Developing statistical and bioinformatic analysis of genomic data from tumours

Previous prognostic signatures for melanoma based on tumour transcriptomic data were developed predominantly on cohorts of AJCC (American Joint Committee on Cancer) stages III and IV melanoma. Since 92% of melanoma patients are diagnosed at AJCC stages I and II, there is an urgent need for better prognostic biomarkers to allow patient stratification for receiving early adjuvant therapies. This study uses genome-wide tumour gene expression levels and clinico-histopathological characteristics of patients from the Leeds Melanoma Cohort (LMC). Several unsupervised and supervised classification approaches were applied to the transcriptomic data, to identify biological classes of melanoma, and to develop prognostic classification models respectively. Unsupervised clustering identified six biologically distinct primary melanoma classes (LMC classes). Unlike previous molecular classes of melanoma, the LMC classes were prognostic in both the whole LMC dataset and in stage I tumours. The prognostic value of the LMC classes was replicated in an independent dataset, but insufficient data were available to replicate in an AJCC stage I subset. Supervised classification using the Random Forest (RF) approach provided improved performances when adjustments were made to deal with class imbalance, while this did not improve performance of the Support Vector Machine (SVM). However, RF and SVM had similar results overall, with RF only marginally better. Combining clinical and transcriptomic information in the RF further improved the performance of the prediction model in comparison to using clinical information alone. Finally, the agnostically derived LMC classes and the supervised RF model showed convergence in their association with outcome in some groups of patients, but not in others. In conclusion, this study reports six molecular classes of primary melanoma with prognostic value in stage I disease and overall, and a prognostic classification model that predicts outcome in primary melanoma

IoT-GChain:internet of things-assisted secure and tractable grain supply chain framework leveraging blockchain

The grain supply chain is crucial for any nation’s self-sustainability due to its huge impact on food security, economic stability, and the livelihoods of several people. The path grain takes from farmers to consumers is opaque and complicated, due to which consumers cannot trust grain quality and its origin. Although blockchain is widely used for fair and secure transactions between farmers and buyers, issues related to transparency and traceability in the grain supply chain, such as counterfeiting and middlemen involvement, have not been adequately addressed. To tackle these issues, a blockchain-based solution is proposed that unites farmers, warehouses, government central and state agencies, transporters, and food corporations on a single platform to enhance transparency, traceability, and trust among all parties. This system involves minting a non-fungible token (NFT) corresponding to each lot of grain approved by government officials. The NFT comprises grain quality, type, temperature data from sensors, weight, and ownership information, which updates as the grain lot moves across the supply chain from central agencies to state agencies and so on. NFTs enable stakeholders to track the grain lot from cultivation to end-users, providing insights into grain conditions and quality. An Internet of Things-based circuit is designed using a Digital-output relative humidity & temperature (DHT22) sensor, which offers real-time temperature and humidity readings, and geolocation coordinates are gathered from the GPS module across the supply chain. Farmers can directly interact with warehouses to sell grains, eliminating the need for middlemen and fostering trust among all parties. The proposed four-tier framework is implemented and deployed on the Ethereum network, with smart contracts interacting with React-based web pages. Analysis and results of the proposed model illustrate that it is viable, secure, and superior to the existing grain supply chain system

Neuro-imaging in severe hypertensive disorders of pregnancy: a study from North Indian tertiary health care institution

Background: Hypertensive disorders of pregnancy comprising of pre-eclampsia and eclampsia are a major cause of adverse pregnancy outcomes. Neurological manifestations of pregnancy induced hypertension are the most common cause of maternal and foetal morbidity and mortality. Cranial neuro-imaging reveals focal regions of symmetric hemispheric oedema; with parietal and occipital regions getting most commonly affected.Methods: The study was conducted among 65 antenatal women diagnosed with pre-eclampsia and eclampsia at gestational age >20 weeks in the department of obstetrics and gynecology, Kamla Nehru State Hospital for Mother and Child IGMC Shimla. Clinical signs and symptoms, neuroimaging findings were recorded for study purpose.Results: About 17.6% of severe pre-eclampsia and 100% of eclampsia had findings observed on cranial MRI. Headache and visual complaints were most frequently recorded. PRES was the predominant neuroradiographic finding in present study and occipital lobe was commonly affected region. No significant difference was observed regarding blood pressure parameters between MRI positive and negative subjects.Conclusions: Neuroimaging in antenatal with severe hypertensive disorders might aid in better understanding of the poorly explained phenomenon. In addition, this would be helpful in better management of the disorders along with their much-dreaded complications. Patients with hypertensive disorders of pregnancy should be subjected routinely to cranial imaging for the better perinatal outcomes

