Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review

Novel approaches that complement and go beyond evidence-based medicine are required in the domain of chronic diseases, given the growing incidence of such conditions on the worldwide population. A promising avenue is the secondary use of electronic health records (EHRs), where patient data are analyzed to conduct clinical and translational research. Methods based on machine learning to process EHRs are resulting in improved understanding of patient clinical trajectories and chronic disease risk prediction, creating a unique opportunity to derive previously unknown clinical insights. However, a wealth of clinical histories remains locked behind clinical narratives in free-form text. Consequently, unlocking the full potential of EHR data is contingent on the development of natural language processing (NLP) methods to automatically transform clinical text into structured clinical data that can guide clinical decisions and potentially delay or prevent disease onset

Discovering medication patterns for high-complexity drug-using diseases through electronic medical records

An Electronic Medical Record (EMR) is a professional document that contains all data generated during the treatment process. The EMR can utilize various data formats, such as numerical data, text, and images. Mining the information and knowledge hidden in the huge amount of EMR data is an essential requirement for clinical decision support, such as clinical pathway formulation and evidence-based medical research. In this paper, we propose a machine-learning-based framework to mine the hidden medication patterns in EMR text. The framework systematically integrates the Jaccard similarity evaluation, spectral clustering, the modified Latent Dirichlet Allocation and cross-matching among multiple features to find the residuals that describe additional knowledge and clusters hidden in multiple perspectives of highly complex medication patterns. These methods work together, step by step to reveal the underlying medication pattern. We evaluated the method by using real data from EMR text (patients with cirrhotic ascites) from a large hospital in China. The proposed framework outperforms other approaches for medication pattern discovery, especially for this disease with subtle medication treatment variances. The results also revealed little overlap among the discovered patterns; thus, the distinct features of each pattern are well studied through the proposed framework

Psychosocial Predictors of Successful Bariatric Surgery

Obesity is an epidemic that can lead to a wide range of physical and mental problems. When traditional weight-loss methods are not effective, bariatric surgery is a viable weight-loss option. While previous researchers have investigated the role of psychological factors in relation to obesity, few have investigated psychological factors as predictors of weight loss and complications after bariatric surgery. The purpose of this study was to determine the prevalence of psychological disorders/conditions (e.g., depression and abuse) in the study population, evaluate weight and psychosocial variables before and 6 months after weight-loss surgery, and identify psychosocial factors that are predictors of weight loss and complications at 5 years post surgery. Three theoretical foundations were important to the present study: the transtheoretical model of behavior change, interpersonal processes, and protection motivation theory. Methods included a retrospective review of archival data of 93 individuals who elected to undergo bariatric surgery, were age 18+, had a BMI \u3e 40kg/m2, and had obesity-related medical conditions Paired sample t tests were used to determine statistically significant changes before and after surgery. Multiple regression was used to predict success of bariatric surgery (measured by weight loss and no or few postsurgical complications). Results indicated that a high proportion (66.7%) of this sample had a behavioral health condition. Weight, depression, and obesity-related quality of life improved at 6 months post surgery. Poor obesity-related quality of life was significant at predicting more weight loss at 5 years postsurgery. Potential social changes may include future development of generalizable methods/tools to determine proper candidates for bariatric surgery, leading to a healthier community and lower healthcare costs

A method to advance adolescent sexual health research: Automated algorithm finds sexual history documentation

Background:We aimed to develop and validate a rule-based Natural Language Processing (NLP) algorithm to detect sexual history documentation and its five key components [partners, practices, past history of sexually transmitted infections (STIs), protection from STIs, and prevention of pregnancy] among adolescent encounters in the pediatric emergency and inpatient settings.MethodsWe iteratively designed a NLP algorithm using pediatric emergency department (ED) provider notes from adolescent ED visits with specific abdominal or genitourinary (GU) chief complaints. The algorithm is composed of regular expressions identifying commonly used phrases in sexual history documentation. We validated this algorithm with inpatient admission notes for adolescents. We calculated the sensitivity, specificity, negative predictive value, positive predictive value, and F1 score of the tool in each environment using manual chart review as the gold standard.ResultsIn the ED test cohort with abdominal or GU complaints, 97/179 (54%) provider notes had a sexual history documented, and the NLP algorithm correctly classified each note. In the inpatient validation cohort, 97/321 (30%) admission notes included a sexual history, and the NLP algorithm had 100% sensitivity and 98.2% specificity. The algorithm demonstrated >97% sensitivity and specificity in both settings for detection of elements of a high quality sexual history including protection used and contraception. Type of sexual practice and STI testing offered were also detected with >97% sensitivity and specificity in the ED test cohort with slightly lower performance in the inpatient validation cohort.ConclusionThis NLP algorithm automatically detects the presence of sexual history documentation and its key components in ED and inpatient settings

