Michael J Becich

• MD PhD
• Chairman and Distinguished University Professor at University of Pittsburgh

This paper summarizes several presentations in the Thresholds in Epidemiology and Risk Assessment session at the Monticello III conference. These presentations described evidence regarding thresholds for particles, including asbestos and silica, and cancer (e.g., mesothelioma) and noncancer (e.g., silicosis) endpoints. In the case of exposure to va...

IMPORTANCE Prior studies have demonstrated the effectiveness of COVID-19 vaccines in children and adolescents. However, the benefits of vaccination in these age groups with prior infection remain underexplored. OBJECTIVE To evaluate the effectiveness of COVID-19 vaccination in preventing reinfection with various Omicron subvariants (BA.1/2, BA.4/5,...

Introduction Managing clinical trials is a complex process requiring careful integration of human, technology, compliance, and operations for success. We collaborated with experts to develop a multi-axial Clinical Trials Management Ecosystem (CTME) maturity model (MM) to help institutions identify best practices for CTME capabilities. Methods A wo...

The COVID-19 pandemic has been associated with increased neuropsychiatric conditions in children and youths, with evidence suggesting that SARS-CoV-2 infection may contribute additional risks beyond pandemic stressors. This study aimed to assess the full spectrum of neuropsychiatric conditions in COVID-19 positive children (ages 5–12) and youths (a...

To develop and evaluate an automated approach using Large Language Models (LLMs) for generating RECORD methodology checklists from full-text articles, aiming to reduce the time burden on researchers while maintaining reporting quality. We randomly sampled 10 Open Access full-text articles from a previous study 3,4. Two independent human readers com...

Importance Obesity is associated with increased severity of COVID-19. Whether obesity is associated with an increased risk of post-acute sequelae of SARS-CoV-2 infection (PASC) among pediatric populations, independent of its association with acute infection severity, is unclear. Objective To quantify the association of body mass index (BMI) status...

Background Social determinants of health (SDoH), such as socioeconomics and neighborhoods, strongly influence health outcomes. However, the current state of standardized SDoH data in electronic health records (EHRs) is lacking, a significant barrier to research and care quality. Methods We conducted a PubMed search using “SDOH” and “EHR” Medical S...

Immunotherapies have demonstrated limited clinical efficacy in malignant mesothelioma treatment. We conducted multiplex immunofluorescence analyses on tissue microarrays (n = 3) from patients with malignant pleural mesothelioma (MPM, n = 88) and malignant peritoneal mesothelioma (MPeM, n = 25). Our study aimed to elucidate spatial distributions of...

We investigated the risks of post-acute and chronic adverse kidney outcomes of SARS-CoV-2 infection in the pediatric population via a retrospective cohort study using data from the RECOVER program. We included 1,864,637 children and adolescents under 21 from 19 children’s hospitals and health institutions in the US with at least six months of follo...

IMPORTANCE Obesity increases the severe COVID-19 risk. Whether obesity is associated with an increased risk of post-acute sequelae of SARS-Cov-2 infection (PASC) among pediatrics, independent of its impacts on acute infection severity, is unclear. OBJECTIVE To quantify the association between body mass index (BMI) status before SARS-CoV-2 infection...

Mesothelioma remains an under-researched cancerous disease due to the lack of high-quality patient samples and clinical information especially outcomes and asbestos exposure data. The National Mesothelioma Virtual Bank (NMVB) is a biobank in which mesothelioma annotated biospecimens can be made widely available to the research community. Here, we s...

Background: The impact of COVID-19 on gastrointestinal (GI) outcomes in children during the post-acute and chronic phases of the disease is not well understood. Methods: We conducted a retrospective cohort study across twenty-nine healthcare institutions from March 2020 to September 2023, including 413,455 pediatric patients with confirmed SARS-CoV...

Background Social determinants of health (SDoH) like socioeconomics and neighborhoods strongly influence outcomes, yet standardized SDoH data is lacking in electronic health records (EHR), limiting research and care quality. Methods We searched PubMed using keywords "SDOH" and "EHR", underwent title/abstract and full-text screening. Included record...

Nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH) are highly prevalent but underdiagnosed. We used an electronic health record data network to test a population-level risk stratification strategy using noninvasive tests (NITs) of liver fibrosis. Data were obtained from PCORnet® sites in the East, Midwest, Southwest, a...

PCORnet, the National Patient-Centered Clinical Research Network, provides the ability to conduct prospective and observational pragmatic research by leveraging standardized, curated electronic health records data together with patient and stakeholder engagement. PCORnet is funded by the Patient-Centered Outcomes Research Institute (PCORI) and is c...

Mesothelioma remains an under-researched cancer due to the lack of high-quality patient samples and clinical information, especially outcomes and asbestos exposure data. The National Mesothelioma Virtual Bank (NMVB) is a biobank in which mesothelioma annotated biospecimens can be made widely available to the research community. Here, we summarized...

Objective: Rare disease research requires data sharing networks to power translational studies. We describe novel use of Research Electronic Data Capture (REDCap), a web application for managing clinical data, by the National Mesothelioma Virtual Bank, a federated biospecimen, and data sharing network. Materials and methods: National Mesotheliom...

Rehabilitation research focuses on determining the components of a treatment intervention, the mechanism of how these components lead to recovery and rehabilitation, and ultimately the optimal intervention strategies to maximize patients' physical, psychologic, and social functioning. Traditional randomized clinical trials that study and establish...

The past three decades catapulted biorepositories and their informatics innovation to the forefront of Precision Medicine and particularly Precision Oncology. The National Institute of Health (NIH)‘s programs, particularly the All of Us Research Program and the Biden Cancer Moonshot initiatives, have been key enablers. The importance of biospecimen...

Rehabilitation research focuses on determining the components of a treatment intervention, the mechanism of how these components lead to recovery and rehabilitation, and ultimately the optimal intervention strategies to maximize patients' physical, psychologic, and social functioning. Traditional randomized clinical trials that study and establish...

Background: Malignant mesothelioma is associated with environmental and occupational exposure to certain mineral fibers, especially asbestos. This study aims to examine work histories of mesothelioma patients and their survival time. Method: Using the NIOSH Industry and Occupation Computerized Coding System, we mapped occupations and industries...

The presentations in this session of the Monticello II conference were aimed at summarizing what is known about asbestiform and non-asbestiform elongate mineral particles (EMPs) and mesothelioma risks based on evidence from experimental and epidemiology studies. Dr. Case discussed case reports of mesothelioma over the last several decades. Dr. Taio...

Breast cancer is the most frequent cancer among women worldwide,1the metastatic breast cancer is the main cause of mortality for breast cancer patients. Computational phenotyping, an informatics approach, that extracts phenotypes from real-world data such as electronic health records (EHRs), has the potential to advance medicine’s understanding of...

Mesothelioma remains an under-researched cancerous disease due to the lack of high-quality patient samples and clinical information especially outcomes and asbestos exposure data. The National Mesothelioma Virtual Bank (NMVB) is a biobank in which mesothelioma annotated biospecimens can be made widely available to the research community. Here, we s...

Malignant pleural mesothelioma (MPM), an aggressive cancer of the mesothelial cells lining the pleural cavity, lacks effective treatments. Multiple somatic mutations and copy number losses in tumor suppressor genes (TSGs) BAP1, CDKN2A/B, and NF2 are frequently associated with MPM. The impact of single versus multiple genomic alterations of TSG on M...

Introduction: Obesity, chronic inflammation, and elevated levels of atherogenic lipids have been associated with increased risk of ASCVD events. Current AHA/ACC guidelines identify existing risk enhancers for ASCVD including persistently elevated LDL-C or triglycerides, chronic kidney disease, chronic inflammatory conditions, and elevated inflammat...

Introduction: Patients with ASCVD are at increased risk for CV events. The 2018 AHA/ACC lipid guidelines recommend treating these patients with high intensity or maximally tolerated statin therapy. The objective of this study was to describe lipid lowering treatment (LLT) patterns and lipid values across 7 regional health systems. Methods: We condu...

