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At least 775 records · Page 43Linked to original sources

Annotation: Tourette syndrome: a relentless drumbeat--driven by misguided brain oscillations.

OBJECTIVE: This annotation reviews recent evidence that points to the likely role of aberrant neural oscillations in the pathogenesis of Tourette syndrome (TS). METHODS: The available anatomic and electrophysiological findings in TS are reviewed in the context of an emerging picture of the crucial role that neural oscillations play in maintaining normal central nervous system (CNS) function. RESULTS: Neurons form behavior-dependent oscillating networks of various sizes and frequencies that bias input selection and facilitate synaptic plasticity, mechanisms that cooperatively support temporal representation as well as the transfer and long-term consolidation of information. Coherent network activity is likely to modulate sensorimotor gating as well as focused motor actions. When these networks are dysrhythmic, there may be a loss of control of sensory information and motor action. The known electrophysiological effects of medications and surgical interventions used to treat TS likely have an ameliorative effect on these aberrant oscillations. Similarly, a strong case can be made that successful behavioral treatments involve the willful training regions of the prefrontal cortex to engage in tic suppression and the performance of competing motor responses to unwanted sensory urges such that these prefrontal regions become effective modulators of aberrant thalamocortical rhythms. CONCLUSIONS: A deeper understanding of neural oscillations may illuminate the complex, challenging, enigmatic, internal world that is TS.

Basal Ganglia↗

Annotated bibliography of structural equation modelling: technical work.

Researchers must be familiar with a variety of source literature to facilitate the informed use of structural equation modelling. Knowledge can be acquired through the study of an expanding literature found in a diverse set of publishing forums. We propose that structural equation modelling publications can be roughly classified into two groups: (a) technical and (b) substantive applications. Technical materials focus on the procedures rather than substantive conclusions derived from applications. The focus of this article is the former category; included are foundational/major contributions, minor contributions, critical and evaluative reviews, integrations, simulations and computer applications, precursor and historical material, and pedagogical textbooks. After a brief introduction, we annotate 294 articles in the technical category dating back to Sewall Wright (1921).

Humans↗

Deciphering tuberactinomycin biosynthesis: isolation, sequencing, and annotation of the viomycin biosynthetic gene cluster.

The tuberactinomycin antibiotics are essential components in the drug arsenal against Mycobacterium tuberculosis infections and are specifically used for the treatment of multidrug-resistant tuberculosis. These antibiotics are also being investigated for their targeting of the catalytic RNAs involved in viral replication and for the treatment of bacterial infections caused by methicillin-resistant Staphylococcus aureus strains and vancomycin-resistant enterococci. We report on the isolation, sequencing, and annotation of the biosynthetic gene cluster for one member of this antibiotic family, viomycin, from Streptomyces sp. strain ATCC 11861. This is the first gene cluster for a member of the tuberactinomycin family of antibiotics sequenced, and the information gained can be extrapolated to all members of this family. The gene cluster covers 36.3 kb of DNA and encodes 20 open reading frames that we propose are involved in the biosynthesis, regulation, export, and activation of viomycin, in addition to self-resistance to the antibiotic. These results enable us to predict the metabolic logic of tuberactinomycin production and begin steps toward the combinatorial biosynthesis of these antibiotics to complement existing chemical modification techniques to produce novel tuberactinomycin derivatives.

Amino Acids↗

Study of the five Rickettsia prowazekii proteins annotated as ATP/ADP translocases (Tlc): Only Tlc1 transports ATP/ADP, while Tlc4 and Tlc5 transport other ribonucleotides.

