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Article ; Online: Advanced Proteomics and Cluster Analysis for Identifying Novel Obstructive Sleep Apnea Subtypes before and after Continuous Positive Airway Pressure Therapy.

Kundel, Vaishnavi / Cohen, Oren / Khan, Samira / Patel, Manishkumar / Kim-Schulze, Seunghee / Kovacic, Jason / Suárez-Fariñas, Mayte / Shah, Neomi A

Annals of the American Thoracic Society

2023 Volume 20, Issue 7, Page(s) 1038–1047

Abstract: Rationale: ...

Abstract	Rationale:
MeSH term(s)	Adult ; Humans ; Female ; Middle Aged ; Male ; Continuous Positive Airway Pressure/methods ; Proteomics ; Sleep Apnea, Obstructive/therapy ; Cluster Analysis ; Biomarkers
Chemical Substances	Biomarkers
Language	English
Publishing date	2023-02-13
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2717461-X
ISSN	2325-6621 ; 1943-5665 ; 2325-6621
ISSN (online)	2325-6621 ; 1943-5665
ISSN	2325-6621
DOI	10.1513/AnnalsATS.202210-897OC
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Article ; Online: Field evaluation of the entomopathogenic fungi enriched with organic amendments against Holotrichia consanguinea Blanchard (Coleoptera

Prakash S. Patel / Sushma Deb / Prakash H. Rabari / Manishkumar J. Joshi

Egyptian Journal of Biological Pest Control, Vol 32, Iss 1, Pp 1-

Scarabaeidae) infesting groundnut crop

2022 Volume 11

Abstract: Abstract Background White grubs are highly polyphagous and most destructive soil pests inflicting damage to a groundnut crop that causes economic yield losses in commercial groundnut production in India. In this study, potential of the two ... ...

Abstract	Abstract Background White grubs are highly polyphagous and most destructive soil pests inflicting damage to a groundnut crop that causes economic yield losses in commercial groundnut production in India. In this study, potential of the two entomopathogenic fungi (EPF) viz., Metarhizium anisopliae (Metchnikoff) Sorokin and Beauveria bassiana (Balsamo) Vuillemin enriched with organic amendments like neem cake, castor cake, vermicompost and poultry manure was evaluated to manage buildup of white grub population in groundnut crop. Results Results showed that the plot treated with soil application of vermicompost @ 1 ton/ha + M. anisopliae 1.15 WP (1 × 108 cfu/g) @ 2 kg/ha showed the least amount of plant mortality due to white grub which was at par with castor cake @ 1 ton/ha + M. anisopliae 1.15 WP (1 × 108 cfu/g) @ 2 kg/ha and neem cake @ 1 ton/ha + M. anisopliae 1.15 WP (1 × 108 cfu/g) @ 2 kg/ha which showed only 1.74, 2.00 and 2.24% plant damage, respectively. Plots treated with vermicompost @ 1 ton/ha + M. anisopliae 1.15 WP (1 × 108 cfu/g) @ 2 kg/ha had the fewest (0.19) white grubs per one meter row length. Based on highest pod yield, net realization and net gain, the treatment with soil application of vermicompost @ 1 ton/ha + M. anisopliae 1.15 WP (1 × 108 cfu/g) @ 2 kg/ha was found most effective treatments for the management of white grub in groundnut. Conclusions Results indicated that M. anisopliae supplemented with various organic amendments, such as vermicompost, castor cake, and neem cake can be commercialized as a healthy alternative to minimize the use of synthetic pesticides in groundnut crops for white grub management.
Keywords	Entomopathogenic fungi ; Metarhizium anisopliae ; Beauveria bassiana ; Vermicompost ; Neem cake ; White grub ; Agriculture ; S
Subject code	630
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	SpringerOpen
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Dexamethasone and overall survival and progression free survival in patients with newly diagnosed glioblastoma: a meta-analysis.

Arora, Harshit / Mammi, Marco / Patel, Naisargi Manishkumar / Zyfi, Dea / Dasari, Hema Reddy / Yunusa, Ismael / Simjian, Thomas / Smith, Timothy R / Mekary, Rania A

Journal of neuro-oncology

2023 Volume 166, Issue 1, Page(s) 17–26

Abstract: Purpose: Glioblastomas, the most common primary malignant brain tumors in adults, still hold poor prognosis. Corticosteroids, such as dexamethasone, are usually prescribed to reduce peritumoral edema and limit neurological symptoms, although potential ... ...