Introduction: Per AHA guidelines, adults between 40-75 with borderline (5-7.5%) 10-year ASCVD risk (approximately 2.5% of this population in prior studies) should have the decision to start statin therapy personalized. Per AHA guidelines, elevated apolipoprotein B-100 (apoB) and elevated lipoprotein(a) (Lp(a)) are risk enhancing factors that may be...

Overview Oncology informatics in the era of precision oncology is challenging because no unified comprehensive system exists linking Health Information Technology (HIT) deployed in clinical settings to the translational needs of researchers. Many advanced informatics solutions have been developed for clinical trials, biobanking, cancer imaging, and...

Background: The current computational analyses of multi to hyperplexed fluorescence and/or mass spectrometry image datasets from patient pathology samples are not powerful enough to extract the maximum amount of information or to create the detailed knowledge that is required to advance precision medicine in pathology, including the development of...

e13580 Background: Malignant Pleural mesothelioma (MPM) is a highly aggressive cancer of the pleural surface and represents 80-90% of mesothelioma diagnosis. MPM is broadly subclassified into three histological subgroups (epithelioid, sarcomatoid, biphasic), however tissue heterogeneity has resulted in diagnostic challenges and suboptimal patient c...

Academic industry partnership (AIP) represents an important alliance between academic researchers and industry that helps translate technology and complete the innovation cycle within academic health systems. Despite diverging missions and skillsets the culture for academia and industry is changing in response to the current digital era which is sp...

Research Patient Data Repositories (RPDRs) have become essential infrastructure for traditional Clinical and Translational Science Award (CTSA) programs and increasingly for a wide range of research consortia and learning health system networks.1–5 Almost every institution with a CTSA or Clinical Translational Research (CTR) program (found in state...

Artificial intelligence (AI) is transforming many domains including finance, agriculture, defense and biomedicine. In this paper, we focus on the role of AI in clinical and translational research (CTR) including pre‐clinical research (T1), clinical research (T2), clinical implementation (T3) and public (or population) health (T4). Given the rapid e...

Objective: As a long-standing Clinical and Translational Science Awards (CTSA) Program hub, the University of Pittsburgh and the University of Pittsburgh Medical Center (UPMC) developed and implemented a modern research data warehouse (RDW) to efficiently provision electronic patient data for clinical and translational research. Materials and met...

Sarcoidosis is a multisystem granulomatous disease of unknown origin with a variable and often unpredictable course and pattern of organ involvement. In this study we sought to identify specific bronchoalveolar lavage (BAL) cell gene expression patterns indicative of distinct disease phenotypic traits. RNA sequencing by Ion Torrent Proton was perfo...

Objective As a long-standing Clinical and Translational Science Awards (CTSA) Program hub, the University of Pittsburgh and the University of Pittsburgh Medical Center (UPMC) developed and implemented a modern research data warehouse (RDW) to efficiently provision electronic patient data for clinical and translational research. Methods Because UPMC...

Simple Summary Internal organs like the heart and lungs, and body cavities like the thoracic and abdominal cavities, are covered by a thin, slippery layer called the mesothelium. Malignant pleural mesothelioma (MPM) is an aggressive cancer of the lining of the lung, where genetics and asbestos exposure play a role. It is not diagnosable until it be...

Growing numbers of artificial intelligence applications are being developed and applied to pathology and laboratory medicine. These technologies introduce risks and benefits that must be assessed and managed through the lens of ethics. This article describes how long-standing principles of medical and scientific ethics can be applied to artificial...

Background Alpha-1 antitrypsin deficiency (AATD) is a genetic condition that causes early onset pulmonary emphysema and airways obstruction. The complete mechanisms via which AATD causes lung disease are not fully understood. To improve our understanding of the pathogenesis of AATD, we investigated gene expression profiles of bronchoalveolar lavage...

