Michael E. Bales

Planning against Biological Terrorism: Lessons from Outbreak Investigations

We examined outbreak investigations conducted around the world from 1988 to 1999 by the Centers for Disease Control and Prevention’s Epidemic Intelligence Service. In 44 (4.0%) of 1,099 investigations, identified causative agents had bioterrorism potential. In six investigations, intentional use of infectious agents was considered. Healthcare providers reported 270 (24.6%) outbreaks and infection control practitioners reported 129 (11.7%); together they reported 399 (36.3%) of the outbreaks. Health departments reported 335 (30.5%) outbreaks. For six outbreaks in which bioterrorism or intentional contamination was possible, reporting was delayed for up to 26 days. We confirmed that the most critical component for bioterrorism outbreak detection and reporting is the frontline healthcare profession and the local health departments. Bioterrorism preparedness should emphasize education and support of this frontline as well as methods to shorten the time between outbreak and reporting.

Epidemiologic Responses to Anthrax Outbreaks: A Review of Field Investigations, 1950–2001

We used unpublished reports, published manuscripts, and communication with investigators to identify and summarize 49 anthrax-related epidemiologic field investigations conducted by the Centers for Disease Control and Prevention from 1950 to August 2001. Of 41 investigations in which Bacillus anthracis caused human or animal disease, 24 were in agricultural settings, 11 in textile mills, and 6 in other settings. Among the other investigations, two focused on building decontamination, one was a response to bioterrorism threats, and five involved other causes. Knowledge gained in these investigations helped guide the public health response to the October 2001 intentional release of B. anthracis, especially by addressing the management of anthrax threats, prevention of occupational anthrax, use of antibiotic prophylaxis in exposed persons, use of vaccination, spread of B. anthracis spores in aerosols, clinical diagnostic and laboratory confirmation methods, techniques for environmental sampling of exposed surfaces, and methods for decontaminating buildings.

Qualitative assessment of the International Classification of Functioning, Disability, and Health with respect to the desiderata for controlled medical vocabularies.

BACKGROUND The International Classification of Functioning, Disability, and Health (ICF), a classification system published in 2001 by the World Health Organization (WHO), provides a common language and framework for describing functional status information (FSI) in health records. METHODS Informed by ongoing research in coding FSI in patient records, this paper qualitatively assesses the ICF framework with respect to the desiderata for controlled medical vocabularies, an enumerated a list of desirable qualities for controlled medical vocabularies proposed by Cimino [J.J. Cimino, Desiderata for controlled medical vocabularies in the twenty-first century, Meth. Inform. Med. 37 (1998) 394-403]. RESULTS The ICF satisfies 5 of the 12 desiderata. Five points were not satisfied and two points could not be evaluated. CONCLUSION The ICF is a rich source of relevant terms, concepts, and relationships, but it was not developed in consideration of requirements for formal terminologies. Therefore, it could serve as a base from which to develop a formal terminology of functioning and disability. This assessment is a key next step in the development of the ICF as a sensitive, universal measure of functional status.

Human and automated coding of rehabilitation discharge summaries according to the International Classification of Functioning, Disability, and Health.

OBJECTIVE The International Classification of Functioning, Disability, and Health (ICF) is designed to provide a common language and framework for describing health and health-related states. The goal of this research was to investigate human and automated coding of functional status information using the ICF framework. DESIGN The authors extended an existing natural language processing (NLP) system to encode rehabilitation discharge summaries according to the ICF. MEASUREMENTS The authors conducted a formal evaluation, comparing the coding performed by expert coders, non-expert coders, and the NLP system. RESULTS Automated coding can be used to assign codes using the ICF, with results similar to those obtained by human coders, at least for the selection of ICF code and assignment of the performance qualifier. Coders achieved high agreement on ICF code assignment. CONCLUSION This research is a key next step in the development of the ICF as a sensitive and universal classification of functional status information. It is worthwhile to continue to investigate automated ICF coding.

A Brain Region-Specific Predictive Gene Map for Autism Derived by Profiling a Reference Gene Set

Molecular underpinnings of complex psychiatric disorders such as autism spectrum disorders (ASD) remain largely unresolved. Increasingly, structural variations in discrete chromosomal loci are implicated in ASD, expanding the search space for its disease etiology. We exploited the high genetic heterogeneity of ASD to derive a predictive map of candidate genes by an integrated bioinformatics approach. Using a reference set of 84 Rare and Syndromic candidate ASD genes (AutRef84), we built a composite reference profile based on both functional and expression analyses. First, we created a functional profile of AutRef84 by performing Gene Ontology (GO) enrichment analysis which encompassed three main areas: 1) neurogenesis/projection, 2) cell adhesion, and 3) ion channel activity. Second, we constructed an expression profile of AutRef84 by conducting DAVID analysis which found enrichment in brain regions critical for sensory information processing (olfactory bulb, occipital lobe), executive function (prefrontal cortex), and hormone secretion (pituitary). Disease specificity of this dual AutRef84 profile was demonstrated by comparative analysis with control, diabetes, and non-specific gene sets. We then screened the human genome with the dual AutRef84 profile to derive a set of 460 potential ASD candidate genes. Importantly, the power of our predictive gene map was demonstrated by capturing 18 existing ASD-associated genes which were not part of the AutRef84 input dataset. The remaining 442 genes are entirely novel putative ASD risk genes. Together, we used a composite ASD reference profile to generate a predictive map of novel ASD candidate genes which should be prioritized for future research.

