Medicine and Health Sciences Commons^™

Research Data Management Readiness At Uganda Cancer Institute, Edward Mukiibi, Joyce Bukirwa

Library Philosophy and Practice (e-journal)

The study explored research data management readiness at the Uganda Cancer Institute. Its objectives were to; establish the state of research data and the institutional readiness for research data management practices. The case study applied a survey method using a questionnaire modified from the Data Asset Framework and the Community Capability Model Framework. The respondents were 60 staff members at different professional levels purposively selected. The findings show massive data generated from clinical trials, and routine cancer clinics at the institute. The business processes are mainly manual except for the funded research projects which are hybrid. The existing data sets …

A Review Of How Bioinformatics And Genome Sequencing Are Affecting Precision Medicine, Taylor S. Hickey

Honors Theses

Advancement in genomic sequencing and bioinformatics methods have been affecting biomedical research through precision medicine, especially in the area of cancer. Vaccine therapies can be developed using neoantigens that target specific mutations in tumors. The goals of this research are to identify mutations that lead to cancer and then define subpopulations in which patients can easily be identified. The future goal is to have targeted vaccines that are specific to each subpopulation ready to be used in treatment of their cancer. Limitations to reaching these goals have been due to tumor heterogeneity, cancer location, and difficulty in creating neoantigens for …

Bibliometric Analysis Of Named Entity Recognition For Chemoinformatics And Biomedical Information Extraction Of Ovarian Cancer, Vijayshri Khedkar, Charlotte Fernandes, Devshi Desai, Mansi R, Gurunath Chavan Dr, Sonali Tidke Dr., M. Karthikeyan Dr.

Library Philosophy and Practice (e-journal)

With the massive amount of data that has been generated in the form of unstructured text documents, Biomedical Named Entity Recognition (BioNER) is becoming increasingly important in the field of biomedical research. Since currently there does not exist any automatic archiving of the obtained results, a lot of this information remains hidden in the textual details and is not easily accessible for further analysis. Hence, text mining methods and natural language processing techniques are used for the extraction of information from such publications.Named entity recognition, is a subtask that comes under information extraction that focuses on finding and categorizing specific …

Meeting Overview: Interferon Lambda - Disease Impact And Therapeutic Potential, Thomas R. O'Brien, Howard A. Young, Raymond P. Donnelly, Ludmila Prokunina-Olsson

Public Health Resources

A meeting entitled, "Interferon Lambda: Disease Impact and Translational Potential," was held on the campus of the National Institutes of Health in Bethesda, Maryland, on October 25-26, 2018. To our knowledge, this was the first meeting that focused exclusively on interferon lambda (IFN-λ). The meeting's purpose was to enhance interdisciplinary communication and promote new collaborations. The gathering brought together an international group of scientists from a wide range of disciplines. Sessions included: IFN-λ Biology, Therapy and Genetic Variation; IFN-λ and Hepatitis C Virus Infection; IFN-λ in Other Infections; and IFN-λ - Hepatic Fibrosis and Cancer. The next meeting on IFN-λ …

Endoglin Protein Interactome Profiling Identifies Trim21 And Galectin-3 As New Binding Partners, Eunate Gallardo-Vara, Lidia Ruiz-Llorente, Juan Casado-Vela, María J. Ruiz-Rodríguez, Natalia López-Andrés, Asit K. Pattnaik, Miguel Quintanilla

School of Veterinary and Biomedical Sciences: Faculty Publications

Endoglin is a 180-kDa glycoprotein receptor primarily expressed by the vascular endothelium and involved in cardiovascular disease and cancer. Heterozygous mutations in the endoglin gene (ENG) cause herediatry hemorrhagic telangiectasia type 1, a vascular disease that presents with nasal and gastrointestinal bleeding, skin and mucosa telangiectase, and arteriovenous malformations in internal organs. A circulating form of endoglin (alias soluble endoglin, sEng), proteolytically released from the membrane-bound protein, has been observed in several inflammation-related pathological conditions and appears to contribute to endothelial dysfunction and cancer development through unknown mechanisms. Membrane-bound endoglin is an auxiliary component of the TGF-B receptor complex and …

