NaII-Pred: An ensemble-learning framework for the identification and interpretation of sodium ion inhibitors by fusing multiple feature representation.

High-affinity ligand peptides for ion channels are essential for controlling the flow of ions across the plasma membrane. These peptides are now being investigated as possible therapeutic possibilities for a variety of illnesses, including cancer and cardiovascular disease. So, the identification and interpretation of ligand peptide inhibitors to control ion flow across cells become pivotal for exploration. In this work, we developed an ensemble-based model, NaII-Pred, for the identification of sodium ion inhibitors. The ensemble model was trained, tested, and evaluated on three different datasets. The NaII-Pred method employs six different descriptors and a hybrid feature set in conjunction with five conventional machine learning classifiers to create 35 baseline models. Through an ensemble approach, the top five baseline models trained on the hybrid feature set were integrated to yield the final predictive model, NaII-Pred. Our proposed model, NaII-Pred, outperforms the baseline models and the current predictors on both datasets. We believe NaII-Pred will play a critical role in screening and identifying potential sodium ion inhibitors and will be an invaluable tool.

An integrative machine learning model for the identification of tumor T-cell antigens.

The escalating global incidence of cancer poses significant health challenges, underscoring the need for innovative and more efficacious treatments. Cancer immunotherapy, a promising approach leveraging the body's immune system against cancer, emerges as a compelling solution. Consequently, the identification and characterization of tumor T-cell antigens (TTCAs) have become pivotal for exploration. In this manuscript, we introduce TTCA-IF, an integrative machine learning-based framework designed for TTCAs identification. TTCA-IF employs ten feature encoding types in conjunction with five conventional machine learning classifiers. To establish a robust foundation, these classifiers are trained, resulting in the creation of 150 baseline models. The outputs from these baseline models are then fed back into the five classifiers, generating their respective meta-models. Through an ensemble approach, the five meta-models are seamlessly integrated to yield the final predictive model, the TTCA-IF model. Our proposed model, TTCA-IF, surpasses both baseline models and existing predictors in performance. In a comparative analysis involving nine novel peptide sequences, TTCA-IF demonstrated exceptional accuracy by correctly identifying 8 out of 9 peptides as TTCAs. As a tool for screening and pinpointing potential TTCAs, we anticipate TTCA-IF to be invaluable in advancing cancer immunotherapy.

IF-AIP: A machine learning method for the identification of anti-inflammatory peptides using multi-feature fusion strategy.

BACKGROUND: The most commonly used therapy currently for inflammatory and autoimmune diseases is nonspecific anti-inflammatory drugs, which have various hazardous side effects. Recently, some anti-inflammatory peptides (AIPs) have been found to be a substitute therapy for inflammatory diseases like rheumatoid arthritis and Alzheimer's. Therefore, the identification of these AIPs is an emerging topic that is equally important. METHODS: In this work, we have proposed an identification model for AIPs using a voting classifier. We used eight different feature descriptors and five conventional machine-learning classifiers. The eight feature encodings were concatenated to get a hybrid feature set. The five baseline models trained on the hybrid feature set were integrated via a voting classifier. Finally, a feature selection algorithm was used to select the optimal feature set for the construction of our final model, named IF-AIP. RESULTS: We tested the proposed model on two independent datasets. On independent data 1, the IF-AIP model shows an improvement of 3%-5.6% in terms of accuracies and 6.7%-10.8% in terms of MCC compared to the existing methods. On the independent dataset 2, our model IF-AIP shows an overall improvement of 2.9%-5.7% in terms of accuracy and 8.3%-8.6% in terms of MCC score compared to the existing methods. A comparative performance analysis was conducted between the proposed model and existing methods using a set of 24 novel peptide sequences. Notably, the IF-AIP method exhibited exceptional accuracy, correctly identifying all 24 peptides as AIPs. The source code, pre-trained models, and all datasets are made available at https://github.com/Mir-Saima/IF-AIP.

Meta-IL4: An ensemble learning approach for IL-4-inducing peptide prediction.

