Cataloging the phylogenetic diversity of human bladder bacterial isolates

BACKGROUND

Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, such as the gut and oral cavity.

RESULTS

To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, we present a bladder-specific bacterial isolate reference collection comprising 1134 genomes, primarily from adult females. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial isolate reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2% of the genera found when re-examining previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis finds that the taxonomies and functions of the bladder microbiota share more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladder Escherichia coli isolates and 387 gut Escherichia coli isolates support the hypothesis that phylogroup distribution and functions of Escherichia coli strains differ dramatically between these two very different niches.

CONCLUSIONS

This bladder-specific bacterial isolate reference collection is a unique resource that will enable bladder microbiota research and comparison to isolates from other anatomical sites.

Cataloging natural sialic acids and other nonulosonic acids (NulOs), and their representation using the Symbol Nomenclature for Glycans

Nonulosonic acids or non-2-ulosonic acids (NulOs) are an ancient family of 2-ketoaldonic acids (α-ketoaldonic acids) with a 9-carbon backbone. In nature, these monosaccharides occur either in a 3-deoxy form (referred to as "sialic acids") or in a 3,9-dideoxy "sialic-acid-like" form. The former sialic acids are most common in the deuterostome lineage, including vertebrates, and mimicked by some of their pathogens. The latter sialic-acid-like molecules are found in bacteria and archaea. NulOs are often prominently positioned at the outermost tips of cell surface glycans, and have many key roles in evolution, biology and disease. The diversity of stereochemistry and structural modifications among the NulOs contributes to more than 90 sialic acid forms and 50 sialic-acid-like variants described thus far in nature. This paper reports the curation of these diverse naturally occurring NulOs at the NCBI sialic acid page (https://www.ncbi.nlm.nih.gov/glycans/sialic.html) as part of the NCBI-Glycans initiative. This includes external links to relevant Carbohydrate Structure Databases. As the amino and hydroxyl groups of these monosaccharides are extensively derivatized by various substituents in nature, the Symbol Nomenclature For Glycans (SNFG) rules have been expanded to represent this natural diversity. These developments help illustrate the natural diversity of sialic acids and related NulOs, and enable their systematic representation in publications and online resources.

Functional interpretation, cataloging, and analysis of 1,341 glucose-6-phosphate dehydrogenase variants

Glucose-6-phosphate dehydrogenase (G6PD) deficiency affects over 500 million individuals who can experience anemia in response to oxidative stressors such as certain foods and drugs. Recently, the World Health Organization (WHO) called for revisiting G6PD variant classification as a priority to implement genetic medicine in low- and middle-income countries. Toward this goal, we sought to collect reports of G6PD variants and provide interpretations. We identified 1,341 G6PD variants in population and clinical databases. Using the ACMG standards and guidelines for the interpretation of sequence variants, we provided interpretations for 268 variants, including 186 variants that were not reported or of uncertain significance in ClinVar, bringing the total number of variants with non-conflicting interpretations to 400. For 414 variants with functional or clinical data, we analyzed associations between activity, stability, and current classification systems, including the new 2022 WHO classification. We corroborated known challenges with classification systems, including phenotypic variation, emphasizing the importance of comparing variant effects across individuals and studies. Biobank data made available by All of Us illustrate the benefit of large-scale sequencing and phenotyping by adding additional support connecting variants to G6PD-deficient anemia. By leveraging available data and interpretation guidelines, we created a repository for information on G6PD variants and nearly doubled the number of variants with clinical interpretations. These tools enable better interpretation of G6PD variants for the implementation of genetic medicine.

Advanced Cataloging of Lysine-63 Polyubiquitin Networks by Genomic, Interactome, and Sensor-Based Proteomic Analyses

