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Article ; Online: Application of supervised machine learning algorithms for the evaluation of utricular function on patients with Meniere's disease: utilizing subjective visual vertical and ocular-vestibular-evoked myogenic potentials.

Bragg, Phillip G / Norton, Benjamin M / Petrak, Michelle R / Weiss, Allyson D / Kandl, Lindsay M / Corrigan, Megan L / Bahner, Cammy L / Matsuoka, Akihiro J

Acta oto-laryngologica

2023 Volume 143, Issue 4, Page(s) 262–273

Abstract: Background: Research on the otolith organs remains inconclusive.: Objectives: This study seeks to further elucidate utricular function in patients with Meniere's disease (MD) in three ways: (1) We aimed to disambiguate the role of the Subjective ... ...

Abstract	Background: Research on the otolith organs remains inconclusive. Objectives: This study seeks to further elucidate utricular function in patients with Meniere's disease (MD) in three ways: (1) We aimed to disambiguate the role of the Subjective Visual Vertical (SVV) and Ocular Vestibular Evoked Myogenic Potential (o-VEMP) tests regarding which utricular subsystem each is measuring. (2) We sought to characterize the acute and chronic state of MD by identifying differences in the relationship of SVV and o-VEMP results across patients with acute and chronic MD. (3) We attempted to find a machine-learning algorithm that could predict acute versus chronic MD using SVV and o-VEMP. Methods: A prospective study with ninety subjects. Results: (1) SVV and o-VEMP tests were found to have a moderate linear relationship in patients with acute MD, suggesting each test measures a different utricular subsystem. (2) Regression analyses statistically differed across the two patient populations, suggesting that SVV results were normalized in chronic MD patients. (3) Logistic regression and Naïve Bayes algorithms were found to predict acute and chronic MD accurately. Significance: A better understanding of what diagnostic tests measure will lead to a better classification system for MD and more targeted treatment options in the future.
MeSH term(s)	Humans ; Meniere Disease ; Vestibular Evoked Myogenic Potentials/physiology ; Prospective Studies ; Bayes Theorem ; Supervised Machine Learning ; Vestibular Function Tests/methods
Language	English
Publishing date	2023-04-17
Publishing country	England
Document type	Journal Article
ISSN	1651-2251
ISSN (online)	1651-2251
DOI	10.1080/00016489.2023.2190163
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Article ; Online: Museum skins enable identification of introgression associated with cytonuclear discordance.

Potter, Sally / Moritz, Craig / Piggott, Maxine P / Bragg, Jason G / Afonso Silva, Ana C / Bi, Ke / McDonald-Spicer, Christiana / Turakulov, Rustamzhon / Eldridge, Mark D B

Systematic biology

2024

Abstract: Increased sampling of genomes and populations across closely related species has revealed that levels of genetic exchange during and after speciation are higher than previously thought. One obvious manifestation of such exchange is strong cytonuclear ... ...

Abstract	Increased sampling of genomes and populations across closely related species has revealed that levels of genetic exchange during and after speciation are higher than previously thought. One obvious manifestation of such exchange is strong cytonuclear discordance, where the divergence in mitochondrial DNA (mtDNA) differs from that for nuclear genes more (or less) than expected from differences between mtDNA and nuclear DNA (nDNA) in population size and mutation rate. Given genome-scale datasets and coalescent modelling, we can now confidently identify cases of strong discordance and test specifically for historical or recent introgression as the cause. Using population sampling, combining exon capture data from historical museum specimens and recently collected tissues we showcase how genomic tools can resolve complex evolutionary histories in the brachyotis group of rock-wallabies (Petrogale). In particular, applying population and phylogenomic approaches we can assess the role of demographic processes in driving complex evolutionary patterns and assess a role of ancient introgression and hybridisation. We find that described species are well supported as monophyletic taxa for nDNA genes, but not for mtDNA, with cytonuclear discordance involving at least four operational taxonomic units (OTUs) across four species which diverged 183-278 kya. ABC modelling of nDNA gene trees supports introgression during or after speciation for some taxon pairs with cytonuclear discordance. Given substantial differences in body size between the species involved, this evidence for gene flow is surprising. Heterogenous patterns of introgression were identified but do not appear to be associated with chromosome differences between species. These and previous results suggest that dynamic past climates across the monsoonal tropics could have promoted reticulation among related species.
Language	English
Publishing date	2024-04-05
Publishing country	England
Document type	Journal Article
ZDB-ID	1482572-7
ISSN	1076-836X ; 1063-5157
ISSN (online)	1076-836X
ISSN	1063-5157
DOI	10.1093/sysbio/syae016
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Article ; Online: Examining infants' visual paired comparison performance in the US and rural Malawi.

