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  1. Article ; Online: Characterizing the West Nile Virus's polyprotein from nucleotide sequence to protein structure - Computational tools.

    Praveen, Mallari

    Journal of Taibah University Medical Sciences

    2024  Volume 19, Issue 2, Page(s) 338–350

    Abstract: Objectives: West Nile virus (WNV) belongs to the Flaviviridae family and causes West Nile fever. The mechanism of transmission involves the culex mosquito species. Infected individuals are primarily asymptomatic, and few exhibit common symptoms. ... ...

    Abstract Objectives: West Nile virus (WNV) belongs to the Flaviviridae family and causes West Nile fever. The mechanism of transmission involves the culex mosquito species. Infected individuals are primarily asymptomatic, and few exhibit common symptoms. Moreover, 10 % of neuronal infection caused by this virus cause death. The proteins encoded by these genes had been uncharacterized, although understanding their function and structure is important for formulating antiviral drugs.
    Methods: Herein, we used in silico approaches, including various bioinformatic tools and databases, to analyse the proteins from the WNV polyprotein individually. The characterization included GC content, physicochemical properties, conserved domains, soluble and transmembrane regions, signal localization, protein disorder, and secondary structure features and their respective 3D protein structures.
    Results: Among 11 proteins, eight had >50 % GC content, eight proteins had basic pI values, three proteins were unstable under in vitro conditions, four were thermostable according to >100 AI values and some had negative GRAVY values in physicochemical analyses. All protein-conserved domains were shared among Flaviviridae family members. Five proteins were soluble and lacked transmembrane regions. Two proteins had signals for localization in the host endoplasmic reticulum. Non-structural (NS) 2A showed low protein disorder. The secondary structural features and tertiary structure models provide a valuable biochemical resource for designing selective substrates and synthetic inhibitors.
    Conclusions: WNV proteins NS2A, NS2B, PM, NS3 and NS5 can be used as drug targets for the pharmacological design of lead antiviral compounds.
    Language English
    Publishing date 2024-01-16
    Publishing country Saudi Arabia
    Document type Journal Article
    ZDB-ID 2817396-X
    ISSN 1658-3612 ; 1658-3612
    ISSN (online) 1658-3612
    ISSN 1658-3612
    DOI 10.1016/j.jtumed.2024.01.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book ; Online: What You Must Remember When Transforming Datawords

    Praveen, M.

    2020  

    Abstract: Streaming Data String Transducers (SDSTs) were introduced to model a class of imperative and a class of functional programs, manipulating lists of data items. These can be used to write commonly used routines such as insert, delete and reverse. SDSTs can ...

    Abstract Streaming Data String Transducers (SDSTs) were introduced to model a class of imperative and a class of functional programs, manipulating lists of data items. These can be used to write commonly used routines such as insert, delete and reverse. SDSTs can handle data values from a potentially infinite data domain. The model of Streaming String Transducers (SSTs) is the fragment of SDSTs where the infinite data domain is dropped and only finite alphabets are considered. SSTs have been much studied from a language theoretical point of view. We introduce data back into SSTs, just like data was introduced to finite state automata to get register automata. The result is Streaming String Register Transducers (SSRTs), which is a subclass of SDSTs. SDSTs can compare data values using a linear order on the data domain, which can not be done by SSRTs. We give a machine independent characterization of SSRTs with origin semantics, along the lines of Myhill-Nerode theorem. Machine independent characterizations for similar models have formed the basis of learning algorithms and enabled us to understand fragments of the models. Origin semantics of transducers track which positions of the output originate from which positions of the input. Although a restriction, using origin semantics is well justified and known to simplify many problems related to transducers. We use origin semantics as a technical building block, in addition to characterizations of deterministic register automata. However, we need to build more on top of these to overcome some challenges unique to SSRTs.
    Keywords Computer Science - Formal Languages and Automata Theory
    Subject code 006
    Publishing date 2020-05-06
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Book ; Online: Realizability Problem for Constraint LTL

    Bhaskar, Ashwin / Praveen, M.

    2022  

    Abstract: Constraint linear-time temporal logic (CLTL) is an extension of LTL that is interpreted on sequences of valuations of variables over an infinite domain. The atomic formulas are interpreted as constraints on the valuations. The atomic formulas can ... ...

