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Liu H, Friedman C. A method for vocabulary development and visualization based on medical language processing and XML. Proc AMIA Symp 2000:502-6. [PMID: 11079934 PMCID: PMC2243989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
A comprehensive controlled clinical vocabulary is critical to the effectiveness of many automated clinical systems. Vocabulary development and maintenance is an important aspect of a vocabulary, and should be linked to terms physicians actually use. This paper presents a method to help vocabulary builders capture, visualize, and analyze both compositional and quantitative information related to terms physicians use. The method includes several components: an MLP system, a corpus of relevant reports and a visualization tool based on XML and JAVA.
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Barrows Jr RC, Busuioc M, Friedman C. Limited parsing of notational text visit notes: ad-hoc vs. NLP approaches. Proc AMIA Symp 2000:51-5. [PMID: 11079843 PMCID: PMC2243829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
This paper describes the extraction of structured data relevant to glaucoma diagnosis and progression from visit notes typed as "notational text" by ophthalmologists during patient encounters. We compared two text processing systems: a limited pattern matching system called GDP (Glaucoma Dedicated Parser) and MedLEE, a proven natural language processing system which is in routine use encoding findings from chest radiograph and mammogram reports at the New York-Presbyterian hospital's Columbia-Presbyterian Center. We also evaluated the use of GDP as a preprocessor program to transform notational text into constructions recognizable by MedLEE. These systems have been evaluated according to their recall and precision in the particular task of processing a corpus of "notational text" documents to extract information related to glaucoma disease.
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Friedman C. A broad-coverage natural language processing system. Proc AMIA Symp 2000:270-4. [PMID: 11079887 PMCID: PMC2243979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Natural language processing systems (NLP) that extract clinical information from textual reports were shown to be effective for limited domains and for particular applications. Because an NLP system typically requires substantial resources to develop, it is beneficial if it is designed to be easily extendible to multiple domains and applications. This paper describes multiple extensions of an NLP system called MedLEE, which was originally developed for the domain of radiological reports of the chest, but has subsequently been extended to mammography, discharge summaries, all of radiology, electrocardiography, echocardiography, and pathology.
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Deng Y, Madan A, Banta AB, Friedman C, Trask BJ, Hood L, Li L. Characterization, chromosomal localization, and the complete 30-kb DNA sequence of the human Jagged2 (JAG2) gene. Genomics 2000; 63:133-8. [PMID: 10662552 DOI: 10.1006/geno.1999.6045] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genomic sequence of the human Jagged2 (JAG2) gene, which encodes a ligand for the Notch receptors, was determined. The 30-kb DNA sequence spanning the JAG2 gene contains 26 exons and a putative promoter region. Several potential binding sites for transcription factors, including NF-kappab, E47, E12, E2F, Ets-1, MyoD, and OCT-1, were found in the human JAG2 promoter region. The JAG2 gene was also mapped to the chromosomal region 14q32 using fluorescence in situ hybridization.
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Friedman C, Dolgin JG. Adverse events of Kytril Injection questioned. Oncol Nurs Forum 1999; 26:1587-9. [PMID: 10573674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
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Friedman C, Barnette M, Buck AS, Ham R, Harris JA, Hoffman P, Johnson D, Manian F, Nicolle L, Pearson ML, Perl TM, Solomon SL. Requirements for infrastructure and essential activities of infection control and epidemiology in out-of-hospital settings: a consensus panel report. Association for Professionals in Infection Control and Epidemiology and Society for Healthcare Epidemiology of America. Infect Control Hosp Epidemiol 1999; 20:695-705. [PMID: 10530650 DOI: 10.1086/501569] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
In 1997 the Association for Professionals in Infection Control and Epidemiology and the Society for Healthcare Epidemiology of America established a consensus panel to develop recommendations for optimal infrastructure and essential activities of infection control and epidemiology programs in out-of-hospital settings. The following report represents the Consensus Panel's best assessment of requirements for a healthy and effective out-of-hospital-based infection control and epidemiology program. The recommendations fall into 5 categories: managing critical data and information; developing and recommending policies and procedures; intervening directly to prevent infections; educating and training of health care workers, patients, and nonmedical caregivers; and resources. The Consensus Panel used an evidence-based approach and categorized recommendations according to modifications of the scheme developed by the Clinical Affairs Committee of the Infectious Diseases Society of America and the Centers for Disease Control and Prevention's Healthcare Infection Control Practices Advisory Committee.
