Virtual reality, ultrasound-guided liver biopsy simulator: development and performance discrimination

OBJECTIVES

The aim of this article was to identify and prospectively investigate simulated ultrasound-guided targeted liver biopsy performance metrics as differentiators between levels of expertise in interventional radiology.

METHODS

Task analysis produced detailed procedural step documentation allowing identification of critical procedure steps and performance metrics for use in a virtual reality ultrasound-guided targeted liver biopsy procedure. Consultant (n=14; male=11, female=3) and trainee (n=26; male=19, female=7) scores on the performance metrics were compared. Ethical approval was granted by the Liverpool Research Ethics Committee (UK). Independent t-tests and analysis of variance (ANOVA) investigated differences between groups.

RESULTS

Independent t-tests revealed significant differences between trainees and consultants on three performance metrics: targeting, p=0.018, t=-2.487 (-2.040 to -0.207); probe usage time, p = 0.040, t=2.132 (11.064 to 427.983); mean needle length in beam, p=0.029, t=-2.272 (-0.028 to -0.002). ANOVA reported significant differences across years of experience (0-1, 1-2, 3+ years) on seven performance metrics: no-go area touched, p=0.012; targeting, p=0.025; length of session, p=0.024; probe usage time, p=0.025; total needle distance moved, p=0.038; number of skin contacts, p<0.001; total time in no-go area, p=0.008. More experienced participants consistently received better performance scores on all 19 performance metrics.

CONCLUSION

It is possible to measure and monitor performance using simulation, with performance metrics providing feedback on skill level and differentiating levels of expertise. However, a transfer of training study is required.

A platform for processing expression of short time series (PESTS)

Background

Time course microarray profiles examine the expression of genes over a time domain. They are necessary in order to determine the complete set of genes that are dynamically expressed under given conditions, and to determine the interaction between these genes. Because of cost and resource issues, most time series datasets contain less than 9 points and there are few tools available geared towards the analysis of this type of data.

Results

To this end, we introduce a platform for Processing Expression of Short Time Series (PESTS). It was designed with a focus on usability and interpretability of analyses for the researcher. As such, it implements several standard techniques for comparability as well as visualization functions. However, it is designed specifically for the unique methods we have developed for significance analysis, multiple test correction and clustering of short time series data. The central tenet of these methods is the use of biologically relevant features for analysis. Features summarize short gene expression profiles, inherently incorporate dependence across time, and allow for both full description of the examined curve and missing data points.

Conclusions

PESTS is fully generalizable to other types of time series analyses. PESTS implements novel methods as well as several standard techniques for comparability and visualization functions. These features and functionality make PESTS a valuable resource for a researcher's toolkit. PESTS is available to download for free to academic and non-profit users at http://www.mailman.columbia.edu/academic-departments/biostatistics/research-service/software-development.

Time-series clustering of gene expression in irradiated and bystander fibroblasts: an application of FBPA clustering

Background

The radiation bystander effect is an important component of the overall biological response of tissues and organisms to ionizing radiation, but the signaling mechanisms between irradiated and non-irradiated bystander cells are not fully understood. In this study, we measured a time-series of gene expression after α-particle irradiation and applied the Feature Based Partitioning around medoids Algorithm (FBPA), a new clustering method suitable for sparse time series, to identify signaling modules that act in concert in the response to direct irradiation and bystander signaling. We compared our results with those of an alternate clustering method, Short Time series Expression Miner (STEM).

Results

While computational evaluations of both clustering results were similar, FBPA provided more biological insight. After irradiation, gene clusters were enriched for signal transduction, cell cycle/cell death and inflammation/immunity processes; but only FBPA separated clusters by function. In bystanders, gene clusters were enriched for cell communication/motility, signal transduction and inflammation processes; but biological functions did not separate as clearly with either clustering method as they did in irradiated samples. Network analysis confirmed p53 and NF-κB transcription factor-regulated gene clusters in irradiated and bystander cells and suggested novel regulators, such as KDM5B/JARID1B (lysine (K)-specific demethylase 5B) and HDACs (histone deacetylases), which could epigenetically coordinate gene expression after irradiation.