    Abstract Constraint linear-time temporal logic (CLTL) is an extension of LTL that is interpreted on sequences of valuations of variables over an infinite domain. The atomic formulas are interpreted as constraints on the valuations. The atomic formulas can constrain valuations over a range of positions along a sequence, with the range being bounded by a parameter depending on the formula. The satisfiability and model checking problems for CLTL have been studied by Demri and D'Souza. We consider the realizability problem for CLTL. The set of variables is partitioned into two parts, with each part controlled by a player. Players take turns to choose valuations for their variables, generating a sequence of valuations. The winning condition is specified by a CLTL formula -- the first player wins if the sequence of valuations satisfies the specified formula. We study the decidability of checking whether the first player has a winning strategy in the realizability game for a given CLTL formula. We prove that it is decidable in the case where the domain satisfies the completion property, a property introduced by Balbiani and Condotta in the context of satisfiability. We prove that it is undecidable over $(\mathbb{Z},<,=)$, the domain of integers with order and equality. We prove that over $(\mathbb{Z},<,=)$, it is decidable if the atomic constraints in the formula can only constrain the current valuations of variables belonging to the second player, but there are no such restrictions for the variables belonging to the first player. We call this single-sided games.

    Comment: 26 pages
    Keywords Computer Science - Logic in Computer Science ; Computer Science - Formal Languages and Automata Theory ; Mathematics - Logic ; F.4.1
    Subject code 511
    Publishing date 2022-07-14
    Publishing country us
    Document type Book ; Online
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  4. Book ; Online: On the piecewise complexity of words and periodic words

    Praveen, M. / Schnoebelen, Philippe / Vialard, Isa / Veron, Julien

    2023  

    Abstract: The piecewise complexity $h(u)$ of a word is the minimal length of subwords needed to exactly characterise $u$. Its piecewise minimality index $\rho(u)$ is the smallest length $k$ such that $u$ is minimal among its order-$k$ class $[u]_k$ in Simon's ... ...

    Abstract The piecewise complexity $h(u)$ of a word is the minimal length of subwords needed to exactly characterise $u$. Its piecewise minimality index $\rho(u)$ is the smallest length $k$ such that $u$ is minimal among its order-$k$ class $[u]_k$ in Simon's congruence. We study these two measures and provide efficient algorithms for computing $h(u)$ and $\rho(u)$. We also provide efficient algorithms for the case where $u$ is a periodic word, of the form $u=v^n$
    Keywords Computer Science - Formal Languages and Automata Theory
    Publishing date 2023-11-26
    Publishing country us
    Document type Book ; Online
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  5. Article ; Online: Management of bronchomalacia in infants post-cardiac surgery using synchronized nasal DuoPAP: A novel technology.

    Kumar, Alok / Praveen, M / Tiwari, Nikhil / Ramamoorthy, H Ravi / Joshi, Ankur / Parikh, Badal

    Annals of cardiac anaesthesia

    2022  Volume 25, Issue 4, Page(s) 531–535

    Abstract: Background: Tracheo-bronchomalacia (TBM) is the weakness in the structural integrity of the cartilaginous ring and arch. It may occur in isolation with prematurity or secondarily in association with various congenital anomalies. Bronchomalacia is more ... ...

