Investigating the Precise Identification of Citrullination Sites with High-Performance Score Metrics using a Powerful Computation Predicting Tool.

BACKGROUND: To elucidate the detailed mechanisms of citrullination at the molecular level and design drugs applicable to major human diseases, predicting protein citrullination sites (PCSs) is essential. Using experimental approaches to predict PCSs is time-consuming and costly. However, there is a limited scope of the current PCS predictors. In particular, most predictors are commonly used for PCS prediction and have limited performance scores. OBJECTIVE: This work aims to provide an improved sophisticated predictor of citrullination sites using a benchmark dataset in a machine learning platform. METHODS: This study presents a reliable citrullination site predictor based on a benchmark dataset containing a 1:1 ratio of positive and negative samples. We classified citrullination sites using the Composition of the K-Spaced Amino Acid Pairs (CKSAAP) and Support Vector Machine (SVM). RESULTS: We developed PCS predictors using integrated machine-learning methods that produced the highest average scores. Using 10-fold cross-validation on test datasets, the True Positive Rate (TPR) was 98.34%, the True Negative Rate (TNR) was 99.44%, the accuracy was 98.89%, the Mathew Correlation Coefficient (MCC) was 98.21%, the Area Under the ROC Curve (AUC) was 0.999, and the partial Area Under the ROC Curve (pAUC) was 0.1968. CONCLUSION: According to overall performance, our developed predictor has a significantly higher implementation in comparison with the current tools on the same benchmark dataset. Moreover, it showed better performance metrics on both test and training datasets. Our developed predictor is promising and can be implemented as a complementary technique for identifying fast and precise citrullination sites.

Design and evaluation of a power tiller vegetable seedling transplanter with dibbler and furrow type.

Vegetable production plays a vital role in ensuring food security in Bangladesh. However, the majority of vegetable seedlings are currently transplanted manually, which is not only time-consuming but also labor-intensive and costly. In this context, a semi-automated transplanter can be considered as an alternative solution for mechanized seedling transplanting. To mechanize seedling operations, two types of transplanters were designed, fabricated and tested: the power tiller-operated semi-automatic dibbler vegetable seedling (DVS) transplanter and the furrow opener vegetable seedling (FVS) transplanter. The goal was to evaluate their performance and impact on field crop productivity. In the DVS transplanter design, the larger sprocket was adjusted to enhance the precision of hole-making by pressing the dibbler into the soil, creating holes where seedlings would be transplanted. On the other hand, the FVS transplanter utilized a furrow opener to create furrows, and the seedling is placed in these furrow at a specific distance from the furrow opener wall, where the distance between seedlings within the furrow could be adjusted based on the specific requirements of the seedling crop. The results of the evaluation indicated that both transplanters successfully planted seedlings without any missing placements, while hole covering was achieved at 115 and 118.2% for the DVS and FVS transplanters, respectively. The field capacity and field efficiency for both transplanters were determined to be 0.05 ha h-1 and 61.18%, respectively, with a coefficient of variation of 5% or less. Field tests conducted with brinjal crops at a forward speed of 1.2 km h-1 and a spacing of 0.7 × 0.6 m demonstrated that both designs yielded higher yield productivity compared to manual transplantation. Additionally, no issues related to vegetative development were observed. Both transplanters exhibited promising performance and significant potential in terms of accurately transplanting seedlings, and ensuring satisfactory transplantation quality. Furthermore, these transplanters offer several advantages, including less time-consuming, lower labor demands and even distribution of seedlings. This design encourages small to medium-level farmers seeking to engage in mechanized vegetable farming practices.

Clinically proven natural products, vitamins and mineral in boosting up immunity: A comprehensive review.

