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  1. Article: A rare case of Boerhaave syndrome with cervico-thoracic esophageal junction rupture causing bilateral empyema; case report from Nepal.

    Khadka, Bikash / Khanal, Kishor / Dahal, Puja / Adhikari, Hemant

    International journal of surgery case reports

    2023  Volume 105, Page(s) 108018

    Abstract: Introduction and importance: Boerhaave syndrome is a rare finding where spontaneous rupture of esophagus occurs, usually in distal segment. It is a life threatening condition that requires urgent surgical intervention.: Case presentation: We present ... ...

    Abstract Introduction and importance: Boerhaave syndrome is a rare finding where spontaneous rupture of esophagus occurs, usually in distal segment. It is a life threatening condition that requires urgent surgical intervention.
    Case presentation: We present a case of 70 years male who presented with pleural effusion and later empyema following spontaneous rupture of cervico-thoracic junction of esophagus who was managed successfully with primary surgical repair.
    Clinical discussion: Although Boerhaave syndrome is tricky to diagnose but it should be considered in all cases with a combination of gastrointestinal and pulmonary signs and symptoms.
    Conclusion: Clinical correlation along with imaging such as HRCT chest or gastrografin study is required to come to a diagnosis, however surgical intervention should not be delayed to reduce the mortality.
    Language English
    Publishing date 2023-03-21
    Publishing country Netherlands
    Document type Case Reports
    ISSN 2210-2612
    ISSN 2210-2612
    DOI 10.1016/j.ijscr.2023.108018
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  2. Article: Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory.

    Ching, Wai-Yim / Adhikari, Puja / Jawad, Bahaa / Podgornik, Rudolf

    Biomedicines

    2023  Volume 11, Issue 2

    Abstract: The spike protein (S-protein) is a crucial part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with its many domains responsible for binding, fusion, and host cell entry. In this review we use the density functional theory (DFT) ... ...

    Abstract The spike protein (S-protein) is a crucial part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with its many domains responsible for binding, fusion, and host cell entry. In this review we use the density functional theory (DFT) calculations to analyze the atomic-scale interactions and investigate the consequences of mutations in S-protein domains. We specifically describe the key amino acids and functions of each domain, which are essential for structural stability as well as recognition and fusion processes with the host cell; in addition, we speculate on how mutations affect these properties. Such unprecedented large-scale ab initio calculations, with up to 5000 atoms in the system, are based on the novel concept of
    Language English
    Publishing date 2023-02-10
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2720867-9
    ISSN 2227-9059
    ISSN 2227-9059
    DOI 10.3390/biomedicines11020517
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  3. Article ; Online: Ab initio study of mechanical and thermal properties of GeTe-based and PbSe-based high-entropy chalcogenides.

    Hasan, Sahib / Adhikari, Puja / San, Saro / Ching, Wai-Yim

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 16218

    Abstract: GeTe-based and PbSe-based high-entropy compounds have outstanding thermoelectric (TE) performance and crucial applications in mid and high temperatures. Recently, the optimization of TE performance of high-entropy compounds has been focused on reducing ... ...

    Abstract GeTe-based and PbSe-based high-entropy compounds have outstanding thermoelectric (TE) performance and crucial applications in mid and high temperatures. Recently, the optimization of TE performance of high-entropy compounds has been focused on reducing thermal conductivity by strengthening the phonon scattering process to improve TE performance. We report a first-principles investigation on nine GeTe-based high-entropy chalcogenide solid solutions constituted of eight metallic elements (Ag, Pb, Sb, Bi, Cu, Cd, Mn, and Sn) and 13 PbSe-based high-entropy chalcogenide solid solutions: Pb
    Language English
    Publishing date 2023-09-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-42101-5
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  4. Article ; Online: Impact of BA.1, BA.2, and BA.4/BA.5 Omicron mutations on therapeutic monoclonal antibodies.

    Jawad, Bahaa / Adhikari, Puja / Podgornik, Rudolf / Ching, Wai-Yim

    Computers in biology and medicine

    2023  Volume 167, Page(s) 107576

    Abstract: The emergence of Omicron SARS-CoV-2 subvariants (BA.1, BA.2, BA.4, and BA.5), with an unprecedented number of mutations in their receptor-binding domain (RBD) of the spike-protein, has fueled a resurgence of COVID-19 infections, posing a major challenge ... ...

