Charles J. Mullett

Assessment of commercial NLP engines for medication information extraction from dictated clinical notes.

PURPOSE We assessed the current state of commercial natural language processing (NLP) engines for their ability to extract medication information from textual clinical documents. METHODS Two thousand de-identified discharge summaries and family practice notes were submitted to four commercial NLP engines with the request to extract all medication information. The four sets of returned results were combined to create a comparison standard which was validated against a manual, physician-derived gold standard created from a subset of 100 reports. Once validated, the individual vendor results for medication names, strengths, route, and frequency were compared against this automated standard with precision, recall, and F measures calculated. RESULTS Compared with the manual, physician-derived gold standard, the automated standard was successful at accurately capturing medication names (F measure=93.2%), but performed less well with strength (85.3%) and route (80.3%), and relatively poorly with dosing frequency (48.3%). Moderate variability was seen in the strengths of the four vendors. The vendors performed better with the structured discharge summaries than with the clinic notes in an analysis comparing the two document types. CONCLUSION Although automated extraction may serve as the foundation for a manual review process, it is not ready to automate medication lists without human intervention.

Left-sided CHILD syndrome caused by a nonsense mutation in the NSDHL gene

Congenital hemidysplasia with ichthyosiform nevus and limb defects (CHILD) syndrome is a rare X‐linked dominant malformation syndrome characterized by unilaterally distributed ichthyosiform nevi, often sharply delimited at the midline, and ipsilateral limb defects. At least two‐thirds of cases demonstrate involvement of the right side. Mutations in an essential enzyme of cholesterol biosynthesis, NAD(P)H steroid dehydrogenase‐like [NSDHL], have been reported in five unrelated patients with right‐sided CHILD syndrome and in a sixth patient with bilaterally, symmetric nevi and mild skeletal anomalies, but not with CHILD syndrome as originally defined. Although all of the molecularly diagnosed cases with the CHILD phenotype to date have had right‐sided disease, we report here a novel nonsense mutation (E151X) of NSDHL in an infant with left‐sided CHILD syndrome. This result demonstrates that both right‐ and left‐sided CHILD syndrome can be caused by mutations in the same gene.

Impact of a Multimodal Antimicrobial Stewardship Program on Pseudomonas aeruginosa Susceptibility and Antimicrobial Use in the Intensive Care Unit Setting

Objective. To study the impact of our multimodal antibiotic stewardship program on Pseudomonas aeruginosa susceptibility and antibiotic use in the intensive care unit (ICU) setting. Methods. Our stewardship program employed the key tenants of published antimicrobial stewardship guidelines. These included prospective audits with intervention and feedback, formulary restriction with preauthorization, educational conferences, guidelines for use, antimicrobial cycling, and de-escalation of therapy. ICU antibiotic use was measured and expressed as defined daily doses (DDD) per 1,000 patient-days. Results. Certain temporal relationships between antibiotic use and ICU resistance patterns appeared to be affected by our antibiotic stewardship program. In particular, the ICU use of intravenous ciprofloxacin and ceftazidime declined from 148 and 62.5 DDD/1,000 patient-days to 40.0 and 24.5, respectively, during 2004 to 2007. An increase in the use of these agents and resistance to these agents was witnessed during 2008–2010. Despite variability in antibiotic usage from the stewardship efforts, we were overall unable to show statistical relationships with P. aeruginosa resistance rate. Conclusion. Antibiotic resistance in the ICU setting is complex. Multimodal stewardship efforts attempt to prevent resistance, but such programs clearly have their limits.

Natural Language Processing Framework to Assess Clinical Conditions

OBJECTIVE The authors developed a natural language processing (NLP) framework that could be used to extract clinical findings and diagnoses from dictated physician documentation. DESIGN De-identified documentation was made available by i2b2 Bio-informatics research group as a part of their NLP challenge focusing on obesity and its co-morbidities. The authors describe their approach, which used a combination of concept detection, context validation, and the application of a variety of rules to conclude patient diagnoses. RESULTS The framework was successful at correctly identifying diagnoses as judged by NLP challenge organizers when compared with a gold standard of physician annotations. The authors overall kappa values for agreement with the gold standard were 0.92 for explicit textual results and 0.91 for intuited results. The NLP framework compared favorably with those of the other entrants, placing third in textual results and fourth in intuited results in the i2b2 competition. CONCLUSIONS The framework and approach used to detect clinical conditions was reasonably successful at extracting 16 diagnoses related to obesity. The system and methodology merits further development, targeting clinically useful applications.

Octreotide efficacy in the treatment of chylothoraces following cardiac surgery in infants and children.

Objective: To examine the efficacy of octreotide in resolving chylothoraces in infants and children following cardiac surgery. Design: Retrospective chart review. Setting: Pediatric intensive care unit of a tertiary care center. Patients: All children who received octreotide for the treatment of chylothoraces following surgery for congenital heart disease over a 30-month period between 2001–2004. Interventions: Octreotide infusion. Measurements and main results: Eight courses of octreotide treatment were identified in seven patients who met our inclusion criteria. The median duration of therapy was 5 days, and dosing ranged from 1 to 4 &mgr;g/kg/hr. Treatment did not result in an overall decrease in average chest tube output after 3 days of therapy. However, in two patients (29%) the chylothoraces ultimately resolved during the octreotide infusion. Treatment was well tolerated, and no serious side effects were noted. Conclusion: In contrast to previously published reports, we find octreotide therapy for postoperative chylothoraces to be successful in only a minority of cases.

