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Article: Auditory feedback decreases timing variability for discontinuous and continuous motor tasks in autistic adults.

Richard Williams, Nicole / Tremblay, Luc / Hurt-Thaut, Corene / Brian, Jessica / Kowaleski, Julia / Mertel, Kathrin / Shlüter, Sebastian / Thaut, Michael

Frontiers in integrative neuroscience

2024 Volume 18, Page(s) 1379208

Abstract: Introduction: Autistic individuals demonstrate greater variability and timing error in their motor performance than neurotypical individuals, likely due at least in part to atypical cerebellar characteristics and connectivity. These motor difficulties ... ...

Abstract	Introduction: Autistic individuals demonstrate greater variability and timing error in their motor performance than neurotypical individuals, likely due at least in part to atypical cerebellar characteristics and connectivity. These motor difficulties may differentially affect discrete as opposed to continuous movements in autistic individuals. Augmented auditory feedback has the potential to aid motor timing and variability due to intact auditory-motor pathways in autism and high sensitivity in autistic individuals to auditory stimuli. Methods: This experiment investigated whether there were differences in timing accuracy and variability in autistic adults as a function of task (discontinuous vs. continuous movements) and condition (augmented auditory feedback vs. no auditory feedback) in a synchronization-continuation paradigm. Ten autistic young adults aged 17-27 years of age completed the within-subjects study that involved drawing circles at 800 milliseconds intervals on a touch screen. In the discontinuous task, participants traced a series of discrete circles and paused at the top of each circle for at least 60 milliseconds. In the continuous task, participants traced the circles without pausing. Participants traced circles in either a non-auditory condition, or an auditory condition in which they heard a tone each time that they completed a circle drawing. Results: Participants had significantly better timing accuracy on the continuous timing task as opposed to the discontinuous task. Timing consistency was significantly higher for tasks performed with auditory feedback. Discussion: This research reveals that motor difficulties in autistic individuals affect discrete timing tasks more than continuous tasks, and provides evidence that augmented auditory feedback may be able to mitigate some of the timing variability present in autistic persons' movements. These results provide support for future investigation on the use of music-based therapies involving auditory feedback to address motor dysfunction in autistic individuals.
Language	English
Publishing date	2024-04-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2452962-X
ISSN	1662-5145
ISSN	1662-5145
DOI	10.3389/fnint.2024.1379208
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Deep Learning Localization of Pneumonia: 2019 Coronavirus (COVID-19) Outbreak.

Hurt, Brian / Kligerman, Seth / Hsiao, Albert

Journal of thoracic imaging

2020 Volume 35, Issue 3, Page(s) W87–W89

MeSH term(s)	Betacoronavirus ; COVID-19 ; Coronavirus Infections/diagnostic imaging ; Deep Learning ; Humans ; Image Interpretation, Computer-Assisted ; Pandemics ; Pneumonia, Viral/diagnostic imaging ; Radiography, Thoracic ; SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-03-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	632900-7
ISSN	1536-0237 ; 0883-5993
ISSN (online)	1536-0237
ISSN	0883-5993
DOI	10.1097/RTI.0000000000000512
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Article ; Online: Augmenting Interpretation of Chest Radiographs With Deep Learning Probability Maps.

Hurt, Brian / Yen, Andrew / Kligerman, Seth / Hsiao, Albert

Journal of thoracic imaging

2020 Volume 35, Issue 5, Page(s) 285–293

Abstract: Purpose: Pneumonia is a common clinical diagnosis for which chest radiographs are often an important part of the diagnostic workup. Deep learning has the potential to expedite and improve the clinical interpretation of chest radiographs. While earlier ... ...

