bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Overview of Multiple Sequence Alignment
Authors: Simossis Victor , Kleinjung Jens , Heringa Jaap 
Published: June 2004

AbstractMultiple sequence alignment is perhaps the most commonly applied bioinformatics technique. It often leads to fundamental biological insight into sequence‐structure‐function relationships of nucleotide or protein sequence families. In this unit, an overview of multiple sequence alignment techniques is presented, covering a history of nearly 30 years from the early pioneering methods to the current state‐of‐the‐art techniques. Methodological and biological issues and end‐user considerations, as well as alignment evaluation issues, are discussed.
Using TWINSCAN to Predict Gene Structures in Genomic DNA Sequences
Authors: Hu Ping , Brent Michael R. 
Published: June 2004

AbstractTWINSCAN is a gene‐prediction system that combines the methods of ab initio predictors like GENSCAN with information derived from genome comparison. This unit describes the use of TWINSCAN to identify gene structures in eukaryotic genomic sequences. Protocols for using TWINSCAN through its Web interface and from the command line in a Linux environment are provided. Detailed discussion about the appropriate parameter settings, input sequence processing, and choice of genome for comparison are included.
Modeling Protein Structure from its Sequence
Authors: Marti‐Renom Marc A. , Madhusudhan M.S. , Eswar Narayanan , Pieper Ursula , Shen Min‐yi , Sali Andrej , Fiser Andras , Mirkovic Nebojsa , John Bino , Stuart Ashley 
Published: June 2004

AbstractFunctional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three‐dimensional (3‐D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3‐D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3‐D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target‐template alignment, model building, and model evaluation. This unit describes generic considerations in all four steps of comparative modeling, typical modeling errors, and applications of comparative protein structure models. Finally, it illustrates these considerations in practice by discussing in detail one application of our program MODELLER.
FAMS and FAMSBASE for Protein Structure
Authors: Umeyama Hideaki , Iwadate Mitsuo 
Published: June 2004

AbstractThe computer program FAMS (Full Automatic Modeling System) performs homology modeling of protein structures by means of an algorithm consisting of database searches and simulated annealing. FAMS produces a model in which the torsion angles of the backbone and sidechains are highly accurate. The operations of the FAMS algorithm are fully automated, and, therefore, special knowledge, techniques or experience are not required in order to obtain a biologically worthwhile protein structure.
Modeling Membrane Proteins Utilizing Information from Silent Amino Acid Substitutions
Authors: Kochva Uzi , Leonov Hadas , Arkin Isaiah T. , Adams Paul D. 
Published: June 2004

AbstractThis unit describes predicting the structure of simple transmembrane α‐helical bundles. The protocol is based on a global molecular dynamics search (GMDS) of the configuration space of the helical bundle, yielding several candidates structures. The correct structure amongst these candidates is selected using information from silent amino acid substitutions, employing the following premise: Only the correct structure must (by definition) accept all of the silent amino acid substitutions. Thus, the correct structure is found by repeating the GMDS for several close homologues and selecting the structure that persists in all of the trials.
Inferring Evolutionary Trees with PAUP*
Authors: Wilgenbusch James C. , Swofford David 
Published: June 2004

AbstractThis unit provides a general description of reconstructing evolutionary trees using PAUP* 4.0. The protocol takes users through an example analysis of mitochondrial DNA sequence data using the parsimony and the likelihood criteria to infer optimal trees. The protocol also discusses searching options available in PAUP* and demonstrates how to import non‐NEXUS formats. Finally, a general discussion is given regarding the pros and cons of the “model‐free” and “model‐based” methods used throughout the protocol.
Using MODELTEST and PAUP* to Select a Model of Nucleotide Substitution
Authors: Posada David 
Published: June 2004

