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PubMed2002

Perazine for schizophrenia.

BACKGROUND: Perazine is an old phenothiazine derivative used for the treatment of people with schizophrenia which has a reputed low level of extrapyramidal side-effects. However, its use is restricted in the sense that - to the best knowledge of the reviewers - it is only marketed in Germany, Poland, Yugoslavia and the Netherlands. OBJECTIVES: To examine the effects of perazine for those with schizophrenia, and schizophrenia-like psychoses. SEARCH STRATEGY: Electronic searches of the Cochrane Schizophrenia Group's register which includes relevant randomised controlled trials from the bibliographic databases Biological Abstracts, CINAHL, The Cochrane Library, EMBASE, MEDLINE, PsycLIT, LILACS, PSYNDEX, Sociological Abstracts and Sociofile were undertaken. References of all included studies were searched for further trials. Pharmaceutical companies and authors of trials were contacted. SELECTION CRITERIA: All randomised controlled trials that compared perazine with other treatments for people with schizophrenia and/or schizophrenia-like psychoses. DATA COLLECTION AND ANALYSIS: Citations and, where possible, abstracts were independently inspected by two reviewers, papers ordered, re-inspected and quality assessed. Data were independently extracted. Data were excluded if loss to follow up was greater than 50%. For homogeneous dichotomous data the Relative Risk (RR), 95% confidence interval (CI) and, where appropriate, the number needed to treat (NNT) were calculated on an intention-to-treat basis. For continuous data, weighted mean differences were calculated (WMD). All data were inspected for heterogeneity. MAIN RESULTS: Six trials with a total of 288 participants are included. According to only one trial with 95 participants perazine appeared superior to active placebo (trimipramine) at five weeks for the outcome of 'no important global improvement' (n=95, RR 0.6, CI 0.3-0.9, NNT 4, CI 2-17), but there was no difference in various measures of mental state. The side-effect risk of perazine compared to placebo could not be estimated because they were not reported. Five small trials including only 193 participants which compared perazine with other antipsychotics were incompletely reported and the outcomes were presented in various ways so that meta-analysis was not possible in most occasions. A similar number of participants receiving perazine or comparator antipsychotics left the studies early (n=193, RR 0.9, CI 0.5-1.4). The results on efficacy were controversial and need further assessment by randomised controlled trials. No obvious differences in adverse events between perazine and other antipsychotics could be derived from these limited data. Two haloperidol comparisons did not present extrapyramidal side-effects in a way usable for meta-analysis, but three small comparisons with the atypical antipsychotics zotepine and amisulpride showed no higher risk of akathisia (n=111, RR 0.3, CI 0.1-1.1), dyskinesia (n=111, RR 0.5, CI 0.1-3.5), parkinsonism (n=81, RR 1.2, CI 0.5-2.8) or tremor (n=40, RR 0.8, CI 0.3-2.3) with perazine. REVIEWER'S CONCLUSIONS: The number, size and reporting of randomised controlled perazine trials is insufficient to present firm conclusions about the properties of this antipsychotic. It is possible that perazine is associated with a similar risk of extrapyramidal side-effects as some atypical antipsychotics, and this should be clarified in larger, well-designed trials.

Antipsychotic Agents↗
PubMed2006

Perazine for schizophrenia.

