Association of Age, Gender, and Site of Implant Placement: An Institution-Based Retrospective Study.

Tooth loss is an undesirable condition that leads to functional, esthetic and social damage, having an impact on an individual's quality of life. Dental implants are man-made tooth root replacements that are increasingly used to replace a missing tooth. It is important to gather demographic data in order to take precautions before the possible failures. Hence the objective of this study was to retrospectively determine the association between age, gender, and site of implant placement in patients reporting to a private dental institution. This study was carried out from the data obtained from the case records of 1281 patients who had undergone implant therapy. Chi-square test was applied to see associations of gender, age and implant site. The results show that a maximum number of 348 implants (27.7%) were placed in patients aged between 41-50 years. The patient pool consisted of 705 (55%) females and 576 (45%) males. A maximum of 228 implants (17.80%) were placed in region 46 and 224 implants (17.49%) in region 36. Only 2 implants (0.2%) were placed in region 41. There was a positive association between age, gender and site of implant. In those aged 20-30 years, 20.53% of implants were placed, 26.23% in 31-40 years, 27.1% in 41-50 years, 17.95% in 51-60 years and 8.11% in 61-70 years of age. In male, a maximum of 124 implants (54.4%) were placed in region 46 and only 1 implant (50%) in region 41. In females, region 36 had a maximum of 110 implants (49.1%), and the least number of implants were placed in regions 31 and 41. In this study, it can be concluded that general factors such as age and gender had a significant effect on the site of implant placement.

PRA-Pred: Structure-based prediction of protein-RNA binding affinity.

Understanding crucial factors that affect the binding affinity of protein-RNA complexes is vital for comprehending their recognition mechanisms. This study involved compiling experimentally measured binding affinity (ΔG) values of 217 protein-RNA complexes and extracting numerous structure-based features, considering RNA, protein, and interactions between protein and RNA. Our findings indicate the significance of RNA base-step parameters, interaction energies, number of atomic contacts in the complex, hydrogen bonds, and contact potentials in understanding the binding affinity. Further, we observed that these factors are influenced by the type of RNA strand and the function of the protein in a protein-RNA complex. Multiple regression equations were developed for different classes of complexes to perform the prediction of the binding affinity between the protein and RNA. We evaluated the models using the jack-knife test and achieved an overall correlation 0.77 between the experimental and predicted binding affinities with a mean absolute error of 1.02 kcal/mol. Furthermore, we introduced a web server, PRA-Pred, intended for the prediction of protein-RNA binding affinity, and it is freely accessible through https://web.iitm.ac.in/bioinfo2/prapred/. We propose that our approach could function as a potential resource for investigating protein-RNA recognitions and developing therapeutic strategies.

Starvation Protects Hepatocytes from Inflammatory Damage through Paradoxical mTORC1 Signaling.

Background and aims: Sepsis-related liver failure is associated with a particularly unfavorable clinical outcome. Calorie restriction is a well-established factor that can increase tissue resilience, protect against liver failure and improve outcome in preclinical models of bacterial sepsis. However, the underlying molecular basis is difficult to investigate in animal studies and remains largely unknown. METHODS: We have used an immortalized hepatocyte line as a model of the liver parenchyma to uncover the role of caloric restriction in the resilience of hepatocytes to inflammatory cell damage. In addition, we applied genetic and pharmacological approaches to investigate the contribution of the three major intracellular nutrient/energy sensor systems, AMPK, mTORC1 and mTORC2, in this context. RESULTS: We demonstrate that starvation reliably protects hepatocytes from cellular damage caused by pro-inflammatory cytokines. While the major nutrient- and energy-related signaling pathways AMPK, mTORC2/Akt and mTORC1 responded to caloric restriction as expected, mTORC1 was paradoxically activated by inflammatory stress in starved, energy-deprived hepatocytes. Pharmacological inhibition of mTORC1 or genetic silencing of the mTORC1 scaffold Raptor, but not its mTORC2 counterpart Rictor, abrogated the protective effect of starvation and exacerbated inflammation-induced cell death. Remarkably, mTORC1 activation in starved hepatocytes was uncoupled from the regulation of autophagy, but crucial for sustained protein synthesis in starved resistant cells. CONCLUSIONS: AMPK engagement and paradoxical mTORC1 activation and signaling mediate protection against pro-inflammatory stress exerted by caloric restriction in hepatocytes.

