bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morphology of polyanhydride copolymers: Time‐resolved small‐angle X‐ray scattering studies of crystallization
Authors: Kipper Matt J. , Seifert Soenke , Thiyagarajan P. , Narasimhan Balaji 
Published: January 2005

AbstractSynchrotron small‐angle X‐ray scattering (SAXS) was used to study the isothermal crystallization kinetics of a family of polyanhydride copolymers consisting of 1,6‐bis(p‐carboxyphenoxy)hexane and sebacic acid monomers. In situ SAXS experiments permitted the direct observation of the crystallization kinetics. The structural parameters (the long period, lamellar thickness, and degree of crystallinity) were obtained from Lorentz‐corrected intensity profiles, one‐dimensional correlation functions, and interface distribution functions to form a comprehensive picture of the crystal morphology. The combination of these three analyses provided information not only on the lamellar dimensions but also on the polydispersity (nonuniformity) of these dimensions. Where possible, the crystallization kinetics were interpreted with a modified version of the Avrami equation. The results can be used to perform the rational design of controlled‐drug‐release formulations because crystallinity affects drug‐release kinetics. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 463–477, 2005
Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology
Authors: Ponomarenko Julia V. , Bourne Philip E. , Shindyalov Ilya N. 
Published: January 2005

AbstractAccompanying the discovery of an increasing number of proteins, there is the need to provide functional annotation that is both highly accurate and consistent. The Gene Ontology™ (GO) provides consistent annotation in a computer readable and usable form; hence, GO annotation (GOA) has been assigned to a large number of protein sequences based on direct experimental evidence and through inference determined by sequence homology. Here we show that this annotation can be extended and corrected for cases where protein structures are available. Specifically, using the Combinatorial Extension (CE) algorithm for structure comparison, we extend the protein annotation currently provided by GOA at the European Bioinformatics Institute (EBI) to further describe the contents of the Protein Data Bank (PDB). Specific cases of biologically interesting annotations derived by this method are given. Given that the relationship between sequence, structure, and function is complicated, we explore the impact of this relationship on assigning GOA. The effect of superfolds (folds with many functions) is considered and, by comparison to the Structural Classification of Proteins (SCOP), the individual effects of family, superfamily, and fold. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Crystal structure of the ferredoxin component of carbazole 1,9a‐dioxygenase of Pseudomonas resinovorans strain CA10, a novel Rieske non‐heme iron oxygenase system
Authors: Nam Jeong‐Won , Noguchi Haruko , Fujimoto Zui , Mizuno Hiroshi , Ashikawa Yuji , Abo Mitsuru , Fushinobu Shinya , Kobashi Nobuyuki , Wakagi Takayoshi , Iwata Kenichi , Yoshida Takako , Habe Hiroshi , Yamane Hisakazu , Omori Toshio , Nojiri Hideaki 
Published: January 2005

AbstractThe carbazole 1,9a‐dioxygenase (CARDO) system of Pseudomonas resinovorans strain CA10 catalyzes the dioxygenation of carbazole; the 9aC carbon bonds to a nitrogen atom and its adjacent 1C carbon as the initial reaction in the mineralization pathway. The CARDO system is composed of ferredoxin reductase (CarAd), ferredoxin (CarAc), and terminal oxygenase (CarAa). CarAc acts as a mediator in the electron transfer from CarAd to CarAa. To understand the structural basis of the protein–protein interactions during electron transport in the CARDO system, the crystal structure of CarAc was determined at 1.9 Å resolution by molecular replacement using the structure of BphF, the biphenyl 2,3‐dioxygenase ferredoxin from Burkholderia cepacia strain LB400 as a search model. CarAc is composed of three β‐sheets, and the structure can be divided into two domains, a cluster‐binding domain and a basal domain. The Rieske [2Fe–2S] cluster is located at the tip of the cluster‐binding domain, where it is exposed to solvent. While the overall folding of CarAc and BphF is strongly conserved, the properties of their surfaces are very different from each other. The structure of the cluster‐binding domain of CarAc is more compact and protruding than that of BphF, and the distribution of electric charge on its molecular surface is very different. Such differences are thought to explain why these ferredoxins can act as electron mediators in respective electron transport chains composed of different‐featured components. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Prediction of protein B‐factor profiles
Authors: Yuan Zheng , Bailey Timothy L. , Teasdale Rohan D. 
Published: January 2005

