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Global mapping of pharmacological space.

We present the global mapping of pharmacological space by the integration of several vast sources of medicinal chemistry structure-activity relationships (SAR) data. Our comprehensive mapping of pharmacological space enables us to identify confidently the human targets for which chemical tools and drugs have been discovered to date. The integration of SAR data from diverse sources by unique canonical chemical structure, protein sequence and disease indication enables the construction of a ligand-target matrix to explore the global relationships between chemical structure and biological targets. Using the data matrix, we are able to catalog the links between proteins in chemical space as a polypharmacology interaction network. We demonstrate that probabilistic models can be used to predict pharmacology from a large knowledge base. The relationships between proteins, chemical structures and drug-like properties provide a framework for developing a probabilistic approach to drug discovery that can be exploited to increase research productivity.

Computational Biology↗

Migraine prophylactic drugs: proof of efficacy, utilization and cost.

OBJECTIVES: In order to understand the pattern of utilization of migraine prophylactic drugs by US physicians, we reviewed the scientific rigor of published trials of anti-migraine medications, assessed their cost, and tested the correlation, if any, between utilization, scientific rigor and cost. MATERIALS AND METHODS: Scientific rigor of published reports. We identified all placebo-controlled, randomized, double-blind trials of migraine prophylactic agents through Medline search, major Headache textbooks and proceedings of major scientific meetings where headache-related topics are discussed. We excluded trials that did not include placebo treatment during the active phase of the study. The trials were reviewed and rated for scientific rigor using a 5-point scale (scientific score [ss]; 1 = low, 5 = good), blinded to the physicians' utilization data and cost of the drugs. Studies that did not show benefit of the active drug over placebo were scored -1 to -5, thus allowing for the reverse logic of negative studies. US physicians utilization. Neurologists and primary care physicians (PCP) completed phone-mail-phone questionnaires which inquired about first and second choices of migraine prophylaxis. These choices were averaged to obtain a weighted average percent usage of each drug. Cost. The average wholesale price (AWP) of each drug was obtained from data published by Adelman and Von Seggern, and from the Amerisource (7/9/96) catalog. STATISTICAL ANALYSIS: Spearman's correlation coefficient was used to assess the relationship between the average ss, physician use, and cost of each drug. RESULTS: Propranolol (ss = 1.44), amitriptyline (ss = 2.33) and verapamil (ss = 1.00) were the three preferred migraine prophylactic drugs by both neurologists and PCPs. Approximately 10% of neurologists said that divalproex (ss = 3.75) would be their first or second choice. The selective serotonin reuptake blockers were favored by 13.21% of PCPs. All other prophylactic drugs were felt to be first or second line of treatment by less than 10% of either neurologists or PCPs. Except for one study (ss = 1) that showed that propranolol reduced the migraine frequency by 76% over placebo, trials of the three most preferred medications failed to demonstrate that the active drug is > 50% better than placebo, i.e. the difference in headache frequency when on placebo vs active drug is > 50%. Of the drugs available in the United States, flurbiprofen and metoprolol achieved the best ss (5.00 and 4.33, respectively) but their efficacy over placebo (23% and 14-33%, respectively) and cost ($67.2 and $65.6) were unfavorable. Neurologists and PCPs chose migraine prophylaxis on the basis of scientific merit (r = 0.644, p = 0.018; r = 0.576, p = 0.05, respectively) but not cost (r = -0.254, p = 0.45; r = -0.255, p = 0.455). CONCLUSION: The three most commonly chosen migraine prophylactic agents have not been shown irrefutably to prevent migraine. Furthermore, their benefit, if any, does not exceed 50% over placebo. The well-conducted recent trials that demonstrated the efficacy of divalproex in migraine prevention are steps in the right direction of finding the "ideal migraine preventative agent". Until that drug is discovered, it is difficult to argue that one migraine prophylactic medication is superior to another and accordingly should be used as a first line of treatment.

Adult↗

[Early detection of cancer of the prostate. Pros and cons].

