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Biomedical subjects

C Friedman

Publications and source records attributed to C Friedman.

At least 73 records · Page 4Linked to original sources
PubMed1997

Analysis of the variation in chromosome size among diverse human populations by bivariate flow karyotyping.

Chromosomes sampled from seven human populations were analyzed by flow cytometry to survey normal variation in chromosome size. The populations include two African Pygmy groups, two Amerindian tribes, Druze, Khmer Cambodians, and Melanesians. Mitotic chromosomes were isolated from cultured cells and stained with Hoechst 33,258 and chromomycin A3. The relative DNA content and base-pair composition of each homolog was quantified by bivariate flow karyotyping. Significant variation in DNA content, ranging from 10-40%, was observed for chromosomes 1, 13-16, 19, 21, 22, and Y. The measurements for each population appeared to be a random sampling of the total set of 33 individuals for the majority of chromosomes. A few significant differences in the distributions of chromosomal DNA content were observed among the populations, however. The data, when combined with an earlier study of 33 unrelated individuals of unknown ethnic origin, provide a good representation of the variation in chromosome size among humans.

Base Composition↗
PubMed1997

Towards a comprehensive medical language processing system: methods and issues.

Natural language processing (NLP) systems can help solve the data entry problem by providing coded data from textual reports for clinical applications. A number of NLP systems have shown promise, but have not yet achieved wide-spread use for practical applications. In order to achieve such use, a system must have broad coverage of the clinical domain and not be restricted to limited applications. In addition, an NLP system must perform satisfactorily for real-world applications. This paper describes methods and issues associated with an ongoing extension of MedLEE, an operational NLP system, from a limited domain to a domain that encompasses comprehensive clinical information.

Humans↗
PubMed1997

Identification of findings suspicious for breast cancer based on natural language processing of mammogram reports.

There is need for encoded data for computerized clinical decision support, but most such data are unavailable as they are in free-text reports. Natural language processing offers one alternative for encoding such data. MedLEE is a natural language processing system which is in routine use for encoding chest radiograph and mammogram reports. In this paper, we study MedLEE's ability to identify mammogram findings suspicious for breast cancer by comparing MedLEE's encoding with a logbook of all suspicious findings maintained by the mammography center. While MedLEE was able to identify all the suspicious findings, it varied in the level of granularity, particularly about the location of the suspicious finding. Thus, natural language processing is a useful technique for encoding mammogram reports in order to detect suspicious findings.

Breast Neoplasms↗
PubMed1996

A double-blind comparison of the efficacy of two dose regimens of oral granisetron in preventing acute emesis in patients receiving moderately emetogenic chemotherapy.

BACKGROUND: The purpose of this study was to define an optimal administration schedule of granisetron for patients receiving moderately emetogenic chemotherapy by comparing the antiemetic efficacy and safety of 2 mg of the drug administrated orally. METHODS: In this double-blind, randomized, parallel study, 2-dose regimens of oral granisetron were evaluated in 697 adult cancer patients. Patients were stratified by gender and randomized to receive 2 mg oral granisetron, either as a divided dose given 1 hour prior to chemotherapy and 12 hours after the start of chemotherapy, or as a single dose 1 hour prior to chemotherapy at Cycle 1. The primary efficacy endpoints assessed were the percentage of patients with complete response (no nausea, no emesis, and no additional antiemetic medication during the 24-hour post-chemotherapy interval) and the incidence of emesis and nausea. Following completion of Cycle 1, patients were given the opportunity to receive open-label granisetron (2 mg once daily) on the first day of each remaining cycle of chemotherapy. RESULTS: No statistically significant differences in any of the endpoints were observed between the two treatment groups. Approximately 50% of patients in both treatment groups achieved complete response. The proportion of patients with no episodes of emesis occurred with similar frequency in the two treatment groups. Approximately 52% of patients in either treatment group were free of nausea during the postchemotherapy period. There was no difference between treatment groups regarding the use of antiemetic rescue medication. Finally, the incidence of adverse experiences was similar for both treatment groups. CONCLUSIONS: Both dose regimens of oral granisetron were similarly effective in controlling nausea and vomiting in the 24-hour interval following chemotherapy. Granisetron was well tolerated with few adverse events attributable to the study drug.

Administration, Oral↗
PubMed1996

The reinforcement of cancellous bone screws with calcium phosphate cement.

