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Article ; Online: Lethal mutagenesis as an antiviral strategy.

Swanstrom, Ronald / Schinazi, Raymond F

2022 Volume 375, Issue 6580, Page(s) 497–498

Abstract: Figure: see text]. ...

Abstract	[Figure: see text].
MeSH term(s)	Animals ; Antiviral Agents/adverse effects ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; COVID-19/drug therapy ; COVID-19/virology ; Cytidine/adverse effects ; Cytidine/analogs & derivatives ; Cytidine/metabolism ; Cytidine/pharmacology ; Cytidine/therapeutic use ; Cytidine/toxicity ; DNA/biosynthesis ; Evolution, Molecular ; Genome, Viral ; Humans ; Hydroxylamines/adverse effects ; Hydroxylamines/metabolism ; Hydroxylamines/pharmacology ; Hydroxylamines/therapeutic use ; Mutagenesis ; Mutagenicity Tests ; Phosphorylation ; RNA Virus Infections/drug therapy ; RNA Virus Infections/virology ; RNA Viruses/drug effects ; RNA Viruses/genetics ; RNA, Viral/biosynthesis ; RNA, Viral/genetics ; Ribonucleosides/metabolism ; SARS-CoV-2/drug effects ; SARS-CoV-2/genetics
Chemical Substances	Antiviral Agents ; Hydroxylamines ; RNA, Viral ; Ribonucleosides ; Cytidine (5CSZ8459RP) ; DNA (9007-49-2) ; N(4)-hydroxycytidine (C3D11PV2O4) ; molnupiravir (YA84KI1VEW)
Language	English
Publishing date	2022-02-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abn0048
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Zs.MG 77: Show issues

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Article ; Online: Informatics and Computational Approaches for the Discovery and Optimization of Natural Product-Inspired Inhibitors of the SARS-CoV-2 2'-

Hanna, George S / Benjamin, Menny M / Choo, Yeun-Mun / De, Ramyani / Schinazi, Raymond F / Nielson, Sarah E / Hevel, Joan M / Hamann, Mark T

Journal of natural products

2024 Volume 87, Issue 2, Page(s) 217–227

Abstract: The urgent need for new classes of orally available, safe, and effective antivirals─covering a breadth of emerging viruses─is evidenced by the loss of life and economic challenges created by the HIV-1 and SARS-CoV-2 pandemics. As frontline interventions, ...

Abstract	The urgent need for new classes of orally available, safe, and effective antivirals─covering a breadth of emerging viruses─is evidenced by the loss of life and economic challenges created by the HIV-1 and SARS-CoV-2 pandemics. As frontline interventions, small-molecule antivirals can be deployed prophylactically or postinfection to control the initial spread of outbreaks by reducing transmissibility and symptom severity. Natural products have an impressive track record of success as prototypic antivirals and continue to provide new drugs through synthesis, medicinal chemistry, and optimization decades after discovery. Here, we demonstrate an approach using computational analysis typically used for rational drug design to identify and develop natural product-inspired antivirals. This was done with the goal of identifying natural product prototypes to aid the effort of progressing toward safe, effective, and affordable broad-spectrum inhibitors of
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Biological Products/pharmacology ; Informatics ; Antiviral Agents/pharmacology
Chemical Substances	Biological Products ; Antiviral Agents
Language	English
Publishing date	2024-01-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	304325-3
ISSN	1520-6025 ; 0163-3864
ISSN (online)	1520-6025
ISSN	0163-3864
DOI	10.1021/acs.jnatprod.3c00875
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Article ; Online: Test-retest reliability of spectral parameterization by 1/f characterization using SpecParam.

McKeown, Daniel J / Finley, Anna J / Kelley, Nicholas J / Cavanagh, James F / Keage, Hannah A D / Baumann, Oliver / Schinazi, Victor R / Moustafa, Ahmed A / Angus, Douglas J

Cerebral cortex (New York, N.Y. : 1991)

2024 Volume 34, Issue 1

Abstract: SpecParam (formally known as FOOOF) allows for the refined measurements of electroencephalography periodic and aperiodic activity, and potentially provides a non-invasive measurement of excitation: inhibition balance. However, little is known about the ... ...