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Friedman C, Barnette M, Buck AS, Ham R, Harris JA, Hoffman P, Johnson D, Manian F, Nicolle L, Pearson ML, Perl TM, Solomon SL. Requirements for infrastructure and essential activities of infection control and epidemiology in out-of-hospital settings: a Consensus Panel report. Am J Infect Control 1999; 27:418-30. [PMID: 10511489 DOI: 10.1016/s0196-6553(99)70008-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In 1997 the Association for Professionals in Infection Control and Epidemiology and the Society for Healthcare Epidemiology of America established a consensus panel to develop recommendations for optimal infrastructure and essential activities of infection control and epidemiology programs in out-of-hospital settings. The following report represents the Consensus Panel's best assessment of requirements for a healthy and effective out-of-hospital-based infection control and epidemiology program. The recommendations fall into 5 categories: managing critical data and information; developing and recommending policies and procedures; intervening directly to prevent infections; educating and training of health care workers, patients, and nonmedical caregivers; and resources. The Consensus Panel used an evidence-based approach and categorized recommendations according to modifications of the scheme developed by the Clinical Affairs Committee of the Infectious Diseases Society of America and the Centers for Disease Control and Prevention's Healthcare Infection Control Practices Advisory Committee.
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Friedman C, Hripcsak G. Natural language processing and its future in medicine. ACADEMIC MEDICINE : JOURNAL OF THE ASSOCIATION OF AMERICAN MEDICAL COLLEGES 1999; 74:890-895. [PMID: 10495728 DOI: 10.1097/00001888-199908000-00012] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
If accurate clinical information were available electronically, automated applications could be developed to use this information to improve patient care and lower costs. However, to be fully retrievable, clinical information must be structured or coded. Many online patient reports are not coded, but are recorded in natural-language text that cannot be reliably accessed. Natural language processing (NLP) can solve this problem by extracting and structuring text-based clinical information, making clinical data available for use. NLP systems are quite difficult to develop, as they require substantial amounts of knowledge, but progress has definitely been made. Some NLP systems have been developed and tested and have demonstrated promising performance in practical clinical applications; some of these systems have already been deployed. The authors provide background information about NLP, briefly describe some of the systems that have been recently developed, and discuss the future of NLP in medicine.
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Friedman C, Elstein A, Wolf F, Murphy G, Franz T, Fine P, Heckerling P, Miller T. Measuring the quality of diagnostic hypothesis sets for studies of decision support. Stud Health Technol Inform 1999; 52 Pt 2:864-8. [PMID: 10384584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Within medical informatics there is widespread interest in computer-based decision support and the evaluation of its impact. It is widely recognized that the measurement of dependent variables, or outcomes, represents the most challenging aspect of this work. This paper describes and reports the reliability and validity of an outcome metric for studies of diagnostic decision support. The results of this study will guide the analytic methods used in our ongoing multi-site study of the effects of decision support on diagnostic reasoning. Our measurement approach conceptualizes the quality of a diagnostic hypothesis set as having two components summed to generate a composite index: a Plausibility Component derived from ratings of each hypothesis in the set, whether correct or incorrect; and a Location Component derived from the location of the correct diagnosis if it appears in the set. The reliability of this metric is determined by the extent of interrater agreement on the plausibility of diagnostic hypotheses. Validity is determined by the extent to which the index generates scores that make sense on inspection (face validity), as well as the extent to which the component scores are non-redundant and discriminate the performance of novices and experts (construct validity). Using data from the pilot and main phases of our ongoing study (n = 124 subjects working 1116 cases), the reliability of our diagnostic quality metric was found to be 0.85-0.88. The metric was found to generate, on inspection, no clearly counterintuitive scores. Using data from the pilot phase of our study (n = 12 subjects working 108 cases), the component scores were moderately correlated (r = 0.68). The composite index, computed by equally weighting both components, was found to discriminate the hypotheses of medical students and attending physicians by 0.97 standard deviation units. Based on these findings, we have adopted this metric for use in our further research exploring the impact of decision support systems on diagnostic reasoning and will make it available to the informatics research community.
