CEP: a conformational epitope prediction server

CEP server () provides a web interface to the conformational epitope prediction algorithm developed in-house. The algorithm, apart from predicting conformational epitopes, also predicts antigenic determinants and sequential epitopes. The epitopes are predicted using 3D structure data of protein antigens, which can be visualized graphically. The algorithm employs structure-based Bioinformatics approach and solvent accessibility of amino acids in an explicit manner. Accuracy of the algorithm was found to be 75% when evaluated using X-ray crystal structures of Ag–Ab complexes available in the PDB. This is the first and the only method available for the prediction of conformational epitopes, which is an attempt to map probable antibody-binding sites of protein antigens

A 32-bit Ultrafast Parallel Correlator using Resonant Tunneling Devices

An ultrafast 32-bit pipeline correlator has been implemented using resonant tunneling diodes (RTD) and hetero-junction bipolar transistors (HBT). The negative differential resistance (NDR) characteristics of RTD's is the basis of logic gates with the self-latching property that eliminates pipeline area and delay overheads which limit throughput in conventional technologies. The circuit topology also allows threshold logic functions such as minority/majority to be implemented in a compact manner resulting in reduction of the overall complexity and delay of arbitrary logic circuits. The parallel correlator is an essential component in code division multi-access (CDMA) transceivers used for the continuous calculation of correlation between an incoming data stream and a PN sequence. Simulation results show that a nano-pipelined correlator can provide and effective throughput of one 32-bit correlation every 100 picoseconds, using minimal hardware, with a power dissipation of 1.5 watts. RTD plus HBT based logic gates have been fabricated and the RTD plus HBT based correlator is compared with state of the art complementary metal oxide semiconductor (CMOS) implementations

Narrative Review of Nimesulide in Adults: Current Scenario

Nimesulide, a nonsteroidal anti-inflammatory drug (NSAID), has been used as an effective treatment regimen for patients aged >12 years for fever, acute pain, acute tendinitis, osteoarthritis and dysmenorrhea. It is reported to be a superior antipyretic and anti-inflammatory drug than paracetamol and aspirin, respectively, and is equal to any of the NSAIDs alone in terms of analgesia. This paper reviews the current scenario of nimesulide in adult patients, concerning clinical evidence, use in special population and expert opinion. Overall, in comparison to other NSAIDs, including coxibs, nimesulide has a promising overall efficacy, safety and tolerability profile, as well as a satisfactory benefit/risk evaluation

Analysis of an LSTM-based NOMA Detector Over Time Selective Nakagami-m Fading Channel Conditions, Journal of Telecommunications and Information Technology, 2022, nr 3

This work examines the efficacy of deep learning (DL) based non-orthogonal multiple access (NOMA) receivers in vehicular communications (VC). Analytical formulations for the outage probability (OP), symbol error rate (SER), and ergodic sum rate for the researched vehicle networks are established Rusing i.i.d. Nakagami-m fading links. Standard receivers, such as least square (LS) and minimum mean square error (MMSE), are outperformed by the stacked long-short term memory (S-LSTM) based DL-NOMA receiver. Under real time propagation circumstances, including the cyclic prefix (CP) and clipping distortion, the simulation curves compare the performance of MMSE and LS receivers with that of the DL-NOMA receiver. According to numerical statistics, NOMA outperforms conventional orthogonal multiple access (OMA) by roughly 20% and has a high sum rate when considering i.i.d. fading links

