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Biomedical subjects

S H Brown

Publications and source records attributed to S H Brown.

At least 19 recordsLinked to original sources
PubMed2003

Integrating pharmacokinetics knowledge into a drug ontology: as an extension to support pharmacogenomics.

The newly developed U.S. Common Medication Information Infrastructure was used as a basis to capture and formally express the properties of drugs relevant to research and the clinical application of pharmacogenomics. Two associated taxonomies within the model, Mechanism of Action and Physiologic Effect, were enriched to accommodate pharmacogenomic use-cases; the 4,000 active ingredients in the VA NDF-RT drug file were related to the enhanced taxonomies. Pharmacokinetics were independently modeled for pharmacogenomics and tested against thirty-one high-profile drugs to demonstrate our approach.

Databases as Topic↗
PubMed2001

A novel carbohydrate:acceptor oxidoreductase from Microdochium nivale.

A Microdochium nivale carbohydrate:acceptor oxidoreductase was purified, cloned, heterologously expressed, and characterized. The gene encoding the protein showed one intron, and the ORF showed a sequence with low homology (< or = 25% identity or 65% similarity) to other known flavin-containing carbohydrate oxidases. The maturation of the protein required the cleavage of a tetrameric propeptide in addition to an 18 amino-acid signal peptide. The enzyme was found to have a relative molecular mass of 55 000 Da, an isoelectric point of 9, and one FAD per protein. It could oxidize mono-, oligo-, or polymeric saccharides, and transfer their electrons to O2 or other acceptors. When D-glucose served as electron-donating substrate, an activity of 2 s(-1) was observed at pH 5.5 and 23 degrees C. Among various oligosaccharides, the enzyme preferred tetrameric dextrins, indicating a favorable interaction of four linked glucose units with the substrate pocket. The unique structure and ability of oxidizing oligo/polymeric saccharides suggest a promising prospect of this enzyme for various industrial/medicinal applications.

Alcohol Oxidoreductases↗
PubMed2001

Development of a homogeneous MAP kinase reporter gene screen for the identification of agonists and antagonists at the CXCR1 chemokine receptor.

Agonist activity at G protein-coupled receptors (GPCRs) that regulate heterotrimeric G proteins of the Galpha(i/o) or Galpha(q) families has been shown to result in activation of the mitogen-activated protein (MAP) kinase cascade. To facilitate compound screening for these classes of GPCR, we have developed a reporter gene that detects the activation of the ternary complex transcription factor Sap1a following MAP kinase activation. In contrast to other reporter gene assays for Galpha(i/o)-coupled GPCRs, the MAP kinase reporter generates an increase in signal in the presence of agonist. The reporter gene has been transfected into Chinese hamster ovary cells to generate a "host" reporter gene-containing cell line. The Galpha(i)-coupled human CXCR1 chemokine receptor was subsequently transfected into this cell line in order to develop a 384-well format screen for both agonists and antagonists of this receptor. Agonists activated the reporter gene with the expected rank order of potency and with similar concentration dependence as seen with the regulation of other signal transduction cascades in mammalian cells: interleukin-8 (IL-8) (pEC(50) = 7.0 +/- 0.1) > GCP-2 (pEC(50) = 6.3 +/- 0.1) > NAP-2 (pEC(50) < 6). CXCR1-mediated activation of MAP kinase was inhibited by pertussis toxin and the MEK inhibitor PD98059, demonstrating that receptor activation of MAP kinase is due to pertussis toxin-sensitive Galpha(i/o)-family G proteins to cause the activation of MEK kinase. Using the 384-well format, assay performance was unaffected by solvent concentrations of 0.5% ethanol, 0.15% glycerol, or 1% DMSO. Signal crosstalk between adjacent wells was less than 1%. The assay exhibited a Z factor of 0.53 and a coefficient of variation of response to repeated application of IL-8 (100 nM) of 15.9%.

Animals↗
PubMed2001

Guideline for health informatics: controlled health vocabularies--vocabulary structure and high-level indicators.

Developers and purchasers of controlled health terminologies require valid mechanisms for comparing terminological systems. By Controlled Health Vocabularies we refer to terminologies and terminological systems designed to represent clinical data at a granularity consistent with the practice of today's healthcare delivery. Comprehensive criterion for the evaluation of such systems are lacking and the known criteria are inconsistently applied. Although there are many papers, which describe specific desirable features of a controlled health vocabulary, to date there is not a consistent guide for evaluators of terminologies to reference, which will help them compare implementations of terminological systems on an equal footing 1,2 This guideline serves to fill the gap between academic enumeration of desirable terminological characteristics and the practical implementation or rigorous evaluations which will yield comparable data regarding the quality of one or more controlled health vocabularies.

