Word2Vec inversion and traditional text classifiers for phenotyping lupus.

BACKGROUND: Identifying patients with certain clinical criteria based on manual chart review of doctors' notes is a daunting task given the massive amounts of text notes in the electronic health records (EHR). This task can be automated using text classifiers based on Natural Language Processing (NLP) techniques along with pattern recognition machine learning (ML) algorithms. The aim of this research is to evaluate the performance of traditional classifiers for identifying patients with Systemic Lupus Erythematosus (SLE) in comparison with a newer Bayesian word vector method. METHODS: We obtained clinical notes for patients with SLE diagnosis along with controls from the Rheumatology Clinic (662 total patients). Sparse bag-of-words (BOWs) and Unified Medical Language System (UMLS) Concept Unique Identifiers (CUIs) matrices were produced using NLP pipelines. These matrices were subjected to several different NLP classifiers: neural networks, random forests, naïve Bayes, support vector machines, and Word2Vec inversion, a Bayesian inversion method. Performance was measured by calculating accuracy and area under the Receiver Operating Characteristic (ROC) curve (AUC) of a cross-validated (CV) set and a separate testing set. RESULTS: We calculated the accuracy of the ICD-9 billing codes as a baseline to be 90.00% with an AUC of 0.900, the shallow neural network with CUIs to be 92.10% with an AUC of 0.970, the random forest with BOWs to be 95.25% with an AUC of 0.994, the random forest with CUIs to be 95.00% with an AUC of 0.979, and the Word2Vec inversion to be 90.03% with an AUC of 0.905. CONCLUSIONS: Our results suggest that a shallow neural network with CUIs and random forests with both CUIs and BOWs are the best classifiers for this lupus phenotyping task. The Word2Vec inversion method failed to significantly beat the ICD-9 code classification, but yielded promising results. This method does not require explicit features and is more adaptable to non-binary classification tasks. The Word2Vec inversion is hypothesized to become more powerful with access to more data. Therefore, currently, the shallow neural networks and random forests are the desirable classifiers.

Intervention to Improve Quality of life for African-AmericaN lupus patients (IQAN): study protocol for a randomized controlled trial of a unique a la carte intervention approach to self-management of lupus in African Americans.

BACKGROUND: Systemic Lupus Erythematosus (lupus) is a chronic autoimmune disease that can impact any organ system and result in life-threatening complications. African-Americans are at increased risk for morbidity and mortality from lupus. Self-management programs have demonstrated significant improvements in health distress, self-reported global health, and activity limitation among people with lupus. Despite benefits, arthritis self-management education has reached only a limited number of people. Self-selection of program could improve such trends. The aim of the current study is to test a novel intervention to improve quality of life, decrease indicators of depression, and reduce perceived and biological indicators of stress in African-American lupus patients in South Carolina. METHODS/DESIGN: In a three armed randomized, wait list controlled trial, we will evaluate the effectiveness of a patient-centered 'a-la-carte' approach that offers subjects a variety of modes of interaction from which they can choose as many or few as they wish, compared to a 'set menu' approach and usual care. This unique 'a-la-carte' self-management program will be offered to 50 African-American lupus patients participating in a longitudinal observational web-based SLE Database at the Medical University of South Carolina. Each individualized intervention plan will include 1-4 options, including a mail-delivered arthritis kit, addition and access to an online message board, participation in a support group, and enrollment in a local self-management program. A 'set menu' control group of 50 lupus patients will be offered a standardized chronic disease self-management program only, and a control group of 50 lupus patients will receive usual care. Outcomes will include changes in (a) health behaviors, (b) health status, (c) health care utilization, and (d) biological markers (urinary catecholamines). DISCUSSION: Such a culturally sensitive educational intervention which includes self-selection of program components has the potential to improve disparate trends in quality of life, disease activity, depression, and stress among African-American lupus patients, as better outcomes have been documented when participants are able to choose/dictate the content and/or pace of the respective treatment/intervention program. Since there is currently no "gold standard" self-management program specifically for lupus, this project may have a considerable impact on future research and policy decisions. TRIAL REGISTRATION: NCT01837875 ; April 18, 2013.

