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PubMed2000

Minimum dataset activity for hospice and hospital palliative care services in the UK 1997/98.

This study reports on the third in an annual series of surveys covering England, Wales, Scotland and Northern Ireland on the activity of palliative care services. This report concentrates on inpatient (hospice and hospital) services. All 640 known UK palliative services were sent a standardized questionnaire asking about the characteristics and numbers of patients cared for. Results were analysed for those services primarily for adults. From the 189 inpatient units (2955 beds) there was an 84% response rate in total, but the response to many of the questions was lower than this. Sixty per cent of services recorded 24,362 new patients, and about 50% provided details showing that 96.7% patients had cancer, and one-third were aged under 65 years. This is higher than the national distribution of cancer deaths where 24% are under 65 years. Conversely, only 7% were in the over 84 age group, which has 14% of cancer deaths. Most patients (73%) were admitted from their own home. Half of the admissions ended in death, and the majority of discharges were to the patient's own home. The mean length of stay was 13.1 days, with larger units tending to have a longer length of stay. Forty per cent of admissions were for one week or less (2.3% of patients died on the day of admission) and 15% were for more than three weeks. Bed occupancy varied between 99.7 and 48.9%. Responses were received from 74% of the 326 hospital support services, although again many questions were answered by less than half of those eligible to do so. Details of 37,194 new patients were reported (5.9% did not have cancer, although there was a wide range between services). Patients typically had four contacts with the service, although almost a quarter were single contacts. Three-quarters of the contacts were by a clinical nurse specialist. National estimates suggest that of the 155,000 patients dying of cancer in the UK each year 27,600 (18%) die in a hospice. There are 39,000 new hospice admissions each year and about 100,000 patients have contact with a hospital support service. Overall, the national provision of palliative care is increasing but there are groups who still appear to be missing out on palliative care, especially older people. Increasingly, patients appear to be admitted to a hospice earlier in care and are discharged home.

England↗
PubMed2006

Are statewide trauma registries comparable? Reaching for a national trauma dataset.

BACKGROUND: Statewide trauma registries have proliferated in the last decade, suggesting that information could be aggregated to provide an accurate depiction of serious injury in the United States. OBJECTIVES: To determine whether variability exists in the composition and content of statewide trauma registries, specifically addressing case-acquisition, case-definition (inclusion criteria), and registry-coding conventions. METHODS: A cross-sectional, two-part survey was administered to managers of all statewide trauma registries. State trauma registrars also provided inclusion and exclusion criteria from their state registry and abstracted a clinical vignette designed to identify coding inconsistencies. RESULTS: Thirty-two states maintain a centralized registry, but requirements for data submission vary significantly. Inclusion and exclusion criteria also vary, particularly for nontraumatic injuries. Coding conventions adopted by states for vague or missing information are dissimilar. When abstractions of the clinical vignette are compared, only 19% and 47% of states provided similar quantity or content for injury e-coding and diagnostic coding, respectively. Injury severity scores (based on diagnostic coding) demonstrated a range from 2 to 18. CONCLUSIONS: Statewide trauma registries are prevalent but vary significantly in composition and content. Standardizing inclusion criteria, variable definitions, and coding conventions would greatly enhance the usability of an aggregated, national trauma registry.

Cross-Sectional Studies↗
PubMed1996

Multicomponent criteria for predicting carcinogenicity: dataset of 30 NTP chemicals.

This article is in response to the challenge issued to the scientific community by the National Toxicology Program to predict the carcinogenicity potential of 30 chemicals previously selected for long-term carcinogenicity testing. Utilizing the available toxicologic, genetic, and structural information on 30 chemicals previously selected for long-term carcinogenicity testing, we predict that 16 chemicals (53%) would induce some indication of carcinogenic activity in rodents; we further predict that 10 chemicals (33%) would be associated with weak or equivocal carcinogenic responses, and another 4 (13%) would give no indication of carcinogenicity. Our level of certainty is indicated for many of these predictions. Nonetheless, we believe that most instances of guessing whether a chemical would eventually induce cancer in experimental animals and hence represent a carcinogenic hazard to humans are fraught with considerable uncertainty: uncertainty that can only be relieved by long-term testing for carcinogenicity in animals or by conducting an epidemiologic investigation of exposed individuals or groups. We further believe that the day may come when our predictive acumen will be upgraded to such an extent that we might eventually obviate cancer testing. Until then, and in the best interests of public health, however, we urge long term testing of chemicals in animals be continued, at increased pace.