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Horan-Murphy E, Barnard B, Chenoweth C, Friedman C, Hazuka B, Russell B, Foster M, Goldman C, Bullock P, Docken L, McDonald L. APIC/CHICA-Canada Infection Control and Epidemiology: Professional and Practice Standards. Association for Professionals in Infection Control and Epidemiology, Inc, and the Community and Hospital Infection Control Association-Canada. Am J Infect Control 1999; 27:47-51. [PMID: 10223902 DOI: 10.1016/s0196-6553(99)70073-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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61
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Friedman C, Hripcsak G, Shagina L, Liu H. Representing information in patient reports using natural language processing and the extensible markup language. J Am Med Inform Assoc 1999; 6:76-87. [PMID: 9925230 PMCID: PMC61346 DOI: 10.1136/jamia.1999.0060076] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVE To design a document model that provides reliable and efficient access to clinical information in patient reports for a broad range of clinical applications, and to implement an automated method using natural language processing that maps textual reports to a form consistent with the model. METHODS A document model that encodes structured clinical information in patient reports while retaining the original contents was designed using the extensible markup language (XML), and a document type definition (DTD) was created. An existing natural language processor (NLP) was modified to generate output consistent with the model. Two hundred reports were processed using the modified NLP system, and the XML output that was generated was validated using an XML validating parser. RESULTS The modified NLP system successfully processed all 200 reports. The output of one report was invalid, and 199 reports were valid XML forms consistent with the DTD. CONCLUSIONS Natural language processing can be used to automatically create an enriched document that contains a structured component whose elements are linked to portions of the original textual report. This integrated document model provides a representation where documents containing specific information can be accurately and efficiently retrieved by querying the structured components. If manual review of the documents is desired, the salient information in the original reports can also be identified and highlighted. Using an XML model of tagging provides an additional benefit in that software tools that manipulate XML documents are readily available.
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Shablinsky I, Starren J, Friedman C. What do ER physicians really want? A method for elucidating ER information needs. Proc AMIA Symp 1999:390-4. [PMID: 10566387 PMCID: PMC2232515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023] Open
Abstract
Prior discharge summaries are a critical source of information for treating emergency room patients. However, reading discharge summaries may occupy more time than emergency care clinicians can afford. It would be beneficial to present vital information in the reports to them so that they would be able to quickly extract and digest it. There are several possible ways to present the information without changing the structure or content of the report itself. As a prelude to an effective study concerning the efficiency of the various presentation approaches, it is first necessary to know which diagnoses would benefit from past history, and what kind of information is most important to present for each of the diagnoses. In this study, we present a method for elucidating emergency care information needs from clinicians. Analysis of the data obtained from clinicians resulted in generation of a list of important diagnoses and informational categories. For validation, the clinicians were shown sample reports and were asked to highlight critical information. Overall, predicted important items correlated with physicians highlighting (Pearson correlation coefficient of 0.650, significance level 0.01).
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Friedman C, Knirsch C, Shagina L, Hripcsak G. Automating a severity score guideline for community-acquired pneumonia employing medical language processing of discharge summaries. Proc AMIA Symp 1999:256-60. [PMID: 10566360 PMCID: PMC2232753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023] Open
Abstract
Obtaining encoded variables is often a key obstacle to automating clinical guidelines. Frequently the pertinent information occurs as text in patient reports, but text is inadequate for the task. This paper describes a retrospective study that automates determination of severity classes for patients with community-acquired pneumonia (i.e. classifies patients into risk classes 1-5), a common and costly clinical problem. Most of the variables for the automated application were obtained by writing queries based on output generated by MedLEE1, a natural language processor that encodes clinical information in text. Comorbidities, vital signs, and symptoms from discharge summaries as well as information from chest x-ray reports were used. The results were very good because when compared with a reference standard obtained manually by an independent expert, the automated application demonstrated an accuracy, sensitivity, and specificity of 93%, 92%, and 93% respectively for processing discharge summaries, and 96%, 87%, and 98% respectively for chest x-rays. The accuracy for vital sign values was 85%, and the accuracy for determining the exact risk class was 80%. The remaining 20% that did not match exactly differed by only one class.
