Genome Informatics (GI) involves accurate computational investigations of strongly correlated subsystems that demands inter-disciplinary approaches for problem solving. With the growing volume of ...genomic sequencing data at an alarming rate, High Performance Computing (HPC) solutions offer the right platform to address the computational needs. GI requires algorithm-architecture co-design of parallel and accelerated biocomputing involving reconfigurable hardware like FPGAs and graphics accelerators or GPUs, to bridge the gap between growing data volumes and compute capabilities. Such platforms offer high degrees of parallelism and scalability, while accelerating the multi-stage GI computational pipeline. Amidst such high computing power, it is the choice of algorithms and implementations in the entirety of the GI pipeline that decides the precision of bio-computing in revealing biologically relevant information. Through this paper, we present ReneGENE-GI, an innovatively engineered GI pipeline. This paper details the performance analysis of ReneGENE-GI’s Comparative Genomics Module (CGM), the compute intensive stage of the pipeline. This module comes in two flavours, designed to run on GPUs and FPGAs respectively, hosted on HPC platforms. The pipeline uses a very efficient reference indexing algorithm based on the dynamic Monotonic Minimal Perfect Hashing Function (MMPH), allowing an absolute indexing for the reference genome, thus avoiding heuristics. Alignment time for our FPGA version is about one-tenth the time taken by our single GPU implementation, which itself is 2.62x faster than CUSHAW2-GPU (the GPU CUDA implementation of CUSHAW). With the single-GPU implementation demonstrating a speed up of 150+ x over standard heuristic aligners in the market like BFAST, the FPGA version of our CGM is several orders faster than the competitors, offering precision over heuristics.
On F-index of Certain Generalized Thorny Graphs Natarajan, C.; Ayyaswamy, S. K.; Sarala, D. ...
National Academy of Sciences, India. Proceedings. Section A. Physical Sciences,
06/2021, Letnik:
91, Številka:
2
Journal Article, Conference Proceeding
Recenzirano
Let
G
=
(
V
,
E
)
be a graph with
n
vertices and
m
edges. The forgotten topological index or
F
-index of
G
is defined as
F
(
G
)
=
∑
v
∈
V
(
G
)
d
G
(
v
)
3
=
∑
u
v
∈
E
(
G
)
d
G
(
u
)
2
+
d
G
(
v
)
...2
where
d
G
(
v
)
stands for the degree of the vertex
v
in
G
. In this paper, we compute the
F
-index of certain generalized thorny graphs.
Abstract
Silver/Zinc Oxide nanocomposites (Ag-ZnO NCs) were fabricated by varying the weight percentages of both Ag and ZnO for investigating its photocatalytic activity. The structural, morphology ...and optical response of the prepared nanocomposites were examined with PXRD, FESEM, TEM, EDAX, XPS, FT-IR, UV–vis-DRS and PL spectroscopy. The effect of Ag and ZnO concentrations on these nanocomposites was examinedby analyzing thephotocatalytic activity towards Methylene Blue (MB) dye degradationunder the UV irradiation. The overall results suggested that, AZ
1:1
NC achieved better photocatalytic activity than AZ
1:2
and AZ
2:1
composition. Therefore, the present study demonstrated the viability of the Ag-ZnO NCs in remediation of environmental pollutant and treatment of waste water.
Rehabilitation of maxillofacial defects is an arduous task that involves restoring the form and function of the resected part of the defect. Obturators are the preferred choice of treatment for ...patients after resection involving the maxilla. Rehabilitation aims to separate the oral and nasal cavity and maintain anatomy while also assisting the patient with mastication, maintaining occlusion, supporting the mandible and facial tissues, and reestablishing speech and esthetics. Following surgery, a prosthetic evaluation is performed in which magnets are attached to the prosthesis to restore function and speech, as well as retention, stability, and quality of life. This case report describes how a hollow bulb obturator was used to treat a partial maxillectomy patient with magnets and clasps for patient rehabilitation.
Sr2SiO4 is an important inorganic host for lanthanide doped white light emitting diodes (LEDs). Strontium silicate (Sr2SiO4) samples doped with 1.0 mol% of Eu3+ and Dy3+ content were prepared via ...sol-gel route and characterized by X-ray diffraction (XRD), Raman spectroscopy and positron annihilation spectroscopy (PAS). The concentration of the dopant ion and the temperature of annealing were optimized for maximum luminescence intensity. The positron annihilation lifetime and coincidence Doppler broadening (CDB) measurements indicated that the local environment around the positron annihilation site is different in Eu+3 doped and Dy+3 doped samples. The results could be explained based on the different local site occupancy of Eu+3 and Dy+3 in the matrix.
Sulphur dioxide (SO2) is a common atmospheric contaminant which has a deleterious effect on fuel cells. The performance of a Polymer Electrolyte Fuel Cell (PEFC) utilising a Pt on nitrogen doped ...graphene support as the cathode catalyst was studied in the presence of air contaminated with known levels of SO2. The nitrogen doped graphene supported platinum was synthesized by a hydrothermal method. At levels of 25 ppm SO2 in air there was within 15 min a 28% reduction in the PEFC performance at 0.5 V. The performance degradation was more severe at higher SO2 concentrations. At 100 ppm SO2 in air the performance degraded by 91% at the same potential. The power loss of the fuel cell could not be recovered by externally polarising the PEFC at 1.6 V. Even after continuous potential cycling of the cell for 9 h only 80% of the initial performance could be recovered. However, a 15 min treatment with 0.4% O3 in air showed almost a 100% performance recovery of the 100 ppm SO2 contaminated fuel cell. The enhanced recovery of the fuel cell is related both to the chemical reaction of O3 with the adsorbed sulphur contaminant, and an increase of cathode potential during the electrochemical treatment.
