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Article ; Online: R

2022 Volume 59, Issue 5

Abstract: Background: Chronic airway inflammation is the main driver of pathogenesis in respiratory diseases such as severe asthma, chronic obstructive pulmonary disease, cystic fibrosis (CF) and bronchiectasis. While the role of common pathogens in airway ... ...

Abstract	Background: Chronic airway inflammation is the main driver of pathogenesis in respiratory diseases such as severe asthma, chronic obstructive pulmonary disease, cystic fibrosis (CF) and bronchiectasis. While the role of common pathogens in airway inflammation is widely recognised, the influence of other microbiota members is still poorly understood. Methods: We hypothesised that the lung microbiota contains bacteria with immunomodulatory activity which modulate net levels of immune activation by key respiratory pathogens. Therefore, we assessed the immunomodulatory effect of several members of the lung microbiota frequently reported as present in CF lower respiratory tract samples. Results: We show that Conclusions: These findings indicate that the presence of
MeSH term(s)	Animals ; Anti-Inflammatory Agents/pharmacology ; Bacteria ; Bronchiectasis/microbiology ; Cystic Fibrosis ; Humans ; Inflammation ; Lung ; Mice ; NF-kappa B ; Sputum/microbiology
Chemical Substances	Anti-Inflammatory Agents ; NF-kappa B
Language	English
Publishing date	2022-05-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639359-7
ISSN	1399-3003 ; 0903-1936
ISSN (online)	1399-3003
ISSN	0903-1936
DOI	10.1183/13993003.01293-2021
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Article ; Online: Caregiver-reported infant motor and imitation skills predict M-CHAT-R/F.

Levick, Samantha / Staples, Angela D / Warschausky, Seth / Huth-Bocks, Alissa / Taylor, H Gerry / Gidley Larson, Jennifer C / Peterson, Catherine / Lukomski, Angela / Lajiness-O'Neill, Renée

Child neuropsychology : a journal on normal and abnormal development in childhood and adolescence

2024 , Page(s) 1–19

Abstract: Altered motor and social-communicative abilities in infancy have been linked to later ASD diagnosis. Most diagnostic instruments for ASD cannot be utilized until 12 months, and the average child is diagnosed substantially later. Imitation combines motor ... ...

Abstract	Altered motor and social-communicative abilities in infancy have been linked to later ASD diagnosis. Most diagnostic instruments for ASD cannot be utilized until 12 months, and the average child is diagnosed substantially later. Imitation combines motor and social-communicative skills and is commonly atypical in infants at risk for ASD. However, few measures have been developed to assess infant imitation clinically. One barrier to the diagnostic age gap of ASD is accessibility of screening and diagnostic services. Utilization of caregiver report to reliably screen for ASD mitigates such barriers and could aid in earlier detection. The present study developed and validated a caregiver-report measure of infant imitation at 4, 6, and 9 months and explored the relationship between caregiver-reported imitation and motor abilities with later ASD risk. Participants (
Language	English
Publishing date	2024-01-26
Publishing country	England
Document type	Journal Article
ZDB-ID	1262599-1
ISSN	1744-4136 ; 0929-7049
ISSN (online)	1744-4136
ISSN	0929-7049
DOI	10.1080/09297049.2024.2304378
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Article ; Online: Gastrointestinal Tolerability and Absorption of R- Versus R,S-Lipoic Acid in Progressive Multiple Sclerosis: A Randomized Crossover Trial.

Cameron, Michelle / Taylor, Cassidy / Lapidus, Jodi / Ramsey, Katrina / Koop, Dennis / Spain, Rebecca

Journal of clinical pharmacology

2020 Volume 60, Issue 8, Page(s) 1099–1106

Abstract: We compared the gastrointestinal (GI) tolerability and assessed for bioequivalent absorption of R ... randomized crossover trial. Participants randomly assigned to formulation sequence took 600 mg of R-LA or ... 1200 mg of a 1:1 racemic R,S-LA mixture in single daily doses for 7 to 10 days, underwent a washout ...