Sarcoidosis is a multisystem granulomatous disease of unknown origin with a variable and often unpredictable course and pattern of organ involvement. In this study we sought to identify specific bronchoalveolar lavage (BAL) cell gene expression patterns indicative of distinct disease phenotypic traits. RNA sequencing by Ion Torrent Proton was perfo...

Pathologists are adopting whole slide images (WSIs) for diagnosis, thanks to recent FDA approval of WSI systems as class II medical devices. In response to new market forces and recent technology advances outside of pathology, a new field of computational pathology has emerged that applies artificial intelligence (AI) and machine learning algorithm...

Pathologists are adopting whole slide images (WSIs) for diagnostic purposes. While doing so, pathologists should have all the information needed to make best diagnoses rapidly, while supervising computational pathology tools in real-time. Computational pathology has great potential for augmenting pathologists’ accuracy and efficiency, but concern e...

Background The National Cancer Institute Informatics Technology for Cancer Research (ITCR) program provides a series of funding mechanisms to create an ecosystem of open-source software (OSS) that serves the needs of cancer research. As the ITCR ecosystem substantially grows, it faces the challenge of the long-term sustainability of the software be...

UNSTRUCTURED The Sustainability and Industry Partnership Work Group (SIP-WG) is a part of the National Cancer Institute (NCI) Informatics Technology for Cancer Research (ITCR) program. The charter of the SIP-WG is to investigate options of long-term sustainability of open source software (OSS) developed by the ITCR, in part by developing a collecti...

Background: The burden and prognosis of malignant mesothelioma in the United States have remained largely unchanged for decades, with approximately 3200 new cases and 2400 deaths reported annually. To address care and research gaps contributing to poor outcomes, in March of 2019 the Mesothelioma Applied Research Foundation convened a workshop on t...

Background : Malignant mesothelioma (MM) is a rare but deadly malignancy with about 3,000 new cases being diagnosed each year in the US. Very few studies have been performed to analyze factors associated with mesothelioma survival, especially for peritoneal presentation. The overarching aim of this study is to examine survival of the cohort of pati...

Pathologists are adopting digital pathology for diagnosis, using whole slide images (WSIs). Explainable AI (xAI) is a new approach to AI that can reveal underlying reasons for its results; this is intended to promote safety, reliability, and accountability of machine learning for critical tasks such as pathology diagnosis. HistoMapr is a proprietar...

Introduction/background: Cancer registries in the US collect timely and systematic data on new cancer cases, extent of disease, staging, biomarker status, treatment, survival, and mortality of cancer cases. Existing methodologies for accessing local cancer registry data for research are time-consuming and often rely on the manual merging of data b...

Background : Malignant mesothelioma (MM) is a rare but deadly malignancy with about 3,000 new cases being diagnosed each year in the US. Very few studies have been performed to analyze factors associated with mesothelioma survival, especially for peritoneal presentation. The overarching aim of this study is to examine survival of the cohort of pati...

The Accrual to Clinical Trials (ACT) network is a federated network of sites from the National Clinical and Translational Science Award (CTSA) Consortium that has been created to significantly increase participant accrual to multi-site clinical trials. The ACT network represents an unprecedented collaboration among diverse CTSA sites. The network h...

Background : Malignant mesothelioma (MM) is a rare but deadly malignancy with about 3,000 new cases being diagnosed each year in the US. Very few studies have been performed to analyze factors associated with mesothelioma survival, especially for peritoneal presentation. The overarching aim of this study is to examine survival of the cohort of pati...

Gynecologic cancers pose significant morbidity and mortality burden for US women. Endometrial cancer is the most common gynecologic malignancy in the US, while ovarian cancer is one of the deadliest. Since research funding for some of the gynecologic malignancies has been limited, novel research on the existing datasets needs to be harnessed to imp...

Increased reactive species (RS; reactive oxygen and nitrogen species) are a byproduct of both enzymatic and non-enzymatic systems, and critical in cancer development, including breast tumorigenesis. To investigate the role of RS-related genes in breast cancer, expression levels of the most common annotated genes involved in regulating cellular RS l...