The self-expanding V-POD is a second-generation flow-diverting device with a low-porosity PTFE patch on a self-expanding microstent. The authors evaluated this device for the treatment of ...elastase-induced aneurysms in rabbits.
Three V-POD types (A, circumferential patch closed-cell stent n = 9; B, asymmetric patch closed-cell stent n = 7; and C, asymmetric patch open-cell stent n = 4) were evaluated by using angiography, conebeam micro-CT, histology, and SEM. Aneurysm flow modifications were expressed in terms of immediate poststent/prestent ratios of maximum CA volume entering the aneurysm dome tracked on procedural angiograms. Flow modifications were correlated with 4 weeks' follow-up angiographic, micro-CT, histologic, and SEM results.
Mechanical stent-deployment difficulties in 4 aneurysms (1 type A; 3 type B) led to suboptimal results and exclusion from analysis. Of the remaining 16 aneurysms, 4-week post-treatment angiograms showed no aneurysm filling in 10 (63%), 3 (∼19%) had no filling with a small remnant neck, and 3 (∼19%) had <0.25 filling. Successfully treated aneurysms (n = 16) demonstrated an immediate poststent/prestent CA maximum volume ratio of 0.13 ± 0.18% (0.0%-0.5%). Favorable contrast-flow modification on immediate angiography after deployment correlated significantly with aneurysm occlusion on follow-up angiography, micro-CT, and histology. The occlusion percentage derived from micro-CT was 96 ± 6.8%. Histology indicated advanced healing (grade ≥3) in the aneurysm dome in 13 of 16 cases. SEM revealed 15 of 16 stents in an advanced state of endothelialization.
This study showed the feasibility and effectiveness of V-POD for aneurysm healing in a rabbit elastase model.
An ICP-AES based method was developed for the direct determination of Phosphorous and Sulphur in U, Th and Zr matrices. Different analytical lines of P and S were identified and the calibration ...curves were established. Analytical performance of these analytical lines and the spectral interference of U, Th and Zr on these lines were studied systematically. The methodology for direct and trace level determination of P and S was found to be promissing, simple and less time consuming and it was validated using synthetic samples. The method was also found to be compared satisfactorily with the existing methods for their determination.
The objective of this study is to determine the impact of intensity modulated proton therapty (IMPT) optimization techniques on the proton dose comparison of commercially available magnetic resonance ...for calculating attenuation (MRCA T) images, a synthetic computed tomography CT (sCT) based on magnetic resonance imaging (MRI) scan against the CT images and find out the optimization technique which creates plans with the least dose differences against the regular CT image sets.
Regular CT data sets and sCT image sets were obtained for 10 prostate patients for the study. Six plans were created using six distinct IMPT optimization techniques including multi-field optimization (MFO), single field uniform dose (SFUD) optimization, and robust optimization (RO) in CT image sets. These plans were copied to MRCA T, sCT datasets and doses were computed. Doses from CT and MRCA T data sets were compared for each patient using 2D dose distribution display, dose volume histograms (DVH), homogeneity index (HI), conformation number (CN) and 3D gamma analysis. A two tailed t-test was conducted on HI and CN with 5% significance level with a null hypothesis for CT and sCT image sets.
Analysis of ten CT and sCT image sets with different IMPT optimization techniques shows that a few of the techniques show significant differences between plans for a few evaluation parameters. Isodose lines, DVH, HI, CN and t-test analysis shows that robust optimizations with 2% range error incorporated results in plans, when re-computed in sCT image sets results in the least dose differences against CT plans compared to other optimization techniques. The second best optimization technique with the least dose differences was robust optimization with 5% range error.
This study affirmatively demonstrates the impact of IMPT optimization techniques on synthetic CT image sets dose comparison against CT images and determines the robust optimization with 2% range error as the optimization technique which gives the least dose difference when compared to CT plans.
Introduction Climate change, nutritional security, land shrinkage, and an increasing human population are the most concerning factors in agriculture, which are further complicated by deteriorating ...soil health. Among several ways to address these issues, the most prominent and cost-effective means is to adopt an integrated farming system (IFS). Integrating farming systems with livestock enables a way to increase economic yield per unit area per unit of time for farmers in small and marginal categories. This system effectively utilizes the waste materials by recycling them via linking appropriate components, thereby minimizing the pollution caused to the environment. Further integrating livestock components with crops and the production of eggs, meat, and milk leads to nutritional security and stable farmer's income generation. So, there is a dire need to develop an eco-friendly, ecologically safe, and economically profitable IFS model. Methods An experiment was conducted to develop a crop–livestock-based integrated farming system model for the benefit of irrigated upland farmers in the semi-arid tropics for increasing productivity, farm income, employment generation, and food and nutritional security through efficient utilization of resources in the farming system. Results and discussion The IFS model has components, viz., crop (0.85 ha) + horticulture (0.10 ha) + 2 cattles along with 2 calves in dairy (50 m 2 ) + 12 female goats and 1 male goat (50 m 2 ) + 150 numbers of poultry birds (50 m 2 ) + vermicompost (50 m 2 ) + kitchen garden (0.02 ha) + boundary planting + supporting activities (0.01 ha) in a one-hectare area. The model recorded a higher total MEY (162.31 t), gross return (689,773), net return (317,765), and employment generation (475 mandays). Further negative emissions of −15,118 CO 2 -e (kg) greenhouse gases were recorded under this model. The study conclusively reveals that integration of crop, horticulture, dairy, goat, poultry, vermicompost production, kitchen garden, and boundary planting models increases the net returns, B:C ratio, employment generation, nutritional security, and livelihoods of small and marginal farmers.
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