The obligate intracytoplasmic pathogen Rickettsia prowazekii relies on the transport of many essential compounds from the cytoplasm of the eukaryotic host cell in lieu of de novo synthesis, an evolutionary outcome undoubtedly linked to obligatory growth in this metabolite-replete niche. The paradigm for the study of rickettsial transport systems is the ATP/ADP translocase Tlc1, which exchanges bacterial ADP for host cell ATP as a source of energy, rather than as a source of adenylate. Interestingly, the R. prowazekii genome encodes four open reading frames that are highly homologous to the well-characterized ATP/ADP translocase Tlc1. Therefore, by annotation, the R. prowazekii genome encodes a total of five ATP/ADP translocases: Tlc1, Tlc2, Tlc3, Tlc4, and Tlc5. We have confirmed by quantitative reverse transcriptase PCR that mRNAs corresponding to all five tlc homologues are expressed in R. prowazekii growing in L-929 cells and have shown their heterologous protein expression in Escherichia coli, suggesting that none of the tlc genes are pseudogenes in the process of evolutionary meltdown. However, we demonstrate by heterologous expression in E. coli that only Tlc1 functions as an ATP/ADP transporter. A survey of nucleotides and nucleosides has determined that Tlc4 transports CTP, UTP, and GDP. Intriguingly, although GTP was not transported by Tlc4, it was an inhibitor of CTP and UTP uptake and demonstrated a K(i) similar to that of GDP. In addition, we demonstrate that Tlc5 transports GTP and GDP. We postulate that Tlc4 and Tlc5 serve the primary function of maintaining intracellular pools of nucleotides for rickettsial nucleic acid biosynthesis and do not provide the cell with nucleoside triphosphates as an energy source, as is the case for Tlc1. Although heterologous expression of Tlc2 and Tlc3 was observed in E. coli, we were unable to identify substrates for these proteins.

Adenosine Diphosphate↗

Functional annotation of class I lysyl-tRNA synthetase phylogeny indicates a limited role for gene transfer.

Functional and comparative genomic studies have previously shown that the essential protein lysyl-tRNA synthetase (LysRS) exists in two unrelated forms. Most prokaryotes and all eukaryotes contain a class II LysRS, whereas most archaea and a few bacteria contain a less common class I LysRS. In bacteria the class I LysRS is only found in the alpha-proteobacteria and a scattering of other groups, including the spirochetes, while the class I protein is by far the most common form of LysRS in archaea. To investigate this unusual distribution we functionally annotated a representative phylogenetic sampling of LysRS proteins. Class I LysRS proteins from a variety of bacteria and archaea were characterized in vitro by their ability to recognize Escherichia coli tRNA(Lys) anticodon mutants. Class I LysRS proteins were found to fall into two distinct groups, those that preferentially recognize the third anticodon nucleotide of tRNA(Lys) (U36) and those that recognize both the second and third positions (U35 and U36). Strong recognition of U35 and U36 was confined to the pyrococcus-spirochete grouping within the archaeal branch of the class I LysRS phylogenetic tree, while U36 recognition was seen in other archaea and an example from the alpha-proteobacteria. Together with the corresponding phylogenetic relationships, these results suggest that despite its comparative rarity the distribution of class I LysRS conforms to the canonical archaeal-bacterial division. The only exception, suggested from both functional and phylogenetic data, appears to be the horizontal transfer of class I LysRS from a pyrococcal progenitor to a limited number of bacteria.

Acylation↗

Improving functional annotation of non-synonomous SNPs with information theory.

Automated functional annotation of nsSNPs requires that amino-acid residue changes are represented by a set of descriptive features, such as evolutionary conservation, side-chain volume change, effect on ligand-binding, and residue structural rigidity. Identifying the most informative combinations of features is critical to the success of a computational prediction method. We rank 32 features according to their mutual information with functional effects of amino-acid substitutions, as measured by in vivo assays. In addition, we use a greedy algorithm to identify a subset of highly informative features. The method is simple to implement and provides a quantitative measure for selecting the best predictive features given a set of features that a human expert believes to be informative. We demonstrate the usefulness of the selected highly informative features by cross-validated tests of a computational classifier, a support vector machine (SVM). The SVM's classification accuracy is highly correlated with the ranking of the input features by their mutual information. Two features describing the solvent accessibility of "wild-type" and "mutant" amino-acid residues and one evolutionary feature based on superfamily-level multiple alignments produce comparable overall accuracy and 6% fewer false positives than a 32-feature set that considers physiochemical properties of amino acids, protein electrostatics, amino-acid residue flexibility, and binding interactions.

Analysis of Variance↗

Bioie: retargetable information extraction and ontological annotation of biological interactions from the literature.