Medical Informatics↗
PubMed2001

Usability evaluation of the progress note construction set.

OVERVIEW: The Veterans Administration (VA) Computerized Patient Record System (CPRS) is a nationally deployed software product that integrates provider order entry, progress notes, vitals, consults, discharge summaries, problem lists, medications, labs, radiology, transcribed documents, study reports, and clinical reminders. Users rapidly adopted the graphical user interface for data retrieval, but demanded options to typing for data entry. We programmed "point and click" forms that integrate with CPRS individually, but were soon overwhelmed by requests. Subsequently, we developed the Progress Note Construction Set (PNCS); a tool suite that permits subject matter experts without programming skills to create reusable "point and click" forms. In this study, we evaluate the usability of these user-constructed forms. METHODS: An untrained, non-VA subject matter expert used the PNCS to create a graphical form for "skin tear" documentation. Ten VA nurses used the skin tear form to document findings for 7 standardized clinical scenarios. Following each scenario the subjects answered usability questions about the form. RESULTS: The subject matter expert created the skin tear form in 78 minutes. Users found the form to facilitate their data entry (p 0.0265), and to be at least as fast (p 0.0029) and as easy to use as expected (p 0.0166). Average note entry time was 3.4 minutes. CONCLUSION: The PNCS allowed a non-programmer to quickly create a usable, CPRS-integrated point and click form. Users found the subject matter expert s form fast and easy to use. The tool suite is a more scaleable form creation method because capacity is no longer limited by programmer availability.

Medical Records Systems, Computerized↗
PubMed2001

A randomized controlled trial of the accuracy of clinical record retrieval using SNOMED-RT as compared with ICD9-CM.

BACKGROUND: Concept-based Indexing is purported to provide more granular data representation for clinical records.1,2 This implies that a detailed clinical terminology should be able to provide improved access to clinical records. To date there is no data to show that a clinical reference terminology is superior to a precoordinated terminology in its ability to provide access to the clinical record. Today, ICD9-CM is the most commonly used method of retrieving clinical records. OBJECTIVE: In this study, we compare the sensitivity, specificity, positive likelihood ratio, positive predictive value and accuracy of SNOMED-RT vs. ICD9-CM in retrieving ten diagnoses from a random sample of 2,022 episodes of care. METHOD: We randomly selected 1,014 episodes of care from the inpatient setting and 1,008 episodes of care from the outpatient setting. Each record had associated with it, the free text final diagnoses from the Master Sheet Index at the Mayo Clinic and the ICD9-CM codes used to bill for the encounters within the episode of care. The free text diagnoses were coded by two expert indexers (disagreements were addressed by a Staff Clinician) as to whether queries regarding one of 5 common or 5 uncommon diagnoses should return this encounter. The free text entries were automatically coded using the Mayo Vocabulary Processor. Each of the ten diagnoses was exploded in both SNOMED-RT and ICD9-CM and using these entry points, a retrieval set was generated from the underlying corpus of records. Each retrieval set was compared with the Gold Standard created by the expert indexers. RESULTS: SNOMED-RT produced significantly greater specificity in its retrieval sets (99.8% vs. 98.3%, p<0.001 McNemar Test). The positive likelihood ratios were significantly better for SNOMED-RT retrieval sets (264.9 vs. 33.8, p<0.001 McNemar Test). The positive predictive value of a SNOMED-RT retrieval was also significantly better than ICD9-CM (92.9% vs. 62.4%, p<0.001 McNemar Test). The accuracy defined as 1 (the total error rate (FP+FN) / Total # episodes queried (20,220)) was significantly greater for SNOMED-RT (98.2% vs. 96.8%, p=0.002 McNemar Test). Interestingly, the sensitivity of the SNOMED-RT generated retrieval set was not significantly different from ICD9-CM, but there was a trend toward significance (60.4% vs. 57.6%, p=0.067 McNemar Test). However, if we examine only the outpatient practice SNOMED-RT produced a more sensitive retrieval set than ICD9-CM (54.8% vs. 46.4%, p=0.002 McNemar Test). CONCLUSIONS: Our data clearly shows that information regarding both common and rare disorders is more accurately identified with automated SNOMED-RT indexing using the Mayo Vocabulary Processor than it is with traditional hand picked constellations of codes using ICD9-CM. SNOMED-RT provided more sensitive retrievals of outpatient episodes of care than ICD9-CM.

Decision Support Systems, Management↗
PubMed2000

Using DNA-tagged mutagenesis to improve heterologous protein production in Aspergillus oryzae.

