bluuebunny/crossref_metadata_2025_split huggingface dataset:
Symptoms, cognition, treatment adherence and functional outcome in first-episode psychosis
Authors: MALLA A. K. , NORMAN R. M. G. , MANCHANDA R. , TOWNSEND L. 
Published: September 2002

Background. The differential strength of correlation between symptoms, cognition and other patient characteristics with community functioning in first-episode psychosis has not been fully investigated.Method. In a sample of 66 first-episode psychosis patients demographic variables, ratings of pre-morbid adjustment, positive and negative symptoms, duration of untreated psychosis (DUP) and assessment of cognitive functions at baseline, and symptoms, cognitive functions and adherence to medication at 1 year, were correlated with scores on social relations and activities of daily living (ADL) (outcome) at 1 year. Hierarchical regression analysis was used to confirm the independent contribution of baseline and concurrent variables to functional outcome at 1 year.Results. Scores on functioning related to social relations and ADL were both significantly correlated with pre-morbid adjustment, all dimensions of residual positive and negative symptoms and adherence to medication at 1 year. Scores on social relations were also modestly correlated with DUP and several cognitive measures at baseline and 1 year (verbal IQ, attention, visual memory, word fluency and working memory). Hierarchical regression confirmed independent contribution of pre-morbid adjustment, total residual symptoms and adherence to medication at 1 year for both dimensions of outcome, and psychomotor poverty and working memory for social relations.Conclusions. In addition to pre-morbid adjustment potentially malleable variables such as level of residual (but not acute) symptoms, adherence to medication and cognitive deficits are likely to influence outcome on aspects of community functioning in individuals treated for first episode of psychosis.
Short screening scales to monitor population prevalences and trends in non-specific psychological distress
Authors: KESSLER R. C. , ANDREWS G. , COLPE L. J. , HIRIPI E. , MROCZEK D. K. , NORMAND S.-L. T. , WALTERS E. E. , ZASLAVSKY A. M. 
Published: September 2002

Background. A 10-question screening scale of psychological distress and a six-question short-form scale embedded within the 10-question scale were developed for the redesigned US National Health Interview Survey (NHIS).Methods. Initial pilot questions were administered in a US national mail survey (N = 1401). A reduced set of questions was subsequently administered in a US national telephone survey (N = 1574). The 10-question and six-question scales, which we refer to as the K10 and K6, were constructed from the reduced set of questions based on Item Response Theory models. The scales were subsequently validated in a two-stage clinical reappraisal survey (N = 1000 telephone screening interviews in the first stage followed by N = 153 face-to-face clinical interviews in the second stage that oversampled first-stage respondents who screened positive for emotional problems) in a local convenience sample. The second-stage sample was administered the screening scales along with the Structured Clinical Interview for DSM-IV (SCID). The K6 was subsequently included in the 1997 (N = 36116) and 1998 (N = 32440) US National Health Interview Survey, while the K10 was included in the 1997 (N = 10641) Australian National Survey of Mental Health and Well-Being.Results. Both the K10 and K6 have good precision in the 90th–99th percentile range of the population distribution (standard errors of standardized scores in the range 0·20–0·25) as well as consistent psychometric properties across major sociodemographic subsamples. The scales strongly discriminate between community cases and non-cases of DSM-IV/SCID disorders, with areas under the Receiver Operating Characteristic (ROC) curve of 0·87–0·88 for disorders having Global Assessment of Functioning (GAF) scores of 0–70 and 0·95–0·96 for disorders having GAF scores of 0–50.Conclusions. The brevity, strong psychometric properties, and ability to discriminate DSM-IV cases from non-cases make the K10 and K6 attractive for use in general-purpose health surveys. The scales are already being used in annual government health surveys in the US and Canada as well as in the WHO World Mental Health Surveys. Routine inclusion of either the K10 or K6 in clinical studies would create an important, and heretofore missing, crosswalk between community and clinical epidemiology.
Using an interleukin-6 challenge to evaluate neuropsychological performance in chronic fatigue syndrome
Authors: ARNOLD M. C. , PAPANICOLAOU D. A. , O'GRADY J. A. , LOTSIKAS A. , DALE J. K. , STRAUS S. E. , GRAFMAN J. 
Published: September 2002

