Identification of MHC Class II Binders/ Non-binders using Negative Selection Algorithm

The identification of major histocompatibility complex (MHC) class-II restricted peptides is an important goal in human immunological research leading to peptide based vaccine design. These MHC class–II peptides are predominantly recognized by CD4+ T-helper cells, which when turned on, have profound immune regulatory effects. Thus, prediction of such MHC class-II binding peptides is very helpful towards epitope-based vaccine design. HLA-DR proteins were found to be associated with autoimmune diseases e.g. HLA-DRB1*0401 with rheumatoid arthritis. It is important for the treatment of autoimmune diseases to determine which peptides bind to MHC class II molecules. The experimental methods for identification of these peptides are both time consuming and cost intensive. Therefore, computational methods have been found helpful in classifying these peptides as binders or non-binders. We have applied negative selection algorithm, an artificial immune system approach to predict MHC class–II binders and non-binders. For the evaluation of the NSA algorithm, five fold cross validation has been used and six MHC class–II alleles have been taken. The average area under ROC curve for HLA-DRB1*0301, DRB1*0401, DRB1*0701, DRB1*1101, DRB1*1501, DRB1*1301 have been found to be 0.75, 0.77, 0.71, 0.72, and 0.69, and 0.84 respectively indicating good predictive performance for the small training set

Fire Safety Analysis of a Railway Compartment using Computational Fluid Dynamics

Trains are considered to be the safest on-land transportation means for both passengers and cargo. Train accidents have been mainly disastrous, especially in case of fire, where the consequences are extensive loss of life and goods. The fire would generate smoke and heat which would spread quickly inside the railway compartments. Both heat and smoke are the primary reasons of casualties in a train. This study has been carried out to perform numerical analysis of fire characteristics in a railway compartment using commercial Computational Fluid Dynamics code ANSYS. Non-premixed combustion model has been used to simulate a fire scenario within a railway compartment, while Shear Stress Transport k-ω turbulence model has been used to accurately predict the hot air turbulence parameters within the compartment. The walls of the compartment have been modelled as no-slip stationary adiabatic walls, as is observed in real life conditions. Carbon dioxide concentration (CO2), temperature distribution and air flow velocity within the railway compartment has been monitored. It has been observed that the smoke above the fire source flows to both sides of the compartment. The highest temperature zone is located downstream the fire source, and gradually decreases with the increase in the distance from the fire source. It can be seen that CFD can be used as an effective tool in order to analyse the evolution of fire in railway compartments with reasonable accuracy. The paper also briefly discusses the topical reliability issues

Aggressive Fibromatosis in Neck.

Aggressive fibromatosis (AF) is a locally aggressive infiltrative low-grade benign tumor that accounts for approximately less than 3% of all soft tissue tumors. In the head and neck region this tumor tends to be more aggressive and associated with significant morbidity. Aggressive surgery is a viable management option and may be successfully used as a single modality treatment, or in combination with radiotherapy. We report a rare case of AF in a 38 year old female, who presented with a painless mass over the left supraclavicular fossa, extending inferiorly into the thoracic inlet, which was excised successfully in toto with the help of cardiothoracic vascular surgeon (CTVS)

A microfluidic device for the study of the orientational dynamics of microrods

We describe a microfluidic device for studying the orientational dynamics of microrods. The device enables us to experimentally investigate the tumbling of microrods immersed in the shear flow in a microfluidic channel with a depth of 400 mu and a width of 2.5 mm. The orientational dynamics was recorded using a 20 X microscopic objective and a CCD camera. The microrods were produced by shearing microdroplets of photocurable epoxy resin. We show different examples of empirically observed tumbling. On the one hand we find that short stretches of the experimentally determined time series are well described by fits to solutions of Jeffery's approximate equation of motion [Jeffery, Proc. R. Soc. London. 102 (1922), 161-179]. On the other hand we find that the empirically observed trajectories drift between different solutions of Jeffery's equation. We discuss possible causes of this orbit drift.Comment: 11 pages, 8 figure

