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Article ; Online: ABPA and AFRS: addressing prevalence, early diagnosis, allergens, and occupational concerns.

Minhas, Anu Priya / Das, Santasabuj

The Journal of asthma : official journal of the Association for the Care of Asthma

2024 , Page(s) 1–13

Abstract: Objective: This study aimed to comprehensively investigate the prevalence of ABPA and AFRS, scrutinize existing diagnostic criteria and immunoassays, pinpoint their limitations, highlight ABPA as an occupational health implication, and identify ... ...

Abstract	Objective: This study aimed to comprehensively investigate the prevalence of ABPA and AFRS, scrutinize existing diagnostic criteria and immunoassays, pinpoint their limitations, highlight ABPA as an occupational health implication, and identify suggestive measures to improve ABPA diagnosis in the context of Occupational Health Nursing and primary healthcare. Data sources: The data sources such as PubMed, Health and Safety Science Abstracts, OSH Update, Medline, and Google Scholar were searched. Study selections: All published studies in the English language from 1990 till Oct, 2023 using Mesh terms keywords "Allergic bronchopulmonary aspergillosis," "Allergic fungal rhinosinusitis," "Signs and Symptoms," "Rapid Diagnostic Tests," "Diagnosis," "Occupational Health," "Occupational Health Nursing," "Prevalence," "Allergens" following "Boolean operators" search strategy were selected. Results: This review succinctly covered signs, symptoms, and prevalence data concerning ABPA and AFRS. It briefly discussed existing diagnostic criteria and immunoassays, highlighted factors influencing the assay's variability, and underscored the role and scope of specific allergens toward improved, simple, and early ABPA diagnosis. ABPA as a neglected occupational health concern was emphasized, and the importance of RDTs in the context of healthcare professionals and OHNs was stated. Finally, this study suggested analyzing the impact of compromised post-pandemic immune status and the use of immunosuppressive drugs on ABPA prevalence among vulnerable communities and occupations. Conclusion: To conclude, global and Indian ABPA and AFRS prevalence data, factors influencing existing assay variability, and the scope of improvement in RDTs for ABPA diagnosis in the background of primary healthcare professionals and OHNs were addressed.
Language	English
Publishing date	2024-01-12
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	603816-5
ISSN	1532-4303 ; 0277-0903
ISSN (online)	1532-4303
ISSN	0277-0903
DOI	10.1080/02770903.2024.2303766
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Article: ABDpred: Prediction of active antimicrobial compounds using supervised machine learning techniques.

Jana, Tanmoy / Sarkar, Debasree / Ganguli, Debayan / Mukherjee, Sandip Kumar / Mandal, Rahul Shubhra / Das, Santasabuj

The Indian journal of medical research

2024 Volume 159, Issue 1, Page(s) 78–90

Abstract: Background objectives: Discovery of new antibiotics is the need of the hour to treat infectious diseases. An ever-increasing repertoire of multidrug-resistant pathogens poses an imminent threat to human lives across the globe. However, the low success ... ...

Abstract	Background objectives: Discovery of new antibiotics is the need of the hour to treat infectious diseases. An ever-increasing repertoire of multidrug-resistant pathogens poses an imminent threat to human lives across the globe. However, the low success rate of the existing approaches and technologies for antibiotic discovery remains a major bottleneck. In silico methods like machine learning (ML) deem more promising to meet the above challenges compared with the conventional experimental approaches. The goal of this study was to create ML models that may be used to successfully predict new antimicrobial compounds. Methods: In this article, we employed eight different ML algorithms namely, extreme gradient boosting, random forest, gradient boosting classifier, deep neural network, support vector machine, multilayer perceptron, decision tree, and logistic regression. These models were trained using a dataset comprising 312 antibiotic drugs and a negative set of 936 non-antibiotic drugs in a five-fold cross validation approach. Results: The top four ML classifiers (extreme gradient boosting, random forest, gradient boosting classifier and deep neural network) were able to achieve an accuracy of 80 per cent and above during the evaluation of testing and blind datasets. Interpretation conclusions: We aggregated the top performing four models through a soft-voting technique to develop an ensemble-based ML method and incorporated it into a freely accessible online prediction server named ABDpred ( http://clinicalmedicinessd.com.in/abdpred/ ).
MeSH term(s)	Humans ; Algorithms ; Machine Learning ; Anti-Infective Agents ; Supervised Machine Learning ; Anti-Bacterial Agents/therapeutic use
Chemical Substances	Anti-Infective Agents ; Anti-Bacterial Agents
Language	English
Publishing date	2024-03-04
Publishing country	India
Document type	Journal Article
ZDB-ID	390883-5
ISSN	0971-5916 ; 0019-5340
ISSN	0971-5916 ; 0019-5340
DOI	10.4103/ijmr.ijmr_1832_22
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Article ; Online: A network biology approach to identify crucial host targets for COVID-19.