AbstractModels of nucleotide substitution are commonly used in the analysis of DNA sequences. This unit describes the use of the program MODELTEST (coupled with PAUP*) to find the best‐fit model of substitution for the sequence alignment at hand. An example data file is analyzed and the interpretation of the results is discussed. Some background theory on model selection and a discussion of the relevance of models is included at the end of the unit.
Introduction to Comparing Large Sequence Sets
Authors: Page Roderic D.M. 
Published: June 2004

AbstractComparisons of whole genomes can yield important insights into the evolution of genome structure, such as the role of inversions in bacterial evolution and the identification of large‐scale duplications in the human genome. This unit briefly compares two tools for aligning whole genome sequences: MUMmer and PipMaker. These tools differ in both the underlying algorithms used, and in the interface they present to the user.
PipMaker: A World Wide Web Server for Genomic Sequence Alignments
Authors: Elnitski Laura , Riemer Cathy , Schwartz Scott , Hardison Ross , Miller Webb 
Published: June 2004

AbstractPipMaker is a World‐Wide Web site used to compare two long genomic sequences and identify conserved segments between them. This unit describes the use of the PipMaker server and explains the resulting output files. PipMaker provides an efficient method of aligning genomic sequences and returns a compact, but easy‐to‐interpret form of output, the percent identity plot (pip). For each aligning segment between two sequences the pip shows both the position relative to the first sequence and the degree of similarity. Optional annotations on the pip provide additional information to assist in the interpretation of the alignment. The default parameters of the underlying blastz alignment program are tuned for human‐mouse alignments.
Using MUMmer to Identify Similar Regions in Large Sequence Sets
Authors: Delcher Arthur L. , Salzberg Steven L. , Phillippy Adam M. 
Published: June 2004

AbstractThe MUMmer sequence alignment package is a suite of computer programs designed to detect regions of homology in long biological sequences. Version 2.1 makes several improvements to the package, including: increased speed and reduced memory requirements; the ability to handle both protein and DNA sequences; the ability to handle multiple sequence fragments; and new algorithms for clustering together basic matches. The system is particularly efficient at comparing highly similar sequences, such as alternative versions of fragment assemblies or closely related strains of the same bacterium.
Large Scale Sequencing
Authors: Stein Lincoln 
Published: June 2004

AbstractDNA sequencing and assembly is the Philosopher's Stone of bioinformatics, where the raw material of wet lab enzymatic chemistry is transformed into the bits and bytes of sequence information. The sequence information becomes the foundation for extensive downstream analyses. This unit provides a brief overview of the sequencing process. It describes several software programs typically used for base calling, assembling, and finishing sequence data such as STADEN, Phred, Phrap, and Consed.
An Overview of RNA Structure Prediction
Authors: Stormo Gary D. 
Published: June 2004

AbstractThis unit briefly describes the two fundamentally different methods for predicting RNA structures. The first is to find that structure with the minimum free energy of folding, as predicted by various thermodynamic parameters related to base‐pair stacking, loop lengths, and other features. If one has only a single sequence, this thermodynamic approach is the best available method. The second fundamental approach to RNA structure prediction is to use multiple, homologous sequences for which one can infer a common structure, and then try and predict a structure common to all of the sequences. Such an approach is referred to as a comparative method or phylogenetic method of RNA structure prediction.
IUPAC/IUB Single‐Letter Codes Within Nucleic Acid and Amino Acid Sequences
Authors: Leonard Shonda A. 
Published: June 2004

AbstractThe International Union of Pure and Applied Chemistry (IUPAC) and the International Union of Biochemistry and Molecular Biology (IUBMB) have established standards for representing nucleic acids and amino acids with single capital letters. The tables provided in this appendix summarize the codes for bases in nucleic acid sequences and individual amino acid residues within protein sequences.
Optimal sensor placement for state reconstruction of distributed process systems
Authors: Alonso Antonio A. , Frouzakis Christos E. , Kevrekidis Ioannis G. 
Published: June 2004

