bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasma phenylalanine is asociated with decreased serum ubiquine‐10 concentrations in phenylketonuria
Authors: Artuch R. , Colomé C. , Vilaseca M. A. , Sierra C. , Cambra F. J. , Lambruschini N. , Campistol J. 
Published: December 2002

AbstractDecreased serum ubiquinone‐10 concentrations is a common condition in patients with phenylketonuria (PKU) under dietary treatment. Our aim was to investigate the implication of the metabolic abnormalities of PKU (low concentrations of tyrosine and high concentrations of phenylalanine) and the effect of treatment with phenylalanine‐restricted diets in decreased ubiquinone‐10 concentrations in PKU patients. We studied 30 PKU patients (age range 5 months to 35 years; median age 7 years) under dietary treatment. Correlation between plasma tyrosine or phenylalanine and serum ubiquinone‐10 concentrations was investigated. Daily cholesterol intake was caulculated from the data obtained through a dietary questionnaire. The index of dietary control (IDC) was calculated as the average of the medians of plasma phenylalanine concentrations obtained every 6 months in the metabolic control of patients. Negative correlations were observed between serum ubiquinone and the IDC (r=−0.46; p<0.01) in PKU patients. No correlation was observed between tyrosine or daily cholesterol intake by multiple linear regression analysis, for each 113 units of increase in IDC values serum ubiquinone decreased 0.1 µmol/L. According to our results, the main factor associated with the decreased serum ubiquinone concentrations was high plasma phenylalanine values. Although daily cholesterol intake seems to be associated with ubiquinone concentrations, it may not be relevant if we take into account the low intake of cholesterol in treated PKU patients.
Effect of timing of critical incident stress debriefing (CISD) on posttraumatic symptoms
Authors: Campfield Kerrianne M. , Hills Adelma M. 
Published: December 2002

AbstractSeventy‐seven civilian employees who were victims of robbery were randomly assigned to either an immediate (< 10 hr) or delayed (> 48 hr) debriefing group, using the J. Mitchell (1983) CISD protocol. Scores on the Posttraumatic Stress Diagnostic Scale were obtained at 4 time intervals: debrief, 2 and 4 days post‐debrief, and 2 weeks postrobbery. The number and severity of symptoms did not differ at debrief, but were lower for the immediate than for the delayed group at each subsequent time interval. The number and severity of symptoms declined across time intervals; however, although this reduction was pronounced for the immediate group it was minimal for the delayed group. The results supported use of immediate debriefing with this type of incident and victim.
Sleep difficulties and alcohol use motives in female rape victims with posttraumatic stress disorder
Authors: Nishith Pallavi , Resick Patricia A. , Mueser Kim T. 
Published: December 2002

AbstractThe purpose of this study was to assess the relationship between sleep difficulties and drinking motives in female rape victims with posttraumatic stress disorder (PTSD). Seventy‐four participants were assessed for PTSD symptoms, depression, sleep difficulties, and drinking motives. Results demonstrated that neither PTSD symptoms nor depression were related to any motives for using alcohol. On the other hand, after controlling for education, sleep difficulties were significantly related to drinking motives for coping with negative affect, but not pleasure enhancement or socialization. The findings suggest that sleep difficulties may be an important factor contributing to alcohol use in rape victims with PTSD.
Genetic and environmental influences on the relationship among combat exposure, posttraumatic stress disorder symptoms, and alcohol use
Authors: McLeod D. Scott , Koenen Karestan C. , Meyer Joanne M. , Lyons Michael J. , Eisen Seth , True William , Goldberg Jack 
Published: December 2002

