Journal of the American Medical Informatics Association : JAMIA
To evaluate a new system, ISAID (Internet-based Semi-automated Indexing of Documents), and to gen... more To evaluate a new system, ISAID (Internet-based Semi-automated Indexing of Documents), and to generate textbook indexes that are more detailed and more useful to readers. Pilot evaluation: simple, nonrandomized trial comparing ISAID with manual indexing methods. Methods evaluation: randomized, cross-over trial comparing three versions of ISAID and usability survey. Pilot evaluation: two physicians. Methods evaluation: twelve physicians, each of whom used three different versions of the system for a total of 36 indexing sessions. Total index term tuples generated per document per minute (TPM), with and without adjustment for concordance with other subjects; inter-indexer consistency; ratings of the usability of the ISAID indexing system. Compared with manual methods, ISAID decreased indexing times greatly. Using three versions of ISAID, inter-indexer consistency ranged from 15% to 65% with a mean of 41%, 31%, and 40% for each of three documents. Subjects using the full version of ISA...
information sources, including databases, web servers, document repositories, ftp servers, specia... more information sources, including databases, web servers, document repositories, ftp servers, special-purpose application servers, and Web service applications. For example, diagnosing a problem with the International Space Station (ISS) communications systems might require a flight controller to access multiple pieces of information, including the repair history of specific system components (e. g., from a relational database), a historical listing of system anomalies (from a text file accessed through a web server), and crew communication procedures (stored as Microsoft Word documents on a document server). Even more challenging is the ability to discern how the information stored on these different data sources in different formats is semantically related, and therefore how it can be coherently integrated. The presence of similar field names (e. g., database column names, HTML labels, Web form descriptors, etc. ) is no guarantee of conceptual similarity. For example, a field called ...
We describe the construction of MYCIN II, a prototype system that provides for content-based mark... more We describe the construction of MYCIN II, a prototype system that provides for content-based markup and search of a forthcoming clinical therapeutics textbook, Antimicrobial Therapy and Vaccines.
Studies in health technology and informatics, 2001
Information needs in clinical practice take the form of specific questions about a given clinical... more Information needs in clinical practice take the form of specific questions about a given clinical situation, and are best satisfied by concise and specific information retrieval. We sought to develop a comprehensive set of generic queries for information retrieval from electronic medical information resources. We collected one hundred and ten real-world questions asked at the point of care in a variety of settings, and from these developed a set of generic queries of which each of the real-world queries could be shown to be a special case. To provide allowed values for each of the concept terms in the queries, we defined generic nouns as unions of UMLS semantic types, and specified which of these were appropriate to each query. We have begun to use the set to index reference texts from general and subspecialty medicine, and found it capable of full text indexing in the clinical domain. We hypothesize that the query set can serve as a basis for more specialized query sets, and that i...
Our group has built an information retrieval system based on a complex semantic markup of medical... more Our group has built an information retrieval system based on a complex semantic markup of medical textbooks. We describe the construction of a set of web-based knowledge-acquisition tools that expedites the collection and maintenance of the concepts required for text markup and the search interface required for information retrieval from the marked text. In the text markup system, domain experts (DEs) identify sections of text that contain one or more elements from a finite set of concepts. End users can then query the text using a predefined set of questions, each of which identifies a subset of complementary concepts. The search process matches that subset of concepts to relevant points in the text. The current process requires that the DE invest significant time to generate the required concepts and questions. We propose a new system--called ACQUIRE (Acquisition of Concepts and Queries in an Integrated Retrieval Environment)--that assists a DE in two essential tasks in the text-m...
Indexing medical text in journals or textbooks requires a tremendous amount of resources. We test... more Indexing medical text in journals or textbooks requires a tremendous amount of resources. We tested two algorithms for automatically indexing nouns, noun-modifiers, and noun phrases, and inferring selected binary relations between UMLS concepts in a textbook of infectious disease. Sixty-six percent of nouns and noun-modifiers and 81% of noun phrases were correctly matched to UMLS concepts. Semantic relations were identified with 100% specificity and 94% sensitivity. For some medical sub-domains, these algorithms could permit expeditious generation of more complex indexing.
