An Interoperable Similarity-based Cohort Identification Method Using the OMOP Common Data Model version 5.0.

Cohort identification for clinical studies tends to be laborious, time-consuming, and expensive. Developing automated or semi-automated methods for cohort identification is one of the "holy grails" in the field of biomedical informatics. We propose a high-throughput similarity-based cohort identification algorithm by applying numerical abstractions on Electronic Health Records (EHR) data.

EliIE: An open-source information extraction system for clinical trial eligibility criteria.

Objective: To develop an open-source information extraction system called Eligibility Criteria Information Extraction (EliIE) for parsing and formalizing free-text clinical research eligibility criteria (EC) following Observational Medical Outcomes Partnership Common Data Model (OMOP CDM) version 5.0.

Materials And Methods: EliIE parses EC in 4 steps: (1) clinical entity and attribute recognition, (2) negation detection, (3) relation extraction, and (4) concept normalization and output structuring.

A multi-site cognitive task analysis for biomedical query mediation.

Objective: To apply cognitive task analyses of the Biomedical query mediation (BQM) processes for EHR data retrieval at multiple sites towards the development of a generic BQM process model.

Materials And Methods: We conducted semi-structured interviews with eleven data analysts from five academic institutions and one government agency, and performed cognitive task analyses on their BQM processes. A coding schema was developed through iterative refinement and used to annotate the interview transcripts.

A data-driven concept schema for defining clinical research data needs.

Objectives: The Patient, Intervention, Control/Comparison, and Outcome (PICO) framework is an effective technique for framing a clinical question. We aim to develop the counterpart of PICO to structure clinical research data needs.

Methods: We use a data-driven approach to abstracting key concepts representing clinical research data needs by adapting and extending an expert-derived framework originally developed for defining cancer research data needs.

Facilitating biomedical researchers' interrogation of electronic health record data: Ideas from outside of biomedical informatics.

Electronic health records (EHR) are a vital data resource for research uses, including cohort identification, phenotyping, pharmacovigilance, and public health surveillance. To realize the promise of EHR data for accelerating clinical research, it is imperative to enable efficient and autonomous EHR data interrogation by end users such as biomedical researchers. This paper surveys state-of-art approaches and key methodological considerations to this purpose.

Use of Self-Service Query Tools Varies by Experience and Research Knowledge.

The lack of understanding of user experience with self-service query tools is a barrier to designing effective query tools and is what propelled this study. User actions were documented and transformed into networks of actions for qualitative analysis. Proficient use of self-service query tools requires significant technical experience.

Toward a cognitive task analysis for biomedical query mediation.

In many institutions, data analysts use a Biomedical Query Mediation (BQM) process to facilitate data access for medical researchers. However, understanding of the BQM process is limited in the literature. To bridge this gap, we performed the initial steps of a cognitive task analysis using 31 BQM instances conducted between one analyst and 22 researchers in one academic department.

What Is Asked in Clinical Data Request Forms? A Multi-site Thematic Analysis of Forms Towards Better Data Access Support.

Many academic medical centers have aggregated data from multiple clinical systems into centralized repositories. These repositories can then be queried by skilled data analysts who act as intermediaries between the data stores and the research teams. To obtain data, researchers are often expected to complete a data request form.

Characterization of the biomedical query mediation process.

To most medical researchers, databases are obscure black boxes. Query analysts are often indispensable guides aiding researchers to perform mediated data queries. However, this approach does not scale up and is time-consuming and expensive.

An Integrated Model for Patient Care and Clinical Trials (IMPACT) to support clinical research visit scheduling workflow for future learning health systems.

We describe a clinical research visit scheduling system that can potentially coordinate clinical research visits with patient care visits and increase efficiency at clinical sites where clinical and research activities occur simultaneously. Participatory Design methods were applied to support requirements engineering and to create this software called Integrated Model for Patient Care and Clinical Trials (IMPACT). Using a multi-user constraint satisfaction and resource optimization algorithm, IMPACT automatically synthesizes temporal availability of various research resources and recommends the optimal dates and times for pending research visits.

A centralized research data repository enhances retrospective outcomes research capacity: a case report.

This paper describes our considerations and methods for implementing an open-source centralized research data repository (CRDR) and reports its impact on retrospective outcomes research capacity in the urology department at Columbia University. We performed retrospective pretest and post-test analyses of user acceptance, workflow efficiency, and publication quantity and quality (measured by journal impact factor) before and after the implementation. The CRDR transformed the research workflow and enabled a new research model.

Socioeconomic and clinical factors influence the interval between positive prostate biopsy and radical prostatectomy.

Objective: To examine socioeconomic and clinical factors that may predict a longer interval between prostate biopsy and radical prostatectomy (RP).

Methods: The Columbia University Urologic Oncology Database was queried for patients who underwent RP from 1990-2010. Time to surgery (TTS) was defined as the period between the most recent positive prostate biopsy and date of surgery.

Partial nephrectomy online: a preliminary evaluation of the quality of health information on the Internet.

