Publications by authors named "Yash Gupta"

This short paper presents an educational approach to teaching three popular methods for encoding DNA sequences: one-hot encoding, binary encoding, and integer encoding. Aimed at bioinformatics and computational biology students, our learning intervention focuses on developing practical skills in implementing these essential techniques for efficient representation and analysis of genetic data. The primary goal of this study is to enhance students' understanding and practical application of DNA encoding methods, which are crucial for various computational analyses in bioinformatics.

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Aptamers are short DNA or RNA sequences that adopt 3D structures and can bind to protein targets with high binding affinity and specificity. Aptamers exhibit excellent tissue penetration, are inexpensive to produce, and can be internalized by cells. Therefore, aptamers are attractive targeting ligands to direct the delivery of theranostic agents to the desired cells.

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Introduction: Adjuvants added to subunit vaccines augment antigen-specific immune responses. One mechanism of adjuvant action is activation of pattern recognition receptors (PRRs) on innate immune cells. colonization factor A (BcfA); an outer membrane protein with adjuvant function, activates T1/T17-polarized immune responses to protein antigens from and SARS CoV-2.

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Chemical insecticides (organophosphates and pyrethroids) in the form of IRS (Indoor Residual Sprays) and LLINs (Long Lasting Insecticidal Nets) are the cornerstone for vector control, globally. However, their incessant use has resulted in widespread development of resistance in mosquito vectors, warranting continuous monitoring and investigation of the underlying mechanisms of resistance. Here, we identified a previously uncharacterized- Cub and Sushi Domain containing Insecticide Resistance (CSDIR) protein and generated evidence for its role in mediating insecticide resistance in the Anopheles stephensi.

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Background: The aim of the study is to assess the possible predictors of microvascular free flap failure and determine the critical postoperative timing of flap failure, thereby minimizing this adverse outcome.

Methods: This is a retrospective single-institutional review of 1569 free flap operations. All free flaps with outcome status recorded were analyzed for possible predictors in the development of microvascular compromise.

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In this study, we report the assembly and annotation of the mitochondrial genome (mitogenome) of from breeding facility, a species commonly known as the house cricket. This species is considered to be an important edible cricket. The mitogenome was assembled using a reproducible protocol implemented on the Galaxy Europe Server, which involved uploading paired-end fastq reads for bioinformatic analysis.

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As the new SARS-CoV-2 Omicron variants and subvariants emerge, there is an urgency to develop intranasal, broadly protective vaccines. Here, we developed highly efficacious, intranasal trivalent SARS-CoV-2 vaccine candidates (TVC) based on three components of the MMR vaccine: measles virus (MeV), mumps virus (MuV) Jeryl Lynn (JL1) strain, and MuV JL2 strain. Specifically, MeV, MuV-JL1, and MuV-JL2 vaccine strains, each expressing prefusion spike (preS-6P) from a different variant of concern (VoC), were combined to generate TVCs.

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Bifidobacterium bifidum strain BB1 causes a strain-specific enhancement in intestinal epithelial tight junction (TJ) barrier. Tumor necrosis factor (TNF)-α induces an increase in intestinal epithelial TJ permeability and promotes intestinal inflammation. The major purpose of this study was to delineate the protective effect of BB1 against the TNF-α-induced increase in intestinal TJ permeability and to unravel the intracellular mechanisms involved.

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Despite global vaccination, pertussis caused by () is resurging. Pertussis resurgence is correlated with the switch from whole cell vaccines (wPV) that elicit T1/T17 polarized immune responses to acellular pertussis vaccines (aPV) that elicit primarily T2 polarized immune responses. One explanation for the increased incidence in aPV-immunized individuals is the lack of bacterial clearance from the nose.

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Background: Atherosclerotic cardiovascular disease (ASCVD) is the leading cause of death worldwide, driven primarily by coronary artery disease (CAD). ASCVD risk estimators such as the pooled cohort equations (PCE) facilitate risk stratification and primary prevention of ASCVD but their accuracy is still suboptimal.

Methods: Using deep electronic health record data from 7,116,209 patients seen at 70+ hospitals and clinics across 5 states in the USA, we developed an artificial intelligence-based electrocardiogram analysis tool (ECG-AI) to detect CAD and assessed the additive value of ECG-AI-based ASCVD risk stratification to the PCE.

