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.

Peripheral blood mononuclear cell transcriptome profiles suggest T-cell immunosuppression after uncomplicated mechanical circulatory support device surgery

Mechanical circulatory support device (MCSD) surgery in patients with advanced heart failure patients is often complicated by infections that are linked to altered cell-mediated immunity. Using a transcriptome-wide peripheral blood mononuclear cell (PBMC) gene expression profiling approach, we analyzed expression patterns directly before and after MCSD implantation in 11 patients who had an uncomplicated course after MCSD implantation (Day 0-24 hours before, Day 1-24 hours after, and Day 7-1 week after implantation). Data were analyzed using Significance Analysis of Microarrays (SAM) and High-Throughput GoMiner on post-implantation profiles (Day 1, Day 7) in comparison with baseline (Day 0). Day1 profiles included differential expression of 821 genes (SAM, FDR <0.1, fold change >1.5), enriching >60 Gene Ontology (GO) categories. Grouping by component genes revealed GO clusters, which we term "interleukin related" (primarily upregulated), "T-cell related" (primarily downregulated), and "apoptosis related" (both up- and down-regulated genes). Day 7 profiles included GO categories related to repair processes. In conclusion, transcriptome-wide expression profiling of PBMCs suggests a response pattern to MCSD implantation of inflammatory activation and simultaneous T-cell suppression.

Aerosolized L-epinephrine vs budesonide for post extubation stridor: a randomized controlled trial

OBJECTIVE

To compare the efficacy and adverse effects of aerosolized L-epinephrine vs budesonide in the treatment of post-extubation stridor.

STUDY DESIGN

Randomized controlled trial.

SETTING

Pediatric intensive care unit (PICU) of a tertiary teaching and referral hospital.

SUBJECTS

Sixty two patients with a stridor score ?4 following extubation.

INTERVENTION

Patients were randomized to receive either aerosolized L-epinephrine (n=32) or budesonide (n =30). Respiratory rate, heart rate, stridor score, blood pressure and oxygen saturation were recorded from 0 min to 24 hours.

OUTCOME MEASURES

Stridor score remaining at >4, need for renebulization and reintubation between 20 min to 24 hours were primary outcome measures. Tachycardia (HR > normal for age), hypertension (BP >95th centile for age) and hypoxia (SpO2 < 92% for 5 min) were secondary outcome measures.

RESULTS

Both drugs showed a significant and comparable decline in the median (95% CI) stridor scores from baseline to 60 min [4 (4.10-4.50) to 2.00 (1.46-2.67) for budesonide vs 4 (4.12-5.00) to 2.00 (1.31 -2.75) for epinephrine]. At 2 hours, the stridor scores were significantly lower in the epinephrine as compared to budesonide group [0.00 (0.69-1.81) vs 3.00(1.75-3.32); P =0.02)]. However, the proportion of patients with stridor score >4 at any time between 20 min to 24 hrs (53.3% vs 53.1%; P=0.99), need for renebulization (40% vs 43.8%; P=0.76) and reintubation (20% vs 25%, P=0.638), and adverse effects were similar in both groups.

CONCLUSIONS

Both aerosolized L-epinephrine and budesonide were equally effective in their initial therapeutic response in post-extubation stridor. However, epinephrine showed a more sustained effect.

Relationship between a validated molecular cardiac transplant rejection classifier and routine organ function parameters

BACKGROUND

As acute cellular cardiac allograft rejection is a systemic process affecting the entire organism, we hypothesized that scores of a peripheral blood mononuclear cell gene expression profiling (GEP) test developed and validated to rule out International Society of Heart and Lung Transplantation (ISHLT) grade > or = 3A/2R acute cellular cardiac allograft rejection also reflects biologically plausible changes of the routinely assessed clinical parameters.

METHODS

We retrospectively analyzed 76 patients who underwent GEP testing, at the time of their routine clinical follow-up in our Institution between February 1, 2006 and January 31, 2007. Data were analyzed with t-test, nonparametric tests, bivariate Spearman's correlation, and multivariate linear regression modeling.

RESULTS

More activated GEP-score correlated with longer corrected QT (QTc)-interval (r = 0.377, p = 0.001, n = 63), longer QRS duration (r = 0.231, p = 0.03, n = 66), higher heart rate (r = 0.221, p = 0.037, n = 66), higher serum creatinine (r = 0.26, p = 0.01, n = 75), higher gamma-glutamyl transferase (GGT) GGT (r = 0.266, p = 0.037, n = 46), lower pulmonary artery oxygen saturation (r = -0.313, p = 0.003, n = 76), lower platelet count (r = -0.372, p = 0.001, n = 74), lower monocyte count (r = -0.208, p = 0.040, n = 72), and lower high-density lipoprotein (HDL) HDL level (r = -0.242, p = 0.041, n = 53). Multivariate analysis showed a significant amount of variance in the GEP score independently explained by the variability of QTc-interval (beta = 1.998, p = 0.001) and platelet count (beta = -1.540, p = 0.017). Post hoc analysis of the 11 individual GEP-classifier genes showed WDRA40 (p = 0.02) and ras homolog gene family, member U (RHOU) RHOU (p = 0.01) independently related to mixed venous O(2)Sat%.

