Evaluation of calling algorithms for array-CGH

Copy number variation (CNV) detection has become an integral part many of genetic studies and new technologies promise to revolutionize our ability to detect and link them to disease. However, recent studies highlight discrepancies in the genome wide CNV profile when measured by different technologies and even by the same technology. Furthermore, the change point algorithms used to call CNVs can have substantial disagreement on the same data set. We focus this article on comparative genomic hybridization (CGH) arrays because this platform lends itself well to accurate statistical modeling. We describe some newer methodological developments in local statistics that are well suited for CNV detection and calling on CGH arrays. Then we use both simulation studies and public data to compare these new local methods with the global methods that currently dominate literature. These results offer suggestions for choosing a particular method and provide insight to the lack of reproducibility that has been seen in the field so far

Effect of trimethoprim-sulfamethoxazole vs. norfloxacin on fecal E. coli resistance pattern and efficacy in patients receiving prophylaxis for spontaneous bacterial peritonitis

Background: Spontaneous Bacterial Peritonitis (SBP) is an infection of ascitic fluid. It is highly mortal and recurrent condition, so prophylaxis with Norfloxacin (NOR) or Trimethoprim-sulfamethoxazole (TMP-SMX) seems to play an important role in the prevention of further episodes of SBP. Aims of the study were to assess the effect of TMP-SMX/NOR on the sensitivity pattern of fecal E. coli after long term prophylaxis in Spontaneous Bacterial Peritonitis (SBP) and to compare the efficacy of TMP-SMX and NOR in prophylaxis of SBP.Methods: An interventional, prospective, open label, single center study conducted in Maulana Azad medical college, New Delhi, India. 52 patients of SBP or with high risk of SBP were screened and finally 39 patients were recruited. Stool sensitivity testing of fecal E. coli was done and they were divided into TMP-SMX group(n=18) and NOR group(n=21) according to sensitivity. After 45±3 days (7 weeks) their stool sample was re-examined for change sensitivity pattern of E. coli. Efficacy variables like any episode of SBP, fever (FEV) resolution of ascites (ASC), bacteremia (BACT), extraperitoneal infection (EPI), liver transplantation (LT) or death (D) were noted throughout the period of 24 weeks.Results: Resistance developed in 60% vs. 48% in TMP-SMX vs. NOR group(p=0.46) after 45 days of prophylaxis. By the end of 24 weeks, Incidence of SBP (29%vs. 25%, p>0.99), episodes of FEV(P=0.60), EPI(p>0.99), ASC(p>0.99) and death (14% vs. 16%, p>0.99) were almost similar in both the groups (TMP-SMX vs. NOR) respectively.Conclusions: Both TMP-SMX and NOR showed same degree of resistance and found equi-efficacious when administered as long-term prophylactic therapy in SBP. TMP-SMX can be a suitable as well as cost effective alternative to NOR for the prophylaxis of SBP

Correlation of clinical examination, ultrasound, magnetic resonance imaging and arthroscopy as diagnostic tools in shoulder pathology

Background: Shoulder pathologies can cause significant pain, discomfort, and affect the activity of daily living. The aim of this study was to compare the efficacy of clinical examination, ultrasound, magnetic resonance imaging (MRI) with shoulder arthroscopy in diagnosing various shoulder pathologies, considering shoulder arthroscopy as the gold standard tool.Methods: This was a prospective, comparative study conducted over 35 patients, between 18-75 years of age presenting with chronic shoulder pain or instability of more than 2 months duration. All patients were examined clinically, followed by high resolution ultrasound, MRI, arthroscopy of the affected shoulder.Results: The sensitivity and specificity of ultrasonography (USG) for diagnosing full thickness tear was 100% each and for MRI was 88% and 100% respectively. For subacromial impingement USG had sensitivity of 66.67%, specificity of 94.12%, positive predictive value of 50% and negative predictive value of 88.89%. For rotator cuff tear USG had sensitivity of 92.86%, specificity of 50%, positive predictive value of 81.25% and negative predictive value of 75% considering shoulder arthroscopy as gold standard.Conclusions: USG and MRI both are sensitive techniques for diagnosing of rotator cuff pathologies. USG has high accuracy in diagnosing partial thickness tears as compare to MRI. MRI proved to be superior in estimation of site and extent of tear. Considering shoulder arthroscopy as gold standard, it can be reserved for patients with suspicious of USG/MRI findings or those who may need surgical intervention simultaneously

Sustainable HPC: Modeling, Characterization, and Implications of Carbon Footprint in Modern HPC Systems

The rapid growth in demand for HPC systems has led to a rise in energy consumption and carbon emissions, which requires urgent intervention. In this work, we present a comprehensive framework for analyzing the carbon footprint of high-performance computing (HPC) systems, considering the carbon footprint during both the hardware production and system operational stages. Our work employs HPC hardware component carbon footprint modeling, regional carbon intensity analysis, and experimental characterization of the system life cycle to highlight the importance of quantifying the carbon footprint of an HPC system holistically