Patient and Family Outcomes of Community Neurologist Palliative Education and Telehealth Support in Parkinson Disease

Importance

Parkinson disease and related disorders (PDRD) are the fastest growing neurodegenerative illness in terms of prevalence and mortality. As evidence builds to support palliative care (PC) for PDRD, studies are needed to guide implementation.

Objective

To determine whether PC training for neurologists and remote access to a PC team improves outcomes in patients with PDRD in community settings.

Design, Setting, and Participants

This pragmatic, stepped-wedge comparative effectiveness trial enrolled and observed participants from 19 community neurology practices supported by PC teams at 2 academic centers from March 8, 2017, to December 31, 2020. Participants were eligible if they had PDRD and moderate to high PC needs. A total of 612 persons with PDRD were referred; 253 were excluded. Patients were excluded if they had another diagnosis meriting PC, were receiving PC, or were unable or unwilling to follow study procedures. Patients received usual care or the intervention based on when their community neurologist was randomized to start the intervention. Data were analyzed from January 2021 to September 2023.

Intervention

The intervention included (1) PC education for community neurologists and (2) team-based PC support via telehealth.

Main Outcomes and Measures

The primary outcomes were differences at 6 months in patient quality of life (QOL; measured by the Quality of Life in Alzheimer Disease Scale [QOL-AD]) and caregiver burden (Zarit Burden Interview) between the intervention and usual care.

Results

A total of 359 patients with PDRD (233 men [64.9%]; mean [SD] age, 74.0 [8.8] years) and 300 caregivers were enrolled. At 6 months, compared with usual care, participants receiving the intervention had better QOL (QOL-AD score, 0.09 [95% CI, -0.63 to 0.82] vs -0.88 [95% CI, -1.62 to -0.13]; treatment effect estimate, 0.97; 95% CI, 0.07-1.86; P = .03). No significant difference was observed in caregiver burden (Zarit Burden Interview score, 1.19 [95% CI, 0.16 to 2.23] vs 0.55 [95%, -0.44 to 1.54]; treatment effect estimate, 0.64; 95% CI, -0.62 to 1.90; P = .32). Advance directive completion was higher under the intervention (19 of 38 [50%] vs 6 of 31 [19%] among those without directives at the beginning of the study; P = .008). There were no differences in other outcomes.

Conclusions and Relevance

PC education for community neurologists and provision of team-based PC via telehealth is feasible and may improve QOL and advance care planning. Overall treatment effects were small and suggest opportunities to improve both the intervention and implementation.

Trial Registration

ClinicalTrials.gov Identifier: NCT03076671.

Comparison of Integrated Outpatient Palliative Care With Standard Care in Patients With Parkinson Disease and Related Disorders: A Randomized Clinical Trial

Importance

Parkinson disease and related disorders (PDRD) have consequences for quality of life (QoL) and are the 14th leading cause of death in the United States. Despite growing interest in palliative care (PC) for persons with PDRD, few studies are available supporting its effectiveness.

Objective

To determine if outpatient PC is associated with improvements in patient-centered outcomes compared with standard care among patients with PDRD and their caregivers.

Design, Setting, and Participants

This randomized clinical trial enrolled participants at 3 academic tertiary care centers between November 1, 2015, and September 30, 2017, and followed them up for 1 year. A total of 584 persons with PDRD were referred to the study. Of those, 351 persons were excluded by phone and 23 were excluded during in-person screenings. Patients were eligible to participate if they had PDRD and moderate to high PC needs. Patients were excluded if they had urgent PC needs, another diagnosis meriting PC, were already receiving PC, or were unable or unwilling to follow the study protocol. Enrolled participants were assigned to receive standard care plus outpatient integrated PC or standard care alone. Data were analyzed between November 1, 2018, and December 9, 2019.

Interventions

Outpatient integrated PC administered by a neurologist, social worker, chaplain, and nurse using PC checklists, with guidance and selective involvement from a palliative medicine specialist. Standard care was provided by a neurologist and a primary care practitioner.

Main Outcomes and Measures

The primary outcomes were the differences in patient quality of life (QoL; measured by the Quality of Life in Alzheimer Disease scale) and caregiver burden (measured by the Zarit Burden Interview) between the PC intervention and standard care groups at 6 months.

