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Article ; Online: K

Sikdar, Papiya / Choudhuri, Tathagata / Paul, Suvam / Das, Sourav / Bagdi, Avik Kumar

ACS omega

2023 Volume 8, Issue 26, Page(s) 23851–23859

Abstract: A one-pot methodology has been developed to synthesize 3-halo-pyrazolo[1,5- ...

Abstract	A one-pot methodology has been developed to synthesize 3-halo-pyrazolo[1,5-
Language	English
Publishing date	2023-06-22
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.3c02270
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Article: Mutational spectrum of K-ras oncogene among Indian patients with gallbladder cancer.

Singh, Mahendra Kumar / Chetri, Kamal / Pandey, Udai Bhan / Kapoor, Vinay Kumar / Mittal, Balraj / Choudhuri, Gourdas

Journal of gastroenterology and hepatology

2004 Volume 19, Issue 8, Page(s) 916–921

Abstract: ... of dysplasia and metaplasia, mutation in the K-ras gene may be an important marker for GBC. The aim ... of the present study was to detect K-ras mutation in cytological smears from GBC.: Methods: Malignant cells ... with restriction fragment length polymorphism (RFLP) analysis was performed to detect the point mutation in codon 12 of the K-ras gene ...

Abstract	Background and aim: Gallbladder cancer (GBC) is a common abdominal malignancy in India with an obscure etiology. However, long-standing stones and chronic infection in gallbladder have been suspected as possible etiologic factors. As carcinogenesis complicating chronic inflammation proceeds through the stages of dysplasia and metaplasia, mutation in the K-ras gene may be an important marker for GBC. The aim of the present study was to detect K-ras mutation in cytological smears from GBC. Methods: Malignant cells were marked on slides of cytological smears obtained from 39 patients with cytologically proven GBC. Marked cells were scraped off and DNA was extracted. Polymerase chain reaction coupled with restriction fragment length polymorphism (RFLP) analysis was performed to detect the point mutation in codon 12 of the K-ras gene. Results: Mutation in codon 12 of K-ras oncogene was detected in eight (38%) of 21 PCR amplified samples by this technique. Six of eight specimens with K-ras (codon 12) mutation corresponded to coexisting gallstone disease. Five patients with K-ras (codon 12) mutation were found to have stage IV malignancy. Conclusions: Mutation in codon 12 of the K-ras oncogene occurs in more than one-third of GBC in northern India. Its detection from fine-needle aspirates may prove useful as an adjunct to cytological examination. The presence of this mutation suggests that chronic inflammation may play an etiologic role in gallbladder carcinogenesis.
MeSH term(s)	Adult ; Aged ; Carcinoma/epidemiology ; Carcinoma/genetics ; Carcinoma/pathology ; DNA Mutational Analysis ; DNA, Neoplasm/analysis ; Female ; Gallbladder Neoplasms/epidemiology ; Gallbladder Neoplasms/genetics ; Gallbladder Neoplasms/pathology ; Genes, ras/genetics ; Humans ; Incidence ; India/epidemiology ; Male ; Middle Aged ; Mutation ; Neoplasm Staging ; Polymerase Chain Reaction
Chemical Substances	DNA, Neoplasm
Language	English
Publishing date	2004-08
Publishing country	Australia
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	632882-9
ISSN	0815-9319
ISSN	0815-9319
DOI	10.1111/j.1440-1746.2004.03355.x
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Article ; Online: CodonU: A Python Package for Codon Usage Analysis.

Choudhuri, Souradipto / Sau, Keya

IEEE/ACM transactions on computational biology and bioinformatics

2024 Volume 21, Issue 1, Page(s) 36–44

Abstract: Codon Usage Analysis (CUA) has been accompanied by several web servers and independent programs written in several programming languages. Also this diversity speaks for the need of a reusable software that can be helpful in reading, manipulating and ... ...

