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Article ; Online: N-Phase Local Expansion Ratio for Characterizing Out-of-Phase Lung Ventilation.

Shao, Wei / Patton, Taylor J / Gerard, Sarah E / Pan, Yue / Reinhardt, Joseph M / Durumeric, Oguz C / Bayouth, John E / Christensen, Gary E

IEEE transactions on medical imaging

2019 Volume 39, Issue 6, Page(s) 2025–2034

Abstract: ... the N-phase local expansion ratio (LER ...

Abstract	Out-of-phase ventilation occurs when local regions of the lung reach their maximum or minimum volumes at breathing phases other than the global end inhalation or exhalation phases. This paper presents the N-phase local expansion ratio (LER
MeSH term(s)	Animals ; Four-Dimensional Computed Tomography ; Lung/diagnostic imaging ; Lung Neoplasms/diagnostic imaging ; Respiration ; Respiration, Artificial ; Sheep
Language	English
Publishing date	2019-12-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	622531-7
ISSN	1558-254X ; 0278-0062
ISSN (online)	1558-254X
ISSN	0278-0062
DOI	10.1109/TMI.2019.2963083
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Article ; Online: The Omicron variant BQ.1* with mutations at positions 28,311 and 28,312 in the SARS-CoV-2 N gene have minimal impact on CDC N1 target detection

Ren, Guoping / Langhorst, Bradley W / Patton, Gregory C.

bioRxiv

Abstract: ... with a commonly used fluorescent probe for N gene detection in many Emergency Use Authorization (EUA) assays ... therefore it is important to verify the impacts of this additional mutation. Using in vitro transcribed (IVT) N ... both of which include the CDC 2019-nCoV_N1 primer-probe set. Both assays successfully detected the mutant N ...

Abstract	Ensuring COVID-19 testing remains accurate and reliable is of critical importance as the SARS-CoV-2 virus continues to evolve. Currently, a number of Omicron variants are dominating infection across the globe in including BQ.1 and XBB. Both variants and their sublineages (BQ.1* and XBB) contain a 28,311 C/U mutation inherited from the original Omicron variant (BA.1). This mutation overlaps with a commonly used fluorescent probe for N gene detection in many Emergency Use Authorization (EUA) assays, as this target was originally established by the U.S. Centers for Disease Control and Prevention (CDC) in their EUA test for COVID-19 (2019-nCoV_N1). This C to U mutation was previously shown to have no impact on CDC N1 target detection. The rise of Omicron sublineages has increased the likelihood of additional point mutations occurring within the same assay target. A subpopulation of BQ.1 has an additional 28,312 C/U mutation within the CDC 2019_nCoV_N1 fluorescent probe in addition to the 28,311 C/U mutation. The double mutation could adversely affect the ability of diagnostic assays to detect the virus in patient samples and therefore it is important to verify the impacts of this additional mutation. Using in vitro transcribed (IVT) N gene RNA representing the wildtype (GenBank/GISAID ID MN908947.3) and Omicron BQ.1.1 variant (BQ.1, GISAID ID EPI_ISL_ 15155651), we evaluated the performance of two different amplification protocols, both of which include the CDC 2019-nCoV_N1 primer-probe set. Both assays successfully detected the mutant N gene sequence efficiently even at 10 copies of input, although the double mutation caused a 0.5~1 Cq delay on average when compared to the wild-type sequence. These data suggest that circulating BQ.1* lineage viruses with this double mutation likely have minimal impact on diagnostic assays that use the 2019-nCoV-N1 primer-probe.
Keywords	covid19
Language	English
Publishing date	2023-01-27
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2023.01.26.525759
Database	COVID19

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Article ; Online: Monoclonal Human Antibodies That Recognise the Exposed N and C Terminal Regions of the Often-Overlooked SARS-CoV-2 ORF3a Transmembrane Protein.

Tan, Tyng Hwey / Patton, Elizabeth / Munro, Carol A / Corzo-Leon, Dora E / Porter, Andrew J / Palliyil, Soumya

Viruses

2021 Volume 13, Issue 11

Abstract: ... located towards the extracellular N terminal and cytosolic C terminal domains of the protein using peptide ... for COVID-19 infections. Both ORF3a N and C termini, epitope-specific monoclonal antibodies were identified ...

