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Article ; Online: Protein Identification from Tandem Mass Spectra by Database Searching.

Edwards, Nathan J

Methods in molecular biology (Clifton, N.J.)

2017 Volume 1558, Page(s) 357–380

Abstract: Protein identification from tandem mass spectra is one of the most versatile and widely used proteomics workflows, able to identify proteins, characterize post-translational modifications, and provide semiquantitative measurements of relative protein ... ...

Abstract	Protein identification from tandem mass spectra is one of the most versatile and widely used proteomics workflows, able to identify proteins, characterize post-translational modifications, and provide semiquantitative measurements of relative protein abundance. This manuscript describes the concepts, prerequisites, and methods required to analyze a tandem mass spectrometry dataset in order to identify its proteins, by using a tandem mass spectrometry search engine to search protein sequence databases. The discussion includes instructions for extraction, preparation, and formatting of spectral datafiles, selection of appropriate search parameter settings, and basic interpretation of the results.
Language	English
Publishing date	2017
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-6783-4_17
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Article ; Online: Temporal and spatial drivers of the structure of macroinvertebrate assemblages associated with Laminaria hyperborea detritus in the northeast Atlantic.

Gouraguine, Adam / Smale, Dan A / Edwards, Arwyn / King, Nathan G / Jackson-Bué, Mathilde / Kelly, Sean / Earp, Hannah S / Moore, Pippa J

Marine environmental research

2024 Volume 198, Page(s) 106518

Abstract: Kelp forests occur on more than a quarter of the world's coastlines, serving as foundation species supporting high levels of biodiversity. They are also a major source of organic matter in coastal ecosystems, with the majority of primary production ... ...

Abstract	Kelp forests occur on more than a quarter of the world's coastlines, serving as foundation species supporting high levels of biodiversity. They are also a major source of organic matter in coastal ecosystems, with the majority of primary production released and exported as detritus. Kelp detritus also provides food and shelter for macroinvertebrates, which comprise important components of inshore food-webs. Hitherto, research on kelp detritus-associated macroinvertebrate assemblages remains relatively limited. We quantified spatiotemporal variability in the structure of detritus-associated macroinvertebrate assemblages within Laminaria hyperborea forests and evaluated the influence of putative drivers of the observed variability in assemblages across eight study sites within four regions of the United Kingdom in May and September 2015. We documented 5167 individuals from 106 taxa with Malacostraca, Gastropoda, Isopoda and Bivalvia the most abundant groups sampled. Assemblage structure varied across months, sites, and regions, with highest richness in September compared to May. Many taxa were unique to individual regions, with few documented in all regions. Finally, key drivers of assemblage structure included detritus tissue nitrogen content, depth, sea surface temperature, light intensity, as well as L. hyperborea canopy density and canopy biomass. Despite their dynamic composition and transient existence, accumulations of L. hyperborea detritus represent valuable repositories of biodiversity and represent an additional kelp forest component which influences secondary productivity, and potentially kelp forest food-web dynamics.
Language	English
Publishing date	2024-04-16
Publishing country	England
Document type	Journal Article
ZDB-ID	1502505-6
ISSN	1879-0291 ; 0141-1136
ISSN (online)	1879-0291
ISSN	0141-1136
DOI	10.1016/j.marenvres.2024.106518
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Article ; Online: Use of accelerometers and inertial measurement units to quantify movement of tactical athletes: A systematic review.

Edwards, Nathan A / Talarico, Maria K / Chaudhari, Ajit / Mansfield, Cody J / Oñate, James

Applied ergonomics

2023 Volume 109, Page(s) 103991

Abstract: The dynamic work environments of tactical athletes are difficult to replicate in a laboratory. Accelerometers and inertial measurement units provide a way to characterize movement in the field. This systematic review identified how accelerometers and ... ...

