bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of distant residue contacts with the use of evolutionary information
Authors: Vicatos Spyridon , Reddy Boojala V.B. , Kaznessis Yiannis 
Published: January 2005

AbstractIn this work we present a novel correlated mutations analysis (CMA) method that is significantly more accurate than previously reported CMA methods. Calculation of correlation coefficients is based on physicochemical properties of residues (predictors) and not on substitution matrices. This results in reliable prediction of pairs of residues that are distant in protein sequence but proximal in its three dimensional tertiary structure. Multiple sequence alignments (MSA) containing a sequence of known structure for 127 families from PFAM database have been selected so that all major protein architectures described in CATH classification database are represented. Protein sequences in the selected families were filtered so that only those evolutionarily close to the target protein remain in the MSA. The average accuracy obtained for the alpha beta class of proteins was 26.8% of predicted proximal pairs with average improvement over random accuracy (IOR) of 6.41. Average accuracy is 20.6% for the mainly beta class and 14.4% for the mainly alpha class. The optimum correlation coefficient cutoff (cc cutoff) was found to be around 0.65. The first predictor, which correlates to hydrophobicity, provides the most reliable results. The other two predictors give good predictions which can be used in conjunction to those of the first one. When stricter cc cutoff is chosen, the average accuracy increases significantly (38.76% for alpha beta class), but the trade off is a smaller number of predictions. The use of solvent accessible area estimations for filtering false positives out of the predictions is promising. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Protein classification based on text document classification techniques
Authors: Cheng Betty Yee Man , Carbonell Jaime G. , Klein‐Seetharaman Judith 
Published: January 2005

AbstractThe need for accurate, automated protein classification methods continues to increase as advances in biotechnology uncover new proteins. G‐protein coupled receptors (GPCRs) are a particularly difficult superfamily of proteins to classify due to extreme diversity among its members. Previous comparisons of BLAST, k‐nearest neighbor (k‐NN), hidden markov model (HMM) and support vector machine (SVM) using alignment‐based features have suggested that classifiers at the complexity of SVM are needed to attain high accuracy. Here, analogous to document classification, we applied Decision Tree and Naïve Bayes classifiers with chi‐square feature selection on counts of n‐grams (i.e. short peptide sequences of length n) to this classification task. Using the GPCR dataset and evaluation protocol from the previous study, the Naïve Bayes classifier attained an accuracy of 93.0 and 92.4% in level I and level II subfamily classification respectively, while SVM has a reported accuracy of 88.4 and 86.3%. This is a 39.7 and 44.5% reduction in residual error for level I and level II subfamily classification, respectively. The Decision Tree, while inferior to SVM, outperforms HMM in both level I and level II subfamily classification. For those GPCR families whose profiles are stored in the Protein FAMilies database of alignments and HMMs (PFAM), our method performs comparably to a search against those profiles. Finally, our method can be generalized to other protein families by applying it to the superfamily of nuclear receptors with 94.5, 97.8 and 93.6% accuracy in family, level I and level II subfamily classification respectively. Proteins 2005. © 2005 Wiley‐Liss, Inc.
S‐adenosylhomocysteine hydrolase from the archaeon Pyrococcus furiosus: Biochemical characterization and analysis of protein structure by comparative molecular modeling
Authors: Porcelli Marina , Moretti Maria Angela , Concilio Luigi , Forte Sabrina , Merlino Antonello , Graziano Giuseppe , Cacciapuoti Giovanna 
Published: January 2005