Abstract	SpecParam (formally known as FOOOF) allows for the refined measurements of electroencephalography periodic and aperiodic activity, and potentially provides a non-invasive measurement of excitation: inhibition balance. However, little is known about the psychometric properties of this technique. This is integral for understanding the usefulness of SpecParam as a tool to determine differences in measurements of cognitive function, and electroencephalography activity. We used intraclass correlation coefficients to examine the test-retest reliability of parameterized activity across three sessions (90 minutes apart and 30 days later) in 49 healthy young adults at rest with eyes open, eyes closed, and during three eyes closed cognitive tasks including subtraction (Math), music recall (Music), and episodic memory (Memory). Intraclass correlation coefficients were good for the aperiodic exponent and offset (intraclass correlation coefficients > 0.70) and parameterized periodic activity (intraclass correlation coefficients > 0.66 for alpha and beta power, central frequency, and bandwidth) across conditions. Across all three sessions, SpecParam performed poorly in eyes open (40% of participants had poor fits over non-central sites) and had poor test-retest reliability for parameterized periodic activity. SpecParam mostly provides reliable metrics of individual differences in parameterized neural activity. More work is needed to understand the suitability of eyes open resting data for parameterization using SpecParam.
MeSH term(s)	Young Adult ; Humans ; Reproducibility of Results ; Electroencephalography/methods ; Cognition
Language	English
Publishing date	2024-03-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1077450-6
ISSN	1460-2199 ; 1047-3211
ISSN (online)	1460-2199
ISSN	1047-3211
DOI	10.1093/cercor/bhad482
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Article: The structural and mechanistic bases for the viral resistance to allosteric HIV-1 integrase inhibitor pirmitegravir.

Dinh, Tung / Tber, Zahira / Rey, Juan S / Mengshetti, Seema / Annamalai, Arun S / Haney, Reed / Briganti, Lorenzo / Amblard, Franck / Fuchs, James R / Cherepanov, Peter / Kim, Kyungjin / Schinazi, Raymond F / Perilla, Juan R / Kim, Baek / Kvaratskhelia, Mamuka

bioRxiv : the preprint server for biology

2024

Abstract: Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are investigational antiretroviral agents which potently impair virion maturation by inducing hyper-multimerization of IN and inhibiting its interaction with viral genomic RNA. The pyrrolopyridine- ... ...

Abstract	Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are investigational antiretroviral agents which potently impair virion maturation by inducing hyper-multimerization of IN and inhibiting its interaction with viral genomic RNA. The pyrrolopyridine-based ALLINI pirmitegravir (PIR) has recently advanced into Phase 2a clinical trials. Previous cell culture based viral breakthrough assays identified the HIV-1
Language	English
Publishing date	2024-01-26
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.26.577387
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Article: Stably-Inverted Apical-Out Human Upper Airway Organoids for SARS-CoV-2 Infection and Therapeutic Testing.

Lee, Ji-Hoon / LeCher, Julia C / Parigoris, Eric / Shinagawa, Noriyuki / Sentosa, Jason / Manfredi, Candela / Goh, Shu Ling / De, Ramyani / Tao, Sijia / Zandi, Keivan / Amblard, Franck / Sorscher, Eric J / Spence, Jason R / Tirouvanziam, Rabindra / Schinazi, Raymond F / Takayama, Shuichi

bioRxiv : the preprint server for biology

2024

Abstract: Apical-out organoids produced through eversion triggered by extra-organoid extracellular matrix (ECM) removal or degradation are generally small, structurally variable, and limited for viral infection and therapeutics testing. This work describes ECM- ... ...

Abstract	Apical-out organoids produced through eversion triggered by extra-organoid extracellular matrix (ECM) removal or degradation are generally small, structurally variable, and limited for viral infection and therapeutics testing. This work describes ECM-encapsulating, stably-inverted apical-out human upper airway organoids (AORBs) that are large (~500 μm diameter), consistently spherical, recapitulate
Language	English
Publishing date	2024-01-04
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.02.573939
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Article ; Online: An interpretable machine learning approach to multimodal stress detection in a simulated office environment.