Background. Individuals with acute infections experience a range of symptoms including fatigue, malaise, muscle aches, and difficulties with concentration and memory that are usually self-limited. This cluster of symptoms is otherwise, similar to those that characterize chronic fatigue syndrome (CFS). The goal of the present study was to evaluate the cognitive and psychological functioning of CFS patients and normal controls (NCs) when they both were experiencing acute influenza-like symptoms. To induce influenza-like symptoms, we administered interleukin-6 (IL-6), a cytokine that temporarily activates the acute phase immunological and endocrine responses.Methods. Nineteen patients who met the 1994 International CFS Study Group Criteria and ten normal controls (NCs) completed routine clinical evaluations, neuropsychological tests of short-term memory, selective attention, and executive control, and self-ratings of somatic symptoms and psychological mood before, shortly following, and 1 day after IL-6 administration.Results. CFS patients consistently reported more somatic symptoms, even when both groups perceived that they were ill. Both groups somatic symptoms increased during the IL-6 challenge, but the CFS patients symptoms increased more rapidly than controls. In general, the CFS patients performed similarly to NCs on the cognitive measures before, during, and after the IL-6. In contrast to predictions, IL-6 provocation did not impair the cognitive performance of either CFS patients or NCs.Conclusions. The IL-6 provocation exacerbated the patients self-reported symptoms but did not reveal notable cognitive impairments between patients and controls during cytokine-induced acute influenza-like symptoms.
The effect of feral cats on the population viability of black‐vented shearwaters (Puffinus opisthomelas) on Natividad Island, Mexico
Authors: Keitt Bradford S. , Wilcox Chris , Tershy Bernie R. , Croll Donald A. , Donlan C. Josh 
Published: September 2002

AbstractInsular breeding seabirds are likely to be particularly vulnerable to introduced mammalian predators because they often lack behavioural, morphological and life‐history defenses against predation. We studied the life‐history of the black‐vented shearwater (Puffinus opisthomelas) on Natividad Island, Baja California Sur, Mexico, to examine its vulnerability to introduced feral cats. Using an allometric equation, we estimated that feral cats consumed 328 g of food day‐1 to satisfy their nutritional requirements. We used stable isotope analysis of cat scat to estimate that 90% of the cats' diet was composed of shearwaters. Using data from our focal species and from the closely related manx shearwater (Puffinus puffinus), we created a demographic model to evaluate the effects of cat population size on the annual growth rate (λ) of the shearwater. The annual growth rate for black‐vented shearwaters was estimated to be 1.006 in the absence of cat predation. With predation, we estimated that annual growth rate declined approximately 5% for every 20 cats in a population of 150,000 birds. Persistence times of bird colonies decreased both with an increase in the size of the feral cat population and with a decrease in the size of the initial bird population.
Dealing with errors in interactive sequencing by hybridization
Authors: Phan Vinhthuy T. , Skiena Steven S. 
Published: September 2002

Abstract
Motivation: A realistic approach to sequencing by hybridization must deal with realistic sequencing errors. The results of such a method can surely be applied to similar sequencing tasks.
Results: We provide the first algorithms for interactive sequencing by hybridization which are robust in the presence of hybridization errors. Under a strong error model allowing both positive and negative hybridization errors without repeated queries, we demonstrate accurate and efficient reconstruction with error rates up to 7%. Under the weaker traditional error model of Shamir and Tsur (Proceedings of the Fifth International Conference on Computational Molecular Biology (RECOMB-01) , pp 269–277, 2000), we obtain accurate reconstructions with up to 20% false negative hybridization errors. Finally, we establish theoretical bounds on the performance of the sequential probing algorithm of Skiena and Sundaram (J. Comput. Biol. , 2, 333–353, 1995) under the strong error model.
Availability: Freely available upon request.
Contact: skiena@cs.sunysb.edu
Enrichment of regulatory signals in conserved non-coding
genomic sequence
Authors: Levy Samuel , Hannenhalli Sridhar , Workman Christopher 
Published: September 2002