The ability of calcium phosphate cement (CPC) to reinforce cancellous screws placed in previously stripped holes was studied in vitro. The distal end of canine femurs were harvested. A total of 15 screws were placed in six femurs. The pullout strength (failure force), failure displacement, stiffness, and energy absorbed were determined for the screws in the intact cancellous bone. Next, these stripped screw holes were packed with CPC. The pullout test was repeated, and the results were compared using a paired, Student's t test. We found that the CPC was able to reinforce the previously stripped holes and significantly increase the pullout strength (1,159 +/- 278 N versus 678 +/- 297 N) and the stiffness (1,990 +/- 569 N/mm versus 1,519 +/- 609 N/mm) of the constructs, as well as the energy absorbed by the constructs until failure (467 +/- 180 N.mm versus 278 +/- 140 N.mm). There was no difference in the failure displacement (0.94 +/- 0.23 versus 0.85 +/- 0.51 mm). This study documents the ability of CPC to acutely reinforce cancellous bone screws in a region with no or poor-quality cancellous bone.

Animals↗
PubMed1996

Progress towards the year 2000: assessing the health status of minorities in Texas.

In 1991, the Centers for Disease Control and Prevention released a consensus set of 18 health status indicators to help communities assess their general health status and focus local, state, and national efforts on tracking the year 2000 objectives. States and local communities were encouraged also to analyze the indicators for each major racial and ethnic population in their jurisdictions. This article presents an update of trends in Texas for the health status indicators for the total population, along with comparisons by race and Hispanic origin for the most recent data. Analysis of these data reveals that the health status for the total population is improving as we approach the year 2000. Yet despite these overall gains, significant disparities exist between the total population and the racial and ethnic minorities in Texas. Further efforts are needed to reduce these health disparities.

Adult↗
PubMed1996

Integrating data from natural language processing into a clinical information system.

Demographic data extracted from discharge summaries by natural language processing was compared to data gathered by a conventional hospital admitting system. Discrepancies in data were noted in names, age, sex, race, and ethnicity. Some differences are attributable to errors in collection: interaction with patient, dictation, transcription, and data entry. Very few differences were due to errors in natural language processing. Other differences can be used to critique existing data, or to enhance data with more detailed information. Discrepancies in data as elementary as patient demographics raise the issue of resolving conflicts when neither source of data is known to be more reliable. Clinical repositories can represent conflicting data from multiple sources, but clinical information systems must bear the cost of increased complexity in the application programs that will use the data.

Evaluation Studies as Topic↗
PubMed1996

Identification of suspected tuberculosis patients based on natural language processing of chest radiograph reports.

Identification of eligible patients from electronically available patient data is a key difficulty in computerizing clinical practice guidelines because a large amount of the relevant data is stored as free text. We have been using MedLEE (Medical Language Extraction and Encoding System), a natural language processing system, to encode the clinical information in all chest radiograph and mammogram reports. This paper describes a retrospective study to determine if MedLEE can identify patients at risk for having tuberculosis (TB) based on their admission chest radiographs. Reports of 171 adult inpatients with culture-positive TB during 1992 and 1993 were manually coded (by a TB specialist) using seven terms suggestive of TB, and were also encoded by MedLEE. Using manual coding as the gold standard, MedLEE agreed on the classification of 152/171 (88.9%) reports--129/142 (90.8%) suspicious for TB and 23/29 (79.3%) not suspicious for TB; and 1072/1197 (89.6%) terms indicative of TB. Analysis showed that most of the discrepancies were caused by MedLEE not finding the location of the infiltrate. By ignoring the location of the infiltrate, the agreement became 157/171 (91.8%) reports and 946/1026 (92.2%) terms. Thus, natural language processing offers a practical alternative for using free-text reports to determine patient eligibility for computerized clinical practice guidelines.

Adult↗
PubMed1995

Unlocking clinical data from narrative reports: a study of natural language processing.