The Mars Society's Desert Research Station (MDRS) Rotation 38, April 3-17, 2005, was dedicate... more The Mars Society's Desert Research Station (MDRS) Rotation 38, April 3-17, 2005, was dedicated to field tests of NASA's Mobile Agents EVA communications system. MDRS provided an excellent, cost-effective venue for bringing together teams from NASA Ames and Johnson Space Center, including six distinct projects, in an intensive two weeks of system integration and experiments. The flexibility of the Mobile
InvestigationOrganizer (IO) is a collaborative semantic Web application designed to support misha... more InvestigationOrganizer (IO) is a collaborative semantic Web application designed to support mishap investigations, and has been used for accidents ranging from those involving only minor property damage to the loss of the Space Shuttle Columbia. The development and use of IO in support of these investigations has provided significant lessons about the use of semantic Web technologies in real-world systems.
JAMA: The Journal of the American Medical Association, 1995
To determine the costs and outcomes associated with intensive care unit (ICU) admission for patie... more To determine the costs and outcomes associated with intensive care unit (ICU) admission for patients with acquired immunodeficiency syndrome (AIDS)-related Pneumocystis carinii pneumonia (PCP), and severe respiratory failure. Survival and cost-effectiveness analysis. A large municipal teaching hospital serving an indigent population. Consecutive patients intubated and mechanically ventilated for AIDS, PCP, and respiratory failure from 1981 through 1991 (n = 113). The cohort was separated into three groups for analysis: patients admitted to the ICU in 1981 through 1985 (era I, n = 43), those admitted in 1986 through 1988 (era II, n = 33), and those admitted in 1989 through 1991 (era III, n = 37). Hospital charges and survival time; cost per year of life saved, using a zero-cost, zero-life assumption. Twenty-eight (25%) of the 113 patients mechanically ventilated for PCP and respiratory failure survived to hospital discharge: six (14%) of 43 in era I, 13 (39%) of 33 in era II, and nine (24%) of 37 in era III (P = .04). Post-ICU admission charges averaged $57,874 for the entire cohort, remaining relatively stable across the three eras. Cost of care for survivors was significantly more expensive than for those dying before discharge. The cost of ICU admission and subsequent hospitalization averaged $174,781 per year of life saved; $305,795 in era I, $94,528 in era II, and $215,233 in era III. Improved survival rates and shorter lengths of ICU stay led to the improved cost-effectiveness in era II, while the opposite trends resulted in worsening cost-effectiveness in recent years. The strongest predictors of hospital mortality in era III were low CD4 cell counts on hospital admission and the development of pneumothorax during mechanical ventilation. The cost-effectiveness of intensive care for patients with PCP and severe respiratory failure improved during the first 8 years of the AIDS epidemic but fell in recent years such that it is now below that of many accepted medical interventions.
JAMA: The Journal of the American Medical Association, 1993
To determine the prevalence of testing for human immunodeficiency virus (HIV) antibody among adul... more To determine the prevalence of testing for human immunodeficiency virus (HIV) antibody among adults with various risk factors for infection, particularly those residing in large metropolitan areas where the bulk of cases of acquired immunodeficiency syndrome (AIDS) have occurred. A nationwide, population-based telephone survey eliciting testing, sexual, and injection drug use histories. A total of 2673 randomly chosen US residents and 8263 randomly chosen residents of 23 metropolitan areas containing 64% of reported cases of AIDS. None. Testing for HIV antibody. Overall, rates of individuals ever tested were only slightly higher in the urban areas (23%) than in the nation as a whole (21%). Testing frequencies were low among all risk groups (less than 40%), except men engaging in same-sex sexual activity (60%) and male and female injection drug users (46% and 73%, respectively). The low rate of testing (35%) among the largest risk group, heterosexual men and women engaging in unprotected sexual intercourse with multiple partners, was particularly worrisome. To encourage antibody testing among the many at risk for infection who have not yet been tested, promotional campaigns should explain the universal susceptibility to infection among those at risk, and the availability of prophylactic medical therapies and social support services to persons who are HIV-seropositive. As there were comparable levels of risk-taking behavior among subjects in both samples, these campaigns must be designed to reach all segments of the population.