AbstractIn this contribution we propose a systematic approach to field reconstruction of distributed process systems from a limited and usually reduced number of measurements. The method exploits the time scale separation property of dissipative processes and concepts derived from principal angles between subspaces, to optimally placing a given number of sensors in the spatial domain. Basic ingredients of the approach include the identification of a low‐dimensional subspace capturing most of the relevant dynamic features of the distributed system, and the solution of a max–min optimization problem through a guided search technique. The low‐dimensional subspace can be defined either through a spectral basis (eigenfunctions of a linear or linearized part of the operator) or through a semiempirical expansion known in the engineering literature as the Proper Orthogonal Decomposition (POD) or Karhunen–Loeve expansion. For both cases, the optimal sensor placement problem will be solved by taking advantage of the underlying algebraic structure of the low‐dimensional subspace. The implications of this approach for dynamic observer design will be discussed together with examples illustrating the proposed methodology. © 2004 American Institute of Chemical Engineers AIChE J, 50: 1438–1452, 2004
A cluster of male breast cancer in office workers
Authors: Milham Samuel 
Published: June 2004

AbstractThree cases of male breast cancer were diagnosed among a small group of men who worked in a basement office of a multi‐story office building. This office was adjacent to an electrical switchgear room which generated high magnetic fields in their work space. The risk of male breast cancer in this group was increased about 100‐fold (observe three cases, expect 0.03 cases; P < 0.00001). Since 1991, 15 epidemiologic studies have associated male breast cancer with exposure to electromagnetic field. Am. J. Ind. Med. 46:86–87, 2004. © 2004 Wiley‐Liss, Inc.
Good practices in managing work‐related indoor air problems: A psychosocial perspective
Authors: Lahtinen Marjaana , Huuhtanen Pekka , Vähämäki Kari , Kähkönen Erkki , Mussalo‐Rauhamaa Helena , Reijula Kari 
Published: June 2004

AbstractBackgroundIndoor air problems at workplaces are often exceedingly complex. Technical questions are interrelated with the dynamics of the work community, and the cooperation and interaction skills of the parties involved in the problem solving process are also put to the test. The objective of our study was to analyze the process of managing and solving indoor air problems from a psychosocial perspective.MethodsThis collective case study was based on data from questionnaires, interviews and various documentary materials. Technical inspections of the buildings and indoor air measurements were also carried out.ResultsThe following four factors best differentiated successful cases from impeded cases: extensive multiprofessional collaboration and participative action, systematic action and perseverance, investment in information and communication, and process thinking and learning. The study also proposed a theoretical model for the role of the psychosocial work environment in indoor air problems.ConclusionsThe expertise related to social and human aspects of problem solving plays a significant role in solving indoor air problems. Failures to properly handle these aspects may lead to resources being wasted and result in a problematic situation becoming stagnant or worse. Am. J. Ind. Med. 46:71–85, 2004. © 2004 Wiley‐Liss, Inc.
Impacts of health and safety education: Comparison of worker activities before and after training
Authors: Becker Paul , Morawetz John 
Published: June 2004

AbstractBackgroundThe International Chemical Workers Union Council (ICWUC) Center for Worker Health and Safety Education in Cincinnati, Ohio, trains workers to protect themselves from hazards due to chemical spills and other chemical exposures. We evaluated whether the ICWUC Hazardous Waste Worker Training Program affects the attitudes and post‐training activities, of trained union workers.MethodsDetailed survey questionnaires were administered to 55 workers prior to and 14–18 months following training. Surveys queried trainees' interest and involvement in safety and health, use of information resources, training activities at their worksite, and their attempts and successes at making worksite improvements.ResultsPost‐training, the study population showed an increase in training of other workers, use of resources, attempts at improvements, success rates for those attempting change, and overall success at making improvements. Self‐reported interest decreased, and self reported involvement in health and safety did not significantly change.ConclusionThe study demonstrates that workers are more willing to attempt to change worksite conditions following training, and that their efficacy at making changes is substantially greater than before they were trained. The study confirms earlier work and strengthens these conclusions by using statistically tested comparisons of impact measures pre‐ and post‐training. Am. J. Ind. Med. 46:63–70, 2004. © 2004 Wiley‐Liss, Inc.
Working conditions and health among female and male employees at a call center in Sweden
Authors: Norman Kerstin , Nilsson Tohr , Hagberg Mats , Tornqvist Ewa Wigaeus , Toomingas Allan 
Published: June 2004

