An Integrated Oncology Data Warehouse for Clinical Decision Support and Complex Patient Cohort Identification in a Hybrid Cancer Center

BACKGROUND: A data warehouse is a repository that centralizes and integrates data from disparate systems to provide the ability to easily access historical, consistent data. Integration of disparate source systems into one centralized location can enable rapid identification of more robust research cohorts and enable data-driven decision making. The objective of the Miami Cancer Institute (MCI) Oncology Data Warehouse (ODW) is to collect and organize data from clinical records, research, and administrative systems to support information retrieval, business intelligence, and analytics for high-level decision making for oncology patients. The design, architecture, and implementation aligns with industry best practices which includes Data Governance, Enterprise Data Modeling, and Metadata Management. METHODS: We integrated structured and unstructured data from disparate sources into one centralized data model optimized for querying known as the ODW. The ODW is modeled as a star schema, with fact tables and conformed dimension tables, and expands to a galaxy schema with constellation facts and dimensions that can snowflake to other data models as needed. Each fact table represents a subject area (i.e. pathology), that is directly related to the conformed dimension tables using surrogate and foreign keys. Conformed dimensions represent the attributes associated to the subject area (i.e. date of encounter). The source data is extracted, transformed and loaded (ETL) automatically from different databases into a set of tables. The ETL code performs incremental loads at regular prescribed intervals into two parallel storage areas, a relational database management system (RDMS) as well as a Big Data file storage system. RESULTS: An interdisciplinary team of physicians, engineers, scientists, and subject matter experts at the Miami Cancer Institute of Baptist Health South Florida, has designed, developed, and implemented the ODW with information originating from different data sources which include: Electronic Medical Record (EMR) systems, Financial Systems, Clinical Trial Management Systems, Tumor Registries, Biospecimen Repositories, Pathology synoptic reports and archives, and Next Generation Sequencing services. Structurally it is a subject-oriented, integrated collection of data leveraging conformed dimensions. The ODW is capable of connecting most business intelligence (i.e. Tableau) or statistical (i.e. SAS) tools for automated or static report development. CONCLUSION: The growing ODW enables physicians, clinical management teams, and medical analysts to systematically mine and review the molecular, genomic, and associated clinical or administrative information of patients, and identify patterns that may influence treatment decisions and potential outcomes. By implementing an innovative combination of technology tools and methods, we were able to organize enterprise information about oncology patients which can be utilized for clinical decision support and precision medicine use cases

A national surveillance project on chronic kidney disease management in Canadian primary care: a study protocol.

INTRODUCTION: Effective chronic disease care is dependent on well-organised quality improvement (QI) strategies that monitor processes of care and outcomes for optimal care delivery. Although healthcare is provincially/territorially structured in Canada, there are national networks such as the Canadian Primary Care Sentinel Surveillance Network (CPCSSN) as important facilitators for national QI-based studies to improve chronic disease care. The goal of our study is to improve the understanding of how patients with chronic kidney disease (CKD) are managed in primary care and the variation across practices and provinces and territories to drive improvements in care delivery. METHODS AND ANALYSIS: The CPCSSN database contains anonymised health information from the electronic medical records for patients of participating primary care practices (PCPs) across Canada (n=1200). The dataset includes information on patient sociodemographics, medications, laboratory results and comorbidities. Leveraging validated algorithms, case definitions and guidelines will help define CKD and the related processes of care, and these enable us to: (1) determine prevalent CKD burden; (2) ascertain the current practice pattern on risk identification and management of CKD and (3) study variation in care indicators (eg, achievement of blood pressure and proteinuria targets) and referral pattern for specialist kidney care. The process of care outcomes will be stratified across patients' demographics as well as provider and regional (provincial/territorial) characteristics. The prevalence of CKD stages 3-5 will be presented as age-sex standardised prevalence estimates stratified by province and as weighted averages for population rates with 95% CIs using census data. For each PCP, age-sex standardised prevalence will be calculated and compared with expected standardised prevalence estimates. The process-based outcomes will be defined using established methods. ETHICS AND DISSEMINATION: The CPCSSN is committed to high ethical standards when dealing with individual data collected, and this work is reviewed and approved by the Network Scientific Committee. The results will be published in peer-reviewed journals and presented at relevant national and international scientific meetings

The European Registered Toxicologist (ERT) : Current status and prospects for advancement

Acknowledgements We would like to thank the participants of the five workshops in which the issues presented in this paper were discussed and the revised guidelines prepared, as well as the EUROTOX Executive Committee and the societies of toxicology of Sweden, the Netherlands, Switzerland, Austria and France for their support which allowed the workshops to take place.Peer reviewedPostprin

