Scaling-up NLP Pipelines to Process Large Corpora of Clinical Notes.

INTRODUCTION: This article is part of the Focus Theme of Methods of Information in Medicine on "Big Data and Analytics in Healthcare". OBJECTIVES: This paper describes the scale-up efforts at the VA Salt Lake City Health Care System to address processing large corpora of clinical notes through a natural language processing (NLP) pipeline. The use case described is a current project focused on detecting the presence of an indwelling urinary catheter in hospitalized patients and subsequent catheter-associated urinary tract infections. METHODS: An NLP algorithm using v3NLP was developed to detect the presence of an indwelling urinary catheter in hospitalized patients. The algorithm was tested on a small corpus of notes on patients for whom the presence or absence of a catheter was already known (reference standard). In planning for a scale-up, we estimated that the original algorithm would have taken 2.4 days to run on a larger corpus of notes for this project (550,000 notes), and 27 days for a corpus of 6 million records representative of a national sample of notes. We approached scaling-up NLP pipelines through three techniques: pipeline replication via multi-threading, intra-annotator threading for tasks that can be further decomposed, and remote annotator services which enable annotator scale-out. RESULTS: The scale-up resulted in reducing the average time to process a record from 206 milliseconds to 17 milliseconds or a 12- fold increase in performance when applied to a corpus of 550,000 notes. CONCLUSIONS: Purposely simplistic in nature, these scale-up efforts are the straight forward evolution from small scale NLP processing to larger scale extraction without incurring associated complexities that are inherited by the use of the underlying UIMA framework. These efforts represent generalizable and widely applicable techniques that will aid other computationally complex NLP pipelines that are of need to be scaled out for processing and analyzing big data.

Intention to adhere to HIV treatment: a patient-centred predictor of antiretroviral adherence.

OBJECTIVES: Despite the effectiveness of highly active antiretroviral therapy (HAART), HIV remains a major cause of mortality in the USA, largely as a result of poor HIV treatment adherence. In this study we assessed the association between five patient-centred factors and adherence to HIV treatment. METHODS: We surveyed 244 adults at two HIV clinics in Houston, Texas between October 2009 and April 2010. Participants were given a questionnaire and their charts were reviewed for clinical data. Survey items assessed the following factors: self-assessed HIV knowledge, awareness of disease biomarkers, intention to adhere to HIV treatment, health literacy and decision-making style. The primary outcome measure was HAART adherence during the previous month. Logistic regressions were performed to calculate the effect of each factor on adherence. RESULTS: All participants had HIV/AIDS and were on HAART at enrolment. Eight per cent of participants were female, 57% were African-American and 16% were Hispanic. Mean age was 58.1 years. Sixty-eight per cent were adherent to HAART during the last month. On univariate analysis, a preference for wanting choices, correct knowledge of recent HIV viral load level, and intention to adhere to HIV treatment were significantly associated with adherence. On multivariate analysis, only intention to adhere to HIV treatment remained statistically significant after adjusting for other factors (odds ratio 2.2; 95% confidence interval 1.1 to 4.3). CONCLUSIONS: Intention to adhere to HIV treatment was significantly associated with self-reported adherence to HAART. Interventions that bolster patients' intentions to adhere to HIV treatment during clinical encounters may improve adherence to HAART and HIV control.

Bacteriophages are synergistic with bacterial interference for the prevention of Pseudomonas aeruginosa biofilm formation on urinary catheters.