Abstract	ORF3a has been identified as a viroporin of SARS-CoV-2 and is known to be involved in various pathophysiological activities including disturbance of cellular calcium homeostasis, inflammasome activation, apoptosis induction and disruption of autophagy. ORF3a-targeting antibodies may specifically and favorably modulate these viroporin-dependent pathological activities. However, suitable viroporin-targeting antibodies are difficult to generate because of the well-recognized technical challenge associated with isolating antibodies to complex transmembrane proteins. Here we exploited a naïve human single chain antibody phage display library, to isolate binders against carefully chosen ORF3a recombinant epitopes located towards the extracellular N terminal and cytosolic C terminal domains of the protein using peptide antigens. These binders were subjected to further characterization using enzyme-linked immunosorbent assays and surface plasmon resonance analysis to assess their binding affinities to the target epitopes. Binding to full-length ORF3a protein was evaluated by western blot and fluorescent microscopy using ORF3a transfected cells and SARS-CoV-2 infected cells. Co-localization analysis was also performed to evaluate the "pairing potential" of the selected binders as possible alternative diagnostic or prognostic biomarkers for COVID-19 infections. Both ORF3a N and C termini, epitope-specific monoclonal antibodies were identified in our study. Whilst the linear nature of peptides might not always represent their native conformations in the context of full protein, with carefully designed selection protocols, we have been successful in isolating anti-ORF3a binders capable of recognising regions of the transmembrane protein that are exposed either on the "inside" or "outside" of the infected cell. Their therapeutic potential will be discussed.
MeSH term(s)	Animals ; Antibodies, Monoclonal/immunology ; Biomarkers ; COS Cells ; COVID-19/immunology ; COVID-19/virology ; Cell Surface Display Techniques/methods ; Chlorocebus aethiops ; Epitopes/immunology ; HEK293 Cells ; Humans ; Membrane Proteins/immunology ; Protein Domains ; SARS-CoV-2/immunology ; Vero Cells ; Viroporin Proteins/immunology
Chemical Substances	Antibodies, Monoclonal ; Biomarkers ; Epitopes ; Membrane Proteins ; ORF3a protein, SARS-CoV-2 ; Viroporin Proteins
Language	English
Publishing date	2021-11-02
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13112201
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Article: Monoclonal Human Antibodies That Recognise the Exposed N and C Terminal Regions of the Often-Overlooked SARS-CoV-2 ORF3a Transmembrane Protein

Tan, Tyng Hwey / Patton, Elizabeth / Munro, Carol A. / Corzo-Leon, Dora E. / Porter, Andrew J. / Palliyil, Soumya

Viruses. 2021 Nov. 02, v. 13, no. 11

2021

Abstract	ORF3a has been identified as a viroporin of SARS-CoV-2 and is known to be involved in various pathophysiological activities including disturbance of cellular calcium homeostasis, inflammasome activation, apoptosis induction and disruption of autophagy. ORF3a-targeting antibodies may specifically and favorably modulate these viroporin-dependent pathological activities. However, suitable viroporin-targeting antibodies are difficult to generate because of the well-recognized technical challenge associated with isolating antibodies to complex transmembrane proteins. Here we exploited a naïve human single chain antibody phage display library, to isolate binders against carefully chosen ORF3a recombinant epitopes located towards the extracellular N terminal and cytosolic C terminal domains of the protein using peptide antigens. These binders were subjected to further characterization using enzyme-linked immunosorbent assays and surface plasmon resonance analysis to assess their binding affinities to the target epitopes. Binding to full-length ORF3a protein was evaluated by western blot and fluorescent microscopy using ORF3a transfected cells and SARS-CoV-2 infected cells. Co-localization analysis was also performed to evaluate the “pairing potential” of the selected binders as possible alternative diagnostic or prognostic biomarkers for COVID-19 infections. Both ORF3a N and C termini, epitope-specific monoclonal antibodies were identified in our study. Whilst the linear nature of peptides might not always represent their native conformations in the context of full protein, with carefully designed selection protocols, we have been successful in isolating anti-ORF3a binders capable of recognising regions of the transmembrane protein that are exposed either on the “inside” or “outside” of the infected cell. Their therapeutic potential will be discussed.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; Western blotting ; apoptosis ; autophagy ; bacteriophages ; biomarkers ; calcium ; epitopes ; fluorescence microscopy ; homeostasis ; humans ; inflammasomes ; peptides ; surface plasmon resonance ; therapeutics ; transmembrane proteins
Language	English
Dates of publication	2021-1102
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v13112201
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: N-Alkynyl Derivatives of 5-Fluorouracil

Jason T Weiss / Craig eFraser / Belén eRubio-Ruiz / Samuel eMyers / Richard eCrispin / John C Dawson / Valerie G Brunton / E Elizabeth Patton / Neil O Carragher / Asier eUnciti-Broceta

Frontiers in Chemistry, Vol

Susceptibility to Palladium-Mediated Dealkylation and Toxigenicity in Cancer Cell Culture

2014 Volume 2

Abstract: Palladium-activated prodrug therapy is an experimental therapeutic approach that relies on the unique chemical properties and biocompatibility of heterogeneous palladium catalysis to enable the spatially-controlled in vivo conversion of a biochemically- ... ...