PDA-Pred: Predicting the binding affinity of protein-DNA complexes using machine learning techniques and structural features.

Protein-DNA interactions play an important role in various biological processes such as gene expression, replication, and transcription. Understanding the important features that dictate the binding affinity of protein-DNA complexes and predicting their affinities is important for elucidating their recognition mechanisms. In this work, we have collected the experimental binding free energy (ΔG) for a set of 391 Protein-DNA complexes and derived several structure-based features such as interaction energy, contact potentials, volume and surface area of binding site residues, base step parameters of the DNA and contacts between different types of atoms. Our analysis on relationship between binding affinity and structural features revealed that the important factors mainly depend on the number of DNA strands as well as functional and structural classes of proteins. Specifically, binding site properties such as number of atom contacts between the DNA and protein, volume of protein binding sites and interaction-based features such as interaction energies and contact potentials are important to understand the binding affinity. Further, we developed multiple regression equations for predicting the binding affinity of protein-DNA complexes belonging to different structural and functional classes. Our method showed an average correlation and mean absolute error of 0.78 and 0.98 kcal/mol, respectively, between the experimental and predicted binding affinities on a jack-knife test. We have developed a webserver, PDA-PreD (Protein-DNA Binding affinity predictor), for predicting the affinity of protein-DNA complexes and it is freely available at https://web.iitm.ac.in/bioinfo2/pdapred/.

WITHDRAWN: Non-Anti-TNF Biologics as Salvage Therapy for Refractory Acute Severe Ulcerative Colitis, A Systematic Review

Since the authors are not responding to the editor's requests to fulfill the editorial requirement, therefore, the article has been withdrawn.Bentham Science apologizes to the readers of the journal for any inconvenience this may have caused.The Bentham Editorial Policy on Article Withdrawal can be found at https://benthamscience.com/editorial-policies-main.php BENTHAM SCIENCE DISCLAIMER: It is a condition of publication that manuscripts submitted to this journal have not been published and will not be simultaneously submitted or published elsewhere. Furthermore, any data, illustration, structure or table that has been published elsewhere must be reported, and copyright permission for reproduction must be obtained. Plagiarism is strictly forbidden, and by submitting the article for publication the authors agree that the publishers have the legal right to take appropriate action against the authors, if plagiarism or fabricated information is discovered. By submitting a manuscript, the authors agree that the copyright of their article is transferred to the publishers if and when the article is accepted for publication.

The role and timing of endoscopic retrograde cholangiopancreatography in acute biliary pancreatitis without cholangitis: A nationwide analysis.

BACKGROUND/PURPOSE: The role and optimal timing of endoscopic retrograde cholangiopancreatography (ERCP) in acute biliary pancreatitis without cholangitis (ABPwoC) remains unclear. Using a large national database, we aimed to examine hospitalization outcomes of patients with ABPwoC as a function of the performance and timing of ERCP. METHODS: This was a retrospective study of adult patients with ABPwoC utilizing the National Inpatient Sample from 2016-2017. Patients who underwent inpatient ERCP were stratified into performance: within 24, 24-48, 48-72, and >72 h of hospital admission. The primary outcome was all-cause inpatient mortality as a function of the performance and timing of ERCP; secondary outcomes, including healthcare utilization, were assessed. Multivariate modeling was used to adjust for potential confounders. Statistical analyses were conducted using STATA, version 16.0. RESULTS: Of the 70 030 patients with ABPwoC, 31.37% underwent inpatient ERCP. Performance (aOR: 0.6, p < .05), but not timing (aOR: 0.98, p = .9), of inpatient ERCP was associated with significantly lower all-cause inpatient mortality. Urgent ERCP (within 24 h) was associated with shorter hospital length of stay, lower charges and cost, and less need for pancreatic drainage procedures, while ERCP within 72 h was associated with less frequent intensive care unit admission (all p < .05). DISCUSSION: Based on this large, nationwide analysis, inpatient ERCP for ABPwoC is associated with lower all-cause mortality. ERCP within 24 and 72 h, though not associated with lower mortality, are associated with multiple improved clinical outcomes, including lower healthcare charges and costs.