Abstract	Codon Usage Analysis (CUA) has been accompanied by several web servers and independent programs written in several programming languages. Also this diversity speaks for the need of a reusable software that can be helpful in reading, manipulating and acting as a pipeline for such data and file formats. This kind of analyses use multiple tools to address the multifaceted aspects of CUA. So, we propose CodonU, a package written in Python language to integrate all aspects. It is compatible with existing file formats and can be used solely or with a group of other such packages. The proposed package incorporates various statistical measures necessary for codon usage analysis. The measures vary with nature of the sequences, viz. for nucleotide, codon adaptation index (CAI), codon bias index (CBI), tRNA adaptation index (tAI) etc. and for protein sequences Gravy score etc. Users can also perform the correspondence analysis (COA). This package also provides the liberty to generate graphics to users, and also develop phylogenetic tree. Capabilities of the proposed package were checked thoroughly on a genomic set of Staphylococcus aureus.
MeSH term(s)	Codon Usage ; Phylogeny ; Software ; Programming Languages ; Codon/genetics
Chemical Substances	Codon
Language	English
Publishing date	2024-02-05
Publishing country	United States
Document type	Journal Article
ISSN	1557-9964
ISSN (online)	1557-9964
DOI	10.1109/TCBB.2023.3335823
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Article: Effect of pyrethrum on CNS and haemolymph monovalent (Na(+), K(+)) cations and also on the level of CNS acetylcholine and activities of esterase and choline acetyltransferase in the insect Schizodactylus monstrosus drury.

Banerjee, U / Choudhuri, D K

Neurochemistry international

2009 Volume 10, Issue 2, Page(s) 135–141

Abstract: ... K(+)) concentrations and also to examine changes in acetylcholine concentration and the activities ...

Abstract	The organic compound pyrethrum is recognised as a highly neurotoxic insecticide. Experiments were conducted to see whether the substance influences the central nervous system and haemolymph cationic (Na(+), K(+)) concentrations and also to examine changes in acetylcholine concentration and the activities of esterase and choline acetyltransferase. Pyrethrum treatment exhibits dissimilar changes in respect of sodium and potassium ion concentrations in the haemolymph and CNS of the carnivorous, orthopteran insect Schizodactylus monstrosus. Application of pyrethrum insecticides decreased the activities of esterase and choline acetyltransferase but increased the concentrations of acetylcholine. The release of the neurotransmitter acetylcholine is related to the ionic balance in the nerve membrane. The changes in the level of both sodium and potassium when exposed to pyrethrum impair the ionic balance in the nerve membrane, and for that matter the nerve conductor is blocked due to non release of acetylcholine ultimately causing paralysis of the insect concerned.
Language	English
Publishing date	2009-11-16
Publishing country	England
Document type	Journal Article
ZDB-ID	283190-9
ISSN	1872-9754 ; 0197-0186
ISSN (online)	1872-9754
ISSN	0197-0186
DOI	10.1016/0197-0186(87)90120-3
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Article: Membrane positioning across antigen-induced synaptic contacts tunes CAR-T cell signaling and effector responses.

Li, Fenglei / Choudhuri, Kaushik

bioRxiv : the preprint server for biology

2023

Abstract: Tumor antigen recognition by chimeric antigen receptors (CAR) triggers phosphorylation of their cytoplasmic portions resulting in CAR-T cell activation. We and others have shown that immunoreceptor triggering depends on the formation of close synaptic ... ...

Abstract	Tumor antigen recognition by chimeric antigen receptors (CAR) triggers phosphorylation of their cytoplasmic portions resulting in CAR-T cell activation. We and others have shown that immunoreceptor triggering depends on the formation of close synaptic contacts, determined by the span of immunoreceptor-ligand complexes, from which large inhibitory phosphatases such as CD45 are sterically excluded. Here, we show, varying CAR-antigen complex span, that CAR-T cell activation depends on a formation of close contacts with target cells. CAR-antigen complexes with a span of 4 immunoglobulin superfamily (IgSF) domains maximize CAR-T cell activation, closely matching the span of endogenous TCR-pMHC complexes. Longer CAR-antigen complexes precipitously reduced triggering and cytokine production, but notably, anti-tumor cytotoxicity was largely preserved due to a ∼10-fold lower signaling threshold for mobilization of cytolytic effector function. Increased intermembrane spacing disrupted short-spanned PD-1-PD- L1 interactions, reducing CAR-T cell exhaustion. Together, our results show that membrane positioning across the immunological synapse can be engineered to generate CAR-T cells with clinically desirable functional profiles
Language	English
Publishing date	2023-10-02
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.10.01.560371
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Article ; Online: A novel tin based hydroxamic acid complex induces apoptosis through redox imbalance and targets Stat3/JNK1/MMP axis to overcome drug resistance in cancer.

