medpie: an information extraction package for medical message board posts

SUMMARY

We have developed medpie, a software package for preparing medical message board corpora and extracting patient mentions and statistics for drugs, herbs and adverse effects experienced from them. The package is divided into web-crawling, HTML-cleaning, de-identification and information extraction modules. It also includes a sample controlled vocabulary of drugs, herbs and adverse effect terms.

AVAILABILITY

http://www.cis.upenn.edu/~ungar/medpie.zip.

DEPENDENCIES

Python 2.6 or 2.7.

Complete Barrett's excision by stepwise endoscopic resection in short-segment disease: long term outcomes and predictors of stricture

BACKGROUND AND STUDY AIMS

Complete Barrett's excision (CBE) of short-segment Barrett's high grade dysplasia (HGD) and early esophageal adenocarcinoma by stepwise endoscopic resection is a precise staging tool, detects covert synchronous disease, and may produce a sustained treatment response. Esophageal stricture is the most commonly reported complication of CBE although risk factors have not yet been clearly defined.

PATIENTS AND METHODS

Data were recorded prospectively on patients with limited co-morbidity and age ≤ 80 years undergoing CBE for histologically proven HGD or esophageal adenocarcinoma within ≤ C3M5 segments. Endoscopic resection was performed by standardized protocol every 6 - 8 weeks until CBE was achieved. Esophageal dilation was performed when patients reported dysphagia. Dysphagia scores were recorded at scheduled endoscopic surveillance or by telephone interview.

RESULTS

By intention-to-treat analysis, complete eradication of neoplasia and intestinal metaplasia was achieved in 95 % and 82 %, respectively, in 77 patients undergoing a median of 2 resection sessions (interquartile range [IQR] 1 - 3). Esophageal dilation was required in 33 % (median 3 dilations, IQR 1 - 3.5) at median follow-up of 20 months (IQR 6 - 40). Independent risk factors for dilation requirement were the number of mucosal resections at the index procedure (odds ratio [OR] 1.3 per resection, 95 % confidence interval [CI] 1.0 - 1.9; P = 0.043) and maximal extent of the Barrett's segment (OR 2.2 per cm, 95 %CI 1.2 - 3.9; P = 0.009).

CONCLUSIONS

Although CBE is highly effective in the treatment of Barrett's HGD and esophageal adenocarcinoma, the risk of post-CBE dysphagia increases with the maximal extent of the Barrett's segment and the number of mucosal resections at the index procedure. These data could be used to inform treatment decisions and identify those patients who may benefit from prophylactic therapies such as dilation.

Combined heart-liver transplantation with extended cardiopulmonary bypass

We report a case of combined heart and liver transplantation for familial amyloid polyneuropathy. This is the first such combined transplant performed in Asia, and differs from previously described cases, in that cardiopulmonary bypass was continued at partial flow during liver transplantation in our case. This was done in order to provide haemodynamic support to the cardiac graft and to protect it from the impending reperfusion insult that frequently accompanies liver transplantation. The utility of this management course is discussed, along with its actual and potential complications. We also describe the impact of a lung-protective ventilation strategy employed during cardiac transplantation.

"Eye-tracking" for assessment of image perception in gastrointestinal endoscopy with narrow-band imaging compared with white-light endoscopy

BACKGROUND AND STUDY AIMS

Narrow-band imaging (NBI) is a new imaging methodology for improving the detection rate of gastrointestinal lesions. We aimed to evaluate perception of images by NBI and corresponding standard white-light-endoscopy (WLE) using a computer-guided eye-tracking system.

METHODS

A total of 23 NBI images of various lesions with the 23 corresponding WLE images were assessed in random order by 18 subjects with various endoscopy experience. Before evaluation, a teaching set of three NBI and corresponding WLE images was shown to highlight the characteristics of lesions. An eye-tracking system (Tobii X series with integrated 17-inch monitor) was used to record the eye movements of the subjects while they examined respective images. The following parameters were measured: total time spent on image, time until first fixation of lesion, total number of fixations per image and per lesion, and number of fixations until finding the lesion.

RESULTS

In total, 828 experiments were conducted. Lesions could not be detected in 6.5 % (NBI) and 4.1 % (WLE) of images ( P = NS). The total number of fixations and total time spent on respective figures as a whole were significantly greater for NBI images compared with WLE images ( P < 0.003). However, the number of fixations until the lesion was found, the number of fixations on the lesion, and the time until first fixation of the lesion did not differ between the two image groups ( P > 0.1).