The cytokine interleukin-4 (IL-4) plays an important role in our immune system. IL-4 leads the way in the differentiation of naïve T-helper 0 cells (Th0) to T-helper 2 cells (Th2). The Th2 responses are characterized by the release of IL-4. CD4+ T cells produce the cytokine IL-4 in response to exogenous parasites. IL-4 has a critical role in the growth of CD8+ cells, inflammation, and responses of T-cells. We propose an ensemble model for the prediction of IL-4 inducing peptides. Four feature encodings were extracted to build an efficient predictor: pseudo-amino acid composition, amphiphilic pseudo-amino acid composition, quasi-sequence-order, and Shannon entropy. We developed an ensemble learning model fusion of random forest, extreme gradient boost, light gradient boosting machine, and extra tree classifier in the first layer, and a Gaussian process classifier as a meta classifier in the second layer. The outcome of the benchmarking testing dataset, with a Matthews correlation coefficient of 0.793, showed that the meta-model (Meta-IL4) outperformed individual classifiers. The highest accuracy achieved by the Meta-IL4 model is 90.70%. These findings suggest that peptides that induce IL-4 can be predicted with reasonable accuracy. These models could aid in the development of peptides that trigger the appropriate Th2 response.

Investigating the effect of insertion torque on marginal bone loss around dental implants.

BACKGROUND/PURPOSE: The use of dental implants in restoring function, esthetics, speech, and health of oral tissues has been growing in recent years. Evaluating marginal bone resorption and the survival rate of implants placed with different torques values is crucial. The primary aim of the present study was to evaluate the effect of different insertion torque values on marginal bone loss around dental implants placed in the posterior region of the mandible. MATERIALS AND METHODS: 37 patients were involved in this study. Patient data (age, gender), implant characteristics (length, diameter), insertion torque values, gingival biotype, and bone quality were recorded, and parallel periapical radiographs measured marginal bone loss. The relationship between variables was obtained using independent t-tests, Pearson correlations, and regressions. RESULTS: The present study found a positive and significant correlation between implant insertion torque and marginal bone loss (MBL)around the dental implants during the first year after placement. Furthermore, patients with D2 bone density at the implant placement site and thin gingival biotype also had significantly higher MBLs from baseline until crown delivery and first-year follow-up than those with D3 bone density and thick gingival biotypes, respectively. CONCLUSION: A lower torque is necessary for high-risk patients to increase implantation success due to identifying patients with an increased risk for MBL.

Morpho-Biochemical characterization of Kalazeera (Bunium persicum Boiss. Fedts) germplasm grown in Global temperate ecologies.

The present investigation explores the variability of Bunium persicum populations belonging to different regions. Variability among 74 genotypes for thirty-seven traits (29 quantitative and 8 qualitative) were studied to ascertain the population structure of the Bunium persicum. Among the agro-morphological traits, wide range of variability was recorded in tuber shape, tuber colour, seed shape, seed colour, growth habit, leaf shape, leaf colour, umbel shape, umbel colour, plant height (22.90-96.52 cm), primary branches plant-1 (1-6), umbel diameter of primary umbel (6.17 - 13.67 cm), number of primary umbels plant-1 (1-12), umbels plant-1 (8-40), seed yield per plant (0.55-13.10 g), essential oil content (3.2-9.3 %) etc. Significant and positive association was observed between number of seeds primary-1 umbel (r = 0.91), plant height (r = 0.65), number of seeds primary-1 umbel (0.52), number of seeds primary-1 umbel (0.43), number of seeds secondary-1 umbel (0.38) with number of umblets secondary-1 umbel. Cluster analysis classified the genotypes with different geographical origin into two major clusters and sub-clusters. Cluster-I comprises of 50 genotypes and cluster - II of 24 genotypes while the genotype SRS-KZ-189 from Kargil population was separated as an individual sub-group. Principal component (PC1) and (PC2) harbors accounted 20.2% and 14% of total variation. Variability of Kalazeera genotypes would facilitate the plant breeders to implement and design various crop improvement programme in future.

Peri-implant squamous cell carcinoma mimicking peri-implantitis: a case report.

Peri-implant oral lesions, benign or malignant, may be misdiagnosed as peri-implantitis. Squamous cell carcinoma is the most common cancer reported around dental implants. Malignant peri-implant lesions are life-threatening, and their resemblance to peri-implantitis, especially in their early stage, necessitates a precise differential diagnosis. This report presents a case of a 55-year-old woman with a peri-implant squamous cell carcinoma mimicking peri-implantitis.

Byar's flaps in the management of congenital megaprepuce.