Abstract	We compared the gastrointestinal (GI) tolerability and assessed for bioequivalent absorption of R-lipoic acid (LA) in people with progressive multiple sclerosis (MS) in a single-center, double-blind, randomized crossover trial. Participants randomly assigned to formulation sequence took 600 mg of R-LA or 1200 mg of a 1:1 racemic R,S-LA mixture in single daily doses for 7 to 10 days, underwent a washout of at least 7 days, and then took the other form of LA for 7 to 10 days. At the end of each period on LA, GI symptoms were assessed with GI questions from the Monitoring of Side Effects Scale. Serum LA concentrations were measured before and 60, 90, 120, 180, and 240 minutes after the first and last day's dose of each form of LA to derive an area under the plasma concentration-time curve (AUC) and maximum serum concentration (C
Language	English
Publishing date	2020-03-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	188980-1
ISSN	1552-4604 ; 0091-2700 ; 0021-9754
ISSN (online)	1552-4604
ISSN	0091-2700 ; 0021-9754
DOI	10.1002/jcph.1605
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Article ; Online: Probing the Catalytic Mechanism and Inhibition of SAMHD1 Using the Differential Properties of R

Morris, Elizabeth R / Kunzelmann, Simone / Caswell, Sarah J / Purkiss, Andrew G / Kelly, Geoff / Taylor, Ian A

Biochemistry

2021 Volume 60, Issue 21, Page(s) 1682–1698

Abstract: SAMHD1 is a fundamental regulator of cellular dNTPs that catalyzes their hydrolysis into 2'-deoxynucleoside and triphosphate, restricting the replication of viruses, including HIV-1, in ... ...

Abstract	SAMHD1 is a fundamental regulator of cellular dNTPs that catalyzes their hydrolysis into 2'-deoxynucleoside and triphosphate, restricting the replication of viruses, including HIV-1, in CD4
MeSH term(s)	Allosteric Regulation ; Catalysis ; Catalytic Domain ; Crystallography, X-Ray/methods ; Deoxyguanine Nucleotides/chemistry ; Deoxyribonucleotides/chemistry ; Deoxyribonucleotides/metabolism ; Humans ; Hydrolysis ; Kinetics ; Models, Molecular ; Monomeric GTP-Binding Proteins/chemistry ; SAM Domain and HD Domain-Containing Protein 1/antagonists & inhibitors ; SAM Domain and HD Domain-Containing Protein 1/chemistry ; SAM Domain and HD Domain-Containing Protein 1/metabolism ; Virus Replication/physiology
Chemical Substances	Deoxyguanine Nucleotides ; Deoxyribonucleotides ; SAM Domain and HD Domain-Containing Protein 1 (EC 3.1.5.-) ; SAMHD1 protein, human (EC 3.1.5.-) ; Monomeric GTP-Binding Proteins (EC 3.6.5.2)
Language	English
Publishing date	2021-05-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.0c00944
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Article: Wearables: An R Package With Accompanying Shiny Application for Signal Analysis of a Wearable Device Targeted at Clinicians and Researchers.

de Looff, Peter / Duursma, Remko / Noordzij, Matthijs / Taylor, Sara / Jaques, Natasha / Scheepers, Floortje / de Schepper, Kees / Koldijk, Saskia

Frontiers in behavioral neuroscience

2022 Volume 16, Page(s) 856544

Abstract: ... processed. This paper describes the creation of a "Wearables" R package and a Shiny "E4 dashboard ...

Abstract	Physiological signals (e.g., heart rate, skin conductance) that were traditionally studied in neuroscientific laboratory research are currently being used in numerous real-life studies using wearable technology. Physiological signals obtained with wearables seem to offer great potential for continuous monitoring and providing biofeedback in clinical practice and healthcare research. The physiological data obtained from these signals has utility for both clinicians and researchers. Clinicians are typically interested in the day-to-day and moment-to-moment physiological reactivity of patients to real-life stressors, events, and situations or interested in the physiological reactivity to stimuli in therapy. Researchers typically apply signal analysis methods to the data by pre-processing the physiological signals, detecting artifacts, and extracting features, which can be a challenge considering the amount of data that needs to be processed. This paper describes the creation of a "Wearables" R package and a Shiny "E4 dashboard" application for an often-studied wearable, the Empatica E4. The package and Shiny application can be used to visualize the relationship between physiological signals and real-life stressors or stimuli, but can also be used to pre-process physiological data, detect artifacts, and extract relevant features for further analysis. In addition, the application has a batch process option to analyze large amounts of physiological data into ready-to-use data files. The software accommodates users with a downloadable report that provides opportunities for a careful investigation of physiological reactions in daily life. The application is freely available, thought to be easy to use, and thought to be easily extendible to other wearable devices. Future research should focus on the usability of the application and the validation of the algorithms.
Language	English
Publishing date	2022-06-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2452960-6
ISSN	1662-5153
ISSN	1662-5153
DOI	10.3389/fnbeh.2022.856544
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Article: Ammonization of the R- and S-Epimers of Ergot Alkaloids to Assess Detoxification Potential

Cherewyk, Jensen E. / Grusie-Ogilvie, Taylor J. / Parker, Sarah E. / Blakley, Barry R. / Al-Dissi, Ahmad N.

