Sharif Digital Repository

Purpose Whole genome sequencing of SARS-CoV2 is important to find useful information about the viral lineages, variants of interests and variants of concern. As there are not enough data about the circulating SARS-CoV2 variants in Iran, we sequenced 54 SARS-CoV2 genomes during the 5 waves of pandemic in Iran. Methods After viral RNA extraction from clinical samples collected during the COVID-19 pandemic, next generation sequencing was performed using the Nextseq platform. The sequencing data were analyzed and compared with reference sequences. Results During the 1st wave, V and L clades were detected. The second wave was recognized by G, GH and GR clades. Circulating clades during the 3rd... 

This paper presents a VLSI architecture of a novel softoutput K-Best MIMO detector. The proposed detector attains low computational complexity using three improvement ideas: relevant discarded paths selection, last stage on-demand expansion, and relaxed LLR computation. A deeply pipelined architecture for a soft-output MIMO detector is implemented for a 4x4 64-QAM MIMO system realizing a peak throughput of 655Mbps, while consuming 174K gates and 195mW in 0.13um CMOS. Synthesis results in 65nm CMOS show the potential to support a sustained throughput up to 2Gbps achieving the data rates envisioned by emerging IEEE 802.16m and LTE-Advanced wireless standards  

In this paper, a novel hard-output detection algorithm for the complex multiple-input multiple-output (MIMO) detectors is proposed, which results in a significant throughput enhancement, a near-ML performance, and an SNR-independent fixed-throughput. Moreover, a high-throughput VLSI implementation is proposed, which is based on a novel method of the node generation and sorting scheme. The proposed design achieves the throughput of 10Gbps in a 0.13 μ CMOS process, which is the highest throughput reported in the literature for both the real and the complex domains. Synthesis results in 90nm CMOS also show that the proposed scheme can achieve the throughput of up to 15Gbps. Moreover, the FPGA... 

Background: Once aligned, long-reads can be a useful source of information to identify the type and position of structural variations. However, due to the high sequencing error of long reads, long-read structural variation detection methods are far from precise in low-coverage cases. To be accurate, they need to use high-coverage data, which in turn, results in an extremely time-consuming pipeline, especially in the alignment phase. Therefore, it is of utmost importance to have a structural variation calling pipeline which is both fast and precise for low-coverage data. Results: In this paper, we present SVNN, a fast yet accurate, structural variation calling pipeline for PacBio long-reads... 

Background: Once aligned, long-reads can be a useful source of information to identify the type and position of structural variations. However, due to the high sequencing error of long reads, long-read structural variation detection methods are far from precise in low-coverage cases. To be accurate, they need to use high-coverage data, which in turn, results in an extremely time-consuming pipeline, especially in the alignment phase. Therefore, it is of utmost importance to have a structural variation calling pipeline which is both fast and precise for low-coverage data. Results: In this paper, we present SVNN, a fast yet accurate, structural variation calling pipeline for PacBio long-reads... 

An integrated microsampling approach based on solid-phase microextraction (SPME) was developed to provide a complete solution to highly efficient and accurate pharmacokinetic studies. The microsampling system included SPME probes that are made of poly(ethylene glycol) (PEG) and C18-bonded silica, a fast and efficient sampling strategy with accurate kinetic calibration, and a high-throughput desorption device based on a modified 96-well plate. The sampling system greatly improved the quantitative capability of SPME in two ways. First, the use of the C18-bonded silica/PEG fibers minimized the competition effect from analogues of the target analytes in a complicated sample matrix such as blood... 

This paper quantifies the difference in resource demand between modern and classic NoC workloads. In the paper, we show that modern workloads are able to better utilize higher numbers of VCs and smaller C factors in order to attain performance and energy efficiency. This is because of the high throughput and possible local congestions in their traffic pattern. As a result, such workloads are more suitable for concurrency and redundancy energy reduction techniques where the voltage and frequency are reduced simultaneously and the increased power budget is used for introducing additional resources to the network in order to improve the performance  

Multivariate curve resolution-particle swarm optimization (MCR-PSO) algorithm is proposed to exploit pure chromatographic and spectroscopic information from multi-component hyphenated chromatographic signals. This new MCR method is based on rotation of mathematically unique PCA solutions into the chemically meaningful MCR solutions. To obtain a proper rotation matrix, an objective function based on non-fulfillment of constraints is defined and is optimized using particle swarm optimization (PSO) algorithm. Initial values of rotation matrix are calculated using local rank analysis and heuristic evolving latent projection (HELP) method. The ability of MCR-PSO in resolving the chromatographic... 