Abstract	Purpose: Pneumonia is a common clinical diagnosis for which chest radiographs are often an important part of the diagnostic workup. Deep learning has the potential to expedite and improve the clinical interpretation of chest radiographs. While earlier approaches have emphasized the feasibility of "binary classification" to accomplish this task, alternative strategies may be possible. We explore the feasibility of a "semantic segmentation" deep learning approach to highlight the potential foci of pneumonia on frontal chest radiographs. Materials and methods: In this retrospective study, we trained a U-net convolutional neural network (CNN) to predict pixel-wise probability maps for pneumonia using a public data set provided by the Radiological Society of North America (RSNA) comprised of 22,000 radiographs and radiologist-defined bounding boxes. We reserved 3684 radiographs as an independent validation data set and assessed overall performance for localization using Dice overlap and classification performance using the area under the receiver-operator characteristic curve. Results: For classification/detection of pneumonia, area under the receiver-operator characteristic curve on frontal radiographs was 0.854 with a sensitivity of 82.8% and specificity of 72.6%. Using this strategy of neural network training, probability maps localized pneumonia to lung parenchyma for essentially all validation cases. For segmentation of pneumonia for positive cases, predicted probability maps had a mean Dice score (±SD) of 0.603±0.204, and 60.0% of these had a Dice score >0.5. Conclusions: A "semantic segmentation" deep learning approach can provide a probabilistic map to assist in the diagnosis of pneumonia. In combination with the patient's history, clinical findings and other imaging, this strategy may help expedite and improve diagnosis.
MeSH term(s)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Deep Learning ; Female ; Humans ; Infant ; Lung/diagnostic imaging ; Male ; Middle Aged ; Pneumonia/diagnostic imaging ; Probability ; Radiographic Image Interpretation, Computer-Assisted/methods ; Radiography, Thoracic/methods ; Retrospective Studies ; Young Adult
Language	English
Publishing date	2020-03-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	632900-7
ISSN	1536-0237 ; 0883-5993
ISSN (online)	1536-0237
ISSN	0883-5993
DOI	10.1097/RTI.0000000000000505
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Article ; Online: Conservation genomics of urban populations of Streamside Salamander (Ambystoma barbouri).

Hubbs, N Wade / Hurt, Carla R / Niedzwiecki, John / Leckie, Brian / Withers, David

PloS one

2022 Volume 17, Issue 6, Page(s) e0260178

Abstract: In Tennessee, populations of the state endangered Streamside Salamander (Ambystoma barbouri) are in decline as their distribution lies mostly within rapidly developing areas in the Nashville Basin. Information regarding the partitioning of genetic ... ...

Abstract	In Tennessee, populations of the state endangered Streamside Salamander (Ambystoma barbouri) are in decline as their distribution lies mostly within rapidly developing areas in the Nashville Basin. Information regarding the partitioning of genetic variation among populations of A. barbouri and the taxonomic status of these populations relative to northern populations and their congener, the Small-mouthed Salamander (A. texanum), have important implications for management and conservation of this species. Here we combined mitochondrial sequencing and genome-wide single nucleotide polymorphism (SNP) data generated using Genotyping-by-Sequencing (GBS) to investigate patterns of genetic variation within Tennessee populations of A. barbouri, to assess their relationship to populations in Kentucky, and to examine their phylogenetic relationship to the closely related A. texanum. Results from phylogenetic reconstructions reveal a complex history of Tennessee A. barbouri populations with regards to northern populations, unisexual A. barbouri, and A. texanum. Patterns of mitochondrial sequence variation suggest that A. barbouri may have originated within Tennessee and expanded north multiple times into Kentucky, Ohio, Indiana, and West Virginia. Phylogenetic reconstructions based on genome-wide SNP data contradict results based on mitochondrial DNA and correspond to geographic and taxonomic boundaries. Variation in allele frequencies at SNP genotypes, as identified by multivariate analyses and Bayesian assignment tests, identified three evolutionary significant units (ESUs) for A. barbouri within Tennessee. Collectively, these results emphasize the need for prioritizing conservation needs for Tennessee populations of A. barbouri to ensure the long-term persistence of this species.
MeSH term(s)	Ambystoma ; Animals ; Bayes Theorem ; Genomics ; Humans ; Phylogeny ; Urban Population ; Urodela/genetics
Language	English
Publishing date	2022-06-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0260178
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Data-driven mechanistic framework with stratified immunity and effective transmissibility for COVID-19 scenario projections.