Abstract
Motivation: Whole genome shotgun sequencing strategies generate sequence data prior to the application of assembly methodologies that result in contiguous sequence. Sequence reads can be employed to indicate regions of conservation between closely related species for which only one genome has been assembled. Consequently, by using pairwise sequence alignments methods it is possible to identify novel, non-repetitive, conserved segments in non-coding sequence that exist between the assembled human genome and mouse whole genome shotgun sequencing fragments. Conserved non-coding regions identify potentially functional DNA that could be involved in transcriptional regulation.
Results: Local sequence alignment methods were applied employing mouse fragments and the assembled human genome. In addition, transcription factor binding sites were detected by aligning their corresponding positional weight matrices to the sequence regions. These methods were applied to a set of transcripts corresponding to 502 genes associated with a variety of different human diseases taken from the Online Mendelian Inheritance in Man database. Using statistical arguments we have shown that conserved non-coding segments contain an enrichment of transcription factor binding sites when compared to the sequence background in which the conserved segments are located. This enrichment of binding sites was not observed in coding sequence. Conserved non-coding segments are not extensively repeated in the genome and therefore their identification provides a rapid means of finding genes with related conserved regions, and consequently potentially related regulatory mechanism. Conserved segments in upstream regions are found to contain binding sites that are co-localized in a manner consistent with experimentally known transcription factor pairwise co-occurrences and afford the identification of novel co-occurring Transcription Factor (TF) pairs. This study provides a methodology and more evidence to suggest that conserved non-coding regions are biologically significant since they contain a statistical enrichment of regulatory signals and pairs of signals that enable the construction of regulatory models for human genes.
Contact: samuel.levy@celera.com
* To whom correspondence should be addressed.
Predicting class II MHC/peptide multi-level binding with an
iterative stepwise discriminant analysis meta-algorithm
Authors: Mallios R. R. 
Published: September 2002

Abstract
Motivation: Predicting peptides that bind to both Major Histocompatibility Complex (MHC) molecules and T cell receptors provides crucial information for vaccine development. An agretope is that portion of a peptide that interacts with an MHC molecule. The identification and prediction of agretopes is the first step towards vaccine design.
Results: An iterative stepwise discriminant analysis meta-algorithm is utilized to derive a quantitative motif for classifying potential agretopes as high-, moderate- or non-binders for HLA-DR1, a class II MHC molecule. A large molecular online database provides the input for this data-driven algorithm. The model correctly classifies over 85% of the peptides in the database.
Availability: Stepwise discriminant analysis software is available commercially in SPSS and BMDP statistical software packages. Peptides known to bind MHC molecules can be downloaded from http://wehih.wehi.edu.au/mhcpep/. Peptides known not to bind HLA-DR1 are available from the author upon request.
Contact: ronna@ucsfresno.edu
Determining the minimum number of types necessary to represent
the sizes of protein atoms
Authors: Tsai Jerry , Voss Neil , Gerstein Mark 
Published: September 2002