Exploring the medicinally important secondary metabolites landscape through the lens of transcriptome data in fenugreek (Trigonella foenum graecum L.).

Fenugreek (Trigonella foenum-graecum L.) is a self-pollinated leguminous crop belonging to the Fabaceae family. It is a multipurpose crop used as herb, spice, vegetable and forage. It is a traditional medicinal plant in India attributed with several nutritional and medicinal properties including antidiabetic and anticancer. We have performed a combined transcriptome assembly from RNA sequencing data derived from leaf, stem and root tissues. Around 209,831 transcripts were deciphered from the assembly of 92% completeness and an N50 of 1382 bases. Whilst secondary metabolites of medicinal value, such as trigonelline, diosgenin, 4-hydroxyisoleucine and quercetin, are distributed in several tissues, we report transcripts that bear sequence signatures of enzymes involved in the biosynthesis of such metabolites and are highly expressed in leaves, stem and roots. One of the antidiabetic alkaloid, trigonelline and its biosynthesising enzyme, is highly abundant in leaves. These findings are of value to nutritional and the pharmaceutical industry.

Formulation and evaluation of oral disintegrating films using a natural ingredient against Streptococcus mutans.

Background: Oral disintegrating films (ODFs) are one of the forms of drug delivery system with better patient compliance. The advantage is that it disintegrates quickly when placed on the tongue and has better bioavailability. Aim: The aim of this study is to develop an ODF using Vaccinium oxycoccos and Plectranthus amboinicus targeting Streptococcus mutans. Setting and Design: This in vitro study was conducted at an institutional laboratory. Materials and Methods: The chemical composition of aqueous extracts of Vaccinium oxycoccos and Plectranthus amboinicus was examined using gas chromatography (GC)-mass spectrometry (MS). Extracts were added at its minimal inhibitory concentration (MIC) into the hydroxy propylmethyl cellulose (HPMC) polymer matrix solution to develop active ODF. The study concentrated on assessing the physical properties such as thickness of film, PH of the film, folding endurance, swelling test, disintegration, and dissolution test. Color analysis, Fourier transform infrared (FTIR), spectroscopy, and scanning electron microscope (SEM) were the mechanical properties of the film assessed. Statistical Analysis: Data were analyzed statistically, one-way analysis of variance followed by post hoc analysis for the assessment of MIC. Descriptive statistics were performed for the analysis of film properties. Results: MIC was 25 µg/ml for Vaccinium oxycoccos and 50 µg/ml for Plectranthus amboinicus. Three percentage HPMC with 1% citric acid and 1% aspartame was used to develop a polymer matrix. Films pH was between 6 and 7. FTIR and SEM analysis were done to confirm the attachment of active compound in a polymer matrix. Conclusion: Vaccinium oxycoccos and Plectranthus amboinicus showed good antibacterial activity, therefore could be a potent source to minimize the incidence of S. mutans.

Ligand Docking Methods to Recognize Allosteric Inhibitors for G-Protein-Coupled Receptors.

