Detecting biomarkers from microarray data using distributed correlation based gene selection

Alok Kumar Shukla,Diwakar Tripathi 한국유전학회 2020 Genes & Genomics Vol.42 No.4

Background Over the past few decades, DNA microarray technology has emerged as a prevailing process for early identification of cancer subtypes. Several feature selection (FS) techniques have been widely applied for identifying cancer from microarray gene data but only very few studies have been conducted on distributing the feature selection process for detecting cancer subtypes. Objective Not all the gene expressions are needed in prediction, this research article objective is to select discriminative biomarkers by using distributed FS method which helps in accurately diagnosis of cancer subtype. Traditional feature selection techniques have several drawbacks like unrelated features that could perform well in terms of classification accuracy with a suitable subset of genes will be left out of the selection. Method To overcome the issue, in this paper a new filter-based method for gene selection is introduced which can select the highly relevant genes for distinguishing tissues from the gene expression dataset. In addition, it is used to compute the relation between gene–gene and gene–class and simultaneously identify subset of essential genes. Our method is tested on Diffuse Large B cell Lymphoma (DLBCL) dataset by using well-known classification techniques such as support vector machine, naïve Bayes, k-nearest neighbor, and decision tree. Results Results on biological DLBCL dataset demonstrate that the proposed method provides promising tools for the prediction of cancer type, with the prediction accuracy of 97.62%, precision of 94.23%, sensitivity of 94.12%, F-measure of 90.12%, and ROC value of 99.75%. Conclusion The experimental results reveal the fact that the proposed method is significantly improved classification accuracy and execution time, compared to existing standard algorithms when applied to the non-partitioned dataset. Furthermore, the extracted genes are biologically sound and agree with the outcome of relevant biomedical studies.

Genetic Transformation of Pigeonpea (Cajanus cajan L.) and Screening Transgenic Progenies Based on Lateral Root Inhibition

Alok Das,Manoj Kumar,Arvind Kumar Singh,Alok Shukla,Jamal Ansari,Subhojit Datta,Narendra Pratap Singh 한국작물학회 2016 Journal of crop science and biotechnology Vol.19 No.4

Production of transgenic pigeonpea is becoming increasingly important, but the methods currently employed in production and subsequent screening still requires improvement. Here, we describe Agrobacterium-mediated genetic transformation of pigeonpea with reporter uidA (gus) gene and selectable marker, neomycin phospho-transferase (nptII) gene. Histochemical assay demonstrate localization of gus activity in cells and transformed plants. Overall, a transformation frequency of 0.33% was achieved using the protocol. Grafting of in vitro-regenerated healthy shoots indicates higher survival percent (72.6%), when stock and scion are of the same variety. Seeds harvested from primary transgenic plants can be screened based on lateral root inhibition strategy. Approximately 87% of the screened T1 plants were found to be PCR positive. In conclusion, in vitro grafting of transgenic pigeonpea shoots leads to better plant establishment and screening based on lateral root inhibition leads to quick identification of positive segregants.

Au-nanoparticle/nanopillars TiO2 meso-porous thin films in the degradation of tetracycline using UV-A light

Alka Tiwari,Alok Shukla,Lalliansanga,Diwakar Tiwari,이승목 한국공업화학회 2019 Journal of Industrial and Engineering Chemistry Vol.69 No.-

Novel meso-porous nanoparticles Au/TiO2 thin films were obtained by template synthesis using polyethylene glycol as filler medium. The materials were characterized by advanced analytical methods. The photocatalysts were employed for the photocatalytic degradation of tetracycline from aqueous solutions using UV-A light (λmax 330 nm). Various physico-chemical parametric studies enabled to deduce the mechanism of degradation. A significant percentage of tetracycline was mineralized by the treatment. The stability of thin film was evidenced with the repeated use of thin film. The degradation of tetracycline was proceeded predominantly by the OH radicals generated at the valance and conduction band of semiconductor.

Titanium Dioxide Nanomaterials and its Derivatives in the Remediation of Water: Past, Present and Future

( Alka Tiwari ),( Alok Shukla ),( Diwakar Tiwari ),( Suk Soon Choi ),( Hyun-gon Shin ),( Seung-mok Lee ) 한국공업화학회 2019 공업화학 Vol.30 No.3

The aim of this review article is to summarize the role of titanium oxide (TiO₂) nanomaterials in the remediation of the aquatic environment contaminated with various emerging pollutants. The advanced oxidation process led by the semiconductor TiO₂ is an impetus in the remediation technology. Therefore, a vast number of literature works are available in this area. Further, the role of modified TiO₂ or thin film materials were discussed in the review. Also, the Localized Surface Plasmon Resonance (LSPR) effect of using noble metaldoped TiO₂ played an interesting role in the remediation process.