Glycosphingolipid Levels in Urine Extracellular Vesicles Enhance Prediction of Therapeutic Response in Lupus Nephritis.

The development of nephritis increases the risk of morbidity and mortality in systemic lupus erythematosus (SLE) patients. While standard induction therapies, such as mycophenolate mofetil (MMF) induce clinical remission (i.e., complete response) in approximately 50% of SLE patients with nephritis, many patients fail to respond. Therapeutic response is often not assessed until 6-12 months after beginning treatment. Those patients that fail to respond to treatment continue to accumulate organ damage, thus, there is a critical need to predict which patients will fail therapy before beginning treatment, allowing physicians to optimize therapy. Our previous studies demonstrated elevated urine, but not serum, glycosphingolipids (GSLs) in SLE patients with nephritis compared to SLE patients without nephritis, suggesting the urine GSLs were derived from the kidney. In this study, we measured the GSLs hexosylceramide and lactosylceramide in extracellular vesicles isolated from longitudinal urine samples of LN patients that were treated with MMF for 12 months. GSL levels were significantly elevated in the baseline samples (prior to treatment) of non-responders compared to complete responders. While a few other proteins measured in the whole urine were higher in non-responders at baseline, only GSLs demonstrated a significant ability to discriminate treatment response in lupus nephritis patients.

Differential DNA Methylation Landscape in Skin Fibroblasts from African Americans with Systemic Sclerosis.

The etiology and reasons underlying the ethnic disparities in systemic sclerosis (SSc) remain unknown. African Americans are disproportionally affected by SSc and yet are underrepresented in research. The aim of this study was to comprehensively investigate the association of DNA methylation levels with SSc in dermal fibroblasts from patients of African ancestry. Reduced representation bisulfite sequencing (RRBS) was performed on primary dermal fibroblasts from 15 SSc patients and 15 controls of African ancestry, and over 3.8 million CpG sites were tested for differential methylation patterns between cases and controls. The dermal fibroblasts from African American patients exhibited widespread reduced DNA methylation. Differentially methylated CpG sites were most enriched in introns and intergenic regions while depleted in 5' UTR, promoters, and CpG islands. Seventeen genes and eleven promoters showed significant differential methylation, mostly in non-coding RNA genes and pseudogenes. Gene set enrichment analysis (GSEA) and gene ontology (GO) analyses revealed an enrichment of pathways related to interferon signaling and mesenchymal differentiation. The hypomethylation of DLX5 and TMEM140 was accompanied by these genes' overexpression in patients but underexpression for lncRNA MGC12916. These data show that differential methylation occurs in dermal fibroblasts from African American patients with SSc and identifies novel coding and non-coding genes.

Race disparity in blood sphingolipidomics associated with lupus cardiovascular comorbidity.

Systemic lupus erythematous (SLE) is a chronic multi-organ autoimmune disease. Genetic and environmental factors contribute to disease onset and severity. Sphingolipids are signaling molecules involved in regulating cell functions and have been associated with multiple genetic disease processes. African-Americans are more likely to suffer from SLE morbidity than Whites. The Medical University of South Carolina has banked plasma samples from a well-characterized lupus cohort that includes African-Americans and Whites. This study examined the influence of race on plasma sphingolipid profiles in SLE patients and association of sphingolipid levels with comorbid atherosclerosis and SLE disease activity. Mass spectrometry revealed that healthy African-Americans had higher sphingomyelin levels and lower lactosylcermide levels compared to healthy Whites. SLE patients, irrespective of race, had higher levels of ceramides, and sphingoid bases (sphingosine and dihydrosphingosine) and their phosphates compared to healthy subjects. Compared to African-American controls, African-American SLE patients had higher levels of ceramides, hexosylceramides, sphingosine and dihydrosphingosine 1-phosphate. Compared to White controls, White SLE patients exhibited higher levels of sphingoid bases and their phosphates, but lower ratios of C16:0 ceramide/sphingosine 1-phosphate and C24:1 ceramide/sphingosine 1-phosphate. White SLE patients with atherosclerosis exhibited lower levels of sphingoid bases compared to White SLE patients without atherosclerosis. In contrast, African-American SLE patients with atherosclerosis had higher levels of sphingoid bases and sphingomyelins compared to African-American SLE patients without atherosclerosis. Compared to White SLE patients with atherosclerosis, African-American SLE patients with atherosclerosis had higher levels of select sphingolipids. Plasma levels of sphingosine, C16:0 ceramide/sphingosine 1-phosphate ratio and C24:1 ceramide/sphingosine 1-phosphate ratio significantly correlated with SLEDAI in the African-American but not White SLE patients. The C16:0 ceramide/sphingosine 1-phosphate ratio in SLE patients, and levels of C18:1 and C26:1 lactosylcermides, C20:0 hexosylceramide, and sphingoid bases in SLE patients with atherosclerosis could be dependent on race. Further ethnic studies in SLE cohorts are necessary to verify use of sphingolipidomics as complementary diagnostic tool.