OBJECTIVE: To evaluate the automated detection of clinical conditions described in narrative reports. DESIGN: Automated methods and human experts detected the presence or absence of six clinical conditions in 200 admission chest radiograph reports. STUDY SUBJECTS: A computerized, general-purpose natural language processor; 6 internists; 6 radiologists; 6 lay persons; and 3 other computer methods. MAIN OUTCOME MEASURES: Intersubject disagreement was quantified by "distance" (the average number of clinical conditions per report on which two subjects disagreed) and by sensitivity and specificity with respect to the physicians. RESULTS: Using a majority vote, physicians detected 101 conditions in the 200 reports (0.51 per report); the most common condition was acute bacterial pneumonia (prevalence, 0.14), and the least common was chronic obstructive pulmonary disease (prevalence, 0.03). Pairs of physicians disagreed on the presence of at least 1 condition for an average of 20% of reports. The average intersubject distance among physicians was 0.24 (95% Cl, 0.19 to 0.29) out of a maximum possible distance of 6. No physician had a significantly greater distance than the average. The average distance of the natural language processor from the physicians was 0.26 (Cl, 0.21 to 0.32; not significantly greater than the average among physicians). Lay persons and alternative computer methods had significantly greater distance from the physicians (all > 0.5). The natural language processor had a sensitivity of 81% (Cl, 73% to 87%) and a specificity of 98% (Cl, 97% to 99%); physicians had an average sensitivity of 85% and an average specificity of 98%. CONCLUSIONS: Physicians disagreed on the interpretation of narrative reports, but this was not caused by outlier physicians or a consistent difference in the way internists and radiologists read reports. The natural language processor was not distinguishable from the physicians and was superior to all other comparison subjects. Although the domain of this study was restricted (six clinical conditions in chest radiographs), natural language processing seems to have the potential to extract clinical information from narrative reports in a manner that will support automated decision-support and clinical research.

Humans↗
PubMed1995

Assignment of the human p27Kip1 gene to 12p13 and its analysis in leukemias.

The p27Kip1 (p27) gene encodes an inducible inhibitor of cyclin-dependent kinase activity. Using a murine p27 cDNA as probe, we obtained a human cDNA clone and subsequently used it to isolate a genomic clone of this gene. The coding region of the human p27 gene was contained in two exons. Both the amino acid sequence and intron-exon organization of p27 were similar to those previously found for the related cyclin-dependent kinase inhibitor p21Waf1 (p21). The p27 gene was localized to chromosome band 12p13 by a combination of somatic cell hybrid and fluorescence in situ hybridization analyses. The p27 gene product is thought to control the leukocyte cell cycle and the 12p13 chromosomal band is known to be deleted in leukemias, suggesting that the p27 gene may act as a tumor suppressor gene in leukemias. Although p27 was found to reside in the minimal region of chromosomal loss in hematological malignancies, no mutations of p27 were observed in leukemia samples. Haploinsufficiency of p27 may confer a growth advantage to leukemia cells.

Base Sequence↗
PubMed1995

Dinucleotide repeats in the human surfactant protein-B gene and respiratory-distress syndrome.

Pulmonary surfactant, a lipoprotein complex, is essential for normal lung function, and deficiency of surfactant can result in respiratory-distress syndrome (RDS) in the prematurely born infant. Some studies have pointed towards a genetic contribution to the aetiology of RDS. Because the surfactant protein B (SP-B) is important for optimal surfactant function and because it is involved in the pathogenesis of pulmonary disease, we investigated the genetic variability of the SP-B gene in individuals with and without RDS. We identified a 2.5 kb BamHI polymorphism and studied its location, nature and frequency. We localized this polymorphism in the first half of intron 4 and found that it is derived by gain or loss in the number of copies of a motif that consists of two elements, a 20 bp conserved sequence and a variable number of CA dinucleotides. Variability in the number of motifs resulting from either deletion (in 55.3% of the cases with the variation) or insertion (44.7%) of motifs was observed in genomic DNAs from unrelated individuals. Analysis of 219 genomic DNAs from infants with (n = 82) and without (n = 137) RDS showed that this insertion/deletion appears with significantly higher frequency in the RDS population (29.3 as against 16.8%, P < 0.05).

Base Sequence↗
PubMed1995

Comparison of case-finding methodologies for endometritis after cesarean section.

BACKGROUND: Endometritis is a possible complication of delivery among patients undergoing cesarean section, resulting in increased costs and patient morbidity. However, traditional case-finding methods for endometritis may not identify most cases. We compared various case-finding methods with a reference method to determine a simple and accurate method for collecting data on endometritis after cesarean section. METHODS: We reviewed charts of all patients undergoing cesarean section (N = 167) during March 1 through July 31, 1991. These data were compared with study case-finding methods that used microbiology data, infection report forms from nursing, and computerized reports linking patients undergoing cesarean section with intravenous antibiotic use data and admission and discharge diagnoses. RESULTS: Each case-finding method was compared separately with the reference method ("gold standard"), which was designed to capture all cases among the patients in the study population (N = 145). This review yielded nine cases of endometritis (infection rate of 5.4/100 procedures). The computerized report method linking patients who underwent cesarean section with antibiotic use had a positive predictive value of 0.53. Methods that used microbiology data and nursing report forms had lower positive predictive values of 0.18 and 0.20, respectively. CONCLUSIONS: In our institution, case finding for postcesarean endometritis by means of a computerized report linking patients undergoing cesarean section with i.v. antibiotic use data and admission and discharge diagnoses is the most effective method of detecting postcesarean endometritis. It also represents the most efficient use of the infection control department's resources.

