K+, Rb+, or Cs+ cations are the 1 : 1 type with the oxygen atoms of the trioxaalkyl chains, as well as the O1H or O1′H group coordinating the cation. The structures of the complexes are calculated by the PM5 semiempirical method and discussed. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Studies on acute human infections using FTIR microspectroscopy and cluster analysis
Authors: Mordehai Jacov , Ramesh Jagannathan , Huleihel Mahmoud , Cohen Zahavi , Kleiner Oleg , Talyshinsky Marina , Erukhimovitch Vitaly , Cahana Aviv , Salman Ahmad , Sahu Ranjit Kumar , Guterman Hugo , Mordechai Shaul 
Published: February 2004

AbstractA novel methodology for the diagnosis of acute infections using FTIR microspectroscopy (FTIR‐MSP) data on blood components and cluster analysis is presented. Blood samples were collected from 11 patients suffering from various infections and 16 age‐matched healthy human controls. Blood components such as white blood cells, red blood cells, and plasma were isolated using standard procedures and FTIR‐MSP of these components was utilized. A cluster analysis of the FTIR spectra was performed. The spectra obtained from the three blood components of patients were different from those of controls. The FTIR spectra of white blood cells from patients suffering infections were significantly different from the controls. Cluster analyses of averaged FTIR‐MSP spectra of white blood cells provided 100% classification between patients and healthy controls. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Inclusion complex of fenbufen with β‐cyclodextrin
Authors: Bratu I. , Gavira‐Vallejo J. M. , Hernanz A. , Bogdan M. , Bora Gh. 
Published: February 2004

AbstractAn inclusion complex of fenbufen with β‐cyclodextrin (β‐CD) in aqueous solution was characterized by 1H‐NMR spectroscopy. The [1:1] stoichiometry was determined and a stability constant of several 1000s (M−1) was calculated. The geometry of the inclusion complex was established based on MM+ molecular mechanics calculations. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Fourier transform infared spectroscopy investigation of protein conformation in spray‐dried protein/trehalose powders
Authors: French Donna L. , Arakawa Tsutomu , Li Tiansheng 
Published: February 2004

AbstractSpray drying is a way to generate protein solids (powders), which is also true for lyophilization. Sugars are used to protect proteins from conformational changes and chemical degradations arising from drying processes and storage conditions such as the humidity. The influence of trehalose and humidity on the conformation and hydration of spray‐dried recombinant human granolucyte colony stimulating factor (rhG‐CSF) and recombinant consensus interferon‐α (rConIFN) was investigated using Fourier transform IR spectroscopy. The spectral analysis of spray‐dried powders in the amide I region demonstrated that trehalose stabilized the α‐helical conformation of both rhG‐CSF and rConIFN proteins. Exposure of the pure protein powders to 33% relative humidity (RH) resulted in the formation of β sheets and loss of turns but no change in α‐helical structure. Trehalose reduced the magnitude of the changes in β sheets and turns. Exposure of the pure protein powders to 75% RH resulted in the loss of α‐helical conformation with a corresponding increase in β structures (β sheets and turns). Trehalose did not protect proteins from the loss of α‐helical structures, but it reduced the formation of antiparallel β sheets. Hydrogen–deuterium exchange (H–D exchange) was used to further characterize these hydration‐induced conformational changes. At 33% RH the percent exchange of the protein decreased with increasing trehalose content, indicating a greater protection of the protein from H–D exchange by a higher concentration of trehalose. Such protection correlates with decreased conformational changes of the protein by trehalose at this humidity. At 75% RH the degree of H–D exchange of the protein was insensitive to the powder composition in all powders. Surprisingly, the H–D exchange of trehalose was low at about 20–25%, which was nearly independent of the protein/trehalose ratio and humidity, indicating that the exchangeable protons on trehalose molecules are highly protected in protein‐containing powders. The observed protein hydration is related to the effect of trehalose on the conformational changes of the protein under humidity. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Interactions of Alzheimer amyloid peptides with cultured cells and brain tissue, and their biological consequences
Authors: Bateman David A. , Chakrabartty Avijit 
Published: February 2004

