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Barry Robson, Thomas P Caruso, Ulysses G J Balis
We describe here the applications of our recently proposed Q-UEL language to continuity of patient care between physicians, specialists and institutions as mediated via the Internet, giving examples derived from HL7 CDA and VistA of particular interest to workflow. Particular attention is given to the Universal Exchange Language for healthcare as requested by the US President׳s Council of Advisors on Science and Technology (PCAST) released in December 2010, especially in regard to disaggregation of the patient record on the Internet...
January 2015: Computers in Biology and Medicine
Edward J Kim, Vaibhav Sahai, Ethan V Abel, Kent A Griffith, Joel K Greenson, Naoko Takebe, Gazala N Khan, John L Blau, Ronald Craig, Ulysses G Balis, Mark M Zalupski, Diane M Simeone
PURPOSE: The hedgehog (HH) signaling pathway is a key regulator in tumorigenesis of pancreatic adenocarcinoma and is upregulated in pancreatic adenocarcinoma cancer stem cells (CSCs). GDC-0449 is an oral small-molecule inhibitor of the HH pathway. This study assessed the effect of GDC-0449-mediated HH inhibition in paired biopsies, followed by combined treatment with gemcitabine, in patients with metastatic pancreatic adenocarcinoma. EXPERIMENTAL DESIGN: Twenty-five patients were enrolled of which 23 underwent core biopsies at baseline and following 3 weeks of GDC-0449...
December 1, 2014: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Jason D Hipp, Jerome Cheng, Jeffrey C Hanson, Avi Z Rosenberg, Michael R Emmert-Buck, Michael A Tangrea, Ulysses J Balis
SIVQ-LCM is a new methodology that automates and streamlines the more traditional, user-dependent laser dissection process. It aims to create an advanced, rapidly customizable laser dissection platform technology. In this report, we describe the integration of the image analysis software Spatially Invariant Vector Quantization (SIVQ) onto the ArcturusXT instrument. The ArcturusXT system contains both an infrared (IR) and ultraviolet (UV) laser, allowing for specific cell or large area dissections. The principal goal is to improve the speed, accuracy, and reproducibility of the laser dissection to increase sample throughput...
2014: Journal of Visualized Experiments: JoVE
J Mark Tuthill, Bruce A Friedman, Ulysses J Balis, Andrew Splitz
No abstract text is available yet for this article.
2014: Journal of Pathology Informatics
Jason M Baron, Anand S Dighe, Ramy Arnaout, Ulysses J Balis, W Stephen Black-Schaffer, Alexis B Carter, Walter H Henricks, John M Higgins, Brian R Jackson, Jiyeon Kim, Veronica E Klepeis, Long P Le, David N Louis, Diana Mandelker, Craig H Mermel, James S Michaelson, Rakesh Nagarajan, Mihae E Platt, Andrew M Quinn, Luigi Rao, Brian H Shirts, John R Gilbertson
BACKGROUND: Pathologists and informaticians are becoming increasingly interested in electronic clinical decision support for pathology, laboratory medicine and clinical diagnosis. Improved decision support may optimize laboratory test selection, improve test result interpretation and permit the extraction of enhanced diagnostic information from existing laboratory data. Nonetheless, the field of pathology decision support is still developing. To facilitate the exchange of ideas and preliminary studies, we convened a symposium entitled: Pathology data integration and clinical decision support...
2014: Journal of Pathology Informatics
Barry Robson, Thomas P Caruso, Ulysses G J Balis
Mining biomedical and pharmaceutical data generates huge numbers of interacting probabilistic statements for inference, which can be supported by mining Web text sources. This latter can also be probabilistic, in a sense described in this report. However, the diversity of tools for probabilistic inference is troublesome, suggesting a need for a unifying best practice. Physicists often claim that quantum mechanics is the universal best practice for probabilistic reasoning. We discuss how the Dirac notation and algebra suggest the form and algebraic and semantic meaning of XML-like Web tags for a clinical and biomedical universal exchange language formulated to make sense directly to the eye of the physician and biomedical researcher...
December 2013: Computers in Biology and Medicine
Akbar K Waljee, Ashin Mukherjee, Amit G Singal, Yiwei Zhang, Jeffrey Warren, Ulysses Balis, Jorge Marrero, Ji Zhu, Peter Dr Higgins
OBJECTIVES: Missing laboratory data is a common issue, but the optimal method of imputation of missing values has not been determined. The aims of our study were to compare the accuracy of four imputation methods for missing completely at random laboratory data and to compare the effect of the imputed values on the accuracy of two clinical predictive models. DESIGN: Retrospective cohort analysis of two large data sets. SETTING: A tertiary level care institution in Ann Arbor, Michigan...
