Comparison of orthogonal NLP methods for clinical phenotyping and assessment of bone scan utilization among prostate cancer patients.

OBJECTIVE: Clinical care guidelines recommend that newly diagnosed prostate cancer patients at high risk for metastatic spread receive a bone scan prior to treatment and that low risk patients not receive it. The objective was to develop an automated pipeline to interrogate heterogeneous data to evaluate the use of bone scans using a two different Natural Language Processing (NLP) approaches. MATERIALS AND METHODS: Our cohort was divided into risk groups based on Electronic Health Records (EHR). Information on bone scan utilization was identified in both structured data and free text from clinical notes. Our pipeline annotated sentences with a combination of a rule-based method using the ConText algorithm (a generalization of NegEx) and a Convolutional Neural Network (CNN) method using word2vec to produce word embeddings. RESULTS: A total of 5500 patients and 369,764 notes were included in the study. A total of 39% of patients were high-risk and 73% of these received a bone scan; of the 18% low risk patients, 10% received one. The accuracy of CNN model outperformed the rule-based model one (F-measure = 0.918 and 0.897 respectively). We demonstrate a combination of both models could maximize precision or recall, based on the study question. CONCLUSION: Using structured data, we accurately classified patients' cancer risk group, identified bone scan documentation with two NLP methods, and evaluated guideline adherence. Our pipeline can be used to provide concrete feedback to clinicians and guide treatment decisions.

Dilution Factor of Quantitative Bacterial Cultures Obtained by Bronchoalveolar Lavage in Patients with Ventilator-Associated Bacterial Pneumonia.

Ventilator-associated bacterial pneumonia (VABP) is a difficult therapeutic problem. Considerable controversy exists regarding the optimal chemotherapy for this entity. The recent guidelines of the Infectious Diseases Society of America and the American Thoracic Society recommend a 7-day therapeutic course for VABP based on the balance of no negative impact on all-cause mortality, less resistance emergence, and fewer antibiotic treatment days, counterbalanced with a higher relapse rate for patients whose pathogen is a nonfermenter. The bacterial burden causing an infection has a substantial impact on treatment outcome and resistance selection. We describe the baseline bronchoalveolar lavage (BAL) fluid burden of organisms in suspected VABP patients screened for inclusion in a clinical trial. We measured the urea concentrations in plasma and BAL fluid to provide an index of the dilution of the bacterial and drug concentrations in the lung epithelial lining fluid introduced by the BAL procedure. We were then able to calculate the true bacterial burden as the diluted colony count times the dilution factor. The median dilution factor was 28.7, with the interquartile range (IQR) being 11.9 to 53.2. Median dilution factor-corrected colony counts were 6.18 log10(CFU/ml) [IQR, 5.43 to 6.46 log10(CFU/ml)]. In a subset of patients, repeat BAL on day 5 showed a good stability of the dilution factor. We previously showed that large bacterial burdens reduce or stop bacterial killing by granulocytes. (This study has been registered at ClinicalTrials.gov under registration no. NCT01570192.).

Biologic differences between peripheral and transition zone prostate cancer.

BACKGROUND: Prostate cancer arises in the transition zone (TZ) in approximately 20-25% of cases. Modern biopsy and surveillance protocols, and advances in prostate cancer imaging, have renewed interest in TZ prostate cancers. We compared TZ and PZ prostate cancer to determine if cancer location is independently associated with better outcomes. METHODS: We evaluated an expanded cohort of 1354 men who underwent radical prostatectomy between 1983 and 2003 with updated long-term clinical follow-up. Regression models were used to compare the volume of high-grade (Gleason 4 or 5) cancer and total cancer volume by location. Uni- and multi-variable logistic regression models tested the associations between cancer location and adverse pathologic features. Multivariable proportional hazard models were fit to examine cancer recurrence. RESULTS: Patients with TZ cancer presented with higher pre-operative serum PSA values (11.07 vs. 7.86 ng/ml) and larger total cancer volume (7.1 vs. 3.8 cc). Patients with TZ cancer had decreased odds of seminal vesicle invasion (OR 0.08, 95% CI 0.03, 0.21), extra-capsular extension (OR 0.56, 95% CI 0.35, 0.92), and lymphovascular invasion (OR 0.48, 95% CI 0.27, 0.87) in multivariable models. TZ cancers were independently associated with decreased hazard of tumor recurrence (HR 0.62, 95% CI 0.43, 0.90). CONCLUSIONS: TZ cancer prostate is associated with favorable pathologic features and better recurrence-free survival despite being diagnosed with larger cancers and higher PSA values. Tumor location should be taken into account when stratifying patient risk before and after prostatectomy, particularly with the evolving role of imaging in prostate cancer management.

