scholarly journals TRISHUL: A single-pass optimal two-level inclusive data cache hierarchy selection process for real-time MPSoCs

2013 ◽  
Author(s):  
M. S. Haque ◽  
A. Kumar ◽  
Yajun Ha ◽  
Qiang Wu ◽  
Shaobo Luo
Keyword(s):  
Real Time ◽  
Selection Process ◽  
Data Cache ◽  
Cache Hierarchy ◽  
Single Pass

Design of an Intelligent Data Cache with Replacement Policy

2019 ◽  
Vol 10 (2) ◽  
pp. 87-107
Author(s):  
B. Shameedha Begum ◽  
N. Ramasubramanian
Keyword(s):  
Real Time ◽  
Replacement Policy ◽  
Data Cache ◽  
Cache Performance ◽  
Performance Requirements ◽  
Novel Approach ◽  
Reconfigurable Caches ◽  
Real Time Applications ◽  
Hard Real Time ◽  
Replacement Algorithms

Embedded systems are designed for a variety of applications ranging from Hard Real Time applications to mobile computing, which demands various types of cache designs for better performance. Since real-time applications place stringent requirements on performance, the role of the cache subsystem assumes significance. Reconfigurable caches meet performance requirements under this context. Existing reconfigurable caches tend to use associativity and size for maximizing cache performance. This article proposes a novel approach of a reconfigurable and intelligent data cache (L1) based on replacement algorithms. An intelligent embedded data cache and a dynamic reconfigurable intelligent embedded data cache have been implemented using Verilog 2001 and tested for cache performance. Data collected by enabling the cache with two different replacement strategies have shown that the hit rate improves by 40% when compared to LRU and 21% when compared to MRU for sequential applications which will significantly improve performance of embedded real time application.

scholarly journals Selection and exploitation of prevalent, tandemly repeated genomic targets for improved real-time PCR-based detection of Wuchereria bancrofti and Plasmodium falciparum in mosquitoes

2020 ◽  
Author(s):  
Michael F. Zulch ◽  
Nils Pilotte ◽  
Jessica R. Grant ◽  
Corrado Minetti ◽  
Lisa J. Reimer ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Real Time ◽  
Real Time Pcr ◽  
Tandem Repeats ◽  
Selection Process ◽  
Wuchereria Bancrofti ◽  
Complete Information ◽  
Detection Sensitivity ◽  
Superior Performance ◽  
Systematic Analysis

BackgroundOptimization of polymerase chain reaction (PCR)-based diagnostics requires the careful selection of molecular targets that are both highly repetitive and pathogen-specific. Advances in both next-generation sequencing (NGS) technologies and bioinformatics-based analysis tools are facilitating this selection process, informing target choices and reducing labor. Once developed, such assays provide disease control and elimination programs with an additional set of tools capable of evaluating and monitoring intervention successes. The importance of such tools is heightened as intervention efforts approach their endpoints, as accurate and complete information is an essential component of the informed decision-making process. As global efforts for the control and elimination of both lymphatic filariasis and malaria continue to make significant gains, the benefits of diagnostics with improved analytical and clinical/field-based sensitivities and specificities will become increasingly apparent.Methodology/Principal Findings Coupling Illumina-based NGS with informatics approaches, we have successfully identified the tandemly repeated elements in both the Wuchereria bancrofti and Plasmodium falciparum genomes of putatively greatest copy number. Utilizing these sequences as quantitative real-time PCR (qPCR)-based targets, we have developed assays capable of exploiting the most abundant tandem repeats for both organisms. For the detection of P. falciparum, analysis and development resulted in an assay with improved analytical and field-based sensitivity vs. an established ribosomal sequence-targeting assay. Surprisingly, analysis of the W. bancrofti genome predicted a ribosomal sequence to be the genome’s most abundant tandem repeat. While resulting cycle quantification values comparing a qPCR assay targeting this ribosomal sequence and a commonly targeted repetitive DNA sequence from the literature supported our finding that this ribosomal sequence was the most prevalent tandemly repeated target in the W. bancrofti genome, the resulting assay did not significantly improve detection sensitivity in conjunction with field sample testing. Conclusions/Significance Examination of pathogen genomes facilitates the development of PCR-based diagnostics targeting the most abundant and specific genomic elements. While in some instances currently available tools may deliver equal or superior performance, systematic analysis of potential targets provides confidence that the selected assays represent the most advantageous options available and that informed assay selection is occurring in the context of a particular study’s objectives.

