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Article ; Online: African American English intensifier

Jones, Taylor

Frontiers in artificial intelligence

2023 Volume 5, Page(s) 683104

Abstract: There are some linguistic forms that may be known to both speakers and linguists, but that occur naturally with such low frequency that traditional sociolinguistic methods do not allow for study. This study investigates one such phenomenon: the ... ...

Abstract	There are some linguistic forms that may be known to both speakers and linguists, but that occur naturally with such low frequency that traditional sociolinguistic methods do not allow for study. This study investigates one such phenomenon: the grammatical reanalysis of an intensifier in some forms of African American English-from a full phrase
Language	English
Publishing date	2023-01-27
Publishing country	Switzerland
Document type	Journal Article
ISSN	2624-8212
ISSN (online)	2624-8212
DOI	10.3389/frai.2022.683104
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Article ; Online: Early Care and Education Settings Are Vital for Childhood Obesity Prevention.

Jones-Taylor, Myra

Childhood obesity (Print)

2015 Volume 11, Issue 5, Page(s) 489–490

MeSH term(s)	Child ; Child Nutritional Physiological Phenomena ; Child, Preschool ; Health Education/organization & administration ; Health Education/standards ; Health Promotion/organization & administration ; Humans ; Parents/education ; Pediatric Obesity/prevention & control ; Practice Guidelines as Topic ; Program Evaluation ; School Health Services/organization & administration ; School Health Services/standards ; Social Environment
Language	English
Publishing date	2015-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	2639910-6
ISSN	2153-2176 ; 2153-2168
ISSN (online)	2153-2176
ISSN	2153-2168
DOI	10.1089/chi.2015.0156
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Article: A transcription factor (TF) inference method that broadly measures TF activity and identifies mechanistically distinct TF networks.

Jones, Taylor / Sigauke, Rutendo F / Sanford, Lynn / Taatjes, Dylan J / Allen, Mary A / Dowell, Robin D

bioRxiv : the preprint server for biology

2024

Abstract: TF profiler is a method of inferring transcription factor regulatory activity, i.e. when a TF is present and actively regulating transcription, directly directly from nascent sequencing assays such as PRO-seq and GRO-seq. Transcription factors ... ...

Abstract	TF profiler is a method of inferring transcription factor regulatory activity, i.e. when a TF is present and actively regulating transcription, directly directly from nascent sequencing assays such as PRO-seq and GRO-seq. Transcription factors orchestrate transcription and play a critical role in cellular maintenance, identity and response to external stimuli. While ChIP assays have measured DNA localization, they fall short of identifying when and where transcription factors are actively regulating transcription. Our method, on the other hand, uses RNA polymerase activity to infer TF activity across hundreds of data sets and transcription factors. Based on these classifications we identify three distinct classes of transcription factors: ubiquitous factors that play roles in cellular homeostasis, driving basal gene programs across tissues and cell types, tissue specific factors that act almost exclusively at enhancers and are themselves regulated at transcription, and stimulus responsive TFs which are regulated post-transcriptionally but act predominantly at enhancers. TF profiler is broadly applicable, providing regulatory insights on any PRO-seq sample for any transcription factor with a known binding motif.
Language	English
Publishing date	2024-03-16
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.15.585303
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Article: A Survey of Virginia Vineyards Revealed High Incidences of Grapevine Rupestris Stem Pitting-Associated Virus, Grapevine Red Blotch Virus, and Two Mealybug Species

Jones, Taylor / Nita, Mizuho

Plant health progress. 2019 Sept. 12, v. 20, no. 4

2019

Abstract: We investigated the prevalence of viruses infecting grapevines in Virginia, identity of disease vectors, and potential factors affecting virus incidence. Tested viruses were grapevine leafroll-associated virus (GLRaV-1 and -4), grapevine fleck virus ( ... ...