Results

A total of 210 patients with PDRD (135 men [64.3%]; mean [SD] age, 70.1 [8.2] years) and 175 caregivers (128 women [73.1%]; mean [SD] age, 66.1 [11.1] years) were enrolled in the study; 193 participants (91.9%) were white and non-Hispanic. Compared with participants receiving standard care alone at 6 months, participants receiving the PC intervention had better QoL (mean [SD], 0.66 [5.5] improvement vs 0.84 [4.2] worsening; treatment effect estimate, 1.87; 95% CI, 0.47-3.27; P = .009). No significant difference was observed in caregiver burden (mean [SD], 2.3 [5.0] improvement vs 1.2 [5.6] improvement in the standard care group; treatment effect estimate, -1.62; 95% CI, -3.32 to 0.09; P = .06). Other significant differences favoring the PC intervention included nonmotor symptom burden, motor symptom severity, completion of advance directives, caregiver anxiety, and caregiver burden at 12 months. No outcomes favored standard care alone. Secondary analyses suggested that benefits were greater for persons with higher PC needs.

Conclusions and Relevance

Outpatient PC is associated with benefits among patients with PDRD compared with standard care alone. This study supports efforts to integrate PC into PDRD care. The lack of diversity and implementation of PC at experienced centers suggests a need for implementation research in other populations and care settings.

Trial Registration

ClinicalTrials.gov Identifier: NCT02533921.

Development of a battery of tests to measure attitudes and intended behaviours of dental students towards people with disability or those in marginalised groups

INTRODUCTION

Recommended curricula in Special Care Dentistry (SCD) outline learning objectives that include the domain of attitudes and behaviours, but these are notoriously difficult to measure. The aims of this study were (i) to develop a test battery comprising adapted and new scales to evaluate values, attitudes and intentions of dental students towards people with disability and people in marginalised groups and (ii) to determine reliability (interitem consistency) and validity of the scales within the test battery.

MATERIALS AND METHODS

A literature search identified pre-existing measures and models for the assessment of attitudes in healthcare students. Adaptation of three pre-existing scales was undertaken, and a new scale was developed based upon the Theory of Planned Behaviour (TPB) using an elicitation survey. These scales underwent a process of content validation. The three adapted scales and the TPB scale were piloted by 130 students at 5 different professional stages, from 4 different countries.

RESULTS

The scales were adjusted to ensure good internal reliability, variance, distribution, and face and content validity. In addition, the different scales showed good divergent validity.

DISCUSSION

These results are positive, and the scales now need to be validated in the field.

CONCLUSIONS

It is hoped that these tools will be useful to educators in SCD to evaluate the impact of teaching and clinical exposure on their students.

Hemodialysis-Associated Febrile Episodes: Surveillance before and after Major Alteration in the Water Treatment System

Surveillance for bacteremic or pyrogenic episodes associated with hemodialysis was undertaken before and after the reconstruction of the water treatment system at our University medical center. The new water system included a holding tank with iodination treatment. The water delivered to individual dialysis stations had only occasional positive bacterial cultures (3 of 21 samples before completion of construction, 2 of 16 samples afterwards) and intermittent detection of endotoxin (6 of 21 samples before completion of construction, 9 of 16 samples afterwards) at monthly sampling. Among 51 individual dialysis treatments (25 patients) before reconstruction and 56 treatments (29 patients), after, only 2 and 3 febrile events were identified, respectively. All of these were associated with underlying infectious illness and not with the hemodialysis procedure itself. Overall, we conclude that pyrogenic episodes associated directly with hemodialysis treatment are infrequent, and that the addition of a water storage tank with iodination treatment does not appear to increase the risk of bacteremia or pyrogenic episodes.

Evaluating Natural Language Processors in the Clinical Domain

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) [1-41. 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.

Extracting Findings from Narrative Reports: Software Transferability and Sources of Physician Disagreement

While natural language processing systems are beginning to see clinical use, it remains unclear whether they can be disseminated effectively through the health care community. MedLEE, a general-purpose natural language processor developed for Columbia-Presbyterian Medical Center, was compared to physicians' ability to detect seven clinical conditions in 200 Brigham and Women's Hospital chest radiograph reports. Using the system on the new institution's reports resulted in a small but measurable drop in performance (it was distinguishable from physicians at p = 0.011). By making adjustments to the interpretation of the processor's coded output (without changing the processor itself), local behavior was better accommodated, and performance improved so that it was indistinguishable from the physicians. Pairs of physicians disagreed on at least one condition for 22% of reports; the source of disagreement appeared to be interpretation of findings, gauging likelihood and degree of disease, and coding errors.