Matched comparison of robot-assisted, laparoscopic and open radical prostatectomy regarding pathologic and oncologic outcomes in obese patients.

OBJECTIVES: To investigate pathological and oncological outcomes of obese patients who underwent robot-assisted radical prostatectomy (RARP) compared with laparoscopic radical prostatectomy (LRP) or open retropubic radical prostatectomy (RRP) since limited comparative data exist with regard to oncological and survival outcomes. METHODS: A total of 869 patients with body mass index ≥ 30 from two academic centers were identified. A total of 194 patients who underwent RARP were propensity score (PS) matched 1:1 to LRP or RRP cases. PS-matching variables included prostate-specific antigen (PSA), biopsy Gleason score, clinical stage, surgeon experience, and nerve-sparing technique. Predictors of positive surgical margins (PSMs) were analyzed using logistic regression. Predictors of recurrence-free survival (RFS) were analyzed within Cox regression models. Overall survival was compared with RFS using the log-rank test. RESULTS: Pathologic Gleason scores <7, =7, and >7 were found in 24.2, 63.6, and 11.7 % of patients, respectively. There were no statistically significant differences related to pathologic stage or lymph node metastases between surgical techniques. PSM for pT2 disease were observed in 22.9, 17.4, and 19.3 % of patients undergoing RARP, LRP, and RRP, respectively (not significantly different). Preoperative PSA and clinical stage cT2 disease were independently associated with PSM. There were no significant differences in mean 3-year RFS for RARP, LRP, and RRP (87.4, 91.0, and 85.7 %). Biopsy Gleason score >7, PSM, and clinical stage two were independent predictors of decreased RFS. CONCLUSIONS: RARP demonstrates similar pathological and oncological results compared with LRP or RRP for obese patients.

Experiences of diabetes self-management: a focus group study among Australians with type 2 diabetes.

AIMS AND OBJECTIVES: The aim of this study was to explore the experiences and concerns of individuals with type 2 diabetes mellitus, in a predominantly low socio-economic setting. BACKGROUND: Currently, approximately 1 million Australians have diabetes and rates have more than doubled since 1989. Type 2 diabetes mellitus accounts for approximately 85% of diabetes cases. Risk factors include obesity, older age, low socio-economic status, sedentary lifestyle and ethnicity. Older individuals from low socio-economic backgrounds are particularly at risk of both developing and of mismanaging their condition. DESIGN: Exploratory qualitative design. METHODS: Focus groups were used to collect data from 22 individuals, aged 40 to more than 70 years, with type 2 diabetes mellitus, who were attending local health services for their diabetes care. Focus groups ranged in size from four to eight individuals and all were recorded, transcribed and analysed. Data were analysed using a thematic analysis approach. RESULTS: Participants described their experiences of managing their diabetes as emotionally, physically and socially challenging. Data analysis revealed four main themes including: (1) diabetes the silent disease; (2) a personal journey (3) the work of managing diabetes; and (4) access to resources and services. Throughout, participants highlighted the impact of diabetes on the family, and the importance of family members in providing support and encouragement to assist their self-management efforts. CONCLUSIONS: Participants in this study were generally satisfied with their diabetes care but identified a need for clear simple instruction immediately post-diagnosis, followed by a need for additional informal information when they had gained some understanding of their condition. RELEVANCE TO CLINICAL PRACTICE: Findings reveal a number of unmet information and support needs for individuals with type 2 diabetes mellitus. In particular, it is important for healthcare professionals and family members to recognise the significant emotional burden that diabetes imposes, and the type and quantity of information individuals with diabetes prefer. It is also important to consider levels of health literacy in the community when developing diabetes-related information or programmes.

