Indian Institute of Technology Palakkad&nbsp;(IIT Palakkad or IIT PKD) is a public autonomous&nbsp;engineering&nbsp;and&nbsp;research&nbsp;institute located in&nbsp;Palakkad,&nbsp;Kerala. It was&nbsp;one of the five new&nbsp;IITs&nbsp;proposed in the&nbsp;2014 Union budget of India. The campus was inaugurated on 3 August 2015. The institute has 94 faculty, 978 students, and 63 non-teaching staffs.

IT Palakkad currently offers four-year Bachelor of Technology (B.Tech) and two years MS programmes in 8 different engineering disciplines including&nbsp;Computer Science, Electrical, Mechanical, Civil among others.

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IIT Palakkad

In this paper, we study two optimization problems where solutions on a dense set yield global solution. We study these problems for spaces of Bochner integrable functions and for spaces of continuous functions. The first one deals with expressing the length of a vector as a sum of the distance to a best approximation and minimal best approximation and the second one relates to approximating a subsequence of a minimizing sequence with a sequence of proximinal vectors. © 2016 Belgian Mathematical Society. All rights reserved.

Department of Mathematics

World University root node

Bulletin of the Belgian Mathematical Society - Simon Stevin

Optimization through dense sets

In this expository paper, we present proofs of Grothendieck-Serre formula for multi-graded algebras and Rees algebras for admissible multi-graded filtrations. As applications, we derive formulas of Sally for postulation number of admissible filtrations and Hilbert coefficients. We also discuss a partial solution of Itoh’s conjecture by Kummini and Masuti. We present an alternate proof of Huneke-Ooishi Theorem and a generalisation for multi-graded filtrations. © Springer Science+Business Media Singapore 2016.

Springer Proceedings in Mathematics and Statistics

Variations on the Grothendieck-Serre formula for Hilbert functions and their applications

The purpose of this article is to provide an exposition of domains of convergence of power series of several complex variables without recourse to relatively advanced notions of convexity.

arXiv preprint arXiv:1601.

Power Series in Several Complex Variables

We describe the design and characterization of a DNA polymerase-nanopore protein construct on an integrated chip. This system is able to incorporate all four DNA bases and distinguish single tagged nucleotide addition in real-time. Coupling protein catalysis and nanopore-based detection to an electrode array could provide the foundation of a highly-scalable, single-molecule, electronic DNA sequencing platform.

Department of Chemistry

20th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2016

Design and characterization of a nanopore-coupled polymerase for single molecule DNA sequencing by synthesis on an integrated electronic array

Scalable, high-throughput DNA sequencing is a prerequisite for precision medicine and biomedical research. Recently, we presented a nanopore-based sequencing-by-synthesis (Nanopore-SBS) approach, which used a set of nucleotides with polymer tags that allow discrimination of the nucleotides in a biological nanopore. Here, we designed and covalently coupled a DNA polymerase to an a-hemolysin (aHL) heptamer using the SpyCatcher/SpyTag conjugation approach. These porin-polymerase conjugates were inserted into lipid bilayers on a complementary metal oxide semiconductor (CMOS)-based electrode array for high-throughput electrical recording of DNA synthesis. The designed nanopore construct successfully detected the capture of tagged nucleotides complementary to a DNA base on a provided template. We measured over 200 tagged-nucleotide signals for each of the four bases and developed a classification method to uniquely distinguish them from each other and background signals. The probability of falsely identifying a background event as a true capture event was less than 1.2%. In the presence of all four tagged nucleotides, we observed sequential additions in real time during polymerase-catalyzed DNA synthesis. Single-polymerase coupling to a nanopore, in combination with the Nanopore-SBS approach, can provide the foundation for a low-cost, single-molecule, electronic DNA-sequencing platform.

Fulltext

Proceedings of the National Academy of Sciences of the United States of America

Design and characterization of a nanopore-coupled polymerase for single-molecule DNA sequencing by synthesis on an electrode array

DNA sequencing by synthesis (SBS) offers a robust platform to decipher nucleic acid sequences. Recently, we reported a singlemolecule nanopore-based SBS strategy that accurately distinguishes four bases by electronically detecting and differentiating four different polymer tags attached to the 5′-phosphate of the nucleotides during their incorporation into a growing DNA strand catalyzed by DNA polymerase. Further developing this approach, we report here the use of nucleotides tagged at the terminal phosphate with oligonucleotidebased polymers to perform nanopore SBS on an α-hemolysin nanopore array platform. We designed and synthesized several polymer-tagged nucleotides using tags that produce different electrical current blockade levels and verified they are active substrates for DNA polymerase. A highly processive DNA polymerase was conjugated to the nanopore, and the conjugates were complexed with primer/template DNA and inserted into lipid bilayers over individually addressable electrodes of the nanopore chip. When an incoming complementary-tagged nucleotide forms a tight ternary complex with the primer/template and polymerase, the tag enters the pore, and the current blockade level is measured. The levels displayed by the four nucleotides tagged with four different polymers captured in the nanopore in such ternary complexes were clearly distinguishable and sequence-specific, enabling continuous sequence determination during the polymerase reaction. Thus, real-time singlemolecule electronic DNA sequencing data with single-base resolution were obtained. The use of these polymer-tagged nucleotides, combined with polymerase tethering to nanopores and multiplexed nanopore sensors, should lead to new high-throughput sequencing methods.

Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array

We demonstrate for the first time the use of Fe-based nanoparticles on N-doped graphene as spacer and cavity materials and study their plasmonic effect on the spontaneous emission of a radiating dipole. Fe-C-MF was produced by pyrolizing FeOOH and melamine formaldehyde precursor on graphene, while Fe-C-PH was produced by pyrolizing the Fe-phenanthroline complex on graphene. The use of the Fe-C-MF composite consisting of Fe-rich crystalline phases supported on N-doped graphene presented a spacer material with 116-fold fluorescence enhancements. On the other hand, the Fe-C-PH/Ag based cavity resulted in an 82-fold enhancement in Surface Plasmon-Coupled Emission (SPCE), with high directionality and polarization of Rhodamine 6G (Rh6G) emission owing to Casimir and Purcell effects. The use of a mobile phone as a cost-effective fluorescence detection device in the present work opens up a flexible perspective for the study of different nanomaterials as tunable substrates in cavity mode and spacer applications. © 2016 American Chemical Society.

ACS Applied Materials and Interfaces

Earth Abundant Iron-Rich N-Doped Graphene Based Spacer and Cavity Materials for Surface Plasmon-Coupled Emission Enhancements

Mammalian sirtuins (SIRT1-7) are members of a highly conserved family of nicotinamide adenine dinucleotide (NAD+)-dependent protein deacetylases that regulate many biological processes including metabolism, genome stability, and transcription. Among the seven human sirtuins, SIRT7 is the least understood, to a large extent due to the lack of enzymatic activity in vitro. Here, we reported that SIRT7 can be activated by DNA to hydrolyze the acetyl group from lysine residues in vitro on histone peptides and histones in the chromatin context. Both N- and C- termini of SIRT7 are important for the DNA-activated deacetylase activity. The regulatory mechanism of SIRT7 is different from that of SIRT6, which also showed increased activity on chromatin substrates, but the deacetylase activity of SIRT6 on a peptide substrate cannot be activated by DNA. This finding provides an improved enzymatic activity assay of SIRT7 that will promote the development of SIRT7 modulators. Further investigation into the activation mechanism of SIRT7 by DNA could provide new insights into its biological function and help the development of sirtuin activators. © 2016 American Chemical Society.

ACS Chemical Biology

SIRT7 Is Activated by DNA and Deacetylates Histone H3 in the Chromatin Context

In this paper, a robust nonlinear proportional–integral–derivative (PID)-like fuzzy control scheme is presented and applied to complex trajectory tracking control of a 2PRP-PPR (P-prismatic, R-revolute) planar parallel manipulator (motion platform) with three degrees-of-freedom (DOF) in the presence of parameter uncertainties and external disturbances. The proposed control law consists of mainly two parts: first part uses a feed forward term to enhance the control activity and estimated perturbed term to compensate for the unknown effects namely external disturbances and unmodeled dynamics, and the second part uses a PID-like fuzzy logic control as a feedback portion to enhance the overall closed-loop stability of the system. Experimental results are presented to show the effectiveness of the proposed control scheme. © 2016 ISA

Department of Mechanical Engineering

ISA Transactions

Robust nonlinear PID-like fuzzy logic control of a planar parallel (2PRP-PPR) manipulator

Recent past has seen an inexorable shift towards the use of deep learning techniques to solve a myriad of problems in the field of medical imaging. In this paper, a novel segmentation method involving a fully-connected deep neural network called Deep Segmentation Network (DSN) is proposed to perform supervised regression for brain extraction from T1-weighted magnetic resonance (MR) images. In contrast to the existing patch-based feature learning techniques, DSN works on full 3D volumes, simplifying pre- and postprocessing operations, to efficiently provide a voxel-wise binary mask delineating the brain region. The model is evaluated using three publicly available datasets and is observed to either outdo or perform comparably to the state-of-the-art methods. DSN is able to achieve a maximum and minimum Dice Similarity Coefficient (DSC) of 97:57 and 92:82 respectively across all the datasets. Experiments conducted in this paper highlight the ability of the DSN model to automatically learn feature representations; making it a simple yet highly effective approach for brain segmentation. Preliminary experiments also suggest that the proposed model has the potential to segment sub-cortical structures accurately.