AbstractThe Alzheimer amyloid peptides are the main constituent of the diagnostic hallmark of Alzheimer disease, the senile plaque. A halo of neurodegeneration surrounds the senile plaques observed in the brains of Alzheimer patients. Significant efforts are under way to determine whether the Alzheimer peptides are the causal agents of this neurodegeneration. We review the developments in identifying the putative interaction sites of Alzheimer amyloid peptides on cells and intact brain tissue. We focus on the specificity of this interaction and on the molecular nature of potential receptors. These studies form the bases for developing therapeutics that target potential interaction sites and inhibit Alzheimer amyloid peptide deposition. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2004
External reversible control of recognition behavior of alpha‐peptide ribonucleic acid (α‐PRNA) through anti‐syn orientational switching of the nucleobase induced by borate esterification of the cis‐2′,3′‐diol
Authors: Wada Takehiko , Sato Hirofumi , Inoue Yoshihisa 
Published: February 2004

AbstractA novel nucleic acid model using peptide ribonucleic acid (PRNA), which contains 5′‐amino‐5′‐deoxypyrimidine ribonucleoside as a recognition site for nucleic acids, has been designed, synthesized and applied to the external reversible control of recognition behavior of the complementary polynucleotide through the orientational switching of the nucleobase induced by borate. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2004
Synthetic heterotrimeric collagen peptides as mimics of cell adhesion sites of the basement membrane
Authors: Renner Christian , Saccà Barbara , Moroder Luis 
Published: February 2004

AbstractCollagen type IV forms a network in the basement membrane into which other constituents of the tissue are incorporated. It also provides cell‐adhesion sites that are specifically recognized by cell‐surface receptors, i.e., the integrins. Different from the ubiquitous sequential RGD adhesion motif found in most of the matrix proteins, in collagen type IV, the responsible binding sites for α1β1 integrin have been identified as Asp461 of the two α1 chains and Arg461 of the α2 chain. Because of the heterotrimeric character of this collagen, the spatial geometry of the binding epitope depends not only on the triple‐helical fold, but decisively even on the stagger of the chains. To investigate the effects of chain registration on the conformational properties and binding affinities of this adhesion epitope, two synthetic heterotrimeric collagen peptides consisting of the identical three chains were assembled by an artificial cystine knot in two different registers, i.e., in the most plausible α2α1α1′ and less probable α1α2α1′ chain alignment. A detailed conformational characterization of both trimers allowed to correlate their different binding affinities for α1β1 integrin with the degree of local plasticity of the two different triple helices. Optimal local breathing of the rod‐shaped collagens is apparently crucial for selective recognition by proteins interacting with these main components of the extracellular matrix. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2004
Ribonucleopeptides: Functional RNA–peptide complexes
Authors: Hagihara Masaki , Hasegawa Tetsuya , Sato Shin‐ichi , Yoshikawa Susumu , Ohkubo Katsutoshi , Morii Takashi 
Published: February 2004

AbstractSelection of functional RNAs from randomized pool of RNA molecules successfully affords RNA aptamers that specifically bind to small molecules, and that have catalytic activities. Recent structural analyses of the ribosomal RNA complex suggest that the RNA–protein complex would be a new structural candidate for the design of tailor‐made receptors and enzymes. We have designed an ATP binding domain that consists of an RNA subunit and a peptide subunit by means of structure‐based design approach and successive in vitro selection method. The RNA subunit is designed to consist of two functional domains; an ATP binding domain with 20 randomized nucleotides and an adjacent stem region that serves as a binding site for the RNA‐binding peptide. The randomized nucleotide region was placed next to the HIV‐1 Rev response element to enable the formation of “ribonucleopeptide” pools in the presence of the Rev peptide. In vitro selection of RNA oligonucleotides from the randomized pool afforded a ribonucleopeptide receptor specific for ATP. The ATP‐binding ribonucleopeptide did not share the known consensus nucleotide sequence for ATP aptamers, and completely lost its ATP‐binding ability in the absence of the Rev peptide. The ATP‐binding activity of the ribonucleopeptide was increased by a substitution of the N‐terminal amino acid of the Rev peptide. These results demonstrate that the peptide stabilizes the functional structure of RNA and suggest that amino acids outside the RNA binding region of the peptide participate in the ATP binding. Our approach would provide a new strategy for the design of tailor‐made ribonucleopeptide receptors. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2004
Molecular design of functional peptides by utilizing unnatural amino acids: Toward artificial and photofunctional protein
Authors: Ishida Hitoshi , Kyakuno Masato , Oishi Shigero 
Published: February 2004

