Positive predictive value of CT urography in the evaluation of upper tract urothelial cancer.

Objective: The purpose of this study was to determine the positive predictive value of CT urography in the diagnosis of upper tract urothelial malignancies.

Materials And Methods: Retrospective review of the records of patients who underwent 2,602 CT urographic examinations revealed that 81 (3%) examinations of 77 patients had findings suggesting upper tract urothelial cancer. Two radiologists in consensus categorized the findings as large masses (> 5 mm), small masses (≤ 5 mm), or urothelial thickening.

A potential role for intragenic miRNAs on their hosts' interactome.

Background: miRNAs are small, non-coding RNA molecules that mainly act as negative regulators of target gene messages. Due to their regulatory functions, they have lately been implicated in several diseases, including malignancies. Roughly half of known miRNA genes are located within previously annotated protein-coding regions ("intragenic miRNAs").

Automating pressure ulcer risk assessment using documented patient data.

Objective: A rule-based prototype decision support tool; Braden-scale based Automated Risk-assessment Tool (BART) was developed to test whether pressure ulcer risk scores can be determined automatically based on the documented patient data.

Methods: The data items required for assessing pressure ulcer risk were identified by analyzing the parameter definitions of the Braden scale and by consulting the nurses specialized in pressure ulcer prevention and care. Documentation coverage and formats of the required data was evaluated.

Smart medical environment at the point of care: auto-tracking clinical interventions at the bed side using RFID technology.

We developed a wireless auto-tracking system for tracking clinical intervention such as drug administrations and blood tests at the patient bedside. The system can not only authenticate patients and nurses, but also confirm medications and provide relevant information, depending on the clinical situation and personnel location. We conducted a feasibility experiment and examined whether or not the system could work as a patient safety measure in terms of reducing misidentifications of patients and medical errors including wrong medication type, dose, time, and route.

DSGeo: software tools for cross-platform analysis of gene expression data in GEO.

The Gene Expression Omnibus (GEO) is the largest resource of public gene expression data. While GEO enables data browsing, query and retrieval, additional tools can help realize its potential for aggregating and comparing data across multiple studies and platforms. This paper describes DSGeo-a collection of valuable tools that were developed for annotating, aggregating, integrating, and analyzing data deposited in GEO.

Towards large-scale sample annotation in gene expression repositories.

Background: Large repositories of biomedical research data are most useful to translational researchers if their data can be aggregated for efficient queries and analyses. However, inconsistent or non-existent annotations describing important sample details such as name of tissue or cell line, histopathological type, and subject characteristics like demographics, treatment, and survival are seldom present in data repositories, making it difficult to aggregate data.

Results: We created a flexible software tool that allows efficient annotation of samples using a controlled vocabulary, and report on its use for the annotation of over 12,500 samples.

Evaluation of a large-scale biomedical data annotation initiative.

Background: This study describes a large-scale manual re-annotation of data samples in the Gene Expression Omnibus (GEO), using variables and values derived from the National Cancer Institute thesaurus. A framework is described for creating an annotation scheme for various diseases that is flexible, comprehensive, and scalable. The annotation structure is evaluated by measuring coverage and agreement between annotators.

Is there an advantage in scoring early embryos on more than one day?

Background: This study was undertaken to determine what characteristics should be recorded on which days to build a predictive model for selection of Day 3 embryos.

Methods: Embryos failing to form a clinical sac or that formed a viable fetus (to > or =12 weeks), and transferred singly (n = 269) or in pairs (n = 1326) were scored for early cleavage and pronuclear status on Day 1, and cell number, fragmentation, and symmetry on Days 2 and 3, with number of nuclei per blastomere also recorded on Day 2. Seven candidate models were identified using a priori clinical knowledge and univariate analyses.

Validation of an automated safety surveillance system with prospective, randomized trial data.

Objective: We sought to validate 3 methods for automated safety monitoring by evaluating clinical trials with elevated adverse events.

Methods: An automated outcomes surveillance system was used to retrospectively analyze data from 2 randomized, TIMI multicenter trials. Trial A was stopped early due to elevated 30-day mortality rates in the intervention arm.

Comparison of RFID systems for tracking clinical interventions at the bedside.

In recent years, there have been high expectations for RFID technologies applied in the medical field, particularly for automatic identification and location of patients and medical supplies. However, few studies have measured the applicability of currently available RFID technologies in a medical environment. To determine the technical factors that affect the performance of RFID systems, we examined the performance of different types of tags for medications, medical equipment, nurses, and patients under different experimental conditions.

Improving calibration of logistic regression models by local estimates.

Objective: To improve the calibration of logistic regression (LR) estimates using local information.

Background: Individualized risk assessment tools are increasingly being utilized. External validation of these tools often reveals poor model calibration.

Current status of the Japanese cancer registry system: results of a nationwide survey.