Higher rates of upgrading and upstaging in older patients undergoing radical prostatectomy and qualifying for active surveillance.

OBJECTIVE: To determine pathological and oncological outcomes of patients diagnosed with low-risk prostate cancer in two age cohorts who underwent radical prostatectomy (RP) and qualified for active surveillance (AS) according to Prostate Cancer Research International: Active Surveillance (PRIAS) criteria, as AS for low-risk prostate cancer represents an acceptable management strategy especially for older patients. PATIENTS AND METHODS: In all, 320 patients aged ≥65 years who underwent RP and were eligible for AS according to PRIAS criteria were propensity score matched 1:1 to patients aged <65 years. Patient characteristics were compared with chi-square, Kruskal-Wallis, and one-way anova tests. Predictors of RP pathological upgrading or upstaging were analysed using logistic regression. Recurrence-free survival (RFS) and overall survival (OS) were calculated using the Kaplan-Meier method. Predictors of RFS were analysed within Cox regression models. RESULTS: Pathological upgrading and upstaging were significantly higher among older (≥65 years) vs younger (<65 years) patients (53.1% vs 44.1% and 12.2% vs 7.2%, respectively). Higher prostate-specific antigen levels and increasing age were independent predictors of upgrading among patients aged <65 years. There were no differences in RFS or OS between the two age groups. Positive surgical margin status was the only independent predictor of shorter RFS. CONCLUSIONS: Patients aged ≥65 years who are eligible for AS by PRIAS criteria have a higher risk of being upgraded and upstaged at RP than those aged <65 years. These findings should be taken into consideration when discussing treatment options for patients diagnosed with prostate cancer.

Matched comparison of outcomes following open and minimally invasive radical prostatectomy for high-risk patients.

PURPOSE: Comparative data related to the use of open and minimally invasive surgical approaches for the treatment of high-risk prostate cancer (PCa) remain limited. We determined outcomes of open radical prostatectomy (RRP), laparoscopic RP (LRP), and robot-assisted RP (RARP) in matched cohorts of patients with high-risk prostate cancer. MATERIALS AND METHODS: A total of 805 patients with high-risk PCa [prostate-specific antigen (PSA) >20 ng/mL, Gleason score ≥8, or clinical stage ≥cT2c] were identified. A total of 407 RRP cases were propensity score (PS) matched 1:1 to 398 LRP or RARP cases to yield 3 cohorts (RARP, LRP, and RRP) of 110 patients each for analysis. PS matching variables included the following: age, clinical stage, preoperative PSA, biopsy Gleason score, surgeon experience, and nerve-sparing technique. Overall survival (OS) and recurrence-free survival (RFS) were compared with log-rank test. RFS predictor analysis was calculated within Cox regression models. RESULTS: Pathological Gleason scores <7, =7, and >7 were found in 3.3, 50.9, and 45.8 % of patients. There were no statistically significant differences for pathological stage and positive surgical margins between surgical techniques. Mean 3-year RFS was 41.4, 77.9, and 54.1 %, for RARP, LRP, and RRP, respectively (p < 0.0001 for RARP vs. LRP). There were no significant differences for mean estimated 3-year OS for patients treated with RARP, LRP, or RRP (95.4, 98.1, and 100 %). CONCLUSIONS: RARP demonstrated similar oncologic outcomes compared to RRP and LRP in a PS-matched cohort of patients with high-risk prostate cancer.

A model for the design and construction of a resource for the validation of prognostic prostate cancer biomarkers: the Canary Prostate Cancer Tissue Microarray.

Tissue microarrays (TMAs) provide unique resources for rapid evaluation and validation of tissue biomarkers. The Canary Foundation Retrospective Prostate Tissue Microarray Resource used a rigorous statistical design, quota sampling, a variation of the case-cohort study, to select patients for inclusion in a multicenter, retrospective prostate cancer TMA cohort. The study is designed to definitively validate tissue biomarkers of prostate cancer recurrence after radical prostatectomy. Tissue samples from over 1000 participants treated for prostate cancer with radical prostatectomy between 1995 and 2004 were selected at 6 participating institutions in the United States and Canada. This design captured the heterogeneity of screening and clinical practices in the contemporary North American population. Standardized clinical data were collected in a centralized database. The project has been informative in several respects. The scale and complexity of assembling TMAs with over 200 cases at each of 6 sites involved unanticipated levels of effort and time. Our statistical design promises to provide a model for outcome-based studies where tissue localization methods are applied to high-density TMAs.