Animals↗
PubMed2002

Interactive 3D segmentation and inspection of volumetric medial datasets.

We propose an interactive method providing 3D real-time visualization of segmentation results while tuning some of the algorithmic parameters. Visual inspection in volume reduces the time spent in tuning cumbersome parameters and may increase accuracy in medical applications. To allow fast interaction, volume rendering is achieved by using 3D texture mapping. The output of the segmentation stage is then dynamically updated in the graphic pipeline through a color lookup table related to the tuned parameters. This technique enables our approach with immediate rendering of the user interaction during the segmentation. Isosurface methods and connectivity filters have been implemented with this technique. CT and MR modalities have been tested for anatomical structures extraction. For application in craniofacial surgical planning, measurements present improvement in accuracy and efficiency for 7 pathological cases. However, manual refinement is still necessary in order to realize clinical applicable 3D models.

Computer Simulation↗
PubMed2002

Interactive PC-based volume rendering of CT datasets.

In radiology, the reading of large CT volumes is a time consuming task. Interactive volume rendering (iVRT) is a promising new technique. Using dedicated hardware (VP1000, Terarecon Inc.) it can now be realized on a standard PC in a cost effective manner. For this purpose, a program built using the Visualization Toolkit with integrated functionality for the VP 1000 is used for almost real-time iVRT (8-9 frames/second). It is possible to embed opaque and translucent polygon surfaces (e.g., segmented structures). By interactively varying the opacity, color and gradient transfer functions as well as using freely placable cutting planes, the visualization can easily be adapted to different diagnostic needs.

Humans↗
PubMed1985

The classification of subjects with joint complaints on incomplete biochemical and haematological datasets.

We performed a retrospective study on 163 subjects suffering from rheumatic fever (16), rheumatoid arthritis (36), lupus erythematosus (17), gout (21), arthrosis (50) and osteomyelitis (23). The number of variables evaluated was 39. These were all of a general biochemical and haematological nature. A feature reduction resulted in sixteen variables that matched well with those known from the literature. Linear discriminant analysis yielded poor results in classifying the six disease categories (with 18 variables 61.8%). A reduction to three disease categories improved the classification results remarkably. This, and the excellent discriminating power between patients and the reference group, shows that the selected variables are illustrative only for general clinical pictures, such as infection, and not for the desired differential diagnosis.

Arthritis, Rheumatoid↗
PubMed2006

Gene expression profile exploration of a large dataset on chronic fatigue syndrome.

OBJECTIVE: To gain understanding of the molecular basis of chronic fatigue syndrome (CFS) through gene expression analysis using a large microarray data set in conjunction with clinically administrated questionnaires. METHOD: Data from the Wichita (KS, USA) CFS Surveillance Study was used, comprising 167 participants with two self-report questionnaires (multidimensional fatigue inventory [MFI] and Zung depression scale [Zung]), microarray data, empiric classification, and others. Microarray data was analyzed using bioinformatics tools from ArrayTrack. RESULTS: Correspondence analysis was applied to the MFI questionnaire to select the 23 samples having either the most or the least fatigue, and to the Zung questionnaire to select the 26 samples having either the most or least depression; ten samples were common, resulting in a total of 39 samples. The MFI and Zung-based CFS/non-CFS (NF) classifications on the 39 samples were consistent with the empiric classification. Two differentially-expressed gene lists were determined, 188 fatigue-related genes and 164 depression-related genes, which shared 24 common genes and involved 11 common pathways. Principal component analysis based on 24 genes clearly separates 39 samples with respect to their likelihood to be CFS. Most of the 24 genes are not previously reported for CFS, yet their functions are consistent with the prevailing model of CFS, such as immune response, apoptosis, ion channel activity, signal transduction, cell-cell signaling, regulation of cell growth and neuronal activity. Hierarchical cluster analysis was performed based on 24 genes to classify 128 (=167-39) unassigned samples. Several of the 11 identified common pathways are supported by earlier findings for CFS, such as cytokine-cytokine receptor interaction and neuroactive ligand-receptor interaction. Importantly, most of the 11 common pathways are interrelated, suggesting complex biological mechanisms associated with CFS. CONCLUSION: Bioinformatics is critical in this study to select definitive sample groups, analyze gene expression data and gain insight into biological mechanisms. The 24 identified common genes and 11 common pathways could be important in future studies of CFS at the molecular level.