Abstract	Palladium-activated prodrug therapy is an experimental therapeutic approach that relies on the unique chemical properties and biocompatibility of heterogeneous palladium catalysis to enable the spatially-controlled in vivo conversion of a biochemically-stable prodrug into its active form. This strategy, which would allow inducing local activation of systemically administered drug precursors by mediation of an implantable activating device made of Pd(0), has been proposed by our group as a way to reduce drug’s systemic toxicity while reaching therapeutic levels of the active drug in the affected tissue / organ. In the seminal study of such an approach, we reported that propargylation of the N1 position of 5-fluorouracil suppressed the drug’s cytotoxic properties, showed high stability in cell culture and facilitated the bioorthogonal restoration of the drug’s pharmacological activity in the presence of extracellular Pd(0)-functionalized resins. To provide additional insight on the properties of this system, we have investigated different N1-alkynyl derivatives of 5-fluorouracil and shown that the presence of substituents near the triple bond influence negatively on its sensitivity to palladium catalysis under biocompatible conditions. Comparative studies of the N1- versus the N3-propargyl derivatives of 5-fluorouracil revealed that masking each or both positions equally led to inactive derivatives (>200-fold reduction of cytotoxicity relative to the unmodified drug), whereas the depropargylation process occurred faster at the N1 position than at the N3, thus resulting in greater toxigenic properties in cancer cell culture.
Keywords	Palladium ; Prodrugs ; chemotherapeutics ; 5-fluorouracil ; bioorthogonal chemistry ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2014-07-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: N-terminal pro-B-type natriuretic peptide is associated with sudden cardiac death risk: the Cardiovascular Health Study.

Patton, Kristen K / Sotoodehnia, Nona / DeFilippi, Christopher / Siscovick, David S / Gottdiener, John S / Kronmal, Richard A

Heart rhythm

2010 Volume 8, Issue 2, Page(s) 228–233

Abstract: ... the relationship between N-terminal pro-B-type natriuretic peptide (NT-proBNP) and SCD in the Cardiovascular Health ...

Abstract	Background: Sudden cardiac death (SCD), the cause of 250,000-450,000 deaths per year, is a major public health problem. The majority of those affected do not have a prior cardiovascular diagnosis. Elevated B-type natriuretic peptide levels have been associated with the risk of heart failure and mortality as well as with sudden death in women. Objective: The purpose of this study was to examine the relationship between N-terminal pro-B-type natriuretic peptide (NT-proBNP) and SCD in the Cardiovascular Health Study population. Methods: The risk of SCD associated with baseline NT-proBNP was examined in 5,447 participants. Covariate-adjusted Cox model regressions were used to estimate the hazard ratios of developing SCD as a function of baseline NT-proBNP. Results: Over a median follow-up of 12.5 years (maximum 16), there were 289 cases of SCD. Higher NT-proBNP levels were strongly associated with SCD, with an unadjusted hazard ratio of 4.2 (95% confidence interval [2.9, 6.1]; P <.001) in the highest quintile compared with in the lowest. NT-proBNP remained associated with SCD even after adjustment for numerous clinical characteristics and risk factors (age, sex, race, and other associated conditions), with an adjusted hazard ratio for the fifth versus the first quintile of 2.5 (95% confidence interval [1.6, 3.8]; P <.001). Conclusion: NT-proBNP provides information regarding the risk of SCD in a community-based population of older adults, beyond other traditional risk factors. This biomarker may ultimately prove useful in targeting the population at risk with aggressive medical management of comorbid conditions.
MeSH term(s)	Age Distribution ; Aged ; Biomarkers/blood ; Cardiovascular Diseases/blood ; Cardiovascular Diseases/mortality ; Cohort Studies ; Confidence Intervals ; Death, Sudden, Cardiac/epidemiology ; Death, Sudden, Cardiac/etiology ; Female ; Humans ; Incidence ; Kaplan-Meier Estimate ; Male ; Middle Aged ; Natriuretic Peptide, Brain/blood ; Peptide Fragments/blood ; Predictive Value of Tests ; Proportional Hazards Models ; Retrospective Studies ; Risk Assessment ; Sex Distribution ; Time Factors ; United States/epidemiology
Chemical Substances	Biomarkers ; Peptide Fragments ; pro-brain natriuretic peptide (1-76) ; Natriuretic Peptide, Brain (114471-18-0)
Language	English
Publishing date	2010-10-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2229357-7
ISSN	1556-3871 ; 1547-5271
ISSN (online)	1556-3871
ISSN	1547-5271
DOI	10.1016/j.hrthm.2010.10.038
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Article ; Online: Incorporation of the HIV-1 microbicide cyanovirin-N in a food product.