Small prostate size and high grade disease--biology or artifact?

PURPOSE: Prior radical prostatectomy series have shown an inverse association between prostate size and high grade cancer. It has been suggested that smaller size prostates arise in a low androgen environment, enabling development of more aggressive cancer. We propose that this observation is the result of ascertainment bias driven by prostate specific antigen performance. MATERIALS AND METHODS: We identified 1,404 patients from the Stanford Radical Prostatectomy Database with clinical stage T1c (723) and T2 (681) disease who underwent surgery between 1988 and 2002, and underwent detailed morphometric mapping by a single pathologist. Multivariate linear regression was performed to assess for the effects of age, prostate weight and prostate specific antigen on total and high grade (Gleason grade 4/5) cancer volume and percentage of high grade disease. RESULTS: In patients who underwent biopsy due to abnormal prostate specific antigen (stage T1c), prostate weight was negatively associated (p = 0.0002) with total cancer volume, volume of high grade disease and percentage of high grade disease. For patients who underwent biopsy based on abnormal digital rectal examination (stage T2) these associations were not observed. CONCLUSIONS: Improved prostate specific antigen performance for high grade disease results in ascertainment bias in patients with T1c disease. Thus, the association between prostate size and high grade disease may be a consequence of grade dependent performance of prostate specific antigen rather than true tumor biology.

Length of site-specific positive surgical margins as a risk factor for biochemical recurrence following radical prostatectomy.

OBJECTIVES: Positive surgical margins (PSM) have been associated with biochemical recurrence (BCR) after radical prostatectomy, but the significance of PSM length and location are debated. We assessed the impact of PSM lengths at specific locations for BCR in an open radical prostatectomy series. METHODS: Detailed clinical and pathological data were collected from 117 post-prostatectomy patients with PSM from 1984 to 2004 at our institution. PSM locations were classified as apex, mid-gland, base, bladder neck, and anterior fibromuscular region with lengths measured at each site. Aggregate PSM length was obtained by summing lengths of all PSM areas in contact with the inked surface. BCR was defined as serum prostate specific antigen level 0.2 ng/mL or greater. Cox proportional hazards regression analyses of PSM lengths were conducted either as a continuous or categorical variable relative to location as a predictor of BCR. RESULTS: Multivariate analyses demonstrated that as a continuous variable, PSM length at the anterior fibromuscular region (Hazard ratio [HR] = 1.17; P = 0.027) and bladder neck (HR = 1.29; P = 0.046) were significant predictors for BCR. As a categorical variable, PSM length ≥ 2 mm at the anterior fibromuscular area was significant for BCR (HR = 3.02; P = 0.036). Increasing Gleason grade and positive lymph node status were also found to be significant independent predictors for BCR. CONCLUSION: PSM length at the anterior fibromuscular region (continuous and categorical) and the bladder neck (continuous) was significantly associated with BCR. Site-specific PSM length, along with Gleason grade and lymph node status, can be predictive of BCR and assist in risk stratification of patients with PSM following radical prostatectomy.

Fecal containment in bedridden patients: economic impact of 2 commercial bowel catheter systems.

