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Biomedical subjects

Thomas J Lee

Publications and source records attributed to Thomas J Lee.

15 recordsLinked to original sources
PubMed2006

BioWarehouse: a bioinformatics database warehouse toolkit.

BACKGROUND: This article addresses the problem of interoperation of heterogeneous bioinformatics databases. RESULTS: We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. CONCLUSION: BioWarehouse embodies significant progress on the database integration problem for bioinformatics.

Computational Biology↗
PubMed2006

Mortality rates in conflict zones in Karen, Karenni, and Mon states in eastern Burma.

OBJECTIVES: To estimate mortality rates for populations living in civil war zones in Karen, Karenni, and Mon states of eastern Burma. METHODS: Indigenous mobile health workers providing care in conflict zones in Karen, Karenni, and Mon areas of eastern Burma conducted cluster sample surveys interviewing heads of households during 3-month time periods in 2002 and 2003 to collect demographic and mortality data. RESULTS: In 2002 health workers completed 1290 household surveys comprising 7496 individuals. In 2003, 1609 households with 9083 members were surveyed. Estimates of vital statistics were as follows: infant mortality rate: 135 (95% CI: 96-181) and 122 (95% CI: 70-175) per 1000 live births; under-five mortality rate: 291 (95% CI: 238-348) and 276 (95% CI: 190-361) per 1000 live births; crude mortality rate: 25 (95% CI: 21-29) and 21 (95% CI: 15-27) per 1000 persons per year. CONCLUSIONS: Populations living in conflict zones in eastern Burma experience high mortality rates. The use of indigenous mobile health workers provides one means of measuring health status among populations that would normally be inaccessible due to ongoing conflict.

Adolescent↗
PubMed2005

Endoluminal therapy for gastroesophageal reflux disease: is the evidence for efficacy any stronger?

Gastroesophageal reflux disease is a common disorder often requiring chronic treatment. Joining the conventional options of antisecretory medications and fundoplication, endoluminal therapies have emerged in recent years. These techniques have entered US and European markets, claiming effectiveness comparable with antireflux surgery. Nevertheless, a paucity of data is available to support that efficacy, even as more devices are coming onto the market. This review examines published reports of endoluminal reflux therapies from January 2004 to January 2005. After another year, there are still no compelling data supporting the efficacy of any of the available endoluminal treatments.

Esophagoscopy↗
PubMed2005

Pathophysiology of gastroesophageal reflux disease.

From a pathophysiologic viewpoint, GERD results from the excessive reflux of gastric contents into the distal esophagus. Under normal conditions, this is prevented as a function of the antireflux barrier at the EGJ, the integrity of which is dependent on the delicate interplay of a host of anatomic and physiologic factors, including the integrity of the LES, TLESR, and anatomic degradation of the EGJ inclusive of but not limited to hiatus hernia. Considerable investigative focus is aimed at describing the subtle aberrations of the EGJ that may contribute to the root causes of GERD. The net result is an increased number of reflux events, an increasing diversity of potential mechanisms of reflux, and a diminished ability of the stomach to selectively vent gas, as opposed to gas and gastric juice, during TLESR. Once reflux occurs, the duration of resultant esophageal acid exposure is determined by the effectiveness of esophageal acid clearance, the dominant determinants of which are peristalsis, salivation, and, again, the anatomic integrity of the EGJ. Approximately half of patients who have GERD have abnormal acid clearance and the major contributor to this is hiatus hernia. Abnormalities of acid clearance probably are the major determining factor influencing which patients who have GERD are most prone to developing esophagitis as opposed to symptomatic GERD. In summary, GERD is a multifactorial process involving physiologic and anatomic abnormalities. These abnormalities exhibit a complicated interplay that degrades the ability of the EGJ to contain gastric juice within the stomach and to clear the esophagus of gastric juice effectively once reflux has occurred.

Disease Progression↗
PubMed2005

Comparison of the Bravo wireless and Digitrapper catheter-based pH monitoring systems for measuring esophageal acid exposure.