Li, Ming / Patton, Dorothy L / Cosgrove-Sweeney, Yvonne / Ratner, Deena / Rohan, Lisa C / Cole, Alexander M / Tarwater, Patrick M / Gupta, Phalguni / Ramratnam, Bharat

Journal of acquired immune deficiency syndromes (1999)

2011 Volume 58, Issue 4, Page(s) 379–384

Abstract: ... of lactic acid bacteria bioengineered to secrete cyanovirin-N. We fed pigtail macaques a yogurt formulation that used ... bioengineered strains as a starter culture. Cyanovirin-N expression could be detected in the rectal vault during ...

Abstract	An urgent need exists for HIV-1 microbicides. Here, we describe the in vivo testing of lactic acid bacteria bioengineered to secrete cyanovirin-N. We fed pigtail macaques a yogurt formulation that used bioengineered strains as a starter culture. Cyanovirin-N expression could be detected in the rectal vault during and immediately after feeding. Ex vivo viral challenge of rectal tissue biopsies revealed that peak viral burden was significantly lower in tissue obtained from experimental animals compared with control animals. Formulation of candidate compounds in lactic acid bacteria and their oral administration seems to be a feasible strategy for mucosal delivery of microbicides.
MeSH term(s)	Animals ; Anti-HIV Agents/administration & dosage ; Bacterial Proteins/administration & dosage ; Carrier Proteins/administration & dosage ; Feces/chemistry ; Feces/virology ; Female ; Food Additives/administration & dosage ; HIV Infections/prevention & control ; HIV-1/drug effects ; Macaca nemestrina ; Rectum/chemistry ; Rectum/drug effects ; Rectum/virology ; Virus Replication/drug effects ; Yogurt
Chemical Substances	Anti-HIV Agents ; Bacterial Proteins ; Carrier Proteins ; Food Additives ; cyanovirin N (184539-38-6)
Language	English
Publishing date	2011-10-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	645053-2
ISSN	1944-7884 ; 1077-9450 ; 0897-5965 ; 0894-9255 ; 1525-4135
ISSN (online)	1944-7884 ; 1077-9450
ISSN	0897-5965 ; 0894-9255 ; 1525-4135
DOI	10.1097/QAI.0b013e31823643fe
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Article: N-alkynyl derivatives of 5-fluorouracil: susceptibility to palladium-mediated dealkylation and toxigenicity in cancer cell culture.

Weiss, Jason T / Fraser, Craig / Rubio-Ruiz, Belén / Myers, Samuel H / Crispin, Richard / Dawson, John C / Brunton, Valerie G / Patton, E Elizabeth / Carragher, Neil O / Unciti-Broceta, Asier

Frontiers in chemistry

2014 Volume 2, Page(s) 56

Abstract	Palladium-activated prodrug therapy is an experimental therapeutic approach that relies on the unique chemical properties and biocompatibility of heterogeneous palladium catalysis to enable the spatially-controlled in vivo conversion of a biochemically-stable prodrug into its active form. This strategy, which would allow inducing local activation of systemically administered drug precursors by mediation of an implantable activating device made of Pd(0), has been proposed by our group as a way to reach therapeutic levels of the active drug in the affected tissue/organ while reducing its systemic toxicity. In the seminal study of such an approach, we reported that propargylation of the N1 position of 5-fluorouracil suppressed the drug's cytotoxic properties, showed high stability in cell culture and facilitated the bioorthogonal restoration of the drug's pharmacological activity in the presence of extracellular Pd(0)-functionalized resins. To provide additional insight on the properties of this system, we have investigated different N1-alkynyl derivatives of 5-fluorouracil and shown that the presence of substituents near the triple bond influence negatively on its sensitivity to palladium catalysis under biocompatible conditions. Comparative studies of the N1- vs. the N3-propargyl derivatives of 5-fluorouracil revealed that masking each or both positions equally led to inactive derivatives (>200-fold reduction of cytotoxicity relative to the unmodified drug), whereas the depropargylation process occurred faster at the N1 position than at the N3, thus resulting in greater toxigenic properties in cancer cell culture.
Language	English
Publishing date	2014-07-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2711776-5
ISSN	2296-2646
ISSN	2296-2646
DOI	10.3389/fchem.2014.00056
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Article ; Online: Influence of Error-Augmentation on the Dynamics of Visuomotor Skill Acquisition: Insights from Proxy-Process Models.

