Biomedical subjects

D C Berrios

Publications and source records attributed to D C Berrios.

10 recordsLinked to original sources

PubMed2001

Empirical formulation of a generic query set for clinical information retrieval systems.

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 it will remain generalizable to other electronic medical resources, indexing tasks, and non-UMLS controlled vocabularies.

Abstracting and Indexing↗

PubMed2000

Automated indexing for full text information retrieval.

We report our experience with a statistically based method of generating sentence-level indexing based on identified UMLS concepts and query and vector-space models. We evaluated the system using the consensus markup of two domain experts as the gold standard. UMLS concepts identified both from HTML headings and in paragraph text were valuable in proposing markup. Using both sources of concepts, the model proposed the correct set of concepts in the form of a query prototype 71% of the time. The correct query prototype was ranked first or second in 79% of cases.

Abstracting and Indexing↗

PubMed1999

Knowledge requirements for automated inference of medical textbook markup.

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.

Abstracting and Indexing↗

PubMed1999

Automation and integration of components for generalized semantic markup of electronic medical texts.

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-markup process. First, it helps her to develop, edit, and maintain the concept model: the set of concepts with which she marks the text. Second, ACQUIRE helps her to develop a query model: the set of specific questions that end users can later use to search the marked text. The DE incorporates concepts from the concept model when she creates the questions in the query model. The major benefit of the ACQUIRE system is a reduction in the time and effort required for the text-markup process. We compared the process of concept- and query-model creation using ACQUIRE to the process used in previous work by rebuilding two existing models that we previously constructed manually. We observed a significant decrease in the time required to build and maintain the concept and query models.

Abstracting and Indexing↗

PubMed1998

MYCIN II: design and implementation of a therapy reference with complex content-based indexing.

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. Existing commercial search technology for digital references utilizes generic tools such as textword-based searches with geographical or statistical refinements. We suggest that the drawbacks of such systems significantly restrict their use in everyday clinical practice. This is in spite of the fact that there is a great need for the information contained within these same references. The system we describe is intended to supplement keyword searching so that certain important questions can be asked easily and can be answered reliably (in terms of precision and recall). Our method attacks this problem in a restricted domain of knowledge-clinical infectious disease. For example, we would like to be able to answer the class of questions exemplified by the following query: "What antimicrobial agents can be used to treat endocarditis caused by Eikenella corrodens?" We have compiled and analyzed a list of such questions to develop a concept-based markup scheme. This scheme was then applied within an HTML markup to electronically "highlight" passages from three textbook chapters. We constructed a functioning web-based search interface. Our system also provides semi-automated querying of PubMed using our concept markup and the user's actions as a guide.

Abstracting and Indexing↗

PubMed1995

Cost and outcome of intensive care for patients with AIDS, Pneumocystis carinii pneumonia, and severe respiratory failure.

OBJECTIVE: 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. DESIGN: Survival and cost-effectiveness analysis. SETTING: A large municipal teaching hospital serving an indigent population. PATIENTS: 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). MAIN OUTCOME MEASURES: Hospital charges and survival time; cost per year of life saved, using a zero-cost, zero-life assumption. RESULTS: 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. CONCLUSIONS: 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.

AIDS-Related Opportunistic Infections↗

PubMed1995

Screening for human immunodeficiency virus antibody in urine.

OBJECTIVE: To determine the diagnostic accuracy of an investigational test for human immunodeficiency virus (HIV) envelope antibodies in urine. DESIGN: Matched blood and urine specimens were tested for HIV by two independent laboratories, both of which were blinded to all results at the other site. Duplicate positive enzyme-linked immunoassay (EIA) results were confirmed by immunofluorescent antibody or western blot. SETTING: Six alcohol treatment centers in the San Francisco metropolitan area. PATIENTS: Five hundred ninety-two recovering alcoholics. MAIN OUTCOME MEASURES: Diagnosis of HIV infection by blood and urine EIA and western blot. RESULTS: The experimental urine EIA, when confirmed by urine western blot, led to a correct diagnosis in all samples. One sample was negative by urine EIA screening, positive by blood EIA, and exhibited an indeterminate blood western blot pattern (p24 band only). CONCLUSIONS: We encountered no false positive or false negative results using an investigational HIV antibody test for urine samples. There are several important advantages to HIV testing of urine versus serum or blood; however, there are also cogent reasons for limiting the use of alternative specimens for HIV testing.

Adolescent↗

PubMed1993

HIV antibody testing among those at risk for infection. The National AIDS Behavioral Surveys.

OBJECTIVE: 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. DESIGN: A nationwide, population-based telephone survey eliciting testing, sexual, and injection drug use histories. PARTICIPANTS: A total of 2673 randomly chosen US residents and 8263 randomly chosen residents of 23 metropolitan areas containing 64% of reported cases of AIDS. INTERVENTIONS: None. MAIN OUTCOME MEASURE: Testing for HIV antibody. MAIN RESULTS: 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. CONCLUSIONS: 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.

AIDS Serodiagnosis↗

PubMed1992

HIV antibody testing in young, urban adults.

We surveyed men and women aged 21 to 34 years to determine the rates of human immunodeficiency virus (HIV) antibody testing in blacks and whites of diverse education levels in four US cities. Responses to the anonymous, mailed questionnaire were received from 90% of 777 white women, 64% of 734 black women, 79% of 677 white men, and 48% of 541 black men. The percentages reporting HIV testing for these four race-gender groups were 29%, 22%, 30%, and 38%, respectively. The percentages reporting testing that was voluntarily sought (ie, not in connection with blood donation, military service) were 16%, 14%, 18%, and 22%, respectively. In each race-gender group, roughly half of those who had not been tested said they "might have a blood test for the AIDS virus in the future". Education level was not correlated with HIV-testing frequency. Blacks were significantly less likely than whites to be aware of "a blood test that can detect the AIDS virus infection" (58% vs 77%), but blacks who knew of the test were more likely than whites to have been tested (47% vs 37%). Eleven percent of subjects reported at least one major risk factor for HIV infection. In these people, HIV testing was most common among homosexually active men (56% tested; 52% voluntarily sought), intermediate among injection drug users (40% tested; 31% voluntarily sought), and least common among the sexual partners of injection-drug users (21% tested; 11% voluntarily sought). Health education programs need to communicate the availability of, and need for, anonymous HIV testing.

AIDS Serodiagnosis↗

PubMed1991

Domestic violence. Risk factors and outcomes.

Domestic violence is a pervasive and frequently unrecognized cause of injury among women. We reviewed data from standardized interviews with 218 women who presented to an emergency department with injuries due to domestic violence. Victims ranged in age from 16 to 66 years and constituted a wide range of socioeconomic and ethnic backgrounds. Domestic violence often resulted in severe injury; 28% of the women interviewed required admission to hospital for injuries, and 13% required major surgical treatment. The typical presentation was injuries to the face, skull, eyes, extremities, and upper torso. A third of the cases involved a weapon, such as a knife, club, or gun. In all, 10% of the victims were pregnant at the time of abuse, and 10% reported that their children had also been abused by the batterer. Most victims (86%) had suffered at least one previous incident of abuse, and about 40% had previously required medical care for abuse. Victim recognition and referral to appropriate agencies could be improved if primary care physicians were more aware of the prevalence, severity, frequency of occurrence, and typical presentation of domestic violence.

Adolescent↗