Machine learning-based coreference resolution of concepts in clinical documents

OBJECTIVE Coreference resolution of concepts, although a very active area in the natural language processing community, has not yet been widely applied to clinical documents. Accordingly, the 2011 i2b2 competition focusing on this area is a timely and useful challenge. The objective of this research was to collate coreferent chains of concepts from a corpus of clinical documents. These concepts are in the categories of person, problems, treatments, and tests. DESIGN A machine learning approach based on graphical models was employed to cluster coreferent concepts. Features selected were divided into domain independent and domain specific sets. Training was done with the i2b2 provided training set of 489 documents with 6949 chains. Testing was done on 322 documents. RESULTS The learning engine, using the un-weighted average of three different measurement schemes, resulted in an F measure of 0.8423 where no domain specific features were included and 0.8483 where the feature set included both domain independent and domain specific features. CONCLUSION Our machine learning approach is a promising solution for recognizing coreferent concepts, which in turn is useful for practical applications such as the assembly of problem and medication lists from clinical documents.

Comparison of Intraoperative Aminophylline Versus Furosemide in Treatment of Oliguria During Pediatric Cardiac Surgery.

Objectives: To determine if intraoperative aminophylline was superior to furosemide to prevent or attenuate postoperative cardiac surgery-associated acute kidney injury. Design: Single-center, historical control, retrospective cohort study. Setting: PICU, university-affiliated children’s hospital. Patients: Children with congenital heart disease in PICU who received furosemide or aminophylline to treat intraoperative oliguria. Interventions: Intraoperative oliguria was treated either with furosemide (September 2007 to February 2012) or with aminophylline (February 2012 to June 2013). The postoperative 48 hours renal outcomes of the aminophylline group were compared with the furosemide group. The primary outcomes were acute kidney injury and renal replacement therapy use at 48 hours postoperatively. Surgical complexity was accounted for by the use of Risk Adjustment for Congenital Heart Surgery-1 score. Measurements and Main Results: The study involves 69 months of observation. There were 200 cases younger than 21 years old reviewed for this study. Eighty-five cases (42.5%) developed acute kidney injury. The aminophylline group patients produced significantly more urine (mL/kg/hr) during the first 8 hours postoperatively than furosemide patients (5.1 vs 3.4 mL/kg/hr; p = 0.01). The urine output at 48 hours postoperatively was similar between the two groups. There was no difference in acute kidney injury incidence at 48 hours between the aminophylline and furosemide groups (38% vs 47%, respectively; p = 0.29). Fewer aminophylline group subjects required renal replacement therapy compared to the furosemide group subjects (n = 1 vs 7, respectively; p = 0.03). In the multi-variant predictive model, intraoperative aminophylline infusion was noted as a negative predictive factor for renal replacement therapy, but not for cardiac surgery-associated acute kidney injury. Conclusion: The intraoperative use of aminophylline was more effective than furosemide in reversal of oliguria in the early postoperative period. There were less renal replacement therapy-requiring acute kidney injury in children in the aminophylline group. Future prospective studies of intraoperative aminophylline to prevent cardiac surgery-associated acute kidney injury may be warranted.

Pharmacological management of acute bronchiolitis

This article reviews the current knowledge base related to the pharmacological treatments for acute bronchiolitis. Bronchiolitis is a common lower respiratory illness affecting infants worldwide. The mainstays of therapy include airway support, supplemental oxygen, and support of fluids and nutrition. Frequently tried pharmacological interventions, such as ribavirin, nebulized bronchodilators, and systemic corticosteroids, have not been proven to benefit patients with bronchiolitis. Antibiotics do not improve the clinical course of patients with bronchiolitis, and should be used only in those patients with proven concurrent bacterial infection. Exogenous surfactant and heliox therapy also cannot be recommended for routine use, but surfactant replacement holds promise and should be further studied.

Acute subdural hematoma: potential soccer injury in an otherwise healthy child.

A 16-year-old adolescent boy presented with headache, dizziness, loss of consciousness, and a tonic-clonic seizure after heading a soccer ball in a competitive match. A computed tomographic scan of the head revealed an acute subdural hematoma with a mass effect. The patient was emergently referred to a tertiary care facility where he eventually recovered completely with conservative care. No predisposing medical conditions were found. To the best of our knowledge, this is the first report of an intracranial hemorrhage secondary to the heading of a soccer ball alone in an otherwise healthy child without any underlying predisposing central nervous system abnormalities.

LDL cholesterol level in fifth-grade schoolchildren associates with stature

Short stature is associated with increased LDL-cholesterol levels and coronary artery disease in adults. We investigated the relationship of stature to LDL levels in children in the West Virginia Coronary Artery Risk Detection in Appalachian Communities (CARDIAC) Project to determine whether the genetically determined inverse relationship observed in adults would be evident in fifth graders. A cross-sectional survey of schoolchildren was assessed for cardiovascular risk factors. Data collected at school screenings over 18 years in WV schools were analyzed for 63,152 fifth-graders to determine relationship of LDL to stature with consideration of age, gender, and BMI. The first (shortest) quartile showed an LDL level of 93.6 mg/dl compared with an LDL level of 89.7 mg/dl for the fourth (tallest) quartile. Each incremental increase of 1 SD of height lowered LDL by 0.049 mg/dl (P < 0.0001). Multivariate analysis showed LDL to vary inversely as a function of the first (lowest) quartile of height after controlling for gender, median age, BMI percentile for age and gender, and year of screening. The odds ratio for LDL ≥ 130 mg/dl for shortest versus tallest quartile is 1.266 (95% CL 1.162–1.380). The odds ratio for LDL ≥ 160 mg/dl is 1.456 (95% CL 1.163–1.822). The relationship between short stature and LDL, noted in adults, is confirmed in childhood.