BACKGROUND: Perazine is an old phenothiazine derivative used for the treatment of people with schizophrenia and is reputed to have a low level of extrapyramidal adverse effects. As far as we are aware, its use is limited to Germany, Poland, the former Yugoslavia and the Netherlands. OBJECTIVES: To examine the effects of perazine for those with schizophrenia, and schizophrenia-like psychoses. SEARCH STRATEGY: We searched the Cochrane Schizophrenia Group's register which includes relevant randomised controlled trials from the bibliographic databases Biological Abstracts, CINAHL, The Cochrane Library, EMBASE, MEDLINE, PsycLIT, LILACS, PSYNDEX, Sociological Abstracts and Sociofile (last update of the review March 2005). We searched references of all included studies for further trials. We contacted pharmaceutical companies and authors of trials. SELECTION CRITERIA: We selected all randomised controlled trials that compared perazine with other treatments for people with schizophrenia and/or schizophrenia-like psychoses. DATA COLLECTION AND ANALYSIS: We independently (SL, BH) inspected citations and where possible abstracts and ordered papers for re-inspection and quality assessment. We independently extracted data. We excluded data if loss to follow up was greater than 50%. For homogeneous dichotomous data we calculated the Relative Risk (RR), 95% confidence interval (CI) and, where appropriate, the number needed to treat (NNT) on an intention-to-treat basis. For continuous data, we calculated weighted mean differences (WMD). We inspected all data for heterogeneity. MAIN RESULTS: We included six trials with a total of 288 participants. In only one trial with 95 participants, perazine appeared superior to 'active placebo' (trimipramine) at five weeks for the outcome of 'no important global improvement' (n=95, RR 0.43 CI 0.2 to 0.8, NNT 4 CI 2 to 13), but there was no statistically significant difference in most measures of mental state. Perazine did not induce more general adverse events than placebo, but more participants received at least one dose of antiparkinson medication (n=95, RR 4.50 CI 1.0 to 19.5, NNH 6 CI 4 to 33). Five small trials comparing perazine with other antipsychotics, including in total only 193 participants, were incompletely reported and the outcomes were presented in various ways so that meta-analysis was not possible in most occasions. A similar number of participants receiving perazine or comparator antipsychotics left the studies early (n=193, RR 0.85, CI 0.5 to 1.4). The results on efficacy were controversial and need further assessment by randomised controlled trials. No obvious differences in adverse events between perazine and other antipsychotics could be derived from the limited data. Two haloperidol comparisons did not present extrapyramidal side-effects in a suitable way for use in meta-analysis, but three small comparisons with the atypical antipsychotics zotepine and amisulpride showed no higher risk of akathisia (n=111, RR 0.31 CI 0.1 to 1.1), dyskinesia (n=111, RR 0.47 CI 0.1 to 3.5), parkinsonism (n=81, RR 1.21 CI 0.5 2.8) or tremor (n=40, RR 0.80 CI 0.3 to 2.6) with perazine. AUTHORS' CONCLUSIONS: The number, size and reporting of randomised controlled perazine trials is insufficient to present firm conclusions about the properties of this antipsychotic. It is possible that perazine is associated with a similar risk of extrapyramidal side-effects as some atypical antipsychotics, and this should be clarified in larger, well-designed trials.

Antipsychotic Agents↗
PubMed2002

Benperidol for schizophrenia.

BACKGROUND: Benperidol is a relatively old antipsychotic drug, marketed since 1966, used in Germany for 30 years, but also available in Belgium, Greece, Italy, the Netherlands and the UK. Benperidol is a butyrophenone antipsychotic, with the highest neuroleptic potency in terms of D2 receptor blockade. Those taking it are, therefore, reputed to be at high risk of extrapyramidal side effects, but benperidol's unusual profile may render it of value to subgroups of people with schizophrenia. OBJECTIVES: To examine the clinical effects and safety of benperidol for those with schizophrenia and schizophrenia-like psychoses. SEARCH STRATEGY: The reviewers searched the Cochrane Schizophrenia Group's register (January 2001) which includes relevant randomised controlled trials from the bibliographic databases Biological Abstracts, CINAHL, The Cochrane Library, EMBASE, MEDLINE, PsycLIT, LILACS, PSYNDEX, Sociological Abstracts and Sociofile. We also searched the references of all included studies and contacted pharmaceutical companies and authors of included studies in order to identify further trials. SELECTION CRITERIA: Randomised controlled trials that compared benperidol with other treatments for people with schizophrenia and/or schizophrenia-like psychoses. DATA COLLECTION AND ANALYSIS: Citations and, where possible, abstracts were independently inspected by two reviewers and papers were ordered, re-inspected and quality assessed. We independently extracted data but excluded data if loss to follow up was greater than 50%. For homogeneous dichotomous data, we calculated the relative risk (RR), the 95% confidence interval (CI) and, where appropriate, the number needed to treat/harm (NNT/H), on an intention-to-treat basis. MAIN RESULTS: We identified only one unpublished poorly randomised controlled trial (N=40, duration 30 days, comparison perphenazine). Although benperidol was inferior to perphenazine (1 RCT, N=40, global state no better or worse RR 8.0 CI 2.1 to 30, NNH 1.4 CI 1 to 2) poor reporting suggests that an overestimate of effect is likely. It was not possible to report other outcomes. REVIEWER'S CONCLUSIONS: Currently, there are insufficient data from randomised trials to assess the clinical effects of benperidol. This interesting compound merits further research.