    Abstract Background: Tracheo-bronchomalacia (TBM) is the weakness in the structural integrity of the cartilaginous ring and arch. It may occur in isolation with prematurity or secondarily in association with various congenital anomalies. Bronchomalacia is more commonly associated with congenital heart diseases. The conventional treatment options include positive pressure ventilation with or without tracheostomy, surgical correction of external compression and airway stenting.
    Aim: To use "synchronized" nasal Dual positive airway pressure (DuoPAP), a non-invasive mode of ventilation as an alternative treatment option for bronchomalacia to avoid complications associated with conventional treatment modalities.
    Study design: Prospective observational study conducted in Army Hospital Research and Referral from Jul 2019 to Dec 2020.
    Material and methods: We diagnosed seven cases of TBM post-cardiac surgery at our institute, incidence of 4.2%. Four infants were diagnosed with left sided bronchomalacia, 2 were diagnosed with right sided bronchomalacia and one with tracheomalacia. Those infants were managed by "synchronized" nasal DuoPAP, a first in ventilation technology by Fabian Therapy Evolution ventilator (Acutronic, Switzerland).
    Results: All seven infants showed significant improvement with synchronized nasal DuoPAP both clinically as well as radiologically. None of the infant required tracheostomy and discharged to home successfully.
    Conclusion: The synchronized nasal DuoPAP is a low cost and effective treatment option for infants with TBM. It could be attributed to synchronization of the breaths leading to better tolerance and compliance in paediatric age group.
    MeSH term(s) Bronchomalacia/diagnosis ; Bronchomalacia/surgery ; Cardiac Surgical Procedures ; Child ; Humans ; Infant ; Intermittent Positive-Pressure Ventilation ; Technology ; Tracheomalacia/diagnosis
    Language English
    Publishing date 2022-10-18
    Publishing country India
    Document type Journal Article ; Observational Study
    ZDB-ID 2106866-5
    ISSN 0974-5181 ; 0971-9784
    ISSN (online) 0974-5181
    ISSN 0971-9784
    DOI 10.4103/aca.aca_112_21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Human C1q Regulates Influenza A Virus Infection and Inflammatory Response via Its Globular Domain.

    Varghese, Praveen M / Kishore, Uday / Rajkumari, Reena

    International journal of molecular sciences

    2022  Volume 23, Issue 6

    Abstract: The Influenza A virus (IAV) is a severe respiratory pathogen. C1q is the first subcomponent of the complement system's classical pathway. C1q is composed of 18 polypeptide chains. Each of these chains contains a collagen-like region located at the N ... ...

    Abstract The Influenza A virus (IAV) is a severe respiratory pathogen. C1q is the first subcomponent of the complement system's classical pathway. C1q is composed of 18 polypeptide chains. Each of these chains contains a collagen-like region located at the N terminus, and a C-terminal globular head region organized as a heterotrimeric structure (ghA, ghB and ghC). This study was aimed at investigating the complement activation-independent modulation by C1q and its individual recombinant globular heads against IAV infection. The interaction of C1q and its recombinant globular heads with IAV and its purified glycoproteins was examined using direct ELISA and far-Western blotting analysis. The effect of the complement proteins on IAV replication kinetics and immune modulation was assessed by qPCR. The IAV entry inhibitory properties of C1q and its recombinant globular heads were confirmed using cell binding and luciferase reporter assays. C1q bound IAV virions via HA, NA and M1 IAV proteins, and suppressed replication in H1N1, while promoting replication in H3N2-infected A549 cells. C1q treatment further triggered an anti-inflammatory response in H1N1 and pro-inflammatory response in H3N2-infected cells as evident from differential expression of TNF-α, NF-κB, IFN-α, IFN-β, IL-6, IL-12 and RANTES. Furthermore, C1q treatment was found to reduce luciferase reporter activity of MDCK cells transfected with H1N1 pseudotyped lentiviral particles, indicative of an entry inhibitory role of C1q against infectivity of IAV. These data appear to demonstrate the complement-independent subtype specific modulation of IAV infection by locally produced C1q.
    MeSH term(s) Complement C1q ; Complement System Proteins ; Humans ; Influenza A Virus, H1N1 Subtype ; Influenza A Virus, H3N2 Subtype ; Influenza A virus ; Influenza, Human
    Chemical Substances Complement C1q (80295-33-6) ; Complement System Proteins (9007-36-7)
    Language English
    Publishing date 2022-03-11
    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/ijms23063045
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  7. Article ; Online: Innate and adaptive immune responses against Influenza A Virus: Immune evasion and vaccination strategies.

    Varghese, Praveen M / Kishore, Uday / Rajkumari, Reena

    Immunobiology

    2022  Volume 227, Issue 6, Page(s) 152279

    Abstract: Influenza A virus (IAV) is a contagious respiratory infection causing pathogen responsible for high morbidity and mortality rates across the planet. The human immune system contains a wide range of soluble activators, membrane-bound receptors, and ... ...