Identification and validation of reference genes for real time PCR expression studies in heads of nurse honeybees

Biologia ◽  
2013 ◽  
Vol 68 (6) ◽  
Author(s):  
Lenka Kohútová ◽  
Jaroslav Klaudiny ◽  
Róbert Nádašdy ◽  
Mária Šedivá ◽  
Ján Kopernický ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Reference Genes ◽  
Selection Process ◽  
Constitutive Expression ◽  
Larval Food ◽  
Gene Encoding ◽  
Age Related ◽  
Expression Studies ◽  
Suitable Reference

AbstractThe primary aim of this study was to identify reference genes and workers of particular role and ages that would be suitable for exploring genetic/epigenetic variations in constitutive expression of a gene encoding antimicrobial peptide defensin1 in worker heads using real-time PCR. This peptide is an integral component of larval food and honey and has potential to act against some brood pathogens. Expression levels of distinct genes may vary in worker heads due to genetic factors, age of bee, and particular role of a worker that depends on its age or colony needs. Prerequisite for exploring the variations in defensin1 expression was therefore to identify such workers in which correlated expression of defensin1 and suitable reference genes occurs. Selection process was done by carefully designed quantitative real-time PCR procedure in two colonies showing different age-related division of labor. Expression of ten candidate reference genes, defensin1 and amylase, as a marker of forager bees, was assessed in pooled head samples of workers aged 2 to 30 days. Correlated and moreover stable expression of defensin1 and six candidate genes was detected in nursing bees in both colonies. The suitable reference genes were therefore selected on the basis of their expression stability. This was evaluated by geNorm and NormFinder algorithms in pooled head samples and through plotted Cq data in head samples of individual nurse bees. As the best reference genes were selected: psa1, tctp1, cyclophilin, gapdh and mrjp4 (in this order). They are suitable for aforementioned defensin1 expression studies and also for studies of other genes expressed in heads of nurses. In addition, an amylase expression-based procedure for reliable distinguishing nurses from foragers was elaborated.

A real-time capable coherent data cache for multicores

2013 ◽  
Vol 26 (6) ◽  
pp. 1342-1354 ◽  
Author(s):  
Arthur Pyka ◽  
Mathias Rohde ◽  
Sascha Uhrig
Keyword(s):  
Real Time ◽  
Data Cache

scholarly journals Ideal and Predictable Hit Ratio for Matrix Transposition in Data Caches

Mathematics ◽  
2020 ◽  
Vol 8 (2) ◽  
pp. 184
Author(s):  
Alba Pedro-Zapater ◽  
Clemente Rodríguez ◽  
Juan Segarra ◽  
Rubén Gran Tejero ◽  
Víctor Viñals-Yúfera
Keyword(s):  
Energy Consumption ◽  
Real Time ◽  
High Performance ◽  
Negative Impact ◽  
Data Cache ◽  
Real Time Systems ◽  
Worst Case ◽  
Tile Size ◽  
Matrix Transposition ◽  
Time Systems

Matrix transposition is a fundamental operation, but it may present a very low and hardly predictable data cache hit ratio for large matrices. Safe (worst-case) hit ratio predictability is required in real-time systems. In this paper, we obtain the relations among the cache parameters that guarantee the ideal (predictable) data hit ratio assuming a Least-Recently-Used (LRU) data cache. Considering our analytical assessments, we compare a tiling matrix transposition to a cache oblivious algorithm, modified with phantom padding to improve its data hit ratio. Our results show that, with an adequate tile size, the tiling version results in an equal or better data hit ratio. We also analyze the energy consumption and execution time of matrix transposition on real hardware with pseudo-LRU (PLRU) caches. Our analytical hit/miss assessment enables the usage of a data cache for matrix transposition in real-time systems, since the number of misses in the worst case is bound. In general and high-performance computation, our analysis enables us to restrict the cache resources devoted to matrix transposition with no negative impact, in order to reduce both the energy consumption and the pollution to other computations.

scholarly journals DNA Methylation Biomarkers for Blood-Based Colorectal Cancer Screening

2008 ◽  
Vol 54 (2) ◽  
pp. 414-423 ◽  
Author(s):  
Catherine Lofton-Day ◽  
Fabian Model ◽  
Theo DeVos ◽  
Reimo Tetzner ◽  
Juergen Distler ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Real Time ◽  
Restriction Enzyme ◽  
Real Time Pcr ◽  
Selection Process ◽  
Pcr Analysis ◽  
Plasma Samples ◽  
Tissue Samples ◽  
High Performing ◽  
Healthy Control

Abstract Background: Sensitive, specific blood-based tests are difficult to develop unless steps are taken to maximize performance characteristics at every stage of marker discovery and development. We describe a sieving strategy for identifying high-performing marker assays that detect colorectal cancer (CRC)-specific methylated DNA in plasma. Methods: We first used restriction enzyme–based discovery methods to identify marker candidates with obviously different methylation patterns in CRC tissue and nonpathologic tissue. We then used a selection process incorporating microarrays and/or real-time PCR analysis of tissue samples to further test marker candidates for maximum methylation in CRC tissue and minimum amplification in tissues from both healthy individuals and patients with other diseases. Real-time assays of 3 selected markers were validated with plasma samples from 133 CRC patients and 179 healthy control individuals in the same age range. Results: Restriction enzyme–based testing identified 56 candidate markers. This group was reduced to 6 with microarray and real-time PCR testing. Three markers, TMEFF2, NGFR, and SEPT9, were tested with plasma samples. TMEFF2 methylation was detected in 65% [95% confidence interval, 56%–73%] of plasma samples from CRC patients and not detected in 69% (62%–76%) of the controls. The corresponding results for NGFR were 51% (42%–60%) and 84% (77%–89%); for SEPT9, the values were 69% (60%–77%) and 86% (80%–91%). Conclusions: The stringent criteria applied at all steps of the selection and validation process enabled successful identification and ranking of blood-based marker candidates.

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