Banerjee, Kaushik / Choudhuri, Soumitra Kumar

Free radical research

2022 Volume 55, Issue 9-10, Page(s) 1018–1035

Abstract: Undesired toxicity and emergence of multidrug resistance (MDR) are the major impediments to the successful application of organotin-based compounds against cancer. Since oxalyl-bis(N-phenyl)hydroxamic acid (OBPHA) exerts significant efficacy against ... ...

Abstract	Undesired toxicity and emergence of multidrug resistance (MDR) are the major impediments to the successful application of organotin-based compounds against cancer. Since oxalyl-bis(N-phenyl)hydroxamic acid (OBPHA) exerts significant efficacy against cancer, we believe that derivatives of OBPHA including organotin molecule can show a promising effect against cancer. Herein, we have selected three previously characterized OBPHA derivatives viz., succinyl-bis(N-phenyl)hydroxamic acid (SBPHA), diphenyl-tin succinyl-bis(N-phenyl)hydroxamic acid (Sn-SBPHA), malonyl-bis(N-phenyl)hydroxamic acid (MBPHA) and evaluated their antiproliferative efficacy against both drug-resistant (CEM/ADR5000; EAC/Dox) and sensitive (CCRF-CEM; HeLa; EAC/S) cancers. Data revealed that Sn-SBPHA selectively targets drug-resistant and sensitive cancers without inducing any significant toxicity to normal cells (Chang Liver). Moreover, shortening of the backbone of SBPHA enhances the efficacy of the newly formed molecule MBPHA by targeting only drug-sensitive cancers. Sn-SBPHA induces caspase3-dependent apoptosis through redox-imbalance in both drug-resistant and sensitive cancer. Sn-SBPHA also reduced the activation and expression of both MMP2 and MMP9 without altering the expression status of TIMP1 and TIMP2 in drug-resistant cancer. In addition, Sn-SBPHA reduced the activation of both STAT3 and JNK1, the transcriptional modulator of MMPs, in a redox-dependent manner in CEM/ADR5000 cells. Thus, Sn-SBPHA targets MMPs by modulating STAT3 and JNK1 in a redox-dependent manner. However, MBPHA and SBPHA fail to target drug resistance and both drug-resistant and sensitive cancer respectively. Furthermore, Sn-SBPHA significantly increases the lifespan of doxorubicin-resistant and sensitive Ehrlich Ascites Carcinoma-bearing mice without inducing any significant systemic toxicity. Therefore, Sn-SBPHA has the therapeutic potential to target and overcome MDR in cancer.
MeSH term(s)	Animals ; Apoptosis ; Cell Line, Tumor ; Doxorubicin/pharmacology ; Drug Resistance, Neoplasm ; Humans ; Hydroxamic Acids/pharmacology ; Matrix Metalloproteinases/metabolism ; Mice ; Neoplasms/drug therapy ; Oxidation-Reduction ; Reactive Oxygen Species/metabolism ; STAT3 Transcription Factor/metabolism ; Tin/metabolism ; Tin/pharmacology
Chemical Substances	Hydroxamic Acids ; Reactive Oxygen Species ; STAT3 Transcription Factor ; STAT3 protein, human ; Tin (7440-31-5) ; Doxorubicin (80168379AG) ; Matrix Metalloproteinases (EC 3.4.24.-)
Language	English
Publishing date	2022-01-17
Publishing country	England
Document type	Journal Article
ZDB-ID	1194130-3
ISSN	1029-2470 ; 1071-5762
ISSN (online)	1029-2470
ISSN	1071-5762
DOI	10.1080/10715762.2021.2013480
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Article: MPO Expression of Background Neutrophils in MPO Negative Acute Promyelocytic Leukemia, An Easy Clue to Corroborate a Challenging Diagnosis: A Case Report and Review of Literature.

Krishnamurthy, Kritika / Choudhuri, Jui / Ramesh, K H / Wang, Yanhua

Case reports in hematology

2023 Volume 2023, Page(s) 7979261

Abstract: Acute promyelocytic leukemia (APL) is characterized by the pathogenic driver fusion transcript PML-RARA resulting from the t(15;17) translocation. Early recognition of APL with prompt ATRA induction has a decisive impact on the early death rate. The ... ...