Abstract	The dynamic work environments of tactical athletes are difficult to replicate in a laboratory. Accelerometers and inertial measurement units provide a way to characterize movement in the field. This systematic review identified how accelerometers and inertial measurement units are currently being used to quantify movement patterns of tactical athletes. Seven research and military databases were searched, producing 26,228 potential articles with 78 articles included in this review. The articles studied military personnel (73.1%), firefighters (19.2%), paramedics (3.8%), and law enforcement officers (3.8%). Accelerometers were the most used type of sensor, and physical activity was the primarily reported outcome variable. Seventy of the studies had fair or poor quality. Research on firefighters, emergency medical services, and law enforcement officers was limited. Future research should strive to make quantified movement data more accessible and user-friendly for non-research personnel, thereby prompting increased use in tactical athlete groups, especially first responder agencies.
MeSH term(s)	Humans ; Accelerometry ; Emergency Responders ; Firefighters ; Military Personnel ; Motor Activity ; Movement ; Paramedics ; Police
Language	English
Publishing date	2023-02-24
Publishing country	England
Document type	Systematic Review ; Journal Article ; Review
ZDB-ID	2003513-5
ISSN	1872-9126 ; 0003-6870
ISSN (online)	1872-9126
ISSN	0003-6870
DOI	10.1016/j.apergo.2023.103991
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Article ; Online: High-throughput detection of T-DNA insertion sites for multiple transgenes in complex genomes.

Edwards, Brianne / Hornstein, Eli D / Wilson, Nathan J / Sederoff, Heike

BMC genomics

2022 Volume 23, Issue 1, Page(s) 685

Abstract: Background: Genetic engineering of crop plants has been successful in transferring traits into elite lines beyond what can be achieved with breeding techniques. Introduction of transgenes originating from other species has conferred resistance to biotic ...

Abstract	Background: Genetic engineering of crop plants has been successful in transferring traits into elite lines beyond what can be achieved with breeding techniques. Introduction of transgenes originating from other species has conferred resistance to biotic and abiotic stresses, increased efficiency, and modified developmental programs. The next challenge is now to combine multiple transgenes into elite varieties via gene stacking to combine traits. Generating stable homozygous lines with multiple transgenes requires selection of segregating generations which is time consuming and labor intensive, especially if the crop is polyploid. Insertion site effects and transgene copy number are important metrics for commercialization and trait efficiency. Results: We have developed a simple method to identify the sites of transgene insertions using T-DNA-specific primers and high-throughput sequencing that enables identification of multiple insertion sites in the T Conclusion: This new methodology enables the early selection of desirable transgene location and copy number to generate homozygous lines within two generations.
MeSH term(s)	DNA, Bacterial/genetics ; Plant Breeding ; Plants, Genetically Modified/genetics ; Transgenes
Chemical Substances	DNA, Bacterial ; T-DNA
Language	English
Publishing date	2022-10-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-022-08918-6
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Article ; Online: SARS-CoV and SARS-CoV-2 display limited neuronal infection and lack the ability to transmit within synaptically connected axons in stem cell-derived human neurons.

Luczo, Jasmina M / Edwards, Sarah J / Ardipradja, Katie / Suen, Willy W / Au, Gough G / Marsh, Glenn A / Godde, Nathan / Rootes, Christina L / Bingham, John / Sundaramoorthy, Vinod

Journal of neurovirology

2024 Volume 30, Issue 1, Page(s) 39–51

Abstract: Sarbecoviruses such as SARS and SARS-CoV-2 have been responsible for two major outbreaks in humans, the latter resulting in a global pandemic. While sarbecoviruses primarily cause an acute respiratory infection, they have been shown to infect the nervous ...