Abstract	We investigated the prevalence of viruses infecting grapevines in Virginia, identity of disease vectors, and potential factors affecting virus incidence. Tested viruses were grapevine leafroll-associated virus (GLRaV-1 and -4), grapevine fleck virus (GFkV), grapevine virus A (GVA), grapevine virus B (GVB), grapevine rupestris stem pitting-associated virus (GRSPaV), tomato ringspot virus (ToRSV), grapevine vein clearing virus (GVCV), grapevine red blotch virus (GRBV), and grapevine Pinot gris virus (GPGV). We documented wide distributions of GRSPaV (54%) and GRBV (24%) and common occurrences of grape (Pseudococcus maritimus) and Gill’s (Ferrisia gilli) mealybugs among vineyards. This is the first report of GLRaV-1, GLRaV-4, GVA, GVB, GRSPaV, and obscure mealybug (Pseudococcus viburni) in Virginia. We also documented significant association (P ≤ 0.05) of the presence of mealybugs and GVA and GVB. With younger vines, significantly lower incidences were found for viruses that were listed (i.e., tested for a certification) by the Foundation Planting Service’s and the National Clean Plant Network’s grape programs. On the other hand, there was a lack of the age effect on incidence of GRSPaV and GRBV, which were not listed until recently. These results suggest the importance of clean plant material and vector management for grapevine virus disease management in Virginia.
Keywords	age ; certification ; disease control ; disease vectors ; Ferrisia ; grapes ; Grapevine fleck virus ; Grapevine leafroll-associated virus ; Grapevine red blotch virus ; Grapevine rupestris stem pitting-associated virus ; Grapevine virus A ; Grapevine virus B ; plant diseases and disorders ; plant viruses ; planting ; Pseudococcus maritimus ; Pseudococcus viburni ; surveys ; Tomato ringspot virus ; vines ; vineyards ; viruses ; Vitis ; Virginia
Language	English
Dates of publication	2019-0912
Size	p. 207-214.
Publishing place	The American Phytopathological Society
Document type	Article
ISSN	1535-1025
DOI	10.1094/PHP-04-19-0026-S
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Light-Inducible Generation of Membrane Curvature in Live Cells with Engineered BAR Domain Proteins.

Jones, Taylor / Liu, Aofei / Cui, Bianxiao

ACS synthetic biology

2020 Volume 9, Issue 4, Page(s) 893–901

Abstract: Nanoscale membrane curvature is now understood to play an active role in essential cellular processes such as endocytosis, exocytosis, and actin dynamics. Previous studies have shown that membrane curvature can directly affect protein function and ... ...

Abstract	Nanoscale membrane curvature is now understood to play an active role in essential cellular processes such as endocytosis, exocytosis, and actin dynamics. Previous studies have shown that membrane curvature can directly affect protein function and intracellular signaling. However, few methods are able to precisely manipulate membrane curvature in live cells. Here, we report the development of a new method of generating nanoscale membrane curvature in live cells that is controllable, reversible, and capable of precise spatial and temporal manipulation. For this purpose, we make use of Bin/Amphiphysin/Rvs (BAR) domain proteins, a family of well-studied membrane-remodeling and membrane-sculpting proteins. Specifically, we engineered two optogenetic systems, opto-FBAR and opto-IBAR, that allow light-inducible formation of positive and negative membrane curvature, respectively. Using opto-FBAR, blue light activation results in the formation of tubular membrane invaginations (positive curvature), controllable down to the subcellular level. Using opto-IBAR, blue light illumination results in the formation of membrane protrusions or filopodia (negative curvature). These systems present a novel approach for light-inducible manipulation of nanoscale membrane curvature in live cells.
MeSH term(s)	Animals ; COS Cells ; Cell Line, Tumor ; Cell Membrane/genetics ; Cell Membrane/metabolism ; Cell Membrane/physiology ; Cell Membrane/radiation effects ; Chlorocebus aethiops ; Fatty Acid-Binding Proteins/genetics ; Fatty Acid-Binding Proteins/metabolism ; Light ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Nerve Tissue Proteins/genetics ; Nerve Tissue Proteins/metabolism ; Optogenetics/methods ; Protein Engineering ; Pseudopodia/genetics ; Pseudopodia/metabolism
Chemical Substances	BAIAP2 protein, human ; FNBP1 protein, human ; Fatty Acid-Binding Proteins ; Membrane Proteins ; Nerve Tissue Proteins ; amphiphysin (147954-52-7)
Language	English
Publishing date	2020-04-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	2161-5063
ISSN (online)	2161-5063
DOI	10.1021/acssynbio.9b00516
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Article ; Online: Coordination variability during running in adolescents with autism spectrum disorder.

Bennett, Hunter J / Jones, Taylor / Valenzuela, Kevin A / Haegele, Justin A

Autism : the international journal of research and practice

2021 Volume 26, Issue 5, Page(s) 1201–1215

Abstract: Lay abstract: Walking and running are popular forms of physical activity that involve the whole body (pelvis/legs and arms/torso) and are coordinated by the neuromuscular system, generally without much conscious effort. However, autistic persons tend ... ...