Journal of the American Medical Informatics Association : JAMIA
To evaluate a new system, ISAID (Internet-based Semi-automated Indexing of Documents), and to gen... more To evaluate a new system, ISAID (Internet-based Semi-automated Indexing of Documents), and to generate textbook indexes that are more detailed and more useful to readers. Pilot evaluation: simple, nonrandomized trial comparing ISAID with manual indexing methods. Methods evaluation: randomized, cross-over trial comparing three versions of ISAID and usability survey. Pilot evaluation: two physicians. Methods evaluation: twelve physicians, each of whom used three different versions of the system for a total of 36 indexing sessions. Total index term tuples generated per document per minute (TPM), with and without adjustment for concordance with other subjects; inter-indexer consistency; ratings of the usability of the ISAID indexing system. Compared with manual methods, ISAID decreased indexing times greatly. Using three versions of ISAID, inter-indexer consistency ranged from 15% to 65% with a mean of 41%, 31%, and 40% for each of three documents. Subjects using the full version of ISA...
information sources, including databases, web servers, document repositories, ftp servers, specia... more information sources, including databases, web servers, document repositories, ftp servers, special-purpose application servers, and Web service applications. For example, diagnosing a problem with the International Space Station (ISS) communications systems might require a flight controller to access multiple pieces of information, including the repair history of specific system components (e. g., from a relational database), a historical listing of system anomalies (from a text file accessed through a web server), and crew communication procedures (stored as Microsoft Word documents on a document server). Even more challenging is the ability to discern how the information stored on these different data sources in different formats is semantically related, and therefore how it can be coherently integrated. The presence of similar field names (e. g., database column names, HTML labels, Web form descriptors, etc. ) is no guarantee of conceptual similarity. For example, a field called ...
We describe the construction of MYCIN II, a prototype system that provides for content-based mark... more We describe the construction of MYCIN II, a prototype system that provides for content-based markup and search of a forthcoming clinical therapeutics textbook, Antimicrobial Therapy and Vaccines.
Studies in health technology and informatics, 2001
Information needs in clinical practice take the form of specific questions about a given clinical... more Information needs in clinical practice take the form of specific questions about a given clinical situation, and are best satisfied by concise and specific information retrieval. We sought to develop a comprehensive set of generic queries for information retrieval from electronic medical information resources. We collected one hundred and ten real-world questions asked at the point of care in a variety of settings, and from these developed a set of generic queries of which each of the real-world queries could be shown to be a special case. To provide allowed values for each of the concept terms in the queries, we defined generic nouns as unions of UMLS semantic types, and specified which of these were appropriate to each query. We have begun to use the set to index reference texts from general and subspecialty medicine, and found it capable of full text indexing in the clinical domain. We hypothesize that the query set can serve as a basis for more specialized query sets, and that i...
Our group has built an information retrieval system based on a complex semantic markup of medical... more Our group has built an information retrieval system based on a complex semantic markup of medical textbooks. We describe the construction of a set of web-based knowledge-acquisition tools that expedites the collection and maintenance of the concepts required for text markup and the search interface required for information retrieval from the marked text. In the text markup system, domain experts (DEs) identify sections of text that contain one or more elements from a finite set of concepts. End users can then query the text using a predefined set of questions, each of which identifies a subset of complementary concepts. The search process matches that subset of concepts to relevant points in the text. The current process requires that the DE invest significant time to generate the required concepts and questions. We propose a new system--called ACQUIRE (Acquisition of Concepts and Queries in an Integrated Retrieval Environment)--that assists a DE in two essential tasks in the text-m...
Indexing medical text in journals or textbooks requires a tremendous amount of resources. We test... more Indexing medical text in journals or textbooks requires a tremendous amount of resources. We tested two algorithms for automatically indexing nouns, noun-modifiers, and noun phrases, and inferring selected binary relations between UMLS concepts in a textbook of infectious disease. Sixty-six percent of nouns and noun-modifiers and 81% of noun phrases were correctly matched to UMLS concepts. Semantic relations were identified with 100% specificity and 94% sensitivity. For some medical sub-domains, these algorithms could permit expeditious generation of more complex indexing.