Abstract	Acute promyelocytic leukemia (APL) is characterized by the pathogenic driver fusion transcript PML-RARA resulting from the t(15;17) translocation. Early recognition of APL with prompt ATRA induction has a decisive impact on the early death rate. The preliminary diagnosis of APL relies heavily on cytomorphology and flow cytometry. In APL with variant morphology, such as the microgranular variant, immunophenotype, especially the bright MPO positivity is the basis of diagnosis. Till date, only five cases of APL with reduced/absent MPO have been described in literature. The identification of MPO deficiency based on genetic testing would involve at the least a MPO gene scanning with NGS, followed by microarray to identify somatic uniparental disomy in heterozygotes. This testing is not only redundant given the scant clinical implications of heterozygous MPO deficiency but also time consuming. An easy way to identify background MPO deficiency confounding the immunophenotype of a myeloid neoplasm is the MPO expression in background neutrophils gated on the initial flow cytometry. A dim MPO in the background neutrophils, in the morphological setting of APL, can identify underlying MPO deficiency, clarifying the immunophenotypic ambiguity and thus establishing an unequivocal diagnosis as seen in the current case.
Language	English
Publishing date	2023-12-26
Publishing country	United States
Document type	Case Reports
ZDB-ID	2627639-2
ISSN	2090-6579 ; 2090-6560
ISSN (online)	2090-6579
ISSN	2090-6560
DOI	10.1155/2023/7979261
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Article ; Online: UK prescribing practice of anticoagulants in patients with chronic kidney disease: a nephrology and haematology-based survey.

Parker, Kathrine / Choudhuri, Satarupa / Lewis, Penny / Thachil, Jecko / Mitra, Sandip

BMC nephrology

2023 Volume 24, Issue 1, Page(s) 9

Abstract: A survey to gain insight into anticoagulant prescribing practice in the setting of chronic kidney disease (CKD) across the UK was disseminated via renal and haematology networks. Areas of anticoagulant use included patients with venous thromboembolism ( ... ...

Abstract	A survey to gain insight into anticoagulant prescribing practice in the setting of chronic kidney disease (CKD) across the UK was disseminated via renal and haematology networks. Areas of anticoagulant use included patients with venous thromboembolism (VTE), requiring thromboprophylaxis for VTE, Atrial Fibrillation (AF) and nephrotic syndrome.An online-survey was disseminated via British Haematology Society, UK Kidney Association, and Renal Pharmacy Group over a five month period. All responses were voluntary and anonymous.Among 117 responses there were 49 nephrology doctors, 47 renal pharmacists and 20 haematology clinicians. A specialist multidisciplinary team to discuss the specific anticoagulant management of these patients was only available to 3% (4/117) respondents. Renal function estimate used for anticoagulant dosing was mainly Cockcroft-Gault for pharmacists and haematology but lab-based estimates were used by nephrology doctors. Therapeutic dose of Low Molecular Weight Heparin was mostly likely to be reduced by one-third when used for VTE treatment, with the majority of units undertaking anti-Xa monitoring in CKD stage 5 and dialysis. Direct-acting Oral Anticoagulants are being used in patients with nephrotic syndrome, those with CKD stage 5 and on dialysis for VTE and AF in the absence of license in these indications.This survey highlighted the significant differences between anticoagulant prescribing in CKD between two professional specialties and marked variation between centres in anticoagulant management strategies employed for these patients. With gaps still existing in the evidence base and answers to these not expected within the next few years, development of a best-practice guideline would be warranted to support clinicians in this field.
MeSH term(s)	Humans ; Anticoagulants/therapeutic use ; Venous Thromboembolism/drug therapy ; Venous Thromboembolism/prevention & control ; Nephrology ; Nephrotic Syndrome/drug therapy ; Renal Dialysis ; Renal Insufficiency, Chronic/complications ; Renal Insufficiency, Chronic/drug therapy ; Renal Insufficiency, Chronic/epidemiology ; Atrial Fibrillation/drug therapy ; Heparin, Low-Molecular-Weight/therapeutic use ; Kidney Failure, Chronic/drug therapy ; Surveys and Questionnaires ; Hematology ; United Kingdom/epidemiology ; Administration, Oral
Chemical Substances	Anticoagulants ; Heparin, Low-Molecular-Weight
Language	English
Publishing date	2023-01-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2041348-8
ISSN	1471-2369 ; 1471-2369
ISSN (online)	1471-2369
ISSN	1471-2369
DOI	10.1186/s12882-022-03041-w
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Article ; Online: Synthetic antioxidants from a natural source can overtake the oncogenic stress management system and activate the stress‑sensitized death of KSHV‑infected cancer cells.