Background: and Purposes: The terminology "immune boost-up" was the talk of the topic in this Covid-19 pandemic. A significant number of the people took initiative to increase the body's defense capacity through boosting up immunity worldwide. Considering this, the study was designed to explain the natural products, vitamins and mineral that were proved by clinical trail as immunity enhancer. Methods: Information was retrieved from SciVerse Scopus ® (Elsevier Properties S. A, USA), Web of Science® (Thomson Reuters, USA), and PubMed based on immunity, nutrients, natural products in boosting up immunity, minerals and vitamins in boosting up immunity, and immune booster agents. Result: A well-defined immune cells response provide a-well functioning defense system for the human physiological system. Cells of the immune system must require adequate stimulation so that these cells can prepare themselves competent enough to fight against any unintended onslaught. Several pharmacologically active medicinal plants and plants derived probiotics or micronutrients have played a pivotal role in enhancing the immune boost-up process. Their role has been well established from the previous study. Immune stimulating cells, especially cells of acquired immunity are closely associated with the immune-boosting up process because all the immunological reactions and mechanisms are mediated through these cells. Conclusion: This article highlighted the mechanism of action of different natural products, vitamins and mineral in boosting up the immunity of the human body and strengthening the body's defense system. Therefore, it is recommended that until the specific immune-boosting drugs are available in pharma markets, anyone can consider the mentioned products as dietary supplements to boost up the immunity.

Evaluation of the properties of Bungarus caeruleus venom and checking the efficacy of antivenom used in Bangladesh for its bite treatment.

As a disaster-prone country with unique geographical features, snake biting is a major public health concern in Bangladesh. The primary reasons of mortality from snakebite include late presentation to the hospital, low efficacy of antivenom, and a lack of adequate management facilities. Because snake venom characteristics vary depending on geographical location, antivenom should be manufactured from snakes native to the region in which it would be administered. Bungarus caeruleus is a highly venomous snake contributing to the major snakebite issue in Bangladesh. Therefore, the neutralization efficacy of the antivenom against B. caeruleus venom was evaluated in the current study along with the characterization of venom. For biological characterization of venom, RP-HPLC and SDS-PAGE profiling, hemolytic activity, hemorrhagic activity, phospholipases A2 (PLA2) activity, edema inducing activity and histopathological observations were carried out following standard protocol. LD50 of the venom was calculated along with neutralization potency of Incepta antivenom through probit analysis. Results showed that venom possesses phospholipase A2 activity, hemolytic activity and edema inducing activity while hemorrhagic activity was absent in the skin of envenomed mice. Histopathological alterations including necrosis, congestion and infiltrations were observed in envenomed mice organs after hematoxylin and eosin staining. Neutralization study showed that Incepta polyvalent antivenom could neutralize (potency 0.53 mg/ml) the lethal effect in in vitro study on mice. Further investigation on snakebite epidemiology and clinical observations of the envenomed patients will help in combating the snakebite problem more efficiently.

Elevated serum malondialdehyde (MDA), insulin, follicle-stimulating hormone (FSH), luteinizing hormone (LH), and thyroid- stimulating hormone (TSH), and reduced antioxidant vitamins in polycystic ovarian syndrome patients.

Elevated oxidative stress and hormonal imbalance have been suggested to associate with polycystic ovarian syndromes (PCOS), a causal factor for unsuccessful pregnancy outcomes and other associated complications in women. The aim of this study was to compare the oxidative stress markers and different relevant hormones between pregnant women with and without PCOS. The levels of malondialdehyde (MDA), insulin, follicle- stimulating hormone (FSH), luteinizing hormone (LH), thyroid-stimulating hormone (TSH), vitamin A and vitamin C were measured in 80 pregnant women with PCOS and 80 healthy pregnancies. The mean MDA and insulin levels were significantly elevated in pregnant women with PCOS compared to healthy controls (1.98±0.07 vs. 1.06±0.02 nmol/mL and 11.15±0.25 vs. 6.67±0.25 mIU/L, respectively with p<0.001 for both). Compared to healthy controls, the mean concentrations of FSH (3.65±0.16 vs. 1.75±0.10 IU/L) and LH (15.67±0.63 vs. 3.65±0.16 IU/L) were significantly higher in pregnant women with PCOS, p<0.001 for both comparisons. Similarly, the concentration of serum TSH was also higher in PCOS cases compared to controls (2.79±0.22 vs. 2.34±0.06, p=0.048). In contrast, the levels of vitamin A and C were lower in PCOS cases compared to healthy pregnancy group, 0.45±0.01 vs. 1.05±0.01 and 0.26±0.01 vs. 0.53±0.02, respectively with p-values <0.001 for both comparations. In conclusion, in PCOS cases, serum MDA, insulin, FSH, LH and TSH levels were found to be elevated while the levels of antioxidant vitamins were lower compared to healthy pregnant women. Unusual hormonal imbalance and increase of oxidative stress markers during the pregnancy might be important to establish the PCOS diagnosis.