AbstractS‐Adenosylhomocysteine hydrolase (AdoHcyHD) is an ubiquitous enzyme that catalyzes the breakdown of S‐adenosylhomocysteine, a powerful inhibitor of most transmethylation reactions, to adenosine and L‐homocysteine. AdoHcyHD from the hyperthermophilic archaeon Pyrococcus furiosus (PfAdoHcyHD) was cloned, expressed in Escherichia coli, and purified. The enzyme is thermoactive with an optimum temperature of 95°C, and thermostable retaining 100% residual activity after 1 h at 90°C and showing an apparent melting temperature of 98°C. The enzyme is a homotetramer of 190 kDa and contains four cysteine residues per subunit. Thiol groups are not involved in the catalytic process whereas disulfide bond(s) could be present since incubation with 0.8 M dithiothreitol reduces enzyme activity. Multiple sequence alignment of hyperthermophilic AdoHcyHD reveals the presence of two cysteine residues in the N‐terminus of the enzyme conserved only in members of Pyrococcus species, and shows that hyperthermophilic AdoHcyHD lack eight C‐terminal residues, thought to be important for structural and functional properties of the eukaryotic enzyme. The homology‐modeled structure of PfAdoHcyHD shows that Trp220, Tyr181, Tyr184, and Leu185 of each subunit and Ile244 from a different subunit form a network of hydrophobic and aromatic interactions in the central channel formed at the subunits interface. These contacts partially replace the interactions of the C‐terminal tail of the eukaryotic enzyme required for tetramer stability. Moreover, Cys221 and Lys245 substitute for Thr430 and Lys426, respectively, of the human enzyme in NAD‐binding. Interestingly, all these residues are fairly well conserved in hyperthermophilic AdoHcyHDs but not in mesophilic ones, thus suggesting a common adaptation mechanism at high temperatures. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Regional reversion of insecticide resistance in Helicoverpa armigera (Lepidoptera: Noctuidae) is associated with the use of Bt cotton in northern China
Authors: Wu Kongming , Mu Wei , Liang Gemei , Guo Yuyuan 
Published: January 2005

AbstractA continuous programme for monitoring resistance of Helicoverpa armigera (Hübner) to commonly used insecticides was undertaken for assessing the impact of Bt cotton planting on the evolution of the pest resistance from 1994 to 2002 in China. The bioassay results showed that the resistance levels per year in field populations of H armigera to lambda‐cyhalothrin, phoxim and endosulfan decreased, respectively, to 9–15‐fold, 11–14‐fold and 6–8‐fold in 2001–2002 from 197–262‐fold, 52–74‐fold and 18–38‐fold before the cultivation of Bt cotton in 1997. This significant increase in susceptibility to insecticides is expected to result in a reduction in insecticide application for H armigera control in Bt cotton. It is concluded that Bt cotton is playing an important role in the long‐term management of H armigera by increasing the potential for natural and chemical control of the pest. Copyright © 2005 Society of Chemical Industry
Matrix‐assisted ultraviolet laser desorption/ionization time‐of‐flight mass spectrometry of β‐(1 → 3), β‐(1 → 4)‐xylans from Nothogenia fastigiata using nor‐harmane as matrix
Authors: Fukuyama Yuko , Kolender Adriana A. , Nishioka Masae , Nonami Hiroshi , Matulewicz María C. , Erra‐Balsells Rosa , Cerezo Alberto S. 
Published: January 2005

AbstractThree xylan fractions isolated from the red seaweed Nothogenia fastigiata (Nemaliales) were analyzed by ultraviolet matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (UV‐MALDI‐TOFMS). UV‐MALDI‐TOFMS was carried out in the linear and reflectron modes, and as routine in the positive and negative ion modes. Of the several matrices tested, nor‐harmane was the only effective one giving good spectra in the positive ion mode. The number‐average molar masses of two of the fractions, calculated from the distribution profiles, were lower than those determined previously by 1H NMR analysis, suggesting a decrease in the ionization efficiency with increasing molecular weight; weight‐average molar mass and polydispersity index were also determined. As the xylans retained small but significant quantities of calcium salts, the influence of added Ca2+ as CaCl2 on UV‐MALDI‐MS was investigated. The simultaneous addition of sodium chloride and calcium chloride was also analyzed. Addition of sodium chloride did not change the distribution profile of the native sample showing that the inhibitory effect is due to Ca2+ and not to Cl−. Addition of calcium chloride with 1:1 analyte/salt molar ratio gave spectra with less efficient desorption/ionization of oligomers; the signals of these oligomers were completely suppressed when the addition of the salt became massive (1:100 analyte/salt molar ratio). Copyright © 2005 John Wiley & Sons, Ltd.
The inactivation of phospholipase A2 by scalaradial: a biomimetic study by electrospray mass spectrometry
Authors: Monti Maria Chiara , Casapullo Agostino , Riccio Raffaele , Gomez‐Paloma Luigi 
Published: January 2005