The pharmaceutical industry is facing enormous challenges due to high drug attribution rates. For the past decades, novel methods have been developed for safety and efficacy testing, as well as for improving early development stages. In vitro screening methods for drug-receptor binding are considered to be good alternatives for decreasing costs in the identification of drug candidates. However, these methods require lengthy and troublesome labeling steps. Biosensors hold great promise due to the fact that label-free detection schemes can be designed in an easy and low-cost manner. In this paper, for the first time in the literature, we aimed to compare the potential of label-free optical and... 

A high-throughput micro-solid-phase extraction device based on a 96-well plate was constructed and applied to the determination of pesticide residues in various apple samples. Butyl methacrylate and ethylene glycol dimethacrylate were copolymerized as a monolithic polymer and placed in the cylindrically shaped stainless-steel meshes of 96-micro-solid-phase extraction device and used as an extracting unit. Before the micro-solid-phase extraction, microwave-assisted extraction was employed to facilitate the transfer of the pesticide residues from the apple matrix to liquid media. Then, 1 mL of the aquatic samples was transferred into the 96-well plate and the 96-micro-solid-phase extraction... 

Background: Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducing the overall cost of sequencing is related to the time consumption of the aligner. The tradeoff between accuracy and speed is the main challenge in designing long read aligners. Results: We propose Meta-aligner which aligns long and very long reads to the reference genome very efficiently and accurately. Meta-aligner incorporates available short/long aligners as subcomponents and uses statistics from the reference genome to increase the performance. Meta-aligner estimates... 

Monitoring the ratio of 40- and 42-residue amyloid β peptides (i.e., Aβ40 and Aβ42) in human plasma is considered one of the hallmarks of detection of the early stage of Alzheimer's disease (AD). Therefore, development of a specific, yet non-antibody-based method for simultaneous detection of Aβ40 and Aβ42 may have considerable clinical applications. Here, we developed a 'nanoparticle-based colorimetric sensor array' utilizing label-free gold and silver nanoparticles for visual detection of Aβ42 and Aβ40. Different aggregation behaviors of nanoparticles through their conjugation with Aβ42 and Aβ40 followed by the coordination of Aβ42 and Aβ40 with Cu(ii) led to diverse spectral and color... 

We study the tradeoff between the sum rate and the error probability in downlink of wireless networks. Using the recent results on the achievable rates of finite-length codewords, the problem is cast as a joint optimization of the network sum rate and the per-user error probability. Moreover, we develop an efficient algorithm based on the divide-and-conquer technique to simultaneously maximize the network sum rate and minimize the maximum users’ error probability and to evaluate the effect of the codeword length on the system performance. The results show that, in delay-constrained scenarios, optimizing the per-user error probability plays a key role in achieving high throughput. IEEE  

The objective of the present work is development of joint approximate diagonalization of eigenmatrices (JADE) as a member of independent component analysis (ICA) family, for the analysis of gas chromatography-mass spectrometry (GC–MS) and comprehensive two-dimensional gas chromatography-mass spectrometry (GC × GC–MS) data to address incomplete separation problem occurred during the analysis of complex sample matrices. In this regard, simulated GC–MS and GC × GC–MS data sets with different number of components, different degree of overlap and noise were evaluated. In the case of simultaneous analysis of multiple samples, column-wise augmentation for GC–MS and column-wise super-augmentation... 

The inertial microfluidic technique, as a powerful new tool for accurate cell/particle separation based on the hydrodynamic phenomenon, has drawn considerable interest in recent years. Despite numerous microfluidic techniques of particle separation, there are few articles in the literature on separation techniques addressing external outlet geometry to increase the throughput efficiency and purity. In this work, we report on a spiral inertial microfluidic device with high efficiency (>98%). Herein, we demonstrate how changing the outlet geometry can improve the particle separation throughput. We present a complete separation of 4 and 6 μm from 10 μm particles potentially applicable to... 

With the advent of high-throughput assays, a large number of biological experiments can be carried out. Image-based assays are among the most accessible and inexpensive technologies for this purpose. Indeed, these assays have proved to be effective in characterizing unknown functions of genes and small molecules. Image analysis pipelines have a pivotal role in translating raw images that are captured in such assays into useful and compact representation, also known as measurements. CellProfiler is a popular and commonly used tool for this purpose through providing readily available modules for the cell/nuclei segmentation, and making various measurements, or features, for each cell/nuclei.... 

We present a design and implementation of a high-throughput deep packet inspection performing both stream categorization and intrusion detection on GPU platform using CUDA. This implementation is capable of matching 64 ethernet packet streams against 25 given regular expressions at 524 Mb/s rate on a computer system with GeForce GTX 295 graphic card