Naegelin, Mara / Weibel, Raphael P / Kerr, Jasmine I / Schinazi, Victor R / La Marca, Roberto / von Wangenheim, Florian / Hoelscher, Christoph / Ferrario, Andrea

Journal of biomedical informatics

2023 Volume 139, Page(s) 104299

Abstract: Background and objective: Work-related stress affects a large part of today's workforce and is known to have detrimental effects on physical and mental health. Continuous and unobtrusive stress detection may help prevent and reduce stress by providing ... ...

Abstract	Background and objective: Work-related stress affects a large part of today's workforce and is known to have detrimental effects on physical and mental health. Continuous and unobtrusive stress detection may help prevent and reduce stress by providing personalised feedback and allowing for the development of just-in-time adaptive health interventions for stress management. Previous studies on stress detection in work environments have often struggled to adequately reflect real-world conditions in controlled laboratory experiments. To close this gap, in this paper, we present a machine learning methodology for stress detection based on multimodal data collected from unobtrusive sources in an experiment simulating a realistic group office environment (N=90). Methods: We derive mouse, keyboard and heart rate variability features to detect three levels of perceived stress, valence and arousal with support vector machines, random forests and gradient boosting models using 10-fold cross-validation. We interpret the contributions of features to the model predictions with SHapley Additive exPlanations (SHAP) value plots. Results: The gradient boosting models based on mouse and keyboard features obtained the highest average F1 scores of 0.625, 0.631 and 0.775 for the multiclass prediction of perceived stress, arousal and valence, respectively. Our results indicate that the combination of mouse and keyboard features may be better suited to detect stress in office environments than heart rate variability, despite physiological signal-based stress detection being more established in theory and research. The analysis of SHAP value plots shows that specific mouse movement and typing behaviours may characterise different levels of stress. Conclusions: Our study fills different methodological gaps in the research on the automated detection of stress in office environments, such as approximating real-life conditions in a laboratory and combining physiological and behavioural data sources. Implications for field studies on personalised, interpretable ML-based systems for the real-time detection of stress in real office environments are also discussed.
MeSH term(s)	Heart Rate ; Machine Learning ; Mental Health ; Movement ; Random Forest
Language	English
Publishing date	2023-01-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2057141-0
ISSN	1532-0480 ; 1532-0464
ISSN (online)	1532-0480
ISSN	1532-0464
DOI	10.1016/j.jbi.2023.104299
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Article ; Online: Biochemical functions and structure of Caenorhabditis elegans ZK177.8 protein: Aicardi-Goutières syndrome SAMHD1 dNTPase ortholog.

Maehigashi, Tatsuya / Lim, Christopher / Wade, Lydia R / Bowen, Nicole E / Knecht, Kirsten M / Alvarez, Natalie N / Kelly, William G / Schinazi, Raymond F / Kim, Dong-Hyun / Xiong, Yong / Kim, Baek

The Journal of biological chemistry

2023 Volume 299, Issue 9, Page(s) 105148

Abstract: Mutations in sterile alpha motif domain and histidine-aspartate domain-containing protein 1 (SAMHD1) are found in a neurodevelopmental disorder, Aicardi-Goutières syndrome, and cancers, and SAMHD1, which is a deoxynucleoside triphosphate (dNTP) ... ...

Abstract	Mutations in sterile alpha motif domain and histidine-aspartate domain-containing protein 1 (SAMHD1) are found in a neurodevelopmental disorder, Aicardi-Goutières syndrome, and cancers, and SAMHD1, which is a deoxynucleoside triphosphate (dNTP) triphosphorylase, was identified as a myeloid-specific HIV-1 restriction factor. Here, we characterized the enzymology and structure of an SAMHD1 ortholog of Caenorhabditis elegans, ZK177.8, which also reportedly induces developmental defects upon gene knockdown. We found ZK177.8 protein is a dNTPase allosterically regulated by dGTP. The active site of ZK177.8 recognizes both 2' OH and triphosphate moieties of dNTPs but not base moiety. The dGTP activator induces the formation of the enzymatically active ZK177.8 tetramers, and ZK177.8 protein lowers cellular dNTP levels in a human monocytic cell line. Finally, ZK177.8 tetramers display very similar X-ray crystal structure with human and mouse SAMHD1s except that its lack of the canonical sterile alpha motif domain. This striking conservation in structure, function, and allosteric regulatory mechanism for the hydrolysis of the DNA building blocks supports their host developmental roles.
Language	English
Publishing date	2023-08-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.105148
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Article ; Online: Medication-invariant resting aperiodic and periodic neural activity in Parkinson's disease.

