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Article: Validating Immunomodulatory Responses of r-

Pandey, Rajkishor / Gautam, Rohit Kumar / Sharma, Simran / Tedla, Mebrahtu G / Mahantesh, Vijay / Dikhit, Manas Ranjan / Kumar, Akhilesh / Pandey, Krishna / Bimal, Sanjiva

Pathogens (Basel, Switzerland)

2022 Volume 12, Issue 1

Abstract: ... With this background, the r- ...

Abstract	Vaccination is considered the most appropriate way to control visceral leishmaniasis (VL). With this background, the r-
Language	English
Publishing date	2022-12-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens12010016
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Article ; Online: Cyclic Peptide [R

Hernandez, Joshua / Ashley, David / Cao, Ruoqiong / Abrahem, Rachel / Nguyen, Timothy / To, Kimberly / Yegiazaryan, Aram / Akinwale David, Ajayi / Kumar Tiwari, Rakesh / Venketaraman, Vishwanath

Frontiers in immunology

2020 Volume 11, Page(s) 1677

Abstract: Tuberculosis (TB) is currently one of the leading causes of global mortality. Medical non-compliance due to the length of the treatment and antibiotic side effects has led to the emergence of multidrug-resistant (MDR) strains ... ...

Abstract	Tuberculosis (TB) is currently one of the leading causes of global mortality. Medical non-compliance due to the length of the treatment and antibiotic side effects has led to the emergence of multidrug-resistant (MDR) strains of
MeSH term(s)	Adolescent ; Adult ; Aged ; Antibiotics, Antitubercular/pharmacology ; Autophagy/drug effects ; Cytokines/metabolism ; Drug Therapy, Combination ; Granuloma/drug therapy ; Granuloma/metabolism ; Granuloma/microbiology ; Host-Pathogen Interactions ; Humans ; Isoniazid/pharmacology ; Microbial Viability/drug effects ; Middle Aged ; Mycobacterium tuberculosis/drug effects ; Mycobacterium tuberculosis/growth & development ; Oxidative Stress ; Peptides, Cyclic/pharmacology ; Pyrazinamide/pharmacology ; Tuberculosis/drug therapy ; Tuberculosis/metabolism ; Tuberculosis/microbiology ; Young Adult
Chemical Substances	Antibiotics, Antitubercular ; Cytokines ; Peptides, Cyclic ; cyclic peptide R4W4 ; Pyrazinamide (2KNI5N06TI) ; Isoniazid (V83O1VOZ8L)
Keywords	covid19
Language	English
Publishing date	2020-08-13
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2020.01677
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Article ; Online: Linear bis-Coordinate Silver(I) and Iodine(I) Complexes with R

Kumar, Parveen / Komulainen, Joonas / Frontera, Antonio / Ward, Jas S / Schalley, Christoph / Rissanen, Kari / Puttreddy, Rakesh

Chemistry (Weinheim an der Bergstrasse, Germany)

2023 Volume 29, Issue 69, Page(s) e202302162

Abstract: Homoleptic [L-I-L] ...

Abstract	Homoleptic [L-I-L]
Language	English
Publishing date	2023-10-26
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1478547-X
ISSN	1521-3765 ; 0947-6539
ISSN (online)	1521-3765
ISSN	0947-6539
DOI	10.1002/chem.202302162
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Article ; Online: Genome-wide association in Drosophila identifies a role for Piezo and Proc-R in sleep latency.

Eiman, Matthew N / Kumar, Shailesh / Serrano Negron, Yazmin L / Tansey, Terry R / Harbison, Susan T

Scientific reports

2024 Volume 14, Issue 1, Page(s) 260

Abstract: ... Piezo, Proc-R and Rbp6 in sleep latency. Two large-effect mutations in the genes Proc-R and Piezo were ...

Abstract	Sleep latency, the amount of time that it takes an individual to fall asleep, is a key indicator of sleep need. Sleep latency varies considerably both among and within species and is heritable, but lacks a comprehensive description of its underlying genetic network. Here we conduct a genome-wide association study of sleep latency. Using previously collected sleep and activity data on a wild-derived population of flies, we calculate sleep latency, confirming significant, heritable genetic variation for this complex trait. We identify 520 polymorphisms in 248 genes contributing to variability in sleep latency. Tests of mutations in 23 candidate genes and additional putative pan-neuronal knockdown of 9 of them implicated CG44153, Piezo, Proc-R and Rbp6 in sleep latency. Two large-effect mutations in the genes Proc-R and Piezo were further confirmed via genetic rescue. This work greatly enhances our understanding of the genetic factors that influence variation in sleep latency.
MeSH term(s)	Animals ; Drosophila/genetics ; Drosophila Proteins/genetics ; Gene Regulatory Networks ; Genome-Wide Association Study ; Ion Channels/genetics ; Polymorphism, Genetic ; Sleep/genetics ; Sleep Latency
Chemical Substances	Drosophila Proteins ; Ion Channels ; Piezo protein, Drosophila ; Proc-R protein, Drosophila
Language	English
Publishing date	2024-01-02
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/s41598-023-50552-z
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Article ; Online: Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions.