The kinematics of the California sea lion foreflipper during forward swimming

To determine the two-dimensional kinematics of the California sea lion foreflipper during thrust generation, a digital, high-definition video is obtained using a non-research female sea lion at the Smithsonian National Zoological Park in Washington, DC. The observational videos are used to extract maneuvers of interest--forward acceleration from rest using the foreflippers and banked turns. Single camera videos are analyzed to digitize the flipper during the motions using 10 points spanning root to tip in each frame. Digitized shapes were then fitted with an empirical function that quantitatively allows for both comparison between different claps, and for extracting kinematic data. The resulting function shows a high degree of curvature (with a camber of up to 32%). Analysis of sea lion acceleration from rest shows thrust production in the range of 150-680 N and maximum flipper angular velocity (for rotation about the shoulder joint) as high as 20 rad s⁻¹. Analysis of turning maneuvers indicate extreme agility and precision of movement driven by the foreflipper surfaces.

Similarity-based modeling applied to signal detection in pharmacovigilance

One of the main objectives in pharmacovigilance is the detection of adverse drug events (ADEs) through mining of healthcare databases, such as electronic health records or administrative claims data. Although different approaches have been shown to be of great value, research is still focusing on the enhancement of signal detection to gain efficiency in further assessment and follow-up. We applied similarity-based modeling techniques, using 2D and 3D molecular structure, ADE, target, and ATC (anatomical therapeutic chemical) similarity measures, to the candidate associations selected previously in a medication-wide association study for four ADE outcomes. Our results showed an improvement in the precision when we ranked the subset of ADE candidates using similarity scorings. This method is simple, useful to strengthen or prioritize signals generated from healthcare databases, and facilitates ADE detection through the identification of the most similar drugs for which ADE information is available.

Methods for identifying suicide or suicidal ideation in EHRs

Electronic health records contain important data elements for detection of novel adverse drug reactions, genotype/phenotype identification and psychosocial factor analysis, and the role of each of these as risk factors for suicidality warrants further investigation. Suicide and suicidal ideation are documented in clinical narratives. The specific purpose of this study was to define an algorithm for automated detection of this serious event. We found that ICD-9 E-Codes had the lowest positive predictive value: 0.55 (90% CI: 0.42-0.67), while combining ICD-9 and NLP had the best PPV: 0.97 (90% CI: 0.92-0.99). A qualitative analysis and classification of the types of errors by ICD-9 and NLP automated coding compared to manual review are also discussed.

Detection of pharmacovigilance-related adverse events using electronic health records and automated methods

Electronic health records (EHRs) are an important source of data for detection of adverse drug reactions (ADRs). However, adverse events are frequently due not to medications but to the patients' underlying conditions. Mining to detect ADRs from EHR data must account for confounders. We developed an automated method using natural-language processing (NLP) and a knowledge source to differentiate cases in which the patient's disease is responsible for the event rather than a drug. Our method was applied to 199,920 hospitalization records, concentrating on two serious ADRs: rhabdomyolysis (n = 687) and agranulocytosis (n = 772). Our method automatically identified 75% of the cases, those with disease etiology. The sensitivity and specificity were 93.8% (confidence interval: 88.9-96.7%) and 91.8% (confidence interval: 84.0-96.2%), respectively. The method resulted in considerable saving of time: for every 1 h spent in development, there was a saving of at least 20 h in manual review. The review of the remaining 25% of the cases therefore became more feasible, allowing us to identify the medications that had caused the ADRs.

Novel data-mining methodologies for adverse drug event discovery and analysis

An important goal of the health system is to identify new adverse drug events (ADEs) in the postapproval period. Datamining methods that can transform data into meaningful knowledge to inform patient safety have proven essential for this purpose. New opportunities have emerged to harness data sources that have not been used within the traditional framework. This article provides an overview of recent methodological innovations and data sources used to support ADE discovery and analysis.

