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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: Using the R = MC

Craig, Derek W / Walker, Timothy J / Cuccaro, Paula / Sharma, Shreela V / Heredia, Natalia I / Robertson, Michael C / Fernandez, Maria E

BMC public health

2024 Volume 24, Issue 1, Page(s) 207

Abstract: ... implementation of school-based physical activity opportunities. The R = MC: Methods: We analyzed interview ... Method to guide the analysis and coded data using deductive (informed by the R = MC: Results: Four ... to the implementation process. Themes 1-3 aligned with subcomponents of the R = MC: Conclusion: Our results highlight ...

Abstract	Background: Schools are a key setting for supporting youth physical activity, given their broad reach and diverse student populations. Organizational readiness is a precursor to the successful implementation of school-based physical activity opportunities. The R = MC Methods: We analyzed interview data from 15 elementary school staff (principals, assistant principals, physical education teachers, and classroom teachers) from a school district in Texas. We focused on factors related to adopting, implementing, and sustaining a variety of school-based physical activity opportunities. We used the Framework Method to guide the analysis and coded data using deductive (informed by the R = MC Results: Four themes emerged from the data: (1) implementation is aided by the presence of internal and external relationships; (2) physical activity opportunities compete with other school priorities; (3) seeing the benefits of physical activity opportunities motivates school staff toward implementation; and (4) staff buy-in is critical to the implementation process. Themes 1-3 aligned with subcomponents of the R = MC Conclusion: Our results highlight and explain how key readiness constructs impact the implementation of school-based physical activity opportunities. They also highlight the importance of obtaining staff buy-in when implementing in the school setting. This information is critical to developing readiness-building strategies that help schools improve their capacity to deliver physical activity opportunities effectively. Trial registration: Not applicable.
MeSH term(s)	Adolescent ; Humans ; Heuristics ; Exercise ; Qualitative Research ; Students ; Motivation
Language	English
Publishing date	2024-01-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2041338-5
ISSN	1471-2458 ; 1471-2458
ISSN (online)	1471-2458
ISSN	1471-2458
DOI	10.1186/s12889-024-17744-2
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Article ; Online: RLSuite: An Integrative R-Loop Bioinformatics Framework.

Miller, H E / Montemayor, D / Levy, S / Sharma, K / Frost, B / Bishop, A J R

Journal of bioinformatics and systems biology : Open access

2023 Volume 6, Issue 4, Page(s) 364–378

Abstract: We recently described the development of a database of 810 R-loop mapping datasets and used ... this data to conduct a meta-analysis of R-loops. R-loops are three-stranded nucleic acid structures ... containing RNA:DNA hybrids and we were able to verify that 30% of expressed genes have an associated R-loop ...

Abstract	We recently described the development of a database of 810 R-loop mapping datasets and used this data to conduct a meta-analysis of R-loops. R-loops are three-stranded nucleic acid structures containing RNA:DNA hybrids and we were able to verify that 30% of expressed genes have an associated R-loop in a location conserved manner.. Moreover, intergenic R-loops map to enhancers, super enhancers and with TAD domain boundaries. This work demonstrated that R-loop mapping via high-throughput sequencing can reveal novel insight into R-loop biology, however the analysis and quality control of these data is a non-trivial task for which few bioinformatic tools exist. Herein we describe RLSuite, an integrative R-loop bioinformatics framework for pre-processing, quality control, and downstream analysis of R-loop mapping data. RLSuite enables users to compare their data to hundreds of public datasets and generate a user-friendly analysis report for sharing with non-bioinformatician colleagues. Taken together, RLSuite is a novel analysis framework that should greatly benefit the emerging R-loop bioinformatics community in a rapidly expanding aspect of epigenetic control that is still poorly understood.
Language	English
Publishing date	2023-12-21
Publishing country	United States
Document type	Journal Article
ISSN	2688-5107
ISSN (online)	2688-5107
DOI	10.26502/jbsb.5107071
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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: Exploration and analysis of R-loop mapping data with RLBase.

Miller, Henry E / Montemayor, Daniel / Li, Janet / Levy, Simon A / Pawar, Roshan / Hartono, Stella / Sharma, Kumar / Frost, Bess / Chedin, Frédéric / Bishop, Alexander J R

Nucleic acids research

2022 Volume 51, Issue D1, Page(s) D1129–D1137

Abstract: R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA ... In 2012, Ginno et al. introduced the first R-loop mapping method. Since that time, dozens of R-loop ... mapping studies have been conducted, yielding hundreds of publicly available datasets. Current R-loop ...