Since the introduction of PSA determination for the detection of cancer of the prostate, there have been discussions of the pros and cons of PSA screening for early detection of this cancer. The PSA test used in combination with digital rectal examination has proven to be a superior diagnostic instrument for the diagnosis of malignant prostate disease at an early stage. The German Guideline Catalog for the early detection of carcinoma of the prostate recommends measurement of the PSA from the age of 45 onwards in patients who have first been comprehensively informed about the further proceedings in the event of a positive result. To date, PSA screening has not been shown to lower the disease-specific mortality rate. Two ongoing randomized, multicentre studies (ERSPC and PLCO) are expected to throw more light on the matter.

Aged↗

A survey identified publication bias in the secondary literature.

OBJECTIVE: To investigate the existence of publication bias in the translation of evidence from the primary to the secondary literature, using the ACP Journal Club (ACPJC) as a representative of secondary literature and Medline as a representative of primary literature. METHODS: A cross-sectional survey of randomly selected randomized controlled trials of therapy published between 1994 and 2002 in English in Medline and all summaries of therapy trials published by ACPJC between the same dates. The main outcome measure was the rate of positive trials from among those trials aiming to find a difference between groups. RESULTS: 831 trials from Medline and 823 summaries of trials from ACPJC met the inclusion criteria and were included in the study. Compared to trials cataloged in Medline, ACPJC preferentially summarized trials with a positive outcome (P < .001). This bias remained after controlling for other selection biases seen in the ACPJC such as preferentially summarizing multicentered trials with large sample size, no active treatment control, blinding, and in certain disease fields (adjusted odds ratio 2.8, 95% confidence interval 2.02-3.93). CONCLUSION: The ACPJC preferentially summarizes trials with a positive outcome. Efforts should be made to reduce this bias.

Cross-Sectional Studies↗

The ubiquitin superfamily: members, features, and phylogenies.

The ubiquitin superfamily is a rich repository of small, conserved, functionally unique, and important proteins. Its member proteins fold simply and similarly, with kinetic and thermodynamic ease (Sorenson, J. M.; Head-Gordon, T. Toward minimalist models of larger proteins: A ubiquitin-like protein. Proteins 2002, 46, 368-379). They have been implicated in numerous cancers, neurodegenerations, inflammations, and various disorders affecting signal transduction or protein half-life. These proteins serve the cell generally as portable recognition tags with distinct intracellular roles; indeed, tagging with small protein modifiers has become a new hallmark of post-translational modifications and other signal transduction phenomenon (Finley, D. J. Signal transduction. An alternative to destruction. Nature 2001, 412, 283, 285-286). Because many ubiquitin-like proteins bear similarities in sequence, structure, and function, we gathered protein sequences containing the ubiquitin domain from public databases and created a highly granular and defined protein catabolism database to catalog, summarize, reference, and relate them to their targets and specific ligases (to be described elsewhere). In this paper, we reveal a compilation of proteins possessing the ubiquitin domain. This comprises the first and most important part of our database content. We searched available organismal proteomes for sequence-related members of the ubiquitin superfamily and here present over 200 proteins possessing this domain. These proteins were organized phylogenetically and functionally, thereby defining several new families. To our knowledge, this is the most complete assemblage of ubiquitin domains to date.

Animals↗

The exclusion of pregnant, pregnable, and once-pregnable people (a.k.a. women) from biomedical research.

The barriers to women's participation as subjects in biomedical research are currently being challenged as a matter of legislative policy, medicine, and law. This Article catalogs the ways in which women have been disadvantaged by their exclusion and recent developments to redress them, and goes on to dissect the underlying rationales for excluding women from clinical trials. The author reveals the 'fundamental misconception' behind exclusionary rationales, and argues that research sponsors in fact have more to fear in the way of potential liability from the exclusion of women, even pregnant women and women of child-bearing capacity, than from their inclusion. Finally, the Article suggests strategies for achieving reform of these exclusionary practices.

Abnormalities, Drug-Induced↗

[Laparoscopic hernia surgery--status of minimal invasive techniques in a spectrum of surgical indications].