BACKGROUND: Fecal contamination is a major challenge in patients in acute/critical care settings that is associated with increased cost of care and supplies and with development of pressure ulcers, incontinence dermatitis, skin and soft tissue infections, and urinary tract infections. OBJECTIVES: To assess the economic impact of fecal containment in bedridden patients using 2 different indwelling bowel catheters and to compare infection rates between groups. METHODS: A multicenter, observational study was done at 12 US sites (7 that use catheter A, 5 that use catheter B). Patients were followed from insertion of an indwelling bowel catheter system until the patient left the acute/critical care unit or until 29 days after enrollment, whichever came first. Demographic data, frequency of bedding/dressing changes, incidence of infection, and Braden scores (risk of pressure ulcers) were recorded. RESULTS: The study included 146 bedridden patients (76 with catheter A, 70 with catheter B) who had similar Braden scores at enrollment. The rate of bedding/dressing changes per day differed significantly between groups (1.20 for catheter A vs 1.71 for catheter B; P = .004). According to a formula that accounted for personnel resources and laundry cycle costs, catheter A cost $13.94 less per patient per day to use than did catheter B. Catheter A was less likely than was catheter B to be removed during the observational period (P = .03). Observed infection rates were low. CONCLUSION: Catheter A may be more cost-effective than catheter B because it requires fewer unscheduled linen changes per patient day.

Multidetector row computed tomography in the management of penetrating neck injuries.

Penetrating neck trauma may occur from gun shots, stabbings, and accidental injury. Approximately 50% of gunshot and 10%-20% of stab-wound patients are reported as having severe injuries and the mortality from severe vascular injuries is reported as high as 50%. Penetrating traumatic neck injury is no longer best managed with exploratory surgery or conventional angiography in the stable patient. Computed tomography angiography has proven to be a useful, safe, and reliable means of diagnosis. Experience with interpreting and reconstructing computed tomography images, understanding the clinically important findings, and avoiding pitfalls is critical for successful patient care. Therefore, radiologists and clinicians who treat trauma patients need to familiarize themselves with the computed tomography angiography technique and appearances of vascular injury and know when to recommend further evaluation, such as interventional angiography or open surgery.

Genomic profiling reveals alternative genetic pathways of prostate tumorigenesis.

Prostate cancer is clinically heterogeneous, ranging from indolent to lethal disease. Expression profiling previously defined three subtypes of prostate cancer, one (subtype-1) linked to clinically favorable behavior, and the others (subtypes-2 and -3) linked with a more aggressive form of the disease. To explore disease heterogeneity at the genomic level, we carried out array-based comparative genomic hybridization (array CGH) on 64 prostate tumor specimens, including 55 primary tumors and 9 pelvic lymph node metastases. Unsupervised cluster analysis of DNA copy number alterations (CNA) identified recurrent aberrations, including a 6q15-deletion group associated with subtype-1 gene expression patterns and decreased tumor recurrence. Supervised analysis further disclosed distinct patterns of CNA among gene-expression subtypes, where subtype-1 tumors exhibited characteristic deletions at 5q21 and 6q15, and subtype-2 cases harbored deletions at 8p21 (NKX3-1) and 21q22 (resulting in TMPRSS2-ERG fusion). Lymph node metastases, predominantly subtype-3, displayed overall higher frequencies of CNA, and in particular gains at 8q24 (MYC) and 16p13, and loss at 10q23 (PTEN) and 16q23. Our findings reveal that prostate cancers develop via a limited number of alternative preferred genetic pathways. The resultant molecular genetic subtypes provide a new framework for investigating prostate cancer biology and explain in part the clinical heterogeneity of the disease.

Extracting Patient-Centered Outcomes from Clinical Notes in Electronic Health Records: Assessment of Urinary Incontinence After Radical Prostatectomy.

OBJECTIVE: To assess documentation of urinary incontinence (UI) in prostatectomy patients using unstructured clinical notes from Electronic Health Records (EHRs). METHODS: We developed a weakly-supervised natural language processing tool to extract assessments, as recorded in unstructured text notes, of UI before and after radical prostatectomy in a single academic practice across multiple clinicians. Validation was carried out using a subset of patients who completed EPIC-26 surveys before and after surgery. The prevalence of UI as assessed by EHR and EPIC-26 was compared using repeated-measures ANOVA. The agreement of reported UI between EHR and EPIC-26 was evaluated using Cohen's Kappa coefficient. RESULTS: A total of 4870 patients and 716 surveys were included. Preoperative prevalence of UI was 12.7 percent. Postoperative prevalence was 71.8 percent at 3 months, 50.2 percent at 6 months and 34.4 and 41.8 at 12 and 24 months, respectively. Similar rates were recorded by physicians in the EHR, particularly for early follow-up. For all time points, the agreement between EPIC-26 and the EHR was moderate (all p < 0.001) and ranged from 86.7 percent agreement at baseline (Kappa = 0.48) to 76.4 percent agreement at 24 months postoperative (Kappa = 0.047). CONCLUSIONS: We have developed a tool to assess documentation of UI after prostatectomy using EHR clinical notes. Our results suggest such a tool can facilitate unbiased measurement of important PCOs using real-word data, which are routinely recorded in EHR unstructured clinician notes. Integrating PCO information into clinical decision support can help guide shared treatment decisions and promote patient-valued care.