The need for extracting general biological interactions of arbitrary types from the rapidly growing volume of the biomedical literature is drawing increased attention, while the need for this much diversity also requires both a robust treatment of complex linguistic phenomena and a method to consistently characterize the results. We present a biomedical information extraction system, BioIE, to address both of these needs by utilizing a full-fledged English grammar formalism, or a combinatory categorial grammar, and by annotating the results with the terms of Gene Ontology, which provides a common and controlled vocabulary. BioIE deals with complex linguistic phenomena such as coordination, relative structures, acronyms, appositive structures, and anaphoric expressions. In order to deal with real-world syntactic variations of ontological terms, BioIE utilizes the syntactic dependencies between words in sentences as well, based on the observation that the component words in an ontological term usually appear in a sentence with known patterns of syntactic dependencies.

Abstracting and Indexing↗

Ruleminer: a knowledge system for supporting high-throughput protein function annotations.

In this paper, we present RuleMiner, a knowledge system to facilitate a seamless integration of multi-sequence analysis tools and define profile-based rules for supporting high-throughput protein function annotations. This system consists of three essential components, Protein Function Groups (PFGs), PFG profiles and rules. The PFGs, established from an integrated analysis of current knowledge of protein functions from Swiss-Prot database and protein family-based sequence classifications, cover all possible cellular functions available in the database. The PFG profiles illustrate detailed protein features in the PFGs as in sequence conservations, the occurrences of sequence-based motifs, domains and species distributions. The rules, extracted from the PFG profiles, describe the clear relationships between these PFGs and all possible features. As a result, the RuleMiner is able to provide an enhanced capability for protein function analysis, such as results from the integrated sequence analysis tools for given proteins can be comparatively analyzed due to the clear feature-PFG relationships. Also, much needed guidance is readily available for such analysis. If the rules describe one-to-one (unique) relationships between the protein features and the PFGs, then these features can be utilized as unique functional identifiers and cellular functions of unknown proteins can be reliably determined. Otherwise, additional information has to be provided.

Algorithms↗

Gene annotation: prediction and testing.

Fifty years after the publication of DNA structure, the whole human genome sequence will be officially finished. This achievement marks the beginning of the task to catalogue every human gene and identify each of their function expression patterns. Currently, researchers estimate that there are about 30,000 human genes and approximately 70% of these can be automatically predicted using a combination of ab initio and similarity-based programs. However, to experimentally investigate every gene's function, the research community requires a high-quality annotation of alternative splicing, pseudogenes, and promoter regions that can only be provided by manual intervention. Manual curation of the human genome will be a long-term project as experimental data are continually produced to confirm or refine the predictions, and new features such as noncoding RNAs and enhancers have not been fully identified. Such a highly curated human gene-set made publicly available will be a great asset for the experimental community and for future comparative genome projects.

Alternative Splicing↗

Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes.

To complement cDNA libraries from the human eye at early gestation and to discover candidate genes associated with early ocular development, we used freshly dissected human eyeballs from week 9-14 of gestation to construct the early human fetal eye cDNA library. A total of 15,809 clones were isolated and sequenced from the unamplified and unnormalized library. We screened 11,246 good-quality ESTs, leading to the identification of 5,534 nonredundant clusters. Among them, 4,010 (72%) genes matched in the human protein database (Ensembl). The remaining 28% (1,524) corresponded to potentially novel or previously unidentified ESTs. We used BLASTX to compare our EST data with eight organisms and found common expression of a high portion of genes: Caenorhabditis briggsae (26%), Caenorhabditis elegans (27%), Anopheles gambiae (37%), Drosophila melanogaster (32%), Danio rerio (42%), Fugu rubripes (49%), Rattus norvegicusvalitus (52%), and Mus musculus (59%). Nevertheless, 48% (2,680 of 5,534) of the genes expressed in the early developing eye were not shared with current NEIBank human eye cDNA data. In addition, eight known retinal disease genes existed in our ESTs. Among them, six (COL11A1, BBS5, PDE6B, OAT, VMD2, and PGK1) were conserved among the genomes of other organisms, indicating that our annotated EST set provides not only a valuable resource for gene discovery and functional genomic analysis but also for phylogenetic analysis. Our foremost early gestation human eye cDNA library could provide detailed comparisons across species to identify physiological functions of genes and to elucidate evolutionary mechanisms.

