National Institute of Technology, Durgapur

About: National Institute of Technology, Durgapur is a education organization based out in Durgapur, India. It is known for research contribution in the topics: Particle swarm optimization & Antenna (radio). The organization has 2590 authors who have published 5731 publications receiving 63466 citations. The organization is also known as: Regional Engineering College, Durgapur & NIT Durgapur.

Visualizing and interpreting cancer genomics data via the Xena platform.

Abstract: To the Editor — There is a great need for easy-to-use cancer genomics visualization tools for both large public data resources such as TCGA (The Cancer Genome Atlas)1 and the GDC (Genomic Data Commons)2, as well as smaller-scale datasets generated by individual labs. Commonly used interactive visualization tools are either web-based portals or desktop applications. Data portals have a dedicated back end and are a powerful means of viewing centrally hosted resource datasets (for example, Xena’s predecessor, the University of California, Santa Cruz (UCSC) Cancer Browser (currently retired3), cBioPortal4, ICGC (International Cancer Genomics Consortium) Data Portal5, GDC Data Portal2). However, researchers wishing to use a data portal to explore their own data have to either redeploy the entire platform, a difficult task even for bioinformaticians, or upload private data to a server outside the user’s control, a non-starter for protected patient data, such as germline variants (for example, MAGI (Mutation Annotation and Genome Interpretation6), WebMeV7 or Ordino8). Desktop tools can view a user’s own data securely (for example, Integrated Genomics Viewer (IGV)9, Gitools10), but lack well-maintained, prebuilt files for the ever-evolving and expanding public data resources. This dichotomy between data portals and desktop tools highlights the challenge of using a single platform for both large public data and smaller-scale datasets generated by individual labs. Complicating this dichotomy is the expanding amount, and complexity, of cancer genomics data resulting from numerous technological advances, including lower-cost high-throughput sequencing and single-cell-based technologies. Cancer genomics datasets are now being generated using new assays, such as whole-genome sequencing11, DNA methylation whole-genome bisulfite sequencing12 and ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing13). Visualizing and exploring these diverse data modalities is important but challenging, especially as many tools have traditionally specialized in only one or perhaps a few data types. And although these complex datasets generate insights individually, integration with other omics datasets is crucial to help researchers discover and validate findings. UCSC Xena was developed as a high-performance visualization and analysis tool for both large public repositories and private datasets. It was built to scale with the current and future data growth and complexity. Xena’s privacy-aware architecture enables cancer researchers of all computational backgrounds to explore large, diverse datasets. Researchers use the same system to securely explore their own data, together or separately from the public data, all the while keeping private data secure. The system easily supports many tens of thousands of samples and has been tested with up to a million cells. The simple and flexible architecture supports a variety of common and uncommon data types. Xena’s Visual Spreadsheet visualization integrates gene-centric and genomic-coordinate-centric views across multiple data modalities, providing a deep, comprehensive view of genomic events within a cohort of tumors. UCSC Xena (http://xena.ucsc.edu) has two components: the front end Xena Browser and the back end Xena Hubs (Fig. 1). The web-based Xena Browser empowers biologists to explore data across multiple Xena Hubs with a variety of visualizations and analyses. The back end Xena Hubs host genomics data from laptops, public servers, behind a firewall, or in the cloud, and can be public or private (Supplementary Fig. 1). The Xena Browser receives data simultaneously from multiple Xena Hubs and integrates them into a single coherent visualization within the browser. A private Xena Hub is a hub installed on a user’s own computer (Supplementary Fig. 2). It is configured to only respond to requests from the computer’s localhost network interface (that is, http://127.0.0.1). This ensures that the hub only communicates with the computer on which the hub is installed. A public hub is configured to respond to requests from external computers. There are two types of public Xena Hubs (Supplementary Fig. 2). The first type is an open-public hub, which is a public hub accessible by everyone. While we host several open-public hubs (Supplementary Table 1), users can also set up their own as a way to share data. An example of one is the Treehouse Hub set up by the Childhood Cancer Initiative to share pediatric cancer RNA-seq gene expression data (Supplementary Note). The second type W eb s er ve r

Graphene–metal oxide nanohybrids for toxic gas sensor: A review

Abstract: Sensing of gas molecules is critical to environmental monitoring, control of chemical processes, agricultural, and medical applications In particular, the detection of industrial toxic gases such as CO, NO x , and NH 3 is very important for many industries Metal oxides have been widely studied for the sensitivity of their properties to gases even though they do have some limitations Recently, graphene has been considered as a promising material for gas sensing since its electronic properties are strongly affected by the adsorption of foreign molecules Intrinsic graphene has high sensitivity at low gas concentrations; but the sensor selectivity is poor which limits its use in many practical applications Hence, hybrid architectures formed by blending of nanoparticles of metal–oxides with graphene or its derivatives have been explored by several researchers which showed improved gas sensing ability, especially the sensitivity and selectivity at room temperature Here we review the state of the art of gas sensors based on graphene and metal oxide hybrid nanostructures for detection of various common toxic gases

Leaf extract mediated green synthesis of silver nanoparticles from widely available Indian plants: synthesis, characterization, antimicrobial property and toxicity analysis

Abstract: In recent years, green synthesis of silver nanoparticles (AgNPs) has gained much interest from chemists and researchers. In this concern, Indian flora has yet to divulge innumerable sources of cost-effective non-hazardous reducing and stabilizing compounds utilized in preparing AgNPs. This study investigates an efficient and sustainable route of AgNP preparation from 1 mM aqueous AgNO3 using leaf extracts of three plants, Musa balbisiana (banana), Azadirachta indica (neem) and Ocimum tenuiflorum (black tulsi), well adorned for their wide availability and medicinal property. AgNPs were prepared by the reaction of 1 mM silver nitrate and 5% leaf extract of each type of plant separately. the AgNPs were duely characterized and tested for their antibacterial activity and toxicity. The AgNPs were characterized by UV-visible (vis) spectrophotometer, particle size analyzer (DLS), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and energy-dispersive spectroscopy (EDS). Fourier transform infrared spectrometer (FTIR) analysis was carried out to determine the nature of the capping agents in each of these leaf extracts. AgNPs obtained showed significantly higher antimicrobial activities against Escherichia coli (E. coli) and Bacillus sp. in comparison to both AgNO3 and raw plant extracts. Additionally, a toxicity evaluation of these AgNP containing solutions was carried out on seeds of Moong Bean (Vigna radiata) and Chickpea (Cicer arietinum). Results showed that seeds treated with AgNP solutions exhibited better rates of germination and oxidative stress enzyme activity nearing control levels, though detailed mechanism of uptake and translocation are yet to be analyzed. In totality, the AgNPs prepared are safe to be discharged in the environment and possibly utilized in processes of pollution remediation. AgNPs may also be efficiently utilized in agricultural research to obtain better health of crop plants as shown by our study.