AIMS: We hypothesized that pretreating urinary catheters with benign Escherichia coli HU2117 plus an antipseudomonal bacteriophage (ΦE2005-A) would prevent Pseudomonas aeruginosa biofilm formation on catheters--a pivotal event in the pathogenesis of catheter-associated urinary tract infection (CAUTI). METHODS AND RESULTS: Silicone catheter segments were exposed to one of four pretreatments (sterile media; E. coli alone; phage alone; E. coli plus phage), inoculated with P. aeruginosa and then incubated up to 72 h in human urine before rinsing and sonicating to recover adherent bacteria. Pseudomonas aeruginosa adherence to catheters was almost 4 log(10) units lower when pretreated with E. coli plus phage compared to no pretreatment (P < 0.001) in 24-h experiments and more than 3 log(10) units lower in 72-h experiments (P < 0.05). Neither E. coli nor phage alone generated significant decreases. CONCLUSIONS: The combination of phages with a pre-established biofilm of E. coli HU2117 was synergistic in preventing catheter colonization by P. aeruginosa. SIGNIFICANCE AND IMPACT OF THE STUDY: We describe a synergistic protection against colonization of urinary catheters by a common uropathogen. Escherichia coli-coated catheters are in clinical trials; adding phage may offer additional benefit.

[Surgical management of Pyoderma gangrenosum]. / Chirurgische Therapie beim Pyoderma gangraenosum.

Pyoderma gangrenosum is a rare affection of unknown etiology, which is often associated with systemic diseases such as chronic inflammatory bowel disease, hematologic disorders, carcinomas and arthritis. Treatment may include topical corticosteroids or calcineurin inhibitors in combination with systemic corticosteroids, cyclosporine A, azathioprine, cyclophosphamide, mycophenolate mofetil, intravenous immunoglobulins or monoclonal antibodies against TNFα but all these approaches are off-label. Surgical therapy is difficult because of pathergy. Nevertheless, after having stopped the inflammation, the ulcers can be treated by split thickness skin grafts and simultaneous immunosuppression. We present three cases with successful surgical treatment.

A bacterial interference strategy for prevention of UTI in persons practicing intermittent catheterization.

STUDY DESIGN: Non-randomized pilot trial. OBJECTIVES: To determine whether Escherichia coli 83972-coated urinary catheters in persons with spinal cord injury (SCI) practicing an intermittent catheterization program (ICP) could (1) achieve bladder colonization with this benign organism and (2) decrease the rate of symptomatic urinary tract infection (UTI). SETTING: Outpatient SCI clinic in a Veterans Affairs hospital (USA). METHODS: Participants had neurogenic bladders secondary to SCI, were practicing ICP, had experienced at least one UTI and had documented bacteruria within the past year. All participants received a urinary catheter that had been pre-inoculated with E. coli 83972. The catheter was left in place for 3 days and then removed. Participants were followed with urine cultures and telephone calls weekly for 28 days and then monthly until E. coli 83972 was lost from the urine. Outcome measures were (1) the rate of successful bladder colonization, defined as the detection (>or=10(2) cfu ml(-1)) of E. coli 83972 in urine cultures for >3 days after catheter removal and (2) the rate of symptomatic UTI during colonization with E. coli 83972. RESULTS: Thirteen participants underwent 19 insertions of study catheters. Eight participants (62%) became successfully colonized for >3 days after catheter removal. In these 8 participants, the rate of UTI during colonization was 0.77 per patient-year, in comparison with the rate of 2.27 UTI per patient-year before enrollment. CONCLUSIONS: E. coli 83972-coated urinary catheters are a viable means of achieving bladder colonization with this potentially protective strain in persons practicing ICP.

Proteus bacteriuria is associated with significant morbidity in spinal cord injury.