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Article Synopsis
  • The COVID-19 pandemic necessitated a transition of the Bioinformatics course from in-person to remote learning, prompting changes in teaching methods and lab activities.
  • Students now require foundational knowledge in DNA sequence analysis and are using Jupyter Notebook for practical learning, which allows for coding and results to be integrated into one document.
  • This platform enhances student engagement by enabling interaction with code and results, creating a hybrid learning experience for Python scripting and genomics during remote instruction.
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Background: Dysmotility and postoperative ileus (POI) are frequent major clinical problems post-abdominal surgery. Erythropoietin (EPO) is a multifunctional tissue-protective cytokine that promotes recovery of the intestine in various injury models. While EPO receptors (EPOR) are present in vagal Schwann cells, the role of EPOR in POI recovery is unknown because of the lack of EPOR antagonists or Schwann-cell specific EPOR knockout animals.

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Article Synopsis
  • Mycolactone (MLN) is a toxin that significantly inhibits platelet degranulation and exocytosis, and it also has strong effects on endocytosis by binding to clathrin and a novel SARS-CoV-2 fusion protein.
  • In live viral assays, MLN showed 100% inhibition at 60 nM and was found to be 10 times more effective than the antiviral drugs remdesivir and molnupiravir.
  • The compound demonstrated notable cytotoxicity against various human cell lines, but it maintained a high therapeutic index, making it a promising candidate for treating COVID-19 and other similar viruses.
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New carborane-bearing hydroxamate matrix metalloproteinase (MMP) ligands have been synthesized for boron neutron capture therapy (BNCT) with nanomolar potency against MMP-2, -9 and -13. New analogs are based on MMP inhibitor CGS-23023A, and two previously reported MMP ligands () and () were studied in vitro for BNCT activity. The boronated MMP ligands and showed high in vitro tumoricidal effects in an in vitro BNCT assay, exhibiting IC values for and of 2.

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The landscape of viral strains and lineages of SARS-CoV-2 keeps changing and is currently dominated by Delta and Omicron variants. Members of the latest Omicron variants, including BA.1, are showing a high level of immune evasion, and Omicron has become a prominent variant circulating globally.

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Objective: We aimed to develop a distributed, immutable, and highly available cross-cloud blockchain system to facilitate federated data analysis activities among multiple institutions.

Materials And Methods: We preprocessed 9166 COVID-19 Structured Query Language (SQL) code, summary statistics, and user activity logs, from the GitHub repository of the Reliable Response Data Discovery for COVID-19 (R2D2) Consortium. The repository collected local summary statistics from participating institutions and aggregated the global result to a COVID-19-related clinical query, previously posted by clinicians on a website.

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Broadly neutralizing antibodies (bNAbs) are potent in neutralizing a wide range of HIV strains. VRC01 is a CD4-binding-site (CD4-bs) class of bNAbs that binds to the conserved CD4-binding region of HIV-1 envelope (env) protein. Natural products that mimic VRC01 bNAbs by interacting with the conserved CD4-binding regions may serve as a new generation of HIV-1 entry inhibitors by being broadly reactive and potently neutralizing.

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With more than 5 million fatalities and close to 300 million reported cases, COVID-19 is the first documented pandemic due to a coronavirus that continues to be a major health challenge. Despite being rapid, uncontrollable, and highly infectious in its spread, it also created incentives for technology development and redefined public health needs and research agendas to fast-track innovations to be translated. Breakthroughs in computational biology peaked during the pandemic with renewed attention to making all cutting-edge technology deliver agents to combat the disease.

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The red-whiskered bulbul (s) is a popular avian species in Thailand and many other countries. The red-whiskered bulbul has a high economic value, but breeding is challenging since sex identification is difficult. The PCR method is now used for sex identification.

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Topics expected to influence personalized medicine (PM), where medical decisions, practices, and treatments are tailored to the individual patient, are reviewed. Lack of discrimination due to different biological conditions that express similar values of numerical variables (ambiguity) is regarded to be a major potential barrier for PM. This material explores possible causes and sources of ambiguity and offers suggestions for mitigating the impacts of uncertainties.

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With the uproar of touchless technology, the Virtual Continuum has seen some spark in the upcoming products. Today numerous gadgets support the use of Mixed Reality / Augmented Reality (AR)/ Virtual Reality. The Head Mounted Displays (HMDs) like that of Hololens, Google Lens, Jio Glass manifested reality into virtuality.

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, commonly known as giant cricket one of the important edible cricket species. However, the genetic information of these species is still limited. Therefore, we have assembled and annotated the first mitochondrial genome of .

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Malaria elimination urgently needs novel antimalarial therapies that transcend resistance, toxicity, and high costs. Our multicentric international collaborative team focuses on developing multistage antimalarials that exhibit novel mechanisms of action. Here, we describe the design, synthesis, and evaluation of a novel multistage antimalarial compound, 'Calxinin'.

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Leishmaniasis remains a serious public health problem in many tropical regions of the world. Among neglected tropical diseases, the mortality rate of leishmaniasis is second only to malaria. All currently approved therapeutics have toxic side effects and face rapidly increasing resistance.

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