Distributed Cognition In Cancer Treatment Decision Making: An Application Of The Decide Decision-Making Styles Typology, Janice L. Krieger, Jessica L. Krok-Schoen, Phokeng M. Dailey, Angela L. Palmer-Wackerly, Nancy Schoenberg, Electra D. Paskett, Mark Dignan

Department of Communication Studies: Faculty Publications

Distributed cognition occurs when cognitive and affective schemas are shared between two or more people during interpersonal discussion. Although extant research focuses on distributed cognition in decision making between health care providers and patients, studies show that caregivers are also highly influential in the treatment decisions of patients. However, there are little empirical data describing how and when families exert influence. The current article addresses this gap by examining decisional support in the context of cancer randomized clinical trial (RCT) decision making. Data are drawn from in-depth interviews with rural, Appalachian cancer patients (N = 46). Analysis of transcript …

Short Course In The Microbiome, Kimberly Falana, Rob Knight, Camilia R. Martin, Romina Goldszmid, K. Leigh Greathouse, Joanne Gere, Howard Young, Winston Patrick Kuo

Public Health Resources

Over the past decade, it has become evident that the microbiome is an important environmental factor that affects many physiological processes, such as cell proliferation and differentiation, behaviour, immune function and metabolism. More importantly, it may contribute to a wide variety of diseases, including cancer, inflammatory diseases, metabolic diseases and responses to pathogens. We expect that international, integrative and interdisciplinary translational research teams, along with the emergence of FDA-approved platforms, will set the framework for microbiome-based therapeutics and diagnostics. We recognize that the microbiome ecosystem offers new promise for personalized/precision medicine and targeted treatment for a variety of diseases. The …

Data Mining The Functional Characterizations Of Proteins To Predict Their Cancer-Relatedness, Peter Revesz, Christopher Assi

School of Computing: Faculty Publications

This paper considers two types of protein data. First, data about protein function described in a number of ways, such as, GO terms and PFAM families. Second, data about whether individual proteins are experimentally associated with cancer by an anomalous elevation or lowering of their expressions within cancerous cells. We combine these two types of protein data and test whether the first type of data, that is, the functional descriptors, can predict the second type of data, that is, cancer-relatedness. By using data mining and machine learning, we derive a classifier algorithm that using only GO term and PFAM family …

Annual Report To The Nation On The Status Of Cancer, 1975-2008, Featuring Cancers Associated With Excess Weight And Lack Of Sufficient Physical Activity, Christie Eheman, S. Jane Henley, Rachel Ballard-Barbash, Eric J. Jacobs, Maria J. Schymura, Anne-Michelle Noone, Liping Pan, Robert N. Anderson, Janet E. Fulton, Betsy A. Kohler, Ahmedin Jemal, Elizabeth Ward, Marcus Plescia, Lynn A. G. Ries, Brenda K. Edwards

Public Health Resources

BACKGROUND: Annual updates on cancer occurrence and trends in the United States are provided through collaboration between the American Cancer Society (ACS), the Centers for Disease Control and Prevention (CDC), the National Cancer Institute (NCI), and the North American Association of Central Cancer Registries (NAACCR). This year’s report highlights the increased cancer risk associated with excess weight (overweight or obesity) and lack of sufficient physical activity (<150 minutes of physical activity per week).