AbstractA biomimetic approach was employed to shed light on the nature of chemical reactions occurring in the covalent inactivation of phospholipase A2 (PLA2) by scalaradial (1), a marine dialdehyde terpenoid endowed with potent anti‐inflammatory activity. To this end, a detailed study of the reaction profile between the nitrogenous nucleophile isopropylamine and scalaradial was performed under biologically relevant conditions. Copyright © 2005 John Wiley & Sons, Ltd.
Pro‐oxidant action of phloxine B on fission yeast Schizosaccharomyces pombe
Authors: Mutoh Norihiro , Kawabata Masao , Nakagawa Chiaki W. , Kitajima Satoko 
Published: January 2005

AbstractA Schizosaccharomyces pombe mutant deficient in Cu,Zn‐superoxide dismutase (sod1 mutant) was hypersensitive to phloxine B, which is used as a food‐colouring agent and also to distinguish diploid strains of Sz. pombe from haploid strains, under illumination with light. The pro‐oxidant nature of phloxine B was confirmed biochemically. The carbonyl content of proteins (which represents protein oxidation) increased, and the reduced form of glutathione was transiently decreased by phloxine B treatment under illumination with light. When cells were treated with phloxine B under light, carbonyl content of proteins in the sod1 mutant was greater than that in the wild‐type and amount of glutathione was much decreased in the sod1 mutant compared with the wild‐type. Genes induced by oxidative stress were induced by phloxine B under illumination with light and some were induced by phloxine B without light. Copyright © 2005 John Wiley & Sons, Ltd.
A new mutation in the yeast aspartate kinase induces threonine accumulation in a temperature‐regulated way
Authors: Velasco I. , Arévalo‐Rodríguez M. , Marina P. , Calderón I. L. 
Published: January 2005

AbstractIn Saccharomyces cerevisiae, aspartate kinase (the HOM3 product) regulates the metabolic flux through the threonine biosynthetic pathway through feedback inhibition by the end product. In order to obtain a strain able to produce threonine in a controlled way, we have isolated a mutant allele (HOM3‐ts31d) that gives rise to a deregulated aspartate kinase. This allele has been isolated as an extragenic suppressor of ilv1, which confers an Ilv+ phenotype at 37 °C but not at 22 °C. We have stated that at high temperature the mutant aspartate kinase is slightly more deregulated and shows a higher specific activity, inducing threonine accumulation. The HOM3‐ts31d allele carries a mutation that leads to a Ser399 → Phe substitution in the postulated regulatory region of the enzyme. We have detected other changes in the nucleotide sequence but they are also present in the parental strain, reflecting the genetic differences between different wild‐type strains. A sequence comparison among all the reported mutant aspartate kinases suggests that not all residues involved in regulation of the activity are clustered in the so‐called regulatory domain, as is the case of that mutated in AK‐R7, another deregulated aspartate kinase obtained with the same strategy of ilv1 suppression. Copyright © 2005 John Wiley & Sons, Ltd.
Influence of low glycolytic activities in gcr1 and gcr2 mutants on the expression of other metabolic pathway genes in Saccharomyces cerevisiae
Authors: Sasaki Hiromi , Uemura Hiroshi 
Published: January 2005

AbstractA complex of the transcription factors Gcr1p and Gcr2p coordinately regulates the expression of glycolytic genes in Saccharomyces cerevisiae. To understand the effects of gcr mutations on other metabolic pathways, genome‐wide gene expression profiles in gcr1 and gcr2 mutants were examined. The biggest effects of gcr1 and gcr2 mutations were observed on the glycolytic genes and the expressions of most of the glycolytic genes were substantially decreased compared to those in the wild‐type strain in both glucose and glycerol + lactate growth conditions. On the other hand, the expressions of genes encoding the TCA cycle and respiration were increased in gcr mutants when the cells were grown in glucose. RT‐PCR analyses revealed that the expression of SIP4 and HAP5, which are known to affect the expression of some of the gluconeogenic, TCA cycle and respiratory genes, were also increased under this condition. The growth of gcr mutants on glucose was impaired by adding respiration inhibitor antimycin A, whereas the growth of the wild‐type strain was not. The conversion of glucose to biomass was higher and, to the contrary, ethanol yield was lower in the gcr2 mutant compared to those in the wild‐type strain. These results suggest the possibility that the gcr mutants, in which glycolytic activities are low, changed their metabolic patterns under glucose growth condition to enhance the expression of TCA cycle and respiratory genes to produce more energy. Copyright © 2005 John Wiley & Sons, Ltd.
Attitudes toward genetic testing for cystic fibrosis among college students
Authors: Neiger Ran , Abuelo Dianne N. , Passero Mary Ann 
Published: January 2005