Biclustering of adverse drug events in the FDA's spontaneous reporting system

In this article, we present a new pharmacovigilance data mining technique based on the biclustering paradigm, which is designed to identify drug groups that share a common set of adverse events (AEs) in the spontaneous reporting system (SRS) of the US Food and Drug Administration (FDA). A taxonomy of biclusters is developed, revealing that a significant number of bona fide adverse drug event (ADE) biclusters have been identified. Statistical tests indicate that it is extremely unlikely that the bicluster structures thus discovered, as well as their content, could have arisen by mere chance. Some of the biclusters classified as indeterminate provide support for previously unrecognized and potentially novel ADEs. In addition, we demonstrate the potential importance of the proposed methodology in several important aspects of pharmacovigilance such as providing insight into the etiology of ADEs, facilitating the identification of novel ADEs, suggesting methods and a rationale for aggregating terminologies, highlighting areas of focus, and providing an exploratory tool for data mining.

Biological nomenclatures: a source of lexical knowledge and ambiguity

There has been increased work in developing automated systems that involve natural language processing (NLP) to recognize and extract genomic information from the literature. Recognition and identification of biological entities is a critical step in this process. NLP systems generally rely on nomenclatures and ontological specifications as resources for determining the names of the entities, assigning semantic categories that are consistent with the corresponding ontology, and assignment of identifiers that map to well-defined entities within a particular nomenclature. Although nomenclatures and ontologies are valuable for text processing systems, they were developed to aid researchers and are heterogeneous in structure and semantics. A uniform resource that is automatically generated from diverse resources, and that is designed for NLP purposes would be a useful tool for the field, and would further database interoperability. This paper presents work towards this goal. We have automatically created lexical resources from four model organism nomenclature systems (mouse, fly, worm, and yeast), and have studied performance of the resources within an existing NLP system, GENIES. Using nomenclatures is not straightforward because issues concerning ambiguity, synonymy, and name variations are quite challenging. In this paper we focus mainly on ambiguity. We determined that the number of ambiguous gene names within the individual nomenclatures, across the four nomenclatures, and with general English ranged from 0%-10.18%, 1.187%-20.30%, and 0%-2.49% respectively. When actually processing text, we found the rate of ambiguous occurrences (not counting ambiguities stemming from English words) to range from 2.4%-32.9% depending on the organisms considered.

Hormonal regulation of interleukin-6 production in human adipocytes

OBJECTIVE

To elucidate the hormonal regulation of interleukin-6 (IL-6) production by human adipose tissue and its relation to leptin.

DESIGN

In vitro study. Human adipocytes were incubated with dexamethasone (with or without RU486), norepinephrine and epinephrine (with or without propranolol), or insulin.

MEASUREMENTS

IL-6 and leptin secretion by human adipocytes.

RESULTS

A gradual increase in IL-6 secretion by adipocytes during differentiation was observed. A positive correlation was found between basal IL-6 release and both glycerol 3-phosphate dehydrogenase activity--a marker of adipocyte differentiation-and leptin release. Dexamethasone decreased IL-6 secretion and increased leptin secretion in a dose-dependent manner. Both catecholamines increased IL-6 and leptin secretion. The effects of dexamethasone and catecholamines on IL-6 and leptin were abrogated by RU486 and propranolol, respectively. Incubation with insulin resulted in a dose-dependent stimulation of IL-6 and leptin secretion.

CONCLUSIONS

IL-6 is produced by human adipocytes and is a potential marker of adipocyte differentiation. Furthermore it is a hormonally regulated cytokine, suppressed by glucocorticoids, and stimulated by catecholamines and insulin in physiological concentrations.

GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles

Systems that extract structured information from natural language passages have been highly successful in specialized domains. The time is opportune for developing analogous applications for molecular biology and genomics. We present a system, GENIES, that extracts and structures information about cellular pathways from the biological literature in accordance with a knowledge model that we developed earlier. We implemented GENIES by modifying an existing medical natural language processing system, MedLEE, and performed a preliminary evaluation study. Our results demonstrate the value of the underlying techniques for the purpose of acquiring valuable knowledge from biological journals.

