predForm-Site: Formylation site prediction by incorporating multiple features and resolving data imbalance

Formylation is one of the newly discovered post-translational modifications in lysine residue which is responsible for different kinds of diseases. In this work, a novel predictor, named predForm-Site, has been developed to predict formylation sites with higher accuracy. We have integrated multiple sequence features for developing a more informative representation of formylation sites. Moreover, decision function of the underlying classifier have been optimized on skewed formylation dataset during prediction model training for prediction quality improvement. On the dataset used by LFPred and Formator predictor, predForm-Site achieved 99.5% sensitivity, 99.8% specificity and 99.8% overall accuracy with AUC of 0.999 in the jackknife test. In the independent test, it has also achieved more than 97% sensitivity and 99% specificity. Similarly, in benchmarking with recent method CKSAAP_FormSite, the proposed predictor significantly outperformed in all the measures, particularly sensitivity by around 20%, specificity by nearly 30% and overall accuracy by more than 22%. These experimental results show that the proposed predForm-Site can be used as a complementary tool for the fast exploration of formylation sites. For convenience of the scientific community, predForm-Site has been deployed as an online tool, accessible at http://103.99.176.239:8080/predForm-Site.     

Influence of the laser parameters on the space and time characteristics of an aluminum laser-induced plasma

In this work, an aluminum laser plasma produced in ambient air at atmospheric pressure by laser pulses at a fluence of 10 J/cm² is characterized by time- and space-resolved measurements of electron density and temperature. Varying the laser pulse duration from 6 ns to 80 fs and the laser wavelength from ultraviolet to infrared only slightly influences the plasma properties. The temperature exhibits a slight decrease both at the plasma edge and close to the target surface. The electron density is found to be spatially homogeneous in the ablation plume during the first microsecond. Finally, the plasma expansion is in good agreement with the Sedov's model during the first 500 ns and it becomes subsonic, with respect to the velocity of sound in air, typically 1 μs after the plasma creation. The physical interpretation of the experimental results is also discussed to the light of a one-dimensional fluid model which provides a good qualitative agreement with measurements.     

The high-temperature heat capacity of LnPO4 (Ln = La,Ce, Gd) by drop calorimetry

The high-temperature heat capacity of three lanthanide orthophosphates of monazite structure have been measured in the temperature range (450 to 1570) K. The data have been analysed in terms of a lattice term, represented by the 4f⁰ and 4f⁷ compounds LaPO₄ and GdPO₄, and an electronic term for CePO₄. The calculated excess heat capacity thus obtained is in reasonable agreement with that calculated from the crystal field energies.     

Interferometric studies of VT relaxation times in a regime of strong laser excitation

In this paper we describe the analysis of non-linearities in the vibrational relaxation rates of SF₆ molecules in a regime of strong laser excitation. Our studies were carried out using an interferometric technique which is particularly suitable to the investigation of the time dependence of VT relaxation times in molecular systems. At very high excitation energies a dramatic decrease in the VT relaxation time was found. This behaviour is related to the beginning of multiphoton dissociation processes of SF₆ molecules.     

On the nonlinear dielectric function of CuCl in pump and probe experiments

We study the dispersion and the absorption changes of CuCl under high excitation conditions in two-beam experiments with parallel and crossed linear polarizations of both beams. The induced optical non linearities are shown to depend sensitively on the presence of interactions between the degenerate transverse exciton states.     

Absorption spectra of NH4MnCl3 and NH4MnF3

The absorption spectra of NH₄MnCl₃ and NH₄MnF₃ crystals have been measured down to 10 K in the 250 to 600 nm region. The observed bands are assigned to electronic transitions from the ⁶A_1g(S) ground state to various excited levels of Mn²⁺ ions in an octahedral crystalline field. The position of the bands have been fitted within the strong crystal field scheme. Resulting parameters at room temperature are B=741, C=2990 and Dq=520 cm⁻¹ for NH₄MnCl₃ and B=800, C=3139 and Dq=694 cm⁻¹ for NH₄MnF₃. At low temperature some bands show a rich fine structure in which some phonon progressions have been identified.     

Mott transition for picosecond all-optical nor gate in CdSe

Using picosecond time resolved spectroscopy, we study the extinction kinetics of the optical transmission of CdSe platelets induced by strong optical pumping. We investigate particularly the all-optical gate capabilities (resulting from the bandgap shrinkage due to the Mott transition) for laser beams the wavelength of which ranges from 676 to 678 nm. The electron-hole plasma density necessary to enable the optical switching is determined (ϱ ∼ 2 × 10¹⁷cm⁻³ at 20K). The switch-off time (i.e. the transparency recovery time) is also studied at different wavelengths by picosecond spectroscopy.     

Vibrational predissociation induced by exciton trapping in inert-gas clusters

The dynamics of exciton trapping, vibrational energy transfer and vibrational predissociation in an electronically excited state of Ar₁₃ clusters was explored by classical molecular dynamics. Two distinct time scales were established for vibrational energy flow, which result in a molecular-type, reactive dissociation process of Ar atoms for this cluster.