AbstractBackgroundThe call center industry is one of the most expansive labor market sectors in Sweden today. The purpose of this study was to investigate the working conditions and symptoms among employees at a call center in Sweden.MethodsThis study represents the cross‐sectional baseline survey, which was part of a prospective cohort study. Fifty‐seven call center workers were compared with a reference group of 1,459 professional computer users from other occupations. A questionnaire covered physical and psychosocial working conditions and symptoms during the last month. Structured observations in accordance with an ergonomic checklist were used to assess workstation design during the subject's ordinary work.ResultsThe call center group had worked for a shorter time in their present tasks and spent longer continuous time in front of the computer than the reference group. There were deficiencies in workspace, keyboard‐ and input device placement. The subjects reported poor support from their immediate supervisor, low control and limited opportunities to influence their work. A higher proportion of the call center group reported musculoskeletal symptoms.ConclusionThe call center operators were exposed to working conditions that in other studies have indicated an increased risk of developing musculoskeletal disorders. The study also shows that young computer operators in the call center group with a short working career had a higher prevalence of neck‐ and upper extremity symptoms than older computer workers in other labor market sectors. Am. J. Ind. Med. 46:55–62, 2004. © 2004 Wiley‐Liss, Inc.
Czech Dysplasia Metatarsal Type
Authors: Kozlowski K. , Marik I. , Marikova O. , Zemkova D. , Kuklik M. 
Published: June 2004

AbstractWe report three further patients of the recently described new bone dysplasia—dominantly inherited pseudorheumatoid arthritis. The patients of this report have a similar clinical history, the same distinctive phenotype and almost identical radiographic findings. The only major difference is absence of weather dependent articular pain which characterized the family of the previous study. This report expands the clinical data of this bone dysplasia. All patients are Caucasians and originate from different parts of the Czech Republic. It seems that this disorder is quite a common constitutional bone disorder in this country. We propose the name of Czech Dysplasia Metatarsal Type for this unique disease. © 2004 Wiley‐Liss, Inc.
Changes in social interactions during adolescence in male mandrills (Mandrillus sphinx)
Authors: Charpentier Marie , Peignot Patricia , Hossaert‐Mckey Martine , Wickings E. Jean 
Published: June 2004

AbstractThe adolescent period in male mandrills extends from the time the testicles descend (at the age of 3–4 years) to the time adult characteristics develop (at the age of 10 years), and is thus one of the longest adolescent periods in cercopithecines. In this short cross‐sectional study of 11 male mandrills (4.7–9.1 years old), we analyzed social behavioral patterns to investigate partner preference and changes in types of interactions throughout puberty. The mandrills were separated into two clusters on the basis of all of the social interactions scored, as well as the age and sex of the protagonist. During early to mid puberty, immature individuals interacted preferentially with other male adolescents and juveniles. Playing was an important activity, and some affiliative interactions with juveniles were observed. Older adolescents interacted more with adult males and females. These older adolescents were predominantly aggressive toward other adolescents, females, and juveniles, and showed little or no affiliative or playful behaviors. These results indicate a shift in social partners: older males interacted more frequently with adult males, and their behavior involved more aggression and less submission compared to younger adolescents, which showed predominantly submissive and playful behavior. These changes are consistent with preparation for dispersal and future intermale competition. Am. J. Primatol. 63:63–73, 2004. © 2004 Wiley‐Liss, Inc.
Genotyping aids field study of unhabituated wild chimpanzees
Authors: McGrew W.C. , Ensminger A.L. , Marchant L.F. , Pruetz J.D. , Vigilant L. 
Published: June 2004