METHODS: Data on cancer incidence were obtained from the CDC, NCI, and NAACCR; data on cancer deaths were obtained from the CDC’s National Center for Health Statistics. Annual percent changes in …

Incidence Of Cancers Of The Oral Cavity And Pharynx Among American Indians And Alaska Natives, 1999–2004, Marsha E. Reichman, Janet J. Kelly, Carol L. Kosary, Steven S. Coughlin, Melissa Jim, Anne P. Lanier

Public Health Resources

BACKGROUND. Previous studies identified disparities in incidence rates of cancers of the oral cavity and pharynx between American Indians/Alaska Natives (AI/AN) and non-Hispanic whites (NHW) and differences between various AI/AN populations. Reporting among AI/AN has been hampered by: 1) heterogeneity among various anatomic sites of oral cavity and pharyngeal cancers obscuring unique patterns of individual anatomic sites; 2) race misclassification and under-reporting of AI/AN; and 3) sparseness of data needed to identify regional variations.

METHODS. To improve race classification of AI/AN, data from US central cancer registries were linked with Indian Health Service (IHS) records. AI/AN incidence data …

Gastric Cancer Among American Indians And Alaska Natives In The United States, 1999–2004, Charles Wiggins, David G. Perdue, Jeffrey A. Henderson, Michael G. Bruce, Anne P. Lanier, Janet J. Kelly, Brenda F. Seals, David K. Espey

Public Health Resources

BACKGROUND. Gastric cancer incidence rates for American Indians and Alaska Natives (AI/ANs) historically have exceeded those for non-Hispanic whites (NHWs). Previous reports may have underestimated the true burden of gastric cancer in AI/AN populations because of misclassification of AI/AN race in cancer registries.

METHODS. Population-based cancer registry data from 1999 through 2004 were used to describe gastric cancer incidence in AI/ANs and NHWs in the US. To address misclassification of race, registry data were linked with Indian Health Service administrative records, and analyses were restricted to residents of Contract Health Service Delivery Areas (CHSDA). Disease patterns were assessed …

Cancer In American Indian And Alaska Native Young Adults (Ages 20–44 Years): Us, 1999–2004, Hannah K. Weir, Melissa Jim, Loraine D. Marrett, Temeika L. Fairley

Public Health Resources

BACKGROUND. An examination of cancer incidence patterns in American Indians and Alaska Native (AI/AN) young adults may provide insight into their present and future cancer burden.

METHODS. To reduce racial misclassification, incidence data were linked with the Indian Health Service (IHS) patient services database. Age-adjusted cancer incidence rates per 100,000 (AAR) and corresponding rate ratios (RR) for young adults (ages 20-44 years) were compared across IHS regions and for selected cancers within Contract Health Service Delivery Area counties by race (AI/AN vs non-Hispanic whites [NHW]) and sex.

RESULTS. The all-sites cancer incidence rate was lower for AI/ANs …

Lung Cancer Incidence Among American Indians And Alaska Natives In The United States, 1999–2004, Anne Bliss, Nathaniel Cobb, Teshia Solomon, Kym Cravatt, Melissa A. Jim, Latisha Marshall, Janis Campbell

Public Health Resources

BACKGROUND. Lung cancer incidence rates among American Indians and Alaska Natives (AI/ANs) in the United States have not been described well, primarily because of race misclassification and, until the 1990s, incomplete coverage of their population by cancer registries. Smoking, the predominant cause of lung cancer, is particularly prevalent among this population.

METHODS. Data from the National Program of Cancer Registries and the Surveillance, Epidemiology, and End Results Program were combined to estimate age adjusted incidence rates of lung cancer during 1999 through 2004. Cases were linked to Indian Health Service (IHS) registration databases to identify AI/ANs whose race …

Methods For Improving Cancer Surveillance Data In American Indian And Alaska Native Populations, David K. Espey, Charles Wiggins, Melissa A. Jim, Barry A. Miller, Christopher J. Johnson, Tom M. Becker

Public Health Resources

BACKGROUND. The misclassification of race decreases the accuracy of cancer incidence data for American Indians and Alaska Natives (AI/ANs) in some central cancer registries. This article describes the data sources and methods that were used to address this misclassification and to produce the cancer statistics used by most of the articles in this supplement.