Endoscopic surgery led in the nineties to a discussion on surgical treatment of hernias. At the present time there are three groups of operative procedures: the conventional procedure--Shouldice, Bassini--the open tension-free procedure with implantation of a mesh--Lichtenstein, Gilbert-Rutkow--and the endoscopic procedure (predominantly transabdominal preperitoneal hernioplasty (TAPP) and total extraperitoneal hernioplasty (TEP)). The debate on the optimal therapy of hernias is understandable in view of the large number of hernia operations which are carried out. Numerous studies, some randomized, have demonstrated both the advantages and the disadvantages of the individual operative procedures. In addition to the recurrence rate and the complications, the cost factor and the associated socio-economic aspects of the particular operation play an increasingly important role in the decision on the method that should be used. In December 1995 some Austrian surgeons, who concerned themselves with problems of hernia repair already before the definitive introduction of laparoscopic hernia repair in today's surgery, came together on the occasion of a "Consensus Conference". During the meeting a summary of all relevant aspects of the complex of problems was worked out and summarized in a catalog of indications for the different operative interventions. The main statement was that the traditional open surgery, which can be performed under local anesthesia is indicated for an unilateral primary hernia. In case of an unclear finding at the contralateral side, as well as in case of a recurrent hernia, an endoscopic procedure is indicated. Meanwhile the Hernia Forum of Zürs ("Zürser Hernienforum") was founded. The function of this forum is the realization of a prospective randomized study for hernia repair in Austria.

Hernia, Inguinal↗

A survey and evaluation of human genetic traits used in classroom laboratory studies.

Twenty-six selected introductory biology and genetics laboratory manuals were examined and were found to include 57 human "inherited" traits as examples for classroom study. Forty-three of these 57 traits are included in McKusick's catalog of human inherited characteristics, Mendelian Inheritance in Man. Of these 43 traits, 26 are annotated with an asterisk, indicating that their modes of inheritance are well documented, while 17 traits are not so annotated, suggesting uncertain mechanisms of inheritance. Fourteen of the 57 traits are not found in McKusick's catalog, implying that they may not be inherited traits at all or that their modes of inheritance may be polygenic. Current literature also suggest that certain traits included in the McKusick catalog may, in fact, not have a genetic basis. Notable examples of such questionable traits are handedness, hand clasping, and tongue rolling. Clearly, a need exists for reliable morphological and easily detected biochemical human genetic traits for use in classroom instruction. Authors preparing instructional manuals for introductory biology and genetics laboratory studies should carefully select the traits with which they illustrate human inheritance. A first requisite for selection of such characteristics must be conclusive evidence that the trait does, indeed, have an established genetic basis. Additional criteria for selection of such traits are also discussed.

Bibliographies as Topic↗

Counterexamples in chemical ring perception.

Ring information is a large part of the structural topology used to identify and characterize molecular structures. It is hence of crucial importance to obtain this information for a variety of tasks in computational chemistry. Many different approaches for "ring perception", i.e., the extraction of cycles from a molecular graph, have been described. The chemistry literature on this topic, however, reports a surprisingly large number of incorrect statements about the properties of chemically relevant ring sets and, in particular, about the mutual relationships of different sets of cycles in a graph. In part these problems seem to have arisen from a sometimes rather idiosyncratic terminology for notions that are fairly standard in graph theory. In this contribution we translate the definitions of concepts such as the Smallest Set of Smallest Rings, Essential Set of Essential Rings, Extended Set of Smallest Rings, Set of Smallest Cycles at Edges, Set of Elementary Rings, K-rings, and beta-rings into a more widely used mathematical language. We then outline the basic properties of different cycle sets and provide numerous counterexamples to incorrect claims in the published literature. These counterexamples may have a serious practical impact because at least some of them are molecular graphs of well-known molecules. As a consequence, we propose a catalog of desirable properties for chemically useful sets of rings.

Journal Article↗

Canonical labeling of proteome maps.

We propose a canonical labeling of proteome maps, which enables one to sort and catalog the maps in a simple way. The canonical label of a proteome map is based on the canonical labeling of vertexes of Hasse diagram embedded in the map resulting in the adjacency matrix, the rows of which when viewed as binary numbers are the smallest possible such numbers. The use of the approach in documentation is illustrated with the proteome maps of liver cells of healthy male Fisher F344 rats and the rats treated with different peroxisome proliferators.

Algorithms↗

Electrosurgical methods for arthroscopic meniscectomy: A review of the literature.