AbstractThe polypeptide backbones and side chains of proteins are constantly moving due to thermal motion and the kinetic energy of the atoms. The B‐factors of protein crystal structures reflect the fluctuation of atoms about their average positions and provide important information about protein dynamics. Computational approaches to predict thermal motion are useful for analyzing the dynamic properties of proteins with unknown structures. In this article, we utilize a novel support vector regression (SVR) approach to predict the B‐factor distribution (B‐factor profile) of a protein from its sequence. We explore schemes for encoding sequences and various settings for the parameters used in SVR. Based on a large dataset of high‐resolution proteins, our method predicts the B‐factor distribution with a Pearson correlation coefficient (CC) of 0.53. In addition, our method predicts the B‐factor profile with a CC of at least 0.56 for more than half of the proteins. Our method also performs well for classifying residues (rigid vs. flexible). For almost all predicted B‐factor thresholds, prediction accuracies (percent of correctly predicted residues) are greater than 70%. These results exceed the best results of other sequence‐based prediction methods. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Simulation of pesticide leaching in a cracking clay soil with the PEARL model
Authors: Scorza Júnior Rômulo P , Boesten Jos JTI 
Published: January 2005

AbstractTesting of pesticide leaching models is important to increase confidence in their use in pesticide registration procedures world‐wide. The chromatographic PEARL model was tested against the results of a field leaching study on a cracking clay soil with a tracer (bromide), a mobile pesticide (bentazone) and a moderately sorbing, persistent pesticide (imidacloprid). Input parameters for water flow and solute transport were obtained from site‐specific measurements and from literature. The model was tested using a stepwise approach in which each sub‐model was sequentially and separately tested. Uncalibrated simulations for the water flow resulted in moisture profiles that were too wet. Calibration of the hydraulic relationships resulted in a good description of the moisture profiles. Calibration of the dispersion length was necessary to obtain a good description of bromide leaching. The calibrated dispersion length was 61 cm, which is very long and indicates a large non‐uniformity of solute transport. The half‐life of bentazone had to be calibrated to obtain a good description of its field persistence. The calibrated half‐life was 2.5 times shorter than the half‐life derived from the laboratory studies. Concentrations of bentazone in drain water and groundwater were described reasonably well by PEARL. Although measured and simulated persistence of imidacloprid in soil corresponded well, the bulk of the imidacloprid movement was overestimated by PEARL. However, imidacloprid concentrations in drain water were underestimated. In spite of the extensive calibration of water flow and tracer movement, the behaviour of the moderately sorbing pesticide imidacloprid could not be simulated. This indicates that the convection–dispersion equation cannot be used for accurate simulation of pesticide transport in cracking clay soils (even if extremely long dispersion length is used). Comparison of the model results from a poorly sorbed chemical (bentazone) and a moderately sorbed chemical (imidacloprid) were useful in defining the limitations of using a chromatographic flow model to simulate the effects of preferential flow. Copyright © 2005 Society of Chemical Industry
Development of a method for simultaneous determination of eflucimibe and its three major metabolites in rat plasma by liquid chromatography/electrospray tandem mass spectrometry: a preliminary study
Authors: Mesplet Nathalie , Morin Philippe , Ribet Jean‐Paul 
Published: January 2005