METHODS. Records from United States cancer registries were linked with Indian Health Service (IHS) records to identify AI/AN cases that were misclassified as non-AI/AN. Data were available from 47 registries that linked their data with IHS, met quality criteria, and agreed to participate. Analyses …

Prostate Cancer Incidence Among American Indian And Alaska Native Men, Us, 1999–2004, Jeffrey A. Henderson, David K. Espey, Melissa Jim, Robert R. German, Kate M. Shaw, Richard M. Hoffman

Public Health Resources

BACKGROUND. American Indian and Alaska Native (AI/AN) men experience lower incidence of prostate cancer than other race/ethnic populations in the US, but racial misclassification of AI/AN men threatens the validity of these estimates. To the authors’ knowledge, little is known concerning prostate-specific antigen (PSA) testing in AI/AN men.

METHODS. The authors linked cancer registry data with Indian Health Service enrollment records to improve race classification. Analyses comparing cancer incidence rates and stage at diagnosis for AI/AN and non-Hispanic white (NHW) men for 6 geographic regions focused on counties known to have less race misclassification. The authors also used …

Using Population-Based Cancer Registry Data To Assess The Burden Of Human Papillomavirus-Associated Cancers In The United States: Overview Of Methods, Meg Watson, Mona Saraiya, Faruque Ahmed, Cheryll J. Cardinez, Marsha E. Reichman, Hannah K. Weir, Thomas B. Richards

Public Health Resources

Increased attention to human papillomavirus (HPV)-associated cancers in light of the recent release of an HPV vaccine, as well as increased availability of cancer registry data that now include reporting from a large proportion of the US population, prompted the current assessment of HPV-associated cancers. This article describes methods used to assess the burden of HPV-associated cervical, vulvar, vaginal, penile, anal, and oral cavity/oropharyngeal cancers in the United States during 1998 through 2003 using cancer registry data, and it provides a brief overview of the epidemiology of these cancers.

Persistent infection with the human papillomavirus (HPV) is considered to be …

Cancer Among American Indians And Alaska Natives In The United States, 1999–2004, Charles Wiggins, David K. Espey, Phyllis A. Wingo, Judith S. Kaur, Robin Taylor Wilson, Judith Swan, Barry A. Miller, Melissa Jim, Janet J. Kelly, Anne P. Lanier

Public Health Resources

BACKGROUND. Cancer incidence rates vary among American Indian and Alaska Native (AI/AN) populations and often differ from rates among non-Hispanic whites (NHWs). However, the misclassification of race for AI/AN cancer cases in central cancer registries may have led to underestimates of the AI/AN cancer burden in previous reports.

METHODS. Cases diagnosed during 1999 through 2004 were identified from population- based cancer registries in the United States. Age-adjusted rates were calculated for the 25 most common sites for AI/ANs and NHWs. To minimize the misclassification of race, cancer registry records were linked with patient registration files from the Indian …

Chlorothalonil Exposure And Cancer Incidence Among Pesticideapplicator Participants In The Agricultural Health Study, Alicia M. Mozzachio, Jennifer A. Rusiecki, Jane A. Hoppin, Rajeev Mahajan, Rahulkumar Patel, Laura Beane-Freeman, Michael Cr Alavanja

Uniformed Services University of the Health Sciences

Background: Chlorothalonil is a broad spectrum, non-systemic fungicide widely used to control diseases affecting over 50 fruit, vegetable, and agricultural crops. Despite its extensive use for over 30 years, little is known about the potential human carcinogenicity associated with the routine application of chlorothalonil. Rodent studies have shown evidence of renal tubular carcinomas and adenomas. We explored cancer incidence with chlorothalonil exposure using data from the Agricultural Health Study, a prospective cohort of licensed pesticide applicators in Iowa and North Carolina.
Methods: Licensed private and commercial pesticide applicators were recruited into this study from 1993 to 1997. Detailed information regarding …