CONCLUSION

This is the first study using eye tracking to evaluate image perception in gastrointestinal endoscopy. Significant differences in the interpretation of NBI and WLE images were observed, which may be relevant for the detection and characterization of lesions during endoscopy.

Feasibility and Accuracy of Sentinel Lymph Node Biopsy in Clinically Node Negative Patients after Neoadjuvant Chemotherapy for Breast Cancer – A Systematic Review and Metaanalysis

BackgroundThe sentinel lymph node biopsy (SLNB) has become an accepted alternative to the axillary lymph node dissection (ALND) for pathologic evaluation of the axillary lymph node status in patients with early breast cancer and a clinically negative axilla. Patients with a negative sentinel lymph node are spared the ALND and its associated morbidities.Currently, there is insufficient evidence to recommend the use of SLNB in patients who have received neoadjuvant chemotherapy (NAC), and treatment of the axilla after neoadjuvant chemotherapy is an ALND.The use of neoadjuvant chemotherapy is increasing, and NAC has been shown to downstage both the primary tumour and axillary lymph nodes. Potentially, an additional proportion of patients who are node negative after NAC may be spared a full ALND and its attendant morbidities.AimsTo determine the feasibility and accuracy of SLNB in patients who have a clinically negative axilla after neoadjuvant chemotherapy for breast cancer.MethodsA systematic review of the English literature of SLNB in patients who have had neoadjuvant chemotherapy (NAC) was conducted and meta analyses performed. Studies selected had an identifiable group of patients with breast cancer who received neoadjuvant chemotherapy and were clinically node negative. These patients had a SLNB prior to the standard ALND regardless of outcome of the SLNB.ResultsTen studies that met the eligibility criteria were identified. A total of 449 patients were studied. Pooled analysis using the fixed effects model was used to calculate successful identification rate and accuracy parameters. The summary rate of identification of SLN was 94% [95% CI: 91.6% – 96.7%]. The pooled sensitivity of SLNB after NAC was 93% [95% CI: 88.5% – 96.8%] and the false negative rate 7.0% [95% CI: 3.2% – 11.5%].ConclusionSLNB in patients with a clinically node negative axilla after neoadjuvant chemotherapy is feasible and accurate.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 1013.

A phase II study of single agent abraxane as second-line therapy in patients with advanced urothelial carcinoma

e16058

Background: Metastatic urothelial cancer progressing on or after first-line platinum-based chemotherapy is incurable and has a very poor prognosis. There is no standard second-line therapy, but the taxanes including paclitaxel, have previously shown activity. Abraxane (ABI-007) is a novel well tolerated albumin-bound nanoparticle formulation of paclitaxel. The goal of this study was to determine the efficacy and tolerability of single agent Abraxane in the second-line metastatic urothelial cancer setting. Methods: Patients with measureable metastatic urothelial cancer, who progressed on or after first-line cisplatin based chemotherapy were enrolled onto this phase II, two-stage multicenter trial. Patients received Abraxane 260 mg/m2 intravenously every 3 weeks. Clinical evaluation, CBC and blood chemistries were performed every cycle and restaging CT scans every 2 cycles. Results: Fourteen patients have been enrolled to date. Patient demographics: M: F 12:2; mean age 64 (range 45–80); ECOG 0:1:2 4:5:5. A total of 57 cycles, avg 4 cycles/ patient (range 1–9) have been administered. There were three dose delays due to neuropathy, pain, and low neutrophil count respectively. There were two dose reductions due to fatigue and neuropathy. Most frequent adverse events (AE) were fatigue, alopecia, anorexia, cough and joint pain; the most frequent grade 3+ AE were fatigue, joint pain, hypertension, joint stiffness and back pain. Fourteen patients are currently evaluable for best response using RECIST criteria. There have been 5 partial responses (PR), 5 stable disease (SD) and 4 progressive disease (PD). Conclusions: Single agent Abraxane was well tolerated in the 2nd line, cisplatin refractory/resistant metastatic urothelial cancer setting. Preliminary efficacy results are encouraging with a clinical benefit rate of 71% (10 out of 14 evaluable pts having either SD or PR). Stage 1 response criteria have been met and accrual is ongoing to a total of 48 patients.

No significant financial relationships to disclose.