Barman, Ranjan Kumar / Mukhopadhyay, Anirban / Maulik, Ujjwal / Das, Santasabuj

Methods (San Diego, Calif.)

2022 Volume 203, Page(s) 108–115

Abstract: The ongoing global pandemic of COVID-19, caused by SARS-CoV-2 has killed more than 5.9 million individuals out of ∼43 million confirmed infections. At present, several parts of the world are encountering the 3rd wave. Mass vaccination has been started in ...

Abstract	The ongoing global pandemic of COVID-19, caused by SARS-CoV-2 has killed more than 5.9 million individuals out of ∼43 million confirmed infections. At present, several parts of the world are encountering the 3rd wave. Mass vaccination has been started in several countries but they are less likely to be broadly available for the current pandemic, repurposing of the existing drugs has drawn highest attention for an immediate solution. A recent publication has mapped the physical interactions of SARS-CoV-2 and human proteins by affinity-purification mass spectrometry (AP-MS) and identified 332 high-confidence SARS-CoV-2-human protein-protein interactions (PPIs). Here, we taken a network biology approach and constructed a human protein-protein interaction network (PPIN) with the above SARS-CoV-2 targeted proteins. We utilized a combination of essential network centrality measures and functional properties of the human proteins to identify the critical human targets of SARS-CoV-2. Four human proteins, namely PRKACA, RHOA, CDK5RAP2, and CEP250 have emerged as the best therapeutic targets, of which PRKACA and CEP250 were also found by another group as potential candidates for drug targets in COVID-19. We further found candidate drugs/compounds, such as guanosine triphosphate, remdesivir, adenosine monophosphate, MgATP, and H-89 dihydrochloride that bind the target human proteins. The urgency to prevent the spread of infection and the death of diseased individuals has prompted the search for agents from the pool of approved drugs to repurpose them for COVID-19. Our results indicate that host targeting therapy with the repurposed drugs may be a useful strategy for the treatment of SARS-CoV-2 infection.
MeSH term(s)	Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Autoantigens ; Cell Cycle Proteins ; Drug Repositioning ; Humans ; Nerve Tissue Proteins ; Pandemics ; SARS-CoV-2 ; COVID-19 Drug Treatment
Chemical Substances	Antiviral Agents ; Autoantigens ; CDK5RAP2 protein, human ; Cell Cycle Proteins ; CEP250 protein, human ; Nerve Tissue Proteins
Language	English
Publishing date	2022-03-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2022.03.016
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Article ; Online: Intranasal immunization of mice with chimera of Salmonella Typhi protein elicits protective intestinal immunity.

Chakraborty, Suparna / Dutta, Pujarini / Pal, Ananda / Chakraborty, Swarnali / Banik, George / Halder, Prolay / Gope, Animesh / Miyoshi, Shin-Ichi / Das, Santasabuj

NPJ vaccines

2024 Volume 9, Issue 1, Page(s) 24

Abstract: Development of safe, highly effective and affordable enteric fever vaccines is a global health priority. Live, oral typhoid vaccines induce strong mucosal immunity and long-term protection, but safety remains a concern. In contrast, efficacy wears off ... ...