Adult↗
PubMed2004

Medulloblastoma and birth date: evaluation of 3 U.S. datasets.

Studies from Norway and Japan have found a higher incidence of medulloblastoma related to births that occur in the fall. The authors sought further evidence concerning this association. For 122 patients in a Duke University database and 90 patients from the Central Cancer Registry of North Carolina, the frequency distribution of birth dates by month was statistically significantly different from the expected North Carolina distribution (p = 0.04 and 0.06). For 75 patients from California Surveillance, Epidemiology, and End Results (SEER) data, the frequency distribution of birth dates by month was marginally different from the expected U.S. distribution (p = 0.14). For 922 patients from national SEER data, the frequency distribution of birth dates by month was not statistically significantly different from the expected U.S. distribution (p = 0.54). Subgroup analysis suggests seasonality of birth dates is most significant for patients aged 5-14 yr diagnosed with medulloblastoma.

Adolescent↗
PubMed2026

Whole-Genome Sequence Dataset of Rhodococcus qingshengii IEGM 267-Terpenoid Biotransformer Toward Genetic Functional Annotation.

Background/Objectives: Microbial biotransformation of monoterpenoids is a promising approach for obtaining bioactive compounds. Rhodococcus species are attractive biocatalysts due to their metabolic versatility and ability to transform hydrophobic substrates. In this study, we investigated the catalytic potential of Rhodococcus qingshengii IEGM 267 toward carveol isomers and explored genomic features that may underlie this activity. Methods: The strain was cultivated in mineral medium supplemented with (-)-trans-carveol. Biotransformation products were analyzed by TLC and GC-MS. The draft genome was sequenced, assembled, taxonomically assigned, and annotated using standard bioinformatics tools. Results: Rhodococcus qingshengii IEGM 267 efficiently converted (-)-trans-carveol to carvone. Genome analysis confirmed the taxonomic assignment of the strain and revealed a large repertoire of oxidoreductases, including monooxygenases, hydroxylases, and dehydrogenases. Seven genes encoding cytochrome P450-dependent oxygenases were identified as candidate enzymes potentially involved in carveol oxidation. Conclusions: R. qingshengii IEGM 267 is an efficient and stereoselective biocatalyst for (-)-trans-carveol oxidation. The results of bioinformatics analysis suggest an alternative enzymatic basis for this transformation and provide a foundation for future functional characterization.

Rhodococcus↗
PubMed2004

The preliminary assessment of the Social Transition in the North dataset: a comparison of STN survey and enumeration data for selected Northwest Alaskan communities.

OBJECTIVE: This study compared the results from STN survey data with a mailback health study of the same communities to assess the reliability of the STN data. STUDY DESIGN. Sample characteristics and respondes to health questions were compared through secondary data analysis. Data from the STN sample was compared to an enumeration study for the same or similar questions, including demographic characteristics and health status indicators, were compared. METHODS: The STN study used the sample of 715 households in 18 Alaskan and Russian Far East communities to obtain data on the demographic transition, epidemiological transition and domestic transition of residents in northern communities. A study of the health and human service needs was conducted in Northwest Alaska using a mailback health questionnaire within a few years of the STN study. RESULTS: Both data sets appear to be taken from similar populations. Responses to health questions show marked similarities. CONCLUSION: The comparison strongly suggests that the STN data is representative of northern Alaska communities surveyed and can be a valuable source of reliable data on the health and welfare of northern communities. The data on the self-reported prevalence of health conditions may not be useful at the community level.

