Sharif Digital Repository

Background: Long reads provide valuable information regarding the sequence composition of genomes. Long reads are usually very noisy which renders their alignments on the reference genome a daunting task. It may take days to process datasets enough to sequence a human genome on a single node. Hence, it is of primary importance to have an aligner which can operate on distributed clusters of computers with high performance in accuracy and speed. Results: In this paper, we presented IMOS, an aligner for mapping noisy long reads to the reference genome. It can be used on a single node as well as on distributed nodes. In its single-node mode, IMOS is an Improved version of Meta-aligner (IM)... 

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... 

Blood transfusion services are vital components of healthcare systems all over the world. In this paper, a generalized network optimization model is developed for a complex blood supply chain in accordance with Iranian blood transfusion organization (IBTO) structure. This structure consist of four types facilities. Blood collection centers, blood collection and processing centers, mobile teams and blood transfusion center have various duties in IBTO structure. The major contribution is to develop a novel hybrid approach based on stochastic programming, ε-constraint and robust optimization (HSERO) to simultaneously model two types of uncertainties by including stochastic scenarios for total... 

Simulation is the gold standard for training in aviation and trauma medicine. Now it is available for diseases diagnosis and treatment. With simulation, clinicians can practice their art in a realistic, consequence free environment, combining both theory and practice in a comprehensive program. Method and materials - In the virtual clinical environment of "VPsoft mentor" software, the practitioner reviews a patient's history, orders laboratory tests and procedures, interprets findings, renders diagnoses, and prescribes medication. Every diagnostic or treatment decision the clinician makes for the patient is analyzed by E-mentor, providing instant feedback.Results - This software have been... 

The use of Computer Science in order to categorize and store information, improve diagnostic and therapeutic procedures, patient education and the training of a skilled labor force, has taken important steps and there are constantly new developments in this area  

MapReduce and its open source implementation, Hadoop, have gained widespread adoption for parallel processing of big data jobs. Since the number of such big data jobs is also rapidly rising, reducing their energy consumption is increasingly more important to reduce environmental impact as well as operational costs. Prior work by Mashayekhy et al. (IEEE Trans. Parallel Distributed Syst. 26, 2720–2733, 2016), has tackled the problem of energy-aware scheduling of a single MapReduce job but we provide a far more efficient heuristic in this paper. We first model the problem as an Integer Linear Program to find the optimal solution using ILP solvers. Then we present a task-based greedy scheduling... 

This paper provides empirical evidence on a novel complementarity between VAT and trade taxes. Downstream domestic firms require VAT receipts from importers to claim VAT on purchases, increasing incentives for honest reporting of imports. Trade gap, the difference between mirror and domestic trade reports in Iran at 6-digit HS disaggregation, is used to measure this complementarity. Iran introduced VAT in 2008 and, since then, has increased its rate from 3 to 9 percent. Difference-in-differences estimates show that a 1 percentage point increase in the VAT rate reduces the trade gap by about 2 percent. Consistent with the compliance mechanisms for VAT, a smaller effect for consumer products... 

A very efficient and mild procedure for the trimethylsilylation of a wide variety of alcohols, including primary, allylic, benzylic, secondary, hindered secondary, tertiary, and phenols with hexamethyldisilazane on the surface of silica gel dispersed with LiClO4 in room temperature at few minutes in excellent yields under neutral conditions is reported. This procedure also allows the excellent selectivity under LP-SiO2 system for silylation of alcohols in the presence of amine and phenolic hydroxy groups  

The recently reported UNIversal QUAsiChemical Segment Activity coefficient (UNIQUAC-SAC) model [developed by Haghtalab and Yousefi Seyf Ind. Eng. Chem. Res. 2015, 54, 8611] provides a practical thermodynamic framework to be used in VLE, LLE, and SLE calculations. The UNIQUAC-SAC model has the advantage of being independent of area (q) and volume (r) structural parameters used in the combinatorial part. While the UNIFAC or UNIFAC-DMD could not apply to the 47% (44 of 94) of the studied molecules because of the undefined groups. Here, the numbers of solvents with identified segment numbers were extended from 82 to 130 with a slight refinement to the previous values. The model parameters... 