G-protein-coupled receptors (GPCRs) are membrane proteins which play an important role in many cellular processes and are excellent drug targets. Despite the existence of several US Food and Drug Administration (FDA)-approved GPCR-targeting drugs, there is a continuing challenge of side effects owing to the nonspecific nature of drug binding. We have investigated the diversity of the ligand binding site for this class of proteins against their cognate ligands using computational docking, even if their structures are known already in the ligand-complexed form. The cognate ligand of some of these receptors dock at allosteric binding site with better score than the binding at the conservative site. Interestingly, amino acid residues at such allosteric binding site are not conserved across GPCR subfamilies. Such a computational approach can assist in the prediction of specific allosteric binders for GPCRs.

Illustrative Tutorials for ProThermDB: Thermodynamic Database for Proteins and Mutants.

ProThermDB (https://web.iitm.ac.in/bioinfo2/prothermdb/index.html) is a primary resource for protein stability, which contains experimentally determined thermodynamic data for proteins and their mutants. The most recent version of ProThermDB accumulates the data obtained from both high- and low-throughput experimental biophysical methods. It includes comprehensive information at four different levels, i.e.: (i) protein sequence and structure; (ii) experimental conditions; (iii) thermodynamic parameters such as Gibbs free energy, melting temperature, enthalpy, etc.; and (iv) literature. In the following protocols, we present detailed tutorials for retrieving data using different search, display and sorting options, interpretation of search results, description of each entry-level information category, data upload and download, cross-links with other databases, and visualization options. This protocol consists of six pictorial exercises, which are useful for biologists/users to understand the contents and organization of data in ProThermDB. Further, potential applications of ProThermDB in protein engineering are discussed. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Retrieval of experimental thermodynamic data for wild-type and mutants of a specific protein using a simple query Basic Protocol 2: Retrieval of stabilizing point mutations, which are located at the interior of α-helical regions, and obtaining data by thermal denaturation methods Basic Protocol 3: Retrieval of destabilizing point mutations, which are in ß-sheets of exposed regions, and obtaining data by chemical denaturation methods (urea and GdnHCl) Basic Protocol 4: Retrieval of stabilizing and destabilizing point mutations in a range of physiological conditions (pH: 6-9 and T: 20°C-25°C) and publication years (2010-2020) Support Protocol: Downloading the entire data of the database for academic research purposes and submission of new data in ProThermDB.

ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years.

ProThermDB is an updated version of the thermodynamic database for proteins and mutants (ProTherm), which has ∼31 500 data on protein stability, an increase of 84% from the previous version. It contains several thermodynamic parameters such as melting temperature, free energy obtained with thermal and denaturant denaturation, enthalpy change and heat capacity change along with experimental methods and conditions, sequence, structure and literature information. Besides, the current version of the database includes about 120 000 thermodynamic data obtained for different organisms and cell lines, which are determined by recent high throughput proteomics techniques using whole-cell approaches. In addition, we provided a graphical interface for visualization of mutations at sequence and structure levels. ProThermDB is cross-linked with other relevant databases, PDB, UniProt, PubMed etc. It is freely available at https://web.iitm.ac.in/bioinfo2/prothermdb/index.html without any login requirements. It is implemented in Python, HTML and JavaScript, and supports the latest versions of major browsers, such as Firefox, Chrome and Safari.

A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways.

This protocol describes a stepwise process to identify proteins of interest from a query proteome derived from NGS data. We implemented this protocol on Moringa oleifera transcriptome to identify proteins involved in secondary metabolite and vitamin biosynthesis and ion transport. This knowledge-driven protocol identifies proteins using an integrated approach involving sensitive sequence search and evolutionary relationships. We make use of functionally important residues (FIR) specific for the query protein family identified through its homologous sequences and literature. We screen protein hits based on the clustering with true homologues through phylogenetic tree reconstruction complemented with the FIR mapping. The protocol was validated for the protein hits through qRT-PCR and transcriptome quantification. Our protocol demonstrated a higher specificity as compared to other methods, particularly in distinguishing cross-family hits. This protocol was effective in transcriptome data analysis of M. oleifera as described in Pasha et al.•Knowledge-driven protocol to identify secondary metabolite synthesizing protein in a highly specific manner.•Use of functionally important residues for screening of true hits.•Beneficial for metabolite pathway reconstruction in any (species, metagenomics) NGS data.