J Biomed Inform

We followed a systematic approach based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses to identify existing clinical natural language processing (NLP) systems that generate structured information from unstructured free text. Seven literature databases were searched with a query combining the concepts of natural language processing and structured data capture. Two reviewers screened all records for relevance during two screening phases, and information about clinical NLP systems was collected from the final set of papers. A total of 7149 records (after removing duplicates) were retrieved and screened, and 86 were determined to fit the review criteria. These papers contained information about 71 different clinical NLP systems, which were then analyzed. The NLP systems address a wide variety of important clinical and research tasks. Certain tasks are well addressed by the existing systems, while others remain as open challenges that only a small number of systems attempt, such as extraction of temporal information or normalization of concepts to standard terminologies. This review has identified many NLP systems capable of processing clinical free text and generating structured output, and the information collected and evaluated here will be important for prioritizing development of new approaches for clinical NLP.CC999999/ImCDC/Intramural CDC HHS/United States2019-11-20T00:00:00Z28729030PMC6864736694

Prescribed hypocaloric nutrition support for critically-ill adults

Background There are controversies about the amount of calories and the type of nutritional support that should be given to critically‐ill people. Several authors advocate the potential benefits of hypocaloric nutrition support, but the evidence is inconclusive. Objectives To assess the effects of prescribed hypocaloric nutrition support in comparison with standard nutrition support for critically‐ill adults Search methods We searched the Cochrane Central Register of Controlled Trials (CENTRAL, Cochrane Library), MEDLINE, Embase and LILACS (from inception to 20 June 2017) with a specific strategy for each database. We also assessed three websites, conference proceedings and reference lists, and contacted leaders in the field and the pharmaceutical industry for undetected/unpublished studies. There was no restriction by date, language or publication status. Selection criteria We included randomized and quasi‐randomized controlled trials comparing hypocaloric nutrition support to normo‐ or hypercaloric nutrition support or no nutrition support (e.g. fasting) in adults hospitalized in intensive care units (ICUs). Data collection and analysis We used standard methodological procedures expected by Cochrane. We meta‐analysed data for comparisons in which clinical heterogeneity was low. We conducted prespecified subgroup and sensitivity analyses, and post hoc analyses, including meta‐regression. Our primary outcomes were: mortality (death occurred during the ICU and hospital stay, or 28‐ to 30‐day all‐cause mortality); length of stay (days stayed in the ICU and in the hospital); and Infectious complications. Secondary outcomes included: length of mechanical ventilation. We assessed the quality of evidence with GRADE. Main results We identified 15 trials, with a total of 3129 ICU participants from university‐associated hospitals in the USA, Colombia, Saudi Arabia, Canada, Greece, Germany and Iran. There are two ongoing studies. Participants suffered from medical and surgical conditions, with a variety of inclusion criteria. Four studies used parenteral nutrition and nine studies used only enteral nutrition; it was unclear whether the remaining two used parenteral nutrition. Most of them could not achieve the proposed caloric targets, resulting in small differences in the administered calories between intervention and control groups. Most studies were funded by the US government or non‐governmental associations, but three studies received funding from industry. Five studies did not specify their funding sources. The included studies suffered from important clinical and statistical heterogeneity. This heterogeneity did not allow us to report pooled estimates of the primary and secondary outcomes, so we have described them narratively. When comparing hypocaloric nutrition support with a control nutrition support, for hospital mortality (9 studies, 1775 participants), the risk ratios ranged from 0.23 to 5.54; for ICU mortality (4 studies, 1291 participants) the risk ratios ranged from 0.81 to 5.54, and for mortality at 30 days (7 studies, 2611 participants) the risk ratios ranged from 0.79 to 3.00. Most of these estimates included the null value. The quality of the evidence was very low due to unclear or high risk of bias, inconsistency and imprecision. Participants who received hypocaloric nutrition support compared to control nutrition support had a range of mean hospital lengths of stay of 15.70 days lower to 10.70 days higher (10 studies, 1677 participants), a range of mean ICU lengths of stay 11.00 days lower to 5.40 days higher (11 studies, 2942 participants) and a range of mean lengths of mechanical ventilation of 13.20 days lower to 8.36 days higher (12 studies, 3000 participants). The quality of the evidence for this outcome was very low due to unclear or high risk of bias in most studies, inconsistency and imprecision. The risk ratios for infectious complications (10 studies, 2804 participants) of each individual study ranged from 0.54 to 2.54. The quality of the evidence for this outcome was very low due to unclear or high risk of bias, inconsistency and imprecision We were not able to explain the causes of the observed heterogeneity using subgroup and sensitivity analyses or meta‐regression. Authors' conclusions The included studies had substantial clinical heterogeneity. We found very low‐quality evidence about the effects of prescribed hypocaloric nutrition support on mortality in hospital, in the ICU and at 30 days, as well as in length of hospital and ICU stay, infectious complications and the length of mechanical ventilation. For these outcomes there is uncertainty about the effects of prescribed hypocaloric nutrition, since the range of estimates includes both appreciable benefits and harms. Given these limitations, results must be interpreted with caution in the clinical field, considering the unclear balance of the risks and harms of this intervention. Future research addressing the clinical heterogeneity of participants and interventions, study limitations and sample size could clarify the effects of this intervention.Fil: Perman, Mario I. Hospital Italiano; ArgentinaFil: Ciapponi, Agustín. Instituto de Efectividad Clínica y Sanitaria; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Franco, Juan V.A.. Hospital Italiano; ArgentinaFil: Loudet, Cecilia. Universidad Nacional de La Plata; ArgentinaFil: Crivelli, Adriana. Hospital HIGA San Martín; ArgentinaFil: Garrote, Virginia. Hospital Italiano; ArgentinaFil: Perman, Gastón. Hospital Italiano; Argentin