I too, am America: a review of research on systemic lupus erythematosus in African-Americans.

Systemic lupus erythematosus (SLE) is a multi-organ autoimmune disorder that can cause significant morbidity and mortality. A large body of evidence has shown that African-Americans experience the disease more severely than other racial-ethnic groups. Relevant literature for the years 2000 to August 2015 were obtained from systematic searches of PubMed, Scopus, and the EBSCOHost platform that includes MEDLINE, CINAHL, etc. to evaluate research focused on SLE in African-Americans. Thirty-six of the 1502 articles were classified according to their level of evidence. The systematic review of the literature reported a wide range of adverse outcomes in African-American SLE patients and risk factors observed in other mono and multi-ethnic investigations. Studies limited to African-Americans with SLE identified novel methods for more precise ascertainment of risk and observed novel findings that hadn't been previously reported in African-Americans with SLE. Both environmental and genetic studies included in this review have highlighted unique African-American populations in an attempt to isolate risk attributable to African ancestry and observed increased genetic influence on overall disease in this cohort. The review also revealed emerging research in areas of quality of life, race-tailored interventions, and self-management. This review reemphasizes the importance of additional studies to better elucidate the natural history of SLE in African-Americans and optimize therapeutic strategies for those who are identified as being at high risk.

Rheumatology Informatics System for Effectiveness: A National Informatics-Enabled Registry for Quality Improvement.

OBJECTIVE: The Rheumatology Informatics System for Effectiveness (RISE) is a national electronic health record (EHR)-enabled registry. RISE passively collects data from EHRs of participating practices, provides advanced quality measurement and data analytic capacities, and fulfills national quality reporting requirements. Here we report the registry's architecture and initial data, and we demonstrate how RISE is being used to improve the quality of care. METHODS: RISE is a certified Centers for Medicare and Medicaid Services Qualified Clinical Data Registry, allowing collection of data without individual patient informed consent. We analyzed data between October 1, 2014 and September 30, 2015 to characterize initial practices and patients captured in RISE. We also analyzed medication use among rheumatoid arthritis (RA) patients and performance on several quality measures. RESULTS: Across 55 sites, 312 clinicians contributed data to RISE; 72% were in group practice, 21% in solo practice, and 7% were part of a larger health system. Sites contributed data on 239,302 individuals. Among the subset with RA, 34.4% of patients were taking a biologic or targeted synthetic disease-modifying antirheumatic drug (DMARD) at their last encounter, and 66.7% were receiving a nonbiologic DMARD. Examples of quality measures include that 55.2% had a disease activity score recorded, 53.6% a functional status score, and 91.0% were taking a DMARD in the last year. CONCLUSION: RISE provides critical infrastructure for improving the quality of care in rheumatology and is a unique data source to generate new knowledge. Data validation and mapping are ongoing and RISE is available to the research and clinical communities to advance rheumatology.

Oral administration of a decaffeinated green tea (Camellia sinensis) extract did not alter urinary 8-epi-prostaglandin F(2 alpha), a biomarker for in-vivo lipid peroxidation.