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Hripcsak G, Kuperman GJ, Friedman C, Heitjan DF. A reliability study for evaluating information extraction from radiology reports. J Am Med Inform Assoc 1999; 6:143-50. [PMID: 10094067 PMCID: PMC61353 DOI: 10.1136/jamia.1999.0060143] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
GOAL To assess the reliability of a reference standard for an information extraction task. SETTING Twenty-four physician raters from two sites and two specialties judged whether clinical conditions were present based on reading chest radiograph reports. METHODS Variance components, generalizability (reliability) coefficients, and the number of expert raters needed to generate a reliable reference standard were estimated. RESULTS Per-rater reliability averaged across conditions was 0.80 (95% CI, 0.79-0.81). Reliability for the nine individual conditions varied from 0.67 to 0.97, with central line presence and pneumothorax the most reliable, and pleural effusion (excluding CHF) and pneumonia the least reliable. One to two raters were needed to achieve a reliability of 0.70, and six raters, on average, were required to achieve a reliability of 0.95. This was far more reliable than a previously published per-rater reliability of 0.19 for a more complex task. Differences between sites were attributable to changes to the condition definitions. CONCLUSION In these evaluations, physician raters were able to judge very reliably the presence of clinical conditions based on text reports. Once the reliability of a specific rater is confirmed, it would be possible for that rater to create a reference standard reliable enough to assess aggregate measures on a system. Six raters would be needed to create a reference standard sufficient to assess a system on a case-by-case basis. These results should help evaluators design future information extraction studies for natural language processors and other knowledge-based systems.
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Yu H, Friedman C, Rhzetsky A, Kra P. Representing genomic knowledge in the UMLS semantic network. Proc AMIA Symp 1999:181-5. [PMID: 10566345 PMCID: PMC2232882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023] Open
Abstract
Genomics research has a significant impact on the understanding and treatment of human hereditary diseases, and biomedical literature concerning the genome project is becoming more and more important for clinicians. The Unified Medical Language System (UMLS) is designed to facilitate the retrieval and integration of information from multiple-readable biomedical information resources. This paper describes our efforts to integrate concepts important to genomics research with the UMLS semantic network. We found that the UMLS contains over 30 semantic types and most of the semantic relations that are essential for representing the underlying genomic knowledge. In addition, we observed that the organization of the network was appropriate for representing the hierarchical organization of the concepts. Because some of the concepts critical to the genomic domain were found to be missing, we propose to extend the network by adding six new semantic types and sixteen new semantic relations.
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Trask BJ, Massa H, Brand-Arpon V, Chan K, Friedman C, Nguyen OT, Eichler E, van den Engh G, Rouquier S, Shizuya H, Giorgi D. Large multi-chromosomal duplications encompass many members of the olfactory receptor gene family in the human genome. Hum Mol Genet 1998; 7:2007-20. [PMID: 9817916 DOI: 10.1093/hmg/7.13.2007] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The human genome contains thousands of genes that encode a diverse repertoire of odorant receptors (ORs). We report here on the identification and chromosomal localization of 74 OR-containing genomic clones. Using fluorescence in situ hybridization (FISH), we demonstrate a striking homology among a set of approximately 20 OR locations, illustrating a history of duplications that have distributed OR sequences across the genome. Half of the OR-containing BACs cloned from total genomic DNA and 86% of cosmids derived from chromosome 3 cross-hybridize to a subset of these locations, many to 17 of them. These paralogous regions are distributed on 13 chromosomes, and eight lie in terminal bands. By analyzing clones from an approximately 250 kb clone-walk across one of these sites (3p13), we show that the homology among these sites is extensive (>150 kb) and encompasses both OR genes and intergenic genomic sequences. The FISH signals appear significantly larger at some sites than at the native location, indicating that portions of some duplicons have undergone local amplification/attrition. More restricted duplications involving pairs of other genomic locations are detected with 12% of the OR-BACs. Only a small subset of OR locations is sufficiently diverged from the others that clones derived from them behave as single-copy FISH probes. We estimate that duplications encompassing members of the OR gene family account for >0.1% of the human genome. A comparison of FISH signals at orthologous locations in other primates indicates that a portion of this OR 'subgenome' has been in flux during the divergence of primates, possibly as a mechanism for evolving the repertoire of olfactory receptors.