Abstract	Development of safe, highly effective and affordable enteric fever vaccines is a global health priority. Live, oral typhoid vaccines induce strong mucosal immunity and long-term protection, but safety remains a concern. In contrast, efficacy wears off rapidly for injectable, polysaccharide-based vaccines, which elicit poor mucosal response. We previously reported Salmonella Typhi outer membrane protein, T2544 as a potential candidate for bivalent (S. Typhi and S. Paratyphi A) vaccine development. Here, we show that intranasal immunization with a subunit vaccine (chimera of T2544 and cholera toxin B subunit) induced strong systemic and intestinal mucosal immunity and protection from S. Typhi challenge in a mouse model. CTB-T2544 augmented gut-homing receptor expression on lymphocytes that produced Th1 and Th17 cytokines, secretory IgA in stool that inhibited bacterial motility and epithelial attachment, antibody recall response and affinity maturation with increased number of follicular helper T cells and CD4+ central and effector memory cells.
Language	English
Publishing date	2024-02-06
Publishing country	England
Document type	Journal Article
ISSN	2059-0105
ISSN (online)	2059-0105
DOI	10.1038/s41541-024-00812-4
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Article ; Online: A candidate glycoconjugate vaccine induces protective antibodies in the serum and intestinal secretions, antibody recall response and memory T cells and protects against both typhoidal and non-typhoidal

Haldar, Risha / Dhar, Amlanjyoti / Ganguli, Debayan / Chakraborty, Suparna / Pal, Ananda / Banik, George / Miyoshi, Shin-Ichi / Das, Santasabuj

Frontiers in immunology

2024 Volume 14, Page(s) 1304170

Abstract: ... ...

Abstract	Human
MeSH term(s)	Child ; Humans ; Animals ; Mice ; Typhoid-Paratyphoid Vaccines ; Memory T Cells ; Intestinal Secretions ; Serogroup ; Typhoid Fever ; Salmonella enteritidis ; Vaccines, Subunit ; Immunoglobulin A, Secretory ; Immunoglobulin G
Chemical Substances	Typhoid-Paratyphoid Vaccines ; Vaccines, Subunit ; Immunoglobulin A, Secretory ; Immunoglobulin G
Language	English
Publishing date	2024-01-09
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1304170
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Article: A network biology approach to identify crucial host targets for COVID-19

Barman, Ranjan Kumar / Mukhopadhyay, Anirban / Maulik, Ujjwal / Das, Santasabuj

Methods. 2022 Mar. 27,

2022

Abstract	The ongoing global pandemic of COVID-19, caused by SARS-CoV-2 has killed more than 5.9 million individuals out of ∼43 million confirmed infections. At present, several parts of the world are encountering the 3rd wave. Mass vaccination has been started in several countries but they are less likely to be broadly available for the current pandemic, repurposing of the existing drugs has drawn highest attention for an immediate solution. A recent publication has mapped the physical interactions of SARS-CoV-2 and human proteins by affinity-purification mass spectrometry (AP-MS) and identified 332 high-confidence SARS-CoV-2-human protein-protein interactions (PPIs). Here, we taken a network biology approach and constructed a human protein-protein interaction network (PPIN) with the above SARS-CoV-2 targeted proteins. We utilized a combination of essential network centrality measures and functional properties of the human proteins to identify the critical human targets of SARS-CoV-2. Four human proteins, namely PRKACA, RHOA, CDK5RAP2, and CEP250 have emerged as the best therapeutic targets, of which PRKACA and CEP250 were also found by another group as potential candidates for drug targets in COVID-19. We further found candidate drugs/compounds, such as guanosine triphosphate, remdesivir, adenosine monophosphate, MgATP, and H-89 dihydrochloride that bind the target human proteins. The urgency to prevent the spread of infection and the death of diseased individuals has prompted the search for agents from the pool of approved drugs to repurpose them for COVID-19. Our results indicate that host targeting therapy with the repurposed drugs may be a useful strategy for the treatment of SARS-CoV-2 infection.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; adenosine monophosphate ; death ; drugs ; guanosine triphosphate ; humans ; mass spectrometry ; pandemic ; protein-protein interactions ; vaccination
Language	English
Dates of publication	2022-0327
Publishing place	Elsevier Inc.
Document type	Article
Note	Pre-press version
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2022.03.016
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Article: A comparative study of sequence- and structure-based features of small RNAs and other RNAs of bacteria

