Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules

Objective

This paper describes the coreference resolution system submitted by Mayo Clinic for the 2011 i2b2/VA/Cincinnati shared task Track 1C. The goal of the task was to construct a system that links the markables corresponding to the same entity.

Materials and methods

The task organizers provided progress notes and discharge summaries that were annotated with the markables of treatment, problem, test, person, and pronoun. We used a multi-pass sieve algorithm that applies deterministic rules in the order of preciseness and simultaneously gathers information about the entities in the documents. Our system, MedCoref, also uses a state-of-the-art machine learning framework as an alternative to the final, rule-based pronoun resolution sieve.

Results

The best system that uses a multi-pass sieve has an overall score of 0.836 (average of B³, MUC, Blanc, and CEAF F score) for the training set and 0.843 for the test set.

Discussion

A supervised machine learning system that typically uses a single function to find coreferents cannot accommodate irregularities encountered in data especially given the insufficient number of examples. On the other hand, a completely deterministic system could lead to a decrease in recall (sensitivity) when the rules are not exhaustive. The sieve-based framework allows one to combine reliable machine learning components with rules designed by experts.

Conclusion

Using relatively simple rules, part-of-speech information, and semantic type properties, an effective coreference resolution system could be designed. The source code of the system described is available at https://sourceforge.net/projects/ohnlp/files/MedCoref.     

Spectrum of visual impairment among urban female school students of Surat

Aim:

Eye morbidities with or without symptoms delineate a significant morbidity among adolescent schoolgirls in India. The study was undertaken to assess the extent of visual impairment and ocular morbidity to identify influencing factors and the impact on scholastic performance.

Materials and Methods:

A population-based cross-sectional study was undertaken among 3002 urban girl students of Surat in Gujarat, India. Overall prevalence of refractive error was found to be 15.22%; myopia affected 91.47%, hyperopia 4.60%, and astigmatism 0.04%. The prevalence of myopia and astigmatism was more in higher age groups, while hyperopia was more in lower age groups; even students with good vision reported ophthalmic symptoms. Of all spectacle users, in 29.73% cases the eyesight was not found to be with the best possible corrections. Refractive error was observed to be higher among the general caste (50.98%) and among Muslims (54.05%). Still, among those with problems of eyesight, 75.93% students had good academic performance. Associated ocular morbidity was noted in 20.35% participants along with the refractive error.

Conclusion:

This study highlighted the load of eye morbidities of adolescent Indian urban girls.     

Per rectal endoscopic myotomy for the treatment of adult Hirschsprung's disease: First human case (with video)

Hirschsprung's disease (HD) is a congenital disorder characterized by the absence of intrinsic ganglion cells in submucosal and myenteric plexuses of the hindgut; and presents with constipation, intestinal obstruction and/or megacolon. HD commonly involves the rectosigmoid region (short segment HD), although shorter and longer variants of the disease are described. Standard treatment involves pull‐through surgery for short segment HD or posterior anorectal myotomy in selected ultrashort segment candidates. Third space endoscopy has evolved during the past few years. Per oral endoscopic myotomy and per oral pyloromyotomy are described for treatment of achalasia cardia and refractory gastroparesis, respectively. Using the same philosophy of muscle/sphincter disruption for spastic bowel segments, per rectal endoscopic myotomy could be considered as a treatment option for short segment HD. A 24‐year‐old male patient presented with refractory constipation since childhood, and habituated to high‐dose laxative combinations. Diagnosis was confirmed as adult short segment HD by barium enema, colonoscopic deep suction mucosal biopsies and anorectal manometry. Histopathology confirmed aganglionosis in the distal 15 cm. By implementing principles of third space endoscopy, per rectal endoscopic myotomy 20 cm in length was successfully carried out. At 24‐week follow up, the patient reported significant relief of constipation and associated symptoms. Sigmoidoscopy, anorectal manometry and barium enema confirm improved rectal distensibility and reduced rectal pressures. The present case report describes the first human experience of per rectal endoscopic myotomy for successful treatment of adult short segment HD.     

Spontaneous perforation--a rare complication of choledochal cyst.

We report a 2-year-old girl with spontaneous perforation of choledochal cyst. Preoperative diagnosis was possible by hepatobiliary scintigraphy. In view of emergency presentation and bile peritonitis, management was a staged procedure with peritoneal lavage and T-tube drainage of the biliary system, followed by excision of the cyst and Roux-en-Y hepatico-jejunostomy 3 months later.     

Early gallbladder cancer

BACKGROUND: The majority of patients with gallbladder cancer (GBC) have advanced disease at the time of diagnosis and are unresectable. Longterm survival is usually seen in a subset of patients with early GBC (EGBC)-cancer confined to the mucosa (pT1a) and muscularis (pT1b). Management guidelines of EGBC are not yet defined and are controversial. The purpose of this article is to evaluate the diagnostic aspects and effects of resectional procedures on survival outcome in patients with EGBC. STUDY DESIGN: EGBC was defined as cancer confined to the mucosa (pT1a) or muscularis (pT1b) according to the TNM classification. Clinicopathological details and survival data of 14 patients who had EGBC were analyzed. There were 9 women and 5 men, with a mean age of 60 years. RESULTS: A definite preoperative diagnosis was possible in only three patients and three patients were diagnosed at operation; the majority of patients were diagnosed incidentally after cholecystectomy for associated gallstones. Two patients underwent extended cholecystectomy and 12 patients underwent simple cholecystectomy. Two patients had pT1a and 12 had pT1b lesions. Mean (SD) survival was 71.5 (12.2) months and median survival was 42 months. There were five treatment failures with locoregional recurrence and death; all with pT1b tumors were treated by simple cholecystectomy. Cumulative 1-, 3-, and 5-year survival was 92%, 68%, and 68% respectively [corrected]. CONCLUSIONS: Simple cholecystectomy is an adequate treatment only for mucosal GBC. Patients with pT1b tumors require extended cholecystectomy. Incidental GBC extending up to the muscularis merits early reoperation for completion of extended cholecystectomy, which offers the only chance of cure.