The efficacy and safety of once-daily Kytril (granisetron hydrochloride) tablets in the prophylaxis of nausea and emesis following fractionated upper abdominal radiotherapy

This multicenter, randomized, double-blind study compared the efficacy and safety of once-daily oral granisetron 2 mg (n = 134) and placebo (n = 126) as prophylaxis for nausea and emesis in patients receiving upper abdominal fractionated radiotherapy. Patients were scheduled to receive 10-30 fractions of radiotherapy; granisetron (two 1-mg tablets) or placebo was administered 1 hr before radiotherapy on each scheduled treatment day. Treatment comparisons were made at 24 hr and at 10 and 20 fractions. Patients treated with granisetron experienced greater emetic control than those treated with placebo as evidenced by median times to first emesis (35 vs. 9 days, p < 0.001) and first nausea (11 vs. 1 day, p < 0.001). Overall endpoint analysis showed that proportionally more granisetron than placebo patients were emesis free (57.5% vs. 42.1%, p = 0.0047) and nausea free (30.6% vs. 16.7%, p = 0.0042). Furthermore, 25% more granisetron-treated than placebo-treated patients were emesis free and 20% more were nausea free on at least 80% of study treatment days. The most commonly reported adverse experiences in granisetron-treated patients were diarrhea, asthenia, and constipation. These findings demonstrate that a once-daily, 2-mg dose of oral granisetron is well tolerated and significantly more effective than placebo in preventing nausea and emesis induced by fractionated radiotherapy to the upper abdomen.

Identification of non-functional human VNO receptor genes provides evidence for vestigiality of the human VNO

In mammals, the vomeronasal organ (VNO) contains chemosensory receptor cells that bind to pheromones and induce a variety of social and reproductive behaviors. It has been traditionally assumed that the human VNO (Jacobson's organ) is a vestigial structure, although recent studies have shown minor evidence for a structurally intact and possibly functional VNO. The presence and function of the human VNO remains controversial, however, as pheromones and VNO receptors have not been well characterized. In this study we screened a human Bacterial Artificial Chromosome (BAC) library with multiple primer sets designed from human cDNA sequences homologous to mouse VNO receptor genes. Utilizing these BAC sequences in addition to mouse VNO receptor sequences, we screened the High Throughput Genome Sequence (HTGS) database to find additional human putative VNO receptor genes. We report the identification of 56 BACs carrying 34 distinct putative VNO receptor gene sequences, all of which appear to be pseudogenes. Sequence analysis indicates substantial homology to mouse V1R and V2R VNO receptor families. Furthermore, chromosomal localization via FISH analysis and RH mapping reveal that the majority of the BACs are localized to telomeric and centromeric chromosomal localizations and may have arisen through duplication events. These data yield insight into the present state of pheromonal olfaction in humans and into the evolutionary history of human VNO receptors.

Transcriptional activity of multiple copies of a subtelomerically located olfactory receptor gene that is polymorphic in number and location

We report here on the transcriptional activity of multiple copies of a subtelomerically located olfactory receptor (OR) gene, OR-A. Due to recent duplication events, both the copy number and chromosomal location of OR-A vary among humans. Sequence analyses of 180 copies of this gene, derived from 12 chromosome ends in 22 individuals, show that the main coding exon of all but one copy is an intact open reading frame with 0-5 predicted amino acid differences. We detected transcription of OR-A in both olfactory epithelium and testis tissue using RT-PCR amplification with primers designed on the basis of a computationally predicted gene structure. Two alternatively spliced forms of transcripts, one encoding an isoform with an extended N-terminus, were found in both tissues. A third transcript, derived from a second promoter, was also observed in testes. The start methionine is predicted in all transcripts to lie in an upstream exon rather than the main coding exon, as is typical for most other OR genes. By examining sequence variants among transcripts, we show that transcription of this gene occurs at multiple chromosomal locations. Our results lend credence to the idea that OR diversity could be generated in rearrangement-prone subtelomeric regions and show that polymorphism in subtelomeric regions could lead to individual-to-individual variation in the expressed repertoire of OR genes.

Electronic chart review as an aid to postdischarge surgical site surveillance: increased case finding

BACKGROUND

At the University of Michigan Hospitals and Health Centers, there is increasing use of an electronic medical record. Because orthopedic surgeons dictate all outpatient visits to the patient's electronic record, total knee arthroplasties were chosen to determine whether the use of electronic medical records increased case finding.

METHODS

All patients who underwent a total knee arthroplasty during the study period (1996-1999) were followed prospectively with the use of the National Nosocomial Infection Surveillance System definitions. Traditional surveillance methods were used to ascertain infections. In addition, each patient's postdischarge outpatient clinic chart was reviewed electronically for 1 year after operation.