Abstract	Purpose: Glioblastomas, the most common primary malignant brain tumors in adults, still hold poor prognosis. Corticosteroids, such as dexamethasone, are usually prescribed to reduce peritumoral edema and limit neurological symptoms, although potential detrimental effects of these drugs have been described. The present meta-analysis aimed to explore the association of dexamethasone with overall survival (OS) and progression free survival (PFS) in patients with newly diagnosed glioblastoma. Methods: PubMed, Cochrane Library, Embase, and ClinicalTrials.gov were searched for pertinent studies following the Preferred Reporting Items of Systematic Review and Meta-Analysis checklist. Pooled multivariable-adjusted hazard ratios (HR) for OS and PFS and their associated 95% confidence intervals (CIs) were calculated using the random-effects model and the heterogeneity among studies was assessed using I Results: Seven studies were included, pooling data of 1,257 patients, with age varying from 11 to 81 years. Glioblastoma patients on pre- or peri-operative dexamethasone were associated with a significantly poorer overall survival (HR: 1.33, 95% CI: 1.15, 1.55; 7 studies; I Conclusion: Dexamethasone appeared to be associated with poor survival outcomes of glioblastoma patients.
MeSH term(s)	Adult ; Humans ; Child ; Adolescent ; Young Adult ; Middle Aged ; Aged ; Aged, 80 and over ; Glioblastoma/drug therapy ; Progression-Free Survival ; Dexamethasone/therapeutic use ; Disease-Free Survival
Chemical Substances	Dexamethasone (7S5I7G3JQL)
Language	English
Publishing date	2023-12-27
Publishing country	United States
Document type	Meta-Analysis ; Systematic Review ; Journal Article ; Review
ZDB-ID	604875-4
ISSN	1573-7373 ; 0167-594X
ISSN (online)	1573-7373
ISSN	0167-594X
DOI	10.1007/s11060-023-04549-3
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Article ; Online: Clenbuterol attenuates immune reaction to lipopolysaccharide and its relationship to anhedonia in adolescents.

Nguyen, Tram N B / Ely, Benjamin A / Pick, Danielle / Patel, Manishkumar / Xie, Hui / Kim-Schulze, Seunghee / Gabbay, Vilma

Brain, behavior, and immunity

2022 Volume 106, Page(s) 89–99

Abstract: While inflammation has been implicated in psychopathology, relationships between immune-suppressing processes and psychiatric constructs remain elusive. This study sought to assess whether ... ...

Abstract	While inflammation has been implicated in psychopathology, relationships between immune-suppressing processes and psychiatric constructs remain elusive. This study sought to assess whether β
MeSH term(s)	Anhedonia ; Biomarkers ; Chemokine CCL3 ; Chemokine CCL4 ; Chemokine CXCL10 ; Clenbuterol/pharmacology ; Cytokines/metabolism ; Epidermal Growth Factor ; Humans ; Interleukin 1 Receptor Antagonist Protein ; Interleukin-6 ; Lipopolysaccharides/pharmacology ; Transforming Growth Factor alpha ; Tumor Necrosis Factor-alpha
Chemical Substances	Biomarkers ; Chemokine CCL3 ; Chemokine CCL4 ; Chemokine CXCL10 ; Cytokines ; Interleukin 1 Receptor Antagonist Protein ; Interleukin-6 ; Lipopolysaccharides ; Transforming Growth Factor alpha ; Tumor Necrosis Factor-alpha ; Epidermal Growth Factor (62229-50-9) ; Clenbuterol (XTZ6AXU7KN)
Language	English
Publishing date	2022-07-29
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	639219-2
ISSN	1090-2139 ; 0889-1591
ISSN (online)	1090-2139
ISSN	0889-1591
DOI	10.1016/j.bbi.2022.07.163
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Article ; Online: Multimodal single-cell analyses reveal mechanisms of perianal fistula in diverse patients with Crohn's disease.