Parmar, Pritesh N / Patton, James L

Journal of neurophysiology

2024

Abstract: Our study addresses the critical question of how learners acquire skills without the constant crutch of feedback, utilizing a specialized training approach with intermittent feedback. Despite recognized benefits in skill retention, the underlying ... ...

Abstract	Our study addresses the critical question of how learners acquire skills without the constant crutch of feedback, utilizing a specialized training approach with intermittent feedback. Despite recognized benefits in skill retention, the underlying mechanisms of intermittent feedback in motor control neuroscience remain elusive. Leveraging a previously published dataset from visuomotor learning experiments with intermittent feedback, we tested a wide range of proxy-process models that posit the presence of an inferred error signal even when an explicit sensory performance is not present. Furthermore, these proxy-process models investigated the impact of error-augmentation (EA) training on visuomotor learning dynamics. Rigorous cross-validation consistently identified a second-order proxy-process model structure accurately predicting motor learning across subjects and learning tasks. Model parameters elucidated the varying influences of EA settings on the rates of change in error, inter-trial variability, and steady-state performance. We then introduced a dynamic-Proxy support Multi-Rate Motor Learning (dPxMRML) model, which shed light on EA's effects on the fast and slow learning dynamics. The dPxMRML model accurately predicted subjects' performance during and beyond training phases, highlighting EA settings conducive to long-term retention. This research yields crucial insights for personalized training program design, applicable in neuro-rehabilitation, sports, and performance training.
Language	English
Publishing date	2024-05-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	80161-6
ISSN	1522-1598 ; 0022-3077
ISSN (online)	1522-1598
ISSN	0022-3077
DOI	10.1152/jn.00051.2024
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Article: RAFT Polymerization of “Splitters” and “Cryptos”: Exploiting Azole-N-carboxamides As Blocked Isocyanates for Ambient Temperature Postpolymerization Modification

Hoff, EmilyA / Abel Brooks A / McCormick Charles L / Patton Derek L / Tretbar Chase A

Macromolecules. 2016 Jan. 26, v. 49, no. 2

2016

Abstract: ... deblocking of polymer scaffolds bearing N-heterocycle-blocked isocyanate moieties is reported. Room ... temperature RAFT polymerization of three azole-N-carboxamide methacrylates, including 3,5-dimethylpyrazole ... molecular weights and narrow dispersities (Đ < 1.2). Model analogues possessing the same N-heterocycle blocking ...

Abstract	A postpolymerization modification strategy based on ambient temperature nucleophilic chemical deblocking of polymer scaffolds bearing N-heterocycle-blocked isocyanate moieties is reported. Room temperature RAFT polymerization of three azole-N-carboxamide methacrylates, including 3,5-dimethylpyrazole, imidazole, and 1,2,4-triazole derivatives, afforded reactive polymer scaffolds with well-defined molecular weights and narrow dispersities (Đ < 1.2). Model analogues possessing the same N-heterocycle blocking agents with varied leaving group abilities were synthesized to determine optimal deblocking conditions. The reactivity of the azole-N-carboxamide moieties toward nucleophiles can be tuned simply by varying the structure of the azole blocking agents (reactivity order: pyrazole < imidazole < triazole). DBU-catalyzed reactions of thiols with imidazole- and 1,2,4-triazole-blocked isocyanate scaffolds were shown to occur rapidly and quantitatively under ambient conditions. Differences in reactivity of 1,2,4-triazole- and 3,5-dimethylpyrazole-blocked isocyanate copolymers with various nucleophiles at room temperature facilitated sequential and postpolymerization modification. This strategy advances the utility of blocked isocyanates and promotes the chemistry as a powerful postmodification tool to access multifunctional polymeric materials.
Keywords	ambient temperature ; arsenic ; composite polymers ; models ; moieties ; molecular weight ; polymerization ; thiols ; triazoles
Language	English
Dates of publication	2016-0126
Size	p. 554-563.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1491942-4
ISSN	1520-5835 ; 0024-9297
ISSN (online)	1520-5835
ISSN	0024-9297
DOI	10.1021%2Facs.macromol.5b02377
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