Abstract
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. Informaticians and domain experts were recruited to design an annotation guideline and generate a training corpus of annotated EC for 230 Alzheimer’s clinical trials, which were represented as queries against the OMOP CDM and included 8008 entities, 3550 attributes, and 3529 relations. A sequence labeling–based method was developed for automatic entity and attribute recognition. Negation detection was supported by NegEx and a set of predefined rules. Relation extraction was achieved by a support vector machine classifier. We further performed terminology-based concept normalization and output structuring.
Results
In task-specific evaluations, the best F1 score for entity recognition was 0.79, and for relation extraction was 0.89. The accuracy of negation detection was 0.94. The overall accuracy for query formalization was 0.71 in an end-to-end evaluation.
Conclusions
This study presents EliIE, an OMOP CDM–based information extraction system for automatic structuring and formalization of free-text EC. According to our evaluation, machine learning-based EliIE outperforms existing systems and shows promise to improve.
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•There is no standard complexity measure to assess EHR data requests.•How a researcher’s cognitive style affects EHR data seeking is unknown.•No formalized structure guiding ...researchers to express their EHR data need.•The need-negotiation process performed informaticians is poorly understood.
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. We adapted a previously published conceptual framework for interactive information retrieval, which defines three entities: user, channel, and source, by elaborating on channels for query formulation in the context of facilitating end users to interrogate EHR data. We show the current progress in biomedical informatics mainly lies in support for query execution and information modeling, primarily due to emphases on infrastructure development for data integration and data access via self-service query tools, but has neglected user support needed during iteratively query formulation processes, which can be costly and error-prone. In contrast, the information science literature has offered elaborate theories and methods for user modeling and query formulation support. The two bodies of literature are complementary, implying opportunities for cross-disciplinary idea exchange. On this basis, we outline the directions for future informatics research to improve our understanding of user needs and requirements for facilitating autonomous interrogation of EHR data by biomedical researchers. We suggest that cross-disciplinary translational research between biomedical informatics and information science can benefit our research in facilitating efficient data access in life sciences.
Purpose Vessel sealing capabilities and the peripheral energy spread associated with currently available energy based surgical instruments were evaluated. Materials and Methods Four groups of energy ...based surgical instruments were established for evaluation, including the ACE™ , LCS-C5 (Ethicon, Cincinnati, Ohio), LigaSure™ V and the prototype Trissector™ . In vivo vessel diameter under physiological conditions, bursting pressures and seal failure were recorded and analyzed for arteries and veins separately. After burst testing the vessels were fixed and evaluated histopathologically for peripheral energy damage. ANOVA was used to determine differences between groups. Results The LigaSure V sealed arteries and veins with an average burst pressure of 536 and 386 mm Hg, respectively. The Harmonic ACE sealed arteries and veins with an average burst pressure of 436 and 160 mm Hg, respectively. The Harmonic LCS-C5 sealed arteries and veins with an average burst pressure of 363 and 215 mm Hg, respectively. The Trissector sealed arteries and veins with an average burst pressure of 328 and 237 mm Hg, respectively. For arteries the ACE, LCS-C5, Trissector and LigaSure V measured a full-thickness peripheral energy spread of 0.6, 0.3, 8.0 and 4.5 mm, respectively (p <0.0001). For veins the ACE, LCS-C5, Trissector and LigaSure V measured a full-thickness peripheral energy spread of 1.5, 1.3, 8.5 and 6.3 mm, respectively (p = 0.003). Conclusions The LigaSure 5 was superior to the other devices tested regarding the ability to seal vessels up to 7 mm. The ACE is an efficient vessel sealing system with the ability to seal vessels up to 5 mm.
Value-based care initiatives require accurate quantification of resource utilization. This study explores hospital resource documentation performance for total knee and hip arthroplasty (TKA, THA) ...implants and how this may differ between hospitals. This retrospective study utilized the Premier discharge database, years 2006 to 2020. TKA/THA cases were categorized into 5 tiers based upon the completeness of implant component documentation: Platinum, Gold, Silver, Bronze, Poor. Correlation between TKA and THA documentation performance (per-hospital percentage of Platinum cases) was assessed. Logistic regression analyses measured the association between hospital characteristics (region, teaching status, bed size, urban/rural) and satisfactory documentation. TKA/THA implant documentation performance was compared to documentation for endovascular stent procedures. Individual hospitals tended to have very complete (Platinum) or very incomplete (Poor) documentation for both TKA and THA. TKA and THA documentation performance were correlated (correlation coefficient = .70). Teaching hospitals were less likely to have satisfactory documentation for both TKA (P = .002) and THA (P = .029). Documentation for endovascular stent procedures was superior compared to TKA/THA. Hospitals’ TKA and THA-related implant documentation performance is generally either very proficient or very poor, in contrast with often well-documented endovascular stent procedures. Hospital characteristics, other than teaching status, do not appear to impact TKA/THA documentation completeness.