The lack of resolution when studying the many different ubiquitin chain types found in eukaryotic cells has been a major hurdle to our understanding of their specific roles. We currently have very little insight into the cellular and physiological functions of Lys-63 (K63)-linked ubiquitin chains, although they are the second most abundant forms of ubiquitin in plant cells. To overcome this problem, we developed several large-scale approaches to characterize (1) the E2-E3 ubiquitination machinery driving K63-linked ubiquitin chain formation and (2) K63 polyubiquitination targets to provide a comprehensive picture of K63 polyubiquitin networks in Arabidopsis (Arabidopsis thaliana). Our work identified the ubiquitin-conjugating enzymes (E2s) UBC35/36 as the major drivers of K63 polyubiquitin chain formation and highlights the major role of these proteins in plant growth and development. Interactome approaches allowed us to identify many proteins that interact with the K63 polyubiquitination-dedicated E2s UBC35/36 and their cognate E2 variants, including more than a dozen E3 ligases and their putative targets. In parallel, we improved the in vivo detection of proteins decorated with K63-linked ubiquitin chains by sensor-based proteomics, yielding important insights into the roles of K63 polyubiquitination in plant cells. This work strongly increases our understanding of K63 polyubiquitination networks and functions in plants.

Quality assessment and cataloguing of telemedicine applications

We created a Web catalogue of approved telemedicine systems that authoritative Italian research bodies had made available for more general use. The evaluation process was divided into two stages: (1) classification of the telemedicine systems and rough preliminary evaluation; (2) assessment of the telemedicine products and services. The scoring method was applied to four well-known telemedicine systems that had been tested in health-care settings: an echocardiology teleconsulting and analysis system; a ward nursing management system; a virtual cooperative system for the management of oncology patients and a telepathology system based on remotely controlled microscopy. After technical revision during the standardization/qualification process, the applications were transferred successfully to eight new health-care facilities. The methodology achieved the main goal of providing effective tools, such as a set of quality control procedures for telemedicine and telehealth projects and a Web catalogue of telemedicine applications with a standardized level of quality, available to all interested parties.

Cross-cutting categorization schemes in the digital humanities

Digital access to large amounts of scholarly text presents both challenges and opportunities for researchers in the humanities. Meeting these challenges depends on having high-quality representations of the contents of digital resources suitable for both machines and humans to use. Different ways of categorizing these contents are appropriate for different purposes, leading to the further problem of relating the contents of different categorization schemes to each other. This essay discusses the rationale for categorizing philosophical concepts and surveys some of the main approaches to doing so for materials that are continuously changing. It describes the goals and methods of the Indiana Philosophy Ontology (InPhO) project and provides an example of the kind of analysis that is made possible by powerful modeling methods.

Cataloguing and displaying Web feeds from French language health sites: a Web 2.0 add-on to a health gateway

Among the numerous new functionalities of the Internet, commonly called Web 2.0, Web syndication illustrates the trend for better and faster information sharing. Web feeds (a.k.a RSS feeds), which were used mostly on weblogs at first, are now also widely used in academic, scientific and institutional websites such as PubMed. As very few French language feeds were listed or catalogued in the Health field by the year of 2007, it was decided to implement them in the quality-controlled health gateway CISMeF ([French] acronym for Catalogue and Index of French Language Health Resources on the Internet). Furthermore, making full use of the nature of Web syndication, a Web feed aggregator was put online in to provide a dynamic news gateway called "CISMeF actualités" (http://www.chu-rouen.fr/actualites/). This article describes the process to retrieve and implement the Web feeds in the catalogue and how its terminology was adjusted to describe this new content. It also describes how the aggregator was put online and the features of this news gateway. CISMeF actualités was built accordingly to the editorial policy of CISMeF. Only a part of the Web feeds of the catalogue were included to display the most authoritative sources. Web feeds were also grouped by medical specialties and by countries using the prior indexing of websites with MeSH terms and the so-called metaterms. CISMeF actualités now displays 131 Web feeds across 40 different medical specialities, coming from 5 different countries. It is one example, among many, that static hypertext links can now easily and beneficially be completed, or replaced, by dynamic display of Web content using syndication feeds.