Antipsychotic Agents↗
PubMed1992

Quantitative morphology for biologists and computer scientists: I. Computer-aided tutorial for biological stereology (version 1.0).

This paper describes a computer-aided tutorial for biological stereology. Stereology, a type of quantitative morphology, includes a collection of statistical methods that quantify the structural compartments that can be viewed in sections with light and electron microscopy. These methods provide volume, surface, length, shape, and number data, and help define the quantitative relationships among the structural compartments of biological hierarchies. Hierarchies, which connect structural data ranging in size from molecules to organs, serve as a central core to which the data of biological databases can be linked. The tutorial focuses on two objectives. It provides the user primarily interested in using quantitative morphology databases with background information, and offers a set of state-of-the-art tools to researchers wishing to use these methods in the laboratory. The main topics of the tutorial include: introduction to quantitative morphology, symbols/terms, data types, sampling, hierarchies, data interpretation, and utilities. The tutorial runs under the MS-DOS operating system and requires at least an IBM PC AT (or compatible), a color monitor (EGA, VGA), 540 KB of RAM, and 3 MB of hard disk space.

Animals↗
PubMed1996

Viability and Metabolic Features of Bacteria Indigenous to a Contaminated Deep Aquifer

The quantitation and characterization of indigenous bacteria of a deep aquifer, located in the southwestern United States and contaminated with halogenated aliphatic compounds, was undertaken. Water samples were obtained aseptically from depths of 45 to 151 m from four sites that ranged from 260 to 1,800 m in distance from the location of contaminant release. Sediment samples were also obtained from the proximal and distal sites for analyses. Results for aerobic and anaerobic colony-forming units were obtained on four agar media that were used to retrieve heterotrophs, oligotrophs, and pseudomonads. Most probable number estimates were obtained from a liquid medium favorable for oligotrophs. Representative isolates were tested against Biolog plates (Biolog, Inc., Hayward, Calif.) for patterns of carbon source utilization. Of 103 Gram-negative (GN) isolates, 48 could not be identified and the others were only tentatively identified via the Biolog database, and none of the 35 Gram-positive (GP) isolates were identifiable. However, the metabolic patterns were subjected to average cluster linkage analyses; the GN and GP bacteria were separable into eight and four groups, respectively. The oligotroph group comprised one-third of the GN and one-half of the GP isolates. The consensus carbon source utilization pattern for each group was determined and will be useful in future characterization of additional aquifer bacterial isolates. Although predominantly aerobic and oligotrophic, the microbial community of this aquifer was highly diverse with discernible viability and metabolic features of the microbiota distinctive to each of the four water and two sediment samples.

Journal Article↗
PubMed2000

Problems in Extinction Model Selection and Parameter Estimation.