AbstractThe knowledge and attitudes of 25 college students toward clinical and genetic aspects of cystic fibrosis (CF) were assessed before and after an 80‐minute presentation about the disease. The students were asked about their plans regarding genetic testing for cystic fibrosis prior to, and during future conceptions. While their knowledge about the disease increased significantly following the lecture, there were no significant changes in their attitudes.
Genetic counselor as a member of an outreach education team
Authors: Schmerler Susan , DeConstanzo Rosemary 
Published: January 2005

AbstractAs part of a program to improve maternal and infant health in New Jersey, the Robert Wood Johnson Foundation has funded seven regional consortia throughout the State. One of the goals of the Northern New Jersey Regional Consortium is to provide a comprehensive educational program for ambulatory care staff. An outreach education team was established that includes a perinatal nurse educator, a neonatal nurse educator, a nutritional counselor and a genetic counselor. Many issues in genetics can be initially addressed by the ambulatory care provider. A good understanding and awareness of the impact of genetic issues in patient care is needed to enhance the ability to recognize patients needing special services. Early assessment of possible risk for developmental disabilities can lead to appropriate comprehensive care and improved pregnancy outcome. Regular in‐service programs, addressing the way heredity contributes to developmental disorders, the latest techniques used in genetics and the available management programs, can be provided. The present study is an evaluation of the effectiveness of the program.
Preconceptional family health evaluation: A regional education program for family planning clients and health professionals
Authors: Lea Dale H. , Gardiner Gale B. , Guttmacher Alan E. 
Published: January 2005

AbstractThe Preconceptional Family Health Evaluation Program was a regional project developed and funded for 2 years by the New England Regional Genetics Group (NERGG) to educate family planning health professionals about genetics, and to offer family planning clients preconceptional identification of genetic and environmental exposure risks. To meet these goals, genetic education was provided on a regional basis to 45 family planning professionals. A self‐administered family health risk questionnaire adaptable to individual family planning settings was developed. Five hundred and twenty‐nine family planning clients voluntarily completed the questionnaire. Cigarette smoking (35%) and alcohol use (57%) were two major categories of risks identified. The Preconceptional Family Health Evaluation Program was well received by all participants and provided an effective means for regional education of family planning health professionals. As a result of the program, state program planners, clinical genetics services, and family planning health professionals developed a strong relationship that will serve future educational and genetic risk screening efforts.
Intraductal Papillary‐mucinous Tumors Arising in Santorini’s Duct: Clinicopathologic Features and the Treatment of Choice
Authors: Hirano Satoshi , Kondo Satoshi , Ambo Yoshiyasu , Tanaka Eiichi , Morikawa Toshiaki , Okushiba Shunichi , Katoh Hiroyuki 
Published: January 2005

AbstractAlmost all reported cases of intraductal papillary‐mucinous tumors of the pancreas (IPMTs) originate from Wirsung’s duct (WD), the main pancreatic duct, or their branches. IPMTs arising from Santorini’s duct (SD) and its branches have rarely been reported. This article presents the clinicopathologic features of IPMTs originating in SD and its branches. Of 36 IPMTs resected in our institution, 5 originated in the region of SD: 3 in SD and 2 from its branches. Both SD and WD were dilated in all cases on radiographic and ultrasonographic studies. The maximum diameter of SD, determined by computed tomography or ultrasonography, was larger than that of WD in all cases. Seven reports of IPMT arising from SD have been published. Four lesions originated from SD and the others from its branches. Overall, 9 of 12 lesions (75%) were considered malignant. In conclusion, the coexistence of an IPMT and a dilated SD suggests an origin in the SD. These tumors have a high malignant potential and should be excised.
Staged Abdominal Repair for Treatment of Moderate to Severe Secondary Peritonitis
Authors: Agalar Fatih , Eroglu Erol , Bulbul Mahmut , Agalar Canan , Tarhan Omar Ridvan , Sari Mustafa 
Published: January 2005