Building an anonymized catalogued radiology museum in PACS: a feasibility study

The aim of this study was to test the feasibility of a software application that would allow the anonymization and cataloguing of whole DICOM datasets in order to build searchable radiology museums within PACS. The application was developed on a dedicated networked PC, using C# and HL7 coding. Whole DICOM datasets were pushed from PACS to a networked PC on which the application, Museum Builder, was developed. Museum Builder works by replacing the patient specific data (the forename, surname and hospital number) within each header of each DICOM file with terms from anatomical and surgical sieve menus. The date of birth is anonymized to 1 January of the same year. Whole DICOM datasets comprising hundreds of images can be anonymized and catalogued in a single episode. Museum Builder primes PACS with an HL7 script to receive a "new" patient. DICOM datasets are then pushed back to PACS where they are added to the database as "new" cases. The museum cases can then be searched for, on PACS, by any combination of terms that correspond to appropriate anatomical units, surgical sieve headings or radiological specialty. New radiology reports containing clinical histories, radiological descriptions, differential diagnoses and discussion can be added through the report window. Our institution has developed and used this tool to generate a PACS based radiology museum containing not only full DICOM datasets, but also relevant histological and clinical photographs. In conclusion, this technique offers a mechanism for generating anonymized catalogued radiology museums in PACS. Museum Builder represents a working prototype that demonstrates some of the archiving functions that are expected by teaching institutions from PACS.

Creating and using the urgent metadata catalogue and thesaurus

The Urban Regeneration and the Environment Research Programme (URGENT) required a system for cataloguing its datasets and enabling its scientific community to discover what data were available to it. This community was multidisciplinary in nature and therefore needed a range of facilities for searching. Of particular importance were facilities to help those unfamiliar with specialist terminology. To meet these needs, four applications were designed and developed: a Metadata Capture Tool for describing datasets in compliance with the National Geospatial Data Framework (NGDF) standard, a Term Entry Tool for creating an ISO compliant thesaurus, a Thesaurus Builder for merging thesauri and a Search Tool. To encourage users to help in cataloguing data, the capture tools were written as stand alone applications, which users could keep and use to build their own metadatabases. The tools contained export and import facilities that allowed the URGENT Data Centre to build a central database and publish it upon the web. During the development work, it was found necessary to extend the NGDF standard as it could not adequately describe time variant or 3-D atmospheric datasets. The four applications met their design objectives. However, a number of ergonomic issues will need to be addressed if the system is to meet the needs of the much larger up coming programmes. The main challenges will be moving from the NGDF standard to the ISO standard, hence bringing the work into line with the recommendations of the INSPIRE Project, and merging the metadatabase with the scientific database, which enable metadata maintenance to be semi-automated.

Cataloging on-line health information: a content analysis of the NC Health Info portal

The unrelenting increase of health information on the World Wide Web has resulted in an urgent need for portals that provide consumers with trustworthy health information. In response to this need, the National Library of Medicine initiated the Go Local initiative, which extends MEDLINEplus by providing consumers with links to local health services, programs and providers. NC Health Info (www.nchealthinfo.org) is the first NIH funded Go Local portal. Our goal is to gain insight into the nature of interactions that occur during the cataloging process of online health information resources. We conducted a content analysis of annotations made by catalogers on the NC Health Info portal between January 2000 and September 2004. Our analysis of 2369 online information resources revealed challenges with establishing the navigational, geographical and topical content of an on-line resource. Our analysis provides insight into the mechanisms that catalogers use to overcome those challenges and thus will be of value to future Go Local portal development.

Developing metadata to organize public health datasets

The Centers for Disease Control and Prevention (CDC) has available a large number of datasets from previous and current surveillance and research.1 Until now, these datasets have not been catalogued. Metadata would organize these datasets and enhance CDC's ability to efficiently use this data to quickly gain the broader view of the nation's health status to effectively carry out public health activities. This project was to develop metadata for cataloguing CDC datasets and a system that would allow researchers to search at least 95% of databases within CDC based on the most relevant criteria for research. It also explored the need to involve stakeholders and users in the project. The resulting metadata and system are available only to CDC researchers on the CDC intranet.

A DNA Motif Lexicon: cataloguing and annotating sequences

The rapid proliferation of genomic DNA sequences has created a significant need for software that can both focus on relatively small areas (such as within genes or promoters) and provide wide-zoom views of patterns across entire genomes. We present our DNA Motif Lexicon that enables users to perform genome-wide searches for motifs of interest and create customizable results pages, where results differ in the degree and extent of annotation. Searching for a particular motif is akin to a word search in a natural language; our motif lexicon speaks to this new time when we will increasingly rely upon DNA dictionaries that offer rich types of annotation. Indeed, the concept of "lexomics", introduced in this paper may be appropriate to the types of meta-analyses appropriate to the deciphering of regulatory information. Currently supporting five genomes, our web-based lexicon allows users to look up motifs of interest and build user-defined result pages to include the following: (1) all base pair locations where a motif is found with links to further search the "neighborhoods" near each of these locations; whether each location of the motif is genic (within) a gene, intergenic, or a bridging sequence (overlapping a gene boundary) (2) NCBI hot-links to nearest upstream and downstream genes for each location (3) statistical information about the query (4) whether the motif is a certain type of repeat (5) links for the reverse, complement and reverse-complement of the motif of interest and (6) hot-links to PubMed abstracts which mention the motif of interest. A software framework facilitates the continual development of new annotation modules. The tool is located at: http://genomics.wheatoncollege.edu/cgi-bin/lexicon.exe.