Levantovsky, Rachel M / Tastad, Christopher / Zhang, Jiayu / Gettler, Kyle / Sabic, Ksenija / Werner, Robert / Chasteau, Colleen / Korie, Ujunwa / Paguay, Diana / Bao, Michelle / Han, Huajun / Maskey, Neha / Talware, Sayali / Patel, Manishkumar / Argmann, Carmen / Suarez-Farinas, Mayte / Harpaz, Noam / Chuang, Ling-Shiang / Cho, Judy H

Med (New York, N.Y.)

2024

Abstract: Background: Crohn's disease complicated by perianal fistulae is more prevalent and severe in patients of African ancestry.: Methods: We profiled single cells from diverse patients with Crohn's disease with perianal fistula from colorectal mucosa and ... ...

Abstract	Background: Crohn's disease complicated by perianal fistulae is more prevalent and severe in patients of African ancestry. Methods: We profiled single cells from diverse patients with Crohn's disease with perianal fistula from colorectal mucosa and fistulous tracts. Immunofluorescence was performed to validate predicted cell-cell interactions. Unstimulated monocytes were chronically cultured in diverse cohorts. A subset was analyzed by single-nucleus RNA + ATAC sequencing. Findings: Fistulous tract cells from complete proctectomies demonstrated enrichment of myeloid cells compared to paired rectal tissues. Ligand-receptor analysis highlights myeloid-stromal cross-talk and cellular senescence, with cellular co-localization validated by immunofluorescence. Chitinase-3 like-protein-1 (CHI3L1) is a top upregulated gene in stromal cells from fistulae expressing both destructive and fibrotic gene signatures. Monocyte cultures from patients of African ancestry and controls demonstrated differences in CHI3L1 and oncostatin M (OSM) expression upon differentiation compared to individuals of European ancestry. Activating protein-1 footprints are present in ATAC-seq peaks in stress response genes, including CHI3L1 and OSM; genome-wide chromatin accessibility including JUN footprints was observed, consistent with reported mechanisms of inflammatory memory. Regulon analyses confirm known cell-specific transcription factor regulation and implicate novel ones in fibroblast subsets. All pseudo-bulked clusters demonstrate enrichment of genetic loci, establishing multicellular contributions. In the most significant African American Crohn's genetic locus, upstream of prostaglandin E receptor 4, lymphoid-predominant ATAC-seq peaks were observed, with predicted RORC footprints. Conclusions: Population differences in myeloid-stromal cross-talk implicate fibrotic and destructive fibroblasts, senescence, epigenetic memory, and cell-specific enhancers in perianal fistula pathogenesis. The transcriptomic and epigenetic data provided here may guide optimization of promising mesenchymal stem cell therapies for perianal fistula. Funding: This work was supported by grants U01DK062422, U24DK062429, and R01DK123758.
Language	English
Publishing date	2024-04-18
Publishing country	United States
Document type	Journal Article
ISSN	2666-6340
ISSN (online)	2666-6340
DOI	10.1016/j.medj.2024.03.021
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Article ; Online: Host metabolome predicts the severity and onset of acute toxicities induced by CAR T-cell therapy.

Jalota, Akansha / Hershberger, Courtney E / Patel, Manishkumar S / Mian, Agrima / Faruqi, Aiman / Khademi, Gholamreza / Rotroff, Daniel M / Hill, Brian T / Gupta, Neetu

Blood advances

2022 Volume 7, Issue 17, Page(s) 4690–4700

Abstract: Anti-CD19 chimeric antigen receptor (CAR) T-cell therapy is a highly effective treatment option for patients with relapsed/refractory large B-cell lymphoma. However, widespread use is deterred by the development of clinically significant acute ... ...

