cl-dash: rapid configuration and deployment of Hadoop clusters for bioinformatics research in the cloud.

Unlabelled: : One of the solutions proposed for addressing the challenge of the overwhelming abundance of genomic sequence and other biological data is the use of the Hadoop computing framework. Appropriate tools are needed to set up computational environments that facilitate research of novel bioinformatics methodology using Hadoop. Here, we present cl-dash, a complete starter kit for setting up such an environment.

LONG-TERM STRUCTURAL AND FUNCTIONAL OUTCOMES AFTER MACULAR HOLE SURGERY.

Purpose: To assess the long-term visual outcomes of macular hole surgery and to correlate structural changes on spectral domain optical coherence tomography after surgery with long-term changes in the best-corrected visual acuity.

Methods: A prospective study looking at 36 patients who underwent macular hole surgery between 2008 and 2010. The main outcome measure was change in the best-corrected visual acuity from 4 months to 6 months after surgery until the study visit.

Development of a shared decision-making tool to assist patients and clinicians with decisions on oral anticoagulant treatment for atrial fibrillation.

Objective: Decision aids (DAs) are increasingly used to operationalize shared decision-making (SDM) but their development is not often described. Decisions about oral anticoagulants (OACs) for atrial fibrillation (AF) involve a trade-off between lowering stroke risk and increasing OAC-associated bleeding risk, and consideration of how treatment affects lifestyle. The benefits and risks of OACs hinge upon a patient's risk factors for stroke and bleeding and how they value these outcomes.

Imaging of acute cholecystitis and cholecystitis-associated complications in the emergency setting.

Acute cholecystitis is a common cause of right upper quadrant pain in patients presenting at the emergency department. Early diagnosis and recognition of associated complications, though challenging, are essential for timely management. Imaging studies, including ultrasonography, computed tomography and magnetic resonance imaging, are increasingly utilised for the evaluation of suspected cases of cholecystitis.

Anti-TNFα therapy for inflammatory bowel diseases is associated with Epstein-Barr virus lytic activation.

Anti-TNFα therapy, known to suppress T-cell immunity, is increasingly gaining popularity for treatment of autoimmune diseases including inflammatory bowel diseases (IBD). T-cell suppression increases the risk of B-cell EBV-lymphoproliferative diseases and lymphomas. Since EBV-lytic activation is essential for development of EBV-lymphomas and there have been reports of EBV-lymphomas in patients treated with anti-TNFα therapy, we investigated if patients treated with anti-TNFα antibodies demonstrate greater EBV-lytic activity in blood.

An Approach to Various Gastric Pathologies Using an "Image Appearance-Based Classification" on Computed Tomography.

Although pathologies affecting stomach are commonly encountered in computed tomography imaging of the abdomen, they are frequently overlooked. Their etiologies are often diverse; however, most of them have certain well-documented imaging characteristics. Conventionally the stomach abnormalities were classified according to their etiopathogenesis.

Novel katG mutations causing isoniazid resistance in clinical M. tuberculosis isolates.

We report the discovery and confirmation of 23 novel mutations with previously undocumented role in isoniazid (INH) drug resistance, in catalase-peroxidase (katG) gene of Mycobacterium tuberculosis (Mtb) isolates. With these mutations, a synonymous mutation in fabG1 (g609a), and two canonical mutations, we were able to explain 98% of the phenotypic resistance observed in 366 clinical Mtb isolates collected from four high tuberculosis (TB)-burden countries: India, Moldova, Philippines, and South Africa. We conducted overlapping targeted and whole-genome sequencing for variant discovery in all clinical isolates with a variety of INH-resistant phenotypes.

Imaging findings of swallowed dentures: a case series.

Dental prosthesis is an uncommon ingested non-food foreign body in adults. Once swallowed, it can lead to serious complications and morbidity. Hence, early localization of the offending foreign body is crucial for timely management.

Epigenetic Modulation of Human Podocyte Vitamin D Receptor in HIV Milieu.

HIV (human immunodeficiency virus) has been reported to induce podocyte injury through down regulation of vitamin D receptor (VDR) and activation of renin angiotensin system; however, the involved mechanism is not clear. Since HIV has been reported to modulate gene expression via epigenetic phenomena, we asked whether epigenetic factors contribute to down regulation of VDR. Kidney cells in HIV transgenic mice and HIV-infected podocytes (HIV/HPs) displayed enhanced expression of SNAIL, a repressor of VDR.

Comparative performance of the new Aptima HIV-1 Quant Dx assay with three commercial PCR-based HIV-1 RNA quantitation assays.