Conclusions

In this study, we have shown that a new time series clustering method, FBPA, can provide new leads to the mechanisms regulating the dynamic cellular response to radiation. The findings implicate epigenetic control of gene expression in addition to transcription factor networks.

Orbital rhabdomyosarcoma in an adult

INTRODUCTION

Rhabdomyosarcoma is the most common primary orbital malignant tumor in children. Orbital lesions represent about 10 % of all the cases of rhabdomyosarcoma. Rhabdomyosarcoma is a rare cause of proptosis in adults.

OBJECTIVE

To report a case of primary orbital rhabdomyosarcoma in a 45-year-old female.

DESIGN

Interventional case report. The main outcome measures are a rare cause ofproptosis in an adult, discussion on treatment options and prognosis ofrhabdomyosarcoma.

RESULT

The patient underwent total orbital exenteration and was referred for radiotherapy and chemotherapy.

CONCLUSION

Rhabdomyosarcoma is a rare cause of proptosis in adults. It should be suspected in a case of rapidly-progressive proptosis in adults.

Risk factors for secondary proctectomy in patients with familial adenomatous polyposis

Background

Colectomy and ileorectal anastomosis (IRA) or restorative proctocolectomy are performed for prophylaxis in familial adenomatous polyposis (FAP). After IRA patients may require secondary proctectomy for worsening polyposis or rectal cancer. Outcomes after IRA were evaluated and risk factors predictive of progressive rectal disease identified.

Methods

Parametric survival analysis was used to identify predictors of progressive rectal disease in all patients undergoing an IRA for FAP at a single centre. Hazard ratios (HRs) were calculated for phenotype, genotype, sex, age at surgery and presence of colonic cancer.

Results

Of 427 patients who underwent IRA, 48 (11·2 per cent) developed rectal cancer and 77 (18·0 per cent) required proctectomy for worsening polyposis over a median follow-up of 15 (range 7–25) years. By the age of 60 years half of the patients retained their rectum. Rectal polyp count exceeding 20 (HR 30·99, 95 per cent confidence interval 9·57 to 100·32; P &lt; 0·001), APC mutation codon 1250–1450 (HR 3·91, 1·45 to 10·51; P = 0·007), colonic polyp count 500 or more (HR 2·18, 1·24 to 3·82; P = 0·006) and age less than 25 years at the time of surgery (HR 1·99, 1·17 to 3·37; P = 0·011) were independent predictors of progressive rectal disease.

Conclusion

The risk of proctectomy after IRA for FAP is based on patient genotype, phenotype and age at surgery.

Stigma in leprosy: miles to go!

No disease has been more closely associated with stigma than leprosy such that it has become a metaphor for stigma. Stigma has been difficult to measure and little research has been done on this issue. Stigma reduction has not been an important component of anti-leprosy program. The study was undertaken to measure the stigma associated with leprosy by using P scale which is used for assessing participation restriction of those affected by the disease. This comparative questionnaire based study was carried out in two sets of patients. Two groups of 30 patients each were studied. First group belonged to a Government run Leprosarium and group two from a tertiary care skin and leprosy centre. The study used the Participation (P) scale and data was collected by interviewing the patients. Participation restriction was defined as any score equal to and more than 13. Participation restriction was observed in 27 (90%) cases of group 1while participation restriction was present in only 7 (23.3%) subjects of group 2. It was observed that mean score of participation restriction in group 1 was quite high at 31.9 while it was only 8.3 for group 2. The participation restriction was directly related to the duration of disease and the grade of disability. Longer the duration of disease, greater was the likelihood of restriction. The participation restriction was found to be negatively correlated with the education. Recommendation about prevention of disability would require program about early diagnosis of nerve damage and subsequent action at the patient-family-community level and health care providers.