Isolation and characterization of micro and nanocrystalline cellulose fibers from the walnut shell, corncob and sugarcane bagasse.

The present study aims to extract and characterize the microcrystalline cellulose (MCC) present in different agro-industrial wastes such as walnut shells, corncob, and sugarcane bagasse. Moreover, it is also the aim of this study to convert MCCs to nanocrystalline cellulose fiber (NCCF), to demonstrate the difference in morphological, structural, thermal, and chemical natures. Corncob cellulose was observed to possess a loosely bounded linear bundle structure. Nanocrystalline cellulose fiber yield from walnut shell and sugarcane bagasse cellulose were higher than corncob cellulose. The thermal stability of cellulose was noted to be high for walnut shell NCCF. Nanocrystalline cellulose fiber of corncob and sugarcane bagasse was estimated to have a low thermal degradation temperature. All the MCCs and NCCFs produced from investigated cellulose sources were found to have type I cellulose. Functional group compositions of cellulose were observed to be intact for converted agro-based NCCF's.

Dataset for the combined transcriptome assembly of M. oleifera and functional annotation.

In this paper, we present the data acquired during transcriptome analysis of the plant Moringa oleifera [1] from five different tissues (root, stem, leaf, flower and seed) by RNA sequencing. A total of 271 million reads were assembled with an N50 of 2094 bp. The combined transcriptome was assessed for transcript abundance across five tissues. The protein coding genes identified from the transcripts were annotated and used for orthology analysis. Further, enzymes involved in the biosynthesis of select medicinally important secondary metabolites, vitamins and ion transporters were identified and their expression levels across tissues were examined. The data generated by RNA sequencing has been deposited to NCBI public repository under the accession number PRJNA394193 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA394193).

The transcriptome enables the identification of candidate genes behind medicinal value of Drumstick tree (Moringa oleifera).

Moringa oleifera is a plant well-known for its nutrition value, drought resistance and medicinal properties. cDNA libraries from five different tissues (leaf, root, stem, seed and flower) of M. oleifera cultivar Bhagya were generated and sequenced. We developed a bioinformatics pipeline to assemble transcriptome, along with the previously published M. oleifera genome, to predict 17,148 gene models. Few candidate genes related to biosynthesis of secondary metabolites, vitamins and ion transporters were identified. Expressions were further confirmed by real-time quantitative PCR experiments for few promising leads. Quantitative estimation of metabolites, as well as elemental analysis, was also carried out to support our observations. Enzymes in the biosynthesis of vitamins and metabolites like quercetin and kaempferol are highly expressed in leaves, flowers and seeds. The expression of iron transporters and calcium storage proteins were observed in root and leaves. In general, leaves retain the highest amount of small molecules of interest.

Development of cellulose-based migratory and nonmigratory active packaging films.

The main aim of this work is to develop a transparent bioactive cellulose acetate (CA) film for food packaging applications. The aim of the study is also to optimize the production methods for development of bulk and surface immobilized bioactive CA films. The vacuum drying method was optimized for the production of transparent CA films. The direct infusion and UV-assisted surface immobilization methods were investigated for the development of bioactive CA films. Reduction in the crystalline nature of CA was observed to be responsible for the production of transparent CA films. Thymol, with high antioxidant and antimicrobial properties, was examined to be the major active compound (>40%) present in the polar fraction of oregano. Retention of active compounds analyzed by High Performance Liquid Chromatography (HPLC), surface morphology analyzed by Atomic Force Microscopy (AFM), and surface chemistry analyzed by X-ray Photoelectron Spectroscopy (XPS) proved the efficiency of UV-assisted surface immobilization method. Acetyl cellulose films treated with UV irradiation at 312 nm were examined to have higher retention of active compounds. The bioactive CA films produced by bulk and surface immobilization methods showed >90% and ∼65% thymol retention, respectively. The UV-assisted surface immobilization method was found to decrease the mechanical and barrier properties of CA film. The bioactive CA films produced by bulk and surface immobilization methods were found to have retained the antioxidant and antimicrobial properties of the thymol.

