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Agents, vehicles, and causal inference in bacterial foodborne disease outbreaks: 82 reports (1986-1995).

OBJECTIVE: To examine the study design of, and the practice of causal inference in, investigations of bacterial foodborne disease outbreaks occurring in the United States and to summarize agents and vehicles identified. DESIGN: Retrospective study. PROCEDURE: An online medical reference database was searched for reports of bacterial foodborne disease outbreak investigations published between 1986 and 1995. Reports were retrieved and reviewed for use of 9 causal criteria in investigations. Information on etiologic agents, vehicles, seasonality, and primary study design from each outbreak was also retrieved. RESULTS: 82 reports were retrieved and reviewed. Coherence, consistency, temporality, and strength of association were the causal criteria most commonly used in foodborne disease outbreak investigations. Coherence was used in all investigations. The number of criteria used ranged from 3 to 7. Meat (n = 20) and eggs (12) were the most commonly implicated vehicles. Salmonella sp and Escherichia coli O157:H7 accounted for 55% of agents reportedly isolated. Cohort and case-control methods were the most common study designs. CLINICAL RELEVANCE: Patterns were found in the use of causal criteria in foodborne disease outbreak investigations. These criteria can provide veterinarians and other public health practitioners with a means to effectively conceptualize, communicate, and summarize causal conclusions. The 4 most commonly used criteria may represent core criteria that investigators consider most useful in explaining food-borne disease outbreaks.

Animals↗

Natural menopause and ovarian toxicity associated with breast cancer therapy.

PURPOSE/OBJECTIVES: To provide essential knowledge of the physiologic changes and symptoms associated with declining ovarian function as a basis for assessment and intervention of premenopausal women treated for breast cancer. DATA SOURCES: Published articles selected from computerized databases; reference texts and lay publications on women's health and menopause. DATA SYNTHESIS: In healthy mid-life women, the years preceding and immediately following menopause are characterized by hormonal changes that result in altered menstrual bleeding patterns that progress to cessation of menses. These physiologic changes may be associated with hot flashes; changes in the vaginal epithelium; and mood, cognitive, and sleep alterations that are described as early menopausal symptoms. Adjuvant therapy for breast cancer suppresses ovarian function resulting in a wide variability of menstrual patterns, hormonal changes, and symptom experiences among treated premenopausal women. The natural perimenopausal transition informs our understanding of women who experience chemotherapy-induced premature menopause. IMPLICATIONS FOR NURSING PRACTICE: Knowledge of the underlying physiology and symptom experience of natural and drug-induced menopause provides a foundation for oncology nurses. This foundation is essential to assessment and clinical decision making in the care of women with breast cancer.

Antineoplastic Agents↗

[Validation of a questionnaire of physical sensations in a French-Canadian population].

The objectives of this study are three-fold. The first objective is to present the aspects of reliability and validity of a self-reported questionnaire that evaluates a specific facet of Panic Disorder with Agoraphobia (PDA) for the francophone population of Quebec, mainly the fear of fear. The Body Sensations Questionnaire (17), translated as the Questionnaire des Sensations Physiques (QSP) evaluates the degree to which individuals fear somatic symptoms commonly associated with panic. A second objective is to determine the factorial validity of the QSP and to investigate the dimensionality of the construct as assessed by the questionnaire. The third objective is to establish a reference database for the agoraphobic (N = 141 and N = 70) and the non-clinical population (N = 223). Results suggest that both questionnaires have similar internal consistency, temporal stability, construct validity, and discriminative validity. While the factorial solution of the present study uncovered a three-factor model (somatic, cardiac, and psychosensorial), which points to the multidimensional nature of the construct evaluated by the QSP, it greatly differs from the one obtained by Arrindel's study (5). Nevertheless, the extraction of the three principal components is supported by the results of the screen test and by two different implementations of parallel analysis, i.e., the computation of random eigen values and the use of an interpolation table of eigen values. Finally, it can be concluded that the psychometric properties of the French-Canadian translation of the BSQ are indications that it is an appropriate instrument to use in clinical research and in clinical practice to assess the fear of bodily sensations associated with the fear of fear.