Miller, Henry E / Montemayor, Daniel / Abdul, Jebriel / Vines, Anna / Levy, Simon A / Hartono, Stella R / Sharma, Kumar / Frost, Bess / Chédin, Frédéric / Bishop, Alexander J R

Nucleic acids research

2022 Volume 50, Issue 13, Page(s) 7260–7286

Abstract: R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA ... While the pathological consequences of R-loops have been well-studied to date, the locations, classes, and dynamics ... of physiological R-loops remain poorly understood. R-loop mapping studies provide insight into R-loop dynamics ...

Abstract	R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA. While the pathological consequences of R-loops have been well-studied to date, the locations, classes, and dynamics of physiological R-loops remain poorly understood. R-loop mapping studies provide insight into R-loop dynamics, but their findings are challenging to generalize. This is due to the narrow biological scope of individual studies, the limitations of each mapping modality, and, in some cases, poor data quality. In this study, we reprocessed 810 R-loop mapping datasets from a wide array of biological conditions and mapping modalities. From this data resource, we developed an accurate R-loop data quality control method, and we reveal the extent of poor-quality data within previously published studies. We then identified a set of high-confidence R-loop mapping samples and used them to define consensus R-loop sites called 'R-loop regions' (RL regions). In the process, we identified a stark divergence between RL regions detected by S9.6 and dRNH-based mapping methods, particularly with respect to R-loop size, location, and colocalization with RNA binding factors. Taken together, this work provides a much-needed method to assess R-loop data quality and offers novel context regarding the differences between dRNH- and S9.6-based R-loop mapping approaches.
MeSH term(s)	Consensus ; DNA/chemistry ; Nucleic Acid Hybridization ; R-Loop Structures ; RNA/chemistry ; RNA/genetics
Chemical Substances	RNA (63231-63-0) ; DNA (9007-49-2)
Language	English
Publishing date	2022-06-27
Publishing country	England
Document type	Journal Article ; Meta-Analysis ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkac537
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Article ; Online: Metabolomic biomarkers for (R, S)-ketamine and (S)-ketamine in treatment-resistant depression and healthy controls: A systematic review.

Kumar, Rakesh / Nuñez, Nicolas A / Joshi, Neha / Joseph, Boney / Verde, Alessandra / Seshadri, Ashok / Cuellar Barboza, Alfredo B / Prokop, Larry J / Medeiros, Gustavo C / Singh, Balwinder

Bipolar disorders

2024

Abstract: Background: Ketamine is increasingly used for treatment-resistant depression (TRD) while its mechanism of action is still being investigated. In this systematic review, we appraise the current evidence of metabolomic biomarkers for racemic ketamine and ... ...

Abstract	Background: Ketamine is increasingly used for treatment-resistant depression (TRD) while its mechanism of action is still being investigated. In this systematic review, we appraise the current evidence of metabolomic biomarkers for racemic ketamine and esketamine in patients with TRD and healthy controls (HCs). Methods: A comprehensive search of several databases (Ovid MEDLINE®, Embase, and Epub Ahead of Print) was performed from each database's inception to June 29, 2022, in any language, was conducted. We included studies wherein the metabolomic biomarkers for racemic ketamine or esketamine were investigated in TRD or HCs. Our main outcomes were to examine changes in metabolites among patients treated with ketamine/esketamine and explore the association with response to ketamine/esketamine. Results: A total of 1859 abstracts were screened of which 11 were included for full-text review. Of these, a total of five articles were included (N = 147), including three RCTs (n = 129) and two open-label trials (n = 18). All studies used racemic ketamine; one study additionally used esketamine. The included studies evaluated patients with treatment-resistant bipolar depression (n = 22), unipolar depression (n = 91), and HCs (n = 34). The included studies reported alteration in several metabolites including acylcarnitines, lipids, kynurenine (KYN), and arginine with ketamine in TRD. Studies suggest the involvement of energy metabolism, KYN, and arginine pathways. In HCs, acetylcarnitine decreased post-infusion, whereas inconsistent findings were observed after the ketamine infusion in TRD patients. Conclusions: This systematic review provides preliminary evidence that ketamine may cause changes in several important pathways involved in energy metabolism and inflammation. Larger and more rigorous studies are needed.
Language	English
Publishing date	2024-02-07
Publishing country	Denmark
Document type	Journal Article ; Review
ZDB-ID	1472242-2
ISSN	1399-5618 ; 1398-5647
ISSN (online)	1399-5618
ISSN	1398-5647
DOI	10.1111/bdi.13412
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Article ; Online: Compromised transcription-mRNA export factor THOC2 causes R-loop accumulation, DNA damage and adverse neurodevelopment.