Titanium Dioxide Nanomaterials and its Derivatives in the Remediation of Water: Past, Present and Future

Tiwari, Alka,Shukla, Alok,Tiwari, Diwakar,Choi, Suk Soon,Shin, Hyun-Gon,Lee, Seung-Mok The Korean Society of Industrial and Engineering C 2019 공업화학 Vol.30 No.3

The aim of this review article is to summarize the role of titanium oxide ($TiO_2$) nanomaterials in the remediation of the aquatic environment contaminated with various emerging pollutants. The advanced oxidation process led by the semiconductor $TiO_2$ is an impetus in the remediation technology. Therefore, a vast number of literature works are available in this area. Further, the role of modified $TiO_2$ or thin film materials were discussed in the review. Also, the Localized Surface Plasmon Resonance (LSPR) effect of using noble metaldoped $TiO_2$ played an interesting role in the remediation process.

Surface modified nanostructured-TiO2 thin films for removal of Congo red

Tiwari, Alka,Shukla, Alok,Choi, Suk Soon,Lee, Seung-Mok Springer-Verlag 2018 Korean Journal of Chemical Engineering Vol.35 No.10

Facile synthesis and characterization of nanocomposite Au0(NPs)/titanium dioxide: Photocatalytic degradation of Alizarin Yellow

Lalliansanga,Diwakar Tiwari,Alka Tiwari,Alok Shukla,DONG JIN KIM,Yi-Yong Yoon,Seung-Mok Lee 한국공업화학회 2020 Journal of Industrial and Engineering Chemistry Vol.82 No.-

The present communication aims to synthesise the plasmonic nanocomposite Au0(NPs)/TiO2 by afacile route and to utilize material in the efficient removal of Alizarin Yellow in aqueous solutions usingthe UV-A light. Au0-nanoparticles were in situ doped with titania network using template method. Polyethylene glycol was employed asfiller media. The nanocomposites Au0(NPs)/TiO2 (non-template)and Au0(NPs)/TiO2(T) (template) were characterized by the XRD and DRS (Diffuse ReflectionSpectroscopy) methods. Surface characteristics were discussed by the SEM and TEM pictures of thesematerials. The interplanar distance of Au(NPs) were found to be 0.14 nm and 0.20 nm for the materialsAu0(NPs)/TiO2 and Au0(NPs)/TiO2(T), respectively. The Atomic Force Microscopy (AFM) analysis showedheterogeneous surface structure and TiO2 were pillared on the surface. Physico-chemical studiesdeduced the mechanistic pathways of removal. The pseudo-first order rate constant values weredecreased with the increase in dye concentrations. Further, mineralization of Alizarin Yellow wasobtained at wide range of pH (pH 4.0–8.0). The nanocomposite thinfilms showed fairly a good stabilityfor repeated cycle of operations in removal of Alizarin Yellow. The photocatalyst shown greaterapplicability in the real matrix treatment using Tlwang river water.

Nanopillars TiO2 thin film photocatalyst application in the remediation of aquatic environment

C. Lalhriatpuia,Alka Tiwari,Diwakar Tiwari,Alok Shukla,Seung-Mok Lee 한국화학공학회 2016 Korean Journal of Chemical Engineering Vol.33 No.12

We assessed the photocatalytic behavior of Nanopillars-TiO2 thin films obtained onto a borosilicate glass in the degradation of 17α-ethynylestradiol (EE2) from aqueous solution under batch reactor operations. The thin films were characterized by the XRD, SEM, AFM analytical methods. BET specific surface area and pore sizes were also obtained. The photocatalytic degradation of EE2 using the UV light was studied at wide range of physico-chemical parametric studies to determine the mechanism of degradation as well the practical implacability of the technique. The batch reactor operations were conducted at varied pH (pH 4.0 to 10.0), EE2 initial concentration (1.0 to 5.0mg/L) and presence of several interfering ions, i.e., cadmium nitrate, copper sulfate, zinc chloride, sodium chloride, sodium nitrate, sodium nitrite, glycine, oxalic acid and EDTA in the photocatalytic degradation of EE2. The time dependence photocatalytic degradation of EE2 was demonstrated with the pseudo-first-order rate kinetics. The mineralization of EE2 was assessed using the total organic carbon analysis conducted at varied initial pH and EE2 concentrations. Further, the repeated use of the photocatalyst enhanced the applicability of thin films in the successive photocatalytic operations.

Equivalent circuit model of a PbZr0.6Ti0.4O3 ceramic using impedance spectroscopy

Pramod Chaitanya,O. P. Thakur,Vinod Kumar,Alok Shukla,Lakshman Pandey 한양대학교 세라믹연구소 2011 Journal of Ceramic Processing Research Vol.12 No.3

The ceramic system PbZr0.6Ti0.4O3 was prepared by a solid state method and impedance measurements were carried out as a function of frequency (100 Hz-10MHz) in the temperature range 370 K-869 K. Equivalent circuit models that represent the data below and above the transition temperature were arrived at by comparing the experimental plots with the computersimulated behavior obtained for model circuits. Below the transition temperature the equivalent circuit model comprises a series LCR combination connected in series with a parallel RC network where as for higher temperatures it contains three parallel RC circuits connected in series. Variation of the values of the components as a function of temperature was also studied.