Sequence-based discrimination of protein-RNA interacting residues using a probabilistic approach.

Protein interactions with ribonucleic acids (RNA) are well-known to be crucial for a wide range of cellular processes such as transcriptional regulation, protein synthesis or translation, and post-translational modifications. Identification of the RNA-interacting residues can provide insights into these processes and aid in relevant biotechnological manipulations. Owing to their eventual potential in combating diseases and industrial production, several computational attempts have been made over years using sequence- and structure-based information. Recent comparative studies suggest that despite these developments, many problems are faced with respect to the usability, prerequisites, and accessibility of various tools, thereby calling for an alternative approach and perspective supplementation in the prediction scenario. With this motivation, in this paper, we propose the use of a simple-yet-efficient conditional probabilistic approach based on the application of local occurrence of amino acids in the interacting region in a non-numeric sequence feature space, for discriminating between RNA interacting and non-interacting residues. The proposed method has been meticulously tested for robustness using a cross-estimation method showing MCC of 0.341 and F- measure of 66.84%. Upon exploring large scale applications using benchmark datasets available to date, this approach showed an encouraging performance comparable with the state-of-art. The software is available at https://github.com/ABCgrp/DORAEMON.

Chou's pseudo amino acid composition improves sequence-based antifreeze protein prediction.

Antifreeze proteins (AFP) in living organisms play a key role in their tolerance to extremely cold temperatures and have a wide range of biotechnological applications. But on account of diversity, their identification has been challenging to biologists. Earlier work explored in this area has yet to cover introduction of sequence order information which is known to represent important properties of various proteins and protein systems for prediction purposes. In this study, the effect of Chou's pseudo amino acid composition that presents sequence order of proteins was systematically explored using support vector machines for AFP prediction. Our findings suggest that introduction of sequence order information helps identify AFPs with an accuracy of 84.75% on independent test dataset, outperforming approaches such as AFP-Pred and iAFP. The relative performance calculated using Youden's Index (Sensitivity+Specificity-1) was found to be 0.71 for our predictor (AFP-PseAAC), 0.48 for AFP-Pred and 0.05 for iAFP. We hope this novel prediction approach will aid in AFP based research for biotechnological applications.

Sequence-based prediction of protein-protein interaction sites with L1-logreg classifier.

Protein-protein interactions are of central importance for virtually every process in a living cell. Information about the interaction sites in proteins improves our understanding of disease mechanisms and can provide the basis for new therapeutic approaches. Since a multitude of unique residue-residue contacts facilitate the interactions, protein-protein interaction sites prediction has become one of the most important and challenging problems of computational biology. Although much progress in this field has been reported, this problem is yet to be satisfactorily solved. Here, a novel method (LORIS: L1-regularized LOgistic Regression based protein-protein Interaction Sites predictor) is proposed, that identifies interaction residues, using sequence features and is implemented via the L1-logreg classifier. Results show that LORIS is not only quite effective, but also, performs better than existing state-of-the art methods. LORIS, available as standalone package, can be useful for facilitating drug-design and targeted mutation related studies, which require a deeper knowledge of protein interactions sites.

Tuning in optoelectronic properties of In/Te bilayer heterostructure upon annealing at different temperatures: surface wettability and photo response study for photonic and solar cell applications.

The current study depicted the influence of annealing temperature on In/Te bilayer thin film of 350 nm synthesized by thermal evaporation method. The interfacial diffusion of In into Te sites at different annealing temperatures (100 °C, 150 °C, 200 °C, 250 °C) modified the structural as well as the electro-optical response of the films. The structural study showed the appearance of an orthorhombic In4Te3 peak with annealing. The surface texture showed the particle nature with homogeneous distribution with annealing temperatures. The cross-sectional view of the bilayer and annealed film confirmed the formation of In/Te film with a total thickness of 350 nm. Surface mapping images confirm the homogeneous and uniform elemental distribution. The transmission was enhanced with annealing and showed broad transparency over the NIR region, making them suitable for IR device applications. The enhanced optical bandgap with annealing due to induced local structural changes reduced the optical parameters, such as refractive index, dielectric constant, and nonlinear susceptibility. The surface wettability measurements showed an enhanced hydrophobic nature with annealing. The variation of photocurrent with respect to voltage showed an ohmic nature, with enhancement from nA to ∼mA with annealing. Such alteration opened new ways to be used in solar cells, photodetectors, and photonic device applications.