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Friedman C, Hripcsak G. Evaluating natural language processors in the clinical domain. Methods Inf Med 1998; 37:334-44. [PMID: 9865031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Evaluating natural language processing (NLP) systems in the clinical domain is a difficult task which is important for advancement of the field. A number of NLP systems have been reported that extract information from free-text clinical reports, but not many of the systems have been evaluated. Those that were evaluated noted good performance measures but the results were often weakened by ineffective evaluation methods. In this paper we describe a set of criteria aimed at improving the quality of NLP evaluation studies. We present an overview of NLP evaluations in the clinical domain and also discuss the Message Understanding Conferences (MUC) [1-4]. Although these conferences constitute a series of NLP evaluation studies performed outside of the clinical domain, some of the results are relevant within medicine. In addition, we discuss a number of factors which contribute to the complexity that is inherent in the task of evaluating natural language systems.
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Rouquier S, Friedman C, Delettre C, van den Engh G, Blancher A, Crouau-Roy B, Trask BJ, Giorgi D. A gene recently inactivated in human defines a new olfactory receptor family in mammals. Hum Mol Genet 1998; 7:1337-45. [PMID: 9700185 DOI: 10.1093/hmg/7.9.1337] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The olfactory receptor (OR) gene family constitutes one of the largest multigene families and is distributed among many chromosomal sites in the human genome. Four OR families have been defined in mammals. We previously demonstrated that a high fraction of human OR sequences have incurred deleterious mutations, thus reducing the repertoire of functional OR genes. In this study, we have characterized a new OR gene, 912-93, in primates. This gene is unique and it defines a new OR family. It localizes to human chromosome 11q11-12 and at syntenical sites in other hominoids. The sequence marks a previously unrecognized rearrangement of pericentromeric material from chromosome 11 to the centromeric region of gibbon chromosome 5. The human gene contains a nonsense point mutation in the region corresponding to the extracellular N-terminus of the receptor. This mutation is present in humans of various ethnic groups, but is absent in apes, suggesting that it probably appeared during the divergence of humans from other apes, <4 000 000-5 000 000 years ago. A second mutation, a frameshift at a different location, has occurred in the gorilla copy of this gene. These observations suggest that OR 912-93 has been recently silenced in human and gorilla, adding to a pool of OR pseudogenes whose growth may parallel a reduction in the sense of smell in primates.
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Li L, Huang GM, Banta AB, Deng Y, Smith T, Dong P, Friedman C, Chen L, Trask BJ, Spies T, Rowen L, Hood L. Cloning, characterization, and the complete 56.8-kilobase DNA sequence of the human NOTCH4 gene. Genomics 1998; 51:45-58. [PMID: 9693032 DOI: 10.1006/geno.1998.5330] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The first complete mammalian genomic sequence reported thus far in the Notch gene family, including a putative promoter region and 30 exons of the human NOTCH4 gene spanning 56.8 kb of DNA, were sequenced. The NOTCH4 locus contains a TATA-less promoter with two putative transcription initiation sites (Inr), three RBP-Jkappa sites, and two GATA recognition sites. Two cDNA isoforms, NOTCH4(L) and NOTCH4(S),were identified. Whereas the NOTCH4(S) isoform contains the entire coding sequence, the NOTCH4(L) isoform has two unspliced intronic sequences between exons 11 and 12 and exons 20 and 21 and a misspliced exon 6. Consistent with these results, two alternatively spliced isoforms of transcripts of approximately 9.3 and 6.7 kb were detected by Northern blot analysis. The predicted amino acid sequence of the NOTCH4 protein based on the NOTCH4(S) cDNA sequence contains 2003 amino acids and includes the predominant motifs of the Notch family: 29 epidermal growth factor (EGF)-like repeats, 3 Notch/lin-12 repeats, a transmembrane region, 6 cdc10/Ankyrin repeats, and a PEST domain.