Is it possible to automatically assess pretreatment digital rectal examination documentation using natural language processing? A single-centre retrospective study.

OBJECTIVES: To develop and test a method for automatic assessment of a quality metric, provider-documented pretreatment digital rectal examination (DRE), using the outputs of a natural language processing (NLP) framework. SETTING: An electronic health records (EHR)-based prostate cancer data warehouse was used to identify patients and associated clinical notes from 1 January 2005 to 31 December 2017. Using a previously developed natural language processing pipeline, we classified DRE assessment as documented (currently or historically performed), deferred (or suggested as a future examination) and refused. PRIMARY AND SECONDARY OUTCOME MEASURES: We investigated the quality metric performance, documentation 6 months before treatment and identified patient and clinical factors associated with metric performance. RESULTS: The cohort included 7215 patients with prostate cancer and 426 227 unique clinical notes associated with pretreatment encounters. DREs of 5958 (82.6%) patients were documented and 1257 (17.4%) of patients did not have a DRE documented in the EHR. A total of 3742 (51.9%) patient DREs were documented within 6 months prior to treatment, meeting the quality metric. Patients with private insurance had a higher rate of DRE 6 months prior to starting treatment as compared with Medicaid-based or Medicare-based payors (77.3%vs69.5%, p=0.001). Patients undergoing chemotherapy, radiation therapy or surgery as the first line of treatment were more likely to have a documented DRE 6 months prior to treatment. CONCLUSION: EHRs contain valuable unstructured information and with NLP, it is feasible to accurately and efficiently identify quality metrics with current documentation clinician workflow.

Weakly supervised natural language processing for assessing patient-centered outcome following prostate cancer treatment.

Background: The population-based assessment of patient-centered outcomes (PCOs) has been limited by the efficient and accurate collection of these data. Natural language processing (NLP) pipelines can determine whether a clinical note within an electronic medical record contains evidence on these data. We present and demonstrate the accuracy of an NLP pipeline that targets to assess the presence, absence, or risk discussion of two important PCOs following prostate cancer treatment: urinary incontinence (UI) and bowel dysfunction (BD). Methods: We propose a weakly supervised NLP approach which annotates electronic medical record clinical notes without requiring manual chart review. A weighted function of neural word embedding was used to create a sentence-level vector representation of relevant expressions extracted from the clinical notes. Sentence vectors were used as input for a multinomial logistic model, with output being either presence, absence or risk discussion of UI/BD. The classifier was trained based on automated sentence annotation depending only on domain-specific dictionaries (weak supervision). Results: The model achieved an average F1 score of 0.86 for the sentence-level, three-tier classification task (presence/absence/risk) in both UI and BD. The model also outperformed a pre-existing rule-based model for note-level annotation of UI with significant margin. Conclusions: We demonstrate a machine learning method to categorize clinical notes based on important PCOs that trains a classifier on sentence vector representations labeled with a domain-specific dictionary, which eliminates the need for manual engineering of linguistic rules or manual chart review for extracting the PCOs. The weakly supervised NLP pipeline showed promising sensitivity and specificity for identifying important PCOs in unstructured clinical text notes compared to rule-based algorithms.

hCAP-D3 expression marks a prostate cancer subtype with favorable clinical behavior and androgen signaling signature.