AbstractA high‐performance liquid chromatography/electrospray ionisation tandem mass spectrometry (HPLC/ESI‐MS/MS) method has been developed for the simultaneous determination of eflucimibe, a powerful acyl‐coenzyme A cholesterol O‐acyltransferase (ACAT) inhibitor, and its main metabolites, in plasma. The ESI and MS/MS parameters were investigated and optimised for each of the four compounds in the positive ion mode. Plasma samples were deproteinised by precipitation with acetonitrile and directly analysed by HPLC/ESI‐MS/MS in less than 4 min. Quantitation was performed in the multiple reaction monitoring (MRM) mode for highest sensitivity, selecting the protonated molecules [M+H]+ as precursor ions. The method was demonstrated to be specific and sensitive, and a linear response was observed within a 1–25 ng/mL concentration range. Correlation coefficients (r2) greater than 0.9960 were obtained by least‐squares regression, and limits of detection down to 0.2 ng/mL were calculated. Therefore, this HPLC/ESI‐MS/MS method appears to be an efficient tool, able to provide valuable information for a pharmacological purpose. Copyright © 2005 John Wiley & Sons, Ltd.
Determination of lincomycin and tylosin residues in honey by liquid chromatography/tandem mass spectrometry
Authors: Thompson Thomas S. , Noot Donald K. , Calvert Jane , Pernal Stephen F. 
Published: January 2005

AbstractA simple and rapid analytical method was developed for the determination of lincomycin and tylosin residues in honey as part of field studies examining the efficacy and target animal safety of these antibiotics to control American foulbrood disease in honey bees. Residues of the antibiotics were determined using liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI‐MS/MS). Honey samples were diluted and injected directly into the LC/MS/MS system without additional cleanup by solid‐phase extraction or liquid‐liquid partitioning. A six‐port valve system was utilized to selectively route eluant from the LC column into the mass spectrometer only during a relatively short portion of the chromatographic run corresponding to the elution of the analytes of interest. Minimal contamination of the MS source chamber was observed despite the analysis of large numbers of samples. Using internal standard quantitation, excellent accuracy and precision were obtained with no apparent matrix‐to‐matrix variation. Based on the analysis of fortified replicates, the mean percent deviation from the theoretical concentration and the percent relative standard deviation were both less than 10% for tylosin over an analytical range of 10–1000 μg/kg. Slightly higher mean percent deviations and relative standard deviations were observed for the analysis of lincomycin in fortified replicate samples. The method detection limits were determined to be 5 and 2 μg/kg for lincomycin and tylosin, respectively. Copyright © 2005 John Wiley & Sons, Ltd.
Hydropyrolysis as a preparative method for the compound‐specific carbon isotope analysis of fatty acids
Authors: Sephton Mark A. , Meredith Will , Sun Cheng‐Gong , Snape Colin E. 
Published: January 2005

AbstractCompound‐specific stable carbon isotope analysis by gas chromatography/combustion/isotope ratio mass spectrometry is an effective and risk‐free means of investigating fatty acid metabolism. Straightforward analysis, however, leads to poor chromatographic resolution, while derivatization adds carbon thereby corrupting the starting stable isotopic composition. Hydropyrolysis is a new approach which defunctionalizes fatty acids to yield the corresponding n‐alkanes thus retaining the carbon skeleton intact and improving chromatography, allowing the faithful measurement of carbon isotope ratios. Copyright © 2005 John Wiley & Sons, Ltd.
Genome‐wide survey of non‐essential genes required for slowed DNA synthesis‐induced filamentous growth in yeast
Authors: Kang Christopher Minkyu , Jiang Yi Wei 
Published: January 2005

AbstractWe recently discovered that slowed DNA synthesis induces filamentous differentiation in S. cerevisiae. We screened the BY yeast deletion strains and identified four classes of non‐essential genes that are required for both slowed DNA‐induced filamentous growth and classic forms of filamentous growth: (a) genes encoding regulators of the actin cytoskeleton and cell polarity, ABP1, CAP2 and HUF1 (= YOR300W), in addition to the previously known BNI1, BUD2, PEA2, SPA2 and TPM1; (b) genes that are likely involved in cell wall biosynthesis, ECM25, GAS1 and PRS3; (c) genes encoding possible regulators of protein secretion, SEC66, RPL21A and RPL34B; (d) genes encoding factors for normal mitochondrial function, IML1 and UGO1. These results showed that pseudohyphal formation involves not the only previously known regulation of the actin cytoskeleton/cell polarity but also regulation of cell wall synthesis, protein secretion and mitochondrial function. Identification of multiple classes of genes that are required for both slowed DNA synthesis‐induced and classic forms of filamentous growth confirms that slowed DNA synthesis‐induced filamentous growth is bone fide filamentous differentiation. Copyright © 2005 John Wiley & Sons, Ltd.
Involvement of actin and polarisome in morphological change during spore germination of Saccharomyces cerevisiae
Authors: Kono Keiko , Matsunaga Rino , Hirata Aiko , Suzuki Genjiro , Abe Mitsuhiro , Ohya Yoshikazu 
Published: January 2005