Abstract	Anti-CD19 chimeric antigen receptor (CAR) T-cell therapy is a highly effective treatment option for patients with relapsed/refractory large B-cell lymphoma. However, widespread use is deterred by the development of clinically significant acute inflammatory toxicities, including cytokine release syndrome (CRS) and immune effector cell-associated neurotoxicity syndrome (ICANS), that induce significant morbidity and require close monitoring. Identification of host biochemical signatures that predict the severity and time-to-onset of CRS and ICANS may assist patient stratification to enable timely mitigation strategies. Here, we report pretreatment host metabolites that are associated with CRS and ICANS induced by axicabtagene ciloleucel or tisagenlecleucel therapy. Both untargeted metabolomics analysis and validation using targeted assays revealed a significant association between the abundance of specific pretreatment biochemical entities and an increased risk and/or onset of clinically significant CRS (q < .1) and ICANS (q < .25). Higher pretreatment levels of plasma glucose and lower levels of cholesterol and glutamate were associated with a faster onset of CRS. In contrast, low baseline levels of the amino acids proline and glycine and the secondary bile acid isoursodeoxycholate were significantly correlated with clinically significant CRS. Lower concentration of the amino acid hydroxyproline was associated with higher grade and faster onset of ICANS, whereas low glutamine was negatively correlated with faster development of ICANS. Overall, our data indicate that the pretreatment host metabolome has biomarker potential in determining the risk of clinically significant CRS and ICANS, and may be useful in risk stratification of patients before anti-CD19 CAR T-cell therapy.
MeSH term(s)	Humans ; Immunotherapy, Adoptive/adverse effects ; Metabolome ; Metabolomics ; Adaptor Proteins, Signal Transducing ; Antigens, CD19 ; Cytokine Release Syndrome
Chemical Substances	cell-associated neurotoxicity ; Adaptor Proteins, Signal Transducing ; Antigens, CD19
Language	English
Publishing date	2022-11-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2915908-8
ISSN	2473-9537 ; 2473-9529
ISSN (online)	2473-9537
ISSN	2473-9529
DOI	10.1182/bloodadvances.2022007456
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Article ; Online: Design, synthesis, and evaluation of 4,5,6,7-tetrahydrobenzo[

Pardhi, Triveni R / Patel, Manishkumar S / Sudarsanam, V / Vasu, Kamala K

MedChemComm

2018 Volume 9, Issue 9, Page(s) 1472–1490

Abstract: Casein kinase 2 (CK2) and glycogen synthase kinase-3beta (GSK3β) are responsible for the phosphorylation of a tumor suppressor protein (PTEN) in a cooperative manner which causes its deactivation. Thus, it is essential to inhibit both kinases ... ...

Abstract	Casein kinase 2 (CK2) and glycogen synthase kinase-3beta (GSK3β) are responsible for the phosphorylation of a tumor suppressor protein (PTEN) in a cooperative manner which causes its deactivation. Thus, it is essential to inhibit both kinases simultaneously to prevent PTEN deactivation more efficiently. In this study, we have designed a novel lead from Hit15 which was identified
Language	English
Publishing date	2018-07-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2545949-1
ISSN	2040-2511 ; 2040-2503
ISSN (online)	2040-2511
ISSN	2040-2503
DOI	10.1039/c8md00321a
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Article ; Online: Antitumor immunity as the basis for durable disease-free treatment-free survival in patients with metastatic urothelial cancer.

Anker, Jonathan / Pal, Sumanta K / Kim-Schulze, Seunghee / Wang, Huan / Halperin, Rebecca / Uzilov, Andrew / Imai, Naoko / Eikawa, Shingo / Saito, Takuro / Sebra, Robert / Hahn, Noah M / Patel, Manishkumar / Qi, Jingjing / Xie, Hui / Bhardwaj, Nina / Gnjatic, Sacha / Galsky, Matthew D

Journal for immunotherapy of cancer

2023 Volume 11, Issue 8

Abstract: Cisplatin-based chemotherapy has been associated with durable disease control in a small subset of patients with metastatic urothelial cancer. However, the mechanistic basis for this phenomenon has remained elusive. Antitumor immunity may underlie these ... ...

Abstract	Cisplatin-based chemotherapy has been associated with durable disease control in a small subset of patients with metastatic urothelial cancer. However, the mechanistic basis for this phenomenon has remained elusive. Antitumor immunity may underlie these exceptional responders. In a phase II trial evaluating a phased schedule of gemcitabine and cisplatin followed by gemcitabine and cisplatin with ipilimumab for metastatic urothelial cancer, 4 of 36 patients achieved durable disease-free treatment-free survival (DDFTFS) and remain in remission over 5 years after enrolment on the study. We sought to identify the genomic and immunological mechanisms associated with functional cures of such patients. Whole exome sequencing was performed on pretreatment archival tumor tissue. Neoantigen prediction and ranking were performed using a novel pipeline. For a subset of patients with available biospecimens, selected peptides were tested for neoantigen-specific T cell reactivity in peripheral blood CD4
MeSH term(s)	Humans ; CD8-Positive T-Lymphocytes ; Cisplatin/therapeutic use ; Ipilimumab/therapeutic use ; Proteomics ; Disease-Free Survival ; Carcinoma, Transitional Cell/drug therapy
Chemical Substances	Cisplatin (Q20Q21Q62J) ; Ipilimumab
Language	English
Publishing date	2023-08-22
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2719863-7
ISSN	2051-1426 ; 2051-1426
ISSN (online)	2051-1426
ISSN	2051-1426
DOI	10.1136/jitc-2023-007613
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Article ; Online: Urine supernatant reveals a signature that predicts survival in clear-cell renal cell carcinoma.