AbstractProlonged habituation times for wild great apes delay the collection of behavioral and environmental data, sometimes for years. However, genotyping of noninvasively collected feces can provide useful socioecological information in the meantime. We tested this premise on an unhabituated wild population of western chimpanzees (Pan troglodytes verus) at Mont Assirik, Senegal. Genotyping yielded information on kinship, group size, party size and composition, sex ratio, and ranging. Am. J. Primatol. 63:87–93, 2004. © 2004 Wiley‐Liss, Inc.
Do males have a better chance of mating when the number of estrous females is equal to or greater than the males' ordinal rank? Testing the hypothesis in Japanese macaques
Authors: Takahashi Hiroyuki 
Published: June 2004

AbstractThis study was designed to test the hypothesis that male primates in multi‐male/multi‐female social groups with a clear male dominance hierarchy have a better chance of mating when the number of estrous females is equal to or greater than, as opposed to less than, the males' ordinal rank. I studied a Japanese macaque (Macaca fuscata fuscata) troop during mating seasons from 1992 to 1995. The mean daily operational sex ratio (OSR; the number of estrous females per troop male), which was calculated on observation days, was 0.21, 1.9, 0.48, and 3.1 in 1992–1995, respectively. Overall, focal animal sampling of males yielded 118 male‐day records. The male‐day records for each male were divided into the two estrous female number conditions: 1) the male‐day records when the number of estrous females was equal to or greater than the male's ordinal rank, and 2) the male‐day records when the number of estrous females was less than the male's ordinal rank. In the 1993 and 1995 mating seasons, when the number of estrous females was equal to or greater than the ordinal rank of each male, all of the males were observed mating. Conversely, when the number of estrous females was less than the ordinal rank of some male, they were not observed mating in the 1992 and 1994 mating seasons. The percentage for each male across each male's total mating opportunity was <20% when the number of estrous females was less than the male's ordinal rank. By contrast, the percentage for each male across each male's total mating opportunity exceeded 45% when the number of estrous females was equal to or greater than the male's ordinal rank, except for one male. Of all the male‐day records for males observed mating with ejaculation, 41 were obtained when the number of estrous females was equal to or greater than the male's rank; conversely, only three records were obtained when the number of estrous females was less than the male's ordinal rank. Therefore, it appears that males have a better chance of mating when the number of estrous females is equal to or greater than the males' ordinal rank, as opposed to when the number is less than their ordinal rank. Am. J. Primatol. 63:95–102, 2004. © 2004 Wiley‐Liss, Inc.
Clinical and cytogenetic manifestations of subtelomeric aberrations: Report of six cases
Authors: Font‐Montgomery Esperanza , Weaver David D. , Walsh Laurence , Christensen Celanie , Thurston Virginia C. 
Published: June 2004

AbstractBACKGROUNDFluorescent subtelomeric probes for the 41 different subtelomeric regions (the p arms of the acrocentric chromosomes were excluded) have been developed over the last 10 years. These probes can detect deletions, duplications, and translocations in the gene‐rich subtelomeric regions of human chromosomes, regions where crossing over frequently occurs and where a high number of abnormalities have been found. Recently, commercially produced probes have become available, which has led to the detection of subtelomeric abnormalities in 7.4% of patients with moderate to severe mental retardation (Knight et al., 1999).CASESWe evaluated 43 dysmorphic children with developmental delay and/or mental retardation of unknown etiology and/or autism who were previously assessed for chromosome abnormalities, metabolic disorders, or recognizable dysmorphic syndromes, all of which were ruled out. Of the 43 children tested, 6 (14%) were found to have subtelomeric aberrations.CONCLUSIONSWe recommend that patients with dysmorphic features and mental retardation of unknown etiology who also have a normal standard chromosome analysis should have subtelomeric FISH testing performed earlier in their clinical workup. Birth Defects Research (Part A), 2004. © 2004 Wiley‐Liss, Inc.