Barik, Amita / Das, Santasabuj

RNA biology. 2018 Jan. 2, v. 15, no. 1

2018

Abstract: Small RNAs (sRNAs) in bacteria have emerged as key players in transcriptional and post-transcriptional regulation of gene expression. Here, we present a statistical analysis of different sequence- and structure-related features of bacterial sRNAs to ... ...

Abstract	Small RNAs (sRNAs) in bacteria have emerged as key players in transcriptional and post-transcriptional regulation of gene expression. Here, we present a statistical analysis of different sequence- and structure-related features of bacterial sRNAs to identify the descriptors that could discriminate sRNAs from other bacterial RNAs. We investigated a comprehensive and heterogeneous collection of 816 sRNAs, identified by northern blotting across 33 bacterial species and compared their various features with other classes of bacterial RNAs, such as tRNAs, rRNAs and mRNAs. We observed that sRNAs differed significantly from the rest with respect to G+C composition, normalized minimum free energy of folding, motif frequency and several RNA-folding parameters like base-pairing propensity, Shannon entropy and base-pair distance. Based on the selected features, we developed a predictive model using Random Forests (RF) method to classify the above four classes of RNAs. Our model displayed an overall predictive accuracy of 89.5%. These findings would help to differentiate bacterial sRNAs from other RNAs and further promote prediction of novel sRNAs in different bacterial species.
Keywords	Gibbs free energy ; RNA folding ; comparative study ; entropy ; gene expression regulation ; models ; prediction ; statistical analysis ; transcription (genetics)
Language	English
Dates of publication	2018-0102
Size	p. 95-103.
Publishing place	Taylor & Francis
Document type	Article
ISSN	1555-8584
DOI	10.1080/15476286.2017.1387709
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Article ; Online: Macrophage Cell Lines and Murine Infection by Salmonella enterica Serovar Typhi L-Form Bacteria.

Ganguli, Debayan / Chakraborty, Swarnali / Chakraborty, Suparna / Pal, Ananda / Gope, Animesh / Das, Santasabuj

Infection and immunity

2022 Volume 90, Issue 6, Page(s) e0011922

Abstract: Antibiotic resistance of pathogenic bacteria has emerged as a major threat to public health worldwide. While stable resistance due to the acquisition of genomic mutations or plasmids carrying antibiotic resistance genes is well established, much less is ... ...

Abstract	Antibiotic resistance of pathogenic bacteria has emerged as a major threat to public health worldwide. While stable resistance due to the acquisition of genomic mutations or plasmids carrying antibiotic resistance genes is well established, much less is known about the temporary and reversible resistance induced by antibiotic treatment, such as that due to treatment with bacterial cell wall-inhibiting antibiotics such as ampicillin. Typically, ampicillin concentration in the blood and other tissues gradually increases over time after initiation of the treatment. As a result, the bacterial population is exposed to a concentration gradient of ampicillin during the treatment of infectious diseases. This is different from
MeSH term(s)	Ampicillin/pharmacology ; Animals ; Anti-Bacterial Agents/pharmacology ; Cell Line ; Macrophages/microbiology ; Mice ; Salmonella typhi/genetics
Chemical Substances	Anti-Bacterial Agents ; Ampicillin (7C782967RD)
Language	English
Publishing date	2022-05-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218698-6
ISSN	1098-5522 ; 0019-9567
ISSN (online)	1098-5522
ISSN	0019-9567
DOI	10.1128/iai.00119-22
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Article ; Online: Susceptibility of male reproductive system to bisphenol A, an endocrine disruptor: Updates from epidemiological and experimental evidence.