Subclinical thyroid dysfunction does not affect one-year mortality in elderly patients after hip fracture: a prospective longitudinal study

Mortality after hip fractures in the elderly is one of the most important patient outcome measures. Subclinical thyroid dysfunction is common in the elderly population. This is a prospective study of 131 elderly patients with a mean (SD) age of 82.0 (8.9) years (range: 61-94) admitted consecutively to our trauma unit. The aim of the study was to determine the prevalence of subclinical thyroid dysfunction in an elderly cohort of patients with hip fracture and to determine if this affects the one-year mortality. There were three times more women (n=100) than men (n=31) in this cohort. All patients underwent surgical treatment for the hip fracture. The prevalence of subclinical hypothyroidism (TSH>5.5 mU/L) was 15% (n=20) and of subclinical hyperthyroidism (TSH<0.35 mU/L) was 3% (n=4). Overall 18% (n=24) of patients had a subclinical thyroid dysfunction. The twelve-month mortality was 27% (n=36). Age, gender, heart rate at admission, pre-existing coronary heart disease, ASA grade and presence of overt or subclinical thyroid dysfunction were analysed for association with twelve-month mortality using a forward stepwise logistic regression analysis. Only ASA grade was found to significantly affect mortality at twelve months (chi(2)=3.98, df=1, p=0.046). Independently the presence of subclinical hypo- or hyperthyroidism was not associated with a higher mortality (p=0.477). We conclude that subclinical thyroid dysfunction does not affect the one-year mortality in elderly patients treated surgically for hip fracture.

Risk factors predicting intra-abdominal desmoids in familial adenomatous polyposis: a single centre experience

BACKGROUND

Desmoids are myofibroblastic proliferations occurring in 15% of patients with familial adenomatous polyposis (FAP), 70% being intra-abdominal desmoids (IAD). Since the morbidity and mortality due to desmoids is almost entirely attributable to IAD, we aimed to identify specifically risk factors predicting IAD development in FAP.

METHODS

We undertook a retrospective review of our institutional database. Multivariate analysis was performed, and hazard ratios (HR) calculated for variables including female gender, 3' APC mutation, surgical intervention for FAP (colectomy with ileo-rectal anastomosis or restorative proctocolectomy), age at surgery and family history (FH) of desmoids.

RESULTS

Of the 558 patients analysed, 49 (9%) developed IAD; 22 (4%) diagnosed intra-operatively and 27 (5%) developing over a median post-operative period of 34 (7-120) months. 75% of IAD had developed before age 40. A 3' APC mutation (HR 5.2, 95% CI 2.1-13.3, P = 0.001), positive FH (HR 2.5, 95% CI 1.4-4.6, P = 0.003) and female gender (HR 1.9, 95% CI 1.0-3.5, P = 0.04) were found to be predictive of IAD development. No significant difference in IAD risk was detected between the type of surgical intervention (P = 0.37) or age at surgery (P = 0.29).

CONCLUSIONS

Our analysis confirms 3' APC mutation to be the most significant risk factor for IAD development. The independent association between positive FH and IAD risk suggests the existence of modifier genes, independent of the APC genotype-phenotype correlation. Few of these risk factors can be meaningfully modified. Delaying prophylactic surgery may be appropriate in female patients with a 3' APC mutation and attenuated polyposis.

Large datasets in biomedicine: a discussion of salient analytic issues

Advances in high-throughput and mass-storage technologies have led to an information explosion in both biology and medicine, presenting novel challenges for analysis and modeling. With regards to multivariate analysis techniques such as clustering, classification, and regression, large datasets present unique and often misunderstood challenges. The authors' goal is to provide a discussion of the salient problems encountered in the analysis of large datasets as they relate to modeling and inference to inform a principled and generalizable analysis and highlight the interdisciplinary nature of these challenges. The authors present a detailed study of germane issues including high dimensionality, multiple testing, scientific significance, dependence, information measurement, and information management with a focus on appropriate methodologies available to address these concerns. A firm understanding of the challenges and statistical technology involved ultimately contributes to better science. The authors further suggest that the community consider facilitating discussion through interdisciplinary panels, invited papers and curriculum enhancement to establish guidelines for analysis and reporting.