Using DNA-tagged mutagenesis to improve heterologous protein production in Aspergillus oryzae. Fungal Genetics and Biology 29, 28-37. Restriction enzyme-mediated integration (REMI) has been employed as a mutagen to generate two insertion libraries in an Aspergillus oryzae strain expressing a Thermomyces lanuginosus lipase. The REMI libraries were created using linearized plasmid containing the A. oryzae pyrG and either BamHI or EcoRI enzyme. The libraries were screened for lipase production, and mutants with increased production were isolated. The genomic DNA flanking the integration event was cloned from one of the mutants with increased lipase titers (DEBY10.3). Nucleotide sequence of the flanking DNA revealed similarity to the Aspergillus nidulans palB gene. Disruption of the palB gene in a strain producing lipase resulted in increased lipase expression. Additionally, complementation of the palB phenotype of DEBY10.3 led to a decrease in lipase production. These lines of evidence demonstrate that the increase in lipase yield in DEBY10.3 is linked to the palB phenotype generated by the integration of the pyrG gene into the palB gene. The results also demonstrated that tagged mutagenesis with REMI can be used to identify genes that influence expression of heterologous proteins.

Aspergillus oryzae↗
PubMed2000

Motor control testing of upper limb function after botulinum toxin injection: a case study.

OBJECTIVE: To evaluate changes in upper extremity function in a hemiparetic patient after treatment with botulinum toxin (BTX) using motor-control testing (MCT) techniques. DESIGN: Interventional with longitudinal study, open label. SETTING: A children's hospital and a motor-control laboratory at a major academic center. PARTICIPANTS: A 16-year-old male with right hemiparetic cerebral palsy and a healthy 12-year-old control subject. INTERVENTIONS: BTX injections to the elbow and wrist flexors. MAIN OUTCOME MEASURES: MCT was used to examine 4 upper extremity movements: forward reach, bilateral rhythmic movements (both muscle homologous and direction homologous), isometric pinch, and hand tapping. The patient was tested before treatment and at 2, 4, 6, 12, 18, and 24 weeks after treatment. In addition, range of motion (ROM), the Ashworth scale of spasticity, Functional Independence Measure, and the mobility and activities of daily living (ADL) sections of the Pediatric Evaluation of the Disability Inventory were performed. RESULTS: Forward reach demonstrated little change initially despite patient reports of "feeling looser." Improvement was noted after 18 weeks, but returned to baseline level at 24 weeks. Bilateral rhythmic movements also showed slight improvement at 18 weeks. Pinch force increased significantly after 2 weeks, but declined again at 6 weeks. Improvements occurred in ROM and the Ashworth rating of spasticity, but were not temporally associated with each other or with MCT results. Functional assessment data did not change during the study period. CONCLUSIONS: Improvements in more complex motor tasks were noted after significant delay from the time of treatment, while simpler tasks demonstrated a more rapid improvement, followed by a rapid return to baseline levels. This case suggests that MCT techniques can provide quantitative and qualitative data, which can add new information about upper extremity motor disability and the outcome of treatment.

Adolescent↗
PubMed1999

Empirical derivation of an electronic clinically useful problem statement system.

Problem lists are tools to improve patient management. In the medical record, they connect diagnoses to therapy, prognosis, and psychosocial issues. Computer-based problem lists enhance paper-based approaches by enabling cost-containment and quality assurance applications, but they require clinically expressive controlled vocabularies. Because existing controlled vocabularies do not represent problem statements at a clinically useful level, we derived a new canonical problem statement vocabulary through semi-automated analysis and distillation of provider-entered problem lists collected over 6 years from 74,696 patients. We combined automated and manual methods to condense 891,770 problem statements entered by 1961 care providers at Grady Memorial Hospital in Atlanta, Georgia, to 15,534 Canonical Clinical Problem Statement System (CCPSS) terms. The nature and frequency of problem statements were characterized, interrelations among them were enumerated, and a database capturing the epidemiology of problems was created. The authors identified 23,503 problem relations (co-occurrences, sign-symptom complexes, and differential diagnoses) and 22,690 modifier words that further categorized "canonical" problems. To assess completeness, CCPSS content was compared with that of the 1997 Unified Medical Language System Metathesaurus (containing terms from 44 clinical vocabularies). Unified Medical Language System terms expressed 25% of individual CCPSS terms exactly (71% of problems by frequency), 27% partially, and 48% poorly or not at all. Clinicians judged that CCPSS terms completely captured their clinical intent for 84% of 686 randomly selected free-text problem statements. The CCPSS represents clinical concepts at a level exceeding that of previous approaches. A similar national approach could create a standardized, useful, shared resource for clinical practice.