Recently, moment dual approach of sums of squares relaxations developed for polynomial optimization problems was successfully extended to optimization problems with polynomial matrix inequality constraints. In this paper, we first derive an efficient polynomial formulization for matrix rank minimization problem which does not add any slack variable or additional equality or inequality constraint. Using the aforementioned theory, then we propose a hierarchy of convex LMI relaxations to provide a sequence of increasingly tight lower bounds on the global minimum rank of an arbitrary matrix under linear and polynomial matrix inequality constraints. Surprisingly enough, these lower bounds are... 

The perturbed chain-statistical associating fluid theory equation of state (PC-SAFT EoS) is one of the state-of-the-art thermodynamic models used in the phase equilibrium calculation of associating mixtures, in particular, in the pharmaceutical industry. Accordingly, parametrization of the PC-SAFT EoS for approved solvents reviewed for use in pharmaceutical process design by the International Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH) was done in the present study. First, the PeC-SAFT EoS model parameters for 41 pure solvents were regressed (of 62 solvents). The available high-quality binary vapor-liquid equilibrium (VLE)... 

Effect of alkaline metal salts on the solvent extraction of platinum from leached spent dehydrogenation catalysts (Pt/Al2O3) in aqua-regia by the Trioctylphosphine oxide (TOPO) has been investigated. Best salting out effect was achieved using KCl as the additive salt in which process upto 90% of Platinum extraction achieved. Response Surface methodology utilized in order to design the experiments, model the extraction process for platinum and aluminum as well as; optimize the whole process. It was shown that solvent extraction of platinum by TOPO was kinetically fast and the needed equilibrium time for it was less than 30 seconds. In the present study, proposed models for platinum and... 

This paper presents several efficient architectures of dynamic/static edge-triggered flip-flops with a compact embedded logic. The proposed structure, which benefits from the overlap period, fixes most of the drawbacks of the dynamic logic family. The design issues of setting the appropriate overlap period for this architecture are explained. The proposed overlap-based approach is compared with several state-of-the-art dynamic/static logic styles in implementing a 4-bit shift register and an odd-even sort coprocessor using different CMOS technologies. The simulation results showed that the overlap-based logic cells become much more efficient when the complexity of their embedded logic... 

In this research, data on liquid-liquid extraction of platinum from commercial spent catalysts by trioctylphosphine oxide (TOPO) in toluene were experimentally obtained. Alkaline metal salts were used to optimize the separation process. Best Salting-out effect was obtained by KCl which extracted up to 90% of platinum utilizing TOPO. Furthermore, extraction percentages of Pt and Al depending upon different factors were investigated. It was observed that the extraction process was kinetically fast and achieving the equilibrium time took less than 30 seconds. Optimized points obtained utilizing response surface methodology (RSM) by the "Design Expert" software in order to minimize the... 

Design and manufacturing of a high performance micro-hydro-kinetic turbine is discussed in the present paper. The main goal is manufacturing an equipped experimental model of hydro-kinetic turbine with highest energy absorption from water current. A multi-shape ducted turbine comprised of a multi-part diffuser was manufactured that can be converted to many experimental models for studying various diffuser enhancing effects. Turbine's rotor included a three-blade axial propeller and a mixed six-blade propeller with high power coefficient. Simple experiments on propeller were performed for flow visualization, torque measurement and illustrating dynamic balance at high speed rotation in air and... 

Data aggregation is a key, yet time-consuming functionality introduced to conserve energy in wireless sensor networks (WSNs). In this paper, to minimize time latency, we focus on aggregation scheduling problem and propose an efficient distributed algorithm that generates a collision-free schedule with the least number of time slots. In contrast to others, our approach named FAST mainly contributes to both tree construction, where the former studies employ Connected 2-hop Dominating Sets, and aggregation scheduling that was previously addressed through the Competitor Sets computation. We prove that the latency of FAST under the protocol interference model is upper-bounded by 12R+Δ-2, where R... 

A new predictive model for evaluating the vibration of a sawing machine was developed using a new rock classification system. The predictors are machine parameters and a rock sawability index. The new rock classification system includes four major parameters of the rock: uniaxial compressive strength, abrasivity index, mean Moh's hardness, and Young's modulus. The FAHP approach was used when determining the weights of these parameters by six decision makers. Two groups of carbonate rocks were sawn using a fully-instrumented laboratory sawing rig at different feed rates and depths of cut. During the sawing trials system vibration was monitored as a measure of saw performance. Then, a new...