RESULTS

From 1996 to 1999, 555 procedures were performed. Overall, 25 infections were identified after operation. Seven infections were identified through traditional surveillance methods, which resulted in an average surgical site infection rate of 1.3%. The use of electronic chart review surveillance after discharge revealed a rate of 4.5%, which was significantly higher than traditional surveillance (P <.01). Eighteen of 25 infections (72%) would not have been identified with the use of traditional surveillance methods.

CONCLUSION

Postdischarge electronic chart review enhanced case finding significantly, which resulted in a more accurate infection rate. Awareness should be given to the institutions' surveillance methods and intensity when comparing to published rates.

Disambiguating ambiguous biomedical terms in biomedical narrative text: an unsupervised method

With the growing use of Natural Language Processing (NLP) techniques for information extraction and concept indexing in the biomedical domain, a method that quickly and efficiently assigns the correct sense of an ambiguous biomedical term in a given context is needed concurrently. The current status of word sense disambiguation (WSD) in the biomedical domain is that handcrafted rules are used based on contextual material. The disadvantages of this approach are (i) generating WSD rules manually is a time-consuming and tedious task, (ii) maintenance of rule sets becomes increasingly difficult over time, and (iii) handcrafted rules are often incomplete and perform poorly in new domains comprised of specialized vocabularies and different genres of text. This paper presents a two-phase unsupervised method to build a WSD classifier for an ambiguous biomedical term W. The first phase automatically creates a sense-tagged corpus for W, and the second phase derives a classifier for W using the derived sense-tagged corpus as a training set. A formative experiment was performed, which demonstrated that classifiers trained on the derived sense-tagged corpora achieved an overall accuracy of about 97%, with greater than 90% accuracy for each individual ambiguous term.

Genomic analysis of orthologous mouse and human olfactory receptor loci

Olfactory receptor (OR) genes represent approximately 1% of genomic coding sequence in mammals, and these genes are clustered on multiple chromosomes in both the mouse and human genomes. We have taken a comparative genomics approach to identify features that may be involved in the dynamic evolution of this gene family and in the transcriptional control that results in a single OR gene expressed per olfactory neuron. We sequenced approximately 350 kb of the murine P2 OR cluster and used synteny, gene linkage, and phylogenetic analysis to identify and sequence approximately 111 kb of an orthologous cluster in the human genome. In total, 18 mouse and 8 human OR genes were identified, including 7 orthologs that appear to be functional in both species. Noncoding homology is evident between orthologs and generally is confined within the transcriptional unit. We find no evidence for common regulatory features shared among paralogs, and promoter regions generally do not contain strong promoter motifs. We discuss these observations, as well as OR clustering, in the context of evolutionary expansion and transcriptional regulation of OR repertoires.

A homogeneous fluorometric assay for measuring cell adhesion to immobilized ligand using V-well microtiter plates

We have developed a homogeneous high-capacity assay format for measuring integrin- and selectin-dependent cell binding to immobilized ligand using V-well microtiter plates. 2',7'-Bis(2-carboxyethyl)-5-(and-6)-carboxylfluorescence, acetoxymethylester-labeled cells are added to ligand-coated V-shaped microtiter wells. Bound cells are separated from free cells using centrifugal force to produce shear stress. Nonadherent cells accumulate in the nadir of the well and are measured using a fluorescence plate reader. Antibody or low-molecular-weight inhibitors of either the ligand or the cell surface receptor result in less cell binding, more cells in the pellet, and increased signal. The optimization and validation of the very late antigen-4/vascular cell adhesion molecule-1 assay is described in detail. We demonstrate that this assay can be rapidly adapted to measure other integrin- and selectin-mediated interactions. This assay format has several advantages over conventional assays. The centrifugal process is biologically relevant and eliminates the washing steps to remove nonadherent cells that can cause well-to-well and plate-to-plate variation. Because the assay is robust with a high signal-to-noise ratio and low variability, it is ideally suited for studying multiple parameters of cell adhesion and for high capacity screening.