Background: Quantitative measurement of HIV-1 RNA levels in plasma ('viral load') plays a central role in clinical management. The choice of assay platform can influence results and treatment decisions.

Objective: To compare the analytical performance of the new TMA-based Hologic Aptima(®) HIV-1 Quant Dx assay with that of three PCR-based assays: Abbott RealTime HIV-1, Qiagen Artus(®) HI Virus-1 QS-RGQ, and Roche CAP/CTM HIV-1 Test v2.

Type 2 responses at the interface between immunity and fat metabolism.

Adipose tissue resident leukocytes are often cast solely as the effectors of obesity and its attendant pathologies; however, recent observations have demonstrated that these cells support and effect 'healthy' physiologic function as well as pathologic dysfunction. Importantly, these two disparate outcomes are underpinned by similarly disparate immune programs; type 2 responses instruct and promote metabolic normalcy, while type 1 responses drive tissue dysfunction. In this Review, we summarize the literature regarding type 2 immunity's role in adipose tissue physiology and allude to its potential therapeutic implications.

Simultaneous deletion of the methylcytosine oxidases Tet1 and Tet3 increases transcriptome variability in early embryogenesis.

Dioxygenases of the TET (Ten-Eleven Translocation) family produce oxidized methylcytosines, intermediates in DNA demethylation, as well as new epigenetic marks. Here we show data suggesting that TET proteins maintain the consistency of gene transcription. Embryos lacking Tet1 and Tet3 (Tet1/3 DKO) displayed a strong loss of 5-hydroxymethylcytosine (5hmC) and a concurrent increase in 5-methylcytosine (5mC) at the eight-cell stage.

Clinico- pathological profile and course of malignant pleural effusion in a tertiary care teaching hospital in western U.P. with special reference to lung cancer.

Background: Malignant pleural effusion is a major clinical problem associated with primary and metastatic pleural malignancies. Pleural effusions from an unknown primary are responsible for 7-15% of all malignant pleural effusions. Presence of malignant pleural effusion puts the patient in advanced stage and renders the prognosis as poor.

AT1R blockade in adverse milieus: role of SMRT and corepressor complexes.

ANG II type 1 receptor blockade (AT1R-BLK) is used extensively to slow down the progression of proteinuric kidney diseases. We hypothesized that AT1R-BLK provides podocyte protection through regulation of silencing mediator of retinoic acid and thyroid hormone receptor (SMRT) and vitamin D receptor (VDR) expression under adverse milieus such as high glucose and human immunodeficiency virus infection. Both AT1R-BLK and VDR agonists (VDAs) stimulated VDR complex formation that differed not only in their composition but also in their functionality.

Gap Between Evidence and Patient Access: Policy Implications for Bariatric and Metabolic Surgery in the Treatment of Obesity and its Complications.

Despite consistently supportive evidence of clinical effectiveness and economic advantages compared with currently available non-surgical obesity treatments, patient access to bariatric and metabolic surgery (BMS) is impeded. To address this gap and better understand the relationship between value and access, the objectives of this study were twofold: (i) identify the multidimensional barriers to adoption of BMS created by clinical guidelines, public policies, and health technology assessments; and, most importantly, (ii) develop recommendations for stakeholders to improve patient access to BMS. Updated public policies focused on treatment and clinical guidelines that reflect the demonstrated advantages of BMS, patient education on safety and effectiveness, updated reimbursement policies, and additional data on long-term BMS effectiveness are needed to improve patient access.

The Expected Net Present Value of Developing Weight Management Drugs in the Context of Drug Safety Litigation.

Background: Following withdrawals, failures, and significant litigation settlements, drug product launches in the anti-obesity category slowed despite a large and growing unmet need. Litigation concerns, a more risk-averse regulatory policy, and the difficulty of developing a product with a compelling risk-benefit profile in this category may have limited innovators' expected return on investment and restricted investment in this therapeutic area.

Objective: The objective of the study was to estimate perceived manufacturer risk associated with product safety litigation and increased development costs vs.

Computed Tomography Features of External Auditory Canal Cholesteatoma: A Pictorial Review.

Computed tomography (CT) is widely used for evaluation of patients with otologic conditions. External auditory canal cholesteatoma (EACC), although rare, demonstrates characteristic CT appearance. Moreover, the accurate extent of involvement cannot be accurately assessed clinically.

Diverticulitis of the appendix, a distinctive entity: preoperative diagnosis by computed tomography.

Diverticular disease of the appendix is rare and is usually diagnosed during surgery. We report a case of a 50-year-old man who presented to the emergency department with right lower quadrant pain of 1-day duration. A preoperative diagnosis of appendiceal diverticulitis was made by computed tomography of the abdomen.