Abstract	Sarbecoviruses such as SARS and SARS-CoV-2 have been responsible for two major outbreaks in humans, the latter resulting in a global pandemic. While sarbecoviruses primarily cause an acute respiratory infection, they have been shown to infect the nervous system. However, mechanisms of sarbecovirus neuroinvasion and neuropathogenesis remain unclear. In this study, we examined the infectivity and trans-synaptic transmission potential of the sarbecoviruses SARS and SARS-CoV-2 in human stem cell-derived neural model systems. We demonstrated limited ability of sarbecoviruses to infect and replicate in human stem cell-derived neurons. Furthermore, we demonstrated an inability of sarbecoviruses to transmit between synaptically connected human stem cell-derived neurons. Finally, we determined an absence of SARS-CoV-2 infection in olfactory neurons in experimentally infected ferrets. Collectively, this study indicates that sarbecoviruses exhibit low potential to infect human stem cell-derived neurons, lack an ability to infect ferret olfactory neurons, and lack an inbuilt molecular mechanism to utilise retrograde axonal trafficking and trans-synaptic transmission to spread within the human nervous system.
MeSH term(s)	Humans ; SARS-CoV-2/pathogenicity ; SARS-CoV-2/physiology ; Animals ; COVID-19/virology ; COVID-19/transmission ; Axons/virology ; Ferrets/virology ; Severe acute respiratory syndrome-related coronavirus/physiology ; Severe acute respiratory syndrome-related coronavirus/pathogenicity ; Neurons/virology ; Virus Replication ; Chlorocebus aethiops ; Neural Stem Cells/virology ; Vero Cells
Language	English
Publishing date	2024-01-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1283265-0
ISSN	1538-2443 ; 1355-0284
ISSN (online)	1538-2443
ISSN	1355-0284
DOI	10.1007/s13365-023-01187-3
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Article ; Online: Normative Performance Profiles of College Aged Esport Athletes in a Pilot Study.

Onate, James A / Edwards, Nathan A / Emerson, Angela / Maymir, Caleb L / Kraemer, William J / Fogt, Nick / Fogt, Jennifer S / Conroy, Sara

International journal of esports

2023 Volume 2023

Abstract: Aims: This study aimed to holistically assess the physical and cognitive attributes of esport athletes.: Methods and results: Forty-six adults between 18 and 32 years old with experience playing videogames were enrolled in this study. Participants ... ...

Abstract	Aims: This study aimed to holistically assess the physical and cognitive attributes of esport athletes. Methods and results: Forty-six adults between 18 and 32 years old with experience playing videogames were enrolled in this study. Participants completed assessments in five areas: demographics, self-report questionnaires, cognitive performance, physical performance, and gaming performance. Participants self-reported Overwatch ranking and physical activity participation (Pediatric Physical Activity Measure), and grip strength was measured with a handheld dynamometer. Seven domains of physical, mental, and social health and well-being were measured with the Patient Reported Outcomes Measurement Information System (PROMIS-29). The List Sorting Working Memory Test and Picture Sequence Memory Test from the National Institutes of Health (NIH) Toolbox Cognition Batteries were used to measure cognitive performance. Finally, esports performance was measured using a series of tasks through Alienware Academy and AIM Booster to record accuracy, reaction time, and targets hit. Participants were separated into high and low ranking groups for comparisons. This sample of esport athletes was similar to the general population for grip strength, each of the PROMIS-29 metrics, the List Sorting Working Memory Test, and the Picture Sequence Memory Test. Reaction time was the variable with the only significant difference between ranking groups. Conclusion: This study represents a primary investigation of esport athletes using a holistic approach. By incorporating physical and cognitive components, the most important factors to esport athletes' health and performance can be better understood and applied.
Language	English
Publishing date	2023-04-01
Publishing country	England
Document type	Journal Article
ISSN	2634-1069
ISSN (online)	2634-1069
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Article ; Online: PepArML: A Meta-Search Peptide Identification Platform for Tandem Mass Spectra.

Edwards, Nathan J

Current protocols in bioinformatics

2013 Volume 44, Page(s) 13.23.1–23

Abstract: The PepArML meta-search peptide identification platform for tandem mass spectra provides a unified search interface to seven search engines; a robust cluster, grid, and cloud computing scheduler for large-scale searches; and an unsupervised, model-free, ... ...