Daza, Jorge / Salomé, Bérengère / Okhawere, Kennedy / Bane, Octavia / Meilika, Kirolos N / Korn, Talia G / Qi, Jingjing / Xe, Hui / Patel, Manishkumar / Brody, Rachel / Kim-Schulze, Seunghee / Sfakianos, John P / Lewis, Sara / Rich, Jordan M / Zuluaga, Laura / Badani, Ketan K / Horowitz, Amir

BJU international

2023 Volume 132, Issue 1, Page(s) 75–83

Abstract: Objective: To profile the cell-free urine supernatant and plasma of a small cohort of clear-cell renal cell carcinoma (ccRCC) patients by measuring the relative concentrations of 92 proteins related to inflammation. Using The Cancer Genome Atlas (TCGA), ...

Abstract	Objective: To profile the cell-free urine supernatant and plasma of a small cohort of clear-cell renal cell carcinoma (ccRCC) patients by measuring the relative concentrations of 92 proteins related to inflammation. Using The Cancer Genome Atlas (TCGA), we then performed a targeted mRNA analysis of genes encoding the above proteins and defined their effects on overall survival (OS). Subjects/patients and methods: Samples were collected prospectively from ccRCC patients. A multiplex proximity extension assay was used to measure the concentrations of 92 inflammation-related proteins in cell-free urine supernatants and plasma. Transcriptomic and clinical information from ccRCC patients was obtained from TCGA. Unsupervised clustering and differential protein expression analyses were performed on protein concentration data. Targeted mRNA analysis on genes encoding significant differentially expressed proteins was performed using TCGA. Backward stepwise regression analyses were used to build a nomogram. The performance of the nomogram and clinical benefit was assessed by discrimination and calibration, and a decision curve analysis, respectively. Results: Unsupervised clustering analysis revealed inflammatory signatures in the cell-free urine supernatant of ccRCC patients. Backward stepwise regressions using TCGA data identified transcriptomic risk factors and risk groups associated with OS. A nomogram to predict 2-year and 5-year OS was developed using these risk factors. The decision curve analysis showed that our model was associated with a net benefit improvement compared to the treat-all/none strategies. Conclusion: We defined four novel biomarkers using proteomic and transcriptomic data that distinguish severity of prognosis in ccRCC. We showed that these biomarkers can be used in a model to predict 2-year and 5-year OS in ccRCC across different tumour stages. This type of analysis, if validated in the future, provides non-invasive prognostic information that could inform either management or surveillance strategies for patients.
MeSH term(s)	Humans ; Carcinoma, Renal Cell/genetics ; Proteomics ; Carcinoma ; Inflammation ; Kidney Neoplasms/genetics ; Prognosis
Language	English
Publishing date	2023-03-07
Publishing country	England
Document type	Journal Article
ZDB-ID	1462191-5
ISSN	1464-410X ; 1464-4096 ; 1358-8672
ISSN (online)	1464-410X
ISSN	1464-4096 ; 1358-8672
DOI	10.1111/bju.15989
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Article ; Online: BIOMARKER OF COVID PNEUMONIA VS CONGESTIVE HEART FAILURE: A KEY TO DISEASE DIAGNOSIS

Al-janabi, Laith / Giri, Padmini / Patel, Manishkumar / Khanam, Verisha / Tusha, Jurgena / Zaki, Ahmed / Kumar, Sarwan

Chest

Keywords	covid19
Publisher	Elsevier; PMC
Document type	Article ; Online
DOI	10.1016/j.chest.2020.09.234
Database	COVID19

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