AbstractWe studied the morphological changes of Saccharomyces cerevisiae ascospores during germination. Initiation of germination is followed by polarization of actin patches, maintaining their localization to the site of cell surface growth. Loss of polarisome components, Spa2p, Pea2p, Bud6p or Bni1p, results in depolarization of actin patches. Green fluorescent protein‐fused polarisome components exhibit the polarized localization, implying that polarisome is involved in the polarized outgrowth during germination. At the late stage of germination, we found that actin patches temporally depolarize before bud emergence. The observation that loss of Cla4p extends the polarized growth period suggests that Cla4p is involved in the actin‐depolization step. Actin polarization in the initial stage is accelerated by overexpression of Ras2p, whereas hyperpolarization is continuously observed by overexpression of Rho1p. Thus, yeast spore germination is a morphological event that is regulated by a number of factors implicated in mitotic bud morphogenesis. Copyright © 2005 John Wiley & Sons, Ltd.
SKG1, a suppressor gene of synthetic lethality of kex2Δgas1Δ mutations, encodes a novel membrane protein that affects cell wall composition
Authors: Tomishige Nario , Noda Yoichi , Adachi Hiroyuki , Shimoi Hitoshi , Yoda Koji 
Published: January 2005

AbstractThe fungal GAS1‐related genes encode GPI‐anchored β‐1,3‐glucanosyltransferase, and their loss causes a defect in the assembly of the cell wall. The KEX2 gene encodes a processing protease in the late Golgi compartment and its loss also results in defects in the cell wall. Simultaneous mutations of these genes are lethal in Saccharomyces cerevisiae. To understand the basis of this synthetic lethality, we screened for multicopy suppressors and identified 13 SKG (suppressor of kex2 gas1 synthetic lethality) genes. SKG1 encodes a transmembrane protein that localizes on the inner surface of the plasma membrane at the bud and in the daughter cell. The multicopy SKG1 increases the sensitivity of cells to zymolyase, and the skg1Δ null mutation increases resistance to it. This zymolyase susceptibility corresponds to an increase of alkali‐soluble β‐1,3‐glucan and a decrease of chitin in the cell wall. Thus SKG1 encodes a novel protein that affects the cell wall polymer composition in the growing region of the cell. Copyright © 2005 John Wiley & Sons, Ltd.
Reproductive issues in adults with cystic fibrosis: Implications for genetic counseling
Authors: Lemke Amy 
Published: January 2005

AbstractThis article reviews reproductive issues faced by the growing number of individuals with cystic fibrosis (CF) who reach adulthood. Approximately 97–98% of males with CF are infertile and they may have an increased risk for genitourinary anomalies. Females with CF may experience delayed puberty, irregular menstrual cycles, and decreased fertility. Women with CF who have good clinical scores, good nutritional status, and normal lung volumes with mild to moderate airway obstruction, have a better chance for successful pregnancies. The role of the genetic counselor in counseling adults with CF is discussed and resources for CF adults are provided.
The twisted helix: An essay on genetic counselors, eugenics, and social responsibility
Authors: Resta Robert G. 
Published: January 2005

AbstractThe American eugenics movement had a significant impact on American social history, and analysis of the movement illustrates the relationship among science, scientists, and society. The history of the American eugenics movement as well as more recent examples of eugenic thought and biological determinism are reviewed. The need for genetic counselors to confront eugenic issues in their own profession and in society is discussed.
The utilization of genetic counselors within a newborn screening program
Authors: Bach Janice , Baker Diane , Naber John , Young William 
Published: January 2005