Cardiac disease in dialysis patients in a Jamaican hospital: echocardiographic findings that predict mortality

The aim of the study was to assess, by echocardiography, the cardiac abnormalities in a group of patients with chronic renal failure and to determine the cardiovascular predictors of mortality. The study comprised forty-five patients from the Renal Unit, University Hospital of the West Indies, Kingston, Jamaica, and was undertaken between October 1, 1998 and July 31, 2000. All echocardiography was done by a single operator. The parameters assessed were systolic dysfunction, diastolic dysfunction, ejection fraction, regional wall motion abnormalities and valvular disease. Left ventricular cavity size, septal and posterior wall thickness were measured and left ventricular mass calculated. Demographic data were obtained directly from each patient by interview. The patients were mainly of African/mixed-African origin. Their mean age was 43.2 +/- 16.0 years. The average body mass index was 23.7 +/- 6.9. Twenty-eight (60.9%) patients were male and seventeen (39.1%) female. Hypertension, chronic glomerulonephritis and diabetes mellitus were the leading causes of chronic renal failure. Blood pressure was controlled at a mean value of 145/90 mm Hg pre-dialysis and 140/90 mm Hg postdialysis. The mean duration of renal failure was 2.8 years. Echocardiographic M-mode and two dimensional apical, four chamber view measurements indicated that mean left ventricular internal diameter (LVID) diastole was 55.7 +/- 7.9 mm (normal 38-56 mm) and LVID systole was 38.9 +/- 9.8 mm (normal 24-45 mm); the mean thickness of the chamber walls was 10.3 +/- 2.8 mm and 10.6 +/- 2.4 mm for the interventricular septum (normal 6-11 mm) and left ventricular posterior wall (normal 6-11 mm) respectively. Diastolic dysfunction was seen in 15 (34%) patients and systolic dysfunction in 12 (23%) patients who had ejection fractions less than 50%. The mean left ventricular ejection fraction was 56.3% +/- 16% (normal 65-85%), mean stroke volume was 82.9 +/- 27.2 mls (normal 51-96 ml). After 21 months enrolment in the study, Kaplan Meier analysis revealed a two-year mortality of 28.3%. Cox regression analysis indicated that a history of smoking current or past, low haemoglobin level, high aorta flow velocities, severity of mitral regurgitation and a negative association with serum creatinine were independent predictors of mortality. The correction of anaemia and control of other factors that impact negatively on cardiac function in dialysis patients is vital to enhance survival.

Unexplained agglutination of stored red blood cells in Alsever's solution caused by the gram-negative bacterium Serratia liquefaciens

Alsever's solution has been used for decades as a preservative solution for storage of RBCs. From October 2005 to January 2006, unexplained hemagglutination of approximately 10 to 20 percent of RBCs stored for several days in a modified version of Alsever's solution was noticed in quality control testing at the Canadian Blood Services Serology Laboratory. An investigation, including microbial testing, was initiated to determine the cause of the unexplained hemagglutination. The gram-negative bacterium Serratia liquefaciens was isolated from supernatant solutions of agglutinated RBCs. Further characterization of this strain revealed that it has the ability to form biofilms; presents high levels of resistance to chloramphenicol, neomycin, and gentamicin; and causes mannose-sensitive hemagglutination. The source of S. liquefaciens contamination in RBC supernatants was not found. However, this bacterium has not been isolated since January 2006 after enhanced cleaning practices were implemented in the serology laboratory where the RBCs are stored. This biofilm-forming, antibiotic-resistant S. liquefaciens strain could be directly linked to the unexplained hemagglutination observed in stored RBCs.

Allelic association and recombination hotspots in the mucin gene (MUC) complex on chromosome 11p15.5

A family of four highly polymorphic genes encoding secreted gel forming mucins is located in the middle of a recombination rich region of the short arm of chromosome 11 (11p15.5; tel MUC6-MUC2-MUC5AC-MUC5B cen; approx. 400 kb). These genes are of interest as risk factors for inflammatory diseases of the epithelia, and we have for example reported association of a VNTR polymorphism of the major mucin domain of MUC2 with asthma, despite the fact that MUC2 is not a major respiratory mucin. To understand the significance of this and other mucin gene associations it is important to describe the patterns of linkage disequilibrium (LD) across this chromosomal region, which is still incomplete on HapMap and the UCSC Golden Path sequence. Our previous studies on the 40 core CEPH families provided direct evidence for several recombination events within the immediate region of the gene complex. This study examines these recombination events in more detail, and also the patterns of LD across the gene complex. We refine the location of the breakpoints, and the combined data suggest two probable recombination hotspots. Three breakpoints are located between MUC6 and MUC2: there is no association between MUC6 and MUC2, and the data collected here, combined with that publicly available, maps a hotspot to a region of 4 kb. The other recombinants map between MUC2 and intron 8 of MUC5B. Relatively strong LD is detected between MUC2 and MUC5AC, and although 10/70 of the chromosomes tested shared a common haplotype, which extends from MUC2 to MUC5B, statistically significant association was not detected between MUC2 and the markers tested in MUC5B. We discuss the possibility that the previously reported association between MUC2 and asthma is most likely attributable to association with functional variation in MUC5AC, which encodes one of the two major mucins expressed in both healthy and diseased airways.