Effects of the gay publishing boom on classes of titles retrieved under the subject headings "Homosexuality," "Gay Men," and "Gays" in the OCLC WorldCat database

What do searchers find when they look for literature on homosexuality? This question has profound implications for older as well as younger gays in their coming out, as well as in their subsequent identity development. Library records provide credible data to answer the question, since they represent relatively free sources of information, unlike data from bookstores, publishers, and some World Wide Web sites. The records of WorldCat, the world's largest union database of library records, comprise over 30 million records listed in the Online Computer Library Center. For the purposes of the study, 18,757 records listed under "Homosexuality," "Gay Men," and "Gays" were downloaded; records for "Lesbian" and "Lesbians" were not examined. Findings of the study suggest that while there has indeed been considerable growth in terms of the quantity of gay literature produced since 1969, such gains may be offset by the deteriorating quality of cataloging copy, which makes the experience of browsing records a discouraging and confusing one.

[CISMeF: catalog and index of French-speaking medical sites]

The Internet has now become a major source of health information. The aim of CISMeF is to catalogue and index the main French-speaking sites and documents concerning health. This project was initiated by Rouen University Hospital. Its URL is http://www.chu-rouen.fr/cismef. CISMeF covers all areas of health care and medical sciences, and is indexed both alphabetically and according to subject. It was set up on a Sun workstation under the Sun UNIX operating system and is entirely based on static HTML. By May 1999, the number of sites and documents indexed was already over 6,500, with a mean of 75 new sites added each week. CISMeF is updated via a five-step process: resource collection, filtering, description, classification, and indexing. The Net Scoring criteria are used to assess the quality of health information on the Internet. These criteria concern eight categories: credibility, content, links, design, interactivity, quantitative aspects, ethics and accessibility. CISMeF uses two standard tools to organize information: the MeSH (medical subject heading) thesaurus from the Medline reference database (National Library of Medicine, USA) and the Dublin core metadata format. The sites and documents included in CISMeF are described using the following elements from the Dublin core project: title, author or creator, subject and keywords, description, publisher, date, resource type, format, identifier, and language.

Addressing the issue of cataloging and making chiropractic literature accessible: Part I: Defining the problem

Health science journals are a principle source of new knowledge for chiropractors, chiropractic faculty and students. Regrettably, clinically or educationally relevant articles (appearing in the nearly 20,000 journals annually) are often overlooked due to access difficulties. Innovations are needed to assist the reader to select articles relevant to chiropractic and reduce the time spent sorting through the volumes of literature. A review of the literature shows there is a trend toward database management for cataloging and accessibility of other, nonchiropractic, literature. Most notable of these is an endeavor by National Technical Information Service, commonly referred to as MEDLARS (Medline). It is interesting to note that a computer-assisted library database program does not exist on any chiropractic campus. This is in contrast with the trend on campuses of other health care fields. Manual search strategies within the chiropractic literature are time consuming, subject to a high failure rate, and even if the search produces citations, there is no assurance the journal can be accessed unless a chiropractic campus is nearby. Furthermore, difficulties exist when a chiropractic literature search is attempted in any computerized database, e.g., MEDLARS (Medline). Journals/articles that are unique to chiropractic (national, international or on the state level) are not specifically included in these computerized databases. Aside from these difficulties, there exists the problem of finding those articles that contain valid and relevant information from among those that are less valid or informative.

