Megha | Searcharxiv

arXiv2025

VHE FSRQs with Fermi-LAT: VHE and even brighter states in high-z FSRQs due to an HBL-like component?

Very high-energy (VHE) detected flat-spectrum radio quasars (FSRQs) are relatively few despite being the most persistent bright MeV-GeV sources. Focusing on VHE emission, we investigated the spectral and temporal properties of VHE-detected FSRQs using 14-year Fermi-LAT data. All are highly variable (flux-amplitude$>$100) with VHE detection associated with brighter flux states and relatively harder spectra. Above a flux limit, flux anti-correlates with spectral index, exhibiting a bluer-when-brighter trend. The low-flux state spectral energy distributions (SEDs) for all resembles a power-law, while high-flux and VHE-associated states resemble a log-parabola, accompanied by an almost nil (PKS0736+017, PKS1510-089) to marginal (4C+21.35, 3C279) to significant (B21420+32, TON0599, PKS1441+25, S30218+35, PKS0346-27, OP313) MeV-GeV peak-upshift -- more prominent in high-redshift sources. For no/marginal peak-upshift, the VHE emission is consistent with external Comptonization of infrared photons (EC-IR) driven primarily by a power-law continuation of the particle spectrum to higher energies. For those with a significant MeV-GeV peak-upshift, PKS0346-27 and OP313 shows peak-upshift in the synchrotron spectrum, and thus VHE is EC-IR origin, while for others without synchrotron-peak upshift, we attribute the VHE to an HBL-like component with a Compton-Dominance (CD) like FSRQs, with VHE driven primarily by particle spectrum continuation. In some, even high-state SEDs seem to require an HBL-like component. Thus, VHE activities in FSRQs mainly result from particle spectrum continuation, aided by spectral transition or a new HBL-like component with FSRQ-like CD. Such spectral changes naturally brighten the GeV-VHE flux, overcoming extragalactic background light absorption without requiring extraordinary brightening under the traditional EC-IR scenario than normally exhibited.

astro-ph.HE↗

arXiv2025

CBTOPE2: An improved method for predicting of conformational B-cell epitopes in an antigen from its primary sequence

In 2009, our group pioneered a novel method CBTOPE for predicting conformational B-cell epitopes in a protein from its amino acid sequence, which received extensive citations from the scientific community. In a recent study, Cia et al. (2023) evaluated the performance of conformational B-cell epitope prediction methods on a well-curated dataset, revealing that most approaches, including CBTOPE, exhibited poor performance. One plausible cause of this diminished performance is that available methods were trained on datasets that are both limited in size and outdated in content. In this study, we present an enhanced version of CBTOPE, trained, tested, and evaluated using the well-curated dataset from Cai et al. (2023). Initially, we developed machine learning-based models using binary profiles, achieving a maximum AUC of 0.58 on the validation dataset. The performance of our method improved significantly from an AUC of 0.58 to 0.63 when incorporating evolutionary information in the form of a Position-Specific Scoring Matrix (PSSM) profile. Furthermore, the performance increased from an AUC of 0.63 to 0.64 when we integrated both the PSSM profile and relative solvent accessibility (RSA). All models were trained, tested, and optimized on the training dataset using five-fold cross-validation. The final performance of our models was assessed using a validation or independent dataset that was not used during hyperparameter optimization. To facilitate scientific community working in the field of subunit vaccine, we develop a standalone software and web server CBTOPE2 (https://webs.iiitd.edu.in/raghava/cbtope2/).

q-bio.BM↗