AbstractThe role of genetic and environmental influences on the relationship between combat exposure, posttraumatic stress disorder (PTSD) symptoms, and alcohol use were examined in 4072 male—male twin pairs who served in the United States military during the Vietnam era (1965–1975). Results indicate that the relationship between combat and alcohol use and between PTSD symptom factors and alcohol use were both substantially influenced by genetic factors. Findings are most consistent with a shared vulnerability model for the etiology of the association between PTSD symptoms and alcohol use. Specific unique environmental factors were more important than genetic factors for PTSD symptoms, and both factors were equally important for alcohol use. Further support is also found for the role of the unique environment in PTSD symptoms.
Sertraline, Paroxetine, and Venlafaxine in refugee posttraumatic stress disorder with depression symptoms
Authors: Smajkic Amer , Weine Stevan , Djuric‐Bijedic Zvezdana , Boskailo Esad , Lewis Jonathan , Pavkovic Ivan 
Published: December 2002

AbstractThree new antidepressants were used in treating posttraumatic stress disorder (PTSD) and symptoms of depression in Bosnian refugees. Thirty‐two Bosnian refugees seeking treatment at a mental health clinic participated in a case series study. All received open trials of Sertraline (n = 15), Paroxetine (n = 12), or Venlafaxine (n = 5), with standard clinical doses. Overall, Sertraline and Paroxetine produced statistically significant improvement at 6 weeks in PTSD symptom severity, in depression, and in Global Assessment of Functioning. Venlafaxine produced improvement in PTSD symptom severity and in Global Assessment of Functioning did not yield improvement in symptoms of major depressive disorder, and had a high rate of side effects. Notwithstanding improvement of symptoms, all 32 refugees remained PTSD positive at the diagnostic level at the 6‐week follow‐up.
Enzyme replacement therapy in Fabry disease
Authors: Brady R. O. , Murray G. J. , Moore D. F. , Schiffmann R. 
Published: December 2002

AbstractRecent clinical trials have demonstrated that enzyme replacement therapy with α‐galactosidase A (α‐Gal A) constitutes a major clinical advance in the treatment of patients with Fabry disease. This new therapeutic approach has been shown to be well tolerated and effective in reducing levels of the storage product globo‐triaosylceramide and in normalizing many of the debilitating manifestations of the disorder. A double‐blind placebo‐controlled trial in 26 hemizygous male patients showed that agalsidase alfa (human α‐Gal A) significantly reduced neuropathic pain (p= 0.02), increased creatinine clearance (p = 0.02), improved glomerular histology, reduced the QRS interval on electrocardiography and increased weight gain. Positron emission tomography also revealed normalization of cerebrovascular flow. After the 6‐month controlled period, all patients were given agalsidase alfa for a further12 months. At the end of this period, all patients had a decrease in neuropathic pain, and there was a significant improvement in their ability to sense heat and cold. In addition, renal function stabilized, even in patients with renal insufficiency at the onset of treatment, and patients reported a normalization of sweating and improvements in their level of energy and sense of well‐being. These findings show that enzyme replacement therapy offers promise as an effective management strategy for patients with Fabry disease.
Clinically relevant therapeutic endpoints in type I Gaucher disease
Authors: Hollak C. E. M. , Maas M. , Aerts J. M. 
Published: December 2002

AbstractThe introduction of enzyme supplementation therapy for Gaucherdisease has had a great impact on the lives of many patients. Organomegaly, cytopenia and bone disease have been shown to improve in response to treatment, resulting in an improvement in quality of life. However, the assessment of organ system involvement is not always done in such a way that the relationship with clinically relevant endpoints is clear. The lack of adequately validated methods of assessment, especially for bone disease, has hindered the establishment of treatment goals and guidelines for treatment optimization.
Multidimensional Profiles of Welfare and Work Dynamics: Development, Validation, and Associations with Child Cognitive and Mental Health Outcomes
Authors: Yoshikawa Hirokazu , Seidman Edward 
Published: December 2002