Abstract 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.com search was performed to identify the top 20 websites for each term. The HONcode toolbar was utilized to determine whether each website was HONcode accredited and report the overall frequency of accreditation for each term. The DISCERN Plus instrument was used to score each website in accordance with the DISCERN Handbook. High and low scoring criteria were then compared. Results A total of 60 websites were identified. For the search terms ‘circumcision’, ‘posterior urethral valves’ and ‘vesicoureteral reflux’, 25–30% of the websites were HONcode certified. Out of the maximum score of 80, the average DISCERN Plus score was 60 (SD = 12, range 38–78), 40 (SD = 12, range 22–69) and 45 (SD = 19, range 16–78), respectively. The lowest scoring DISCERN criteria included: ‘Does it describe how the treatment choices affect overall quality of life?’, ‘Does it describe the risks of each treatment?’ and ‘Does it provide details of additional sources of support and information?’ (1.35, 1.83 and 1.95 out of 5, respectively). Conclusions These findings demonstrate the poor quality of information that patients and their parents may use in decision-making and treatment choices. The two lowest scoring DISCERN Plus criteria involved education on quality of life issues and risks of treatment. Physicians should know how to best use these tools to help guide patients and their parents to websites with valid information.
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. Clinical factors examined included: age, D'Amico risk group, year of surgery, body mass index, and comorbidities. Socioeconomic factors included race/ethnicity, relationship status, income, and distance to treatment center. The relationship between clinical/socioeconomic factors and TTS was evaluated using univariate and multivariate regression models. Results Two-thousand five-hundred seventy-three patients were included in the analysis. Median TTS was 48 days (IQR 35-70, range 43-1103), and 71% of patients underwent RP within 60 days after the most recent positive biopsy. On multivariate analysis, living further from the medical center was associated with shorter TTS ( P = .01), whereas more recent year of surgery ( P = .01), comorbid cardiovascular disease ( P = .007), African-American ( P = .005) or Hispanic race ( P = .005), divorced relationship status ( P = .01), and lower income ( P = .003) were all associated with longer TTS. Conclusion Patients often experience widely variable intervals between the diagnosis and treatment of localized prostate cancer. Longer intervals before surgery may point to disparities in access to prostate cancer care, and not increased decision-making time by the patient.
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. In this study we examined the effect of delay from diagnosis to surgery on outcomes in men with localized prostate cancer and found no association between time to surgery and risk of biochemical recurrence, even for patients with longer delays and high‐risk disease. Men with localized prostate cancer can be reassured that reasonable delays in treatment will not influence disease outcomes.
OBJECTIVE
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To examine the effect of time from last positive biopsy to surgery on clinical outcomes in men with localized prostate cancer undergoing radical prostatectomy (RP).
PATIENTS AND METHODS
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We conducted a retrospective review of 2739 men who underwent RP between 1990 and 2009 at our institution.
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Clinical and pathological features were compared between men undergoing RP ≤ 60, 61–90 and >90 days from the time of prostate biopsy.
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A Cox proportional hazards model was used to analyse the association between clinical features and surgical delay with biochemical progression. Biochemical recurrence (BCR)‐free rates were assessed using the Kaplan–Meier method.
RESULTS
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Of the 1568 men meeting the inclusion criteria, 1098 (70%), 303 (19.3%) and 167 (10.7%) had a delay of ≤60, 61–90 and >90 days, respectively, between biopsy and RP. A delay of >60 days was not associated with adverse pathological findings at surgery.
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The 5‐year survival rate was similar among the three groups (78–85%, P= 0.11).
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In a multivariate Cox model, men with higher PSA levels, clinical stages, Gleason sums, and those of African‐American race were all at higher risk for developing BCR.
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A delay to surgery of >60 days was not associated with worse biochemical outcomes in a univariate and multivariate model.
CONCLUSIONS
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A delay of >60 days is not associated with adverse pathological outcomes in men with localized prostate cancer, nor does it correlate with worse BCR‐free survival.
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Patients can be assured that delaying treatment while considering therapeutic options will not adversely affect their outcomes.
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