INTRODUCTION: Early management of congenital megaprepuce (CMP) is necessary to address recurrent urinary tract infections and parental concerns. Different procedures, mostly using the inner preputial skin to cover the phallus, have been described. However, cosmetic appearance with the inner preputial covering of the penis is suboptimal. Owing to this, we conducted this study using outer preputial skin in the form of Byar's flaps to cover the penile shaft and analysed the results. PATIENTS AND METHODS: This prospective study included 19 patients with CMP operated by a single surgeon using the Byar's flap technique. Following surgery patients were assessed on the 4th post-operative day, at 3 months and 1-year post-operative for cosmetic and functional outcomes. Parental satisfaction about cosmetic results was evaluated using a subjective score. Data were collected and analysed. RESULTS: Nineteen patients with CMP were studied with a mean age of 6.3 months. Nineteen patients (100%) patients presented with buried penis and preputial ballooning, malodorous infected urine in 15 (78.9%) patients, thin stream of urine in 17 (89.4%) and dysuria in 12 (63%) patients. One of the patients had associated glanular hypospadias and the other two had isolated chordee. There were no significant complications except for one patient who developed meatal stenosis which was later managed by a meatoplasty. All patients had satisfactory cosmetic appearance. CONCLUSION: CMP is an uncommon but easily identifiable condition. Early surgical correction is recommended to prevent complications. Byar's flap technique yields very good functional and cosmetic results in the management of CMP.

Design, Synthesis, Molecular Modelling, and Biological Evaluation of Oleanolic Acid-Arylidene Derivatives as Potential Anti-Inflammatory Agents.

INTRODUCTION: Oleanolic acid, a pentacyclic triterpenic acid, is widely distributed in medicinal plants and is the most commonly studied triterpene for various biological activities, including anti-allergic, anti-cancer, and anti-inflammatory. METHODS: The present study was carried out to synthesize arylidene derivatives of oleanolic acid at the C-2 position by Claisen Schmidt condensation to develop more effective anti-inflammatory agents. The derivatives were screened for anti-inflammatory activity by scrutinizing NO production inhibition in RAW 264.7 cells induced by LPS and their cytotoxicity. The potential candidates were further screened for inhibition of LPS-induced interleukin (IL-6) and tumour necrosis factor-alpha (TNF-α) production in RAW 264.7 cells. RESULTS: The results of in vitro studies revealed that derivatives 3d, 3e, 3L, and 3o are comparable to that of the oleanolic acid on the inhibition of TNF-α and IL-6 release. However, derivative 3L was identified as the most potent inhibitor of IL-6 (77.2%) and TNF-α (75.4%) when compared to parent compound, and compounds 3a (77.18%), 3d (71.5%), and 3e (68.8%) showed potent inhibition of NO than oleanolic acid (65.22%) at 10µM. Besides, from docking score and Cyscore analysis analogs (3e, 3L, 3n) showed greater affinity towards TNF-α and IL-1ß than dexamethasone. CONCLUSION: Herein, we report a series of 15 new arylidene derivatives of oleanolic acid by Claisen Schmidt condensation reaction. All the compounds synthesized were screened for their anti-inflammatory activity against NO, TNF-α and IL-6. From the data, it was evident that most of the compounds exhibited better anti-inflammatory activity.

Juvenile trabecular ossifying fibroma of the maxilla: Case report of a diagnostic dilemma.

Ossifying fibromas (OFs) are benign, well-demarcated lesions in the craniofacial region, particularly in the jaws, with clinical, radiographic, and histopathological similarities to other lesions, which make their diagnosis challenging. Herein, we report a case of a fibro-osseous lesion in the anterior maxilla of a 13-year-old boy, consisting of an intraosseous and an extra-osseous part, which created a diagnostic dilemma.

Management of Intussusception in the Era of Ultrasound-Guided Hydrostatic Reduction: A 3-Year Experience from a Tertiary Care Center.