Resolution of puzzles from the LSND, KARMEN, and MiniBooNE experiments

This work has attempted to reconcile puzzling neutrino oscillation results from the LSND, KARMEN and MiniBooNE experiments. We show that the LSND evidence for $\bar{\nu}_\mu \to \bar{\nu}_e$ oscillations, its long-standing disagreement with the results from KARMEN, and the anomalous event excess observed by MiniBooNE in $\nu_\mu$ and $\bar{\nu}_\mu$ data could all be explained by the existence of a heavy sterile neutrino ($\nu_h$). All these results are found to be consistent with each other assuming that the $\nu_h$ is created in $\nu_\mu$ neutral-current interactions and decays radiatively into a photon and a light neutrino. Assuming the $\nu_h$ is produced through mixing with $\nu_\mu$, the combined analysis of the LSND and MiniBooNe excess events suggests that the $\nu_h$ mass is in the range from 40 to 80 MeV, the mixing strength is $|U_{\mu h}|^2 \simeq 10^{-3}-10^{-2}$, and the lifetime is $\tau_{\nu_h} \lesssim 10^{-9}$ s. Surprisingly, this LSND-MiniBooNE parameters window is found to be unconstrained by the results from the most sensitive experiments searching for heavy neutrino. We set new limits on $|U_{\mu h}|^2$ for the LSND-MiniBooNE favorable mass region from the precision measurements of the Michel spectrum by the TWIST experiment. The results obtained provide a strong motivation for a sensitive search for the $\nu_h$ in a near future $K$ decay or neutrino experiments, which fit well in the existing/planned experimental programs at CERN or FNAL. The question of whether the heavy neutrino is Dirac or Majorana particle is briefly discussed.Comment: 24 pages, 28 figures, version to appear in PR

Constraints on nuclear matter parameters of an Effective Chiral Model

Within an effective non-linear chiral model, we evaluate nuclear matter parameters exploiting the uncertainties in the nuclear saturation properties. The model is sternly constrained with minimal free parameters, which display the interlink between nuclear incompressibility ($K$), the nucleon effective mass ($m^{\star}$), the pion decay constant ($f_{\pi}$) and the $\sigma-$meson mass ($m_{\sigma}$). The best fit among the various parameter set is then extracted and employed to study the resulting Equation of state (EOS). Further, we also discuss the consequences of imposing constraints on nuclear EOS from Heavy-Ion collision and other phenomenological model predictions.Comment: 10 pages, 8 figure

Globular clusters as gamma ray sources

There are indications now that globular clusters contain a large number of low magnetic field millisecond pulsars. Since millisecond pulsars are expected to emit γ -rays due to curvature radiation, it is likely that globular clusters will themselves be sources of γ -rays bright enough to be detectable by present day instruments. Using the expression derived by Scharlemann, Arons & Fawley (1978) of the energy acquired by the electrons moving along the open magnetic field lines of the pulsars we have calculated the likely luminosity of γ -rays from globular clusters. We discuss our results in the light of the calculations reported in the literature based on some of the other models

Gamma-ray emission from pulsars

We have attempted to devise a scheme by which it may be possible to identify pulsars which are likely to be γ-ray pulsars. We apply this test to a representative population of pulsars and identify the likely candidates for γ emission. We also discuss some individual cases including the Crab and Vela pulsars

Effect of shear force on the separation of double stranded DNA

Using the Langevin Dynamics simulation, we have studied the effects of the shear force on the rupture of short double stranded DNA at different temperatures. We show that the rupture force increases linearly with the chain length and approaches to the asymptotic value in accordance with the experiment. The qualitative nature of these curves almost remains same for different temperatures but with a shift in the force. We observe three different regimes in the extension of covalent bonds (back bone) under the shear force.Comment: 4 pages, 4 figure