Evaluation of simple International ovarian tumor analysis ultra sound rules in differentiating between benign and malignant ovarian tumors and their histopathological correlation

Background: IOTA (International ovarian tumor analysis) study is considered one of the largest studies on ultrasound diagnosis of ovarian pathology conducted in literature till date. It was started in 1999 and included nine European countries. It is a standardized technique for preoperative classification of ovarian pathology defined by IOTA group.Methods: A retrospective study was analyzed from a period of January 2016 to December 2017 (2-year period). The records of all the patients operated for benign and malignant ovarian pathology in the gynae department of hospital were retrieved from medical record sections. USG findings were redefined as per IOTA simple rules by sonologist and its histopathological correlation was done using kappa statistical method.Results: In the present study, out of 61 patients IOTA was applicable to 57 patients. The sensitivity where IOTA simple rules were applicable was 92.8% and the specificity was 93%. The accuracy turned out to be 92.9%. If inconclusive results were taken as malignant then sensitivity increased to 94% and specificity decreased to 87%. Good level of agreement was found between sonological and histopathological findings with Kappa statistics application (K = 0.59).Conclusions: The IOTA simple rules can be considered as an important diagnostic modality in differentiation of benign and malignant ovarian tumors, it has an added advantage of abolishing the subjectivity of routine ultrasound. However inconclusive results demand further expertise in the field and need to be taken care of before interpretation of ovarian pathologies

First report on metagenomics and their predictive functional analysis of fermented bamboo shoot food of Tripura, North East India

Moiya pansung, mileye amileye, moiya koshak, and midukeye are naturally fermented bamboo shoot foods of Tripura. The present study aimed to reveal the whole microbial community structure of naturally fermented moiya pangsung, mileye amileye, moiya koshak, and midukeye along with the prediction of microbial functional profiles by shotgun metagenomic sequence analysis. The metataxonomic profile of moiya pangsung, mileye amileye, moiya koshak, and midukeye samples showed different domains, viz., bacteria (97.70%) followed by the virus (0.76%), unclassified (0.09%), eukaryotes (1.46%) and archaea (0.05%). Overall, 49 phyla, 409 families, 841 genera, and 1,799 species were found in all the fermented bamboo shoot samples collected from different places of Tripura. Firmicutes was the most abundant phylum (89.28%) followed by Proteobacteria (5.13%), Bacteroidetes (4.38%), Actinobacteria (1.02%), and Fusobacteria (0.17%). Lactiplantibacillus plantarum was the most abundant species in moiya pangsung, mileye amileye, moiya koshak, and midukeye followed by Lactococcus lactis, Levilactobacillus brevis, Leuconostoc mesenteroides, Weissella paramesenteroides, Leuconostoc kimchii, Pediococcus pentosaceus, Leuconostoc gasicomitatum, and Lacticaseibacillus casei. A few phyla of fungus were found, viz., Ascomycota, Basidiomycota, and Glomeromycota, where Ascomycota was present in high abundance. Functional analysis of moiya pangsung, mileye amileye, moiya koshak, and midukeye metagenome revealed the genes for the synthesis and metabolism of a wide range of bioactive compounds including, various essential amino acids, and conjugated amino acids. The abundance profile and predictive analysis of fermented bamboo shoots revealed a huge plethora of essential microorganisms and KEGG analysis revealed genes for amino acid metabolism, pectin degradation, lipid metabolism, and many other essential pathways that can be essential for the improvement of nutritional and sensory qualities of the fermented bamboo shoot products

In vitro induction of tuber formation for the synthesis of secondary metabolites in Chlorophytum borivilianum Sant. et Fernand