Associating co-authorship patterns with publications in high-impact journals

OBJECTIVES To develop a method for investigating co-authorship patterns and author team characteristics associated with the publications in high-impact journals through the integration of public MEDLINE data and institutional scientific profile data. METHODS For all current researchers at Columbia University Medical Center, we extracted their publications from MEDLINE authored between years 2007 and 2011 and associated journal impact factors, along with author academic ranks and departmental affiliations obtained from Columbia University Scientific Profiles (CUSP). Chi-square tests were performed on co-authorship patterns, with Bonferroni correction for multiple comparisons, to identify team composition characteristics associated with publication impact factors. We also developed co-authorship networks for the 25 most prolific departments between years 2002 and 2011 and counted the internal and external authors, inter-connectivity, and centrality of each department. RESULTS Papers with at least one author from a basic science department are significantly more likely to appear in high-impact journals than papers authored by those from clinical departments alone. Inclusion of at least one professor on the author list is strongly associated with publication in high-impact journals, as is inclusion of at least one research scientist. Departmental and disciplinary differences in the ratios of within- to outside-department collaboration and overall network cohesion are also observed. CONCLUSIONS Enrichment of co-authorship patterns with author scientific profiles helps uncover associations between author team characteristics and appearance in high-impact journals. These results may offer implications for mentoring junior biomedical researchers to publish on high-impact journals, as well as for evaluating academic progress across disciplines in modern academic medical centers.

Evolution of Coauthorship in Public Health Services and Systems Research

CONTEXT Public health services and systems research (PHSSR) focuses on the structure, organization, and legal basis of domestic public health activities and their effect on population health. An accurate description of the field is needed to empower funding agencies and other stakeholders to coordinate PHSSR activities and to foster the development of the field. The purpose of the study is to characterize the emerging community of researchers engaged in PHSSR. This study (1) describes dynamics of this growing community and (2) identifies research themes, subgroups within the field, and collaboration among groups. EVIDENCE ACQUISITION Coauthorship network visualization of selected research publications in the MEDLINE bibliographic database between 1988 and May 2010. EVIDENCE SYNTHESIS PHSSR has emerged gradually with noticeable growth after 1994 and after 2004. The network of PHSSR research has a core-periphery structure. The core includes highly collaborative researchers focusing on topics pertaining directly to PHSSR, such as workforce, quality improvement and performance, law, and information infrastructure. The periphery consists of groups publishing either on general health services research topics or on epidemiologic and clinical topics. CONCLUSIONS Although a nucleus group of productive and engaged individuals participate in PHSSR, most also publish broadly on health services research and population health. This trend suggests that this emerging field cannot yet support a singular focus on PHSSR. Lack of funding sources and defined career paths likely contribute to this pattern. An overview of collaboration in PHSSR is an important step in advancing a coordinated research agenda and attracting sustainable funding streams for this field.

Topological Analysis of Large-scale Biomedical Terminology Structures

OBJECTIVE To characterize global structural features of large-scale biomedical terminologies using currently emerging statistical approaches. DESIGN Given rapid growth of terminologies, this research was designed to address scalability. We selected 16 terminologies covering a variety of domains from the UMLS Metathesaurus, a collection of terminological systems. Each was modeled as a network in which nodes were atomic concepts and links were relationships asserted by the source vocabulary. For comparison against each terminology we created three random networks of equivalent size and density. MEASUREMENTS Average node degree, node degree distribution, clustering coefficient, average path length. RESULTS Eight of 16 terminologies exhibited the small-world characteristics of a short average path length and strong local clustering. An overlapping subset of nine exhibited a power law distribution in node degrees, indicative of a scale-free architecture. We attribute these features to specific design constraints. Constraints on node connectivity, common in more synthetic classification systems, localize the effects of changes and deletions. In contrast, small-world and scale-free features, common in comprehensive medical terminologies, promote flexible navigation and less restrictive organic-like growth. CONCLUSION While thought of as synthetic, grid-like structures, some controlled terminologies are structurally indistinguishable from natural language networks. This paradoxical result suggests that terminology structure is shaped not only by formal logic-based semantics, but by rules analogous to those that govern social networks and biological systems. Graph theoretic modeling shows early promise as a framework for describing terminology structure. Deeper understanding of these techniques may inform the development of scalable terminologies and ontologies.

Research evaluation support services in biomedical libraries

Objective The paper provides a review of current practices related to evaluation support services reported by seven biomedical and research libraries. Methods A group of seven libraries from the United States and Canada described their experiences with establishing evaluation support services at their libraries. A questionnaire was distributed among the libraries to elicit information as to program development, service and staffing models, campus partnerships, training, products such as tools and reports, and resources used for evaluation support services. The libraries also reported interesting projects, lessons learned, and future plans. Results The seven libraries profiled in this paper report a variety of service models in providing evaluation support services to meet the needs of campus stakeholders. The service models range from research center cores, partnerships with research groups, and library programs with staff dedicated to evaluation support services. A variety of products and services were described such as an automated tool to develop rank-based metrics, consultation on appropriate metrics to use for evaluation, customized publication and citation reports, resource guides, classes and training, and others. Implementing these services has allowed the libraries to expand their roles on campus and to contribute more directly to the research missions of their institutions. Conclusions Libraries can leverage a variety of evaluation support services as an opportunity to successfully meet an array of challenges confronting the biomedical research community, including robust efforts to report and demonstrate tangible and meaningful outcomes of biomedical research and clinical care. These services represent a transformative direction that can be emulated by other biomedical and research libraries.