Adult↗

[EndNote 5 reference manager--functions--improvements--personal experiences].

Bibliography database managers are used to manage information recourses: specifically, to maintain a database to references and create bibliographies and reference lists for written works. A good reference management program should make it easy to read and to record the elements that a reference comprises, e.g. authors name, year of publication, title of article etc. It should offer tools that let you find and retrieve references quickly, and it should be able to produce the bibliography in the format required for a particular publication. You can create your database reference by reference or you can download batches of references from one of the popular searching services (e.g. MEDLINE) and you can search in the Internet. When you want to cite a reference you simply paste the reference wherever you want your intext citation to appear. There are many computer programs, but very few stands out as truly useful, time saving, and work enhancing. One of them is EndNote. The reference manager EndNote 5.0 was recently released in Germany. As long-time fans of this excellent program, we upgraded from the previous version. The use of the software package EndNote 5.0 for Windows is described. The main reason for getting EndNote 5.0 is its clearly improved functions and features: especially the co-operation with Microsoft Word (cite while you write) and the spelling examination. Altogether EndNote 5.0 provides also an excellent combination of features and ease of use.

Database Management Systems↗

[Reference manager: a personal database on literature for consultation and word processing].

The software programme Reference manager serves as a personal database for bibliographic references within a restricted field, especially journal articles (with abstracts). Yet it is more than a digital card index. References can be retrieved via author name, keyword, title word, year of publication, or name of periodical. During the preparation of a manuscript by means of a word processor, references can be simply indicated by one or more of these characteristics. Later Reference manager transforms these provisional references automatically into a bibliography and text references, according to the style of the journal in question. The personal database does not have to be built through laborious copying, but can be captured from Medline databases. Updating with recent references is possible by means of bibliographic services such as Current contents or Reference update.

Data Display↗

Reliable and rapid identification of Listeria monocytogenes and Listeria species by artificial neural network-based Fourier transform infrared spectroscopy.

Differentiation of the species within the genus Listeria is important for the food industry but only a few reliable methods are available so far. While a number of studies have used Fourier transform infrared (FTIR) spectroscopy to identify bacteria, the extraction of complex pattern information from the infrared spectra remains difficult. Here, we apply artificial neural network technology (ANN), which is an advanced multivariate data-processing method of pattern analysis, to identify Listeria infrared spectra at the species level. A hierarchical classification system based on ANN analysis for Listeria FTIR spectra was created, based on a comprehensive reference spectral database including 243 well-defined reference strains of Listeria monocytogenes, L. innocua, L. ivanovii, L. seeligeri, and L. welshimeri. In parallel, a univariate FTIR identification model was developed. To evaluate the potentials of these models, a set of 277 isolates of diverse geographical origins, but not included in the reference database, were assembled and used as an independent external validation for species discrimination. Univariate FTIR analysis allowed the correct identification of 85.2% of all strains and of 93% of the L. monocytogenes strains. ANN-based analysis enhanced differentiation success to 96% for all Listeria species, including a success rate of 99.2% for correct L. monocytogenes identification. The identity of the 277-strain test set was also determined with the standard phenotypical API Listeria system. This kit was able to identify 88% of the test isolates and 93% of L. monocytogenes strains. These results demonstrate the high reliability and strong potential of ANN-based FTIR spectrum analysis for identification of the five Listeria species under investigation. Starting from a pure culture, this technique allows the cost-efficient and rapid identification of Listeria species within 25 h and is suitable for use in a routine food microbiological laboratory.

Bacteriological Techniques↗

IAEA Internet database of natural matrix reference materials.

The International Atomic Energy Agency maintains a database on internationally available certified reference materials of natural origin. The database was updated in 1998 and prepared for an Internet implementation. A user-friendly structure was created, providing two main pathways for browsing, either according to the matrix classification or the producer's name. The database presently contains over 20,000 values for 480 measurands and 1085 reference materials from 43 different producers. Most of the materials entered contain values for trace and minor elements (66%).