Effect of film constituents and different processing conditions on the properties of starch based thermoplastic films.

The main aim of this study is to examine the different film preparation methods (Hot air oven method, Microwave oven method, and UV irradiation method) for development of Bio-thermoplastic films from agro waste polysaccharides. The rheological properties were also studied for different combinations of tamarind seed starch (T), okra mucilage polysaccharide (OK), Residual rice bran starch (R) and sugarcane bagasse cellulose (C). Increase in concentration of okra mucilage polysaccharide and sugarcane bagasse cellulose found to highly influence the rheological viscous properties of tamarind starch solution. Increase in concentration of okra mucilage (above 1.5%) in tamarind film matrix solution significantly increased the elongation properties of starch films. Increase in concentration of cellulose (above 1%) in tamarind film matrix solution significantly increased the tensile strength of starch films. The microwave oven method was found to be the quickest method (~10 to 20 min) for biopolymer film preparation. SEM and AFM analysis revealed that UV - irradiation method produces stable bio-thermoplastic films with low surface roughness and high barrier properties. The interaction of starch molecules with other natural polysaccharide produces stable thermoplastic biopolymer films, that can be developed under different processing conditions to eradicate environmental pollution caused by petrochemical plastics.

Extraction of nano cellulose fibers from the banana peel and bract for production of acetyl and lauroyl cellulose.

The principal aim of the present study is to develop a method for the production of cellulose nanofibers, from the banana peel (BP) and bract (BB). It is also the aim of this study to produce cellulose-based biopolymers through acetyl and lauroyl modifications. The microwave digestion method and ball milling assisted ultra-sonication method was optimized for sustainable extraction of micro and nano cellulose fibers, respectively. The microwave digestion method was found to be effective in the removal of hemicellulose and lignin. Micro and nano cellulose fibers of BP and BB were found to contain type I cellulose structure. Thermal stability and crystallinity index of cellulose nanofibers were examined to be higher than it's native micro cellulose. Nano cellulose fibers were examined to be a potential source for production of acetyl and lauroyl cellulose, with a high degree of substitution and thermal stability. Hence, microwave digestion and ball milling assisted ultra-sonication method was proven to be effective in the extraction of nano cellulose fiber for development of cellulose-based polymers.

Extraction and characterization of polysaccharides from tamarind seeds, rice mill residue, okra waste and sugarcane bagasse for its Bio-thermoplastic properties.

The aim of the present study is to extract potential thermoplastic polysaccharides from agricultural industrial wastes. Polysaccharides were extracted from renewable agro industrial wastes such as tamarind seeds [rich in starch (TSS)], okra head waste [rich in mucilage polysaccharide (OMP)], sugarcane bagasse [rich in cellulose (SBC)] and residual rice mill wastes [rich in starch and fiber (RS)]. Urigam variety of tamarind seed starch found to be an amylose rich starch. Different polysaccharides extracted from agro wastes were found to be having high thermal stability, except okra polysaccharide (comparatively low). X-ray diffraction pattern of tamarind seed starch proved its high crystallinity index. Crystallinity index of investigated polysaccharides were found to be in the order of SBC > TSS > RS > OMP. Chemical nature of extracted polysaccharides was confirmed by Fourier transform infrared spectroscopic analysis. Residual rice bran starch granules and tamarind seed starch globules were found to be having comparatively reduced particle size than sugarcane bagasse cellulose and okra mucilage. Scanning electron microscopic analysis revealed the cluster formations of RS granules and TSS globules. Residual rice bran starch found to be associated with other fibers (present in outer coat of rice). Okra mucilage and SBC were examined to be having linear sheets and linear bundles structures, respectively.