It is a vexing problem to achieve a consensus about the proper scientific way to assess population viability for habitat conservation plans. Rather than a hypothesis-testing approach, here it is proposed to select population models, estimate extinction parameters, and assess prediction uncertainty using a pragmatic, empirical Bayesian approach. The simplest usable models include the effects of population growth, r; carrying capacity, K; Allee threshold, N(A); and environmental stochasticity, v(r). Analytic predictions of expected extinction times are available for such models. Models that are more complex can be elaborated from this basis. Selection from a hierarchy of nesting population models can often be done through the evaluation of parameters. The estimation of the most important extinction parameters can be undertaken in a variety of ways. Time series can be analyzed to estimate r(d), v(r), rho, and K. Habitat models and individualistic population models may help estimate N(A) and K and demographic stochasticity. Fine-scale biogeography and climatological data may be useful in the estimation of a variety of parameters. Because it takes many years to estimate extinction parameters accurately for a given population of interest, the most efficient estimation procedures are desirable. I propose the use of prior information from an (as yet nonexistent) population biology database. The accumulation of local information through monitoring will improve our estimates allowing adaptive management. Uncertainty in the estimates will always remain, but it may be quantified by the posterior distributions. A crude example is discussed using treefrog population data. Although the motivations, beliefs, and biases of competing stakeholders will differ, a habitat conservation plan could accommodate this variation in the prior distributions. Field experience from monitoring will increasingly clear up any discrepancies between the opposing beliefs and the real ecosystem. As the world is an uncertain place and because there is no universal scientific method, there will always be controversy and surprises. The best we can do is (1) agree about our prior information, (2) agree about the strategy of model selection and parameter estimation, and (3) agree about our strategy for adaptive management. Perhaps the greatest impediment to such prior agreements for HCPs is the likely paranoia inspired by the use of unfamiliar statistical methodology. We need to train students of ecology in a more flexible and deeper understanding of statistics and philosophy of science.

Journal Article↗
PubMed2000

Comparative gene mapping workshop: progress in agriculturally important animals.

Following the successful Comparative Mapping Workshop held at Fraser Island, Australia in 1995, HUGO organized a second workshop of 41 invited participants, held at Toulouse, France on May 3 and 4, 1999. The aim of the conference was to focus on recent developments in genome mapping in a variety of vertebrate species, with particular emphasis on progress in farm animals (cattle, pigs, chickens, sheep, horses, goats, and deer). In addition, representatives from important experimental mammalian and vertebrate organisms (e.g. mice, rats, dogs, fugu, and marsupials) also participated in the meeting. After a rapid overview of developments in the construction and comparison of genome maps in a wide variety of species, discussion focused on how comparative genomics will play a vital role in the genetic dissection of multigenic traits and the characterization of agriculturally important loci in agricultural species. Acceleration of gene discovery with heterologous ESTs (Expressed Sequence Tags) or collections of ESTs was discussed. Recent developments in the construction of cDNA libraries and the efficiency of tools such as whole genome radiation hybrids (RH) and large fragment clone libraries (YACs and in particular BACs) were discussed. Proposed criteria to improve the identification of homologous genes between species and recommendations for nomenclatures were identified. Particular emphasis was placed on how the integration of biological databases could help the scientific community.

Agriculture↗
PubMed1989

GENPRO: automatic generation of Prolog clause files for knowledge-based systems in the biomedical sciences.

With the increasing interest in using knowledge-based approaches for protein structure prediction and modelling, there is a requirement for general techniques to convert molecular biological data into structures that can be interpreted by artificial intelligence programming languages (e.g. Prolog). We describe here an interactive program that generates files in Prolog clausal form from the most commonly distributed protein structural data collections. The program is flexible and enables a variety of clause structures to be defined by the user through a general schema definition system. Our method can be extended to include other types of molecular biological database or those containing non-structural information, thus providing a uniform framework for handling the increasing volume of data available to knowledge-based systems in biomedicine.

Database Management Systems↗
PubMed2006

Status of text-mining techniques applied to biomedical text.