Oxidative stress is involved in the pathogenesis of numerous chronic human diseases. The objective of this study was to determine whether administration of a decaffeinated green tea extract providing 844 mg flavonoids daily reduced the urinary excretion of 8-epi-prostaglandin F(2 alpha) (8-epi-PGF(2 alpha)), a product of lipid peroxidation in cellular membranes and of low-density lipoprotein (LDL). Nine healthy male and female subjects were studied at baseline and after 14 days of green tea supplementation. Analysis of urinary 8-epi-PGF(2 alpha) was performed using immunoaffinity extraction-gas chromatography-negative ion chemical ionization-mass spectrometry (GC-NICI-MS). Urinary 8-epi-PGF(2 alpha) concentrations were 0.286+/-0.120 nmol (mmol creatinine)(-1) at baseline and 0.244+/-0.177 nmol mmol(-1) creatinine after green tea supplementation. There were no significant differences in the excretion of urinary 8-epi-PGF(2 alpha) after treatment with green tea. We conclude that 14 days of green tea supplementation did not significantly alter in-vivo lipid peroxidation.

Improving clinical trial accrual by streamlining the referral process.

OBJECTIVE: Poor accrual rates impede clinical trial efficiency and significantly contribute to development costs for new interventions. Many providers recognize investigational treatments are their patients' best opportunities for improvement, but operational clinical burdens impede providers' awareness of, and ability to leverage, such opportunities. We aimed to develop a new workflow for non-intrusively apprising providers of trial opportunities for their patients and enabling providers to efficiently refer potential trial candidates to study teams for preliminary eligibility review. MATERIALS AND METHODS: We developed a small information system to monitor institutional systems, identify patients potentially eligible for ongoing clinical trials, and give providers a non-intrusive, one-click method to refer such patients to study teams for preliminary eligibility vetting. RESULTS: In 18 months of pilot experience, providers invited study teams to vet 11% of 1844 patients found potentially eligible for 38 trials registered with the system. Seventy-nine patients were conservatively estimated to be accrued. Accrual rates were boosted for several trials. Results of a survey indicated most users were satisfied with the system. DISCUSSION: Providers' time constraints impede their pursuit of investigational opportunities for their patients. In pilot experience, our novel approach to facilitating such pursuits yielded improved accrual, benefiting trials and presumably patients, too. Our approach may bear particular fruit for cross-disciplinary referrals for screening. CONCLUSION: Systems for assisting providers in making investigational opportunities available to their patients may benefit from careful attention to provider workflow and time constraints. Our system might further benefit from improved patient/trial matching and shorter messages.

An Intervention to Reduce Psychosocial and Biological Indicators of Stress in African American Lupus Patients: The Balancing Lupus Experiences with Stress Strategies Study.

OBJECTIVE: Very little is known about the impact of psychosocial stress on African American lupus patients. Due to the exposure of African Americans to a unique trajectory of stressors throughout life, it may be critical to understand the relationship between psychosocial stress and underlying biological mechanisms that influence disease activity and pathology in this high risk group. METHODS: The Balancing Lupus Experiences with Stress Strategies (BLESS) study piloted the validated "Better Choices, Better Health" Chronic Disease Self-Management Program (CDSMP) in 30 African-American lupus patients participating in the SLE Clinic Database Project at the Medical University of South Carolina (MUSC). Measures of psychosocial and biological indicators of stress were collected in all of the patients in each of the study conditions before and after intervention activities, as well as four months post-intervention, to assess the effectiveness of the program in reducing perceived and biological indicators of stress. RESULTS: Participation in the workshops had large effects upon depression (d=1.63 and d = 1.68), social/role activities limitations (d =1.15), health distress (d =1.13 and d = 0.78), fatigue (d =1.03), pain (d =0.96), and lupus self-efficacy (d =0.85). Neither the differences in cortisol or DHEA levels pre- and post-intervention were found to be significantly different between intervention participants and controls. CONCLUSION: The intervention workshops acted to reduce perceived stress and improve quality of life. Our findings imply that comparable, if not more significant gains in relevant health indicators are possible in African American patients when provided the opportunity to participate in CDSMP's.

Stress and Depression in Relation to Functional Health Behaviors in African American Patients with Systemic Lupus Erythematosus.