Animals↗

Chicken genomics resource: sequencing and annotation of 35,407 ESTs from single and multiple tissue cDNA libraries and CAP3 assembly of a chicken gene index.

Its accessibility, unique evolutionary position, and recently assembled genome sequence have advanced the chicken to the forefront of comparative genomics and developmental biology research as a model organism. Several chicken expressed sequence tag (EST) projects have placed the chicken in 10th place for accrued ESTs among all organisms in GenBank. We have completed the single-pass 5'-end sequencing of 37,557 chicken cDNA clones from several single and multiple tissue cDNA libraries and have entered 35,407 EST sequences into GenBank. Our chicken EST sequences and those found in public databases (on July 1, 2004) provided a total of 517,727 public chicken ESTs and mRNAs. These sequences were used in the CAP3 assembly of a chicken gene index composed of 40,850 contigs and 79,192 unassembled singlets. The CAP3 contigs show a 96.7% match to the chicken genome sequence. The University of Delaware (UD) EST collection (43,928 clones) was assembled into 19,237 nonredundant sequences (13,495 contigs and 5,742 unassembled singlets). The UD collection contains 6,223 unique sequences that are not found in other public EST collections but show a 76% match to the chicken genome sequence. Our chicken contig and singlet sequences were annotated according to the highest BlastX and/or BlastN hits. The UD CAP3 contig assemblies and singlets are searchable by nucleotide sequence or key word (http://cogburn.dbi.udel.edu), and the cDNA clones are readily available for distribution from the chick EST website and clone repository (http://www.chickest.udel.edu). The present paper describes the construction and normalization of single and multiple tissue chicken cDNA libraries, high-throughput EST sequencing from these libraries, the CAP3 assembly of a chicken gene index from all public ESTs, and the identification of several nonredundant chicken gene sets for production of custom DNA microarrays.

Animals↗

The treatment of attention-deficit hyperactivity disorder: an annotated bibliography and critical appraisal of published systematic reviews and metaanalyses.

CONTEXT: The Agency for Health Care Policy and Research charged the McMaster Evidence-based Practice Center with conducting a comprehensive systematic review of the literature on the treatment of attention-deficit hyperactivity disorder (ADHD), with input from various groups of stakeholders. One strategy used to avoid duplication of work included a critical appraisal of existing systematic reviews and metaanalyses. OBJECTIVE: To identify and appraise published metaanalyses and systematic reviews on the treatment of ADHD and to produce an annotated bibliography. DATA SOURCES: Medline, Cumulative Index in Nursing and Allied Health (CINAHL), Healthstar, Psycinfo, and Embase were searched to September 1998; the Cochrane Database (1998 issue 3), selected Internet sites, and the files of investigators were also reviewed. STUDY SELECTION: Review articles described as systematic reviews or metaanalyses or including a Methods section were identified independently by 3 reviewers. DATA EXTRACTION: Two reviewers extracted, by consensus, relevant information on the name, methodological quality, ADHD-related aspects (comorbid disorders, family characteristics) of those reviews; data on the population, study setting, interventions, and outcomes evaluated by the reviews were also retrieved. RESULTS: Thirteen reviews, published from 1982 to 1998, were included. Eight included metaanalysis and 5 a qualitative review. Nonpharmacological treatments were mentioned in 6 reviews and combination therapies in 3. One review focused on the treatment of adults. Forty-seven drugs and 20 adverse effects were mentioned. Most reviews had major methodological flaws. CONCLUSIONS: Most published systematic reviews and metaanalyses on the treatment of ADHD have limited value for guiding clinical, policy, and research decisions. A rigorous, systematic review following established methodological criteria is warranted.

Attention Deficit Disorder with Hyperactivity↗

The legal status of clinical practice parameters: an annotated bibliography.