Abdominal wall reconstruction (AWR) for post-trauma laparotomy ventral hernia and follow-up assessment of functional quality of life (QOL): experience of a level-1 trauma centre in India.

PURPOSE: The aim of this study was to examine the postoperative outcomes and follow-up QOL of patients after AWR at a level-1 trauma centre in India. METHODS: The study cohort included AWR patients treated between January 2011 and July 2022. The Activities Assessment Scale (AAS) was used to measure QOL, and the Ventral Hernia Recurrence Inventory (VHRI) was used to determine the occurrence of recurrence. In patients suspected of having recurrence, thorough clinical examination and relevant imaging were performed to confirm or rule out recurrence. RESULTS: Out of 89 patients, 35 patients whose complete perioperative and follow-up data were available were enrolled. The mean age of the patients was 28 (SD, 9) years. The mean defect size was 14. 9 (SD, 7) cm. The mean time from laparotomy to AWR surgery was 21 months. During the postoperative course, 37% of patients developed complications, such as SSI and seroma. The mean follow-up time was 53 (SD, 43) months. Upon comparing procedures involving the mesh placed in the sublay position with procedures involving the mesh placed in other positions, no statistically significant difference in the recurrence rate (one in each group, p = 0.99), surgical complication rate (33% v/s 66%, p = 0.6), or mean AAS QOL score (94.7 v/s 98, p = 0.4) was observed. The specificity of the VHRI for diagnosing recurrence was 79%. CONCLUSION: Overall, the recurrence rate was low in these patients despite the presence of large hernia defects. Long-term QOL was not affected by the specific procedure used. Timely planning and execution are more important than the specific repair approach for post-trauma laparotomy ventral hernia.

Annealing-induced phase transformation in In10Se70Te20 thin films and its structural, optical and morphological changes for optoelectronic applications.

In2Se3 and In2Te3 have great importance in various device fabrications. The present report is based on the annealing-induced phase formation of both In2Se3 and In2Te3 from In10Se70Te20 thin films at different annealing temperatures as found from the XRD analysis and well supported by the Raman study. The average crystallite size increased with a decrease in the dislocation density. The surface morphology changed with annealing and increased in particle size as noticed from the FESEM images. The uniform distribution and presence of constituent elements in the film were verified using EDX data. The increase in transmittance is accompanied by a decrease in extinction coefficient, optical density and increase in skin depth with annealing. The increase in optical bandgap from 0.418 eV to 0.645 eV upon annealing at 250 °C is associated with a decrease in disorder. The steepness parameter increased and the Se-p value decreased with annealing. The refractive index decreased with an increase in oscillator energy and decrease in dispersion energy. The quality factor, dielectric loss, optical conductivity and electrical susceptibility decreased. The optical electronegativity and plasma frequency increased with annealing. There is a significant change in the non-linear susceptibility and non-linear refractive index with annealing. The observed changes in the film structure and optical behaviour are due to the annealing-induced phase formation from the In10Se70Te20 host matrix upon annealing. Such materials are suitable for optoelectronic and phase change devices.

Correction: In situ laser irradiation: the kinetics of the changes in the nonlinear/linear optical parameters of As50Se40Sb10 thin films for photonic applications.

[This corrects the article DOI: 10.1039/D1RA02368C.].

Recurrent Cylindroma of the Scalp: A Cytomorphological Evaluation at Fine Needle Aspiration Cytology.