Journal of agricultural and food chemistry. 2022 July 13, v. 70, no. 29

2022

Abstract: ... natural ergot-contaminated wheat was ammoniated. The total concentration of ergot alkaloids (R- and S ... epimers) decreased after exposure to ammonia (8–29%). Separately, the total R-epimers decreased ... the R- and S-epimers of ergot alkaloids, which may lead to a potential practical detoxification process ...

Abstract	Detoxification of ergot-contaminated feed by ammonia would be a practical application, given that ammonia is routinely used in the agriculture industry. To assess the effects of ammonia on ergot alkaloids, natural ergot-contaminated wheat was ammoniated. The total concentration of ergot alkaloids (R- and S-epimers) decreased after exposure to ammonia (8–29%). Separately, the total R-epimers decreased in concentration (40–66%), whereas the total S-epimers increased (21–81%). Specific ergot alkaloids demonstrated degradation and/or epimerization after exposure to ammonia, potentially associated with structural differences, and influenced the total concentrations observed. Ammonization of ergot standards resulted in potential degradation products and epimerization, supporting the above results. The use of ultrahigh-performance liquid chromatography–tandem mass spectrometry provides an updated assessment of the detoxification potential of ammonia for ergot alkaloids and the quantification of the S-epimers. Ammonia alters the R- and S-epimers of ergot alkaloids, which may lead to a potential practical detoxification process of ergot-contaminated feed.
Keywords	agricultural industry ; ammonia ; ergot ; food chemistry ; liquid chromatography ; tandem mass spectrometry ; wheat
Language	English
Dates of publication	2022-0713
Size	p. 8931-8941.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	241619-0
ISSN	1520-5118 ; 0021-8561
ISSN (online)	1520-5118
ISSN	0021-8561
DOI	10.1021/acs.jafc.2c01583
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Article ; Online: Structural snapshots of R-loop formation by a type I-C CRISPR Cascade.

O'Brien, Roisin E / Bravo, Jack P K / Ramos, Delisa / Hibshman, Grace N / Wright, Jacquelyn T / Taylor, David W

Molecular cell

2023 Volume 83, Issue 5, Page(s) 746–758.e5

Abstract: ... mechanism facilitates efficient R-loop formation and prevents dsDNA reannealing. Additionally, we provide ... basis for directional R-loop formation and reveal how different Acr proteins have converged upon common ...

Abstract	Type I CRISPR-Cas systems employ multi-subunit Cascade effector complexes to target foreign nucleic acids for destruction. Here, we present structures of D. vulgaris type I-C Cascade at various stages of double-stranded (ds)DNA target capture, revealing mechanisms that underpin PAM recognition and Cascade allosteric activation. We uncover an interesting mechanism of non-target strand (NTS) DNA stabilization via stacking interactions with the "belly" subunits, securing the NTS in place. This "molecular seatbelt" mechanism facilitates efficient R-loop formation and prevents dsDNA reannealing. Additionally, we provide structural insights into how two anti-CRISPR (Acr) proteins utilize distinct strategies to achieve a shared mechanism of type I-C Cascade inhibition by blocking PAM scanning. These observations form a structural basis for directional R-loop formation and reveal how different Acr proteins have converged upon common molecular mechanisms to efficiently shut down CRISPR immunity.
MeSH term(s)	R-Loop Structures ; Protein Conformation ; Models, Molecular ; DNA/genetics ; CRISPR-Cas Systems ; CRISPR-Associated Proteins/genetics
Chemical Substances	DNA (9007-49-2) ; CRISPR-Associated Proteins
Language	English
Publishing date	2023-02-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2023.01.024
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Article: bistro: An R package for vector bloodmeal identification by short tandem repeat overlap.