CONCLUSION

A GEP test developed and validated to detect the absence of cardiac rejection correlates with electrocardiographic and hemodynamic cardiac parameters as well as renal, hepatic, bone marrow, and lipid metabolism parameters suggesting a complex relationship between rejection, leukocytes, and organ function within the continuum between alloimmunological quiescence and rejection.

A case of gestational diabetes arising following treatment with glucocorticosteroids for pemphigoid gestationis

A case of pemphigoid gestationis, a rare autoimmune disease unique to pregnancy, is described. To control the skin lesions systemic corticosteroids were required. The patient developed gestational diabetes mellitus. The pregnancy continued to 37 weeks and a live male infant was delivered. There was no evidence of macroscopic changes in the placenta. The skin lesions resolved in the postpartum period.

Structural and functional abnormalities in lungs in patients with achalasia

Dilatation and oesophageal body aperistalsis in achalasia can lead to stasis which in turn can induce repeated microaspiration. It is therefore conceivable that patients with achalasia may also have abnormalities in lungs secondary to repeated episodes of microaspiration. There is a lack of systematic study on involvement of lungs in patients with achalasia. Thirty patients with achalasia underwent pulmonary function tests (spirometry, and carbon mono-oxide diffusion capacity) and high resolution computerized tomography (HRCT) of the chest. The mean age of patients and mean duration of disease were 33.5 +/- 10.9 years and 28.1 +/- 27.3 months respectively. Regurgitation was present in 22 (73.3%) of them. Respiratory symptoms in them were dry cough in 17 (56.6%), and chest pain in 18 (60%). The oesophagus was dilated in 26 (86.6%) and 13 (43.3%) had residue in oesophagus. Sixteen (53.3%) patients had either anatomical changes as seen on HRCT or functional changes as observed on pulmonary function tests. Of those with functional abnormalities, five (16.6%) and one (3.3%) had restrictive and obstructive airways disease respectively. While evidence of tracheo-bronchial compression by dilated oesophagus was present in eight (26.6%), 10 (33.3%) patients had parenchymal lung disease [nodular opacities in five (16.6%), ground glass appearance six (20%), patchy pulmonary fibrosis five (16.6%), air trapping two (6.6%), consolidation and bronchiectasis one (3.3%) each]. There was a significant association between presence of regurgitation and dilatation of oesophagus (P = 0.032). More than half (53.3%) of patients with achalasia have structural and/or functional abnormalities in lungs.

Near-grain-boundary characterization by atomic force microscopy

Characterization of near-grain boundary is carried out by atomic force microscopy (AFM). It has been observed to be the most suitable technique owing to its capability to investigate the surface at high resolution. Commercial purity-grade nickel processed under different conditions, viz., (i) cold-rolled and annealed and (ii) thermally etched condition without cold rolling, is considered in the present study. AFM crystallographic data match well with the standard data. Hence, it establishes two grain-boundary relations viz., plane matching and coincidence site lattice (CSL Sigma=9) relation for the two different sample conditions.

A critique of the new ST-segment criteria for the diagnosis of acute myocardial infarction in patients with left bundle-branch block

BACKGROUND

Recently, electrocardiogram (ECG) criteria have been proposed for the diagnosis of acute myocardial infarction (AMI) in the presence of left bundle-branch block (LBBB). However, clinical experience indicates that such ECG changes indicative of AMI are occasionally noted in clinically stable patients with LBBB, raising concerns about the specificity of the proposed criteria.

HYPOTHESIS

The aim of this study was to evaluate the frequency of ST-segment abnormalities suggestive of AMI in ambulatory patients with cardiovascular disease and chronic LBBB, who did not have an AMI. In addition, the ECG determinants of such ST-segment abnormalities were sought.

METHODS

The files of all (4,193) patients followed in the outpatient cardiology clinic were reviewed to identify patients with LBBB. Electrocardiograms of these patients were evaluated as to the duration of the QRS complex, frontal QRS axis, amplitude of QRS in leads V1-V3, and the presence and magnitude of ST-segment depression (-ST) in leads V1-V3, and ST-segment elevation (+ST) in leads with predominantly positive or negative QRS complexes. Correlations of these ECG variables were carried out.

RESULTS

In 124 patients with LBBB only 1 patient with -ST of 1 mm in leads V1-V3, and 1 patient with +ST of 1 mm in a predominantly positive ECG lead were found; the latter patient also had +ST of 6 mm in V3. Nine patients were detected with > or = 5 mm +ST in at least one ECG lead with predominantly negative QRS complex. Regression analysis of amplitude of +STs on corresponding QRS amplitudes in leads V1-V3 yielded Rs of 0.69, 0.68, and 0.69, all with a p value of 0.00005. A similar analysis of the amplitudes of +STs > or = 5 mm with the corresponding QRSs yielded an R = 0.76 and a p value of 0.0018.