Specific diagnosis of adnexal tumours at fine needle aspiration cytology (FNAC) is challenging. In a recurrent scalp tumour, a startling array of lesions ranging from benign to malignant tumours fall into differential diagnosis. Accurate preoperative diagnosis is essential for planning management and to improve clinical outcome. Herein, we report a rare case of recurrent cylindroma of the scalp in a 62-year-old male patient. Cytology smears showed tight clusters of round to oval basaloid cells, few clusters with peripheral palisading. Basement membrane material was seen surrounding the cell clusters. FNAC diagnosis of a benign adnexal tumour, possibly cylindroma, was made. The diagnosis was confirmed at histopathology. We emphasize the decisive role of FNAC in arriving at an accurate diagnosis of a recurrent scalp tumour.

The impact of fluence dependent proton ion irradiation on the structural and optical properties of Bi5In30Se65 thin films for nonlinear optical devices.

This paper reports the effects of ion irradiation on the structural, linear, and nonlinear optical properties of thermally evaporated Bi5In30Se65 thin films. The prepared films were irradiated with 30 keV proton ions with different fluences, such as 5 × 1015 ions per cm2, 1 × 1016 ions per cm2, and 5 × 1016 ions per cm2. Structural analysis via X-ray diffraction (XRD) confirmed the non-crystalline nature of the film after ion irradiation with different doses. However, after the irradiation dose, the surface morphology changed, as shown by atomic force microscopy (AFM) images and field emission scanning electron microscopy (FESEM) images. The compositions of the films were obtained using energy-dispersive X-ray spectroscopy (EDX). Optical analysis via UV-Visible spectroscopy showed a reduction in the transmittance and an increase in the absorption in the higher wavelength region with irradiation. The optical bandgap and Tauc parameter decreased with an increase in the irradiation fluence, which is due to an increase in the irradiation-induced defects and disorder inside the system. The increases in the third order nonlinear susceptibility and the nonlinear refractive index with ion fluence are useful for nonlinear optical applications. The linear refractive index calculated from the transmittance data increased, satisfying Moss's rule. The optical parameters, such as lattice dielectric constant, optical density, skin depth, optical conductivity, real and imaginary dielectric constants, optical conductivity, loss factor, VELF, and SELF, were calculated using several empirical relationships and showed increasing behavior with the ion irradiation dose. The changes obtained in both the linear and nonlinear parameters will be useful for nonlinear optical device applications.

Effect of surface energy and roughness on cell adhesion and growth - facile surface modification for enhanced cell culture.

In vitro, cellular processing on polymeric surfaces is fundamental to the development of biosensors, scaffolds for tissue engineering and transplantation. However, the effect of surface energy and roughness on the cell-surface interaction remains inconclusive, indicating a lack of complete understanding of the phenomenon. Here, we study the effect of surface energy (E s) and roughness ratio (r) of a polydimethylsiloxane (PDMS) substrate on cell attachment, growth, and proliferation. We considered two different cell lines, HeLa and MDA MB 231, and rough PDMS surfaces of different surface energy in the range E s = 21-100 mJ m-2, corresponding to WCA 161°-1°, and roughness ratio in the range r = 1.05-3, corresponding to roughness 5-150 nm. We find that the cell attachment process proceeds through three different stages marked by an increase in the number of attached cells with time (stage I), flattening of cells (stage II), and elongation of cells (III) on the surface. Our study reveals that moderate surface energy (E s ≈ 70 mJ m-2) and intermediate roughness ratio (r ≈ 2) constitute the most favourable conditions for efficient cell adhesion, growth, and proliferation. A theoretical model based on the minimization of the total free energy of the cell-substrate system is presented and is used to predict the spread length of cells that compares well with the corresponding experimental data within 10%. The performance and reusability of the rough PDMS surface of moderate energy and roughness prepared via facile surface modification are compared with standard T-25 cell culture plates for cell growth and proliferation, which shows that the proposed surface is an attractive choice for efficient cell culture.

Observation of high nonlinearity in Bi doped BixIn35-xSe65 thin films with annealing.