Sub-Tenon anaesthesia: reduction in subconjunctival haemorrhage with controlled bipolar conjunctival cautery

PURPOSE

To evaluate the effect of controlled conjunctival cautery on the frequency and extent of subconjunctival haemorrhage (SCH) associated with sub-Tenon anaesthetic (STA) injection in patients with various clotting states.

METHODS

One hundred forty-four patients suitable for cataract surgery with STA were prospectively divided into four groups: group A (n=36) were on warfarin (INR 1.8-4.2); group B (n=48) on aspirin (75 mg); group C (n=12) on clopidogrel (75 mg); and group D (n=48) on no anticoagulant or antiplatelet agents. All patients had no other known coagulopathy. Each group was randomly divided into two subgroups, one of which received localised bipolar cautery under microscope control to the STA conjunctival entry site before tissue dissection, whereas the other served as a control. chi(2) and Fisher's exact tests were used to analyse the data with the SPSS package (v11.0).

RESULTS

Conjunctival cautery reduced the frequency of SCH from 67 to 6% in group A (P=0.0001); from 37.5 to 4% in group B (P=0.005); from 50 to 0% in group C (P=0.9); and from 17 to 0% in group D (P=0.55). This overall reduction in SCH was highly significant (P<0.0001), especially in groups A and B. No statistically significant reduction in the extent of SCH was found.

CONCLUSIONS

Controlled localised bipolar conjunctival cautery before STA injection may significantly reduce the frequency of SCH, especially in patients on warfarin or aspirin.

Novel molecular basis of an Inab phenotype

The Cromer blood group system consists of ten high-prevalence and three low-prevalence antigens carried on decay-accelerating factor (DAF). DAF is found in the cell membranes of RBCs, granulocytes, platelets, and lymphocytes and is widely represented in other body tissues. Sequence analyses of DNA were performed on a blood sample from a 91-year-old Japanese woman whose serum contained an alloantibody to a high-prevalence antigen in the Cromer blood group system (anti-IFC). A blood sample from her daughter was also studied. Sequence analysis revealed a substitution of 508C7>T in exon 4 of DAF in the proband. The proband's daughter was heterozygous for 508C/T. This study describes an Inab phenotype in which the 508C>T nonsense mutation is predicted to change arginine at amino acid residue 136 to a stop codon. This change is in SCR 3 of DAF. This study reports on the molecular basis of a new proband with the Inab phenotype who had no history of intestinal disorders.

Effect of high altitude exposure on spermatogenesis and epididymal sperm count in male rats

The present study was designed to determine the effect of exposure to high altitude on spermatogenesis using transillumination technique and sperm count in male rats. In addition, the effect of oral intubation for intragastric administration of vehicle on testicular parameters in adult male rats in a schedule of 42 days was assessed. Male rats were exposed to Cerro de Pasco (Peru) at 4340 m for 3, 7, 14, 21, 28, 35 and 42 days resulting in a modification of the pattern of the seminiferous tubule stages. At day 3, stages I, IV-V, VI, VII and IX-XI were relatively shorter at high altitude than at sea level. At day 7, stages VIII, IX-XI, XII and XIII-XIV were reduced. At day 14, stages VII, VIII and IX-XI were reduced. At day 21 and 28, stages VIII, XII and XIII-XIV were significantly increased at high altitude. At day 35 an increase in stage XIII-XIV was observed. At day 42, stages II-III, IX-XI and XII were significantly increased at high altitude. Epididymal sperm count was significantly reduced at day 7 of exposure to high altitude and maintained low levels with respect to sea level up to 42 days. In conclusion, high altitude exposure affects spermatogenesis, particularly onset of mitosis and spermiation. This in turn affects epididymal sperm count.