Scientific progress is increasingly based on knowledge and information. Knowledge is now recognized as the driver of productivity and economic growth, leading to a new focus on the role of information in the decision-making process. Most scientific knowledge is registered in publications and other unstructured representations that make it difficult to use and to integrate the information with other sources (e.g. biological databases). Making a computer understand human language has proven to be a complex achievement, but there are techniques capable of detecting, distinguishing and extracting a limited number of different classes of facts. In the biomedical field, extracting information has specific problems: complex and ever-changing nomenclature (especially genes and proteins) and the limited representation of domain knowledge.

Abstracting and Indexing↗
PubMedDate not supplied

Comparative aspects of zebrafish (Danio rerio) as a model for aging research.

The zebrafish has emerged over the past decade as a major model system for the study of development due to its invertebrate-like advantages coupled with its vertebrate biology. These features also make it a potentially valuable organism for gerontological research. The main advantages of zebrafish include its economical husbandry, small yet accessible size, high reproductive capacity, genetic tractability, and a large and growing biological database. Although zebrafish life span is longer than rodents, it shares the feasibility of large-scale mutational analysis with the extremely short-lived invertebrate models. This review compares zebrafish with the more widely used model organisms used for aging research, including yeast, worms, flies, mice, and humans.

Aging↗
PubMed2004

Development of public toxicogenomics software for microarray data management and analysis.

A robust bioinformatics capability is widely acknowledged as central to realizing the promises of toxicogenomics. Successful application of toxicogenomic approaches, such as DNA microarray, inextricably relies on appropriate data management, the ability to extract knowledge from massive amounts of data and the availability of functional information for data interpretation. At the FDA's National Center for Toxicological Research (NCTR), we are developing a public microarray data management and analysis software, called ArrayTrack. ArrayTrack is Minimum Information About a Microarray Experiment (MIAME) supportive for storing both microarray data and experiment parameters associated with a toxicogenomics study. A quality control mechanism is implemented to assure the fidelity of entered expression data. ArrayTrack also provides a rich collection of functional information about genes, proteins and pathways drawn from various public biological databases for facilitating data interpretation. In addition, several data analysis and visualization tools are available with ArrayTrack, and more tools will be available in the next released version. Importantly, gene expression data, functional information and analysis methods are fully integrated so that the data analysis and interpretation process is simplified and enhanced. ArrayTrack is publicly available online and the prospective user can also request a local installation version by contacting the authors.

Databases, Genetic↗
PubMed1998

Unification of protein families.

Computational biology exploits the evolutionary connectivity between proteins and protein families to predict structural and functional properties of uncharacterized gene products. In the past year, conceptual and statistical refinements have substantially improved algorithms for the detection of remote homologues. In conjunction with the rapid growth of biological databases, the global organization of proteins into sequence families, functional families and structural families has become both pertinent and feasible.

Amino Acid Sequence↗
PubMed1996

Integrated access to metabolic and genomic data.

The EcoCyc system consists of a knowledge base (KB) that describes the genes and intermediary metabolism of Escherichia coli, and a graphical user interface (GUI) for accessing that knowledge. This paper addresses two problems: How can we create a GUI that provides integrated access to metabolic and genomic data? We describe the design and implementation of visual presentations that closely mimic those found in the biology literature, and that offer hypertext navigation among related entities, and multiple views of the same entity. We employ a frame knowledge representation system (FRS) called HyperTHEO to manage the EcoCyc knowledge base. Among the advantages of FRSs are an expressive data model for capturing the complexities of biological information, and schema-evolution capabilities that facilitate the constant schema changes that biological databases tend to undergo. HyperTHEO also includes rule-based inference facilities that are the foundation of expert systems, a constraint language for maintaining data integrity, and a declarative query language. A graphic KB editor and browser allow the EcoCyc developers to interactively inspect and modify this evolving KB.

Artificial Intelligence↗
PubMed1994

Simplified user poll and experience report language (SUPER): implementation and application.