Stress, Affect Systems and Eating Pathology in Problematic Weight Regulation

Problematic weight regulation as found in obesity and Anorexia Nervosa (AN) are chronic conditions which require long-term management. In order to develop long-term strategies to manage these conditions, a clearer understanding of the factors that can contribute to the development and also recovery from these conditions are a necessity. Although obesity and AN are at the opposite end of the bodyweight spectrum, some shared psychological processes may drive these states. One factor that has been suggested to contribute to problematic weight regulation is psychosocial stress whilst positive affect systems and affect regulation processes are important for regulating stress-related experiences. Gilbert (2005) describes an affect regulation system which consists of two positive affect systems known as social rank and attachment. Whilst the latter affect system refers to the attachment bond that develops between an infant and its caregiver (which extends to adult relationships), the former is used to form relationships that allow us to compete for limited resources and maintain our status in the social environment. Affect regulation processes in the current research are self-criticism and self-reassurance. Whilst self-critical thoughts and feelings can be triggered by perceptions of being low rank, the idea that people can be self-reassuring or being able to self-reassure at times of difficulty is nested in the positive infant-caregiver attachment bond and a consequence of internalizing parental soothing (Gilbert, 2006). Hence, as stress is suggested to be an important factor in problematic weight regulation and affect systems and processes are central to the regulation of emotional responses to stress-related experiences, the current series of studies examined these factors in relation to problematic weight regulation. The current research consisted of four studies designed to examine the role of stress and affect regulation in relation to weight change, weight regain following weight loss and recovery versus symptom maintenance in AN in women. A longitudinal study (Study One) was conducted to examine the change trajectories of stress, eating pathology and bodyweight, how these changes influence each other and the role of affect regulation systems and processes on these changes in a community based sample (N = 1157). Study Two examined the role of stress and affect regulation as predictors of weight regain in those who have lost weight (N = 42) and Study Three used a measure of life events and difficulties to investigate the role of stressful life changes and affect systems on recovery and relapse following AN (N = 30). Finally, in Study four, an expressive writing task which has been demonstrated to have a positive impact on stress-related health outcomes was used to explore the role of stress, affect systems and processes on problematic weight regulation and eating at times of stress (N = 57). The findings of the research studies demonstrated that there is a concurrent link between stress and the regulation of bodyweight and eating in a community-based sample of women. However, the proposed relationship between stress, bodyweight and eating behaviours was not confirmed when examined longitudinally in a community-based sample, over a 7-month period in women who have lost weight or when examined retrospectively as contributing to symptom maintenance in women with AN. However, the main finding of the current series of studies suggested that affect systems and affect regulation processes do have important implications for regulating stress-related experiences, bodyweight and eating behaviours. Perceived low social status, greater insecurity of attachment, more self-critical and less self-reassuring thoughts and feelings were related to increases in stress levels, higher bodyweight and higher levels of dysfunctional eating patterns. In addition, whilst expressive writing did not reduce stress, influence bodyweight or improve affect regulation at times of difficulty, writing about positive experiences had a positive impact on reducing dietary restraint behaviours during a stressful period. In conclusion, these findings suggest that it may not be stress per se that contributes to unhealthy changes in bodyweight and eating behaviours but how we use our affect systems and processes to manage our emotions at times of difficulty. Consequently, these findings have important implications for practice as weight loss programmes, Eating Disorder prevention programmes and stress management interventions should address the issues of perceived low social status, self-criticism and attachment insecurities