Abstract
Motivation: Traditionally, for packing calculations people have collected atoms together into a number of distinct ‘types’. These, in fact, often represent a heavy atom and its associated hydrogens (i.e. a united atom). Also, atom typing is usually done according to basic chemistry, giving rise to 20–30 protein atom types, such as carbonyl carbons, methyl groups, and hydroxyl groups. No one has yet investigated how similar in packing these chemically derived types are. Here we address this question in detail, using Voronoi volume calculations on a set of high-resolution crystal structures.
Results: We perform a rigorous clustering analysis with cross-validation on tens of thousands of atom volumes and attempt to compile them into types based purely on packing. From our analysis, we are able to determine a ‘minimal’ set of 18 atom types that most efficiently represent the spectrum of packing in proteins. Furthermore, we are able to uncover a number of inconsistencies in traditional chemical typing schemes, where differently typed atoms have almost the same effective size. In particular, we find that tetrahedral carbons with two hydrogens are almost identical in size to many aromatic carbons with a single hydrogen.
Availability: Programs available from http://geometry.molmovdb.org.
Contact: JerryTsai@TAMU.edu; neil.voss@yale.edu; Mark.Gerstein@yale.edu
Supplementary Information: Available at http://geometry.molmovdb.org.
* To whom correspondence should be addressed.
Comprehensive comparison between locations of orthologous genes
on archaeal and bacterial genomes
Authors: Horimoto Katsuhisa , Fukuchi Satoshi , Mori Kentaro 
Published: September 2002

Abstract
Motivation: Following an extensive search for orthologous genes between the complete genomes from archaea and bacteria, the spatial association of the orthologs has been investigated in terms of synteny, the conservation of the order of neighboring genes. However, the relationships between the relative locations of remote orthologs over entire genomes have not been shown.
Results: Comprehensive comparisons between the locations of orthologs on nineteen archaeal and bacterial genomes are presented by the location to location correspondence based on the gene–location distance. When the two genomes are rotated such that a pair of orthologs with the shortest distance is set in the same angle, a statistically significant number of orthologs maintain their relative locations between the genomes. Even by the short distances at the 5% significance level, the rotations are restricted within a narrow range, suggesting an intrinsic angle for realizing similar locations between the orthologs in each genome pair. Furthermore, the rotations in the restricted range agree with the replication origin and terminus sites for the analyzed genomes where such sites are known. The relationship between location-maintained orthologs and gene function is also discussed.
Contact: horimoto@post.saga-med.ac.jp
* To whom correspondence should be addressed.
The HMMTOP transmembrane topology prediction server
Authors: Tusnády Gábor
   E. , Simon István 
Published: September 2002

Abstract
Summary: The HMMTOP transmembrane topology prediction server predicts both the localization of helical transmembrane segments and the topology of transmembrane proteins. Recently, several improvements have been introduced to the original method. Now, the user is allowed to submit additional information about segment localization to enhance the prediction power. This option improves the prediction accuracy as well as helps the interpretation of experimental results, i.e. in epitope insertion experiments.
Availability: HMMTOP 2.0 is freely available to non-commercial users at http://www.enzim.hu/hmmtop. Source code is also available upon request to academic users.
Contact: tusi@enzim.hu
* To whom correspondence should be addressed.
VISTRAJ: exploring protein conformational space
Authors: Salama John J. , Feldman Howard J. , Hogue Christopher W. V. 
Published: September 2002

Abstract
Summary: VISTRAJ is an application which allows 3D visualization, manipulation and editing of protein conformational space using probabilistic maps of this space called ‘trajectory distributions’. Trajectory distributions serve as input to FOLDTRAJ which samples protein structures based on the represented conformational space. VISTRAJ also allows FOLDTRAJ to be used as a tool for homology model creation, and structures may be generated containing post-translationally modified amino acids.
Availability: Binaries are freely available for non-profit use as part of the FOLDTRAJ package at ftp://ftp.mshri.on.ca/pub/TraDES/foldtraj/.
Contact: hogue@mshri.on.ca
Supplementary Information: The Trajectory Directed Ensemble Sampling (TraDES) web site can be visited at http://bioinfo.mshri.on.ca/trades/. The web-based version of INITTRAJ/FOLDTRAJ may be accessed at http://foldtraj.mshri.on.ca/.
* To whom correspondence should be addressed.
Protein motif extraction with neuro-fuzzy optimization
Authors: Chang Bill C.H. , Halgamuge Saman K. 
Published: September 2002