2013: BMJ Open
Ioan C Cucoranu, Anil V Parwani, Andrew J West, Gonzalo Romero-Lauro, Kevin Nauman, Alexis B Carter, Ulysses J Balis, Mark J Tuthill, Liron Pantanowitz
Data protection and security are critical components of routine pathology practice because laboratories are legally required to securely store and transmit electronic patient data. With increasing connectivity of information systems, laboratory work-stations, and instruments themselves to the Internet, the demand to continuously protect and secure laboratory information can become a daunting task. This review addresses informatics security issues in the pathology laboratory related to passwords, biometric devices, data encryption, internet security, virtual private networks, firewalls, anti-viral software, and emergency security situations, as well as the potential impact that newer technologies such as mobile devices have on the privacy and security of electronic protected health information (ePHI)...
2013: Journal of Pathology Informatics
Jaime Rodriguez-Canales, Jeffrey C Hanson, Jason D Hipp, Ulysses J Balis, Michael A Tangrea, Michael R Emmert-Buck, G Steven Bova
Isolation of well-preserved pure cell populations is a prerequisite for sound studies of the molecular basis of any tissue-based biological phenomenon. This updated chapter reviews current methods for obtaining anatomically specific signals from molecules isolated from tissues, a basic requirement for productive linking of phenotype and genotype. The quality of samples isolated from tissue and used for molecular analysis is often glossed over or omitted from publications, making interpretation and replication of data difficult or impossible...
2013: Methods in Molecular Biology
David A Hanauer, Yang Liu, Qiaozhu Mei, Frank J Manion, Ulysses J Balis, Kai Zheng
In this study, we quantified the use of uncertainty expressions, referred to as 'hedge' phrases, among a corpus of 100,000 clinical documents retrieved from our institution's electronic health record system. The frequency of each hedge phrase appearing in the corpus was characterized across document types and clinical departments. We also used a natural language processing tool to identify clinical concepts that were spatially, and potentially semantically, associated with the hedge phrases identified. The objective was to delineate the prevalence of hedge phrase usage in clinical documentation which may have a profound impact on patient care and provider-patient communication, and may become a source of unintended consequences when such documents are made directly accessible to patients via patient portals...
2012: AMIA ... Annual Symposium Proceedings
Roy E Lee, David S McClintock, Ulysses J Balis, Jason M Baron, Michael J Becich, Bruce A Beckwith, Victor B Brodsky, Alexis B Carter, Anand S Dighe, Mehrvash Haghighi, Jason D Hipp, Walter H Henricks, Jiyeon Y Kim, Veronica E Klepseis, Frank C Kuo, William J Lane, Bruce P Levy, Maristela L Onozato, Seung L Park, John H Sinard, Mark J Tuthill, John R Gilbertson
BACKGROUND: Last year, our pathology informatics fellowship added informatics-based interactive case studies to its existing educational platform of operational and research rotations, clinical conferences, a common core curriculum with an accompanying didactic course, and national meetings. METHODS: The structure of the informatics case studies was based on the traditional business school case study format. Three different formats were used, varying in length from short, 15-minute scenarios to more formal multiple hour-long case studies...
2012: Journal of Pathology Informatics
Sinchita Roy Chowdhuri, Jeffrey Hanson, Jerome Cheng, Jaime Rodriguez-Canales, Patricia Fetsch, Ulysses Balis, Armando C Filie, Giuseppe Giaccone, Michael R Emmert-Buck, Jason D Hipp
OBJECTIVE: In the past decade molecular diagnostics has changed the clinical management of lung adenocarcinoma patients. Molecular diagnostics, however, is largely dependent on the quantity and quality of the tumor DNA that is retrieved from the tissue or cytology samples. Frequently, patients are diagnosed on cytology specimens where the tumor cells are scattered within the cell block, making selecting for tumor enrichment difficult. In the past we have used laser capture microdissection (LCM) to select for pure populations of tumor cells to increase the sensitivity of molecular assays...
2012: Acta Cytologica
Jennifer A Hipp, Jason D Hipp, Megan Lim, Gaurav Sharma, Lauren B Smith, Stephen M Hewitt, Ulysses G J Balis
BACKGROUND: Conventional tissue microarrays (TMAs) consist of cores of tissue inserted into a recipient paraffin block such that a tissue section on a single glass slide can contain numerous patient samples in a spatially structured pattern. Scanning TMAs into digital slides for subsequent analysis by computer-aided diagnostic (CAD) algorithms all offers the possibility of evaluating candidate algorithms against a near-complete repertoire of variable disease morphologies. This parallel interrogation approach simplifies the evaluation, validation, and comparison of such candidate algorithms...
2012: Journal of Pathology Informatics
Jason D Hipp, Steven C Smith, Jeffrey Sica, David Lucas, Jennifer A Hipp, Lakshmi P Kunju, Ulysses J Balis
No abstract text is available yet for this article.