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MESH Headings
- Adult
- Alternative Splicing
- Amino Acid Sequence
- Base Sequence
- Chromosome Mapping
- Chromosomes, Human, Pair 6/genetics
- Cloning, Molecular
- DNA, Complementary/genetics
- Exons
- Gene Expression
- Genome, Human
- Humans
- Major Histocompatibility Complex/genetics
- Molecular Sequence Data
- Polymorphism, Genetic
- Promoter Regions, Genetic
- Proto-Oncogene Proteins/genetics
- Receptor, Notch4
- Receptors, Cell Surface
- Receptors, Notch
- Sequence Alignment
- Sequence Analysis, DNA
- Tissue Distribution
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Friedman C, Chenoweth C. A survey of infection control professional staffing patterns at University HealthSystem Consortium institutions. Am J Infect Control 1998; 26:239-44. [PMID: 9638286 DOI: 10.1016/s0196-6553(98)80007-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Proper staffing of infection control departments has long been a topic of interest. The most complete report on the subject, the Study on the Efficacy of Nosocomial Infection Control, was published in 1985. To provide current benchmarking comparison data for expected staff reductions at the University of Michigan Health System, a survey of University HealthSystem Consortium members was performed. METHODS A survey tool was developed to obtain general demographic, staffing, and case-mix information. An infection control professional at each institution was contacted to obtain most of the information. Additional information was obtained from standard references. RESULTS Responses were obtained from 45 University HealthSystem Consortium members (67%). Full-time equivalent ratios were based on the following parameters and compared for the institutions: number of occupied beds (according to occupancy rate, median 137 occupied beds/full-time equivalent), number of intensive care unit beds (median 28 beds/full-time equivalent), number of admissions or discharges (median 6686 admissions/full-time equivalent), number of ambulatory care visits (median 104,426 visits/full-time equivalent), and case-mix index (median 1.75). CONCLUSIONS Many institutions are using benchmarking comparison data to make decisions regarding staff reductions. This survey provides preliminary data for determining the "best practice" in staffing for infection control departments. More information may be needed to evaluate other factors that affect infection control professionals' workload.
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Gralla RJ, Navari RM, Hesketh PJ, Popovic W, Strupp J, Noy J, Einhorn L, Ettinger D, Bushnell W, Friedman C. Single-dose oral granisetron has equivalent antiemetic efficacy to intravenous ondansetron for highly emetogenic cisplatin-based chemotherapy. J Clin Oncol 1998; 16:1568-73. [PMID: 9552067 DOI: 10.1200/jco.1998.16.4.1568] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
PURPOSE To compare the antiemetic efficacy of a single dose of an oral antiemetic (granisetron 2 mg) with a single dose of an intravenous (i.v.) antiemetic (ondansetron 32 mg) given before cisplatin-based chemotherapy. PATIENTS AND METHODS This was a multicenter, randomized, double-blind, parallel-group study. Patients (N = 1,054) scheduled to receive cisplatin (> or = 60 mg/m2)-based chemotherapy were randomized to receive either 2 mg of oral granisetron tablets 1 hour before chemotherapy (n = 534) or i.v. ondansetron (32 mg) 30 minutes before chemotherapy (n = 520). The primary efficacy end point was total control (no emesis, no nausea, and no use of antiemetic rescue medication) over the initial 24 hours after the start of chemotherapy. Dexamethasone or methylprednisolone were permitted, but not required, as concomitant prophylactic antiemetics. RESULTS Total control was equivalent 24 hours after cisplatin chemotherapy for single-dose oral granisetron (54.7%) and i.v. ondansetron (58.3%) (95% confidence interval [CI], -9.6 to 2.4). Similar proportions of patients remained nausea-free in the granisetron group (55.4%) and the ondansetron group (59%) (95% CI, -9.6 to 2.4). The rate of complete control of emesis was 61.2% in the granisetron group and 67.1% in the ondansetron group (95% CI, -11.7 to -0.1). Both treatment regimens were well tolerated, with similar patterns of adverse reactions, generally of a mild degree. The most common side effects included constipation (14%), headache (15%), and diarrhea (10%). CONCLUSION Oral granisetron, administered as a single 2-mg dose, provided equivalent total antiemetic control when compared with i.v. ondansetron (32 mg) in patients who received highly emetogenic, cisplatin-based chemotherapy.