CONCLUSIONS

Thus, recently proposed ST-segment criteria for the diagnosis of AMI in patients with LBBB are appropriate. However, stable > or = 5 mm +STs are occasionally found in leads with predominantly negative QRS complexes, particularly of large amplitude (mean value 46.0, range [28.0-71.0] mm) in the absence of AMI. In such patients presenting with symptoms suggestive of AMI, further non-ECG confirmation of probable underlying AMI should be sought.

Pattern of ocular tumors in the eastern region of Nepal

BACKGROUND

ocular tumors are commonly encountered in ophthalmic practice.

OBJECTIVE

to study the clinical pattern of ocular tumors in the eastern region of Nepal.

MATERIALS AND METHODS

the hospital records of patients with ocular tumors treated at B P Koirala Institute of Health Sciences in the eastern region of Nepal over a period of 5 years (April 2003 - March 2008) were studied retrospectively.

RESULTS

of 115 consecutive patients with ocular tumors, 40 (34.75%) were below the age of 21 years, 41 (35.65%) were in the age group of 21-50 years and 34 (29.56%) of age above 50 years. There were 48 (41.73%) and 67 (58.26%) patients with benign and malignant tumors respectively. The common benign tumors were conjunctival papilloma, dermoid cysts, nevus, cystic lesions and hemangioma. Among the malignant tumors, basal cell carcinoma was the commonest (22.38%). Retinoblastoma was the most common ocular malignant tumor in the pediatric age group (88.8%). Basal cell carcinoma was the commonest eyelid malignancy (53.57%).

CONCLUSION

conjunctival papilloma, dermoid cysts, nevus, cystic lesions and hemangioma are common benign ocular tumors, whereas basal cell carcinoma and retinoblastoma are the commonest ocular malignancies in adults and children respectively.

An ICMR task force study of Prevention of Parent to Child Transmission (PPTCT) service delivery in India

A retrospective survey was conducted during August to December 2007 in 19 medical colleges of India to examine the functioning of the PPTCT service delivery. Data was extracted from records of the PPTCT centers for the year 2005-2006. HIV prevalence was higher than 2005 NACO figures in 11 out of 19 (57.8%) centers. There was wide variation in the proportion of women counseled & tested for HIV in different centers. Antenatal prophylaxis was practiced in 7 out of 19 (36.8%) centers. Overall intra-natal ART was provided to 52.8% of HIV positive women. Early newborn testing was available at 3 out of 19 (15.7%) centers. Improved counseling services are required for better case detection.

Asymmetric breast uptake of radioiodine in a patient with thyroid malignancy: metastases or not?

Various physiological processes can cause potentially misleading appearances in radioiodine whole body scans; proper understanding of the causes of these can therefore obviate diagnostic errors. Whole-body radioiodine scintigraphy with I131 or I123 is an accurate form of imaging used for management of differentiated thyroid carcinoma. Following thyroidectomy, any residual thyroid tissue or metastatic disease is ablated with high dose I131 and diagnostic images are acquired, demonstrating residual thyroid tissue and metastatic disease. However, atypical physiological uptake of I131 can simulate metastases.

Imaging appearance of parasitic infestations of the breast: a report of two cases and review of the literature

Parasitic infestations of the breast are uncommon. They may occur as a part of generalized disease, or present as primary breast infestations, making diagnosis difficult. Clinically, they are difficult to differentiate from the more common breast pathologies. However, imaging plays an important role, and different modalities often help distinguish and diagnose these rare conditions.

Clinical examination, MRI and arthroscopy in meniscal and ligamentous knee Injuries - a prospective study

Data from 565 knee arthroscopies performed by two experienced knee surgeons between 2002 and 2005 for degenerative joint disorders, ligament injuries, loose body removals, lateral release of the patellar retinaculum, plica division, and adhesiolysis was prospectively collected. A subset of 109 patients from the above group who sequentially had clinical examination, MRI and arthroscopy for suspected meniscal and ligament injuries were considered for the present study and the data was reviewed. Patients with previous menisectomies, knee ligament repairs or reconstructions and knee arthroscopies were excluded from the study. Patients were categorised into three groups on objective clinical assessment: those who were positive for either meniscal or cruciate ligament injury [group 1]; both meniscal and cruciate ligament injury [group 2] and those with highly suggestive symptoms and with negative clinical signs [group 3]. MRI was requested for confirmation of diagnosis and for additional information in all these patients. Two experienced radiologists reported MRI films. Clinical and MRI findings were compared with Arthroscopy as the gold standard. A thorough clinical examination performed by a skilled examiner more accurately correlated at Arthroscopy. MRI added no information in group 1 patients, valuable information in group 2 and was equivocal in group 3 patients. A negative MRI did not prevent an arthroscopy. In this study, specificity, positive and negative predictive values were more favourable for clinical examination though MRI was more sensitive for meniscal injuries. The use of MRI as a supplemental tool in the management of meniscal and ligament injuries should be highly individualised by an experienced surgeon.