OBJECTIVE: While increased psychological distress in SLE has been clinically and empirically reported, the relationship between emotional distress, treatment adherence, and disease activity are complex and even more unclear in African American lupus patients. In an effort to elucidate this phenomenon in these patients, this exploratory study aimed to investigate relationships between stress, depression, and various health behaviors in this group. METHODS: Thirty patients invited to participate in this study were African American systemic lupus erythematosus (SLE) patients attending rheumatology clinics at the Medical University of South Carolina (MUSC). This study was part of a larger interventional pilot study, the Balancing Lupus Experiences with Stress Strategies (BLESS) study, that included a comprehensive battery of psychosocial, quality of life, and behavior change measures. RESULTS: When looking at the association between anxiety/stress and functionality, levels of reported stress had strong effects upon functionality, especially between health distress and functionality. When looking at the association between depressive symptoms and functionality, depressive symptoms had moderate effects upon social/role limitations and nights spent in the hospital. CONCLUSION: Not only did the larger pilot project demonstrate significant reductions in stress and depression as a result of workshop participation; this nested study also showed that those improvements were positively associated with improved health behaviors. These results could have implications for developing interventions to improve disease experience and quality of life in SLE patients with stress and depression.

Predictors of non-response and non-compliance in African American lupus patients: Findings from the Balancing Lupus Experiences with Stress Strategies (BLESS) Study.

Arthritis self-management education has demonstrated significant improvements in health distress, self-reported global health, and activity limitation, with trends toward improvement in self efficacy and mental stress management. Consequently, numerous national agencies have recommended arthritis self-management education to complement medical care. Despite these recommendations, arthritis self-management education has reached only a limited number of people. Compliance is also a persistent problem in standardized programs. As part of the Balancing Lupus Experiences with Stress Strategies (BLESS) Study, a validated psychosocial stress intervention was piloted among a cohort of African American lupus patients participating in an SLE database project at the Medical University of South Carolina (MUSC). Recruitment attempts were made with the 330 database participants who met eligibility requirements for the study. While enrollment was limited to 30 participants (n=15 controls and n=15 intervention), two of the participants assigned to the intervention group did not attend any intervention sessions and several participants did not complete post-intervention questionnaires. Therefore, data were analyzed on 30 participants at baseline, 25 (n=13 controls and n=12 intervention) at post-intervention, and 22 (n=12 controls and n=10 intervention) at four months post-intervention. In an effort to characterize those who fully participated in the study and those who were non-compliant or non-responsive to recruitment attempts, we obtained descriptive data from African-American Lupus patients participating in the SLE Clinic Database Project. This information can be used to develop and refine future intervention activities.

Variable association of reactive intermediate genes with systemic lupus erythematosus in populations with different African ancestry.

OBJECTIVE: Little is known about the genetic etiology of systemic lupus erythematosus (SLE) in individuals of African ancestry, despite its higher prevalence and greater disease severity. Overproduction of nitric oxide (NO) and reactive oxygen species are implicated in the pathogenesis and severity of SLE, making NO synthases and other reactive intermediate-related genes biological candidates for disease susceptibility. We analyzed variation in reactive intermediate genes for association with SLE in 2 populations with African ancestry. METHODS: A total of 244 single-nucleotide polymorphisms (SNP) from 53 regions were analyzed in non-Gullah African Americans (AA; 1432 cases and 1687 controls) and the genetically more homogeneous Gullah of the Sea Islands of South Carolina (133 cases and 112 controls). Single-marker, haplotype, and 2-locus interaction tests were computed for these populations. RESULTS: The glutathione reductase gene GSR (rs2253409; p = 0.0014, OR 1.26, 95% CI 1.09-1.44) was the most significant single SNP association in AA. In the Gullah, the NADH dehydrogenase NDUFS4 (rs381575; p = 0.0065, OR 2.10, 95% CI 1.23-3.59) and NO synthase gene NOS1 (rs561712; p = 0.0072, OR 0.62, 95% CI 0.44-0.88) were most strongly associated with SLE. When both populations were analyzed together, GSR remained the most significant effect (rs2253409; p = 0.00072, OR 1.26, 95% CI 1.10-1.44). Haplotype and 2-locus interaction analyses also uncovered different loci in each population. CONCLUSION: These results suggest distinct patterns of association with SLE in African-derived populations; specific loci may be more strongly associated within select population groups.

Efficacy and safety of rituximab in moderately-to-severely active systemic lupus erythematosus: the randomized, double-blind, phase II/III systemic lupus erythematosus evaluation of rituximab trial.

