CNN-BLSTM based deep learning framework for eukaryotic kinome classification: An explainability based approach.

Classification of protein families from their sequences is an enduring task in Proteomics and related studies. Numerous deep-learning models have been moulded to tackle this challenge, but due to the black-box character, they still fall short in reliability. Here, we present a novel explainability pipeline that explains the pivotal decisions of the deep learning model on the classification of the Eukaryotic kinome.

Effect of titanium dioxide nanocoating on the colour stability of room temperature vulcanizing maxillofacial silicone-an invitro study.

Objective: The aim of this in vitro study was to evaluate the effect of an oxide nanocoating to prevent colour degradation of maxillofacial silicone elastomers following accelerated ageing.

Material And Methods: Specimens (N = 40) of specified dimensions were fabricated in Factor II room temperature vulcanizing (RTV) silicone and processed according to the manufacturer's instructions. Two groups were classified with 20 specimens each.

Use of near infrared spectroscopy for the prediction of perioperative complications in patients undergoing elective microsurgical resection of cerebral arteriovenous malformations- a prospective observational trial (NIRSCAM trial).

Purpose: Cerebral arteriovenous malformations (AVM) represent focal abnormal areas of low resistance circulation which render the peri-nidal neuronal tissue susceptible to ischemia. The post-excision cerebral perfusion surge can result in hyperaemic complications.We hypothesised that Near Infrared Spectroscopy (NIRS)-guided perioperative management can aid in the prediction and prevention of perioperative complications in patients presenting for surgical excision of cerebral AVMs.

Evaluation and correlation of nociceptive response index and spectral entropy indices as monitors of nociception in anesthetized patients.

Objectives: During anesthesia, the response to these stimuli depends on the balance between nociception and antinociception. Recently, various monitoring systems based on the variables derived from electroencephalography, plethysmography, autonomic tone, reflex pathways, and composite algorithms have been introduced for monitoring nociception. The main aim of our study was to evaluate and correlate the physiological variables which reflect the autonomic nervous system response to nociception, such as heart rate (HR), systolic blood pressure (SBP), perfusion index (PI), and nociceptive response index (NRI), with the spectral entropy indices response entropy (RE) and RE-state entropy (SE), which reflects electromyographic (EMG) activation as a response to pain.

A Perfusion Index-Based Evaluation and Comparison of Peripheral Perfusion in Sevoflurane and Isoflurane Anaesthesia: A Prospective Randomised Controlled Trial.

Objective: Perfusion index has shown to be helpful in the operative and critical care settings to monitor peripheral tissue perfusion. Randomised controlled trials quantifying different agents' vasodilatory properties using perfusion index has been limited. Therefore, we undertook this study to compare the vasodilatory effects of isoflurane and sevoflurane using perfusion index.

Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation.

The tiger, a poster child for conservation, remains an endangered apex predator. Continued survival and recovery will require a comprehensive understanding of genetic diversity and the use of such information for population management. A high-quality tiger genome assembly will be an important tool for conservation genetics, especially for the Indian tiger, the most abundant subspecies in the wild.

Drug-food Interactions in the Era of Molecular Big Data, Machine Intelligence, and Personalized Health.

The drug-food interaction brings forth changes in the clinical effects of drugs. While favourable interactions bring positive clinical outcomes, unfavourable interactions may lead to toxicity. This article reviews the impact of food intake on drug-food interactions, the clinical effects of drugs, and the effect of drug-food in correlation with diet and precision medicine.

PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe.

Unlabelled: Sequence alignments are models that capture the structural, functional and evolutionary relationships between proteins. Structure-guided sequence alignments are helpful in the case of distantly related proteins with poor sequence identity, thus rendering routine sequence alignment methods ineffective. Protein Alignment organized as Structural Superfamilies or PASS2 database provides such sequence alignments of protein domains within a superfamily as per the Structural Classification of Proteins extended (SCOPe) database.

Comparison of multiple risk scores in assessing medium-to long-term clinical outcomes in unstable angina / non-ST-elevation myocardial infarction patients undergoing multi vessel percutaneous coronary intervention: An observational, registry-based study in India.

Objective: Post-revascularization mortality in multivessel coronary artery disease (MVCAD) has been explored via several risk scores. Here, we assessed and compared various risk scores in predicting medium to long-term clinical outcomes in unstable angina/non-ST-elevation myocardial infarction (UA/NSTEMI) patients with MVCAD undergoing percutaneous coronary intervention (PCI).

Methods: We analyzed a cohort of a tertiary care center registry enrolling patients in South India, Kerala, with MVCAD (N = 200) who had undergone PCI between 2010 and 2018.