Bhattacharjee, Rudrarup / Jolly, Lachlan A / Corbett, Mark A / Wee, Ing Chee / Rao, Sushma R / Gardner, Alison E / Ritchie, Tarin / van Hugte, Eline J H / Ciptasari, Ummi / Piltz, Sandra / Noll, Jacqueline E / Nazri, Nazzmer / van Eyk, Clare L / White, Melissa / Fornarino, Dani / Poulton, Cathryn / Baynam, Gareth / Collins-Praino, Lyndsey E / Snel, Marten F /

Nadif Kasri, Nael / Hemsley, Kim M / Thomas, Paul Q / Kumar, Raman / Gecz, Jozef

Nature communications

2024 Volume 15, Issue 1, Page(s) 1210

Abstract: We implicated the X-chromosome THOC2 gene, which encodes the largest subunit of the highly-conserved TREX (Transcription-Export) complex, in a clinically complex neurodevelopmental disorder with intellectual disability as the core phenotype. To study the ...

Abstract	We implicated the X-chromosome THOC2 gene, which encodes the largest subunit of the highly-conserved TREX (Transcription-Export) complex, in a clinically complex neurodevelopmental disorder with intellectual disability as the core phenotype. To study the molecular pathology of this essential eukaryotic gene, we generated a mouse model based on a hypomorphic Thoc2 exon 37-38 deletion variant of a patient with ID, speech delay, hypotonia, and microcephaly. The Thoc2 exon 37-38 deletion male (Thoc2
MeSH term(s)	Humans ; Male ; Mice ; Animals ; Transcription Factors/metabolism ; R-Loop Structures ; Active Transport, Cell Nucleus ; Intellectual Disability/genetics ; DNA Damage ; Phenotype ; RNA, Messenger/metabolism
Chemical Substances	Transcription Factors ; RNA, Messenger
Language	English
Publishing date	2024-02-08
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-45121-5
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Article ; Online: Measurement of R(D) and R(D^{*}) with a Semileptonic Tagging Method.

Caria, G / Urquijo, P / Adachi, I / Aihara, H / Al Said, S / Asner, D M / Atmacan, H / Aushev, T / Babu, V / Badhrees, I / Bahinipati, S / Bakich, A M / Behera, P / Beleño, C / Bennett, J / Bhuyan, B / Bilka, T / Biswal, J / Bozek, A /

Bračko, M / Browder, T E / Campajola, M / Červenkov, D / Chang, P / Cheaib, R / Chekelian, V / Chen, A / Cheon, B G / Chilikin, K / Cho, H E / Cho, K / Choi, Y / Choudhury, S / Cinabro, D / Cunliffe, S / Dash, N / De Nardo, G / Di Capua, F / Di Carlo, S / Doležal, Z / Dong, T V / Eidelman, S / Epifanov, D / Fast, J E / Ferber, T / Ferlewicz, D / Fulsom, B G / Garg, R / Gaur, V / Gabyshev, N / Garmash, A / Giri, A / Goldenzweig, P / Greenwald, D / Grzymkowska, O / Guan, Y / Hartbrich, O / Hayasaka, K / Hayashii, H / Higuchi, T / Hou, W-S / Hsu, C-L / Iijima, T / Inami, K / Inguglia, G / Ishikawa, A / Itoh, R / Iwasaki, M / Iwasaki, Y / Jacobs, W W / Jeon, H B / Jia, S / Jin, Y / Joffe, D / Joo, K K / Kaliyar, A B / Kang, K H / Karyan, G / Kawasaki, T / Kichimi, H / Kim, C H / Kim, D Y / Kim, H J / Kim, K T / Kim, S H / Kinoshita, K / Kodyš, P / Korpar, S / Kotchetkov, D / Križan, P / Kroeger, R / Krohn, J-F / Krokovny, P / Kuhr, T / Kumar, R / Kwon, Y-J / Lange, J S / Lee, I S / Lee, J K / Lee, S C / Li, L K / Li, Y B / Li Gioi, L / Libby, J / Lieret, K / Liventsev, D / Luo, T / MacQueen, C / Masuda, M / Matsuda, T / Matvienko, D / Merola, M / Metzner, F / Miyabayashi, K / Mohanty, G B / Moon, T J / Mori, T / Mussa, R / Nakamura, K R / Nakao, M / Nath, K J / Nayak, M / Nisar, N K / Nishida, S / Nishimura, K / Ogawa, K / Ono, H / Onuki, Y / Oskin, P / Pakhlov, P / Pakhlova, G / Pal, B / Pang, T / Park, H / Park, S-H / Patra, S / Paul, S / Pedlar, T K / Pestotnik, R / Piilonen, L E / Popov, V / Prencipe, E / Prim, M T / Rabusov, A / Resmi, P K / Ritter, M / Rozanska, M / Russo, G / Sahoo, D / Sakai, Y / Sandilya, S / Santelj, L / Sanuki, T / Savinov, V / Schneider, O / Schnell, G / Schueler, J / Schwanda, C / Schwartz, A J / Seino, Y / Senyo, K / Sevior, M E / Shebalin, V / Shiu, J-G / Shwartz, B / Simon, F / Sokolov, A / Solovieva, E / Starič, M / Stottler, Z S / Sumiyoshi, T / Sutcliffe, W / Takizawa, M / Tamponi, U / Tanida, K / Tenchini, F / Trabelsi, K / Uchida, M / Uglov, T / Uno, S / Usov, Y / Vahsen, S E / Van Tonder, R / Varner, G / Varvell, K E / Vossen, A / Waheed, E / Wang, B / Wang, C H / Wang, M-Z / Wang, P / Wang, X L / Watanuki, S / Wiechczynski, J / Won, E / Yamamoto, H / Yang, S B / Ye, H / Yin, J H / Yuan, C Z / Zhang, Z P / Zhilich, V / Zhukova, V / Zhulanov, V