PURPOSE: To outline the development of electrosurgical (radiofrequency) devices, explain the basic principles, and review the current orthopaedic literature regarding the application of electrosurgery to arthroscopic partial meniscectomy. MATERIALS AND METHODS: The history and principles of electrosurgery were obtained from various pertinent texts and journal articles. A literature search was performed using MEDLINE; reviewed articles consisted of articles in the English language cataloged between 1966 and January 1999. RESULTS: The history and principles of electrosurgery are reviewed. The articles pertaining to arthroscopic electrosurgical meniscectomy are discussed with a separate discussion on the potential complications of using radiofrequency energy for meniscal ablation, including articular cartilage damage, osteonecrosis, and damage caused by irrigant. CONCLUSION: Electrosurgery has been shown to be an effective tool in arthroscopic meniscectomy. Further research and refinement is warranted because it may show superiority to other methods in certain situations.

Arthroscopy↗

Book availability as a performance measure of a library: an analysis of the effectiveness of a health sciences library.

User satisfaction as a measure of library effectiveness has been studied by using Kantor's branching technique. Cleveland Health Sciences Library, Cleveland, Ohio, was used as the center of this study. The study measured independently the user bibliographic information performance, collection development policy performance, acquisition policy performance, user catalog performance, circulation performance, library operation/functioning performance, and the user search performance. Each of these categories represented one or more of the factors of library performance that could account for the possibility of users' failure. The sample size consisted of 1000 requests for book titles. The book availability rates were 59.60% without the help of the librarian and 63.50% with the help of the librarian. The results indicate that a dynamic study of library policies at regular intervals by using the Kantor's method, which is easily reproducible, can maximize library resources for the most effective fulfillment of user demand.

Consumer Behavior↗

Transgenic and knockout databases: behavioral profiles of mouse mutants.

Genetically engineered strains of mice, modified by transgenesis or gene targeting ("knockouts") are being generated at an impressive rate and used, among other areas, as premiere research tools in deciphering the genetic basis of behavior. As behavioral phenotyping strategies continue to evolve, characterization of these "designer" mice will provide models to evaluate the efficacy of new pharmacological and gene therapy treatments in human hereditary diseases. Reported behavioral profiles include aberrant social, reproductive, and parental behaviors, learning and memory deficits, feeding disorders, aggression, anxiety-related behaviors, pain/analgesia, and altered responses to antidepressants, antipsychotics, ethanol, and psychostimulant drugs of abuse. The Induced Mutant Resource (IMR) at The Jackson Laboratory (TJL, Bar Harbor, ME, USA) imports, cryopreserves, develops, maintains, and distributes biomedically important stocks of transgenic and targeted mutant mice to the research community. Information on neurological/behavioral strains--including behavioral performance, husbandry requirements, strain availability, and genetic typing protocols--is provided through the IMR database (http://www.jax.org/resources/documents/imr/). A catalog of available strains is readily accessible via the JAX Mice website at http://jaxmice.jax.org/index.shtml. In addition, TJL is now host to TBASE (http://tbase.jax.org/), a comprehensive, public-domain database with primary emphasis on mouse knockouts. TBASE contains an exhaustive list of knockout-related citations and provides an extensive phenotypic characterization of numerous behavioral mutants that is extracted directly from the literature. Present efforts to merge the two resources into a novel, schematically enhanced database, provisionally named Transgenic and Targeted Mutation Database (TTMD), will be briefly discussed.

Animals↗

International Union of Pharmacology. XLVI. G protein-coupled receptor list.

NC-IUPHAR (International Union of Pharmacology Committee on Receptor Nomenclature and Drug Classification) and its subcommittees provide authoritative reports on the nomenclature and pharmacology of G protein-coupled receptors (GPCRs) that summarize their structure, pharmacology, and roles in physiology and pathology. These reports are published in Pharmacological Reviews (http://www.iuphar.org/nciuphar_arti.html) and through the International Union of Pharmacology (IUPHAR) Receptor Database web site (http://www.iuphar-db.org/iuphar-rd). The essentially complete sequencing of the human genome has allowed the cataloging of all of the human gene sequences potentially encoding GPCRs. The IUPHAR Receptor List (http://www.iuphar-db.org/iuphar-rd/list/index.htm) presents this catalog giving IUPHAR-approved nomenclature (where available), known ligands, and gene names for all of these potential receptors (excluding sensory receptors and pseudogenes) together with links to curated sequence, descriptive information, and additional links in the Entrez Gene database (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene). This list is a major new initiative of NC-IUPHAR that, through continuing curation, defines the target of our ongoing receptor classification and invites further input from the scientific community.