Humans↗
PubMed1999

Targeted mutations in a Trametes villosa laccase. Axial perturbations of the T1 copper.

Trametes villosa laccase was mutated on a tetrapeptide segment near the type 1 site. The mutations F463M and F463L were at the position corresponding to the type 1 copper axial methionine (M517) ligand in Zucchini ascorbate oxidase. The mutations E460S and A461E were near the T1 copper site. The mutated Trametes laccases were expressed in an Aspergillus oryzae host and characterized. The E460S mutation failed to produce a transformant with meaningful expression. The F463L and A461E mutations did not significantly alter the molecular and enzymological properties of the laccase. In contrast, the F463M mutation resulted in a type 1 copper site with an EPR signal intermediate between that of the wild type laccase and plastocyanin, an altered UV-visible spectrum, and a decreased redox potential (by 0.1 V). In oxidizing phenolic substrate, the mutation led to a more basic optimal pH as well as an increase in kcat and Km. These effects are attributed to a significant perturbation of the T1 copper center caused by the coordination of the axial methionine (M463) ligand.

Base Sequence↗
PubMed1999

Molecular characterization of laccase genes from the basidiomycete Coprinus cinereus and heterologous expression of the laccase lcc1.

A laccase from Coprinus cinereus is active at alkaline pH, an essential property for some potential applications. We cloned and sequenced three laccase genes (lcc1, lcc2, and lcc3) from the ink cap basidiomycete C. cinereus. The lcc1 gene contained 7 introns, while both lcc2 and lcc3 contained 13 introns. The predicted mature proteins (Lcc1 to Lcc3) are 58 to 80% identical at the amino acid level. The predicted Lcc1 contains a 23-amino-acid C-terminal extension rich in arginine and lysine, suggesting that C-terminal processing may occur during its biosynthesis. We expressed the Lcc1 protein in Aspergillus oryzae and purified it. The Lcc1 protein as expressed in A. oryzae has an apparent molecular mass of 66 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and absorption maxima at 278 and 614 nm. Based on the N-terminal protein sequence of the laccase, a 4-residue propeptide was processed during the maturation of the enzyme. The dioxygen specificity of the laccase showed an apparent K(m) of 21 +/- 2 microM and a catalytic constant of 200 +/- 10 min(-1) for O(2) with 2, 2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) as the reducing substrate at pH 5.5. Lcc1 from A. oryzae may be useful in industrial applications. This is the first report of a basidiomycete laccase whose biosynthesis involves both N-terminal and C-terminal processing.

Amino Acid Sequence↗
PubMed1999

No free lunch: institutional preparations for computer-based patient records.

The Veterans Administration (VA) is aggressively pursuing computer-based medical records by deploying the Computerized Patient Record System (CPRS) across its 150 medical centers and 400 outpatient clinics. CPRS's client-server, patient-centered approach to clinical computing is a departure from VA's traditional terminal-compatible, department-centered approach. Although the CPRS software is freely distributed, institutional readiness for computer-based patient records has proven expensive. Preparations include organizational changes, human resource development, hardware deployment, physical plant upgrades, and software testing. This paper details CPRS preparations and their costs at one VA Medical Center. Lessons learned during the process are summarized.

Computer Systems↗
PubMed1998

Site-directed mutations in fungal laccase: effect on redox potential, activity and pH profile.

A Myceliophthora thermophila laccase and a Rhizoctonia solani laccase were mutated on a pentapeptide segment believed to be near the type-1 Cu site. The mutation L513F in Myceliophthora laccase and the mutation L470F in Rhizoctonia laccase took place at a position corresponding to the type-1 Cu axial methionine (M517) ligand in Zucchini ascorbate oxidase. The triple mutations V509L,S510E,G511A in Myceliophthora laccase and L466V,E467S,A468G in Rhizoctonia laccase involved a sequence segment whose homologue in ascorbate oxidase is flanked by the M517 and a type-1 Cu-ligating histidine (H512). The single mutation did not yield significant changes in the enzymic properties (including any significant increase in the redox potential of the type-1 Cu). In contrast, the triple mutation resulted in several significant changes. In comparison with the wild type, the Rhizoctonia and Myceliophthora laccase triple mutants had a phenol-oxidase activity whose pH optimum shifted 1 unit lower and higher, respectively. Although the redox potentials were not significantly altered, the Km, kcat and fluoride inhibition of the laccases were greatly changed by the mutations. The observed effects are interpreted as possible mutation-induced structural perturbations on the molecular recognition between the reducing substrate and laccase and on the electron transfer from the substrate to the type-1 Cu centre.