OBJECTIVE: B cells are likely to contribute to the pathogenesis of systemic lupus erythematosus (SLE), and rituximab induces depletion of B cells. The Exploratory Phase II/III SLE Evaluation of Rituximab (EXPLORER) trial tested the efficacy and safety of rituximab versus placebo in patients with moderately-to-severely active extrarenal SLE. METHODS: Patients entered with >or=1 British Isles Lupus Assessment Group (BILAG) A score or >or=2 BILAG B scores despite background immunosuppressant therapy, which was continued during the trial. Prednisone was added and subsequently tapered. Patients were randomized at a ratio of 2:1 to receive rituximab (1,000 mg) or placebo on days 1, 15, 168, and 182. RESULTS: In the intent-to-treat analysis of 257 patients, background treatment was evenly distributed among azathioprine, mycophenolate mofetil, and methotrexate. Fifty-three percent of the patients had >or=1 BILAG A score at entry, and 57% of the patients were categorized as being steroid dependent. No differences were observed between placebo and rituximab in the primary and secondary efficacy end points, including the BILAG-defined response, in terms of both area under the curve and landmark analyses. A beneficial effect of rituximab on the primary end point was observed in the African American and Hispanic subgroups. Safety and tolerability were similar in patients receiving placebo and those receiving rituximab. CONCLUSION: The EXPLORER trial enrolled patients with moderately-to-severely active SLE and used aggressive background treatment and sensitive cutoffs for nonresponse. No differences were noted between placebo and rituximab in the primary and secondary end points. Further evaluation of patient subsets, biomarkers, and exploratory outcome models may improve the design of future SLE clinical trials.

Association of reactive oxygen and nitrogen intermediate and complement levels with apoptosis of peripheral blood mononuclear cells in lupus patients.

OBJECTIVE: Both increased production of reactive oxygen and nitrogen intermediates (RONI) and reduced levels of complement may play a role in the increased apoptosis and reduced clearance of apoptotic cells in systemic lupus erythematosus (SLE). The objective of this study was to evaluate both processes in a parallel, prospective, longitudinal manner. METHODS: Sixty-seven SLE patients were evaluated during multiple visits, and 31 healthy control subjects were evaluated once or twice. Clinical and laboratory features of SLE disease activity were determined, and blood was collected for measurement of serum nitrate plus nitrite (NOx) levels and for isolation of peripheral blood mononuclear cells (PBMCs). PBMCs were cultured with a nitric oxide (NO) donor and SLE or control plasma, with or without heat inactivation, cobra venom factor (CVF), or lipopolysaccharide plus interferon-gamma treatment. Cells were analyzed for apoptotic index (AI), cellular subsets, and RONI production. RESULTS: The PBMC AI was associated with SLE and was inversely associated with complement levels over time. Changes in the AI with addition of a NO donor was longitudinally associated with serum NOx levels, and stimulation of SLE PBMCs led to parallel increases in RONI production and apoptosis. Addition of SLE plasma resulted in a greater PBMC AI, an effect that was increased with heat inactivation and was corrected with CVF treatment. CONCLUSION: These data suggest that the greater AI observed in SLE PBMCs relates to increased PBMC RONI production and reduced complement levels. The longitudinal nature of these parallel associations within individuals suggests that these processes are dynamic and additive.

Leveraging of open EMR architecture for clinical trial accrual.

Accrual to clinical trials is a major bottleneck in scientific progress in clinical medicine. Many methods for identifying potential subjects and improving accrual have been pursued; few have succeeded, and none have proven generally reproducible or scalable. We leveraged the open architecture of the core clinical data repository of our electronic medical record system to prototype a solution for this problem in a manner consistent with contemporary regulations and research ethics. We piloted the solution with a local investigator-initiated trial for which candidate identification was expected to be difficult. Key results in the eleven months of experience to date include automated screening of 7,296,708 lab results from 69,288 patients, detection of 1,768 screening tests of interest, identification of 70 potential candidates who met all further automated criteria, and accrual of three candidates to the trial. Hypotheses for this disappointing impact on accrual, and directions for future research, are discussed.