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Biomedical subjects

C Friedman

Publications and source records attributed to C Friedman.

At least 37 records · Page 2Linked to original sources
PubMed2000

Using BLAST for identifying gene and protein names in journal articles.

We describe a system which automatically identifies gene and protein names in journal articles, an important and non-trivial first step in knowledge extraction of protein and gene actions. Our system uses a database of gene and protein names and is based on BLAST [Altschul et al., Nucleic Acids Res. 25 (1997) 3389-3402], a popular tool for DNA and protein sequence comparison. We describe a method that consists of mapping sequences of text characters into sequences of nucleotides that can be processed by BLAST. We demonstrate that this approach is feasible: the system matches gene and protein names with a recall of 78.8% and a precision of 71.7%, which includes names that are not part of the system database. An analysis of the results suggests techniques that can be used to improve performance further.

Algorithms↗
PubMed2000

PART-1: a novel human prostate-specific, androgen-regulated gene that maps to chromosome 5q12.

Genes regulated by androgenic hormones are of critical importance for the normal physiological function of the human prostate gland, and they contribute to the development and progression of prostate carcinoma. We used cDNA microarrays containing 1500 prostate-derived cDNAs to profile transcripts regulated by androgens in prostate cancer cells. This study identified a novel gene that we have designated PART-1 (prostate androgen-regulated transcript 1), which exhibited increased expression upon exposure to androgens in the LNCaP prostate cancer cell line. Northern analysis demonstrated that PART-1 is highly expressed in the prostate gland relative to other normal human tissues and is expressed as different transcripts using at least three different polyadenylation signals. The PART-1 cDNA and putative protein are not significantly homologous to any sequences in the nonredundant public sequence databases. Cloning and analysis of the putative PART-1 promoter region identified a potential binding site for the homeobox gene PBX-la, but no consensus androgen response element or sterol-regulatory element binding sites were identified. We used a radiation hybrid panel and fluorescence in situ hybridization to map the PART-1 gene to chromosome 5q12, a region that has been suggested to harbor a prostate tumor suppressor gene. These results identify a new gene involved in the androgen receptor-regulated gene network of the human prostate that may play a role in the etiology of prostate carcinogenesis.

Amino Acid Sequence↗
PubMed2000

Characterization, chromosomal localization, and the complete 30-kb DNA sequence of the human Jagged2 (JAG2) gene.

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.

Base Sequence↗
PubMed2000

Coding neuroradiology reports for the Northern Manhattan Stroke Study: a comparison of natural language processing and manual review.

Automated systems using natural language processing may greatly speed chart review tasks for clinical research, but their accuracy in this setting is unknown. The objective of this study was to compare the accuracy of automated and manual coding in the data acquisition tasks of an ongoing clinical research study, the Northern Manhattan Stroke Study(NOMASS). We identified 471 neuroradiology reports of brain images used in the NOMASS study. Using both automated and manual coding, we completed a standardized NOMASS imaging form with the information contained in these reports. We then generated ROC curves for both manual and automated coding by comparing our results to the original NOMASS data, where study in investigators directly coded their interpretations of brain images. The areas under the ROC curves for both manual and automated coding were the main outcome measure. The overall predictive value of the automated system (ROC area 0.85, 95% CI 0.84-0.87) was not statistically different from the predictive value of the manual coding (ROC area 0.87, 95% CI 0.83-0.91). Measured in terms of accuracy, the automated system performed slightly worse than manual coding. The overall accuracy of the automated system was 84% (CI 83-85%). The overall accuracy of manual coding was 86% (CI 84-88%). The difference in accuracy between the two methods was small but statistically significant (P = 0.026). Errors in manual coding appeared to be due to differences between neurologists' and nueroradiologists' interpretation, different use of detailed anatomic terms, and lack of clinical information. Automated systems can use natural language processing to rapidly perform complex data acquisition tasks. Although there is a small decrease in the accuracy of the data as compared to traditional methods, automated systems may greatly expand the power of chart review in clinical research design and implementation.

Brain↗
PubMed2000

Prevention of cerebrospinal fluid rhinorrhea in neurotologic surgery.