Abstract	The PepArML meta-search peptide identification platform for tandem mass spectra provides a unified search interface to seven search engines; a robust cluster, grid, and cloud computing scheduler for large-scale searches; and an unsupervised, model-free, machine-learning-based result combiner, which selects the best peptide identification for each spectrum, estimates false-discovery rates, and outputs pepXML format identifications. The meta-search platform supports Mascot; Tandem with native, k-score and s-score scoring; OMSSA; MyriMatch; and InsPecT with MS-GF spectral probability scores—reformatting spectral data and constructing search configurations for each search engine on the fly. The combiner selects the best peptide identification for each spectrum based on search engine results and features that model enzymatic digestion, retention time, precursor isotope clusters, mass accuracy, and proteotypic peptide properties, requiring no prior knowledge of feature utility or weighting. The PepArML meta-search peptide identification platform often identifies two to three times more spectra than individual search engines at 10% FDR.
MeSH term(s)	Humans ; Peptides/analysis ; Search Engine ; Software ; Tandem Mass Spectrometry/methods
Chemical Substances	Peptides
Language	English
Publishing date	2013-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1934-340X
ISSN (online)	1934-340X
DOI	10.1002/0471250953.bi1323s44
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Article ; Online: The contributions of clinical disease activity, functional disability, and illness intrusiveness to depressive symptoms in pediatric inflammatory bowel disease.

Edwards, Clayton S / Baudino, Marissa N / Roberts, Caroline M / Basile, Nathan L / Dattilo, Taylor M / Gamwell, Kaitlyn L / Jacobs, Noel J / Edwards, Desti S / Tung, Jeanne / Parker, Colton V / Chaney, John M

Journal of pediatric gastroenterology and nutrition

2023 Volume 78, Issue 1, Page(s) 77–84

Abstract: Background: Clinical disease activity associated with inflammatory bowel disease (IBD) can place physical limitations on youths' activities of daily living. In turn, functional limitations potentially contribute to youths' heightened experience of IBD- ... ...

Abstract	Background: Clinical disease activity associated with inflammatory bowel disease (IBD) can place physical limitations on youths' activities of daily living. In turn, functional limitations potentially contribute to youths' heightened experience of IBD-induced intrusions on a wide range of routine and valued activities (i.e., illness intrusiveness), which can increase their risk for depressive symptoms. The present study examined the contributions of clinical disease activity, functional disability, and illness intrusiveness to depressive symptoms in youth with IBD. Methods: Youth (N = 180) completed the Functional Disability Inventory (FDI), Illness Intrusiveness Scale-Child (IIS-C), and Children's Depression Inventory-2 (CDI-2). Physicians completed the Physicians Global Assessment of disease activity (PGA). Results: Results revealed a mediating effect for functional disability in the association between disease activity and depressive symptoms (PGA → FDI → CDI-2); illness intrusiveness mediated the association between functional disability and depressive symptoms (i.e., FDI → IIS-C → CDI-2). Serial mediation revealed that clinical disease activity conferred an indirect effect on youth depressive symptoms through the sequential effects of functional disability and illness intrusiveness (i.e., PGA → FDI → IIS-C → CDI-2). Conclusions: Taken together, these findings indicate that youth who encounter more physical limitations as a function of clinical disease activity are more likely to experience an amplified sense of IBD-related intrusions on their ability to participate in meaningful activities. In turn, heightened illness intrusiveness increases the likelihood of depressive symptoms. Clinical interventions that help youth maintain adequate functional ability in the face of IBD disease activity and encourage involvement in positively valued activities could decrease the negative impact of IBD on youths' emotional adjustment.
MeSH term(s)	Adolescent ; Humans ; Child ; Depression/etiology ; Depression/diagnosis ; Activities of Daily Living ; Inflammatory Bowel Diseases/diagnosis ; Probability
Language	English
Publishing date	2023-12-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	603201-1
ISSN	1536-4801 ; 0277-2116
ISSN (online)	1536-4801
ISSN	0277-2116
DOI	10.1002/jpn3.12056
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Zs.A 1728: Show issues

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Article ; Online: Ten simple rules and a template for creating workflows-as-applications.