AbstractThe aim of this study was to evaluate the effects of planned relaparotomy and to assess factors that may contribute to mortality in patients with moderate to severe secondary peritonitis. A total of 36 consecutive patients with an Acute Physiologic and Clinical Health Evaluation (APACHE) II score of >10 were enrolled the study for a 2‐year period. The mean age of the patients was 56 years (17‐92 years), and 23% of them were male. One‐third of them had postoperative peritonitis; 152 scheduled operations were done, and the overall mortality rate was 36%. For patients whose septic source was in the upper gastrointestinal system, control of the source was more difficult (p = 0.004). Overall, 28 complications developed in 61% of the patients. Initial and second‐day APACHE II scores were 14.5 (11‐27) and 12.0 (9‐25), respectively. The initial APACHE II score of survivors was lower than that of nonsurvivors [p = 0.0001, 95% confidence interval (CI) ‐9.5, ‐3.6]. Second‐day APACHE II scores were not different (p = 0.19; 95% CI ‐3.79, 0.80). Striking end or lateral duodenal leaks were clearly associated with high mortality. It is found that the initial APACHE II score, the success of controlling the source, the occurrence of complications, and the type of illness are independent factors that may affect mortality. We concluded that staged abdominal repair should be used with caution in the treatment of lateral or end duodenal leaks. It is a good alternative to conventional laparotomy for moderate to severe forms of secondary peritonitis from other sources.
AJCP as a Vehicle for Improving Community Life: An Historic–Analytic Review of the Journal's Contents
Authors: Martin Pamela P. , Lounsbury David W. , Davidson William S. 
Published: January 2005

AbstractThe current article is an analysis of the research represented in American Journal of Community Psychology (AJCP) from 1993 to 1998, including a comparison to two previously published analytic reviews by Lounsbury et al. (J. W. Lounsbury, D. S. Leader, E. P. Meares, & M. P. Cook, 1980) and Speer et al. (P. Speer, A. Dey, P. Griggs, C. Gibson, B. Lubin, & J. Hughey, 1992), respectively. Observed trends are examined with references to major epistemological frameworks and methods used to define community psychology. Four guiding principles were examined to determine the representation of the epistemological frameworks of the articles published in the journal. The frameworks include social action, human diversity and cultural relativity, person–environmental fit, and methodological procedures. The results document the transition of community psychology from its early beginnings to an independent field conducting research consistent with the values articulated at the Swampscott Conference. This paper also comments on how well, after three decades of publication, the journal has served as a vehicle for improving community life.
Crime, Social Capital, and Community Participation
Authors: Saegert Susan , Winkel Gary 
Published: January 2005

AbstractSocial disorganization at the neighborhood and community levels has been consistently linked to various forms of criminal activity. However, a very much smaller body of literature addresses the effects of crime on community organizations. In some studies, crime appears to energize communities while in others, crime leads to withdrawal from community life. Using department of health crime victimization data and interviews with 2,985 low‐income inner city residents living in 487 multi‐family dwellings, a multi‐level model examined the relationships among crime victimization, social organization, and participation in neighborhood organizations. Social organization at the individual and building levels was measured using recent formulations of social capital theory. Findings regarding crime suggested more signs of a chilling effect on participation than of an energizing effect, especially at the building level. Social capital at the building level was more strongly and consistently related to participation in community organizations than was crime.
An Empowerment Evaluation Model for Sexual Assault Programs: Empirical Evidence of Effectiveness
Authors: Campbell Rebecca , Dorey Heather , Naegeli Monika , Grubstein Lori K. , Bennett Kelly K. , Bonter Freya , Smith Patricia K. , Grzywacz Jessica , Baker Patsy K. , Davidson William S. 
Published: January 2005

AbstractUsing an empowerment evaluation approach, the Sexual Assault and Rape Prevention (SARP) Evaluation Project brought together university researchers, public health evaluators, state funders, and program staff to provide evaluation training and consultation to all state‐funded rape prevention and victim services programs in Michigan. In this paper, the specific activities of the SARP project are described, and process and outcome data are presented that address the effectiveness of this empowerment evaluation approach. Based on subjective reports from program staff and objective data obtained from state funders, results suggest that this evaluation model was successful in helping 90% of the prevention programs and 75% of the victim services programs successfully develop and launch program evaluations. One‐year follow‐up data indicate that 90% of the programs had sustained their evaluation efforts after the formal work of the SARP project had ended.