Beckner, Aaron G / Arnold, Charles D / Bragg, Megan G / Caswell, Bess L / Chen, Zhijun / Cox, Katherine / DeBolt, Michaela C / George, Matthews / Maleta, Kenneth / Stewart, Christine / Oakes, Lisa M / Prado, Elizabeth

Developmental science

2023 , Page(s) e13439

Abstract: Measures of attention and memory were evaluated in 6- to 9-month-old infants from two diverse contexts. One sample consisted of African infants residing in rural Malawi (N = 228, 118 girls, 110 boys). The other sample consisted of racially diverse ... ...

Abstract	Measures of attention and memory were evaluated in 6- to 9-month-old infants from two diverse contexts. One sample consisted of African infants residing in rural Malawi (N = 228, 118 girls, 110 boys). The other sample consisted of racially diverse infants residing in suburban California (N = 48, 24 girls, 24 boys). Infants were tested in an eye-tracking version of the visual paired comparison procedure and were shown racially familiar faces. The eye tracking data were parsed into individual looks, revealing that both groups of infants showed significant memory performance. However, how a look was operationally defined impacted some-but not other-measures of infant VPC performance. RESEARCH HIGHLIGHTS: In both the US and Malawi, 6- to 9-month-old infants showed evidence of memory for faces they had previously viewed during a familiarization period. Infant age was associated with peak look duration and memory performance in both contexts. Different operational definitions of a look yielded consistent findings for peak look duration and novelty preference scores-but not shift rate. Operationalization of look-defined measures is an important consideration for studies of infants in different cultural contexts.
Language	English
Publishing date	2023-08-31
Publishing country	England
Document type	Journal Article
ZDB-ID	2023952-X
ISSN	1467-7687 ; 1363-755X
ISSN (online)	1467-7687
ISSN	1363-755X
DOI	10.1111/desc.13439
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Article ; Online: Detecting steps in spatial genetic data: Which diversity measures are best?

Sentinella, Alexander T / Moles, Angela T / Bragg, Jason G / Rossetto, Maurizio / Sherwin, William B

PloS one

2022 Volume 17, Issue 3, Page(s) e0265110

Abstract: ... derived from the q-profile, including allelic richness, Shannon Information, GST, and Jost-D, as well ... ineffective at detecting steps. Further, allelic richness-based beta (between-locality) measures (e.g ... GST based measures, a Jost-D related measure, and Bray-Curtis dissimilarity. No one measure was best ...

Abstract	Accurately detecting sudden changes, or steps, in genetic diversity across landscapes is important for locating barriers to gene flow, identifying selectively important loci, and defining management units. However, there are many metrics that researchers could use to detect steps and little information on which might be the most robust. Our study aimed to determine the best measure/s for genetic step detection along linear gradients using biallelic single nucleotide polymorphism (SNP) data. We tested the ability to differentiate between linear and step-like gradients in genetic diversity, using a range of diversity measures derived from the q-profile, including allelic richness, Shannon Information, GST, and Jost-D, as well as Bray-Curtis dissimilarity. To determine the properties of each measure, we repeated simulations of different intensities of step and allele proportion ranges, with varying genome sample size, number of loci, and number of localities. We found that alpha diversity (within-locality) based measures were ineffective at detecting steps. Further, allelic richness-based beta (between-locality) measures (e.g., Jaccard and Sørensen dissimilarity) were not reliable for detecting steps, but instead detected departures from fixation. The beta diversity measures best able to detect steps were: Shannon Information based measures, GST based measures, a Jost-D related measure, and Bray-Curtis dissimilarity. No one measure was best overall, with a trade-off between those measures with high step detection sensitivity (GST and Bray-Curtis) and those that minimised false positives (a variant of Shannon Information). Therefore, when detecting steps, we recommend understanding the differences between measures and using a combination of approaches.
Language	English
Publishing date	2022-03-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0265110
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Book ; Online: An Event-Driven Approach To Genotype Imputation On A Custom RISC-V FPGA Cluster

Morris, Jordan / Rafiev, Ashur / Bragg, Graeme / Vousden, Mark / Thomas, David / Yakovlev, Alex / Brown, Andrew

2023

Abstract: This paper proposes an event-driven solution to genotype imputation, a technique used to statistically infer missing genetic markers in DNA. The work implements the widely accepted Li and Stephens model, primary contributor to the computational ... ...