Roach, Michael J / Pierce-Ward, N Tessa / Suchecki, Radoslaw / Mallawaarachchi, Vijini / Papudeshi, Bhavya / Handley, Scott A / Brown, C Titus / Watson-Haigh, Nathan S / Edwards, Robert A

PLoS computational biology

2022 Volume 18, Issue 12, Page(s) e1010705

MeSH term(s)	Workflow ; Computational Biology
Language	English
Publishing date	2022-12-15
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1010705
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Article ; Online: Tensions and Paradoxes of Scaling Up: A Critical Reflection on Physical Activity Promotion.

Koorts, Harriet / Bauman, Adrian / Edwards, Nancy / Bellew, William / Brown, Wendy J / Duncan, Mitch J / Lubans, David R / Milat, Andrew J / Morgan, Philip J / Nathan, Nicole / Searles, Andrew / Lee, Karen / Plotnikoff, Ronald C

International journal of environmental research and public health

2022 Volume 19, Issue 21

Abstract: Background: Achieving system-level, sustainable 'scale-up' of interventions is the epitome of successful translation of evidence-based approaches in population health. In physical activity promotion, few evidence-based interventions reach implementation ...

Abstract	Background: Achieving system-level, sustainable 'scale-up' of interventions is the epitome of successful translation of evidence-based approaches in population health. In physical activity promotion, few evidence-based interventions reach implementation at scale or become embedded within systems for sustainable health impact. This is despite the vast published literature describing efficacy studies of small-scale physical activity interventions. Research into physical activity scale-up (through case-study analysis; evaluations of scale-up processes in implementation trials; and mapping the processes, strategies, and principles for scale-up) has identified barriers and facilitators to intervention expansion. Many interventions are implemented at scale by governments but have not been evaluated or have unpublished evaluation information. Further, few public health interventions have evaluations that reveal the costs and benefits of scaled-up implementation. This lack of economic information introduces an additional element of risk for decision makers when deciding which physical activity interventions should be supported with scarce funding resources. Decision-makers face many other challenges when scaling interventions which do not relate to formal research trials of scale-up; Methods: To explore these issues, a multidisciplinary two-day workshop involving experts in physical activity scale-up was convened by the University of Newcastle, Australia, and the University of Ottawa, Canada (February 2019); Results: In this paper we discuss some of the scale-up tensions (challenges and conflicts) and paradoxes (things that are contrary to expectations) that emerged from this workshop in the context of the current literature and our own experiences in this field. We frame scale-up tensions according to epistemology, methodology, time, and partnerships; and paradoxes as 'reach without scale', 'planned serendipity' and 'simple complexity'. We reflect on the implications of these scale-up tensions and paradoxes, providing considerations for future scale-up research and practice moving forward; Conclusions: In this paper, we delve deeper into stakeholders' assumptions, processes and expectations of scaling up, and challenge in what ways as stakeholders, we all contribute to desired or undesired outcomes. Through a lens of 'tensions' and 'paradoxes', we make an original contribution to the scale-up literature that might influence current perspectives of scaling-up, provide future approaches for physical activity promotion, and contribute to understanding of dynamic of research-practice partnerships.
MeSH term(s)	Exercise ; Public Health ; Research Design ; Australia ; Canada ; Health Promotion/methods
Language	English
Publishing date	2022-11-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2175195-X
ISSN	1660-4601 ; 1661-7827
ISSN (online)	1660-4601
ISSN	1661-7827
DOI	10.3390/ijerph192114284
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