    Abstract Influenza A virus (IAV) is a contagious respiratory infection causing pathogen responsible for high morbidity and mortality rates across the planet. The human immune system contains a wide range of soluble activators, membrane-bound receptors, and regulators to eliminate IAVs. Despite these various immune mechanisms that neutralize IAVs or restrict their replication, IAVs have developed distinct strategies to evade host immunity and establish a successful infection. Given the higher and continuous rate of mutations in IAVs, decades of research have focused on understanding the host's immune mechanisms against IAVs, and the evasion strategies employed by the virus to overcome the host immune system. Future IAV pandemics or epidemics remain inevitable, and a greater understanding of the host-pathogen interaction involved is required to develop universal vaccines and treatments against IAV. Here, we review how the host immune system responds to IAV infection as well as the strategies employed by the IAV to evade host immune surveillance. Furthermore, this review also focuses on the treatments and vaccines that have been developed to counter IAV infection.
    MeSH term(s) Humans ; Influenza A virus ; Immune Evasion ; Immunity, Innate ; Influenza, Human/prevention & control ; Host-Pathogen Interactions ; Vaccination ; Virus Replication
    Language English
    Publishing date 2022-09-14
    Publishing country Netherlands
    Document type Review ; Journal Article
    ZDB-ID 563292-4
    ISSN 1878-3279 ; 0171-2985
    ISSN (online) 1878-3279
    ISSN 0171-2985
    DOI 10.1016/j.imbio.2022.152279
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  8. Book ; Online: Verification of Flat FIFO Systems

    Finkel, Alain / Praveen, M.

    2019  

    Abstract: The decidability and complexity of reachability problems and model-checking for flat counter machines have been explored in detail. However, only few results are known for flat (lossy) FIFO machines, only in some particular cases (a single loop or a ... ...

    Abstract The decidability and complexity of reachability problems and model-checking for flat counter machines have been explored in detail. However, only few results are known for flat (lossy) FIFO machines, only in some particular cases (a single loop or a single bounded expression). We prove, by establishing reductions between properties, and by reducing SAT to a subset of these properties that many verification problems like reachability, non-termination, unboundedness are NP-complete for flat FIFO machines, generalizing similar existing results for flat counter machines. We also show that reachability is NP-complete for flat lossy FIFO machines and for flat front-lossy FIFO machines. We construct a trace-flattable system of many counter machines communicating via rendez-vous that is bisimilar to a given flat FIFO machine, which allows to model-check the original flat FIFO machine. Our results lay the theoretical foundations and open the way to build a verification tool for (general) FIFO machines based on analysis of flat sub-machines.
    Keywords Computer Science - Computational Complexity ; Computer Science - Logic in Computer Science ; Theory of computation - Parallel computing models
    Subject code 501
    Publishing date 2019-08-20
    Publishing country us
    Document type Book ; Online
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  9. Article ; Online: Metabolite profiling of

    Sulaiman, C T / Ramesh, P R / Mahesh, K / Anandan, E M / Praveen, M / Balachandran, I

    Natural product research

    2021  Volume 36, Issue 14, Page(s) 3726–3730

    Abstract: Cyanthillium ... ...

    Abstract Cyanthillium cinereum
    MeSH term(s) Anti-Inflammatory Agents/pharmacology ; Asteraceae ; Chromatography, High Pressure Liquid/methods ; Flavonoids/chemistry ; Phenols/analysis ; Phytochemicals/analysis ; Plant Extracts/chemistry ; Tandem Mass Spectrometry/methods
    Chemical Substances Anti-Inflammatory Agents ; Flavonoids ; Phenols ; Phytochemicals ; Plant Extracts
    Language English
    Publishing date 2021-01-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 2185747-7
    ISSN 1478-6427 ; 1478-6419
    ISSN (online) 1478-6427
    ISSN 1478-6419
    DOI 10.1080/14786419.2020.1869972
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  10. Article: Exploring

    Praveen, Mallari / Ullah, Ihsan / Buendia, Ricardo / Khan, Imran Ahmad / Sayed, Mian Gul / Kabir, Rahmul / Bhat, Mashooq Ahmad / Yaseen, Muhammad

    Pharmaceuticals (Basel, Switzerland)

    2024  Volume 17, Issue 1

    Abstract: Potentilla ... ...

    Abstract Potentilla nepalensis
    Language English
    Publishing date 2024-01-19
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2193542-7
    ISSN 1424-8247
    ISSN 1424-8247
    DOI 10.3390/ph17010134
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