OBJECTIVE: To determine the efficacy and safety of quick-setting hydroxyapatite cement in eliminating cerebrospinal fluid (CSF) rhinorrhea following neurotologic surgery. STUDY DESIGN: A prospective study of 40 consecutive patients undergoing neurotologic surgery in whom the dura was opened. SETTING: All patients were treated as hospital inpatients at a tertiary referral center. PATIENTS: 25 men and 15 women between the ages of 20 and 72 years (mean age 51 years) underwent neurotologic surgery at the parent institution. INTERVENTION: Various neurotologic procedures were performed for the resection of 25 acoustic tumors, 5 meningiomas, 3 glomus tumors, 2 vestibular nerve sections, 2 chordomas, 1 epidermoid tumor, and 1 meningoencephelocele, and for 2 patients referred to our institution with known CSF leaks following acoustic tumor surgery. A new form of quick-setting hydroxyapatite cement, which that hardens within 3 to 5 minutes was used to seal the air cell tracts of the temporal bone in all cases. MAIN OUTCOME MEASURE: The presence of CSF rhinorrhea postoperatively. RESULTS: CSF rhinorrhea occurred in 2 patients following acoustic tumor surgery, the first through an occult air cell tract at the margin of the drilled internal auditory canal, and the second via an oval window fistula 1 month after a translabyrinthine approach. CONCLUSIONS: This form of hydroxyapatite cement appears safe, reliable, effective, and economical for the prevention of CSF rhinorrhea following neurotologic surgery. CSF rhinorrhea cannot be eliminated unless our ability to identify all potential air cell tract communications improves.

Adult↗
PubMed2000

A knowledge model for analysis and simulation of regulatory networks.

MOTIVATION: In order to aid in hypothesis-driven experimental gene discovery, we are designing a computer application for the automatic retrieval of signal transduction data from electronic versions of scientific publications using natural language processing (NLP) techniques, as well as for visualizing and editing representations of regulatory systems. These systems describe both signal transduction and biochemical pathways within complex multicellular organisms, yeast, and bacteria. This computer application in turn requires the development of a domain-specific ontology, or knowledge model. RESULTS: We introduce an ontological model for the representation of biological knowledge related to regulatory networks in vertebrates. We outline a taxonomy of the concepts, define their 'whole-to-part' relationships, describe the properties of major concepts, and outline a set of the most important axioms. The ontology is partially realized in a computer system designed to aid researchers in biology and medicine in visualizing and editing a representation of a signal transduction system.

Animals↗
PubMed2000

Characterization of nonfunctional V1R-like pheromone receptor sequences in human.

The vomeronasal organ (VNO) or Jacobson's organ is responsible in terrestrial vertebrates for the sensory perception of pheromones, chemicals that elicit stereotyped behaviors among individuals of the same species. Pheromone-induced behaviors and a functional VNO have been described in a number of mammals, but the existence of this sensory system in human is still debated. Recently, two nonhomologous gene families, V1R and V2R, encoding pheromone receptors have been identified in rat. These receptors belong to the seven-transmembrane domain G-protein-coupled receptor superfamily. We sought to characterize V1R-like genes in the human genome. We have identified seven different human sequences by PCR and library screening with rodent sequences. These human sequences exhibit characteristic features of V1R receptors and show 52%-59% of amino acid sequence identity with the rat sequences. Using PCR on a monochromosomal somatic cell hybrid panel and/or FISH, we demonstrate that these V1R-like sequences are distributed on chromosomes 7, 16, 20, 13, 14, 15, 21, and 22 and possibly on additional chromosomes. One sequence hybridizes to pericentromeric locations on all the acrocentric chromosomes (13, 14, 15, 21, and 22). All of the seven V1R-like sequences analyzed show interrupted reading frames, indicating that they represent nonfunctional pseudogenes. The preponderence of pseudogenes among human V1R sequences and the striking anatomical differences between rodent and human VNO raise the possibility that humans may have lost the V1R/VNO-mediated sensory functions of rodents.

Amino Acid Sequence↗
PubMed2000

Infection control outside the hospital: developing a continuum of care.

Pressures to limit or eliminate more expensive inpatient care have led t he way to rapidly expanded use of ambulatory care are extended care services. A consensus panel of infection control specialists have devised new recommendations on what can be addressed when infections occur outside the hospital.

Ambulatory Care↗
PubMed2000

Limited parsing of notational text visit notes: ad-hoc vs. NLP approaches.

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.

Glaucoma↗
PubMed2000

A broad-coverage natural language processing system.

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.

Decision Making, Computer-Assisted↗
PubMed2000

A method for vocabulary development and visualization based on medical language processing and XML.

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.

Humans↗
PubMed1999

Requirements for infrastructure and essential activities of infection control and epidemiology in out-of-hospital settings: a Consensus Panel report.

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.

Allied Health Personnel↗
PubMed1999

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.

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.

Aftercare↗
PubMed1999

Natural language processing and its future in medicine.

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.

Forecasting↗
PubMed1999

Representing genomic knowledge in the UMLS semantic network.

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.

Genome, Human↗
PubMed1999

Automating a severity score guideline for community-acquired pneumonia employing medical language processing of discharge summaries.

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.

Community-Acquired Infections↗
PubMed1999

What do ER physicians really want? A method for elucidating ER information needs.

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).

Emergency Medicine↗