AbstractGenetic counselors have participated in the Michigan Newborn Screening Program on a contractual basis since 1988. Their role includes newborn screening education and training, newborn nursery site visits, and monitoring newborn screening in hospitals. Their impact has been to improve the quality of newborn screening services by reducing errors and increasing completion of data fields on newborn screening cards, improving hospital nursery cooperation and problem solving, and enhancing health department response to specific problems.
An educational program to overcome language and cultural barriers to genetic services
Authors: Dixson Barbara , Dang Vi , Cleveland James O. , Peterson Raymond M. 
Published: January 2005

AbstractProviding genetic services to families who do not speak English and whose cultures are quite diverse presents a unique challenge to genetic specialists. One approach that is being employed successfully is the use of specially trained genetic assistants to provide outreach, case finding, referral, support, interpretation, advocacy, and follow‐up counseling. A basic genetic assistant training program for five bicultural/bilingual Southeast Asian case managers is described. The course syllabus can be used to train health workers who represent a variety of cultures and languages.
Social Support Mediates the Effects of Dual‐Focus Mutual Aid Groups on Abstinence from Substance Use
Authors: Laudet Alexandre B. , Cleland Charles M. , Magura Stephen , Vogel Howard S. , Knight Edward L. 
Published: January 2005

AbstractBackground: Specialized 12‐step based groups have emerged to address the needs of persons recovering from both substance abuse and psychiatric illness. Objective: This study investigates the role of social support in mediating the association between mutual aid participation and subsequent substance use for dually diagnosed persons. Method: A cohort of Double Trouble in Recovery (DTR) members in New York City were studied prospectively over a two‐year period. Findings: Longer DTR participation during the first year of the study was associated with lower substance use in the second year; that effect was partially explained by the maintenance of high level of social support. Conclusion: These findings speak of the enduring influence of 12‐step attendance on reducing substance use, and underline the importance of both 12‐step attendance and supportive networks for dually diagnosed persons.
The Contributions of Community, Family, and School Variables to Student Victimization
Authors: Khoury-Kassabri Mona , Benbenishty Rami , Avi Astor Ron , Zeira Anat 
Published: January 2005

AbstractAn ecological perspective was used to predict school violence from a number of variables describing the students and their families based on nationally representative sample of 10,400 students in grades 7–11 in 162 schools across Israel. Self‐administered anonymous questionnaires that included a scale for reporting victimization by serious and moderate physical violence, threats, and verbal–social victimization were filled out during class. Hierarchical linear modeling (HLM) examined the relationships between students’ reports of victimization and student level variables (gender, age) and the school‐level variables—cultural affiliation (Jewish vs. Arab), the socio‐economic status (SES) of the school's neighborhood and students’ families, school and class size, school level (junior high vs. high), and school climate. Variance between schools accounted for 9–15% of the variance in student victimization (major factors being school climate characteristics and percent of boys at the school). Boys reported higher victimization than girls for all forms of school violence. Students in junior high schools reported more victimization than high school students. Higher levels of victimization were reported in overcrowded classes, while school size was not associated with students’ reports of victimization. Although there were almost no differences between Jewish and Arab schools in students’ reports of victimization, the SES of the school's neighborhood and students did have a moderate effect. The discussion highlights the importance of improving school climate and the need to allocate more resources to schools in low SES contexts in order to protect students from school violence.
The Relationship Between Perceptions of Neighborhood Characteristics and Substance Use Among Urban African American Adolescents
Authors: Lambert Sharon F. , Brown Tamara L. , Phillips Clarenda M. , Ialongo Nicholas S. 
Published: January 2005

AbstractAlthough the neighborhood microsystem is recognized as an important domain for adolescent development, relative to the family and peer contexts, neighborhood factors have been understudied in relation to adolescent substance abuse. In addition, recent research suggests that risk factors for adolescent substance use may differ for African Americans when compared to Caucasian youth. This study investigated the association between perceived neighborhood disorganization and later substance use, as well as possible mediators of that association, among a community sample of urban African American adolescents. Perceptions of neighborhood disorganization (i.e., violence/safety and drug activity) in grade 7 were associated with increased tobacco, alcohol, and marijuana use in grade 9. For females, this association was mediated by attitudes about drug use and perceptions of drug harmfulness. Findings highlight the importance of neighborhood contextual variables for African American substance use. Implications and directions for future research are presented.