Abstract	This paper proposes an event-driven solution to genotype imputation, a technique used to statistically infer missing genetic markers in DNA. The work implements the widely accepted Li and Stephens model, primary contributor to the computational complexity of modern x86 solutions, in an attempt to determine whether further investigation of the application is warranted in the event-driven domain. The model is implemented using graph-based Hidden Markov Modeling and executed as a customized forward/backward dynamic programming algorithm. The solution uses an event-driven paradigm to map the algorithm to thousands of concurrent cores, where events are small messages that carry both control and data within the algorithm. The design of a single processing element is discussed. This is then extended across multiple FPGAs and executed on a custom RISC-V NoC FPGA cluster called POETS. Results demonstrate how the algorithm scales over increasing hardware resources and a 48 FPGA run demonstrates a 270X reduction in wall-clock processing time when compared to a single-threaded x86 solution. Optimisation of the algorithm via linear interpolation is then introduced and tested, with results demonstrating a wall-clock reduction time of approx. 5 orders of magnitude when compared to a similarly optimised x86 solution.
Keywords	Computer Science - Distributed ; Parallel ; and Cluster Computing
Subject code	006
Publishing date	2023-01-22
Publishing country	us
Document type	Book ; Online
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Article: Fluctuation theorem and extended thermodynamics of turbulence.

Porporato, Amilcare / Hooshyar, Milad / Bragg, Andrew D / Katul, Gabriel

Proceedings. Mathematical, physical, and engineering sciences

2020 Volume 476, Issue 2243, Page(s) 20200468

Abstract: Turbulent flows are out-of-equilibrium because the energy supply at large scales and its dissipation by viscosity at small scales create a net transfer of energy among all scales. This energy cascade is modelled by approximating the spectral energy ... ...

Abstract	Turbulent flows are out-of-equilibrium because the energy supply at large scales and its dissipation by viscosity at small scales create a net transfer of energy among all scales. This energy cascade is modelled by approximating the spectral energy balance with a nonlinear Fokker-Planck equation consistent with accepted phenomenological theories of turbulence. The steady-state contributions of the drift and diffusion in the corresponding Langevin equation, combined with the killing term associated with the dissipation, induce a stochastic energy transfer across wavenumbers. The fluctuation theorem is shown to describe the scale-wise statistics of forward and backward energy transfer and their connection to irreversibility and entropy production. The ensuing turbulence entropy is used to formulate an extended turbulence thermodynamics.
Language	English
Publishing date	2020-11-18
Publishing country	England
Document type	Journal Article
ZDB-ID	209241-4
ISSN	1471-2946 ; 1364-5021 ; 0962-8444 ; 0080-4630 ; 0950-1207
ISSN (online)	1471-2946
ISSN	1364-5021 ; 0962-8444 ; 0080-4630 ; 0950-1207
DOI	10.1098/rspa.2020.0468
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Article ; Online: Ergot Alkaloid Biosynthesis in the Maize (Zea mays) Ergot Fungus Claviceps gigantea.

Bragg, Paige E / Maust, Matthew D / Panaccione, Daniel G

Journal of agricultural and food chemistry

2017 Volume 65, Issue 49, Page(s) 10703–10710

Abstract: Biosynthesis of the dihydrogenated forms of ergot alkaloids is of interest because many of the ergot alkaloids used as pharmaceuticals may be derived from dihydrolysergic acid (DHLA) or its precursor dihydrolysergol. The maize (Zea mays) ergot pathogen ... ...