The present work demonstrates the impact of thermal annealing on the structural, linear, and non-linear optical characteristics of thermally evaporated BixIn35-xSe65 (x = 0, 5, 10, 15 at%) thin films. The prominent crystalline phases have been developed for all annealed films at 450 °C whereas the films remain amorphous at 350 °C annealing. The XRD and Raman analysis showed the phase transformation of Bi-doped films and new Bi2Se3 phases developed upon annealing at 450 °C. The phase transformation induced change increased the linear and nonlinear properties with great extent as seen from the UV-visible optical studies. The direct and indirect optical bandgaps decreased with annealing temperature and also with Bi % content due to the formation of surface dangling bonds near the crystallite sites. The static linear refractive index and high-frequency dielectric constants were increased with annealing. The third-order non-linear susceptibility and non-linear refractive index were found to be greatly influenced by annealing temperature and increased with bismuth content. The FESEM micrographs also showed the phase transformation and EDX analysis showed the composition. The results obtained from the materials showed the potentiality to be useful for photovoltaic and optoelectronic applications.

In situ laser irradiation: the kinetics of the changes in the nonlinear/linear optical parameters of As50Se40Sb10 thin films for photonic applications.

The photosensitivity of amorphous chalcogenide thin films brings out light-induced changes in the nonlinear and linear optical parameters upon sub-bandgap and bandgap laser irradiation. The present work reports the in situ laser irradiated changes in the optical properties of As50Se40Sb10 thin films. The thermally evaporated film showed an exponential decrease in optical bandgap and increase in Urbach energy. The decay rate of the bandgap was 6.24 min and growth rate of Urbach energy was 6.67 min respectively. The dynamics of photo-induced changes were observed from the changes in linear refractive index and its dependent parameters such as 3rd order nonlinear susceptibility, nonlinear refractive index, dispersion and dielectric parameters. The conversion of heteropolar to homopolar bonds induced the photodarkening mechanism that changed the dispersion parameters. The decrease in E d and E o reduced the oscillator strength along with the zero-frequency dielectric constant. The optical and electrical conductivity changed significantly with time. The changes were saturated with time which brings stability in the film properties that is useful for various optical applications. However, no structural and compositional changes upon laser irradiation were noticed from the X-ray diffraction and EDX studies respectively. The surface homogeneity was checked from the FESEM picture.

Clinical evaluation of instrumentation time and quality of obturation using paediatric hand and rotary file systems with conventional hand K-files for pulpectomy in primary mandibular molars: a double-blinded randomized controlled trial.

AIM: The present study aims to comparatively evaluate the instrumentation time and obturation quality using paediatric manual (Kedo-SH) and rotary (Kedo-S and Kedo-SG Blue) with conventional manual (Hand K-files) instrumentation technique for pulpectomy in primary mandibular molars. MATERIALS AND METHODS: A double-blinded randomized controlled trial was designed, recruiting participants with pulpally involved primary mandibular molars requiring pulpectomy in the age group of 6-9 years old. Sixty primary mandibular molars were randomly allocated to either of the four intervention groups: Group I: 15 teeth were instrumented using hand K-files (control group); Group II: 15 teeth were instrumented with paediatric rotary files (Kedo-S); Group III: 15 teeth were instrumented with paediatric hand files Kedo-SH (experimental group) and Group IV: 15 teeth were instrumented with paediatric rotary file system Kedo-SG Blue. Instrumentation time was recorded during root canal preparation and post-operative quality of obturation in each group was also assessed. Extracted data was subjected to statistical analysis using Chi-square, One-way ANOVA and post hoc Tukey test. RESULTS: Mean instrumentation time was significantly reduced for Kedo-SG Blue (2.7840 ± 0.34217) min-s followed by Kedo-S (3.4827 ± 0.48657), Kedo-SH (5.8800 ± 0.48345) min-s and hand K-files (6.2167 ± 0.30978) min-s (p = 0.0005). A statistically significant difference was found in the obturation quality (p = 0.001) between the four groups with higher percentage of optimal fillings observed with rotary Kedo-SG Blue (80%) followed by Kedo-SH (46.7%); Kedo-S (40.0%) and hand K-files (20%). CONCLUSIONS: On comparative evaluation, a marked reduction in instrumentation time and superior quality of obturation was found with rotary Kedo-SG Blue file system followed by Kedo-SH, Kedo-S and hand K-files.