INTRODUCTION: We compared esophageal acid exposure data obtained during simultaneous esophageal pH studies using the Bravo wireless and the Slimline catheter-Mark III Digitrapper pH systems. METHODS: Twenty-five asymptomatic subjects underwent endoscopy with endoclip placement at the squamocolumnar junction (SCJ) and manometry to localize the lower esophageal sphincter (LES). A Bravo capsule was placed 6 cm above the SCJ and a Slimline catheter 5 cm above the LES. Relative positions were checked fluoroscopically. Synchronized pH data were compared by manual extraction into Excel spreadsheets. An in vivo pH reference was established with swallows of orange juice (pH 3.88). RESULTS: Median acid exposure time was greater with the Slimline compared to the Bravo system (Slimline, 3.4%; Bravo, 1.76%, p < 0.05) but electrode positions were similar. The dominant source of discrepancy between systems was an offset in recorded pH values around pH 4 as evidenced by the recorded values of the swallowed orange juice. Bench-top testing suggested that this offset was mainly attributable to the software designed to compensate for the difference in electrode recording characteristics between room and body temperature. After adjusting the pH data sets to accurately reflect actual orange juice pH, acid exposure between systems was similar (Slimline, 0.90%; Bravo, 1.15%). CONCLUSION: The Slimline system on average over-recorded esophageal acid exposure compared to the Bravo system largely because of a flawed software scheme for electrode thermal calibration. Accuracy of pH data sets from both systems can be improved by scrutiny for artifacts and use of an in vivo pH reference.

Acids↗
PubMed2005

Bravo capsule placement in the gastric cardia: a novel method for analysis of proximal stomach acid environment.

BACKGROUND: Intragastric pH monitoring is currently done using catheter-based pH systems. This study assessed the feasibility of proximal intragastric pH recording with the Bravo wireless pH monitoring system using novel methodology. METHODS: Nine asymptomatic volunteers and 9 symptomatic patients were studied. One pH capsule was positioned under direct endoscopic visualization so that the device straddled the squamocolumnar junction (SCJ) with the attachment well positioned on squamous mucosa and the pH electrode 1.5-2 cm distal to the SCJ. A second capsule was placed 6 cm proximal to the SCJ. The signal from each capsule was recorded by a separate receiver synchronized for time. RESULTS: Successful placement and interpretable recording for >42 h from both pH capsules was achieved in 16 (88%) of 18 subjects. Data capture were 98.3% in the cardia and 97.7% in the esophagus. Two failures occurred due to premature capsule detachment (one esophageal and one gastric). The acid environment in the cardia was similar in asymptomatic controls and symptomatic patients and exhibited less meal-related buffering than is typical of more distal intragastric recordings. In addition, nadir gastric cardia pH was almost always less than nadir esophageal pH during reflux events. CONCLUSIONS: Twenty-four hour gastric cardia pH monitoring is feasible with the Bravo system and can be added to esophageal pH monitoring to assess concomitant cardia acidity. Instantaneous cardia pH defines the potential nadir esophageal pH during reflux events.

Cardia↗
PubMed2004

Esophagogastric junction morphology predicts susceptibility to exercise-induced reflux.

BACKGROUND AND AIM: Although strenuous exercise has been reported to increase gastroesophageal reflux, there are few data exploring the mechanism behind this relationship. The aim of this study was to use vigorous exercise as a provocation for strain-induced reflux and examine the correlation between endoscopically assessed EGJ integrity and exercise-induced reflux. METHODS: Ten controls and 10 GERD patients were studied for a 2-day period using the wireless Bravo pH monitoring system. The subjects were randomly assigned to perform 60 min of exercise on day 1 or 2 consuming the same diet on both days. Exercise consisted of 30 min of running and 30 min of 5 resistance exercises. Subjects underwent endoscopy to grade the EGJ "flap valve" and manometry to measure basal LES pressure. RESULTS: Nineteen subjects completed the 2-day study with 100% data capture during exercise. Median acid exposure was increased more than threefold for both controls and GERD patients during exercise when compared to nonexercise periods. In addition, a strong correlation existed between EGJ grade and % time pH < 4 during exercise while there was not a significant correlation between LES pressure and EGJ grade. These findings were present even after exclusion of hiatus hernia patients (flap valve grade 4). CONCLUSIONS: Exercise caused a threefold increase in esophageal acid exposure in both controls and GERD patients. The degree of exercise-induced reflux is strongly correlated with EGJ morphology and this supports the hypothesis that anatomical integrity of the EGJ is of cardinal importance in preventing strain-induced reflux.

