Search results for "Array"
showing 10 items of 1264 documents
Computing the Original eBWT Faster, Simpler, and with Less Memory
2021
Mantaci et al. [TCS 2007] defined the \(\mathrm {eBWT}\) to extend the definition of the \(\mathrm {BWT}\) to a collection of strings. However, since this introduction, it has been used more generally to describe any \(\mathrm {BWT}\) of a collection of strings, and the fundamental property of the original definition (i.e., the independence from the input order) is frequently disregarded. In this paper, we propose a simple linear-time algorithm for the construction of the original \(\mathrm {eBWT}\), which does not require the preprocessing of Bannai et al. [CPM 2021]. As a byproduct, we obtain the first linear-time algorithm for computing the \(\mathrm {BWT}\) of a single string that uses …
The New "Maximum Yield Grid" (MYG) Array in Full 3D Resistivity Tomography
2008
Over the past few years geoelectrical prospecting has experienced many innovations, ranging from instrumental refinements to improvement of data interpretation. The consequence of this has been a strong increase in the method s resolution power and, therefore, its field of application has broadened. Nevertheless, the diffusion of 3D surveys in electrical resistivity tomography has been very much limited by the long acquisition time required by this kind of investigation, as compared to 2D ERT or other geophysical exploration methods like GPR. However, 3D ERT has a great advantage in terms of resolution power, that is very important in many applications, such as archeological or cultural her…
Integrated CGH/WES Analyses Advance Understanding of Aggressive Neuroblastoma Evolution: A Case Study
2021
Neuroblastoma (NB) is the most common extra-cranial malignancy in preschool children. To portray the genetic landscape of an overly aggressive NB leading to a rapid clinical progression of the disease, tumor DNA collected pre- and post-treatment has been analyzed. Array comparative genomic hybridization (aCGH), whole-exome sequencing (WES), and pharmacogenetics approaches, respectively, have identified relevant copy number alterations (CNAs), single nucleotide variants (SNVs), and polymorphisms (SNPs) that were then combined into an integrated analysis. Spontaneously formed 3D tumoroids obtained from the recurrent mass have also been characterized. The results prove the power of combining C…
Learning automata based energy-efficient AI hardware design for IoT applications
2020
Energy efficiency continues to be the core design challenge for artificial intelligence (AI) hardware designers. In this paper, we propose a new AI hardware architecture targeting Internet of Things applications. The architecture is founded on the principle of learning automata, defined using propositional logic. The logic-based underpinning enables low-energy footprints as well as high learning accuracy during training and inference, which are crucial requirements for efficient AI with long operating life. We present the first insights into this new architecture in the form of a custom-designed integrated circuit for pervasive applications. Fundamental to this circuit is systematic encodin…
Transcriptómica de la infertilidad masculina
2012
La infertilidad es un problema cada vez más presente en la sociedad actual, especialmente por razones sociales como por ejemplo la postergación de la maternidad por parte de las parejas y en Europa se calcula que afecta alrededor de a 15% de parejas en edad reproductiva. Las causas de la infertilidad son muchas y pueden afectar a uno sólo de los miembros o a ambos, además su etiología es diversa y a veces es desconocida. Las técnicas de reproducción asistida nacieron como consecuencia de estos problemas acuciantes y desde sus inicios han ido mejorando e innovando para mejorar cada vez más sus tasas de éxito. El mayor éxito en estas técnicas radica en la investigación de los factores que int…
Sistema de transferencia de datos en el instrumento TilePPr del proyecto TileCal
2017
El proyecto surge de la implementación del nuevo sistema de lectura de datos FELIX, que aprovecha los Transceptores Gigabit incorporados en las FPGA XC7VX485T y XC7VX690T del fabricante Xilinx. Estos transceptores se usan para establecer enlaces de datos a través de fibra óptica entre la FPGA del Pre-procesador del TileCal o TilePPr (XC7VX485T) y la placa electrónica que está conectada por PCIe al servidor local (XC7VX690T), por lo que el trabajo consiste en alcanzar los siguientes objetivos: a) Poner en marcha en la FPGA XC7VX485T del Pre-procesador o TilePPr la interfaz de transferencia de datos para que sea compatible con el nuevo sistema “Enlace de intercambio en el límite frontal” o FE…
An FPGA aligner for short read mapping
2012
The rapid growth of short read datasets poses a new challenge to the mapping of short reads to a reference genome in terms of sensitivity and execution speed. In this work, we present a parallel architecture for short read mapping utilizing field programmable gate array (FPGA)-based hardware. The computation intensive semi-global alignment and the hash table lookup operations are mapped onto an FPGA. The proposed Align Core is implemented with a parallel block structure to gain computational efficiency. We present a new parallel block-wise alignment structure to approximate the conventional dynamic programming algorithm. The performance of our FPGA aligner is compared to the GASSST and BWA …
A hybrid short read mapping accelerator
2013
Background The rapid growth of short read datasets poses a new challenge to the short read mapping problem in terms of sensitivity and execution speed. Existing methods often use a restrictive error model for computing the alignments to improve speed, whereas more flexible error models are generally too slow for large-scale applications. A number of short read mapping software tools have been proposed. However, designs based on hardware are relatively rare. Field programmable gate arrays (FPGAs) have been successfully used in a number of specific application areas, such as the DSP and communications domains due to their outstanding parallel data processing capabilities, making them a compet…
Event Horizon Telescope imaging of the archetypal blazar 3C 279 at an extreme 20 microarcsecond resolution
2020
Open Access article, published by EDP Sciences, under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Open Access funding provided by Max Planck Society.--All authors: Kim, Jae-Young; Krichbaum, Thomas P.; Broderick, Avery E.; Wielgus, Maciek; Blackburn, Lindy; Gómez, José L.; Johnson, Michael D.; Bouman, Katherine L.; Chael, Andrew; Akiyama, Kazunori; Jorstad, Svetlana; Marscher, Alan P.; Issaoun, Sara; Janssen, Michael; Chan, Chi-kwan; Savolainen, Tuomas; Pesce, Dominic W.; Özel, Feryal; Alberdi, Antxon; Alef, Walt…
An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs
2020
AbstractMicroRNA are small non-coding RNAs that post-transcriptionally regulate the expression levels of messenger RNAs. MicroRNA regulation activity depends on the recognition of binding sites located on mRNA molecules. ComiR is a web tool realized to predict the targets of a set of microRNAs, starting from their expression profile. ComiR was trained with the information regarding binding sites in the 3’utr region, by using a reliable dataset containing the targets of endogenously expressed microRNA in D. melanogaster S2 cells. This dataset was obtained by comparing the results from two different experimental approaches, i.e., inhibition, and immunoprecipitation of the AGO1 protein--a comp…