Annual Report To The Nation On The Status Of Cancer, 1975–2004, Featuring Cancer In American Indians And Alaska Natives, David K. Espey, Xiao-Cheng Wu, Judith Swan, Charles Wiggins, Melissa A. Jim, Elizabeth Ward, Phyllis A. Wingo, Holly L. Howe, Lynn A. G. Ries, Barry A. Miller, Ahmedin Jemal, Faruque Ahmed, Nathaniel Cobb, Judith S. Kaur, Brenda K. Edwards

Public Health Resources

BACKGROUND. The American Cancer Society, the Centers for Disease Control and Prevention, the National Cancer Institute, and the North American Association of Central Cancer Registries collaborate annually to provide updated information on cancer occurrence and trends in the U.S. The 2007 report features a comprehensive compilation of cancer information for American Indians and Alaska Natives (AI/AN).

METHODS. Cancer incidence data were available for up to 82% of the U.S. population. Cancer deaths were available for the entire U.S. population. Long-term (1975 through 2004) and fixed-interval (1995 through 2004) incidence and mortality trends were evaluated by annual percent change …

Annual Report To The Nation On The Status Of Cancer, 1975–2003, Featuring Cancer Among U.S. Hispanic/ Latino Populations, Holly L. Howe, Xiao-Cheng Wu, Lynn A. G. Ries, Vilma Cokkinides, Faruque Ahmed, Ahmedin Jemal, Barry A. Miller, Melanie Williams, Elizabeth Ward, Phyllis A. Wingo, Amelie Ramirez, Brenda K. Edwards

Public Health Resources

BACKGROUND. The American Cancer Society, Centers for Disease Control and Prevention, National Cancer Institute, and North American Association of Central Cancer Registries collaborate annually to provide U.S. cancer information, this year featuring the first comprehensive compilation of cancer information for U.S. Latinos.

METHODS. Cancer incidence was obtained from 90% of the Hispanic/Latino and 82% of the U.S. populations. Cancer deaths were obtained for the entire U.S. population. Cancer screening, risk factor, incidence, and mortality data were compiled for Latino and non-Latino adults and children (incidence only). Long-term (1975– 2003) and fixed-interval (1995–2003) trends and comparative analyses by disease …

Colorectal Cancer In U.S. Adults Younger Than 50 Years Of Age, 1998--2001, Temeika L. Fairley, Cheryll J. Cardinez, Jim Martin, Linda Alley, Carol Friedman, Brenda K. Edwards, Patricia Jamison

Public Health Resources

BACKGROUND. Colorectal cancer (CRC) incidence rates are increasing among persons younger than 50 years of age, a population routinely not screened unless an individual has a high risk of CRC. This population-based study focuses primarily on describing the CRC burden for persons in this age group.

METHODS. The data used for this study were derived from the National Program of Cancer Registries (NPCR) and Surveillance, Epidemiology, and End Results (SEER) surveillance systems. Age-adjusted incidence rates, rate ratios, and their corresponding 95% confidence intervals were calculated.

RESULTS. CRC is ranked among the top 10 cancers occurring in males …

Analysis Of 200 Food Items For Benzo[A]Pyrene And Estimation Of Its Intake Ίη An Epidemiologic Study, Ν. Kazerouni, R. Sinha, Che-Han Hsu, Α. Greenberg, Ν. Rothman

Public Health Resources

Animal stιιdies have shown that dietary intake of benzo[α]pyrene (BaP), a polycyclic aromatic hydrocarbon (ΡΑΗ), causes increased levels of tumors at several sites, particιιlarly ίη the upper gastrointestinal tract. However, the role of dietary intake of BaP and cancer ίη humans is not clear. We CIeated a BaP database of selected food products that could be lίnl(ed to Food Frequency Qnestionnaires (FFQs) to estimate BaP intake. BaP levels were measnred for each food line-item (composite samples) which consisted of a variety of foods ίη a FFQ. Composite sample parts were derived from the Second National Health and Nutrition Examination Survey …