Abstract	Lay abstract: Walking and running are popular forms of physical activity that involve the whole body (pelvis/legs and arms/torso) and are coordinated by the neuromuscular system, generally without much conscious effort. However, autistic persons tend not to engage in sufficient amounts of these activities to enjoy their health benefits. Recent reports indicate that autistic individuals tend to experience altered coordination patterns and increased variability during walking tasks when compared to non-autistic controls. Greater stride-to-stride coordination variability, when the task has not changed (i.e. walking at same speed and on same surface), is likely indicative of motor control issues and is more metabolically wasteful. To date, although, research examining running is unavailable in any form for this population. This study aimed to determine if coordination variability during running differs between autistic adolescents and age, sex, and body mass index matched non-autistic controls. This study found that increased variability exists throughout the many different areas of the body (foot-leg, left/right thighs, and opposite arm-opposite thigh) for autistic adolescents compared to controls. Along with previous research, these findings indicate autistic persons exhibit motor control issues across both forms of locomotion (walking and running) and at multiple speeds. These findings highlight issues with motor control that can be addressed by therapeutic/rehabilitative programming. Reducing coordination variability, inherently lessening metabolic inefficiency, may be an important step toward encouraging autistic youth to engage in sufficient physical activity (i.e. running) to enjoy physiological and psychological benefits.
MeSH term(s)	Adolescent ; Autism Spectrum Disorder ; Biomechanical Phenomena/physiology ; Gait/physiology ; Humans ; Running/physiology ; Walking/physiology
Language	English
Publishing date	2021-09-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1338513-6
ISSN	1461-7005 ; 1362-3613
ISSN (online)	1461-7005
ISSN	1362-3613
DOI	10.1177/13623613211044395
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Article ; Online: Scapular motion is accelerated in asymptomatic individuals with dyskinesis: An observational study.

Day, Joseph M / Jones, Taylor / Eiben, Kayla / Berger, Yitz

Journal of bodywork and movement therapies

2021 Volume 26, Page(s) 134–140

Abstract: Introduction: Individuals with shoulder and upper extremity pathology often present with altered scapular motion. Few studies have looked at variations in scapular acceleration as a way of quantifying scapular motion. The purpose was to determine the ... ...

Abstract	Introduction: Individuals with shoulder and upper extremity pathology often present with altered scapular motion. Few studies have looked at variations in scapular acceleration as a way of quantifying scapular motion. The purpose was to determine the effectiveness of wireless accelerometers for detecting changes in acceleration in individuals with scapular dyskinesis. Materials/methods: Twenty-seven asymptomatic college students (mean age 24 (SD ± 1.54), 65% female, 93% right handed) were visually screened for scapular dyskinesis using previously described criteria. Of the students recruited, fifteen students were determined to have scapular dyskinesis. After securing a wireless accelerometer (MyoResearch 3D DTS) on the dominate scapula, the participants performed five repetitions of standing scaption from 0 to 140°. Linear scapular accelerations along three orthogonal axes (frontal-y, transverse-z, and sagittal-x) were collected. Intraclass correlation coefficients (ICC Results: There was good between day intra-rater reliability for the average of all three axes (ICC = 0.79) and for the x and y axes (ICC > 0.78). Reliability was poor (ICC = 0.31) for the z-axis. There was a significant increase in overall acceleration of the scapula in those with dyskinesis (p = .039). There was also a significant increase in acceleration along the y-axis for those with dyskinesis (p = .003) but not for the other axes (p > .16). Conclusion: Wireless accelerometers reliably quantify scapular acceleration in healthy individuals. In a healthy population with dyskinesis, the overall magnitude of scapular acceleration was greater when compared to a healthy group without dyskinesis.
MeSH term(s)	Adult ; Biomechanical Phenomena ; Female ; Humans ; Male ; Range of Motion, Articular ; Reproducibility of Results ; Scapula ; Shoulder Joint ; Young Adult
Language	English
Publishing date	2021-02-06
Publishing country	United States
Document type	Journal Article ; Observational Study
ZDB-ID	2029441-4
ISSN	1532-9283 ; 1360-8592
ISSN (online)	1532-9283
ISSN	1360-8592
DOI	10.1016/j.jbmt.2020.12.034
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Article ; Online: Inter and intra-limb coordination variability during walking in adolescents with autism spectrum disorder.

