Quick chip assay using locked nucleic acid modified epithelial cell adhesion molecule and nucleolin aptamers for the capture of circulating tumor cells

The role of circulating tumor cells (CTCs) in disease diagnosis, prognosis, monitoring of the therapeutic efficacy, and clinical decision making is immense and has attracted tremendous focus in the last decade. We designed and fabricated simple, flat channel microfluidic devices polydimethylsiloxane (PDMS based) functionalized with locked nucleic acid (LNA) modified aptamers (targeting epithelial cell adhesion molecule (EpCAM) and nucleolin expression) for quick and efficient capture of CTCs and cancer cells. With optimized flow rates (10 μl/min), it was revealed that the aptamer modified devices offered reusability for up to six times while retaining optimal capture efficiency (>90%) and specificity. High capture sensitivity (92%) and specificity (100%) was observed in whole blood samples spiked with Caco-2 cells (10-100 cells/ml). Analysis of blood samples obtained from 25 head and neck cancer patients on the EpCAM LNA aptamer functionalized chip revealed that an average count of 5 ± 3 CTCs/ml of blood were captured from 22/25 samples (88%). EpCAM intracellular domain (EpICD) immunohistochemistry on 9 oral squamous cell carcinomas showed the EpICD positivity in the tumor cells, confirming the EpCAM expression in CTCs from head and neck cancers. These microfluidic devices also maintained viability for in vitro culture and characterization. Use of LNA modified aptamers provided added benefits in terms of cost effectiveness due to increased reusability and sustainability of the devices. Our results present a robust, quick, and efficient CTC capture platform with the use of simple PDMS based devices that are easy to fabricate at low cost and have an immense potential in cancer diagnosis, prognosis, and therapeutic planning

Amplitude measurements of Faraday waves

A light reflection technique is used to measure quantitatively the surface elevation of Faraday waves. The performed measurements cover a wide parameter range of driving frequencies and sample viscosities. In the capillary wave regime the bifurcation diagrams exhibit a frequency independent scaling proportional to the wavelength. We also provide numerical simulations of the full Navier-Stokes equations, which are in quantitative agreement up to supercritical drive amplitudes of 20%. The validity of an existing perturbation analysis is found to be limited to 2.5% overcriticaly.Comment: 7 figure

Nonlinear Measures for Characterizing Rough Surface Morphologies

We develop a new approach to characterizing the morphology of rough surfaces based on the analysis of the scaling properties of contour loops, i.e. loops of constant height. Given a height profile of the surface we perform independent measurements of the fractal dimension of contour loops, and the exponent that characterizes their size distribution. Scaling formulas are derived and used to relate these two geometrical exponents to the roughness exponent of a self-affine surface, thus providing independent measurements of this important quantity. Furthermore, we define the scale dependent curvature and demonstrate that by measuring its third moment departures of the height fluctuations from Gaussian behavior can be ascertained. These nonlinear measures are used to characterize the morphology of computer generated Gaussian rough surfaces, surfaces obtained in numerical simulations of a simple growth model, and surfaces observed by scanning-tunneling-microscopes. For experimentally realized surfaces the self-affine scaling is cut off by a correlation length, and we generalize our theory of contour loops to take this into account.Comment: 39 pages and 18 figures included; comments to [email protected]

Design considerations for workflow management systems use in production genomics research and the clinic

Abstract The changing landscape of genomics research and clinical practice has created a need for computational pipelines capable of efficiently orchestrating complex analysis stages while handling large volumes of data across heterogeneous computational environments. Workflow Management Systems (WfMSs) are the software components employed to fill this gap. This work provides an approach and systematic evaluation of key features of popular bioinformatics WfMSs in use today: Nextflow, CWL, and WDL and some of their executors, along with Swift/T, a workflow manager commonly used in high-scale physics applications. We employed two use cases: a variant-calling genomic pipeline and a scalability-testing framework, where both were run locally, on an HPC cluster, and in the cloud. This allowed for evaluation of those four WfMSs in terms of language expressiveness, modularity, scalability, robustness, reproducibility, interoperability, ease of development, along with adoption and usage in research labs and healthcare settings. This article is trying to answer, which WfMS should be chosen for a given bioinformatics application regardless of analysis type?. The choice of a given WfMS is a function of both its intrinsic language and engine features. Within bioinformatics, where analysts are a mix of dry and wet lab scientists, the choice is also governed by collaborations and adoption within large consortia and technical support provided by the WfMS team/community. As the community and its needs continue to evolve along with computational infrastructure, WfMSs will also evolve, especially those with permissive licenses that allow commercial use. In much the same way as the dataflow paradigm and containerization are now well understood to be very useful in bioinformatics applications, we will continue to see innovations of tools and utilities for other purposes, like big data technologies, interoperability, and provenance

Diagnostic Efficacy of Ultrasound, Ultrasound Elastography and Magnetic Resonance Imaging for Breast Lesions: A Comparative Study

Background: The present study was conducted for comparing the diagnostic efficacy of ultrasound, ultrasound elastography and magnetic resonance imaging for breast lesions. Materials & methods: A total of 100 subjects were enrolled. Complete demographic details and clinical details of all the subjects were enrolled. All the patients were subjected to B-mode USG assessment. US Elastography was also done. The two-dimensional USG was followed by Real Time ultrasound elastography. The stiffness of the lesion was evaluated.  All patients were placed prone on a 0.5 Tesla MRI scanner equipped with a dedicated breast surface coil. The lesion was categorized as benign, probably benign, Malignant and probably Malignant. Fine needle aspiration cytology (FNAC) or biopsy was performed and the specimen was evaluated cytologically/histopathologically to confirm the diagnosis. All the results were recorded and analysed by SPSS software. Results: Sensitivity and specificity of USG was 78.6 percent and 86.2 percent respectively. Sensitivity and specificity of Elastography was 89.5 percent and 92.6 percent respectively. Sensitivity and specificity of MRI was 96.2 percent and 93.1 percent respectively. Conclusion: MRI was most sensitive and most specific followed by USG elastography.&nbsp

Assessment of Role of MRI in the Evaluation of Spinal Trauma: an Observational Study

A total of 100 patients were analysed. Complete demographic and clinical details of all the patients were obtained. The source of data for this study was patients referred to Department of Radio diagnosis, Imaging and Interventional radiology from OPD. After obtaining clinical history relevant clinical examination was done.ASIA grading was done for neurological injury. MRI examinations were done. Every patient lay in supine position with quiet breathing. No movement was allowed during examination. In 71 percent of the patients, compression fracture of the vertebral body was present. Cord oedema of >3cm was seen in 55 percent of the patients. Sensory loss and motor loss was seen in 26 percent and 21 percent of the patients respectively. MRI findings in acute spinal cord injury correlate well with the initial clinical findings and can be helpful to clinician in predicting the outcome and extent of recovery in patients of spinal cord injury