    Abstract The emergence of Omicron SARS-CoV-2 subvariants (BA.1, BA.2, BA.4, and BA.5), with an unprecedented number of mutations in their receptor-binding domain (RBD) of the spike-protein, has fueled a resurgence of COVID-19 infections, posing a major challenge to the efficacy of existing vaccines and monoclonal antibody (mAb) therapeutics. We conducted a systematic molecular dynamics (MD) simulation to investigate how the RBD mutations of these subvariants affect the interactions with broad mAbs including AstraZeneca (COV2-2196 and COV2-2130), Brii Biosciences (BRII-196), Celltrion (CT-P59), Eli Lilly (LY-CoV555 and LY-CoV016), Regeneron (REGN10933 and REGN10987), Vir Biotechnology (S309), and S2X259. Our results show a complete loss of binding for COV2-2196, BRII-196, CT-P59, and LY-CoV555 with all Omicron RBDs. Additionally, REGN10987 totally loses its binding with BA.1, but retains a partial binding with BA.2 and BA.4/5. The binding reduction is significant for LY-CoV016 and REGN10933 but moderate for COV2-2130. S309 and S2X259 retain their binding with BA.1 but exhibit decreased binding with other subvariants. We introduce a mutational escape map for each mAb to identify the key RBD sites and the corresponding critical mutations. Overall, our findings suggest that the majority of therapeutic mAbs have diminished or missing activity against Omicron subvariants, indicating the urgent need for a new therapeutic mAb with a better design.
    MeSH term(s) Humans ; Antibodies, Monoclonal/genetics ; Antibodies, Monoclonal/therapeutic use ; Mutation ; COVID-19/genetics
    Chemical Substances amubarvimab (2AD5KH3SE4) ; S2X259 ; Antibodies, Monoclonal
    Language English
    Publishing date 2023-10-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2023.107576
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  5. Article ; Online: Amino acid interacting network in the receptor-binding domain of SARS-CoV-2 spike protein.

    Adhikari, Puja / Ching, Wai-Yim

    RSC advances

    2020  Volume 10, Issue 65, Page(s) 39831–39841

    Abstract: The relation between amino acid (AA) sequence and biologically active conformation controls the process of polypeptide chains folding into three-dimensional (3d) protein structures. The recent achievements in the resolution achieved in cryo-electron ... ...

    Abstract The relation between amino acid (AA) sequence and biologically active conformation controls the process of polypeptide chains folding into three-dimensional (3d) protein structures. The recent achievements in the resolution achieved in cryo-electron microscopy coupled with improvements in computational methodologies have accelerated the analysis of structures and properties of proteins. However, the detailed interaction between AAs has not been fully elucidated. Herein, we present a
    Language English
    Publishing date 2020-11-02
    Publishing country England
    Document type Journal Article
    ISSN 2046-2069
    ISSN (online) 2046-2069
    DOI 10.1039/d0ra08222h
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  6. Article ; Online: Bond strength between receptor binding domain of spike protein and human angiotensin converting enzyme-2 using machine learning

    Adebiyi, Abdulmateen / Adhikari, Puja / Rao, Praveen / Ching, Wai-Yim

    bioRxiv

    Abstract: The spike protein (S-protein) of SARS-CoV-2 plays an important role in binding, fusion, and host entry. In this study, we have predicted interatomic bond strength between receptor binding domain (RBD) and angiotensin converting enzyme-2 (ACE2) using ... ...

    Abstract The spike protein (S-protein) of SARS-CoV-2 plays an important role in binding, fusion, and host entry. In this study, we have predicted interatomic bond strength between receptor binding domain (RBD) and angiotensin converting enzyme-2 (ACE2) using machine learning (ML), that matches with expensive ab initio calculation result. We collected bond order result from ab initio calculations. We selected a total of 18 variables such as bond type, bond length, elements and their coordinates, and others, to train ML models. We then trained five well-known regression models, namely, Decision Tree regression, KNN Regression, XGBoost, Lasso Regression, and Ridge Regression. We tested these models on two different datasets, namely, Wild type (WT) and Omicron variant (OV). In the first setting, we used 90% of each dataset for training and 10% for testing to predict the bond order. XGBoost model outperformed all the other models in the prediction of the WT dataset. It achieved an R2 Score of 0.997. XGBoost also outperformed all the other models with an R2 score of 0.9998 in the prediction of the OV dataset. In the second setting, we trained all the models on the WT (or OV) dataset and predicted the bond order on the OV (or WT) dataset. Interestingly, Decision Tree outperformed all the other models in both cases. It achieved an R2 score of 0.997.
    Keywords covid19
    Language English
    Publishing date 2024-04-18
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2024.04.16.589808
    Database COVID19

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  7. Article ; Online: Porosity modeling in a TiNbTaZrMo high-entropy alloy for biomedical applications.