McKeown, Daniel J / Jones, Manon / Pihl, Camilla / Finley, Anna J / Kelley, Nicholas / Baumann, Oliver / Schinazi, Victor R / Moustafa, Ahmed A / Cavanagh, James F / Angus, Douglas J

Psychophysiology

2023 Volume 61, Issue 4, Page(s) e14478

Abstract: Parkinson's disease (PD) has been associated with greater total power in canonical frequency bands (i.e., alpha, beta) of the resting electroencephalogram (EEG). However, PD has also been associated with a reduction in the proportion of total power ... ...

Abstract	Parkinson's disease (PD) has been associated with greater total power in canonical frequency bands (i.e., alpha, beta) of the resting electroencephalogram (EEG). However, PD has also been associated with a reduction in the proportion of total power across all frequency bands. This discrepancy may be explained by aperiodic activity (exponent and offset) present across all frequency bands. Here, we examined differences in the eyes-open (EO) and eyes-closed (EC) resting EEG of PD participants (N = 26) on and off medication, and age-matched healthy controls (CTL; N = 26). We extracted power from canonical frequency bands using traditional methods (total alpha and beta power) and extracted separate parameters for periodic (parameterized alpha and beta power) and aperiodic activity (exponent and offset). Cluster-based permutation tests over spatial and frequency dimensions indicated that total alpha and beta power, and aperiodic exponent and offset were greater in PD participants, independent of medication status. After removing the exponent and offset, greater alpha power in PD (vs. CTL) was only present in EO recordings and no reliable differences in beta power were observed. Differences between PD and CTL in the resting EEG are likely driven by aperiodic activity, suggestive of greater relative inhibitory neural activity and greater neuronal spiking. Our findings suggest that resting EEG activity in PD is characterized by medication-invariant differences in aperiodic activity which is independent of the increase in alpha power with EO. This highlights the importance of considering aperiodic activity contributions to the neural correlates of brain disorders.
MeSH term(s)	Humans ; Parkinson Disease ; Electroencephalography ; Rest/physiology
Language	English
Publishing date	2023-11-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	209486-1
ISSN	1469-8986 ; 1540-5958 ; 0048-5772
ISSN (online)	1469-8986 ; 1540-5958
ISSN	0048-5772
DOI	10.1111/psyp.14478
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Article ; Online: Reply to Troth et al.

Zhou, Shuntai / Hill, Collin S / Woodburn, Blaide M D / Schinazi, Raymond F / Swanstrom, Ronald

The Journal of infectious diseases

2021 Volume 224, Issue 8, Page(s) 1443–1444

Language	English
Publishing date	2021-07-12
Publishing country	United States
Document type	Research Support, N.I.H., Extramural ; Letter ; Comment
ZDB-ID	3019-3
ISSN	1537-6613 ; 0022-1899
ISSN (online)	1537-6613
ISSN	0022-1899
DOI	10.1093/infdis/jiab363
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Zs.MO 445: Show issues

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Article ; Online: HIV latency reversal research and the potential effects on the central nervous system: is concern warranted?

Anderson, Albert M / Schinazi, Raymond F / Tyor, William R

Journal of the International AIDS Society

2016 Volume 19, Issue 1, Page(s) 21008

Language	English
Publishing date	2016-05-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2467110-1
ISSN	1758-2652 ; 1758-2652
ISSN (online)	1758-2652
ISSN	1758-2652
DOI	10.7448/IAS.19.1.21008
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