AbstractUnnatural amino acids are effective as building blocks to design functional peptides from the following two points: (1) utilization of rigid unnatural amino acids for the incorporated peptides to control the conformation to appear the function, and (2) incorporation of functional and unnatural amino acids into peptides resulting in appearance of the inherent functions. As a combined strategy, molecular design of artificial metalloproteins utilizing 5′‐amino‐2,2′‐bipyridine‐5‐carboxilic acid (H–5Bpy–OH) as an unnatural amino acid is proposed. The peptide containing three residues of the unnatural amino acid would fold through coordination to a metal ion. In particular, ruthenium(II) ion would yield a ruthenium tris(bipyridine) derivative as the core complex of the artificial protein, which would appear the similar photochemical functions as that of ruthenium(II) tris(bipyridine) complex. The central complex could form two isomers, fac and mer. For selective synthesis of the mer complex, which is expected as the core complex in the artificial protein, dicyclohexylamide as a bulky group is introduced at the C‐terminal of the unnatural amino acid to destabilize the fac complex due to steric hindrance. Furthermore, in order to know the photochemical properties and function of the protein mimics, ruthenium(II) tris(2,2′‐bipyridine) complexes bearing amide groups at 5,5′ positions have been synthesized as the model complexes. As a result, the direction of amide groups (RNHCOor RCONH) in ruthenium complexes is found to significantly affect the emission efficiency: the former reduces the quantum yield and the latter enhances it, respectively. The ruthenium(II) tris(5,5′‐diamide‐2,2′‐bipyridine) complexes are also found to strongly bind with various anions [e.g., halogen ions (Cl−, Br−) and acetate anion] in acetonitrile and to detect these anions through the emission spectral changes under air. The molecular design of artificial protein is expected to develop new fields among peptide, organic, inorganic, and physical chemistry. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2004
Chain‐length dependence of α‐helix to β‐sheet transition in polylysine: Model of protein aggregation studied by temperature‐tuned FTIR spectroscopy
Authors: Dzwolak Wojciech , Muraki Takeshi , Kato Minoru , Taniguchi Yoshihiro 
Published: February 2004

AbstractThe chain‐length dependence of the α‐helix to β‐sheet transition in poly(L‐lysine) is studied by temperature‐tuned FTIR spectroscopy. This study shows that heterogeneous samples of poly(L‐lysine), comprising polypeptide chains with various lengths, undergo the α–β transition at an intermediate temperature compared to homogenous ingredients. This holds true as long as each individual fraction of the polypeptide is capable of adopting an antiparallel β‐sheet structure. The tendency is that the longer chain is, the lower the α–β transition temperature is, which has been linked to the presence of distorted or solvated helices with turns or β sheets in elongating chains of poly(L‐lysine). As such helical structures are apparently conducive to the α–β transition, this draws a comparison to the hypothesis of metastable protein conformational states being a common stage in amyloid‐formation pathways. The antiparallel architecture of the β sheet is likely to reflect the pretransition interhelical interactions in poly(L‐lysine). Namely, the chains are arranged in an antiparallel manner because of energetically favored antiparallel preassembly of dipolar α helices. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004