Role of annealing temperature on optimizing the linear and nonlinear optical properties of As40Se50Ge10 films.

The present work shows the effect of annealing conditions on the linear and nonlinear optical properties of two-year-old thermally evaporated 800 nm As40Se50Ge10 thin films. The aging effect in this film is clearly noticeable as compared with the old observation. The two-year-old films were annealed at different temperatures like 373, 413, 453 and 493 K for 1 h. The optical parameters were calculated from the optical transmittance and reflectance spectra measured at normal incidence of light by spectrometer in the 500-1000 nm range. The linear refractive index (n) and extinction coefficient (k) were decreased with annealing temperature. The observation reveals the increase in optical band gap with increase in annealing temperature while the width of the tail in the gap has an opposite behaviour. The oscillator energy, dispersion energy, dielectric constant, the loss factor, and optical conductivity were discussed in detail. The nonlinear refractive index and optical susceptibility were calculated by using Miller's formula which decreased with annealing temperature. The changes in both linear and nonlinear optical parameters with annealing temperature showed that annealing temperature can be considered as a useful factor for controlling the optical properties of As40Se50Ge10 chalcogenide films which could be the candidate for numerous photonic applications. The structural study was done by X-ray diffraction and Raman spectroscopy.

Feasibility of Endoscopically Assisted Repair of Zygomatico-Maxillary Complex Orbital Fractures: Case Series.

AIM: To assess the feasibility and the outcome of endoscopically assisted repair of zygomatico-maxillary complex orbital fractures in a tertiary care hospital. MATERIALS AND METHODS: A descriptive study was carried out over a period of 2 years (01. 11. 2014-31. 10. 2016). 0°-4 mm endoscopes were used for intra-operative endoscopic exploration. Regular armamentarium for management of maxillofacial trauma along with standard plating systems was used. Commercially available medical grade titanium meshes were utilised for orbital floor reconstruction. RESULTS: Fifty-seven of hundred and twelve surgically managed zygomatico-maxillary complex fractures required orbital exploration. Twenty-one of these had reconstruction of the orbital floor. Endoscopically assisted exploration was performed in 10 of the 21; trans-nasally in three cases, the Caldwell-Luc approach was used in three cases, and in another three, the existing fracture in the anterior wall of the maxilla was utilised. In addition, an endoscopic trans-nasal-sphenoidal approach was opted for to access the orbital apex to manage fractured bone fragments that were impinging on the optic nerve in one of the patients. CONCLUSION: Endoscopes serve as the primary tool in minimally invasive procedures. They are yet to evolve as a major role player in the maxillofacial arena. The authors conclude that endoscopes are truly beneficial as an adjunct to existing techniques. They hold much promise for the future.

Phylogenetic analysis of 3C protease (3C(pro)) coding region of Foot-and-mouth disease virus type A.

Nucleotide sequence analysis of the 3C protease (3C(pro)) region of Foot-and-mouth disease virus type A (FMDV-A) isolates from India has revealed incongruous phylogenetic grouping between 3C(pro) and VP1 region possibly due to the genetic recombination or independent evolution of non-structural and structural protein coding regions. Similar to the VP1 region, the emerging VP3(59)-deletion group maintained its genetic distinctiveness at 3C(pro) region and was found to be diverging with time. Two lineage specific signature aa residues were detected for the deletion group in proof of lineage specific drift or selection events. 3C(pro) region exhibited high degree of conservation as evident from low dN/dS ratio (0.036) and percentage of variable aa positions (20%). A transmembrane domain from aa 27 to 44 could be predicted that possibly anchors 3C to intracellular membranes for better interaction with RNA replication complex. On the basis of sequence conservation, the likelihood that the region aa 121-150 was carrying a vaccine exploitable T-cell epitope was very high.