Lapp, Zena / Abel, Lucy / Mangeni, Judith / Obala, Andrew A / O'Meara, Wendy / Taylor, Steve M / Markwalter, Christine F

medRxiv : the preprint server for health sciences

2023

Abstract: ... We developed bistro, an R package that implements 3 preexisting STR matching methods as well as the package's ... Then we applied it to match 777 newly field-collected mosquito bloodmeals to a database of 645 people. 3. The R ... and robust analyses of vector-human contact in natural settings. The bistro R package and ...

Abstract	1. Measuring vector-human contact in a natural setting can inform precise targeting of interventions to interrupt transmission of vector-borne diseases. One approach is to directly match human DNA in vector bloodmeals to the individuals who were bitten using genotype panels of discriminative short tandem repeats (STRs). Existing methods for matching STR profiles in bloodmeals to the people bitten preclude the ability to match most incomplete profiles and multi-source bloodmeals to bitten individuals. 2. We developed bistro, an R package that implements 3 preexisting STR matching methods as well as the package's namesake, bistro, a new algorithm described here. bistro employs forensic analysis methods to calculate likelihood ratios and match human STR profiles in bloodmeals to people using a dynamic threshold. We evaluated the algorithm's accuracy and compared it to existing matching approaches using a publicly-available panel of 188 single-source and 100 multi-source samples containing DNA from 50 known human sources. Then we applied it to match 777 newly field-collected mosquito bloodmeals to a database of 645 people. 3. The R package implements four STR matching algorithms in user-friendly functions with clear documentation. bistro correctly matched 99% (184/185) of profiles in single-source samples, and 63% (225/359) of profiles from multi-source samples, resulting in a sensitivity of 0.75 (vs < 0.51 for other algorithms). The specificity of bistro was 0.9998 (vs. 1 for other algorithms). Furthermore, bistro identified 80% (729/909) of all possible matches for field-derived mosquitoes, yielding 1.4x more matches than existing algorithms. 4. bistro identifies more correct bloodmeal-human matches than existing approaches, enabling more accurate and robust analyses of vector-human contact in natural settings. The bistro R package and corresponding documentation allow for straightforward uptake of this algorithm by others.
Language	English
Publishing date	2023-09-15
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.09.14.23295566
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Article ; Online: Correction: Structural and Functional Analysis of the Symmetrical Type I Restriction Endonuclease R.EcoR124INT.

Taylor, James E N / Swiderska, Anna / Artero, Jean-Baptiste / Callow, Philip / Kneale, Geoff

PloS one

2024 Volume 19, Issue 3, Page(s) e0301486

Abstract: This corrects the article DOI: 10.1371/journal.pone.0035263.]. ...

Abstract	[This corrects the article DOI: 10.1371/journal.pone.0035263.].
Language	English
Publishing date	2024-03-26
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0301486
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Article ; Online: Design and Synthesis of D 3 R Bitopic Ligands with Flexible Secondary Binding Fragments

Gui-Long Tian / Chia-Ju Hsieh / Michelle Taylor / Ji Youn Lee / Robert R. Luedtke / Robert H. Mach

Molecules, Vol 29, Iss 1, p

Radioligand Binding and Computational Chemistry Studies

2023 Volume 123

Abstract: ... were prepared with the goal of preparing a D 3 R-selective compound. The effect of the flexible linker ... R , S ) -trans -2a – d ), SBFs ( ( R , S ) -trans -2h – j ), and the chirality of orthosteric ... binding fragments (OBFs) ( ( S , R ) -trans -d , ( S , R ) -trans -i , ( S , S ) -trans -d , ( S , S ...

Abstract	A series of bitopic ligands based on Fallypride with a flexible secondary binding fragment (SBF) were prepared with the goal of preparing a D 3 R-selective compound. The effect of the flexible linker ( ( R , S ) -trans -2a – d ), SBFs ( ( R , S ) -trans -2h – j ), and the chirality of orthosteric binding fragments (OBFs) ( ( S , R ) -trans -d , ( S , R ) -trans -i , ( S , S ) -trans -d , ( S , S ) -trans -i, ( R , R ) -trans -d, and ( R , R ) -trans -i ) were evaluated in in vitro binding assays. Computational chemistry studies revealed that the interaction of the fragment binding to the SBF increased the distance between the pyrrolidine nitrogen and ASP110 3.32 of the D 3 R, thereby reducing the D 3 R affinity to a suboptimal level.
Keywords	dopamine 2 receptor ; dopamine 3 receptor ; flexible linker ; bitopic ligands ; molecular dynamic simulation ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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