Amino Acid Sequence↗
PubMed1998

Crystal structure of the type-2 Cu depleted laccase from Coprinus cinereus at 2.2 A resolution.

Laccase catalyses the oxidation of a variety of organic substrates coupled to the reduction of oxygen to water. It is widely believed to be the simplest representative of the ubiquitous blue multi-copper oxidase family. Laccase is implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism in fungi and plants. The structure of laccase from the fungus Coprinus cinereus has been determined by X-ray crystallography at a resolution of 2.2 A. Laccase is a monomer composed of three cupredoxin-like beta-sandwich domains, similar to that found in ascorbate oxidase. In contrast to ascorbate oxidase, however, the mononuclear type-1 Cu site lacks the axial methionine ligand and so exhibits trigonal planar coordination, consistent with its elevated redox potential. Crucially, the structure is trapped in a Cu depleted form in which the putative type-2 Cu atom is completely absent, but in which the remaining type-1 and type-3 Cu sites display full occupancy. Type-2 Cu depletion has unexpected consequences for the coordination of the remaining type-3 Cu atoms.

Amino Acid Sequence↗
PubMed1997

Crystallization and preliminary X-ray analysis of the laccase from Coprinus cinereus.

The laccase from the fungus Coprinus cinereus has been prepared and crystallized in a form suitable for X-ray diffraction analysis. Small plate-like crystals of an enzymatically deglycosylated form of the enzyme have been grown by the hanging-drop method using polyethylene glycol as precipitant. These crystals diffract to at least 2.2 A. They belong to the space group P2(1)2(1)2(1) with cell dimensions a = 45.4, b = 85.7, c = 143.1 A with a single molecule of laccase in the asymmetric unit.

Journal Article↗
PubMed1997

Quantification of upper extremity function using kinematic analysis.

OBJECTIVE: To illustrate the applicability of motor control analytical techniques to the assessment of upper limb dysfunction in children with ataxia. DESIGN: Descriptive case series. SETTING: The study sample was selected from an outpatient pediatric rehabilitation clinic and testing was performed in a research laboratory. PARTICIPANTS: Four children with upper limb ataxia and seven healthy children were examined. All subjects were recruited on a volunteer basis. Criteria for inclusion (ataxic group) included: (1) age 6 to 15 yrs; (2) ambulatory with assistive devices. MAIN OUTCOME MEASURES: Quantitative measures of elbow kinematics (movement speed and duration) and spatio-temporal "portraits" of elbow movement during unilateral and bilateral forward reaching movements. RESULTS: Movements made by ataxic subjects were characterized by lower peak velocities, prolonged durations, and increased variability compared with normal subjects. In the one subject with unilateral ataxia, interlimb coordination was severely disrupted during the performance of coupled, bilateral arm movements. In addition to changes in specific kinematic values (eg, peak velocity), phase plane and angle-angle displacement curves revealed marked spatio-temporal variability throughout the movement, the magnitude of which was correlated with severity of ataxia. CONCLUSION: The application of the quantitative motor control methods described in this report can provide rehabilitation specialists with a simple yet sensitive means to evaluate treatment and progression of a wide variety of motor disorder conditions. These techniques are particularly well suited to pediatric populations as young as 6 years.

Adolescent↗
PubMed1997

Characterization of the gene encoding an extracellular laccase of Myceliophthora thermophila and analysis of the recombinant enzyme expressed in Aspergillus oryzae.

A genomic DNA segment encoding an extracellular laccase was isolated from the thermophilic fungus Myceliophthora thermophila, and the nucleotide sequence of this gene was determined. The deduced amino acid sequence of M. thermophila laccase (MtL) shows homology to laccases from diverse fungal genera. A vector containing the M. thermophila laccase coding region, under transcriptional control of an Aspergillus oryzae alpha-amylase gene promoter and terminator, was constructed for heterologous expression in A. oryzae. The recombinant laccase expressed in A. oryzae was purified to electrophoretic homogeneity by anion-exchange chromatography. Amino-terminal sequence data suggests that MtL is synthesized as a preproenzyme. The molecular mass was estimated to be approximately 100 to 140 kDa by gel filtration on Sephacryl S-300 and to be 85 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Carbohydrate analysis revealed that MtL contains 40 to 60% glycosylation. The laccase shows an absorbance spectrum that is typical of blue copper oxidases, with maxima at 276 and 589 nm, and contains 3.9 copper atoms per subunit. With syringaldazine as a substrate, MtL has optimal activity at pH 6.5 and retains nearly 100% of its activity when incubated at 60 degrees C for 20 min. This is the first report of the cloning and heterologous expression of a thermostable laccase.

Aspergillus oryzae↗