Abstract	Biosynthesis of the dihydrogenated forms of ergot alkaloids is of interest because many of the ergot alkaloids used as pharmaceuticals may be derived from dihydrolysergic acid (DHLA) or its precursor dihydrolysergol. The maize (Zea mays) ergot pathogen Claviceps gigantea has been reported to produce dihydrolysergol, a hydroxylated derivative of the common ergot alkaloid festuclavine. We hypothesized expression of C. gigantea cloA in a festuclavine-accumulating mutant of the fungus Neosartorya fumigata would yield dihydrolysergol because the P450 monooxygenase CloA from other fungi performs similar oxidation reactions. We engineered such a strain, and high performance liquid chromatography and liquid chromatography-mass spectrometry analyses demonstrated the modified strain produced DHLA, the fully oxidized product of dihydrolysergol. Accumulation of high concentrations of DHLA in field-collected C. gigantea sclerotia and discovery of a mutation in the gene lpsA, downstream from DHLA formation, supported our finding that DHLA rather than dihydrolysergol is the end product of the C. gigantea pathway.
MeSH term(s)	Chromatography, High Pressure Liquid/methods ; Claviceps/metabolism ; Ergot Alkaloids/biosynthesis ; Gene Expression ; Lysergic Acid/analogs & derivatives ; Lysergic Acid/chemistry ; Mass Spectrometry/methods ; Mixed Function Oxygenases/metabolism ; Mutation ; Secondary Metabolism ; Transformation, Genetic ; Zea mays/microbiology
Chemical Substances	Ergot Alkaloids ; Mixed Function Oxygenases (EC 1.-) ; 9,10-dihydrolysergol (I39LU14H83) ; Lysergic Acid (ITO20DAO7J)
Language	English
Publishing date	2017-12-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	241619-0
ISSN	1520-5118 ; 0021-8561
ISSN (online)	1520-5118
ISSN	0021-8561
DOI	10.1021/acs.jafc.7b04272
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Article ; Online: The role of canines in the treatment of posttraumatic stress disorder: A systematic review.

Vitte, Pauline / Bragg, Kevin / Graham, David / Davidson, John / Bratten, Truls / Angus-Leppan, Gavin

Psychological trauma : theory, research, practice and policy

2021 Volume 13, Issue 8, Page(s) 899–906

Abstract: Objective: Posttraumatic stress disorder (PTSD) is a syndrome of prolonged stress reactions that can develop following a traumatic event. Treatment usually relies on both psychotherapies and pharmacotherapies. Recently, the use of dogs as adjunct ... ...

Abstract	Objective: Posttraumatic stress disorder (PTSD) is a syndrome of prolonged stress reactions that can develop following a traumatic event. Treatment usually relies on both psychotherapies and pharmacotherapies. Recently, the use of dogs as adjunct intervention for a variety of psychiatric conditions has received widespread attention. The aim of this review was to systematically review the evidence for the use of dogs in the treatment of PTSD. Method: A systematic search was conducted using multiple specialist and generalist databases. Articles targeted were those examining the effects of dogs in the treatment of PTSD. Inclusion criteria were peer review, that participants had a formal diagnosis of PTSD, and that the experimental intervention involved a dog. There were no restrictions on subpopulation, exact type or role of dog, or country or language of publication. Results: 16 papers met the inclusion criteria. All of the included studies examined veterans. Methods and results were widely heterogeneous between studies, making it infeasible to quantify an overall effect size. Multiple studies demonstrated promising results when dogs were used as an adjunct intervention to standard therapy, particularly in symptom reduction and social functioning. However, risk of bias was an issue for most of the studies. While the results in most of the studies were overall promising, the risk of biases and veteran subpopulation limit the validity and generalizability of the results. Conclusions: At best, the current evidence raises the hypothesis that dogs are beneficial in PTSD. Further research is required with a focus on rigorous design. (PsycInfo Database Record (c) 2021 APA, all rights reserved).
MeSH term(s)	Animals ; Dogs ; Humans ; Psychotherapy ; Stress Disorders, Post-Traumatic/therapy ; Veterans
Language	English
Publishing date	2021-09-02
Publishing country	United States
Document type	Journal Article ; Systematic Review
ZDB-ID	2497028-1
ISSN	1942-969X ; 1942-9681
ISSN (online)	1942-969X
ISSN	1942-9681
DOI	10.1037/tra0001074
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Article ; Online: Safety findings from CENTURION, a phase 3 consistency study of lasmiditan for the acute treatment of migraine.

Tassorelli, C / Bragg, S / Krege, J H / Doty, E G / Ardayfio, P A / Ruff, D / Dowsett, S A / Schwedt, T

The journal of headache and pain

2021 Volume 22, Issue 1, Page(s) 132

Abstract: Background: Lasmiditan (LTN) is a selective 5-HT: Methods: Patients were randomized 1:1:1 to LTN 200 mg (LTN200), LTN100, or a control group that received placebo for 3 attacks and LTN50 for either the 3rd or 4th attack (1:1). Safety analyses were ... ...