AbstractThis prospective longitudinal study addresses the research gap in the literature regarding multidimensional variation in welfare use and employment patterns, and relationships of such variation with parent earnings and child development outcomes. This study also aims to address the limitations of welfare dynamics studies that do not examine how multiple dimensions of welfare receipt and employment co‐occur. Cluster analysis was utilized, using monthly welfare and employment data from the National Longitudinal Survey of Youth, to examine variation within the welfare population in their welfare and work patterns across the first 5 years of children's lives. Six cluster profiles of welfare and work dynamics were found: Short‐Term, Short‐Term Work Exit, Working Cyclers, Nonworking Cyclers, Cycle to Long‐Term Exit, and Long‐Term. The clusters were validated using mother's 6th‐year earnings as the criterion. The clusters' associations with child development outcomes in the cognitive and mental health domains (at ages 6 and 7) were then explored. Work following short‐term welfare use was associated with higher child reading scores than that following long‐term use (a moderate‐size effect). Cycling on and off welfare in the context of high levels of employment was associated with higher child internalizing symptoms than cycling accompanied by low levels of employment (a moderate‐size effect). Implications for evaluation of TANF welfare‐to‐work policies are discussed.
Search for structural similarity in proteins
Authors: Leluk Jacek , Konieczny Leszek , Roterman Irena 
Published: December 2002

Abstract
Motivation: The expanding protein sequence and structure databases await methods allowing rapid similarity search. Geometric parameters—dihedral angle between two sequential peptide bond planes (V) and radius of curvature (R) as they appear in pentapeptide fragments in polypeptide chains—are proposed for use in evaluating structural similarity in proteins (VeaR). The parabolic (empirical) function expressing the radius of curvature’s dependence on the V-angle in model polypeptides is altered in real proteins in a form characteristic for a particular protein. This can be used as a criterion for judging similarity.
Results: A structural comparison of proteins representing a wide spectrum of structures was assessed versus sequence similarity analysis based on the genetic semihomology algorithm. The term ‘consensus structure’, analogous to ‘consensus sequence’, was introduced for the serpine family.
Availability: Semihom—sequence comparison freely available on request from J. Leluk. VeaR—structural comparison freely available on request from I. Roterman.
Contact: lulu@bf.uni.wroc.pl for SEMIHOM program myroterm@cyf-kr.edu.pl for VeaR program.
* To whom correspondence should be addressed.
MAVG: locating non-overlapping maximum average segments
in a given sequence
Authors: Lin Yaw-Ling , Huang Xiaoqiu , Jiang Tao , Chao Kun-Mao 
Published: December 2002

Abstract
Summary: MAVG is a software tool for finding k non-overlapping maximum-average segments that are sufficiently long in a given sequence of real numbers, for any k &gt; 0. It has applications in several areas of biomolecular sequence analysis including locating GC-rich regions and CpG islands in a genomic sequence, and annotating multiple sequence alignments.
Availability: http://iubio.bio.indiana.edu/soft/molbio/pattern/cpg_islands/
Contact: kmchao@csie.ntu.edu.tw
* To whom correspondence should be addressed.
Microarray data assembler
Authors: Anbazhagan Ramswamy 
Published: December 2002

Abstract
Summary: Large volumes of microarray data are generated and deposited in public databases. Most of this data is in the form of tab-delimited text files or Excel spreadsheets. Combining data from several of these files to reanalyze these data sets is time consuming. Microarray Data Assembler is specifically designed to simplify this task. The program can list files and data sources, convert selected text files into Excel files and assemble data across multiple Excel worksheets and workbooks. This program thus makes data assembling easy, saves time and helps avoid manual error.
Availability: The program is freely available for non-profit use, via email request from the author, after signing a Material Transfer Agreement with Johns Hopkins University.
Contact: anba@jhmi.edu
* To whom correspondence should be addressed.
Analysis of whole-genome microarray replicates using mixed models
Authors: Wernisch Lorenz , Kendall Sharon L. , Soneji Shamit , Wietzorrek Andreas , Parish Tanya , Hinds Jason , Butcher Philip D. , Stoker Neil G. 
Published: December 2002