INTRODUCTION: Ultrasound-guided hydrostatic reduction (HSR) is currently the initial management tool in the treatment of intussusception. HSR is, however, confronted with failures besides there are still a number of patients who primarily undergo surgical intervention for the management of intussusception. We undertook this study to assess the efficacy of HSR and also to look for factors demanding the surgical exploration in patients with intussusception. MATERIALS AND METHODS: A total of 215 patients with intussusception from June 2014 to June 2017 were prospectively studied. HSR was carried out in 203 patients, which was successful in 187 and unsuccessful in 16. These two groups were compared using the Student's t-test. Significance was set at P < 0.05. Twelve patients undergoing surgery primarily were also assessed for the factors affecting the decision-making. RESULTS: HSR was successful in 187 and unsuccessful in 16. The failed group was more likely to have symptoms over 24 h, appearance of crescent, and ≥10-cm length on ultrasonography (USG). Two of these patients had ischemic bowel, two had ileoileal intussusception, and eight had pathological lead points, whereas no obvious cause could be identified in the rest of the four patients. Among the 12 patients who were primarily operated, four patients had peritonitis and other four patients were neonates. Laparoscopic reduction was done in four patients. CONCLUSION: HSR is a safe and effective treatment modality for intussusception. However, it is met with higher failure rates in patients with risk factors such as delayed presentation, appearance of crescent on USG, and length >10 cm. The role of HSR is also dubious in situations such as neonatal intussusception, small-bowel intussusception, and multiple intussusceptions and also in preventing the future recurrence. Such patients ought to be managed by laparotomy or where feasible by laparoscopy. Furthermore, before embarking on HSR, peritonitis and bowel ischemia should be ruled out clinically and radiologically. In the suspicious cases of bowel ischemia, USG Doppler may be helpful.

Curcuma longa and Trigonella foenum graecum-enriched nutrient mixture from germinated Macrotyloma uniflorum and Vigna radiate ameliorate nonalcoholic fatty liver diseases in rats.

The prevalence of nonalcoholic fatty liver is increasing due to modern lifestyle. Germinated and dehulled Macrotyloma uniflorum and Vigna radiate were shown to have enhanced nutrients. Curcuma longa and Trigonella foenum graecum were proven hepatoprotective.The supplementation of the nutrient herbal mixture to the MCD diet-induced steatosis shows reduced hepatic fat accumulation and lipid profile, and liver injury markers in serum also reserved in normal. Increased serum albumin in the treatment group indicates that the liver function is enhanced than that of steatosis. The supplementation of the herbal mixture has preserved the hepatic antioxidant. Zymographic analysis of matrix metalloproteinase, western blot determination of α-SMA, and histological evolution (H&E, Sirius red) depicted reduced fibrosis and reveled management of hepatic stellate cells in quiescent form. The present study concludes that the herbal mixture has reduced hepatocyte fat accumulation in steatotic animals, and curtailed the oxidative stress, further it prevents the progression of steatohepatitis. PRACTICAL APPLICATIONS: Fatty liver diseases can be treated by modulating the diet composition such as consuming food rich in the nutrient herbal mixture. In this study, the nutrient mixture was made with dynamic food processing techniques such as germination, dehulling, and milling to augment the nutritional contents. Besides, Macrotyloma uniflorum, Vigna radiate, Curcuma longa, and Trigonella foenum graecum were used to improve the medicinal value and antioxidant. This formulation could target the various stages of NAFLD. This study revealed that the nutrient herbal mixture reduces the steatosis of the liver and curtailed the progression of steatohepatitis from hepatic steatosis. Since the edible foodstuff was used to make the nutrient mixture, it has excellent clinical application.

Spectrum of bacteria associated with diabetic foot ulcer and biofilm formation: A prospective study.

BACKGROUND: India has the world's largest number of diabetics. Non-traumatic lower limb amputation is the most common devastating complication of diabetes, primarily due to diabetic foot ulcers (DFU) and diabetic foot infections (DFI). In India, the incidence of foot ulcers ranges from 8-17 per cent. DFIs are predominantly polymicrobial and multidrug-resistant (MDR) with the ability to form biofilm, which is an important virulence factor and results in treatment failure. AIMS: The main objectives of the study are to identify the spectrum of multidrug-resistant bacteria associated with these infections, their antibiotic sensitivity pattern, and to detect the biofilm formation. METHODS: This was a prospective study at a tertiary care hospital. One hundred patients over the age of 18, having chronic diabetic foot ulcer, and attending the surgery outpatient department were included. Samples of pus were collected from deep wounds and processed using standard techniques for culture and sensitivity. Biofilm detection was done. Results were compiled and statistically analysed. RESULTS: One hundred samples were processed and 82 yielded positive cultures. Staphylococcus aureus was the predominant organism, followed by Pseudomonas aeruginosa. Biofilm formation was seen in 38 (46.34 per cent) of the organisms. Biofilms were formed predominantly by Staphylococcus aureus (20 per cent). CONCLUSION: The organisms causing chronic diabetic foot ulcers were commonly multidrug-resistant; this was also observed among biofilm formers. Therefore, screening for biofilm formation, along with the usual antibiogram, needs to be performed as a routine procedure in chronic diabetic ulcers to formulate effective treatment strategies for these patients.