Bennett, Hunter J / Jones, Taylor / Valenzuela, Kevin A / Haegele, Justin A

Clinical biomechanics (Bristol, Avon)

2021 Volume 89, Page(s) 105474

Abstract: Background: Autism spectrum disorder, a neurodevelopmental disorder, is difficult to characterize from a gait biomechanics perspective, possibly due to increased inter and intra-individual variability. Previous research illustrates increased gait ... ...

Abstract	Background: Autism spectrum disorder, a neurodevelopmental disorder, is difficult to characterize from a gait biomechanics perspective, possibly due to increased inter and intra-individual variability. Previous research illustrates increased gait variability in young children with autism, but assessments in older adolescents or at varying speeds are unavailable. The purpose of this study was to determine if adolescents with autism demonstrate increased intra-limb and inter-limb coordination variability during walking compared to age, sex, and body mass index matched controls. Methods: Seventeen adolescents with autism (age 13-18 years) and seventeen matched controls performed walking at two matched speeds: self-selected of adolescents with autism and at 1.3 m/s. Modified vector coding was used to determine the patterns of movement for foot-shank, left/right thigh, and contralateral thigh-arm coupling. Coordination variability, a measure of cycle-to-cycle variability, was determined across the full stride. Mixed-model analyses of variance were used to determine if group by speed interactions and/or main effects existed for coordination variability. Findings: A significant interaction existed for foot-shank variability (p = 0.039). Adolescents with autism had greater variability at self-selected speeds (p = 0.018), but not at 1.3 m/s (p = 0.593) compared to controls. Thigh-thigh coordination was greater for adolescents with ASD compared to controls at both speeds (p = 0.021). Variability was decreased at 1.3 m/s for both foot-shank (p = 0.016) and thigh-thigh (p = 0.021) coupling. Interpretation: This study illustrates that adolescents with autism perform walking with increased coordination variability at both proximal and distal segments. Thus, it is likely intra-individual variability drives the disparity of movement patterns in this population.
MeSH term(s)	Adolescent ; Autism Spectrum Disorder ; Biomechanical Phenomena ; Child ; Child, Preschool ; Gait ; Humans ; Lower Extremity ; Walking
Language	English
Publishing date	2021-08-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	632747-3
ISSN	1879-1271 ; 0268-0033
ISSN (online)	1879-1271
ISSN	0268-0033
DOI	10.1016/j.clinbiomech.2021.105474
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Zs.B 2876: Show issues

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Article ; Online: Benchmarking AlphaFold2 on peptide structure prediction.

McDonald, Eli Fritz / Jones, Taylor / Plate, Lars / Meiler, Jens / Gulsevin, Alican

Structure (London, England : 1993)

2022 Volume 31, Issue 1, Page(s) 111–119.e2

Abstract: Recent advancements in computational tools have allowed protein structure prediction with high accuracy. Computational prediction methods have been used for modeling many soluble and membrane proteins, but the performance of these methods in modeling ... ...

Abstract	Recent advancements in computational tools have allowed protein structure prediction with high accuracy. Computational prediction methods have been used for modeling many soluble and membrane proteins, but the performance of these methods in modeling peptide structures has not yet been systematically investigated. We benchmarked the accuracy of AlphaFold2 in predicting 588 peptide structures between 10 and 40 amino acids using experimentally determined NMR structures as reference. Our results showed AlphaFold2 predicts α-helical, β-hairpin, and disulfide-rich peptides with high accuracy. AlphaFold2 performed at least as well if not better than alternative methods developed specifically for peptide structure prediction. AlphaFold2 showed several shortcomings in predicting Φ/Ψ angles, disulfide bond patterns, and the lowest RMSD structures failed to correlate with lowest pLDDT ranked structures. In summary, computation can be a powerful tool to predict peptide structures, but additional steps may be necessary to analyze and validate the results.
MeSH term(s)	Protein Structure, Secondary ; Benchmarking ; Peptides/chemistry ; Membrane Proteins ; Disulfides ; Protein Conformation
Chemical Substances	Peptides ; Membrane Proteins ; Disulfides
Language	English
Publishing date	2022-12-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2022.11.012
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Article: Cellular zinc status alters chromatin accessibility and binding of transcription factor p53 to genomic sites.

Damon, Leah J / Ocampo, Daniel / Sanford, Lynn / Jones, Taylor / Allen, Mary A / Dowell, Robin D / Palmer, Amy E

bioRxiv : the preprint server for biology

2023

Abstract: ... Zinc ( ... ...

Abstract	Zinc (Zn
Language	English
Publishing date	2023-11-21
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.11.20.567954
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