Utilization of ancillary studies in the cytologic diagnosis of respiratory lesions: The papanicolaou society of cytopathology consensus recommendations for respiratory cytology

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134863/1/dc23549.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134863/2/dc23549_am.pd

Mangroves enhance the biomass of coral reef fish communities in the Caribbean

Mangrove forests are one of the world's most threatened tropical ecosystems with global loss exceeding 35% (ref. 1). Juvenile coral reef fish often inhabit mangroves, but the importance of these nurseries to reef fish population dynamics has not been quantified. Indeed, mangroves might be expected to have negligible influence on reef fish communities: juvenile fish can inhabit alternative habitats and fish populations may be regulated by other limiting factors such as larval supply or fishing. Here we show that mangroves are unexpectedly important, serving as an intermediate nursery habitat that may increase the survivorship of young fish. Mangroves in the Caribbean strongly influence the community structure of fish on neighbouring coral reefs. In addition, the biomass of several commercially important species is more than doubled when adult habitat is connected to mangroves. The largest herbivorous fish in the Atlantic, Scarus guacamaia, has a functional dependency on mangroves and has suffered local extinction after mangrove removal. Current rates of mangrove deforestation are likely to have severe deleterious consequences for the ecosystem function, fisheries productivity and resilience of reefs. Conservation efforts should protect connected corridors of mangroves, seagrass beds and coral reefs

Evaluating the utility of B/Ca ratios in planktic foraminifera as a proxy for the carbonate system: A case study of Globigerinoides ruber

B/Ca ratios in foraminifera have attracted considerable scientific attention as a proxy for past ocean carbonate system. However, the carbonate system controls on B/Ca ratios are not straightforward, with ?[ inline image] ([ inline image]in situ – [ inline image]at saturation) correlating best with B/Ca ratios in benthic foraminifera, rather than pH, inline image, or inline image (as a simple model of boron speciation in seawater and incorporation into CaCO3 would predict). Furthermore, culture experiments have shown that in planktic foraminifera properties such as salinity and [B]sw can have profound effects on B/Ca ratios beyond those predicted by simple partition coefficients. Here, we investigate the controls on B/Ca ratios in G. ruber via a combination of culture experiments and core-top measurements, and add to a growing body of evidence that suggests B/Ca ratios in symbiont-bearing foraminiferal carbonate are not a straightforward proxy for past seawater carbonate system conditions. We find that while B/Ca ratios in culture experiments covary with pH, in open ocean sediments this relationship is not seen. In fact, our B/Ca data correlate best with [ inline image] (a previously undocumented association) and in most regions, salinity. These findings might suggest a precipitation rate or crystallographic control on boron incorporation into foraminiferal calcite. Regardless, our results underscore the need for caution when attempting to interpret B/Ca records in terms of the ocean carbonate system, at the very least in the case of mixed-layer planktic foraminifera

Functioning of patients with chronic idiopathic axonal polyneuropathy (CIAP)

Although patients with Chronic Idiopathic Axonal Polyneuropathy (CIAP) report a slow deterioration of sensory and motor functions, the impact of this deterioration on daily functioning has not yet been investigated in detail. The first aim of this crosssectional study involving 56 patients with CIAP was, therefore, to assess patients’ functioning with use of the International Classification of Functioning, Disability and Health (ICF). The second aim was to find determinants of walking ability, dexterity, and autonomy. Fatigue and limited walking ability were present in most patients and differed considerably. In regression models, age, muscle strength, and fatigue together explained 63% of the variance in walking ability, which by itself explained almost 50% of the variance in patients’ autonomy indoors and outdoors (42% and 49%, respectively). Muscle strength and sensory function scores together explained 30% of the variance in dexterity scores, which in turn explained only 13% of the variance in autonomy indoors. The diminished autonomy of patients with CIAP might be improved by reducing fatigue, by means of training, and by improving walking ability

The dangers of using intention as a surrogate for Retention in brand positioning decision support systems

The purpose of this paper is to explore the dangers of using intention as a surrogate for retention in a decision support system (DSS) for brand positioning. An empirical study is conducted, using structural equations modeling and both data from the internal transactional database and a survey. The study is aimed at evaluating whether the DSS recommends different product benefits for brand positioning when intention is used as opposed to retention as a criterion variable. The results show that different product benefits are recommended contingent upon the criterion variable (intention vs. retention). The findings also indicate that the strength of the structural relationships is inflated when intention is used. This study is limited in that it investigates only one industry; the newspaper industry. This study provides guidance for brand managers in selecting the most appropriate benefit for brand positioning and advices against the use of intention as opposed to retention in DSS. To the best of our knowledge this study is the first to challenge and refute the commonly held belief that intention is a valid surrogate for retention in a DSS for brand positioning