Database Management Systems↗

Population variation of human mitochondrial DNA hypervariable regions I and II in 105 Croatian individuals demonstrated by immobilized sequence-specific oligonucleotide probe analysis.

AIM: To detect sequence variation in 105 Croatian individuals by the use of duplex polymerase chain reaction amplification of full-length hypervariable region I and II (HVI/HVII) products and subsequent hybridization to a linear array of 27 immobilized sequence-specific oligonucleotide (SSO) probes, which targets six regions within HVI and HVII, and two additional sites, 189 and 16093. METHODS: Chelex-extracted bloodstains were used for amplification of HV regions. In all cases, a single robust amplification was sufficient for immobilized SSO probe typing and subsequent direct sequence analysis for both HVI and HVII. This method, suitable for a range of forensic samples (including shaft portions of single hairs), was also applied to the analysis of 18 skeletal elements recovered from a mass grave. Using a panel of immobilized SSO probes, we have developed a rapid screening approach to mitochondrial DNA (mtDNA) haplotyping before direct sequence analysis. RESULTS: We established a reference sequence database of mtDNA haplotypes for 105 randomly selected Croatian individuals. Fifty different mitotypes were observed (33 unique). The most frequent mitotypes occurred 18 times or approximately 17.1% [111111 189 (A) 16093 (T)] and 11 times or approximately 10.5% [131111 189 (A) 16093 (T)]; all other mitotypes occurred 5% or less. The corresponding genetic diversity value for this database was approximately 0.952. The usefulness of establishing an mtDNA reference database with immobilized SSO probe testing has been demonstrated by determining the strength of a match comparison obtained for one skeletal element and a corresponding maternal reference from 18 specimens recovered from a mass grave. CONCLUSION: The sequence variation detected by the panel of immobilized SSO probes is sufficiently diverse to be used for identification of human skeletal remains from mass graves. The immobilized SSO typing strip targets polymorphic regions within HVI and HVII and is a useful identification tool for mass grave and mass disaster analysis, as well as for criminal casework testing.

Base Sequence↗

Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts.

The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the alpha-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely alpha-helix, beta-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time.

Algorithms↗

Pathbase: a new reference resource and database for laboratory mouse pathology.

Pathbase (http://www.pathbase.net) is a web accessible database of histopathological images of laboratory mice, developed as a resource for the coding and archiving of data derived from the analysis of mutant or genetically engineered mice and their background strains. The metadata for the images, which allows retrieval and interoperability with other databases, is derived from a series of orthogonal ontologies and controlled vocabularies. One of these controlled vocabularies, MPATH, was developed by the Pathbase Consortium as a formal description of the content of mouse histopathological images. The database currently has over 1000 images on-line with 2000 more under curation and presents a paradigm for the development of future databases dedicated to aspects of experimental biology.

Animals↗

Storage and utilization of HLA genomic data--new approaches to HLA typing.

Currently available DNA-based HLA typing assays can provide detailed information about sequence motifs of a tested sample. It is still a common practice, however, for information acquired by high-resolution sequence specific oligonucleotide probe (SSOP) typing or sequence specific priming (SSP) to be presented in a low-resolution serological format. Unfortunately, this representation can lead to significant loss of useful data in many cases. An alternative to assigning allele equivalents to suchDNA typing results is simply to store the observed typing pattern and utilize the information with the help of Virtual DNA Analysis (VDA). Interpretation of the stored typing patterns can then be updated based on newly defined alleles, assuming the sequence motifs detected by the typing reagents are known. Rather than updating reagent specificities in individual laboratories, such updates should be performed in a central, publicly available sequence database. By referring to this database, HLA genomic data can then be stored and transferred between laboratories without loss of information. The 13th International Histocompatibility Workshop offers an ideal opportunity to begin building this common database for the entire human MHC.