Adult↗
PubMed2003

Does telephone triage delay significant medical treatment?: Advice nurse service vs on-call pediatricians.

BACKGROUND: Advice nurse call centers are used to ensure access to medical advice, thereby potentially reducing the costs of health services. OBJECTIVE: To determine if medical advice from advice nurses and on-call physicians delays significant medical treatment in a general pediatrics population. DESIGN: Randomized controlled trial. SETTING: A university general pediatrics faculty practice. PARTICIPANTS: Parents or guardians calling for after-hours advice regarding their children.Intervention After-hours medical advice calls were randomized at the time of the call to an advice nurse or an on-call pediatrician. MAIN OUTCOME MEASURES: The proportion of callers who sought medical care not advised by the advice nurse or on-call pediatrician and the proportion who received unadvised significant care. RESULTS: There were 1182 advice calls: 566 in the pediatrician group and 616 in the advice nurse group. There were no significant differences in the types of telephone triage advice in the physician and advice nurse groups. There was no significant difference in the proportion of callers who sought unadvised care (108 [19.9%] in the physician group vs 110 [19.0%] in the advice nurse group) or in the proportion of callers who received unadvised significant care (23 [4.2%] in the physician group vs 25 [4.3%] in the advice nurse group). CONCLUSIONS: The proportions of callers who sought unadvised medical care and who received unadvised significant care were not significantly different in the advice nurse and pediatrician groups. This suggests that advice nurses do not delay significant medical treatment when compared with pediatricians.

Academic Medical Centers↗
PubMed2003

Medical management of Barrett's esophagus.

Barrett's metaplasia of some extent is found commonly in patients with GERD. Detection is possible only by endoscopy and biopsy of the columnar appearing mucosa; no symptoms or signs distinguish patients with Barrett's metaplasia from those without. The management goals in patients with Barrett's are to alleviate reflux symptoms and to control the risk of adenocarcinoma. Symptom control is achieved primarily with PPIs. Acid inhibition does not, however, cause regression of Barrett's metaplasia and has not been shown to reduce the risk of esophageal adenocarcinoma. The risk of adenocarcinoma is managed by surveillance with endoscopy and biopsy searching for dysplastic change. LGD merits more intense surveillance. The optimal management of HGD, however, remains controversial, as evidenced by the multitude of ablation therapies that have been introduced recently. These techniques will be discussed in depth in subsequent articles in this volume.

Adenocarcinoma↗
PubMed2003

Parental compliance with after hours telephone triage advice: nurse advice service versus on-call pediatricians.

To compare parental compliance with after-hours triage advice provided by telephone advice nurses and on-call pediatricians, a randomized controlled trial was undertaken at a university general pediatrics practice that enrolled parents or guardians calling for after-hours advice. Advice calls were randomized to a call center advice nurse or the on-call pediatrician. Parental compliance with the triage advice and agreement of the parental report of advice with the pediatrician/nurse report of advice given was evaluated. There were 566 participants in the pediatrician and 616 in the nurse group. Compliance with advice (pediatrician v. nurse) was not significantly different for emergent/urgent care (75.8% v. 72.6%) and self care (74.3% v. 77.2%) but was significantly higher in the pediatrician group for office care (51.5% v. 29.6%; 95% CI of difference, 8.9%-34.2%). Overall agreement between the caller reported and physician or nurse advice was 84.5% for emergent/ urgent, 42.7% for office care, and 93.7% for self-care.

After-Hours Care↗
PubMed2002

Emergency department triage of patients infected with HIV.