The detection of Dichelobacter nodosus and Fusobacterium necrophorum from ovine footrot in Kashmir, India.

In a study conducted, a total of 450 swab samples from footrot lesions of naturally infected sheep were collected in all the ten districts of the Kashmir valley and were examined for the presence of Dichelobacter nodosus (D. nodosus) and Fusobacterium necrophorum (F. necrophorum), in order to determine if F. necrophorum was associated with ovine footrot. The detection of F. necrophorum and D. nodosus was carried out by polymerase chain reaction targeting the leukotoxin (lktA) and 16S rRNA genes, respectively. In this study, only less than 50% of positive samples contained both the bacteria, so it is not possible to conclude with certainty that both bacteria are together required for the disease manifestation.

Baseline antibody titres against Salmonella typhi in apparently asymptomatic HIV positive individuals in a tertiary care hospital.

BACKGROUND: Enteric fever is common in tropical regions and is caused by Salmonella enterica serotype typhi (S typhi ). For diagnosis of enteric fever, the Widal test is the most widely used test after blood culture. In HIV infected individuals false positive and false negative Widal reactions are common. The result is variable titres and baseline titres that are unusual in this patient population. AIMS: This study was done to determine the baseline antibody titres for S typhi among HIV infected individuals. METHOD: Average baseline antibody titres against O and H antigens of S typhi were measured by standard Widal test in 200 HIV positive asymptomatic individuals, as well as 200 age and sex-matched controls. The results were compiled and statistically analysed. RESULTS: A total of 84 (42%) of the cases had an H antibody titre of >1:20 and 105 (52.5%) had a titre of >1:20 against O antigen. This implies that positive titre of H and O antigen is significantly associated with HIV positive cases with P<0.001. Correlation of CD4 count with antibody titres shows that there is no significant association between CD4 counts and antibody titres against either H (P=0.634) or O antigen (P=0.765). CONCLUSION: This study shows that HIV infected individuals had increased titres of antibodies against S typhi from the baseline. This indicates a need for evaluation of current cut-off values of diagnostic titres for this group. We also suggest that it is best to perform baseline titres against S t yphi for each patient at the time of diagnosis of HIV status, and to use this for future reference.

Closure of large oroantral communication using coronoid process pedicled on temporalis muscle flap: a new alternative approach.

Proximity of maxillary molar teeth roots to the maxillary sinus floor can potentiate oroantral communication (OAC) after extraction. Considering the defect size and situation, surgical treatment may become essential. Surgical treatment modalities are variable and would be indicated in special clinical circumstances.In this article, a chronic case of OAC with a size of 25 × 15 mm(2) in a 30-year old man with history of heavy smoking and drug abuse was treated with combination of buccal fat pad (for covering sinus floor), coronoid process pedicled on temporalis flap, and mucosal closure. There was no complication during and after operation. Short- and long-term follow-up revealed success of this novel technique despite the patient's poor compliance.

Detection and sequencing of plasmid encoded tetracycline resistance determinants (tetA and tetB) from food-borne Bacillus cereus isolates.

OBJECTIVE: To investigate the detection and sequencing of plasmid encoded tetracycline resistance genes (tetA and tetB) from food-borne and standard strains of Bacillus cereus (B. cereus). METHODS: A PCR was carried out to detect the tetracycline resistance genes (tetA and tetB) in food-borne B. cereus strains and the amplified products were sequenced. RESULTS: The phenotypic resistance against tetracycline was observed in 39 of the 118 food-borne isolates and two reference strains (MTCC 430 and MTCC 1307) of B. cereus. Among the phenotypically resistant isolates, tetA was detected in 36 food-borne isolates and two reference strains (MTCC 430 and MTCC 1307), whereas, tetB was detected in 12 food-borne isolates and MTCC 1307 strain. CONCLUSIONS: A close association was therefore found between phenotypic resistance against tetracycline and presence of tetracycline resistance genes. The tetA and tetB gene fragments were amplified, purified and sequenced. The gene sequences of the isolates studied herein were found similar to tetA and tetB gene sequences of other bacteria available in NCBI. The occurrence of tetA and tetB genes in B. cereus indicate the horizontal transfer of antibiotic resistance determinants from other bacteria into B. cereus. The transfer of these resistant determinants to other potentially pathogenic bacteria may be a matter of great concern.