2012: Journal of Pathology Informatics
Jason Hipp, James Monaco, L Priya Kunju, Jerome Cheng, Yukako Yagi, Jaime Rodriguez-Canales, Michael R Emmert-Buck, Stephen Hewitt, Michael D Feldman, John E Tomaszewski, Mehmet Toner, Ronald G Tompkins, Thomas Flotte, David Lucas, John R Gilbertson, Anant Madabhushi, Ulysses Balis
INTRODUCTION: The advent of digital slides offers new opportunities within the practice of pathology such as the use of image analysis techniques to facilitate computer aided diagnosis (CAD) solutions. Use of CAD holds promise to enable new levels of decision support and allow for additional layers of quality assurance and consistency in rendered diagnoses. However, the development and testing of prostate cancer CAD solutions requires a ground truth map of the cancer to enable the generation of receiver operator characteristic (ROC) curves...
2012: Analytical Cellular Pathology (Amsterdam)
Scott R Owens, Ulysses G J Balis, David R Lucas, Jeffrey L Myers
Critical values in anatomic pathology are rare occurrences and difficult to define with precision. Nevertheless, accrediting institutions require effective and timely communication of all critical values generated by clinical and anatomic laboratories. Provisional gating criteria for potentially critical anatomic diagnoses have been proposed, with some success in their implementation reported in the literature. Ensuring effective communication is challenging, however, making the case for programmatic implementation of a turnkey-style integrated information technology solution...
March 2012: American Journal of Surgical Pathology
Jason Hipp, Jerome Cheng, Liron Pantanowitz, Stephen Hewitt, Yukako Yagi, James Monaco, Anant Madabhushi, Jaime Rodriguez-Canales, Jeffrey Hanson, Sinchita Roy-Chowdhuri, Armando C Filie, Michael D Feldman, John E Tomaszewski, Natalie Nc Shih, Victor Brodsky, Giuseppe Giaccone, Michael R Emmert-Buck, Ulysses J Balis
INTRODUCTION: The increasing availability of whole slide imaging (WSI) data sets (digital slides) from glass slides offers new opportunities for the development of computer-aided diagnostic (CAD) algorithms. With the all-digital pathology workflow that these data sets will enable in the near future, literally millions of digital slides will be generated and stored. Consequently, the field in general and pathologists, specifically, will need tools to help extract actionable information from this new and vast collective repository...
2011: Journal of Pathology Informatics
Kai Zheng, Qiaozhu Mei, Lei Yang, Frank J Manion, Ulysses J Balis, David A Hanauer
In this study, we comparatively examined the linguistic properties of narrative clinician notes created through voice dictation versus those directly entered by clinicians via a computer keyboard. Intuitively, the nature of voice-dictated notes would resemble that of natural language, while typed-in notes may demonstrate distinctive language features for reasons such as intensive usage of acronyms. The study analyses were based on an empirical dataset retrieved from our institutional electronic health records system...
2011: AMIA ... Annual Symposium Proceedings
Jason Hipp, Jerome Cheng, Stephanie Daignault, Jefferey Sica, Michael C Dugan, David Lucas, Yukako Yagi, Stephen Hewitt, Ulysses J Balis
Recently, with the advent of the 7th edition of the AJCC Cancer Staging manual, at least one set of criteria (e.g. breast) were modified to now require the measurement of maximal depth of stromal invasion. With the current manual interpretive morphological approaches typically employed by surgical pathologists to assess tumor extent, the specialty now potentially has stumbled upon a crossroads of practice, where the diagnostic criteria have exceeded the capabilities of our commonly available tools. While whole slide imaging (WSI) technology holds the potential to offer many improvements in clinical workflow over conventional slide microscopy including unambiguous utility for facilitating quantitative diagnostic tasks with one important example being the determination of both linear dimension and surface area...
2011: Analytical Cellular Pathology (Amsterdam)
Jason Hipp, Steven Christopher Smith, Jerome Cheng, Scott Arthur Tomlins, James Monaco, Anant Madabhushi, Lakshmi Priya Kunju, Ulysses J Balis
For personalization of medicine, increasingly clinical and demographic data are integrated into nomograms for prognostic use, while molecular biomarkers are being developed to add independent diagnostic, prognostic, or management information. In a number of cases in surgical pathology, morphometric quantitation is already performed manually or semi-quantitatively, with this effort contributing to diagnostic workup. Digital whole slide imaging, coupled with emerging image analysis algorithms, offers great promise as an adjunctive tool for the surgical pathologist in areas of screening, quality assurance, consistency, and quantitation...
2012: Analytical Cellular Pathology (Amsterdam)
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