Efficacy of intravenous granisetron to control nausea and vomiting during multiple cycles of cisplatin-based chemotherapy

The safety and efficacy of granisetron (10 micrograms/kg and 40 micrograms/kg) were evaluated during a second (n = 393) and third (n = 200) cycle of chemotherapy in this multicenter, double-blind, randomized, parallel-group study. Granisetron was administered as a single intravenous dose before the start of cisplatin chemotherapy (> or = 60 mg/m2). Total control (no vomiting, no retching, no nausea, and no use of antiemetic rescue medication) after the first 24 hr following chemotherapy was achieved in 40% and 49% of patients in Cycles 2 and 3, respectively, for the 10 micrograms/kg group, and in 42% and 38% of patients in Cycles 2 and 3, respectively, for the 40 micrograms/kg group. Both dose levels of granisetron were well tolerated. The results demonstrate comparable efficacy between the 10 micrograms/kg and 40 micrograms/kg doses of granisetron in preventing nausea and vomiting during repeat cycles of high-dose cisplatin-based chemotherapy. The results of this study show that granisetron 10 micrograms/kg is safe and well tolerated, and remains effective with repeat cycle use.

Randomized trial of supplemental beta-carotene to prevent second head and neck cancer

Beta-carotene has established efficacy in animal models of oral carcinogenesis and has been shown to regress oral precancerous lesions in humans. The purpose of this study was to see whether these effects extended to the prevention of oral/pharyngeal/laryngeal (head and neck) cancer in humans. The subject population for this randomized, placebo-controlled, double-blinded clinical trial included 264 patients who had been curatively treated for a recent early-stage squamous cell carcinoma of the oral cavity, pharynx, or larynx. Patients were assigned randomly to receive 50 mg of beta-carotene per day or placebo and were followed for up to 90 months for the development of second primary tumors and local recurrences. After a median follow-up of 51 months, there was no difference between the two groups in the time to failure [second primary tumors plus local recurrences: relative risk (RR), 0.90; 95% confidence interval (CI), 0.56-1.45]. In site-specific analyses, supplemental beta-carotene had no significant effect on second head and neck cancer (RR, 0.69; 95% CI, 0.39-1.25) or lung cancer (RR, 1.44; 95% CI, 0.62-3.39). Total mortality was not significantly affected by this intervention (RR, 0.86; 95% CI, 0.52-1.42). Whereas none of the effects were statistically significant, the point estimates suggested a possible decrease in second head and neck cancer risk but a possible increase in lung cancer risk. These effects are consistent with the effects observed in trials using intermediate end point biological markers in humans, in which beta-carotene has established efficacy in oral precancerous lesions but has no effect or slightly worsens sputum cytology, and in animal carcinogenicity studies, in which beta-carotene has established efficacy in buccal pouch carcinogenesis in hamsters but not in animal models of respiratory tract/lung carcinogenesis, with some suggestions of tumor-promoting effects in respiratory tract/lung. If our results are replicated by other ongoing/completed trials, this suggests a critical need for mechanistic studies addressing differential responses in one epithelial site (head and neck) versus another (lung).

A physical map of the human genome

The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.

Are clinicians correct when they believe they are correct? Implications for medical decision support

The process of clinical decision support is linked to the validity of clinicians' confidence in their judgments. Clinicians who are appropriately confident-highly confident when they are correct and less confident when they are incorrect-will access computer-based and other information resources only when they are needed. Clinicians who are consistently underconfident will rely on external resources when they are not needed. Those who are overconfident, who believe they are correct when in fact they are not, will be prone to medical errors. An extensive literature indicates a general tendency toward overconfidence in human judgment. This study explores the relationship between confidence and "correctness", across three levels of clinical experience, in the task domain of diagnosis in internal medicine. We created detailed synopses of 36 diagnostically challenging cases and divided them into four equivalent sets of nine cases each. We asked 216 subjects at three experience levels (72 senior medical students, 72 senior medical residents, and 72 faculty attendings) to generate a differential diagnosis for each of the nine cases in one randomly-assigned set, and simultaneously to indicate their level of confidence in each of their diagnoses. We then examined the relationship between the correctness of these diagnoses (the appearance of the correct diagnosis anywhere in the hypothesis list) and these confidence judgments, for all subjects and separately for subjects at each experience level. Results indicate a small but statistically significant relationship associating correctness with higher confidence for all subjects (Kendall's tau b =.-106;p <.0001). This statistical relationship is strongest for the students ( tau b =.-121;p <.001), somewhat lesser but still significant for the faculty-level attendings ( tau b =.-103;p <.005), and non-significant ( tau b =.-041 ) for the residents. (The negative correlations are a coding artifact.) Subjects in this study showed a tendency toward underconfidence: they had low confidence in correct diagnoses more often than they had high confidence when wrong. Nonetheless, they were overconfident and thus "error prone" for 17% of cases overall. The medical students were possibly overmatched by the difficulty of the cases, so their concordance between confidence and correctness may have resulted from an awareness that they were often guessing. The relatively low concordance seen in the residents and attendings makes a strong argument that decision support systems to reduce medical errors should include both "push" and "pull" models. In sum, these results indicate that medical decision support systems cannot rely exclusively on clinicians' perceptions of their information needs, as such perceptions will frequently be incorrect.

