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Joseph W Rudolf, Christopher A Garcia, Matthew G Hanna, Christopher L Williams, Ulysses G Balis, Liron Pantanowitz, J Mark Tuthill, John R Gilbertson
Background: The alumni of today's Pathology Informatics and Clinical Informatics fellowships fill diverse roles in academia, large health systems, and industry. The evolving training tracks and curriculum of Pathology Informatics fellowships have been well documented. However, less attention has been given to the posttraining experiences of graduates from informatics training programs. Here, we examine the career paths of subspecialty fellowship-trained pathology informaticians. Methods: Alumni from four Pathology Informatics fellowship training programs were contacted for their voluntary participation in the study...
2018: Journal of Pathology Informatics
Christopher L Williams, David S McClintock, Ulysses G J Balis
No abstract text is available yet for this article.
2018: Journal of Pathology Informatics
Monica A Konerman, Dongxia Lu, Yiwei Zhang, Mary Thomson, Ji Zhu, Aashesh Verma, Boang Liu, Nizar Talaat, Ulysses Balis, Peter D R Higgins, Anna S F Lok, Akbar K Waljee
OBJECTIVE: Assessing risk of adverse outcomes among patients with chronic liver disease has been challenging due to non-linear disease progression. We previously developed accurate prediction models for fibrosis progression and clinical outcomes among patients with advanced chronic hepatitis C (CHC). The primary aim of this study was to validate fibrosis progression and clinical outcomes models among a heterogeneous patient cohort. DESIGN: Adults with CHC with ≥3 years follow-up and without hepatic decompensation, hepatocellular carcinoma (HCC), liver transplant (LT), HBV or HIV co-infection at presentation were analyzed (N = 1007)...
2017: PloS One
Akbar K Waljee, Kay Sauder, Anand Patel, Sandeep Segar, Yiwei Zhang, Ji Zhu, Ryan W Stidham, Ulysses Balis, Peter D R Higgins
No abstract text is available yet for this article.
January 5, 2018: Journal of Crohn's & Colitis
Akbar K Waljee, Kay Sauder, Anand Patel, Sandeep Segar, Boang Liu, Yiwei Zhang, Ji Zhu, Ryan W Stidham, Ulysses Balis, Peter D R Higgins
Background and Aims: Big data analytics leverage patterns in data to harvest valuable information, but are rarely implemented in clinical care. Optimising thiopurine therapy for inflammatory bowel disease [IBD] has proved difficult. Current methods using 6-thioguanine nucleotide [6-TGN] metabolites have failed in randomized controlled trials [RCTs], and have not been used to predict objective remission [OR]. Our aims were to: 1) develop machine learning algorithms [MLA] using laboratory values and age to identify patients in objective remission on thiopurines; and 2) determine whether achieving algorithm-predicted objective remission resulted in fewer clinical events per year...
July 1, 2017: Journal of Crohn's & Colitis
Christopher L Williams, Jeffrey C Sica, Robert T Killen, Ulysses G J Balis
OBJECTIVE: Within the information technology (IT) industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise's overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems...
2016: Journal of Pathology Informatics
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...
August 1, 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
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