Growing evidence suggests that only a fraction of prostate cancers detected clinically are potentially lethal. An important clinical issue is identifying men with indolent cancer who might be spared aggressive therapies with associated morbidities. Previously, using microarray analysis we defined 3 molecular subtypes of prostate cancer with different gene-expression patterns. One, subtype-1, displayed features consistent with more indolent behavior, where an immunohistochemical marker (AZGP1) for subtype-1 predicted favorable outcome after radical prostatectomy. Here we characterize a second candidate tissue biomarker, hCAP-D3, expressed in subtype-1 prostate tumors. hCAP-D3 expression, assayed by RNA in situ hybridization on a tissue microarray comprising 225 cases, was associated with decreased tumor recurrence after radical prostatectomy (P=0.004), independent of pathologic tumor stage, Gleason grade, and preoperative prostate-specific antigen levels. Simultaneous assessment of hCAP-D3 and AZGP1 expression in this tumor set improved outcome prediction. We have previously demonstrated that hCAP-D3 is induced by androgen in prostate cells. Extending this finding, Gene Set Enrichment Analysis revealed enrichment of androgen-responsive genes in subtype-1 tumors (P=0.019). Our findings identify hCAP-D3 as a new biomarker for subtype-1 tumors that improves prognostication, and reveal androgen signaling as an important biologic feature of this potentially clinically favorable molecular subtype.

An Automated Feature Engineering for Digital Rectal Examination Documentation using Natural Language Processing.

Digital rectal examination (DRE) is considered a quality metric for prostate cancer care. However, much of the DRE related rich information is documented as free-text in clinical narratives. Therefore, we aimed to develop a natural language processing (NLP) pipeline for automatic documentation of DRE in clinical notes using a domain-specific dictionary created by clinical experts and an extended version of the same dictionary learned by clinical notes using distributional semantics algorithms. The proposed pipeline was compared to a baseline NLP algorithm and the results of the proposed pipeline were found superior in terms of precision (0.95) and recall (0.90) for documentation of DRE. We believe the rule-based NLP pipeline enriched with terms learned from the whole corpus can provide accurate and efficient identification of this quality metric.

The CPC Risk Calculator: A New App to Predict Prostate-specific Antigen Recurrence During Follow-up After Radical Prostatectomy.

BACKGROUND: It can be challenging to predict the risk of biochemical recurrence (BR) during follow-up after radical prostatectomy (RP) in men who have undetectable prostate-specific antigen (PSA), even years after surgery. OBJECTIVE: To establish and validate a contemporary nomogram that predicts the absolute risk of BR every year after RP in men with undetectable PSA while accounting for competing risks of death. DESIGN, SETTING, AND PARTICIPANTS: A total of 3746 patients from Rigshospitalet (Copenhagen, Denmark) and Stanford Urology (Stanford, CA, USA) who underwent RP between 1995 and 2013 were included. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Time to BR was defined as the first PSA result ≥0.2 ng/ml. BR risk was computed using multiple cause-specific Cox regression including preoperative PSA, pT category, RP Gleason score (GS), and surgical margin (R) status. Death without BR was considered a competing event. The nomogram presents the future risk of BR for a man who is alive and without BR at the time of follow-up. Validation assessed the discrimination and accuracy using time-dependent area under the curve and Brier scores. RESULTS AND LIMITATIONS: The nomogram predicts risk of BR up to 12 yr after RP at an individual level. As example, the risk of BR for a man with pT3a, R-, GS 3 + 4, and preoperative PSA ≤10 ng/ml followed for 5 yr with undetectable PSA is 18% for the next 5 yr. External validation demonstrated both high accuracy and discrimination. The CPC Risk Calculator is available as a free Android and iOS App. Declining discrimination and accuracy after 7 yr of follow-up is the main limitation. CONCLUSIONS: This nomogram can be used as a tool to inform men with undetectable PSA during follow-up after RP about their future risk of BR, and may aid in decisions on the necessity for further follow-up. The nomogram is the first to be available as a free app. PATIENT SUMMARY: We developed an easily interpretable nomogram to evaluate the risk of prostate-specific antigen elevation (cancer recurrence) following complete removal of the prostate (radical prostatectomy). The tool can aid both physicians and patients in evaluating the future risk of cancer recurrence during follow-up after surgery. The model is available as a free mobile app that can be downloaded from the App Store.