Base Sequence↗

Database of natural matrix reference materials (NMRM) for organic constituents.

The International Atomic Energy Agency maintains a database of internationally available certified reference materials (CRM) of natural matrices. This database is periodically updated, and presently documents nearly 25,000 measurands in 1,700 materials. The organic constituents are classified in five major groups of analytes aliphatic and aromatic hydrocarbons (A), chlorinated hydrocarbons (B), pesticides (C), organometallic compounds (D) and other organic constituents (nutrients, etc.) (E). The matrices include natural materials such as body fluids, food products, soils, and sediments, terrestrial (e.g. plants), and anthropogenic products (e.g. dust, fly ash). These five organic groups of analytes encompass more than 2000 measurands for 420 different analytes in 230 materials. Of these measurands, 1,682 (68%) are certified, and 768 (32%) are provided as informational values. Within each major group of analytes, measurands reported as informational values accounted for: A (35%); B (35%); C (26%); D (10%), and E (22%). The high proportion of informational values (i.e. non-certified values) for A, B, and C, compares well with a similar but undesirable situation faced in the nineteen-seventies in the inorganic area when simultaneous multielement techniques became available. In the case of D and E, it appears that mostly targeted analytes are measured, leading to a cohesive certification profile. Although the IAEA database is not equally comprehensive for all groups of analytes cited above, it can still serve as an useful indicator of the status of organic constituents in RMs.

Animals↗

[Construction of standard human transcript dataset based on RefSeq and human genome sequence database].

The NCBI Reference Sequence (RefSeq) database aimed to provide a biologically non-redundant collection of DNA, RNA, and protein sequences and to promote the research on genes and proteins of human beings and other species. However, because of widely distributed polymorphisms and different quality control of experiments in individual laboratories, there are potential problems need to be identified in the RefSeq database. Regarding which, we herein define the concept, standard transcript, based on the Central Dogmas of Biology that each standard transcript should be perfectly mapped to the standard genomic DNA sequence at the exon level. A large scale analysis for mapping all of the RefSeq records of human being (2005-4-18) to the officially released human genome sequence database (2005-4-20) was further performed using BLAT, Sim4 and a homemade program, EIparser, which was especially designed for this purpose. The standard transcripts based on the RefSeq database were obtained according to the alignment with standard human genome database. There are 9,771 RefSeq records of human being labeled with "NM_" and "NR_" could be perfectly mapped to human genome sequences, while other 10,943 records could be considered as standard transcripts after reasonable revision by comparing with the genome sequences according to all of the three methods. Moreover, the left 203 unrevisable records and 2,676 inconsistent records reported by the above programs could not be considered as standard transcripts and should be checked critically before using because of potential errors in them. Our study has thus provided a reference standard dataset of human beings with high quality for further bioinformatic and experimental analysis such as polymorphism and mutation of human genes. The reference standard dataset based on above criteria could be retrieved from http://biocompute.bmi.ac.cn/transcriptome/index.htm.

Databases, Genetic↗

PaperChase: a user-friendly program for searching the biomedical literature.

PaperChase is a computer program which provides an efficient interface to the National Library of Medicine's MEDLINE database of references to the biomedical literature. The database includes references (citations) and abstracts compiled from Index Medicus, the International Nursing Index and the Index to Dental Literature. PaperChase may be accessed using any computer terminal or personal computer with modem. No special knowledge of computers or biomedical terms is necessary. Simple menus enable the novice to search the biomedical literature without training. A command language speeds searching for the experienced user. PaperChase does not require the user to know the database's indexing terminology, called Medical Subject Headings. Everyday language may be used and PaperChase will translate, or "map", the user's search term into the required Medical Subject Heading. PaperChase monitors a search in progress and suggests additional Medical Subject Headings which can be used to broaden or narrow a search. The searcher can order a full-text photocopy of any reference found in PaperChase. Support documentation and a subscriber newsletter are provided at no charge. Trained search specialists are available to offer assistance and to answer questions.