Abstract
Motivation: It is attempted to improve the speed and flexibility of protein motif identification. The proposed algorithm is able to extract both rigid and flexible protein motifs.
Results: In this work, we present a new algorithm for extracting the consensus pattern, or motif, from a group of related protein sequences. This algorithm involves a statistical method to find short patterns with high frequency and then neural network training to optimize the final classification accuracies. Fuzzy logic is used to increase the flexibility of protein motifs. C2H2 Zinc Finger Protein and epidermal growth factor protein sequences are used to demonstrate the capability of the proposed algorithm in finding motifs.
Availability: This program is freely available for academic use by request.
Contact: bcch@mame.mu.oz.ausam@mame.mu.oz.au
Probabilistic alignment of motifs with sequences
Authors: Gonnet Pedro , Lisacek Frédérique 
Published: September 2002

Abstract
Motivation: Motif detection is an important component of the classification and annotation of protein sequences. A method for aligning motifs with an amino acid sequence is introduced. The motifs can be described by the secondary (i.e. functional, biophysical, etc...) characteristics of a signal or pattern to be detected. The results produced are based on the statistical relevance of the alignment. The method was targeted to avoid the problems (i.e. over-fitting, biological interpretation and mathematical soundness) encountered in other methods currently available.
Results: The method was tested on lipoprotein signals in B. subtilis yielding stable results. The results of signal prediction were consistent with other methods where literature was available.
Availability: An implementation of the motif alignment, refining and bootstrapping is available for public use online at http://www.expasy.org/tools/patoseq/
Contact: pedro.gonnet@genebio.com
* To whom correspondence should be addressed.
Simplifying amino acid alphabets by means of a branch
and bound algorithm and substitution matrices
Authors: Cannata Nicola , Toppo Stefano , Romualdi Chiara , Valle Giorgio 
Published: September 2002

Abstract
Motivation: Protein and DNA are generally represented by sequences of letters. In a number of circumstances simplified alphabets (where one or more letters would be represented by the same symbol) have proved their potential utility in several fields of bioinformatics including searching for patterns occurring at an unexpected rate, studying protein folding and finding consensus sequences in multiple alignments. The main issue addressed in this paper is the possibility of finding a general approach that would allow an exhaustive analysis of all the possible simplified alphabets, using substitution matrices like PAM and BLOSUM as a measure for scoring.
Results: The computational approach presented in this paper has led to a computer program called AlphaSimp (Alphabet Simplifier) that can perform an exhaustive analysis of the possible simplified amino acid alphabets, using a branch and bound algorithm together with standard or user-defined substitution matrices. The program returns a ranked list of the highest-scoring simplified alphabets. When the extent of the simplification is limited and the simplified alphabets are maintained above ten symbols the program is able to complete the analysis in minutes or even seconds on a personal computer. However, the performance becomes worse, taking up to several hours, for highly simplified alphabets.
Availability: AlphaSimp and other accessory programs are available at http://bioinformatics.cribi.unipd.it/alphasimp
Contact: giorgio.valle@unipd.it
Prediction of Golgi Type II membrane proteins based on
their transmembrane domains
Authors: Yuan Zheng , Teasdale Rohan D. 
Published: September 2002

Abstract
Motivation: A major issue in cell biology today is how distinct intracellular regions of the cell, like the Golgi Apparatus, maintain their unique composition of proteins and lipids. The cell differentially separates Golgi resident proteins from proteins that move through the organelle to other subcellular destinations. We set out to determine if we could distinguish these two types of transmembrane proteins using computational approaches.
Results: A new method has been developed to predict Golgi membrane proteins based on their transmembrane domains. To establish the prediction procedure, we took the hydrophobicity values and frequencies of different residues within the transmembrane domains into consideration. A simple linear discriminant function was developed with a small number of parameters derived from a dataset of Type II transmembrane proteins of known localization. This can discriminate between proteins destined for Golgi apparatus or other locations (post-Golgi) with a success rate of 89.3% or 85.2%, respectively on our redundancy-reduced data sets.
Availability: See http://microarray.imb.uq.edu.au/golgi/
Contact: r.teasdale@imb.uq.edu.au
* To whom correspondence should be addressed.