STUDY DESIGN: Retrospective chart review. OBJECTIVES: We investigated the morbidity associated with Proteus bacteriuria in a spinal cord injured (SCI) population. SETTING: Michael E DeBakey Veterans Affairs Medical Center in Houston, Texas, USA. METHODS: We reviewed the medical records of all veterans with SCI who received care in our medical center during the past 3 years. Proteus bacteriuria was defined as the growth of Proteus species in any urine culture during the study period. Urinary stones were defined as either renal or bladder calculi. RESULTS: During the study period, 71 of the 501 subjects (14%) had Proteus and 90 (18%) had urinary stones. Twenty-seven percent of the subjects with Proteus had stones, and the association of Proteus with stones was significant (P<0.05). Proteus bacteriuria was likewise associated with complete injury, hospitalization, decubitus ulcers, and history of stones (P<0.001). Subjects using indwelling catheters, either transurethral or suprapubic, were significantly more likely to have Proteus, whereas subjects practising spontaneous voiding and clean intermittent catheterization were significantly less likely to have Proteus. In the 90 patients with stones, Proteus was associated with requiring treatment for stones and having multiple stones (P<0.01). Twenty-five of the 90 patients with stones (28%) required treatment, most often with lithotripsy, and 6 (7%) developed urosepsis. CONCLUSIONS: In persons with SCI, Proteus was found in subjects with a greater degree of impairment who were more likely to be hospitalized, to have decubiti, and to use indwelling catheters. Bacteriuria with Proteus predicted urologic complications in persons with SCI. STATEMENT OF ETHICS: All applicable institutional and governmental regulations concerning the ethical use of human volunteers were followed during the course of this research.

Tuberculous pericarditis: optimal diagnosis and management.

Pericarditis is a rare manifestation of tuberculous disease. The appropriate diagnostic workup and optimal therapeutic management are not well defined. We present 10 new cases of tuberculous pericarditis and review the relevant literature. The specific topics addressed are (1) the importance of tissue for diagnosis, (2) the optimal surgical management, (3) the role of corticosteroids, and (4) the impact of human immunodeficiency virus (HIV) on the management of this disease. The cases and the literature suggest that the optimal management includes an open pericardial window with biopsy, both for diagnosis and to prevent reaccumulation of fluid. Corticosteroids probably offer some benefit in preventing fluid reaccumulation as well. The data are inconclusive regarding whether open drainage or corticosteroid use prevents progression to constrictive pericarditis. No studies have addressed these issues specifically in HIV-positive patients, but the 3 HIV-positive patients in our series had an excellent response to drainage and antituberculous therapy.

Clear cell hidradenoma in a young girl.

Clear cell hidradenoma was diagnosed in a girl at 3(1/2) years of age. Only one case of hidradenoma has been documented in the first decade of life, although it remains unclear whether it was clear cell hidradenoma. This case demonstrates that clear cell hidradenoma is a rare differential diagnosis of cutaneous tumors even in young children, which is of special interest, because malignant transformations can occur.

[Persistent erythema and edema of the face associated with rosacea and lymph vessel dysplasia]. / Persistierendes Erythem und Odem des Gesichts bei Rosazea und Lymphgefässdysplasie.

A 24-year-old woman with lymph vessel dysplasia had experienced a progressive edema of her legs since her second year of life and progressive facial edema for the past year. She also had telangiectasias and papules on the background of a diffuse erythema as well as marked seborrhea on her face. Histopathological examination of a representative facial lesion revealed a granulomatous dermatitis with periadnexal distribution mainly consisting of lymphocytes and histiocytes. In addition, there was a moderate fibrosis of the dermis with numerous mast cells. By duplex ultrasound, a diagnosis of a massive edema of the legs without evidence for chronic venous insufficiency was made. The clinical and histopathological findings were consistent with solid persistent erythema and edema of the face associated with rosacea and lymph vessel dysplasia. The chronic course, absence of serological abnormalities and nonspecific histopathological features as well as resistance to therapy are the most important diagnostic criteria of this disease also known as Morbihan's disease.

[Three-quadrant syndrome in Klippel-Trenaunay syndrome and primary lymphedema of both legs]. / Drei-Quadranten-Syndrom bei Klippel-Trenaunay-Syndrom und primären Lymphödemen beider Beine.

A 34-year-old woman with extensive Klippel-Trenaunay syndrome is presented. Clinical and radiological tests demonstrated that three quadrants are affected with haemangiomas, varicose veins and bone abnormalities. In addition, our patient suffers from congenital lymphoedema of both legs. Associated findings such as intestinal haemangiomata, vascular hamartomas, lipoma or arteriovenous abnormalities of the spinal cord were not apparent. The treatment is only symptomatic with compression bandages and an orthopaedic appliance for compensation of the different leg length.