Integration of cytogenetic landmarks into the draft sequence of the human genome

We have placed 7,600 cytogenetically defined landmarks on the draft sequence of the human genome to help with the characterization of genes altered by gross chromosomal aberrations that cause human disease. The landmarks are large-insert clones mapped to chromosome bands by fluorescence in situ hybridization. Each clone contains a sequence tag that is positioned on the genomic sequence. This genome-wide set of sequence-anchored clones allows structural and functional analyses of the genome. This resource represents the first comprehensive integration of cytogenetic, radiation hybrid, linkage and sequence maps of the human genome; provides an independent validation of the sequence map and framework for contig order and orientation; surveys the genome for large-scale duplications, which are likely to require special attention during sequence assembly; and allows a stringent assessment of sequence differences between the dark and light bands of chromosomes. It also provides insight into large-scale chromatin structure and the evolution of chromosomes and gene families and will accelerate our understanding of the molecular bases of human disease and cancer.

Automating SNOMED coding using medical language understanding: a feasibility study

This paper evaluates qualitatively the use of the MedLEE natural language processing system to code medical narratives directly into the SNOMED nomenclature, while retaining the MedLEE information model data structure. A gold standard is produced from narrative text manually coded in SNOMED. An automated parsing and SNOMED-coding of the narrative text is then automatically generated by MedLEE. By comparing MedLEE s output to that of the Gold Standard, the capacities of SNOMED and MedLEE to represent the clinical information are subsequently evaluated leading to qualitative observations on their respective strengths and constraints. In this study, MedLEE did code to SNOMED and captures the codes in a sub-structure amenable to interoperability with the description logic of SNOMED RT, showing an approach that augments and formalizes SNOMED s compositional representation methods to accurately capture information from clinical narratives.

Evaluating the UMLS as a source of lexical knowledge for medical language processing

Medical language processing (MLP) systems rely on specialized lexicons in order to recognize, classify, and normalize medical terminology, and the performance of an MLP system is dependent on the coverage and quality of such lexicons. However, the acquisition of lexical knowledge is expensive and time-consuming. The UMLS is a comprehensive resource that can be used to acquire lexical knowledge needed for medical language processing. This paper describes methods that use these resources to automatically create lexical entries and generate two lexicons. The first lexicon was created primarily using the UMLS, whereas the second was created by supplementing the lexicon of an existing MLP system called MedLEE with entries based on the UMLS. We subsequently carried out a study, which is the primary focus of this paper, using MedLEE with each of the two lexicons and also the current MedLEE lexicon to measure performance. Overall accuracy, sensitivity, and specificity using the lexicon primarily based on the UMLS were.86,.60, and.96 respectively. Those measures using the MedLEE lexicon alone were.93,.81, and.93, which was significantly better except for specificity; performance using the supplemental lexicon was exactly the same as performance using solely the MedLEE lexicon.

A study of abbreviations in the UMLS

Abbreviations are widely used in medicine. The understanding of abbreviations is important for medical language processing and information retrieval systems. The Unified Medical Language System (UMLS) contains a large number of abbreviations. We hypothesized that extracting and studying the UMLS abbreviations can be helpful for understanding the characteristics of abbreviations in medicine. In this paper, we describe a method for extracting abbreviations from the UMLS. We evaluated the method and studied the ambiguous nature of the abbreviations. In addition, the coverage of the UMLS abbreviations in medical reports was studied. Using our method, we extracted 163,666 unique (abbreviation, full form) pairs from the UMLS with a precision of 97.5%, and a recall of 96%. The UMLS abbreviations were highly ambiguous: 33.1% of abbreviations with six characters or less had multiple meanings; the average number of different full forms for all abbreviations with six characters or less was 2.28. The coverage of the UMLS abbreviations in medical reports was over 66%.

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.

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.

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.

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.

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.

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.

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.