Yadav, Shiv K / Bijalwan, Vandana / Yadav, Suresh / Sarkar, Kamalesh / Das, Santasabuj / Singh, Dhirendra P

Journal of biochemical and molecular toxicology

2022 Volume 37, Issue 4, Page(s) e23292

Abstract: Bisphenol A (BPA) is an omnipresent environmental pollutant. Despite being restrictions in-force for its utilization, it is widely being used in the production of polycarbonate plastics and epoxy resins. Direct, low-dose, and long-term exposure to BPA is ...

Abstract	Bisphenol A (BPA) is an omnipresent environmental pollutant. Despite being restrictions in-force for its utilization, it is widely being used in the production of polycarbonate plastics and epoxy resins. Direct, low-dose, and long-term exposure to BPA is expected when they are used in the packaging of food products and are used as containers for food consumption. Occupationally, workers are typically exposed to BPA at higher levels and for longer periods during the manufacturing process. BPA is a known endocrine disruptor chemical (EDC), that causes male infertility, which has a negative impact on human life from emotional, physical, and societal standpoints. To minimize the use of BPA in numerous consumer products, efforts and regulations are being made. Despite legislative limits in numerous nations, BPA is still found in consumer products. This paper examines BPA's overall male reproductive toxicity, including its impact on the hypothalamic-pituitary-testicular (HPT) axis, hormonal homeostasis, testicular steroidogenesis, sperm parameters, reproductive organs, and antioxidant defense system. Furthermore, this paper highlighted the role of non-monotonic dose-response (NMDR) in BPA exposure, which will help to improve the overall understanding of the harmful effects of BPA on the male reproductive system.
MeSH term(s)	Male ; Humans ; Endocrine Disruptors/toxicity ; Semen ; Genitalia, Male ; Testis ; Benzhydryl Compounds/toxicity
Chemical Substances	bisphenol A (MLT3645I99) ; Endocrine Disruptors ; Benzhydryl Compounds
Language	English
Publishing date	2022-12-16
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1410020-4
ISSN	1099-0461 ; 1095-6670
ISSN (online)	1099-0461
ISSN	1095-6670
DOI	10.1002/jbt.23292
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Article ; Online: A comparative study of sequence- and structure-based features of small RNAs and other RNAs of bacteria.

Barik, Amita / Das, Santasabuj

RNA biology

2017 Volume 15, Issue 1, Page(s) 95–103

Abstract	Small RNAs (sRNAs) in bacteria have emerged as key players in transcriptional and post-transcriptional regulation of gene expression. Here, we present a statistical analysis of different sequence- and structure-related features of bacterial sRNAs to identify the descriptors that could discriminate sRNAs from other bacterial RNAs. We investigated a comprehensive and heterogeneous collection of 816 sRNAs, identified by northern blotting across 33 bacterial species and compared their various features with other classes of bacterial RNAs, such as tRNAs, rRNAs and mRNAs. We observed that sRNAs differed significantly from the rest with respect to G+C composition, normalized minimum free energy of folding, motif frequency and several RNA-folding parameters like base-pairing propensity, Shannon entropy and base-pair distance. Based on the selected features, we developed a predictive model using Random Forests (RF) method to classify the above four classes of RNAs. Our model displayed an overall predictive accuracy of 89.5%. These findings would help to differentiate bacterial sRNAs from other RNAs and further promote prediction of novel sRNAs in different bacterial species.
MeSH term(s)	Bacteria/genetics ; Base Composition/genetics ; Base Pairing ; Gene Expression Regulation, Bacterial ; RNA, Bacterial/classification ; RNA, Bacterial/genetics ; RNA, Messenger/classification ; RNA, Messenger/genetics ; RNA, Ribosomal/classification ; RNA, Ribosomal/genetics ; RNA, Small Untranslated/classification ; RNA, Small Untranslated/genetics ; RNA, Transfer/classification ; RNA, Transfer/genetics
Chemical Substances	RNA, Bacterial ; RNA, Messenger ; RNA, Ribosomal ; RNA, Small Untranslated ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2017-11-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1555-8584
ISSN (online)	1555-8584
DOI	10.1080/15476286.2017.1387709
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