OBJECTIVE: The emergency department (ED) and HIV specialty clinics are primary sources of care for persons infected with HIV. HIV disease may be complicated by vague and complex symptomatology, and determining the degree of illness at triage is often difficult. The goals of this project were to characterize the ED presentation of HIV-related conditions, to develop a clinical decision rule to triage HIV-infected patients, and to validate the rule in clinical practice. METHODS: The study population consisted of ambulatory patients with self-reported HIV infection who presented for care to the ED of a 553-bed public hospital that serves a medically indigent, minority population. An Illness Severity Instrument was developed by an expert panel to serve as the criterion standard for defining medical urgency for HIV-infected patients presenting to the ED for care. Two phases of the study were conducted. Data from the first phase, a noninterventional cohort study, were used to develop a clinical decision rule for the ED triage of HIV-infected patients. The second phase was a prospective validation of the clinical decision rule. RESULTS: During phase I, data from 542 patient visits were collected. Data from 441 (81%) patient visits were used in a classification and regression tree (CART) analysis to produce a decision rule, the Clinical Triage Instrument. During phase II, the prospective validation of the Clinical Triage Instrument, 156 patient visits occurred. Of these, 88 (56%) patient visits were triaged using the Clinical Triage Instrument and could be scored using the Illness Severity Instrument. The Clinical Triage Instrument accurately triaged 45 [51%; 95% confidence interval (95% CI) = 40% to 62%] patient visits, undertriaged 11 (13%; 95% CI = 6% to 21%) patient visits, and overtriaged 32 (36%; 95% CI = 26% to 47%) patient visits. Sensitivities and specificities for determining emergent, urgent, and nonurgent medical conditions by the Clinical Triage Instrument were 56% (95% CI = 31% to 75%) and 84% (95% CI = 74% to 92%), 71% (95% CI = 55% to 84%) and 39% (95% CI = 25% to 55%), and 18% (95% CI = 6% to 37%) and 93% (95% CI = 84% to 98%), respectively. The positive and negative predictive values for determining an emergent medical condition using the Clinical Triage Instrument were 48% (95% CI = 26% to 70%) and 88% (95% CI = 78% to 95%), respectively. The positive and negative predictive values for determining a nonurgent medical condition using the Clinical Triage Instrument were 56% (95% CI = 21% to 86%) and 71% (95% CI = 60% to 81%), respectively. CONCLUSIONS: The Clinical Triage Instrument was not sufficiently accurate for clinical use. Until accurate and reliable triage methods are developed, all patients infected with HIV who present to the ED for care should receive timely evaluation and care.

Adult↗
PubMed2002

Caller satisfaction with after-hours telephone advice: nurse advice service versus on-call pediatricians.

OBJECTIVE: To compare caller satisfaction with after-hours medical advice provided by a for-profit nurse advice service with advice provided by on-call pediatricians. METHODS: The study setting was the general pediatrics faculty practice of an urban university medical center. Participants were parents or guardians of a population of approximately 6000 children calling for after-hours medical advice over a 10-month period from January 18 to November 20, 2000. After-hours medical advice calls were randomized to either a nurse advice service or the on-call pediatrician. Caller satisfaction and subsequent health care utilization were measured by a telephone survey of callers and review of all health care visits within 3 days of the initial telephone advice call. RESULTS: Five hundred sixty-six (48%) callers were enrolled in the on-call pediatrician group, and 616 (52%) were enrolled in the advice nurse group. Caller satisfaction was rated as very good or excellent significantly more often for the on-call pediatrician than for the nurse advice service as follows: telephone call overall (68.5% vs 55.0%; 95% confidence interval [CI] of difference: 8.0%-19.0%), thoroughness and competence of the person they spoke with (74.0% vs 59.1%; 95% CI of difference: 9.6%-20.2%), courtesy and friendliness of the person they spoke with (77.4% vs 73.9%; 95% CI of difference: -1.4%-8.4%), length of time spent waiting (70.8% vs 60.1%; 95% CI of difference: 5.4%-16.2%), time spent talking with the on-call pediatrician or advice nurse (68.2% vs 52.4%; 95% CI of difference: 10.2%-21.3%), and the medical advice given (68.6% vs 53.9%; 95% CI of difference: 9.2%-20.1%). Compliance with the advice given was significantly higher for office care in the on-call pediatrician group (51.5% vs 29.6%; 95% CI of difference: 8.9%-34.2%). Repeat calls for advice were significantly more frequent for the nurse advice service, both within 4 hours (13.0% vs 4.8%; 95% CI of difference: 5.0%-11.4%), and within 72 hours (23.4% vs 13.3%; 95% CI of difference: 5.8%-14.5%). CONCLUSION: Callers were less satisfied with medical advice provided by a nurse advice service compared with the traditional on-call pediatrician. The lower satisfaction was associated with somewhat poorer compliance with recommended triage dispositions and more frequent repeat calls for medical advice.

Child↗