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Simple scalable nucleotic FPGA based short read aligner for exhaustive search of substitution errors

Abstract

With the advent of the new and continuously improving technologies, in a couple of years DNA sequencing can be as commonplace as a simple blood test. The growth of sequencing efficiency has a larger exponent than the Moore’s law of standard processors, hence alignment and further processing of sequenced data is the bottleneck. The usage of FPGA (Field Programmable Gate Arrays) technology may provide an efficient alternative. We propose a simple algorithm for DNA sequence alignment, which can be realized efficiently by nucleotic principal agents of Non.Neumann nature. The prototype FPGA implementation runs on a small Terasic DE1-SoC demo board with a Cyclone V chip. We present test results and furthermore analyse the theoretical scalability of this system, showing that the execution time is independent of the length of reference genome sequences. A special advantage of this parallel algorithm is that it performs exhaustive search producing all match variants up to a predetermined number of point (mutation) errors.

Open access
Automatic detection of hard and soft exudates from retinal fundus images

Abstract

According to WHO estimates, 400 million people suffer from diabetes, and this number is likely to double by year 2030. Unfortunately, diabetes can have severe complications like glaucoma or retinopathy, which both can cause blindness. The main goal of our research is to provide an automated procedure that can detect retinopathy-related lesions of the retina from fundus images. This paper focuses on the segmentation of so-called white lesions of the retina that include hard and soft exudates. The established procedure consists of three main phases. The preprocessing step compensates the various luminosity patterns found in retinal images, using background and foreground pixel extraction and a data normalization operator similar to Z-transform. This is followed by a modified SLIC algorithm that provides homogeneous superpixels in the image. The final step is an ANN-based classification of pixels using fifteen features extracted from the neighborhood of the pixels taken from the equalized images and from the properties of the superpixel where the pixel belongs. The proposed methodology was tested using high-resolution fundus images originating from the IDRiD database. Pixelwise accuracy is characterized by a 54% Dice score in average, but the presence of exudates is detected with 94% precision.

Open access
Mesh: A Supply Chain Solution with Locally Private Blockchain Transactions

facts, 2018. https://corporate.walmart.com/our-story/our-locations . [7] Epc™ radio-frequency identity protocols generation-2 uhf rfid standard version 2. EPCglobal Inc. Specification documents, Jul. 2018. https://www.gs1.org/sites/default/files/docs/epc/gs1-epc-gen2v2-uhf-airinterface_i21_r_2018-09-04.pdf . [8] R. AlTawy, R. Rohit, M. He, K. Mandal, G. Yang, and G. Gong. sLiSCP-light: Towards hardware optimized spongespecific cryptographic permutations. ACM Trans. Embeded Computing Systems , 17(4):81:1–81:26, 2018. [9] E. Androulaki, A. Barger, V

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