An important recent development in American medicine has been the strong push in the last few years toward the formal creation, dissemination, and enforcement of explicit clinical practice guidelines or parameters relating to the quality and efficacy of various medical interventions, parameters that would guide the decisions and actions of physicians and other health care providers (1-3). Medical societies (4), governmental agencies such as the federal Agency for Health Care Policy and Research, and insurers are utilizing a variety of approaches to the development of practice parameters for medical diagnosis and intervention, including informal consensus development, formal consensus development, evidence-based guideline development, and explicit guideline development (5). The number and variety of practice parameters has burgeoned in response to the wide national variations in medical practice patterns, without corresponding differences in clinical outcomes, that have been documented by health services researchers. Several commentators have expressed serious skepticism about the probable impact of practice parameters, surmising that they will be used extensively in a negative manner in medical malpractice litigation (6, 7). Many physicians in particular have asked "how they [practice parameters] can be implemented without courting the ruin of the individual practitioner" (8). In response to these anxieties, a new medicolegal literature has arisen to address the relationship between the development of clinical practice parameters and the physician's exposure to malpractice litigation and adverse judgments, as well as the implications for malpractice insurance premiums. This growing literature has now achieved a critical mass. The major contributions to this corpus at present are listed and annotated below.

Humans↗

The legal status of clinical practice parameters: an updated annotated bibliography.

In response to extensive speculation about the probable liability implications for health care providers of the formal creation and dissemination of explicit practice parameters of guidelines, I prepared several years ago an annotated bibliography of emerging literature on that topic (1). Since preparation of that catalogue, little meaningful clarification of these issues has emerged from the courts, legislatures, or regulatory agencies.

Insurance, Liability↗

The effects of breast reduction and breast augmentation surgery on lactation: an annotated bibliography.

An annotated bibliography reviews journal literature, some medical texts and sources cited therein, from the past ten years on the subject of the effects of breast reduction and breast augmentation surgery on the ability to lactate. Far more information is available about the relationship of breast reduction surgery and lactation than about breast augmentation surgery and lactation. Women are often able to breastfeed after breast augmentation surgery. Depending upon the type of breast reduction surgery, estimates of the number of women who can lactate after reduction surgery range from zero to 70 percent.

Female↗

Cultural competence models in nursing: a selected annotated bibliography.

Since the early 1990s, along with a phenomenal growth of nursing literature published on cultural competence, an array of cultural competence and cultural assessment models has been developed. This annotated bibliography provides bibliographic entries to books, book chapters, and journal articles that deal with the construction, development, or conceptualization of cultural competence and cultural assessment models. It also includes entries to books dealing with cultural assessment guides.

Bibliometrics↗

Phenotype-based screening of mechanistically annotated compounds in combination with gene expression and pathway analysis identifies candidate drug targets in a human squamous carcinoma cell model.

The squamous cell carcinoma HeLa cell line and an epithelial cell line hTERT-RPE with a nonmalignant phenotype were interrogated for HeLa cell selectivity in response to 1267 annotated compounds representing 56 pharmacological classes. Selective cytotoxic activity was observed for 14 of these compounds dominated by cyclic adenosine monophosphate (cAMP) selective phosphodiesterase (PDE) inhibitors, which tended to span a representation of the chemical descriptor space of the library. The PDE inhibitors induced delayed cell death with features compatible with classical apoptosis. The PDE inhibitors were largely inactive when tested against a cell line panel consisting of hematological and nonsquamous epithelial phenotypes. In a genome-wide DNA microarray analysis, PDE3A and PDE2A were found to be significantly increased in HeLa cells compared to the other cell lines. The pathway analysis software PathwayAssist was subsequently used to extract a list of proteins and small molecules retrieved from Medline abstracts associated with the hit compounds. The resulting list consisted of major parts of the cAMP-protein kinase A pathway linking to ERK, P38, and AKT. This molecular network may provide a basis for further exploitation of novel candidate targets for the treatment of squamous cell carcinoma.

Carcinoma, Squamous Cell↗

Annotated bibliography of simulations and games in health education.

This annotated bibliography describes 66 simulation games in health education under the headings: diseases; drug use and abuse; ecology; family planning and human sexuality; health care planning; mental health; nursing; nutrition; physical fitness; and safety. Those reviewed are a selection of the more useful games from among a large number available. Few health education games are suitable for classroom use and few include social modeling through simulation. Games in drug education and mental health areas may contain distorted, out-of-date, or false information. Promising areas for development include: aging, venereal disease, sexuality, consumer health, health careers, safety education, and health planning.

Bibliographies as Topic↗