Biological computing is generally organized as stand-alone implementation on a PC-type computer or on a central facility (e.g. a university computer center). Services provided by central facilities need to be tailored to the user community. Unless very work-intensive individual contacts are used, the feedback must be collected with generalized tools, such as questionnaires distributed in the form of a newsletter. We have developed a method to have such polls automated and tailored, as well as having multiple-choice questions combined with branching after fundamental questions. As the evaluation of the results needs to know the questions asked, we have also included a method to process the answers and give detailed tables on the answers. SUPER was applied in a poll to query the academic usership in Switzerland on the usage of molecular biology databases.

Evaluation Studies as Topic↗
PubMed1999

Automated genome sequence analysis and annotation.

MOTIVATION: Large-scale genome projects generate a rapidly increasing number of sequences, most of them biochemically uncharacterized. Research in bioinformatics contributes to the development of methods for the computational characterization of these sequences. However, the installation and application of these methods require experience and are time consuming. RESULTS: We present here an automatic system for preliminary functional annotation of protein sequences that has been applied to the analysis of sets of sequences from complete genomes, both to refine overall performance and to make new discoveries comparable to those made by human experts. The GeneQuiz system includes a Web-based browser that allows examination of the evidence leading to an automatic annotation and offers additional information, views of the results, and links to biological databases that complement the automatic analysis. System structure and operating principles concerning the use of multiple sequence databases, underlying sequence analysis tools, lexical analyses of database annotations and decision criteria for functional assignments are detailed. The system makes automatic quality assessments of results based on prior experience with the underlying sequence analysis tools; overall error rates in functional assignment are estimated at 2.5-5% for cases annotated with highest reliability ('clear' cases). Sources of over-interpretation of results are discussed with proposals for improvement. A conservative definition for reporting 'new findings' that takes account of database maturity is presented along with examples of possible kinds of discoveries (new function, family and superfamily) made by the system. System performance in relation to sequence database coverage, database dynamics and database search methods is analysed, demonstrating the inherent advantages of an integrated automatic approach using multiple databases and search methods applied in an objective and repeatable manner. AVAILABILITY: The GeneQuiz system is publicly available for analysis of protein sequences through a Web server at http://www.sander.ebi.ac. uk/gqsrv/submit

Amino Acid Sequence↗
PubMed2004

Gene clustering by latent semantic indexing of MEDLINE abstracts.

MOTIVATION: A major challenge in the interpretation of high-throughput genomic data is understanding the functional associations between genes. Previously, several approaches have been described to extract gene relationships from various biological databases using term-matching methods. However, more flexible automated methods are needed to identify functional relationships (both explicit and implicit) between genes from the biomedical literature. In this study, we explored the utility of Latent Semantic Indexing (LSI), a vector space model for information retrieval, to automatically identify conceptual gene relationships from titles and abstracts in MEDLINE citations. RESULTS: We found that LSI identified gene-to-gene and keyword-to-gene relationships with high average precision. In addition, LSI identified implicit gene relationships based on word usage patterns in the gene abstract documents. Finally, we demonstrate here that pairwise distances derived from the vector angles of gene abstract documents can be effectively used to functionally group genes by hierarchical clustering. Our results provide proof-of-principle that LSI is a robust automated method to elucidate both known (explicit) and unknown (implicit) gene relationships from the biomedical literature. These features make LSI particularly useful for the analysis of novel associations discovered in genomic experiments. AVAILABILITY: The 50-gene document collection used in this study can be interactively queried at http://shad.cs.utk.edu/sgo/sgo.html.

Abstracting and Indexing↗
PubMed2005

GeneInfoMiner--a web server for exploring biomedical literature using batch sequence ID.

GeneInfoMiner is a web-based system for searching Medline abstracts using sequence ID lists such as GenBank accession numbers derived from high-throughput experiments. It will map query results to MeSH topics to facilitate the exploration of the biological significance of the sequence ID lists. GeneInfoMiner is based on a custom gene and protein name identification engine that can map gene and protein names to important molecular biology databases.

Abstracting and Indexing↗