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Scheckler WE, Brimhall D, Buck AS, Farr BM, Friedman C, Garibaldi RA, Gross PA, Harris JA, Hierholzer WJ, Martone WJ, McDonald LL, Solomon SL. Requirements for infrastructure and essential activities of infection control and epidemiology in hospitals: a consensus panel report. Society for Healthcare Epidemiology of America. Infect Control Hosp Epidemiol 1998; 19:114-24. [PMID: 9510112 DOI: 10.1086/647779] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The scientific basis for claims of efficacy of nosocomial infection surveillance and control programs was established by the Study on the Efficacy of Nosocomial Infection Control project. Subsequent analyses have demonstrated nosocomial infection prevention and control programs to be not only clinically effective but also cost-effective. Although governmental and professional organizations have developed a wide variety of useful recommendations and guidelines for infection control, and apart from general guidance provided by the Joint Commission on Accreditation of Healthcare Organizations, there are surprisingly few recommendations on infrastructure and essential activities for infection control and epidemiology programs. In April 1996, the Society for Healthcare Epidemiology of America established a consensus panel to develop recommendations for optimal infrastructure and essential activities of infection control and epidemiology programs in hospitals. The following report represents the consensus panel's best assessment of needs for a healthy and effective hospital-based infection control and epidemiology program. The recommendations fall into eight categories: managing critical data and information; setting and recommending policies and procedures; compliance with regulations, guidelines, and accreditation requirements; employee health; direct intervention to prevent transmission of infectious diseases; education and training of healthcare workers; personnel resources; and nonpersonnel resources. The consensus panel used an evidence-based approach and categorized recommendations according to modifications of the scheme developed by the Clinical Affairs Committee of the Infectious Diseases Society of America and the Centers for Disease Control and Prevention's Hospital Infection Control Practices Advisory Committee.
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Scheckler WE, Brimhall D, Buck AS, Farr BM, Friedman C, Garibaldi RA, Gross PA, Harris JA, Hierholzer WJ, Martone WJ, McDonald LL, Solomon SL. Requirements for infrastructure and essential activities of infection control and epidemiology in hospitals: A consensus panel report. Society for Healthcare Epidemiology of America. Am J Infect Control 1998; 26:47-60. [PMID: 9503113 DOI: 10.1016/s0196-6553(98)70061-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The scientific basis for claims of efficacy of nosocomial infection surveillance and control programs was established by the Study on the Efficacy of Nosocomial Infection Control project. Subsequent analyses have demonstrated nosocomial infection prevention and control programs to be not only clinically effective but also cost-effective. Although governmental and professional organizations have developed a wide variety of useful recommendations and guidelines for infection control, and apart from general guidance provided by the Joint Commission on Accreditation of Healthcare Organizations, there are surprisingly few recommendations on infrastructure and essential activities for infection control and epidemiology programs. In April 1996, the Society for Healthcare Epidemiology of America established a consensus panel to develop recommendations for optimal infrastructure and essential activities of infection control and epidemiology programs in hospitals. The following report represents the consensus panel's best assessment of needs for a healthy and effective hospital-based infection control and epidemiology program. The recommendations fall into eight categories: managing critical data and information; setting and recommending policies and procedures; compliance with regulations, guidelines, and accreditation requirements; employee health; direct intervention to prevent transmission of infectious diseases; education and training of healthcare workers; personnel resources; and nonpersonnel resources. The consensus panel used an evidence-based approach and categorized recommendations according to modifications of the scheme developed by the Clinical Affairs Committee of the Infectious Diseases Society of America and the Centers for Disease Control and Prevention's Hospital Infection Control Practices Advisory Committee.