Animals↗

The biologic actions of extracellular adenosine triphosphate.

The study of the biologic effects of extracellular ATP is rapidly progressing from cataloging the integrated biologic responses of isolated tissues to characterizing the biochemical basis of signal transduction in isolated cells. Clearly, many fundamental issues remain; these include the classification of receptor subtypes, identification of defined or new signal-transduction pathways, generation of specific high-affinity ligands for the various ATP receptor subtypes, and ultimately, the development of protocols for the identification, isolation, cloning, and physicochemical characterization of the receptor moities per se. Such work will be essential for developing selective ATP-receptor antagonists. Such antagonists, in turn, will facilitate evaluation of the role of these receptors in physiological and/or pathological processes. A possible therapeutic role for drugs selective for these receptors is suggested by the critical pathophysiological roles of the human cell types (phagocytic leukocytes, vascular endothelial cells) known to express such receptors. The earlier, seminal work on the biologic actions of extracellular ATP was largely performed by smooth-muscle physiologists and pharmacologists. With the expanding range of, and interest in, this topic, recent studies have been carried out largely by diverse groups of pharmacologists, neurobiologists, physiologists, and biochemists. Not surprisingly, these various scientists often investigate certain aspects of extracellular ATP action from different perspectives, using the specialized tools and methods of their respective disciplines. Hopefully, by integrating these interdisciplinary perspectives on the biologic actions of extracellular ATP, there will be rapid progress in this field during the next few years.

Adenosine Triphosphate↗

Mechanization of library procedures in the medium-sized medical library. 8. Computer applications in hospital departmental libraries.

To test the hypothesis that a standard library system could be designed for hospital departmental libraries, a system was developed and partially tested for four departmental libraries in the Washington University School of Medicine and Associated Hospitals. The system from determination of needs through design and evaluation, is described. The system was limited by specific constraints to control of the monograph collection. Products of control include catalog cards, accessions list, new book list, location list, fund list, missing book list, and discard book list. Sample data form and pages from a procedure manual are given, and conversion from a manual to an automated system is outlined. The question of standardization of library records and procedures is discussed, with indications of the way in which modular design, as utilized in this system, could contribute to greater flexibility in design of future systems. Reference is made to anticipating needs for organizing departmental libraries in developing regional medical library programs and to exploring the role of the departmental library in a medical library network.

Computers↗

[Health education: object of study in dissertations and theses by Brazillian nurses].

This study was aimed at surveying the quantity of dissertations and theses written by nurses on health education, identifying and analyzing their methodological steps. 17 Catalogs of Information about Research and Researchers from CEPEn/ABEn--published from 1979 to 1999--have been examined. The sample comprises 105 dissertations and 15 theses about the theme. Chronic diseases, pregnancy-puerperal cycle, health education, management and perisurgery situation have stood out as objects of study. The populations were adults, nursing professionals, women, children and adolescents. Interviewing was the most used technique. Authors indicated the need to improve educative practices and considered that health education motivates changes in lifestyle. It was concluded that there is a need to strengthen research into the everyday of Nursing in a historical and social context.

Academic Dissertations as Topic↗

Medicine and the Internet. What can I learn from the Internet?

What is the Internet? The Internet is the biggest network of information resources the world has ever seen and is growing rapidly each day. The Internet and the World Wide Web (The Web) represent the first technology to fully integrate the communications found on bookshelves, magazine racks, catalog files, fax machines, symposiums, in television/radio studios and the common mail system into a global infrastructure with extraordinary capabilities to deliver timely health care information. Unlike conventional media like newspapers or television, the Internet provides rapid one-to-one communication between millions of individuals. Television and newspapers communicate from "a few" (the writers and advertisers) to "many" (the readership). On the Internet, everyone is a "peer," being both an information provider and consumer on a 24-hour, 7-day a week basis. This article will discuss ways you can use the Internet's information resources in your own personal and professional life.

Communication↗