Abstract
Motivation: Microarray experiments are inherently noisy. Replication is the key to estimating realistic fold-changes despite such noise. In the analysis of the various sources of noise the dependency structure of the replication needs to be taken into account.
Results: We analyzed replicate data sets from a Mycobacterium tuberculosis trcS mutant in order to identify differentially expressed genes and suggest new methods for filtering and normalizing raw array data and for imputing missing values. Mixed ANOVA models are applied to quantify the various sources of error. Such analysis also allows us to determine the optimal number of samples and arrays. Significance values for differential expression are obtained by a hierarchical bootstrapping scheme on scaled residuals. Four highly upregulated genes, including bfrB, were analyzed further. We observed an artefact, where transcriptional readthrough from these genes led to apparent upregulation of adjacent genes.
Availability: All methods and data discussed are available in the package YASMAhttp://www.cryst.bbk.ac.uk/wernisch/yasma.html for the statistical data analysis system R (http://www.R-project.org).
Contact: l.wernisch@bbk.ac.uk
* To whom correspondence should be addressed.
Prediction of biologically significant components from microarray data:
Independently Consistent Expression Discriminator (ICED)
Authors: Bijlani Rahul , Cheng Yinhe , Pearce David A. , Brooks Andrew I. , Ogihara Mitsunori 
Published: December 2002

Abstract
Motivation: Class distinction is a supervised learning approach that has been successfully employed in the analysis of high-throughput gene expression data. Identification of a set of genes that predicts differential biological states allows for the development of basic and clinical scientific approaches to the diagnosis of disease. The Independent Consistent Expression Discriminator (ICED) was designed to provide a more biologically relevant search criterion during predictor selection by embracing the inherent variability of gene expression in any biological state. The four components of ICED include (i) normalization of raw data; (ii) assignment of weights to genes from both classes; (iii) counting of votes to determine optimal number of predictor genes for class distinction; (iv) calculation of prediction strengths for classification results. The search criteria employed by ICED is designed to identify not only genes that are consistently expressed at one level in one class and at a consistently different level in another class but identify genes that are variable in one class and consistent in another. The result is a novel approach to accurately select biologically relevant predictors of differential disease states from a small number of microarray samples.
Results: The data described herein utilized ICED to analyze the large AML/ALL training and test data set (Golub et al., 1999, Science, 286, 531–537) in addition to a smaller data set consisting of an animal model of the childhood neurodegenerative disorder, Batten disease, generated for this study. Both of the analyses presented herein have correctly predicted biologically relevant perturbations that can be used for disease classification, irrespective of sample size. Furthermore, the results have provided candidate proteins for future study in understanding the disease process and the identification of potential targets for therapeutic intervention.
Contact: andrew_brooks@urmc.rochester.edu
* To whom correspondence should be addressed.
† The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
Gene selection: a Bayesian variable selection approach
Authors: Lee Kyeong Eun , Sha Naijun , Dougherty Edward R. , Vannucci Marina , Mallick Bani K. 
Published: December 2002

Abstract
Selection of significant genes via expression patterns is an important problem in microarray experiments. Owing to small sample size and the large number of variables (genes), the selection process can be unstable. This paper proposes a hierarchical Bayesian model for gene (variable) selection. We employ latent variables to specialize the model to a regression setting and uses a Bayesian mixture prior to perform the variable selection. We control the size of the model by assigning a prior distribution over the dimension (number of significant genes) of the model. The posterior distributions of the parameters are not in explicit form and we need to use a combination of truncated sampling and Markov Chain Monte Carlo (MCMC) based computation techniques to simulate the parameters from the posteriors. The Bayesian model is flexible enough to identify significant genes as well as to perform future predictions. The method is applied to cancer classification via cDNA microarrays where the genes BRCA1 and BRCA2 are associated with a hereditary disposition to breast cancer, and the method is used to identify a set of significant genes. The method is also applied successfully to the leukemia data.
Supplementary information: http://stat.tamu.edu/people/faculty/bmallick.html
Contact: bmallick@stat.tanu.edu
* To whom correspondence should be addressed.
Using DFT methods for the prediction of the structure and energetics of metal‐binding sites in metalloproteins
Authors: Rulíšek Lubomír , Havlas Zdeněk 
Published: December 2002