[Standardization of the tooth numbering systems]

When identifying a specific tooth, dentists list the dentition, arch, quadrant and tooth name. There are several systems of naming and coding teeth. It is necessary that the dental team be familiar with all systems so that communication between dental offices is possible. In this article, the most popular systems are reviewed and their advantages, disadvantages are discussed. These systems are Universal, Palmer and FDI. Also, other systems are summarized. The Palmer/Zsigmody notation have been used widely in the world, but caused problems in typing and printing. And also, it is not suitable for computer processing. The FDI two-digit system helps to prevent errors when differentiating between right and left sides of the mouth or between upper and lower dental arches. It also has advantages when typing and is capable of being incorporated in computer languages.

Low cost organization of a mental retardation facility staff library

A mental retardation facility staff library of 700 volumes required complete organization. Two restraining factors were lack of personnel and limited funds. A plan was developed to classify titles according to Library of Congress, with the subject heading catalog predominantly based on Medical Subject Headings (MeSH). A cataloging service was located which produced custom card sets and book labels from CATLINE and MARC computer databases. Where necessary, MARC records were edited to alter LC subject headings to MeSH terminology. Organization was accomplished at an average cost per title of less than $1.50.

Online search patterns: NLM CATLINE database

In this article the authors present their analysis of the online search patterns within user searching sessions of the National Library of Medicine ELHILL system and examine the user search patterns on the CATLINE database. In addition to the CATLINE analysis, a comparison is made using data previously analyzed on the MEDLINE database for the same time period, thus offering an opportunity to compare the performance parameters of different databases within the same information system. Data collection covers eight weeks and includes 441,282 transactions and over 11,067 user sessions, which accounted for 1680 hours of system usage. The descriptive analysis contained in this report can assists system design activities, while the predictive power of the transaction log analysis methodology may assists the development of real-time aids.

Library-media production interface

This article presents a detailed discussion of the roles of the health sciences library and the media production service personnel in providing a standardized system for accessing audiovisual and video in-house produced software. A worksheet and guidelines for collecting complete bibliographic information for these programs are also included.

ABC of computing. Computers in the medical library

Images

The NEOUCOM Cooperative Cataloging Service: development and review of the first four years

The Basic Medical Sciences Library of the Northeastern Ohio Universities College of Medicine (NEOUCOM) provided a Cooperative Cataloging Service to fourteen of its affiliated hospitals' libraries since March 1978, using the OCLC system. Analysis of the first four years of service showed that the hospital libraries spent almost $30,000 to catalog more than 18,000 titles. Personnel expenses and other costs eclipsed the savings from a 31.3% duplication rate. Centralized bibliographic control control and the principal by-product of the service, a uniform, machine-related data base, provided the foundation for an on-line integrated library system to serve the consortium. The hospital libraries contributed 44% of the unique titles in this data base, which emphasis the need to share resources and continue cooperation.

OCLC for the hospital library: the justification plan for hospital administration

This paper delineates the necessary steps to provide hospital administrators with the information needed to evaluate an automated system, OCLC, for addition to the medical library. Based on experience at the Norton-Children's Hospitals, included are: (1) cost analyses of present technical processing systems and cost comparisons with OCLC; (2) delineation of start-up costs for installing OCLC; (3) budgetary requirements for 1981; (4) the impact of automation on library systems, personnel, and services; (5) potential as a shared service; and (6) preparation of the proposal for administrative review.

The learning center: what to do until the librarian is hired

By providing a self-instructional learning resources center to employees, a health care institution can expand the training and education function without initially adding to the education staff. This article describes the basic procedures for setting up and managing the learning resources collection until such time as a librarian can be hired.

Descriptive cataloging of serials: the National Library of Medicine versus the Library of Congress

Descriptive cataloging practices for serial differ significantly in some respects between the Library of Congress and the National Library of Medicine. This paper compares some of these differences and indicates the impact they can have on the development of on-line cooperative data bases such as OCLC. Attention is also given to the possible impact of the second edition of the Anglo-American Cataloguing Rules on serials cataloging. The need for standardization is stressed.

Recommended data elements for the descriptive cataloging of computer-based educational materials in the health sciences

A large part of the mission of the National Library of Medicine is to collect, index, and disseminate the world's biomedical literature. Until recently, this related only to serial and monographic material, but as new forms of information appear responsibility for bibliographic control of these also must be assumed by the National Library of Medicine. This paper briefly describes the type of information that will be necessary before descriptive cataloging of computer-based educational materials can be attempted.