Das, Piyanki / Brahmachari, Goutam / Chatterjee, Koustav / Choudhuri, Tathagata

International journal of molecular medicine

2022 Volume 50, Issue 3

Abstract: Synthetic and modified natural derivatives are reported as potential bioactive compounds and are being used therapeutically against various diseases in a widespread manner nowadays. Cancerous cells exhibit high levels of reactive oxygen species (ROS) ... ...

Abstract	Synthetic and modified natural derivatives are reported as potential bioactive compounds and are being used therapeutically against various diseases in a widespread manner nowadays. Cancerous cells exhibit high levels of reactive oxygen species (ROS) internally, and thus successfully manage to sustain themselves and proliferate via antioxidative mechanisms that maintain a redox balance. On this note, various antioxidants are applied as anticancer compounds, which strategically affects the ongoing oncogenic stress management system in both a pro‑ and antioxidative manner, resulting in cancer restriction, as well as sustaining cell proliferation via antioxidative mechanisms that promote cancer progression. Alike non‑viral cancers, viral cancers exhibit varying levels of ROS during different stages of cancer progression. Hence, successful stress balance should be addressed, depending on the cancer cell stress response during the therapeutic management. The application of antioxidants is crucial and needs to be carefully designed in such cases; the respective underlying mechanisms are less understood. The role of antioxidants controlling the varied levels of stress response at different stages of Kaposi's sarcoma‑associated herpes virus malignancy have not been fully reported. Therefore, the present study aimed to analyze the activity of certain antioxidants in KSHV‑infected oncogenic cells. For this purpose, two naturally derived flavonoid‑based antioxidants (theaflavin and novel curcumin derivatives) were selected and tested in different KSHV‑infected cell lines. The findings presented herein demonstrate that these compounds can successfully induce the death of different KSHV‑positive cells and can restrict the growth of KSHV‑infected cell lines restricting viral reactivation by counteracting the oncogenic stress management system.
MeSH term(s)	Antioxidants/metabolism ; Antioxidants/pharmacology ; Antioxidants/therapeutic use ; Carcinogenesis ; Herpesvirus 8, Human/metabolism ; Humans ; Neoplasms/metabolism ; Oxidation-Reduction ; Oxidative Stress ; Reactive Oxygen Species/metabolism
Chemical Substances	Antioxidants ; Reactive Oxygen Species
Language	English
Publishing date	2022-07-20
Publishing country	Greece
Document type	Journal Article
ZDB-ID	1444428-8
ISSN	1791-244X ; 1107-3756
ISSN (online)	1791-244X
ISSN	1107-3756
DOI	10.3892/ijmm.2022.5173
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Article ; Online: Ambient stable solution-processed organic field effect transistors from electron deficient planar aromatics: effect of end-groups on ambient stability.

Giri, Indrajit / Biswas, Sagar / Chhetri, Shant / Choudhuri, Anwesha / Mondal, Indrajit / Senanayak, Satyaprasad P / Iyer, Parameswar Krishnan / Chaudhuri, Debangshu / Vijayaraghavan, Ratheesh K

RSC advances

2024 Volume 14, Issue 11, Page(s) 7915–7923

Abstract: Ambient stable solution processed n-channel organic field effect transistors (OFETs) are essential for next-generation low-cost organic electronic devices. Several molecular features, such as suitable orbital energy levels, easy synthetic steps, ...

Abstract	Ambient stable solution processed n-channel organic field effect transistors (OFETs) are essential for next-generation low-cost organic electronic devices. Several molecular features, such as suitable orbital energy levels, easy synthetic steps,
Language	English
Publishing date	2024-03-06
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d4ra01499e
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