Snail2 is an essential mediator of Twist1-induced epithelial mesenchymal transition and metastasis.

To metastasize, carcinoma cells must attenuate cell-cell adhesion to disseminate into distant organs. A group of transcription factors, including Twist1, Snail1, Snail2, ZEB1, and ZEB2, have been shown to induce epithelial mesenchymal transition (EMT), thus promoting tumor dissemination. However, it is unknown whether these transcription factors function independently or coordinately to activate the EMT program.

Assessing the quality of annotations in asthma gene expression experiments.

Background: The amount of data deposited in the Gene Expression Omnibus (GEO) has expanded significantly. It is important to ensure that these data are properly annotated with clinical data and descriptions of experimental conditions so that they can be useful for future analysis. This study assesses the adequacy of documented asthma markers in GEO.

Feasibility evaluation of Smart Stretcher to improve patient safety during transfers.

Objectives: The integration of noninvasive vital sign sensors and wireless sensor networks into intelligent alarm systems has the potential to improve patient safety. We developed a wireless network-based system ("Smart Stretcher"), which was designed to constantly monitor patient vital signs and detect apnea during transfers within a hospital. The system alerts medical staff in case of an emergency through a wireless network.

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.

TGF-beta1 interactome: metastasis and beyond.

The ubiquitous cytokine transforming growth factor-beta1 (TGF-beta1) is one of the most potent metastatic inducers. Functional interactomic mapping using high-throughput proteomic and genomic data provides valuable insights into the regulation of tumor suppressive and metastatic attributes of TGF-beta1. Polarity changes of the TGF-beta1 interactome at a given time contributes to these contrasting effects.

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.