Alaska↗
PubMed2006

Confirming single nucleotide polymorphisms from expressed sequence tag datasets derived from three cattle cDNA libraries.

Using the Phred/Phrap/Polyphred/Consed pipeline established in the National Livestock Research Institute of Korea, we predicted candidate coding single nucleotide polymorphisms (cSNPs) from 7,600 expressed sequence tags (ESTs) derived from three cDNA libraries (liver, M. longissimus dorsi, and intermuscular fat) of Hanwoo (Korean native cattle) steers. From the 7,600 ESTs, 829 contigs comprising more than two EST reads were assembled using the Phrap assembler. Based on the contig analysis, 201 candidate cSNPs were identified in 129 contigs, in which transitions (69%) outnumbered transversions (31%). To verify whether the predicted cSNPs are real, 17 SNPs involved in lipid and energy metabolism were selected from the ESTs. Twelve of these were confirmed to be real while five were identified as artifacts, possibly due to expressed sequence tag sequence error. Further analysis of the 12 verified cSNPs was performed using the program BLASTX. Five were identified as nonsynonymous cSNPs, five were synonymous cSNPs, and two SNPs were located in 3'-UTRs. Our data indicated that a relatively high SNP prediction rate (71%) from a large EST database could produce abundant cSNPs rapidly, which can be used as valuable genetic markers in cattle.

Animals↗
PubMed2025

A comparative genomic analysis of left- and right-sided colon cancer using real-world data from the AACR project GENIE BPC dataset.

Left- and Right-sided colon cancers (LCC and RCC) are increasingly recognized as distinct clinicopathological and molecular subtypes with divergent prognoses and therapeutic responses. Leveraging a large, multi-institutional cohort from the AACR Project Genomics Evidence Neoplasia Information Exchange (GENIE) Biopharma Collaborative (BPC) (n = 750; LCC: 363 vs. RCC: 387), we conducted a comprehensive analysis of mutational profiles, tumor mutation burden (TMB), and survival outcomes. Our findings revealed a markedly higher TMB in RCC compared to LCC (6.65 &#xb1; 11.3 vs. 3.17 &#xb1; 4.35; adjusted P = 3.12&#xd7;10-32), suggesting greater genomic instability in RCC. After applying functional annotation filters (PolyPhen > 0.85, SIFT < 0.05), RCC tumors were significantly enriched for mutations in BRAF (23.1% vs. 6.7%), KMT2D (8.6% vs. 3.2%), and SMAD4 (13.1% vs. 7.3%), while TP53 mutations predominated in LCC (40.6% vs. 31.8%). Multivariate Cox regression analysis identified RCC as an independent predictor of poorer overall survival (OS) relative to LCC (HR: 1.30, 95% CI: 1.02-1.66, P = 0.033). Notably, KRAS mutations were associated with significantly worse OS in LCC (HR: 1.68, 95% CI: 1.06-2.70, P = 0.027), while BRAF mutations predicted adverse outcomes in RCC (HR: 1.58, 95% CI: 1.05-2.37, P = 0.028). These results underscore the prognostic value of tumor sidedness and specific genetic alterations in colon adenocarcinoma. Our study highlights the need for sidedness-specific molecular profiling to inform precision oncology strategies in colon cancer management.

BRAF↗
PubMed1992

Techniques for dataset design: a utilization management system model.

Designing a clinical information system offers a sense of accomplishment similar to that of a dramatic performance. The development of the data dictionary and proposed system description requires the same attention to detail as stage directions in a script. The people involved in daily system operation are of key importance in developing a clear understanding of how things actually happen in the information flow and decision process. Once the business rules are defined and edits and conditions are developed to ensure data integrity, it is time to step back and let the performance begin. The real power of the user-designed system, like that of a performance before a live audience, comes with the ability to query the data for answers to issues and problems decision makers did not face at the time of the initial system design.

Clinical Medicine↗