MEDLARS↗

Evaluation of computational metabolic-pathway predictions for Helicobacter pylori.

MOTIVATION: We seek to determine the accuracy of computational methods for predicting metabolic pathways in sequenced genomes, and to understand the contributions of both the prediction algorithms, and the reference pathway databases used by those algorithms, to the prediction accuracy. RESULTS: The comparisons we performed were as follows. (1) We compared two predictions of the pathway complements of Helicobacter pylori that were computed by an early version of our pathway-prediction algorithm: prediction A used the EcoCyc E. coli pathway DB as the reference database (DB) for prediction, and prediction B used the MetaCyc pathway DB (a superset of EcoCyc) as the reference pathway DB. The MetaCyc-based prediction contained 75% more pathway predictions, but we believe a significant number of those predictions were false positives. (2) We compared two predictions of the pathway complement of H. pylori that used MetaCyc as the reference pathway DB, but that used different algorithms: the original PathoLogic algorithm, and an enhanced version of the algorithm designed to eliminate false-positive pathway predictions. The improved algorithm predicted 30\% fewer metabolic pathways than the original algorithm; all of the eliminated pathways are believed to be false-positive predictions. (3) We compared the 98 pathways predicted by the enhanced algorithm with the results of a manual analysis of the pathways of H. pylori. Results: 40 of the computationally predicted pathways were consistent with the manual analysis, 13 pathways are considered false-positive predictions, and four pathways had partially overlapping topologies. Twenty-six predicted pathways were not mentioned in the manual analysis; we believe these are correct predictions by PathoLogic that were not found by the manual analysis. Five pathways from the manual analysis were not found computationally. Agreement between the computational and manual predictions was good overall, with the computational analysis inferring many pathways that the manual analysis did not identify. Ultimately the manual analysis is also partially speculative, and therefore is not an absolute measure of correctness. The algorithm is designed to err on the side of more false positives to bring more potential pathways to the user's attention. The resulting H. pylori pathway DB is freely available at http://ecocyc.org:1555/HPY/organism-summary?object=HPY. AVAILABILITY: The Pathway Tools software is freely available to academic users, and is available to commercial users for a fee. Contact pkarp@ai.sri.com for information on obtaining the software.

Algorithms↗

C3: A comprehensive physician activity and billing tool

Purpose: The Clinical Charge Capture system (C3) was developed at the University of Michigan to increase the efficiency and accuracy with which information about physician activity and billing is tracked in academic medical centers. Description: This Oracle-based, Visual Basic system integrates the operating room scheduling system, transcription database, clinical data repository, referring physician database, and IDX to allow physicians and staff to perform paperless and on-line standard tasks such as preauthorizing procedures; creating a bill which describes the charges for procedures performed along with their supporting diagnoses; identifying inpatient daily care and consult charges; dictating, editing, signing, and providing attestations for procedural and inpatient notes (menu-driven boilerplate notes are used for common procedures); submitting of charges on-line to IDX; and downloading of payment data from IDX. A messaging system between physicians and billing specialists allows questions to be posed regarding coding issues and options. Summary information about charges is presented and the status of the bill as it progresses through the internal review and billing process is demonstrated. Any missing data are flagged such that delivery of a bill is accurate, timely, and complete. Outpatient clinic visit charges are acquired on line using bar code technology with direct download of clinic charges to IDX. Generation of charges and referral letters may be performed immediately following the performance of a procedure or patient encounter or subsequently in the office. Resident activity is also tracked. Finally, search functions are provided which allow the program to serve as a clinical information research database. Results: The time to bill submission for operative procedures in fiscal year 1996 (Pre-C3) when compared to 1999 (Post-C3) decreased in each individual surgical division (See figure)as well as for the overall Department (Total: mean Pre-C3=40 days, mean Post-C3=8 days). The average bill was increased by 9% for each primary charge submitted. Conclusions: We conclude that this system has the potential to enhance the efficiency, accuracy, and organization of routine physician documentation, billing, and data collection activities.

Journal Article↗