Computational prediction of potential siRNA and human miRNA sequences to silence orf1ab associated genes for future therapeutics against SARS-CoV-2.

The coronavirus disease 2019 (COVID-19) is an ongoing pandemic caused by an RNA virus termed as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). SARS-CoV-2 possesses an almost 30kbp long genome. The genome contains open-reading frame 1ab (ORF1ab) gene, the largest one of SARS-CoV-2, encoding polyprotein PP1ab and PP1a responsible for viral transcription and replication. Several vaccines have already been approved by the respective authorities over the world to develop herd immunity among the population. In consonance with this effort, RNA interference (RNAi) technology holds the possibility to strengthen the fight against this virus. Here, we have implemented a computational approach to predict potential short interfering RNAs including small interfering RNAs (siRNAs) and microRNAs (miRNAs), which are presumed to be intrinsically active against SARS-CoV-2. In doing so, we have screened miRNA library and siRNA library targeting the ORF1ab gene. We predicted the potential miRNA and siRNA candidate molecules utilizing an array of bioinformatic tools. By extending the analysis, out of 24 potential pre-miRNA hairpins and 131 siRNAs, 12 human miRNA and 10 siRNA molecules were sorted as potential therapeutic agents against SARS-CoV-2 based on their GC content, melting temperature (Tm), heat capacity (Cp), hybridization and minimal free energy (MFE) of hybridization. This computational study is focused on lessening the extensive time and labor needed in conventional trial and error based wet lab methods and it has the potential to act as a decent base for future researchers to develop a successful RNAi therapeutic.

Impact of LFGD (Ar+O2) plasma on seed surface, germination, plant growth, productivity and nutritional composition of maize (Zea mays L.).

In this present study conducted with the LFGD (Low-Frequency Glow Discharge) (Ar + O2) plasma treated maize seeds, to inspect the effect on seed surface modifications, seed germination, growth, development, productivity and nutritional compositions of maize plants. This study reported that LFGD (Ar + O2) plasma treated maize seeds have a potential effect to change its smooth seed surfaces and, it becomes rougher. It also enhances the seed germination rate up to (15.88%), which might help to increase the shoot length (33.42%), root length (10.67%), stem diameter (13.37%), total chlorophyll content (46.93%), total soluble protein (52.48%), total soluble phenol (21.68%) and sugar (1.62%) concentrations in respect controls of our experimental plants. For this reason, the acceptable treatment duration for maize seeds were 30sec, 60sec, 90sec and 120sec. After treatment, the plants exhibited a significant increase in CAT, SOD, APX and GR activities in the leaves and roots, and also significantly changes in H2O2 (208.33 ± 5.87µ molg-1 FW) in the leaves and (61.13 ± 1.72µ molg-1 FW) in the roots, NO was (369.24 ± 213.19µ molg-1FW) and (1094.23 ± 135.44µ molg-1FW) in the leaves and roots. LFGD plasma treatment also contributed to enhancement of productivity (1.27%), nutritional (moisture, ash, fat, and crude fiber) compositions, and iron and zinc micro-nutrition concentrations of maize. From this research, LFGD (Ar + O2) plasma treatment showed a potential impact on the maize cultivation system, which is very effective tools and both in nationally and internationally alter the conventional cultivation system of maize. Because it promotes seed surface modification, improved germination rate, shoot length, root length, chlorophyll content, some of the growths related enzymatic activity, nutrient composition, iron, and zinc micro-nutrients and the productivity of maize.