A survey about the status of the Japanese cancer registry system was administered to certified cancer network hospitals in Japan. It revealed that the cancer registry system was utilized in most of the responding hospitals. However, the degree of data integration with the hospital information system and the levels of data utilization inside the hospital were not high.

Validating an automated outcomes surveillance application using data from a terminated randomized, controlled trial (OPUS [TIMI-16]).

We sought to validate an automated outcomes surveillance system (DELTA) using OPUS (TIMI-16), a multi-center randomized, controlled trial that was stopped early due to elevated mortality in one of the two intervention arms. Methodologies that were incorporated into the application (Statistical Process Control [SPC] and Bayesian Updating Statistics [BUS]) were compared with standard Data Safety Monitoring Board (DSMB) protocols.

Is redundancy in vital signs monitoring useful?

During an ongoing study of wireless vital signs monitoring of post-triage patients with SMART [1] in the waiting area of the emergency department (ED) at the Brigham and Women's Hospital in Boston, Massachusetts, USA, we observed that redundancy in vital signs monitoring can be advantageous.

Rare adverse event monitoring of medical devices with the use of an automated surveillance tool.

Prospective outcomes surveillance using population level data allows for statistical methodologies and confounder adjustment not supported by the FDA's current monitoring system. We explored propensity score matching integrated into an automated surveillance tool as a method for confounder adjustment in an observational cohort. The application analyzed all patients undergoing PCI via femoral access route from 2002-2006.

Peripheral arterial occlusive disease: global gene expression analyses suggest a major role for immune and inflammatory responses.

Background: Peripheral arterial disease (PAD), a major manifestation of atherosclerosis, is associated with significant cardiovascular morbidity, limb loss and death. However, mechanisms underlying the genesis and progression of the disease are far from clear. Genome-wide gene expression profiling of clinical samples may represent an effective approach to gain relevant information.

Validation of oligoarrays for quantitative exploration of the transcriptome.

Background: Oligoarrays have become an accessible technique for exploring the transcriptome, but it is presently unclear how absolute transcript data from this technique compare to the data achieved with tag-based quantitative techniques, such as massively parallel signature sequencing (MPSS) and serial analysis of gene expression (SAGE). By use of the TransCount method we calculated absolute transcript concentrations from spotted oligoarray intensities, enabling direct comparisons with tag counts obtained with MPSS and SAGE. The tag counts were converted to number of transcripts per cell by assuming that the sum of all transcripts in a single cell was 5.

Angiogenic heterogeneity in head and neck squamous cell carcinoma: biological and therapeutic implications.

The literature contains numerous references describing heterogeneity for tumor phenotypes including cell proliferation, invasiveness, metastatic potential, and response to therapies. However, data regarding angiogenic heterogeneity are limited. In this study, we investigated the degree of intertumoral angiogenic heterogeneity present in head and neck squamous cell carcinomas (HNSCC).

Risk-adjusted sequential probability ratio test control chart methods for monitoring operator and institutional mortality rates in interventional cardiology.

Background: The objective of this study was to evaluate risk-adjusted sequential probability ratio test control charts for the detection of significant discrepancies between institution or individual interventional cardiologist postprocedural mortality rates and national or local event rate expectations.

Methods: Eight thousand nine hundred forty-two percutaneous coronary interventional procedures were performed by 27 operators between January 1, 2002, and November 30, 2006. The institution-based evaluation included all procedures, and the individual-based evaluations included 8750 procedures performed by 18 operators who had each done at least 100 PCI procedures.

SMART--an integrated wireless system for monitoring unattended patients.

Monitoring vital signs and locations of certain classes of ambulatory patients can be useful in overcrowded emergency departments and at disaster scenes, both on-site and during transportation. To be useful, such monitoring needs to be portable and low cost, and have minimal adverse impact on emergency personnel, e.g.

Modeling cancer: integration of "omics" information in dynamic systems.

The last 10 years have seen the rise of many technologies that produce an unprecedented amount of genome-scale data from many organisms. Although the research community has been successful in exploring these data, many challenges still persist. One of them is the effective integration of such data sets directly into approaches based on mathematical modeling of biological systems.

Effects of SVM parameter optimization on discrimination and calibration for post-procedural PCI mortality.

Support vector machines (SVM) have become popular among machine learning researchers, but their applications in biomedicine have been somewhat limited. A number of methods, such as grid search and evolutionary algorithms, have been utilized to optimize model parameters of SVMs. The sensitivity of the results to changes in optimization methods has not been investigated in the context of medical applications.

Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates.

Background: High-throughput systems for gene expression profiling have been developed and have matured rapidly through the past decade. Broadly, these can be divided into two categories: hybridization-based and sequencing-based approaches. With data from different technologies being accumulated, concerns and challenges are raised about the level of agreement across technologies.