Chlorophytum borivilianum Sant. et Fernand an endangered herb is valued for several medicinal properties in its tuberous roots. An efficient and reproducible method for inducing in vitro tubers from stem disc explant has been developed. Stem disc possessing shoot buds were induced to develop multiple shoots in Murashige and Skoog (MS) medium supplemented with vitamins, 3% sucrose, 0.8% agar and 5 mg/L benzylaminopurine (BAP). Healthy regenerated shoots were rooted in MS basal medium containing 3% sucrose (w/v), 0.8% agar supplemented with indole-3-acetic acid (2 mg/L). On further sub culturing, the maximum percentage of tuber formation was obtained in growth hormone free half (½) MS liquid media supplemented with vitamins and 1.5% sucrose after 8 to 9 weeks. The saponin contents of the in vitro and in vivo raised tubers were qualitatively and quantitatively analyzed by highperformance liquid chromatography (HPLC) and liquid chromatography electrospray ionization mass spectrometry (LC-ESI-MS). There was a significant similarity in the saponins in both tubers. The in vitro raised tubers showed similar high metabolite content than in vivo grown tubers which is required for medicinal applications. The rooted plantlets were transferred to peat and sand (2:1) with more than 80% success. This is the 1st report of in vitro tuber formation and secondary metabolites screening of C. borivilianum. This work will give a strong impetus to the pharmaceutical and neutraceutical sectors.Keywords: Chlorophytum borivilianum, tuber formation, saponin, liquid medium, high-performance liquid chromatography (HPLC)African Journal of Biotechnology Vol. 12(20), pp. 2900-2907

Differential susceptibility of catheter biomaterials to biofilm-associated infections and their remedy by drug-encapsulated Eudragit RL100 nanoparticles

Biofilms are the cause of major bacteriological infections in patients. The complex architecture of Escherichia coli (E. coli) biofilm attached to the surface of catheters has been studied and found to depend on the biomaterial’s surface properties. The SEM micrographs and water contact angle analysis have revealed that the nature of the surface a ects the growth and extent of E. coli biofilm formation. In vitro studies have revealed that the Gram-negative E. coli adherence to implanted biomaterials takes place in accordance with hydrophobicity, i.e., latex > silicone > polyurethane > stainless steel. Permanent removal of E. coli biofilm requires 50 to 200 times more gentamicin sulfate (G-S) than the minimum inhibitory concentration (MIC) to remove 90% of E. coli biofilm (MBIC90). Here, in vitro eradication of biofilm-associated infection on biomaterials has been done by Eudragit RL100 encapsulated gentamicin sulfate (E-G-S) nanoparticle of range 140 nm. It is 10–20 times more e ective against E. coli biofilm-associated infections eradication than normal unentrapped G-S. Thus, Eudragit RL100 mediated drug delivery system provides a promising way to reduce the cost of treatment with a higher drug therapeutic index

Effect of fungicidal contamination on survival, morphology, and cellular immunity of Apis mellifera (Hymenoptera: Apidae)

Pesticide residues have been reported in hive-stored products for long periods. Larvae of honey bees experience oral or contact exposure to these products during their normal growth and development inside the cells. We analyzed various toxicological, morphogenic, and immunological effects of residue-based concentrations of two fungicides, captan and difenoconazole, on the larvae of worker honey bees, Apis mellifera. Selected concentrations (0.08, 0.4, 2, 10, and 50 ppm) of both fungicides were applied topically at a volume of 1 µL/larva/cell as single and multiple exposures. Our results revealed a continuous, concentration-dependent decrease in brood survival after 24 h of treatment to the capping and emergence stages. Compared to larvae with a single exposure, the multiply exposed youngest larvae were most sensitive to fungicidal toxicity. The larvae that survived higher concentrations, especially multiple exposures, showed several morphological defects at the adult stage. Moreover, difenoconazole-treated larvae showed a significantly decreased number of granulocytes after 1 h of treatment followed by an increase after 24 h of treatment. Thus, fungicidal contamination poses a great risk as the tested concentrations showed adverse effects on the survival, morphology, and immunity of larval honey bees

Metal coordinated macrocyclic complexes in different chemical transformations

Macrocyclic ligand chemistry is seen by a growing number of scientists as a tool for designing new molecules with inherently selective properties. Metal coordinated macrocyclic rings are featured with exceptionally stable π-conjugated cyclic systems containing the metal ion in the central cavity. The cyclic tetra dentate framework of the four central nitrogen atoms makes these macrocyclic rings system unique chelating agents, in addition, these conjugated double bonds impart a vital effect in electrons transportation. Because of inimitable characteristics, these metal coordinated macrocyclic compounds have been effectively applied as catalysts in various important organic transformations. Hence, this review portrays the overview of metal coordinated macrocyclic molecules, classifications, and their catalytic application in redox reactions. This comprehensive and up-to-date review is particularly aligned toward the catalytic applications of four types of metal-coordinated macrocyclic rings, i.e., porphyrin, porphyrazine, corrole, and corrolazines, in different organic transformations. The different synthetic approaches for the preparation of metal coordinated macrocyclic rings and their UV spectrums are also outlined in this review