Subacute oral toxicity of ayurvedic anti-diabetic preparation Jambadyarista in Sprague-Dawley rats.

BACKGROUND: Jambadyarista is an Ayurvedic polyherbal formulation widely prescribed by Ayurvedic practitioners for the management of diabetes and its associated complications. About 39 companies have marketed this formulation in Bangladesh with consent from the Directorate General of Drug Administration (DGDA). AIM: This study investigated the sub-acute oral toxicity of Jambadyarista in the Sprague-Dawley rat model. METHODS: The sub-acute toxicity studies were executed in Sprague-Dawley rats. Jambadyarista formulation was given for 28-days through oral gavage at 10 mL/kg and 20 mL/kg dose to two different groups comprising 6 rats of both sex/groups. Across the experimental period mortality, adverse reactions were closely monitored. After 28-day feeding hematological, biochemical, and relative organ weights were quantified. RESULTS: No mortality and/or signs of morbidity were observed for 28-day of repeated-dose sub-acute toxicity. Any pernicious change in body weight, biochemical, and hematological parameters along with relative organ weight were not observed for Jambadyarista. Correlation study among parameters of the renal profile, liver profile, lipid profile also metabolic hormones (T3 and TSH), and enzymes showed the non-toxic rather beneficial role (hypolipidemic) of Jambadyarista in Sprague-Dawley rats. CONCLUSION: Jambadyarista preparation did not cause any potential toxic effect in repeated dose subacute toxicity study over Sprague-Dawley rats orally. Therefore, low dose administration of Jambadyarista could have a beneficial effect on diabetes and can be considered safe before the chronic study.

An immunoinformatics study on the spike protein of SARS-CoV-2 revealing potential epitopes as vaccine candidates.

BACKGROUND: The pandemic situation of SARS-CoV-2 infection has sparked global concern due to the disease COVID-19 caused by it. Since the first cluster of confirmed cases in China in December 2019, the infection has been reported across the continents and inflicted upon a substantial number of populations. METHOD: This study is focused on immunoinformatics analyses of the SARS-CoV-2 spike glycoprotein (S protein) which is key for the viral attachment to human host cells. Computational analyses were carried out for the prediction of B-cell and T-cell (MHC class I and II) epitopes of S protein and the analyses were extended further for the prediction of their immunogenic properties. The interaction and binding affinity of T-cell epitopes with HLA-B7 were also investigated by molecular docking. RESULT: Three distinct epitopes for vaccine design were predicted from the sequence of S protein. The potential B-cell epitope was KNHTSPDVDLG possessing the highest antigenicity score of 1.4039 among other B-cell epitopes. T-cell epitope for human MHC class I was VVVLSFELL with an antigenicity score of 1.0909 and binding ability to 29 MHC-I alleles. The predicted T-cell epitope for human MHC class II molecule was VVIGIVNNT with a corresponding 1.3063 antigenicity score, less digesting enzymes, and 7 MHC-II alleles binding ability. All these three peptides were predicted to be highly antigenic, non-allergenic, and non-toxic. Analyses of the physiochemical properties of these predicted epitopes indicate their stable nature for plausible vaccine design. Furthermore, molecular docking investigation between the MHC class-I epitopes and human HLA-B7 reflects the stable interaction with high affinity among them. CONCLUSION: The present study posits three potential epitopes of S protein of SARS-CoV-2 predicted by immunoinformatic methods based on their immunogenic properties and interactions with the host counterpart that can facilitate the development of vaccine against SARS-CoV-2. This study can act as the springboard for the future development of the COVID-19 vaccine.