Anti-Bacterial Agents↗
PubMed1995

Molecular analysis of a novel subtelomeric repeat with polymorphic chromosomal distribution.

DNA from a 50-kb yeast artificial chromosome (YAC) containing one human telomere was characterized. Cloned sequences from the centromeric end of this YAC (designated yRM2001) localized to several human chromosomes by somatic hybrid panel mapping. The telomeric end of the YAC contained both (TTAGGG)n sequences and the previously characterized TelBam3.4 subterminal repeat element. A novel low-copy repeat element (designated HC1103) mapped 19 kb from the telomeric end of the YAC. This repeat was shown by fluorescence in situ hybridization to be present in several subtelomeric regions (3q, 12p, 15q, 19p, and 20p) and at an interstitial site (2q13-->q14) in all individuals studied, but to be polymorphically distributed at several other telomeres. The YAC vector-insert EcoRI cloning site was positioned 50 kb to 70 kb from chromosome termini in human genomic DNA using RecA-assisted restriction endonuclease (RARE) cleavage analysis. Our results suggest that the DNA segment cloned in yRM2001 contains a novel block of low-copy DNA consistently present at some human telomeres, but polymorphically distributed at others.

Base Sequence↗
PubMed1995

Comparative clinical trial of granisetron and ondansetron in the prophylaxis of cisplatin-induced emesis. The Granisetron Study Group.

PURPOSE: To compare the efficacy and safety of granisetron and ondansetron, serotonin (5-HT3) receptor antagonists shown to be effective in the prevention of chemotherapy-induced emesis. PATIENTS AND METHODS: In a double-blind, randomized, stratified, parallel-group study, the efficacy and safety of granisetron and ondansetron were compared in 987 chemotherapy-naive patients who received cisplatin in doses > or = 60 mg/m2. Granisetron was administered as a single dose of 10 or 40 micrograms/kg before the start of chemotherapy. Ondansetron was administered in doses of 0.15 mg/kg before and 4 and 8 hours after the start of chemotherapy. The three treatment groups were well-matched with respect to demographic characteristics and the dose of cisplatin administered. RESULTS: For all evaluations, single doses of granisetron 10 or 40 micrograms/kg were as effective as three 0.15-mg/kg doses of ondansetron. Total control (no vomiting, no retching, no nausea, and no use of rescue) was attained by 38%, 41%, and 39% of all patients who received granisetron 10 microgram/kg, granisetron 40 micrograms/kg, and ondansetron, respectively. No vomiting or retching and no use of rescue antiemetics were reported in 47%, 48%, and 51% of patients who received granisetron 10 micrograms/kg, granisetron 40 micrograms/kg, and ondansetron, respectively; no nausea and no use of rescue antiemetics were reported in 39%, 42%, and 40% of patients, respectively. CONCLUSION: All three treatment regimens were well-tolerated. The results of this study indicate that a single dose of granisetron 10 or 40 micrograms/kg is as effective as three doses of ondansetron 0.15 mg/kg in the prevention of nausea and vomiting induced by cisplatin chemotherapy.

Adult↗
PubMed1995

Architectural requirements for a multipurpose natural language processor in the clinical environment.

A considerable amount of research has been concerned with the development of natural language systems to automate the encoding of clinical information that occurs in textual form. The task is very complex, and not many language processors are used routinely within clinical information systems. Those systems that are operational, have been implemented in narrow domains for particular applications. For a system to be truly useful, it should be designed so that it could be widely used within the clinical environment. This paper examines architectural requirements we have identified as being necessary for portability and describes the architecture of the system we developed. Our system was designed so that it could be used in different domains to serve a variety of applications. It has been integrated with the clinical information system at Columbia-Presbyterian Medical Center where it routinely encodes clinical information from radiological reports of patients.

Computer Systems↗
PubMed1995

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Adult↗