Abstract	R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA. In 2012, Ginno et al. introduced the first R-loop mapping method. Since that time, dozens of R-loop mapping studies have been conducted, yielding hundreds of publicly available datasets. Current R-loop databases provide only limited access to these data. Moreover, no web tools for analyzing user-supplied R-loop datasets have yet been described. In our recent work, we reprocessed 810 R-loop mapping samples, building the largest R-loop data resource to date. We also defined R-loop consensus regions and developed a framework for R-loop data analysis. Now, we introduce RLBase, a user-friendly database that provides the capability to (i) explore hundreds of public R-loop mapping datasets, (ii) explore R-loop consensus regions, (iii) analyze user-supplied data and (iv) download standardized and reprocessed datasets. RLBase is directly accessible via the following URL: https://gccri.bishop-lab.uthscsa.edu/shiny/rlbase/.
MeSH term(s)	DNA/genetics ; DNA/chemistry ; Hybridization, Genetic ; Nucleic Acid Hybridization ; R-Loop Structures ; RNA/genetics ; RNA/chemistry ; Databases, Genetic
Chemical Substances	DNA (9007-49-2) ; RNA (63231-63-0)
Language	English
Publishing date	2022-08-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
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/gkac732
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Article ; Online: Buchanania cochinchinensis (Lour.) M.R. Almedia habitat exhibited robust adaptability to diverse socioeconomic scenarios in eastern India.

Garai, Sanjoy / Mishra, Yogeshwar / Malakar, Ayushman / Kumar, Rikesh / Singh, Ronak / Sharma, Jassi / Tiwari, Sharad

Environmental monitoring and assessment

2023 Volume 195, Issue 8, Page(s) 1005

Abstract: One of the greatest challenges to ecosystems is the rapidity of climate change, and their ability to adjust swiftly will be constrained. Climate change will disrupt the ecological balances, causing species to track suitable habitats for survival. ... ...

Abstract	One of the greatest challenges to ecosystems is the rapidity of climate change, and their ability to adjust swiftly will be constrained. Climate change will disrupt the ecological balances, causing species to track suitable habitats for survival. Consequently, understanding the species' response to climate change is crucial for its conservation and management, and for enhancing biodiversity through effective management. This research intends to examine the response of the vulnerable Buchanania cochinchinensis species to climate change. We modeled the potential suitable habitats of B. cochinchinensis for the present and future climatic scenario proxies based on the Shared Socioeconomic Pathways (SSP), i.e. SSP126, 245, 370 and 585. Maxent was used to simulate the potential habitats of B. cochinchinensis. The study found that ~28,313 km
MeSH term(s)	Ecosystem ; Prospective Studies ; Environmental Monitoring ; Biodiversity ; Climate Change ; Socioeconomic Factors
Language	English
Publishing date	2023-07-28
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	782621-7
ISSN	1573-2959 ; 0167-6369
ISSN (online)	1573-2959
ISSN	0167-6369
DOI	10.1007/s10661-023-11611-0
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Article ; Online: C16orf72/HAPSTR1/TAPR1 functions with BRCA1/Senataxin to modulate replication-associated R-loops and confer resistance to PARP disruption.

Sharma, Abhishek Bharadwaj / Ramlee, Muhammad Khairul / Kosmin, Joel / Higgs, Martin R / Wolstenholme, Amy / Ronson, George E / Jones, Dylan / Ebner, Daniel / Shamkhi, Noor / Sims, David / Wijnhoven, Paul W G / Forment, Josep V / Gibbs-Seymour, Ian / Lakin, Nicholas D

Nature communications

2023 Volume 14, Issue 1, Page(s) 5003

Abstract: ... associated R-loops. C16orf72 is critical to facilitate replication fork restart, suppress DNA damage and ... this identifies a C16orf72/Senataxin/BRCA1-dependent pathway to suppress replication-associated R-loop ...