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Knirsch CA, Jain NL, Pablos-Mendez A, Friedman C, Hripcsak G. Respiratory isolation of tuberculosis patients using clinical guidelines and an automated clinical decision support system. Infect Control Hosp Epidemiol 1998; 19:94-100. [PMID: 9510106 DOI: 10.1086/647773] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVE To evaluate a clinical guideline and an automated computer protocol for detection and respiratory isolation of tuberculosis (TB) patients. DESIGN An automated computer protocol was tested on a retrospective cohort of adult culture-positive TB patients admitted from 1992 to 1993 to Columbia-Presbyterian Medical Center and evaluated prospectively from July 1995 until July 1996. SETTING A large teaching hospital in New York City. PATIENTS 171 adult patients admitted from 1992 to 1993 and 43 patients admitted between July 1995 and July 1996. INTERVENTIONS The 1990 Centers for Disease Control and Prevention guidelines for preventing transmission of TB were adapted to formulate clinical guidelines to ensure early isolation of TB patients at Columbia-Presbyterian Medical Center. RESULTS Implementation of a clinical respiratory isolation protocol resulted in a significant improvement in TB patient isolation rates, from 45 (51%) of 88 in 1992 to 62 (75%) of 83 in 1993 (P<.001). In testing automated protocols, the theoretical improvement would have identified an additional 27 patients not isolated by clinicians, making the overall isolation rate 134 (78%) of 171. For the prospective evaluation, 30 (70%) of 43 TB patients were isolated by clinicians adhering to the clinical protocol. Four additional patients were identified by the automated TB protocol, making the combined isolation rate 34 (79%) of 43. CONCLUSIONS A clinical policy to isolate TB patients and suspected human immunodeficiency virus-infected patients with cough, fever, or radiographic abnormalities improved isolation of culture-documented TB patients from 1992 to 1993. Automated computer protocols were successful in identifying additional potentially infectious patients that clinicians failed to place on respiratory isolation. Clinical and automated protocols combined resulted in better isolation rates than a clinical protocol alone.
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Perez EA, Hesketh P, Sandbach J, Reeves J, Chawla S, Markman M, Hainsworth J, Bushnell W, Friedman C. Comparison of single-dose oral granisetron versus intravenous ondansetron in the prevention of nausea and vomiting induced by moderately emetogenic chemotherapy: a multicenter, double-blind, randomized parallel study. J Clin Oncol 1998; 16:754-60. [PMID: 9469367 DOI: 10.1200/jco.1998.16.2.754] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
PURPOSE The antiemetic effectiveness and safety of single-dose oral granisetron were compared with intravenous (I.V.) ondansetron in chemotherapy-naive patients who received moderately emetogenic chemotherapy. PATIENTS AND METHODS In this double-blind, parallel-group study, patients naive to emetogenic chemotherapy (N = 1,085) who were scheduled to receive cyclophosphamide- (500 to 1,200 mg/m2) or carboplatin (> or = 300 mg/m2) based chemotherapy, were randomized to receive either oral granisetron (n = 542) or I.V. ondansetron (n = 543). Efficacy assessments included the proportion of patients in each treatment group with total control over the 24 and 48 hours following chemotherapy initiation, as well as incidence and severity of nausea and emesis and use of antiemetic rescue medication. Prophylactic corticosteroids were allowed. Safety assessment was based on patients' reports of adverse experiences. RESULTS Approximately 80% of patients received prophylactic corticosteroids. Single-dose oral granisetron (2 mg) and I.V. ondansetron (32 mg) resulted in equivalent levels of total emetic control during the first 48 hours after chemotherapy. The proportion of nausea- and emesis-free patients at 24 and 48 hours were also approximately equivalent. The most commonly reported adverse experiences were headache, asthenia, and constipation. More patients who received ondonsetron than granisetron reported dizziness (9.6% v 5.4%, respectively; P = .011) and abnormal vision (4.2% v 0.6%, respectively; P < .001). CONCLUSION A single oral dose of granisetron (2 mg) resulted in equivalent levels of antiemetic protection as I.V. ondansetron (32 mg). Both agents were well tolerated, although more dizziness and abnormal vision were reported with ondansetron. Because the two antiemetic regimens exhibited equivalent efficacies, additional factors such as convenience and cost of therapy should be considered.
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