The Mars Society's Desert Research Station (MDRS) Rotation 38, April 3-17, 2005, was dedicate... more The Mars Society's Desert Research Station (MDRS) Rotation 38, April 3-17, 2005, was dedicated to field tests of NASA's Mobile Agents EVA communications system. MDRS provided an excellent, cost-effective venue for bringing together teams from NASA Ames and Johnson Space Center, including six distinct projects, in an intensive two weeks of system integration and experiments. The flexibility of the Mobile
InvestigationOrganizer (IO) is a collaborative semantic Web application designed to support misha... more InvestigationOrganizer (IO) is a collaborative semantic Web application designed to support mishap investigations, and has been used for accidents ranging from those involving only minor property damage to the loss of the Space Shuttle Columbia. The development and use of IO in support of these investigations has provided significant lessons about the use of semantic Web technologies in real-world systems.
JAMA: The Journal of the American Medical Association, 1995
To determine the costs and outcomes associated with intensive care unit (ICU) admission for patie... more To determine the costs and outcomes associated with intensive care unit (ICU) admission for patients with acquired immunodeficiency syndrome (AIDS)-related Pneumocystis carinii pneumonia (PCP), and severe respiratory failure. Survival and cost-effectiveness analysis. A large municipal teaching hospital serving an indigent population. Consecutive patients intubated and mechanically ventilated for AIDS, PCP, and respiratory failure from 1981 through 1991 (n = 113). The cohort was separated into three groups for analysis: patients admitted to the ICU in 1981 through 1985 (era I, n = 43), those admitted in 1986 through 1988 (era II, n = 33), and those admitted in 1989 through 1991 (era III, n = 37). Hospital charges and survival time; cost per year of life saved, using a zero-cost, zero-life assumption. Twenty-eight (25%) of the 113 patients mechanically ventilated for PCP and respiratory failure survived to hospital discharge: six (14%) of 43 in era I, 13 (39%) of 33 in era II, and nine (24%) of 37 in era III (P = .04). Post-ICU admission charges averaged $57,874 for the entire cohort, remaining relatively stable across the three eras. Cost of care for survivors was significantly more expensive than for those dying before discharge. The cost of ICU admission and subsequent hospitalization averaged $174,781 per year of life saved; $305,795 in era I, $94,528 in era II, and $215,233 in era III. Improved survival rates and shorter lengths of ICU stay led to the improved cost-effectiveness in era II, while the opposite trends resulted in worsening cost-effectiveness in recent years. The strongest predictors of hospital mortality in era III were low CD4 cell counts on hospital admission and the development of pneumothorax during mechanical ventilation. The cost-effectiveness of intensive care for patients with PCP and severe respiratory failure improved during the first 8 years of the AIDS epidemic but fell in recent years such that it is now below that of many accepted medical interventions.
JAMA: The Journal of the American Medical Association, 1993
To determine the prevalence of testing for human immunodeficiency virus (HIV) antibody among adul... more To determine the prevalence of testing for human immunodeficiency virus (HIV) antibody among adults with various risk factors for infection, particularly those residing in large metropolitan areas where the bulk of cases of acquired immunodeficiency syndrome (AIDS) have occurred. A nationwide, population-based telephone survey eliciting testing, sexual, and injection drug use histories. A total of 2673 randomly chosen US residents and 8263 randomly chosen residents of 23 metropolitan areas containing 64% of reported cases of AIDS. None. Testing for HIV antibody. Overall, rates of individuals ever tested were only slightly higher in the urban areas (23%) than in the nation as a whole (21%). Testing frequencies were low among all risk groups (less than 40%), except men engaging in same-sex sexual activity (60%) and male and female injection drug users (46% and 73%, respectively). The low rate of testing (35%) among the largest risk group, heterosexual men and women engaging in unprotected sexual intercourse with multiple partners, was particularly worrisome. To encourage antibody testing among the many at risk for infection who have not yet been tested, promotional campaigns should explain the universal susceptibility to infection among those at risk, and the availability of prophylactic medical therapies and social support services to persons who are HIV-seropositive. As there were comparable levels of risk-taking behavior among subjects in both samples, these campaigns must be designed to reach all segments of the population.
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Papers by Daniel Berrios