Evaluating the psychological predictors of long term weight loss following bariatric surgery.

Introduction: Weight loss surgery (WLS) is cost effective for managing obesity. Yet nearly a third of patients do not achieve successful weight loss (WL) long-term. Furthermore identifying psychological characteristics of long-term successful WL, remain largely undetermined. Aims: To examine the psychological and WL outcomes of patients who had WLS 2-10 years ago and to identify which preoperative and/or postoperative psychological factors might predict successful WL long term. Method: 24 patients, who had undergone WLS 2-10 years ago, participated. Two data sets were used: (1) retrospective data from participants’ medical records on their surgical procedure, physical and psychological health before and after surgery and (2) follow-up data from eight questionnaires, on postoperative psychological functioning, eating behaviours, physical health and adherence to professional support. Results: Participants were predominantly female (n=19), had undergone Roux–en–Y gastric bypass (RYGB, n=19), on average four years prior to follow-up. Mean postoperative WL was 41kg (SD = 18.47) and two thirds of participants (n =16) achieved more than 25% WL. Fifty per cent had a probable anxiety disorder, a third were hazardously drinking alcohol and most had weight related quality of life concerns. RYGB patients with successful WL (n=14) had significantly fewer disordered eating symptoms (p < 0.005), than the unsuccessful WL group (n=5). Disordered eating symptoms also significantly correlated with %WL, even after controlling for years since surgery (F(2,16) = 5.77, p < 0.013.). The relationship between preoperative psychological factors and %WL was not determined due to a lack of data in the medical records. Conclusion: While WLS is successful in reducing obesity, it is unclear whether the presence of postoperative psychological difficulties in this sample is a consequence of this procedure. Further research is required to determine if key psychological characteristics can predict %WL

Can clinical presentation predict response to a non-surgical chronic disease management program for hip and knee osteoarthritis?

Osteoarthritis (OA) is a leading cause of global disability. International guidelines make clear recommendations for evidence-based OA management. However, there is considerable discrepancy between these recommendations and the actual care received by patients. Osteoarthritis management programs (OAMPs) aim to address this evidence-practice gap. There is evidence that some participants improve in pain and function following OAMPs, however, others fail to accomplish these gains. The ability to predict patient outcomes would enable targeting these programs at those people most likely to demonstrate improvement. This Thesis addresses the question: ‘Can clinical presentation can predict response to an OAMP?’ Five studies were conducted to address this question. Two longitudinal cohort studies examined the relationships between participant characteristics and changes in pain and function following 26 weeks of an OAMP. Significant predictors included: sex; knee as treatment joint (vs hip); and total joint arthroplasty (TJR) waitlist status. However, the regression models were not sufficiently sensitive to correctly classify ‘responders’ or ‘worseners’. We then examined patients’ attitudes and capabilities towards OA self-management as a construct that could potentially predict OAMP outcomes. We conducted a systematic review that aimed to identify the instrument assessing OA self-management attitudes and capabilities with the “best” measurement properties. From this review, little extant measurement property evidence was found to recommend any instrument. The fourth study examined the measurement properties of the Patient Activation Measure (PAM-13) in a cross-sectional cohort study. The fifth study examined the relationships between PAM-13 and changes in pain and function. PAM-13 scores were not associated with changes in pain or function following 12 or 26 weeks of the OAMP. Other variables that were independent predictors of outcomes were the Timed-Up-and-Go and employment status. It is difficult to determine who will improve or worsen in an OAMP. This Thesis did identify some patient characteristics that were predictors of response, however, these findings should be replicated in larger cohorts