Background: The Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC, http://www.pcabc.upmc.edu) is one of the first major project-based initiatives stemming from the Pennsylvania Cancer Alliance that was funded for four years by the Department of Health of the Commonwealth of Pennsylvania. The objective of this was to initiate a prototyp...

Background: Patient matching is a key barrier to achieving interoperability. Patient demographic elements must be consistently collected over time and region to be valuable elements for patient matching. Objectives: We sought to determine what patient demographic attributes are collected at multiple institutions in the United States and see how...

The University of Pittsburgh's Department of Biomedical Informatics and Division of Pathology Informatics created a Science, Technology, Engineering, and Mathematics (STEM) pipeline in 2011 dedicated to providing cutting-edge informatics research and career preparatory experiences to a diverse group of highly motivated high-school students. In this...

A molecular test performed using fresh-frozen tissue was proposed for use in the prognosis of patients with pleural mesothelioma. The accuracy of the test and its properties was assessed under Clinical Laboratory Improvement Amendments-approved guidelines using FFPE tissue from an independent multicenter patient cohort. Concordance studies were per...

The importance of biomedical informatics has been proven in the pathology diagnostics over the period of a decade by meeting many challenges that has been accomplished with the improvement in clinical service, telepathology, whole slide imaging, biobanking, and academic endeavors. There is still room for improvements with joint and active participa...

The Computer Science, Biology, and Biomedical Informatics (CoSBBI) program was initiated in 2011 to expose the critical role of informatics in biomedicine to talented high school students.[1] By involving them in Science, Technology, Engineering, and Math (STEM) training at the high school level and providing mentorship and research opportunities t...

Final Computer Science, Biology, and Biomedical Informatics evaluation questionnaire

Advances in cancer research and personalized medicine will require significant new bridging infrastructures, including more robust biorepositories that link human tissue to clinical phenotypes and outcomes. In order to meet that challenge, four cancer centers formed the Text Information Extraction System (TIES) Cancer Research Network, a federated...

Sarcoidosis is a systemic disease characterized by noncaseating granulomatous inflammation with tremendous clinical heterogeneity and uncertain pathobiology and lacking in clinically useful biomarkers. The Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study is an observational cohort study designed to explore the role o...

Severe deficiency of alpha-1 antitrypsin has a highly variable clinical presentation. The GRADS Alpha-1 Study is a prospective, multicenter, cross-sectional, study of adults > age 35 with PiZZ or PiMZ alpha-1 antitrypsin genotypes designed to better understand if microbial factors influence this heterogeneity. Clinical symptoms, pulmonary function...

The Big Data to Knowledge (BD2K) Center for Causal Discovery is developing and disseminating an integrated set of open source tools that support causal modeling and discovery of biomedical knowledge from large and complex biomedical datasets. The Center integrates teams of biomedical and data scientists focused on the refinement of existing and the...

Context: We define the scope and needs within the new discipline of computational pathology, a discipline critical to the future of both the practice of pathology and, more broadly, medical practice in general. Objective: To define the scope and needs of computational pathology. Data sources: A meeting was convened in Boston, Massachusetts, in...

BAP1 is a nuclear deubiquitinase that regulates gene expression, transcription, DNA repair, and more. Several findings underscore the apparent "driver" role of BAP1 in malignant mesothelioma (MM). However the reported frequency of somatic BAP1 mutations in MM varies considerably, a discrepancy that appeared related to either methodological or ethni...

Anatomic Pathology laboratories began to encode and retrieve diagnoses from paper reports using punched cards in the 1960s. When Anatomic Pathology Laboratory Information systems (APLIS) began to be used in the 1970s, pathology departments found that searching free text for diagnoses was hindered by the variability of terms for the same concept and...

Background: Research networking systems hold great promise for helping biomedical scientists identify collaborators with the expertise needed to build interdisciplinary teams. Although efforts to date have focused primarily on collecting and aggregating information, less attention has been paid to the design of end-user tools for using these colle...