AbstractIn recent years, density functional theory (DFT) methods have been successfully applied in the area of quantum bioinorganic chemistry. Often, they are the only methods of choice for the calculations of the accurate molecular properties of model systems containing transition metal(s) (TMs) and up to additional 50 atoms. In our contribution, we present an example of the application of DFT methods for the quantitative estimates of complexation energies of several TM ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+) in general metal‐binding sites in metalloproteins. Our approach is based on the calculations of the interaction energies of model functional groups with the TM ions, defined as the substitution energy of single water molecule from the coordination sphere of a metal ion, and the evaluation of the cooperative effect, defined as the nonadditive part of the substitution of the second water molecule. It is demonstrated that it is possible to derive complexation energy of the given TM ion in “per‐substituted” [MXn]2+ site by combining the above two contributions with 5‐ to 15‐kcal/mol accuracy and thus a number of metal‐binding sites in metalloproteins can be readily scanned for their specificity toward the studied TM ions. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Density functional theory and Hartree–Fock studies of the geometric and electronic structure of neutral and doped ethylenedioxythiophene (EDOT) oligomers
Authors: Dkhissi A. , Beljonne D. , Lazzaroni R. , Louwet F. , Groenendaal L. , Brédas J. L. 
Published: December 2002

AbstractThe geometric and electronic structure of 3,4‐ethylenedioxythiophene oligomers, ranging in size up to the decamer, have been calculated with density functional theory according to Becke's three‐parameter exchange functional and the gradient‐corrected functional of Lee, Yang, and Paar (DFT/B3LYP/6‐31G) and ab initio Hartree–Fock (HF/6‐31G) methods. A comparison between the energetics of the aromatic and quinoid forms in the neutral state shows as expected that the former is more stable. For both the singly and doubly positively charged compounds, HF is found to localize the excess charge around the center of the molecule, whereas DFT leads to delocalization of the charge all along the conjugated path. The optical properties calculated at the semiempirical level (intermediate neglect of differential overlap/single configuration, (INDO/SCI) on the basis of the geometries provided by DFT and HF are also analyzed. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
The Role of Referent and Expert Power in Mutual Help
Authors: Salem Deborah A. , Reischl Thomas M. , Gallacher Fiona , Randall Katie Weaver 
Published: December 2002

AbstractThis study explored the roles of referent power (i.e., influence based on sense of identification) and expert power (i.e., influence based on knowledge and expertise) in Schizophrenics Anonymous (SA), a mutual‐help group for persons experiencing a schizophrenia‐related illness. The study describes SA participants' experience of referent and expert power with SA members, SA leaders, and with mental health professionals. It also examines whether or not referent and expert power ascribed to fellow SA participants predicts the perceived helpfulness of the group. One hundred fifty‐six SA participants were surveyed. Participants reported experiencing higher levels of referent power with fellow SA members and leaders than with mental health professionals. They reported higher levels of expert power for mental health professionals and SA leaders than for SA members. The respondents' ratings of their SA group's helpfulness was significantly correlated with ratings of referent and expert power. Although expert power was the best independent predictor of helpfulness, a significant interaction between referent and expert power indicated that when members reported high referent power, expert power was not related to helpfulness. These results are interpreted to suggest that there are multiple forms of social influence at work in mutual help.
Where the Girls (and Women) Are
Authors: Bertram Corrine , Hall Julia , Fine Michelle , Weis Lois 
Published: December 2002

AbstractThis paper takes up a theoretical and empirical investigation of how two community‐based projects for young women both create safety from community and domestic violence but how, in the process, discourses of multicultural inclusion define one site, and racist discourses of exclusion float through the other site. By relying on two intensive qualitative case studies of community‐based organizations for girls, one exclusively White and working class and the other expressly multicultural and antiracist, we try to identify those structures and practices that support feminist, but inadvertently racist, work and those structures and practices that enable, at once, feminist and antiracist consciousness and praxis.