Physical review letters

2020 Volume 124, Issue 16, Page(s) 161803

Abstract: The experimental results on the ratios of branching fractions R(D)=B(B[over ¯]→Dτ^{-}ν[over ¯]_{τ ... B(B[over ¯]→Dℓ^{-}ν[over ¯]_{ℓ}) and R(D^{*})=B(B[over ¯]→D^{*}τ^{-}ν[over ¯]_{τ})/B(B[over ¯]→D^ ... simultaneous measurement of R(D) and R(D^{*}), based on a data sample containing 772×10^{6} BB[over ¯] events ...

Abstract	The experimental results on the ratios of branching fractions R(D)=B(B[over ¯]→Dτ^{-}ν[over ¯]_{τ})/B(B[over ¯]→Dℓ^{-}ν[over ¯]_{ℓ}) and R(D^{})=B(B[over ¯]→D^{}τ^{-}ν[over ¯]_{τ})/B(B[over ¯]→D^{}ℓ^{-}ν[over ¯]_{ℓ}), where ℓ denotes an electron or a muon, show a long-standing discrepancy with the standard model predictions, and might hint at a violation of lepton flavor universality. We report a new simultaneous measurement of R(D) and R(D^{}), based on a data sample containing 772×10^{6} BB[over ¯] events recorded at the ϒ(4S) resonance with the Belle detector at the KEKB e^{+}e^{-} collider. In this analysis the tag-side B meson is reconstructed in a semileptonic decay mode and the signal-side τ is reconstructed in a purely leptonic decay. The measured values are R(D)=0.307±0.037±0.016 and R(D^{})=0.283±0.018±0.014, where the first uncertainties are statistical and the second are systematic. These results are in agreement with the standard model predictions within 0.2, 1.1, and 0.8 standard deviations for R(D), R(D^{}), and their combination, respectively. This work constitutes the most precise measurements of R(D) and R(D^{*}) performed to date as well as the first result for R(D) based on a semileptonic tagging method.
Language	English
Publishing date	2020-05-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.124.161803
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Article ; Online: Reply to E.R.S. Cliff et al.

D'Souza, Anita / Kumar, Shaji

Journal of clinical oncology : official journal of the American Society of Clinical Oncology

2023 Volume 41, Issue 10, Page(s) 1951–1952

Language	English
Publishing date	2023-01-30
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	604914-x
ISSN	1527-7755 ; 0732-183X
ISSN (online)	1527-7755
ISSN	0732-183X
DOI	10.1200/JCO.22.02691
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Article ; Online: NetVA: an R package for network vulnerability and influence analysis.

Kumar, Swapnil / Pauline, Grace / Vindal, Vaibhav

Journal of biomolecular structure & dynamics

2024 , Page(s) 1–12

Abstract: In biological network analysis, identifying key molecules plays a decisive role in the development of potential diagnostic and therapeutic candidates. Among various approaches of network analysis, network vulnerability analysis is quite important, as it ... ...

Abstract	In biological network analysis, identifying key molecules plays a decisive role in the development of potential diagnostic and therapeutic candidates. Among various approaches of network analysis, network vulnerability analysis is quite important, as it assesses significant associations between topological properties and the functional essentiality of a network. Similarly, some node centralities are also used to screen out key molecules. Among these node centralities, escape velocity centrality (EVC), and its extended version (EVC+) outperform others,
Language	English
Publishing date	2024-01-17
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2024.2303607
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