The PaTH (University of Pittsburgh/UPMC, Penn State College of Medicine, Temple University Hospital, and Johns Hopkins University) clinical data research network initiative is a collaborative effort among four academic health centers in the Mid-Atlantic region. PaTH will provide robust infrastructure to conduct research, explore clinical outcomes,...

This editorial provides insights into how informatics can attract highly trained students by involving them in science, technology, engineering, and math (STEM) training at the high school level and continuing to provide mentorship and research opportunities through the formative years of their education. Our central premise is that the trajectory...

The PaTH (University of Pittsburgh/UPMC, Penn State College of Medicine, Temple University Hospital, and Johns Hopkins University) clinical data research network initiative is a collaborative effort among four academic health centers in the Mid-Atlantic region. PaTH will provide robust infrastructure to conduct research, explore clinical outcomes,...

Endometrial cancer is the most common gynecologic malignancy in the United States but it remains poorly understood at the molecular level. This investigation was conducted to specifically assess whether gene expression changes underlie the clinical and pathologic factors traditionally used for determining treatment regimens in women with stage I en...

Transcript expression from quantitative PCR (top row) and microarray analysis (bottom row) for six selected genes (RORB, PEG3, TRH, S100A8, MELK, and DLG7) differentially expressed between endometrial carcinoma endometrioid (E), papillary serous carcinoma (PS), and normal endometrium (N).

Pathology informatics has evolved to varying levels around the world. The history of pathology informatics in different countries is a tale with many dimensions. At first glance, it is the familiar story of individuals solving problems that arise in their clinical practice to enhance efficiency, better manage (e.g., digitize) laboratory information...

The National Mesothelioma Virtual Bank (NMVB), developed six years ago, gathers clinically annotated human mesothelioma specimens for basic and clinical science research. During this period, this resource has greatly increased its collection of specimens by expanding the number of contributing academic health centers including New York University,...

The National Mesothelioma Virtual Bank (NMVB) was established to provide annotated biospecimens to the mesothelioma research community. The resource provides tissue microarrays (TMA) to evaluate the biomarkers along with a variety of other resected mesothelioma specimens. In this manuscript, we describe the immunohistochemical evaluation of the mes...

This article provides an overview of how functional genomics is likely to impact on the pathology laboratory and highlights how informatics and tissue banking will greatly facilitate the molecular age of medicine. Important aspects of functional genomics in the post-genome era, including the roles of laser capture microdissection, DNA- and compleme...

Recent advances in next-generation sequencing (NGS) methods and technology have substantially reduced costs and operational complexity leading to production of benchtop sequencers and commercial software solutions for implementation in small research and clinical laboratories. This article addresses requirements and limitations to successful implem...

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. The structure of the informatics case studies was based on the tradit...

The Human Genome Project (HGP) provided the initial draft of mankind's DNA sequence in 2001. The HGP was produced by 23 collaborating laboratories using Sanger sequencing of mapped regions as well as shotgun sequencing techniques in a process that occupied 13 years at a cost of ~$3 billion. Today, Next Generation Sequencing (NGS) techniques represe...

Biomedical informatics has made a deep impact in the overall workflow of the surgical pathology practice and has provided a variety of software tools that accelerate the overall turnaround time, cost effectiveness, and accuracy of information. Laboratory Information System functions as a single comprehensive piece of software managing laboratory wo...

Conflicting roles for Slit2, a protein involved in mediating the processes of cell migration and chemotactic response, have been previously described in prostate cancer. Here we use immunohistochemistry to evaluate the expression of Slit2 in normal donor prostate (NDP), benign prostatic hyperplasia (BPH), high-grade prostatic intraepithelial neopla...

Assessing Prior Probabilities. (DOC)

Background: A genome-wide association study (GWAS) typically involves examining representative SNPs in individuals from some population. A GWAS data set can concern a million SNPs and may soon concern billions. Researchers investigate the association of each SNP individually with a disease, and it is becoming increasingly commonplace to also analy...