Curation of viral genomes: challenges, applications and the way forward

BACKGROUND: Whole genome sequence data is a step towards generating the 'parts list' of life to understand the underlying principles of Biocomplexity. Genome sequencing initiatives of human and model organisms are targeted efforts towards understanding principles of evolution with an application envisaged to improve human health. These efforts culminated in the development of dedicated resources. Whereas a large number of viral genomes have been sequenced by groups or individuals with an interest to study antigenic variation amongst strains and species. These independent efforts enabled viruses to attain the status of 'best-represented taxa' with the highest number of genomes. However, due to lack of concerted efforts, viral genomic sequences merely remained as entries in the public repositories until recently. RESULTS: VirGen is a curated resource of viral genomes and their analyses. Since its first release, it has grown both in terms of coverage of viral families and development of new modules for annotation and analysis. The current release (2.0) includes data for twenty-five families with broad host range as against eight in the first release. The taxonomic description of viruses in VirGen is in accordance with the ICTV nomenclature. A well-characterised strain is identified as a 'representative entry' for every viral species. This non-redundant dataset is used for subsequent annotation and analyses using sequenced-based Bioinformatics approaches. VirGen archives precomputed data on genome and proteome comparisons. A new data module that provides structures of viral proteins available in PDB has been incorporated recently. One of the unique features of VirGen is predicted conformational and sequential epitopes of known antigenic proteins using in-house developed algorithms, a step towards reverse vaccinology. CONCLUSION: Structured organization of genomic data facilitates use of data mining tools, which provides opportunities for knowledge discovery. One of the approaches to achieve this goal is to carry out functional annotations using comparative genomics. VirGen, a comprehensive viral genome resource that serves as an annotation and analysis pipeline has been developed for the curation of public domain viral genome data . Various steps in the curation and annotation of the genomic data and applications of the value-added derived data are substantiated with case studies

Quantum MOS circuits and systems.

Device physics limitations of conventional complementary metal-oxide semiconductor (CMOS) transistors are likely to cause diminishing integrated circuit performance improvement in the sub 100-nm regime. At these dimensions, quantum effects become prominent leading to realization of devices utilizing quantum-mechanical tunneling transport mechanisms for obtaining picosecond device switching speeds. The negative differential-resistance (NDR) current-voltage (I-V) characteristic of such devices, achieved due to resonant tunneling, is also ideally suited for the design of compact self-latching logic circuits. While resonant tunneling devices have been demonstrated using III-V materials, their large absolute current values and low integration levels have limited their use to niche high-performance small-scale circuits. Given the advantages of resonant tunneling devices, it is attractive to envision compact, high-functionality NDR circuits implemented in a technology such as CMOS that offers low power dissipation and very high integration levels. Even as research in cointegration of resonant tunneling devices in Silicon, referred to as quantum MOS (QMOS), is ongoing, this dissertation presents novel combinational and bistable logic families, and compact flip-flop circuits using resonant tunneling diodes (RTDs) and MOS transistors. Analytical studies of static and dynamic QMOS performance parameters yield expressions for theoretical circuit comparison with CMOS, and also for optimizing RTD characteristics. QMOS circuits are characterized using SPICE simulation, and simulation-based comparison of QMOS and CMOS circuits highlights potential area-power-delay savings of this new circuit technique. The folded I-V characteristic of RTDs allows gate-level bistable-clocked-mode system operation. Performance improvement of such fine-grained QMOS pipelines arises from compactness of logic design, elimination of pipeline latch area, delay and power overhead, and high switching speed of the RTD. A pipelined carry-save multiplier and a 32-bit parallel correlator are designed to study the system-level advantages of QMOS logic. In particular, signal processing systems and communication systems benefit from fine-grained pipelining due to minimal data dependence and large volume of similar computations at each cycle. In the absence of a fabrication process that cointegrates RTDs in Silicon, a study of various QMOS prototyping schemes is presented that identifies the best means to verify system-level behavior of QMOS circuits while research in RTD-CMOS cointegration continues.Ph.D.Applied SciencesElectrical engineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/132180/2/9959801.pd

Edge-Triggered Flip-Flop Circuit Based on Resonant-Tunneling Diodes and MOSFETs

Abstract This paper presents a novel circuit that combines resonant tunneling diodes with MOSFETs to create a very compact and high-speed flip-flop implementation. This edge-triggered flip-flop circuit offers smaller circuit size and area as compared to a true single-phase CMOS flipflop. The circuit can operate at lower supply voltage as compared to a conventional CMOS flip-flop and provides better noise immunity through isolation of dynamic storage nodes

doi:10.1093/nar/gki460 CEP: a conformational epitope prediction server

CEP serve

A physical design tool for built-in self-repairable RAMs

Abstract—In this paper, we present the description and evaluation of a novel physical design tool, BISRAMGEN, that can generate reconfigurable and fault-tolerant RAM modules. This tool, first proposed in [3], designs a redundant RAM array with accompanying built-in self-test (BIST) and built-in self-repair (BISR) logic that can switch out faulty rows and switch in spare rows. Built-in self-repair causes significant improvement in reliability, production yield, and manufacturing cost of ASICs and microprocessors with embedded RAMs. Index Terms—Built-in self-testing (BIST), die cost, reliability, self repair, yield. I