Applying Knowledge of Enzyme Biochemistry to the Prediction of Functional Sites for Aiding Drug Discovery.

Enzymes are biological catalysts that play an important role in determining the patterns of chemical transformations pertaining to life. Many milestones have been achieved in unraveling the mechanisms in which the enzymes orchestrate various cellular processes using experimental and computational approaches. Experimental studies generating nearly all possible mutations of target enzymes have been aided by rapid computational approaches aiming at enzyme functional classification, understanding domain organization, functional site identification. The functional architecture, essentially, is involved in binding or interaction with ligands including substrates, products, cofactors, inhibitors, providing for their function, such as in catalysis, ligand mediated cell signaling, allosteric regulation and post-translational modifications. With the increasing availability of enzyme information and advances in algorithm development, computational approaches have now become more capable of providing precise inputs for enzyme engineering, and in the process also making it more efficient. This has led to interesting findings, especially in aberrant enzyme interactions, such as hostpathogen interactions in infection, neurodegenerative diseases, cancer and diabetes. This review aims to summarize in retrospection - the mined knowledge, vivid perspectives and challenging strides in using available experimentally validated enzyme information for characterization. An analytical outlook is presented on the scope of exploring future directions.

Evaluation of highly conserved hsp65-specific nested PCR primers for diagnosing Mycobacterium tuberculosis.

OBJECTIVE: To evaluate the sensitivity and specificity of a new nested set of primers designed for the detection of Mycobacterium tuberculosis complex targeting a highly conserved heat shock protein gene (hsp65). DESIGN: The nested primers were designed using multiple sequence alignment assuming the nucleotide sequence of the M. tuberculosis H37Rv hsp65 genome as base. Multidrug-resistant Mycobacterium species along with other non-mycobacterial and fungal species were included to evaluate the specificity of M. tuberculosis hsp65 gene-specific primers. RESULTS: The sensitivity of the primers was determined using serial 10-fold dilutions, and was 100% as shown by the bands in the case of M. tuberculosis complex. None of the other non M. tuberculosis complex bacterial and fungal species yielded any band on nested polymerase chain reaction (PCR). The first round of amplification could amplify 0.3 ng of the template DNA, while nested PCR could detect 0.3 pg. CONCLUSION: The present hsp65-specific primers have been observed to be sensitive, specific and cost-effective, without requiring interpretation of biochemical tests, real-time PCR, sequencing or high-performance liquid chromatography. These primer sets do not have the drawbacks associated with those protocols that target insertion sequence 6110, 16S rDNA, rpoB, recA and MPT 64.

Ensemble Architecture for Prediction of Enzyme-ligand Binding Residues Using Evolutionary Information.

Enzyme interactions with ligands are crucial for various biochemical reactions governing life. Over many years attempts to identify these residues for biotechnological manipulations have been made using experimental and computational techniques. The computational approaches have gathered impetus with the accruing availability of sequence and structure information, broadly classified into template-based and de novo methods. One of the predominant de novo methods using sequence information involves application of biological properties for supervised machine learning. Here, we propose a support vector machines-based ensemble for prediction of protein-ligand interacting residues using one of the most important discriminative contributing properties in the interacting residue neighbourhood, i. e., evolutionary information in the form of position-specific- scoring matrix (PSSM). The study has been performed on a non-redundant dataset comprising of 9269 interacting and 91773 non-interacting residues for prediction model generation and further evaluation. Of the various PSSM-based models explored, the proposed method named ROBBY (pRediction Of Biologically relevant small molecule Binding residues on enzYmes) shows an accuracy of 84.0 %, Matthews Correlation Coefficient of 0.343 and F-measure of 39.0 % on 78 test enzymes. Further, scope of adding domain knowledge such as pocket information has also been investigated; results showed significant enhancement in method precision. Findings are hoped to boost the reliability of small-molecule ligand interaction prediction for enzyme applications and drug design.