Abstract	Background: Lasmiditan (LTN) is a selective 5-HT Methods: Patients were randomized 1:1:1 to LTN 200 mg (LTN200), LTN100, or a control group that received placebo for 3 attacks and LTN50 for either the 3rd or 4th attack (1:1). Safety analyses were conducted for patients who took ≥1 dose of study drug and, in some cases, those who took all 4 doses. Results: Overall, 1471 patients treated 4494 attacks. The incidences of treatment-emergent serious adverse events (SAEs) were - placebo, n=2 (0.4 %); LTN100, n=1 (0.2 %); LTN200, n=2 (0.4 %); no specific treatment-emergent SAE was reported in more than one patient. The most common treatment emergent adverse events (TEAEs) with lasmiditan were dizziness, paresthesia, fatigue, nausea, vertigo, and somnolence; the vast majority were mild or moderate in severity. The incidences of these TEAEs were highest during the first attack and decreased during subsequent attacks. For patients who experienced a common TEAE with the first attack, less than 45 % experienced the same event in subsequent attacks. Patients who did not experience an event in the 1st attack infrequently experienced the same event in subsequent attacks. The time of onset of the common TEAE ranged from ~40 min to 1 h (dependent upon TEAE) and, for individual TEAE, the onset was similar across attacks. Duration was dependent upon TEAE and attack. It was shortest for paresthesia (< 2 h for all attacks); it ranged from 1.8 to 5.5 h for other common TEAEs and was generally similar across attacks. Serotonin syndrome was reported for 2 patients post LTN dosing; there were no meaningful differences across treatment groups in suicidality; there was no evidence of an increase in motor vehicle accidents. Conclusion: In this blinded, controlled, multiple-attack study, LTN was associated with generally mild or moderate CNS-related TEAEs of short duration. TEAEs tended to decrease in frequency across the 4 attacks. Trial registration: NCT03670810.
MeSH term(s)	Adult ; Benzamides ; Double-Blind Method ; Humans ; Migraine Disorders/drug therapy ; Piperidines ; Pyridines ; Serotonin Receptor Agonists ; Treatment Outcome
Chemical Substances	Benzamides ; Piperidines ; Pyridines ; Serotonin Receptor Agonists ; lasmiditan (760I9WM792)
Language	English
Publishing date	2021-11-06
Publishing country	England
Document type	Journal Article ; Randomized Controlled Trial
ZDB-ID	2036768-5
ISSN	1129-2377 ; 1129-2369
ISSN (online)	1129-2377
ISSN	1129-2369
DOI	10.1186/s10194-021-01343-2
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Article ; Online: Limited Introgression between Rock-Wallabies with Extensive Chromosomal Rearrangements.

Potter, Sally / Bragg, Jason G / Turakulov, Rustamzhon / Eldridge, Mark D B / Deakin, Janine / Kirkpatrick, Mark / Edwards, Richard J / Moritz, Craig

Molecular biology and evolution

2021 Volume 39, Issue 1

Abstract: Chromosome rearrangements can result in the rapid evolution of hybrid incompatibilities. Robertsonian fusions, particularly those with monobrachial homology, can drive reproductive isolation amongst recently diverged taxa. The recent radiation of rock- ... ...

Abstract	Chromosome rearrangements can result in the rapid evolution of hybrid incompatibilities. Robertsonian fusions, particularly those with monobrachial homology, can drive reproductive isolation amongst recently diverged taxa. The recent radiation of rock-wallabies (genus Petrogale) is an important model to explore the role of Robertsonian fusions in speciation. Here, we pursue that goal using an extensive sampling of populations and genomes of Petrogale from north-eastern Australia. In contrast to previous assessments using mitochondrial DNA or nuclear microsatellite loci, genomic data are able to separate the most closely related species and to resolve their divergence histories. Both phylogenetic and population genetic analyses indicate introgression between two species that differ by a single Robertsonian fusion. Based on the available data, there is also evidence for introgression between two species which share complex chromosomal rearrangements. However, the remaining results show no consistent signature of introgression amongst species pairs and where evident, indicate generally low introgression overall. X-linked loci have elevated divergence compared with autosomal loci indicating a potential role for genic evolution to produce reproductive isolation in concert with chromosome change. Our results highlight the value of genome scale data in evaluating the role of Robertsonian fusions and structural variation in divergence, speciation, and patterns of molecular evolution.
MeSH term(s)	Animals ; Chromosomes/genetics ; DNA, Mitochondrial/genetics ; Macropodidae/genetics ; Phylogeny ; Reproductive Isolation
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2021-12-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msab333
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