    San, Saro / Adhikari, Puja / Sakidja, Ridwan / Brechtl, Jamieson / Liaw, Peter K / Ching, Wai-Yim

    RSC advances

    2023  Volume 13, Issue 51, Page(s) 36468–36476

    Abstract: High-entropy alloys (HEAs) have attracted great attention for many biomedical applications. However, the nature of interatomic interactions in this class of complex multicomponent alloys is not fully understood. We report, for the first time, the results ...

    Abstract High-entropy alloys (HEAs) have attracted great attention for many biomedical applications. However, the nature of interatomic interactions in this class of complex multicomponent alloys is not fully understood. We report, for the first time, the results of theoretical modeling for porosity in a large biocompatible HEA TiNbTaZrMo using an atomistic supercell of 1024 atoms that provides new insights and understanding. Our results demonstrated the deficiency of using the valence electron count, quantification of large lattice distortion, validation of mechanical properties with available experimental data to reduce Young's modulus. We utilized the novel concepts of the total bond order density (TBOD) and partial bond order density (PBOD)
    Language English
    Publishing date 2023-12-14
    Publishing country England
    Document type Journal Article
    ISSN 2046-2069
    ISSN (online) 2046-2069
    DOI 10.1039/d3ra07313k
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  8. Article: Ultra-large-scale

    Ching, Wai-Yim / Adhikari, Puja / Jawad, Bahaa / Podgornik, Rudolf

    Computational and structural biotechnology journal

    2021  Volume 19, Page(s) 1288–1301

    Abstract: The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. ...

    Abstract The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption.
    Language English
    Publishing date 2021-02-19
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2021.02.004
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  9. Article: Quantum Chemical Computation of Omicron Mutations Near Cleavage Sites of the Spike Protein.

    Adhikari, Puja / Jawad, Bahaa / Podgornik, Rudolf / Ching, Wai-Yim

    Microorganisms

    2022  Volume 10, Issue 10

    Abstract: The attachment of the spike protein in SARS-CoV-2 to host cells and the initiation of viral invasion are two critical processes in the viral infection and transmission in which the presence of unique furin (S1/S2) and TMPRSS2 (S2') cleavage sites play a ... ...

    Abstract The attachment of the spike protein in SARS-CoV-2 to host cells and the initiation of viral invasion are two critical processes in the viral infection and transmission in which the presence of unique furin (S1/S2) and TMPRSS2 (S2') cleavage sites play a pivotal role. We provide a detailed analysis of the impact of the BA.1 Omicron mutations vicinal to these cleavage sites using a novel computational method based on the amino acid-amino acid bond pair unit (AABPU), a specific protein structural unit as a proxy for quantifying the atomic interaction. Our study is focused mainly on the spike region between subdomain 2 (SD2) and the central helix (CH), which contains both S1/S2 and S2' cleavage sites. Based on ab initio quantum calculations, we have identified several key features related to the electronic structure and bonding of the Omicron mutations that significantly increase the size of the relevant AABPUs and the positive charge. These findings enable us to conjecture on the biological role of Omicron mutations and their specific effects on cleavage sites and identify the principles that can be of some value in analyzing new variants.
    Language English
    Publishing date 2022-10-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms10101999
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  10. Article ; Online: Effect of Delta and Omicron Mutations on the RBD-SD1 Domain of the Spike Protein in SARS-CoV-2 and the Omicron Mutations on RBD-ACE2 Interface Complex.

    Ching, Wai-Yim / Adhikari, Puja / Jawad, Bahaa / Podgornik, Rudolf

    International journal of molecular sciences

    2022  Volume 23, Issue 17

    Abstract: The receptor-binding domain (RBD) is the essential part in the Spike-protein (S-protein) of SARS-CoV-2 virus that directly binds to the human ACE2 receptor, making it a key target for many vaccines and therapies. Therefore, any mutations at this domain ... ...

    Abstract The receptor-binding domain (RBD) is the essential part in the Spike-protein (S-protein) of SARS-CoV-2 virus that directly binds to the human ACE2 receptor, making it a key target for many vaccines and therapies. Therefore, any mutations at this domain could affect the efficacy of these treatments as well as the viral-cell entry mechanism. We introduce ab initio DFT-based computational study that mainly focuses on two parts: (1) Mutations effects of both Delta and Omicron variants in the RBD-SD1 domain. (2) Impact of Omicron RBD mutations on the structure and properties of the RBD-ACE2 interface system. The in-depth analysis is based on the novel concept of
    MeSH term(s) Amino Acids/genetics ; Angiotensin-Converting Enzyme 2/genetics ; COVID-19 ; Humans ; Mutation ; Protein Binding ; Receptors, Virus/genetics ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics ; Syndactyly
    Chemical Substances Amino Acids ; Receptors, Virus ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
    Language English
    Publishing date 2022-09-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms231710091
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