Abstract	While the toxicity of PARP inhibitors to cells with defects in homologous recombination (HR) is well established, other synthetic lethal interactions with PARP1/PARP2 disruption are poorly defined. To inform on these mechanisms we conducted a genome-wide screen for genes that are synthetic lethal with PARP1/2 gene disruption and identified C16orf72/HAPSTR1/TAPR1 as a novel modulator of replication-associated R-loops. C16orf72 is critical to facilitate replication fork restart, suppress DNA damage and maintain genome stability in response to replication stress. Importantly, C16orf72 and PARP1/2 function in parallel pathways to suppress DNA:RNA hybrids that accumulate at stalled replication forks. Mechanistically, this is achieved through an interaction of C16orf72 with BRCA1 and the RNA/DNA helicase Senataxin to facilitate their recruitment to RNA:DNA hybrids and confer resistance to PARP inhibitors. Together, this identifies a C16orf72/Senataxin/BRCA1-dependent pathway to suppress replication-associated R-loop accumulation, maintain genome stability and confer resistance to PARP inhibitors.
MeSH term(s)	DNA Damage ; DNA Helicases/genetics ; Poly(ADP-ribose) Polymerase Inhibitors/pharmacology ; R-Loop Structures/genetics ; RNA ; BRCA1 Protein/genetics ; Intracellular Signaling Peptides and Proteins/genetics
Chemical Substances	DNA Helicases (EC 3.6.4.-) ; Poly(ADP-ribose) Polymerase Inhibitors ; RNA (63231-63-0) ; BRCA1 Protein ; Intracellular Signaling Peptides and Proteins
Language	English
Publishing date	2023-08-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-40779-9
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Article ; Online: Evaluation of the oncolytic potential of R

Sharma, Kishan K / Kalyani, Irsadullakhan H / Mohapatra, Jogeswar / Patel, Satish D / Patel, Dharmesh R / Vihol, Priti D / Chatterjee, Abhijit / Patel, Dinesh R / Vyas, Bhavesh

Archives of virology

2017 Volume 162, Issue 9, Page(s) 2705–2713

Abstract: ... communication, we explored the oncolytic potential of R ...

Abstract	Virotherapy is emerging as an alternative treatment of cancer. Among the candidate oncolytic viruses (OVs), Newcastle disease virus (NDV) has emerged as a promising non-engineered OV. In the present communication, we explored the oncolytic potential of R
MeSH term(s)	Animals ; Antibodies, Viral ; Colonic Neoplasms/therapy ; Humans ; Mice ; Mice, Inbred BALB C ; Mice, Nude ; Neoplasms, Experimental/therapy ; Newcastle disease virus/classification ; Oncolytic Virotherapy ; Oncolytic Viruses ; Viral Vaccines/immunology
Chemical Substances	Antibodies, Viral ; Viral Vaccines
Language	English
Publishing date	2017-09
Publishing country	Austria
Document type	Journal Article
ZDB-ID	7491-3
ISSN	1432-8798 ; 0304-8608
ISSN (online)	1432-8798
ISSN	0304-8608
DOI	10.1007/s00705-017-3411-4
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Article ; Online: Author Correction: C16orf72/HAPSTR1/TAPR1 functions with BRCA1/Senataxin to modulate replication-associated R-loops and confer resistance to PARP disruption.

Nature communications

2023 Volume 14, Issue 1, Page(s) 7784

Language	English
Publishing date	2023-11-27
Publishing country	England
Document type	Published Erratum
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-43353-5
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Book ; Online: Classifying Rhoticity of /r/ in Speech Sound Disorder using Age-and-Sex Normalized Formants

Benway, Nina R / Preston, Jonathan L / Salekin, Asif / Xiao, Yi / Sharma, Harshit / McAllister, Tara

2023

Abstract: ... impacting, e.g., /r/. We show age-and-sex normalized formant estimation outperforms cepstral representation ... for detection of fully rhotic vs. derhotic /r/ in the PERCEPT-R Corpus. Gated recurrent neural networks trained ...

Abstract	Mispronunciation detection tools could increase treatment access for speech sound disorders impacting, e.g., /r/. We show age-and-sex normalized formant estimation outperforms cepstral representation for detection of fully rhotic vs. derhotic /r/ in the PERCEPT-R Corpus. Gated recurrent neural networks trained on this feature set achieve a mean test participant-specific F1-score =.81 ({\sigma}x=.10, med = .83, n = 48), with post hoc modeling showing no significant effect of child age or sex. Comment: To appear in Proceedings of the Annual Conference of the International Speech Communication Association, INTERSPEECH 2023
Keywords	Electrical Engineering and Systems Science - Audio and Speech Processing
Publishing date	2023-05-25
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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