Bleeding complications after dual antiplatelet therapy with ticagrelor versus dual antiplatelet therapy with clopidogrel-a propensity-matched comparative study of two antiplatelet regimes in off-pump coronary artery bypass grafting.

Purpose: Ticagrelor combined with aspirin had shown better saphenous vein graft patency than aspirin with clopidogrel after off-pump coronary artery bypass grafting. However, the safety of this drug in regard to bleeding complications remains unknown. The aim of our study was to assess the bleeding complications of dual antiplatelet therapy with aspirin and ticagrelor compared with aspirin and clopidogrel within the first 3 months after off-pump surgery.

Phenotypic expression and clinical outcomes in a South Asian PRKAG2 cardiomyopathy cohort.

The PRKAG2 syndrome is a rare autosomal dominant phenocopy of sarcomeric hypertrophic cardiomyopathy (HCM), characterized by ventricular pre-excitation, progressive conduction system disease and left ventricular hypertrophy. This study describes the phenotype, genotype and clinical outcomes of a South-Asian PRKAG2 cardiomyopathy cohort over a 7-year period. Clinical, electrocardiographic, echocardiographic, and cardiac MRI data from 22 individuals with PRKAG2 variants (68% men; mean age 39.

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 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.

Dataset for the combined transcriptome assembly of and functional annotation.

In this paper, we present the data acquired during transcriptome analysis of the 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 Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins.

Snakebite envenoming is a serious and neglected tropical disease that kills ~100,000 people annually. High-quality, genome-enabled comprehensive characterization of toxin genes will facilitate development of effective humanized recombinant antivenom. We report a de novo near-chromosomal genome assembly of Naja naja, the Indian cobra, a highly venomous, medically important snake.

Draft Genome Sequence of Freshwater-Derived sp. Strain BPSDS2, Isolated from Damte Stream, Northeast India.

We report the draft genome sequence of sp. strain BPSDS2, isolated from freshwater sediments in Northeast India. The draft genome has a size of 8.

Sepsis in the era of data-driven medicine: personalizing risks, diagnoses, treatments and prognoses.

Sepsis is a series of clinical syndromes caused by the immunological response to infection. The clinical evidence for sepsis could typically attribute to bacterial infection or bacterial endotoxins, but infections due to viruses, fungi or parasites could also lead to sepsis. Regardless of the etiology, rapid clinical deterioration, prolonged stay in intensive care units and high risk for mortality correlate with the incidence of sepsis.

Draft Genome Sequence of Streptomyces thermocarboxydus BPSAC147, a Potentially Plant Growth-Promoting Endophytic Bacterium.

strain BPSAC147 is an endophytic actinobacterium isolated from root tissues of in Mizoram, Northeast India. The strain showed potentially plant growth-promoting and biocontrol activities. The draft genome consists of 7.

Draft Genome Sequence of Plant Growth-Promoting Endophytic BPSAC84, Isolated from the Medicinal Plant .

Endophytic strain BPSAC84, which has antimicrobial potential, was isolated from root tissues of in Mizoram, Northeast India. The draft genome consists of 3.58 Mb and 3,444 protein-coding sequences.

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.

PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe.

The number of protein structures is increasing due to the individual initiatives and rapid development of structure determination techniques. Structure-based sequence alignments of distantly related proteins enable the investigation of structural, evolutionary and functional relationships between proteins and their domains leading to their common evolutionary origin. Protein Alignments organized as Structural Superfamilies (PASS2) is a database that provides such alignments of members of protein domain superfamilies of known structure and with less than 40% sequence identity.

RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information.

Background: RNA-binding proteins (RBPs) interact with their cognate RNA(s) to form large biomolecular assemblies. They are versatile in their functionality and are involved in a myriad of processes inside the cell. RBPs with similar structural features and common biological functions are grouped together into families and superfamilies.

PIMADb: A Database of Protein-Protein Interactions in Huge Macromolecular Assemblies.

Protein-protein interactions play a very important role in the process of cellular functionality. Intricate details about the interactions between the proteins in a macromolecular assembly are important to understand the function and significance of protein complexes. We are reporting about a database of protein-protein interactions in huge macromolecular assemblies (PIMADb) that records the intrinsic details of 189,532 interchain interactions in 40,049 complexes from the Protein Data Bank.

An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry.

The modern sequencing technologies are generating large volumes of information at the transcriptome and genome level. Translation of this information into a biological meaning is far behind the race due to which a significant portion of proteins discovered remain as proteins of unknown function (PUFs). Attempts to uncover the functional significance of PUFs are limited due to lack of easy and high throughput functional annotation tools.

PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features.

Structure-based sequence alignment is an essential step in assessing and analysing the relationship of distantly related proteins. PASS2 is a database that records such alignments for protein domain superfamilies and has been constantly updated periodically. This update of the PASS2 version, named as PASS2.