Unlabelled: What's known on the subject? and What does the study add? Patients are highly likely to access the Internet for health information, and studies have reported that inaccurate or low-quality information may alter patients' expectations and negatively impact informed decision-making. In a unique collaboration with the Health On the Internet (HON) Foundation, we evaluated the top 20 search results for the urology search term 'partial nephrectomy,' and identified the highest and lowest scoring criteria to increase awareness of areas of concern and improvement.

Objective: To further evaluate the quality of information available on the Internet with regard to the management of localized renal cancer, we evaluated websites providing information on 'partial nephrectomy' in conjunction with the Health On the Internet (HON) Foundation.

Pathological confirmation of nerve-sparing types performed during robot-assisted radical prostatectomy (RARP).

Unlabelled: WHAT'S KNOWN ON THE SUBJECT? AND WHAT DOES THE STUDY ADD?: Incremental nerve-sparing techniques (NSTs) improve postoperative erectile function after robot-assisted radical prostatectomy (RARP). However, there are no studies to date that histologically confirm the surgeon intended NST. Thus, in the present study, we histologically confirmed that the surgeon performed the nerve preservation as his intended NSTs during RARP.

Comparison of two core biopsy techniques before and after laparoscopic cryoablation of small renal cortical neoplasms.

Introduction: Cryoablation is an acceptable treatment option for small renal cortical neoplasms (RCN). Unlike extirpative interventions, intraoperative needle biopsy is the only pathologic data for ablated tumors. It is imperative that sampled tissue accurately captures pathology.

Comparison of biochemical failure definitions for predicting local cancer recurrence following cryoablation of the prostate.

Background: Various definitions of biochemical failure (BF) have been used to predict cancer recurrence following prostate cryoablation. However to date, none of these definitions have been validated for this use. We have reviewed several definitions of BF to determine their accuracy in predicting biopsy-proven local recurrence following prostate cryoablation.

Prognostic indicators for upper tract urothelial carcinoma after radical nephroureterectomy: the impact of lymphovascular invasion.

Unlabelled: What's known on the subject? and What does the study add? In an array of urological and non-urological malignancies, lymphovascular invasion (LVI) is a pathological feature known to be associated with adverse outcomes for recurrence and survival. For some cancers, LVI has therefore been incorporated into American Joint Committee on Cancer TNM staging algorithms. This study presents an analysis of the impact of LVI in upper urinary tract urothelial carcinoma (UTUC) treated at our institution over a 20-year period.

Dysregulation of circulating microRNAs and prediction of aggressive prostate cancer.

Background: It is becoming increasingly evident that microRNAs (miRNAs) are associated with the development and progression of prostate cancer (PCa).

Methods: We examined the hypothesis that plasma miRNA levels can differentiate patients by aggressiveness in 82 PCa patients. Taqman based quantitative RT-PCR assays were performed to measure copy number of target miRNAs.

Evaluating the quality of Internet health resources in pediatric urology.

Purpose: Many patients and their parents utilize the Internet for health-related information, but quality is largely uncontrolled and unregulated. The Health on the Net Foundation Code (HONcode) and DISCERN Plus were used to evaluate the pediatric urological search terms 'circumcision,' 'vesicoureteral reflux' and 'posterior urethral valves'.

Materials And Methods: A google.

Effect of delaying surgery on radical prostatectomy outcomes: a contemporary analysis.

Unlabelled: Study Type - Therapy (case series). Level of Evidence 4. What's known on the subject? and What does the study add? For patients electing surgical treatment, the question of the effect of surgical delay on clinical outcomes in prostate cancer is controversial.

Vitamin D deficiency in the urological population: a single center analysis.

Purpose: Vitamin D has a well-known role in calcium metabolism and bone health. It may also help prevent a number of chronic diseases, including cardiovascular disease, diabetes and malignancies such as breast, colorectal and prostate cancer. To our knowledge the prevalence of vitamin D deficiency has never been reported in the general urological population.

Tumour diameter and decreased preoperative estimated glomerular filtration rate are independently correlated in patients with renal cell carcinoma.

Objective: To examine the relationship between tumour diameter and estimated GFR (eGFR) in patients with renal cell carcinoma (RCC).

Patients And Methods: In total, 1009 patients undergoing partial or radical nephrectomy for unilateral RCC were identified in the Columbia Urologic Database. eGFR was calculated using the modification of diet in renal disease equation using demographic data and preoperative serum creatinine values.

DNA methylation changes correlate with Gleason score and tumor stage in prostate cancer.

DNA methylation, a widely used epigenetic mark, has been associated with many tumors. However, few studies have addressed the role of cell-free plasma DNA methylation in discriminating aggressive prostate cancer (PCa) from indolent cases. We conducted a case series and a case-control study among histologically confirmed stage II/III cases and matched controls recruited at Columbia University Medical Center.

Evaluation of bioimpedance as novel predictor of extracorporeal shockwave lithotripsy success.

Background And Purpose: Obesity has been identified as a limitation of extracorporeal shockwave lithotripsy (SWL). The obesity metrics of body mass index (BMI) and skin-to-stone distance (SSD) have been evaluated as predictors of SWL success. While SSD has demonstrated a strong correlation with success, BMI has not.