Porebski, Przemyslaw / Venkatramanan, Srinivasan / Adiga, Aniruddha / Klahn, Brian / Hurt, Benjamin / Wilson, Mandy L / Chen, Jiangzhuo / Vullikanti, Anil / Marathe, Madhav / Lewis, Bryan

Epidemics

2024 Volume 47, Page(s) 100761

Abstract: Scenario-based modeling frameworks have been widely used to support policy-making at state and federal levels in the United States during the COVID-19 response. While custom-built models can be used to support one-off studies, sustained updates to ... ...

Abstract	Scenario-based modeling frameworks have been widely used to support policy-making at state and federal levels in the United States during the COVID-19 response. While custom-built models can be used to support one-off studies, sustained updates to projections under changing pandemic conditions requires a robust, integrated, and adaptive framework. In this paper, we describe one such framework, UVA-adaptive, that was built to support the CDC-aligned Scenario Modeling Hub (SMH) across multiple rounds, as well as weekly/biweekly projections to Virginia Department of Health (VDH) and US Department of Defense during the COVID-19 response. Building upon an existing metapopulation framework, PatchSim, UVA-adaptive uses a calibration mechanism relying on adjustable effective transmissibility as a basis for scenario definition while also incorporating real-time datasets on case incidence, seroprevalence, variant characteristics, and vaccine uptake. Through the pandemic, our framework evolved by incorporating available data sources and was extended to capture complexities of multiple strains and heterogeneous immunity of the population. Here we present the version of the model that was used for the recent projections for SMH and VDH, describe the calibration and projection framework, and demonstrate that the calibrated transmissibility correlates with the evolution of the pathogen as well as associated societal dynamics.
Language	English
Publishing date	2024-03-21
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2467993-8
ISSN	1878-0067 ; 1755-4365
ISSN (online)	1878-0067
ISSN	1755-4365
DOI	10.1016/j.epidem.2024.100761
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Article: Deep Learning Localization of Pneumonia: 2019 Coronavirus (COVID-19) Outbreak

Hurt, Brian / Kligerman, Seth / Hsiao, Albert

J Thorac Imaging

Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #11700
Database	COVID19

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Article ; Online: Conservation genomics of urban populations of Streamside Salamander (Ambystoma barbouri).

N Wade Hubbs / Carla R Hurt / John Niedzwiecki / Brian Leckie / David Withers

PLoS ONE, Vol 17, Iss 6, p e

2022 Volume 0260178

Abstract	In Tennessee, populations of the state endangered Streamside Salamander (Ambystoma barbouri) are in decline as their distribution lies mostly within rapidly developing areas in the Nashville Basin. Information regarding the partitioning of genetic variation among populations of A. barbouri and the taxonomic status of these populations relative to northern populations and their congener, the Small-mouthed Salamander (A. texanum), have important implications for management and conservation of this species. Here we combined mitochondrial sequencing and genome-wide single nucleotide polymorphism (SNP) data generated using Genotyping-by-Sequencing (GBS) to investigate patterns of genetic variation within Tennessee populations of A. barbouri, to assess their relationship to populations in Kentucky, and to examine their phylogenetic relationship to the closely related A. texanum. Results from phylogenetic reconstructions reveal a complex history of Tennessee A. barbouri populations with regards to northern populations, unisexual A. barbouri, and A. texanum. Patterns of mitochondrial sequence variation suggest that A. barbouri may have originated within Tennessee and expanded north multiple times into Kentucky, Ohio, Indiana, and West Virginia. Phylogenetic reconstructions based on genome-wide SNP data contradict results based on mitochondrial DNA and correspond to geographic and taxonomic boundaries. Variation in allele frequencies at SNP genotypes, as identified by multivariate analyses and Bayesian assignment tests, identified three evolutionary significant units (ESUs) for A. barbouri within Tennessee. Collectively, these results emphasize the need for prioritizing conservation needs for Tennessee populations of A. barbouri to ensure the long-term persistence of this species.
Keywords	Medicine ; R ; Science ; Q
Subject code	580
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The dual nature of the nucleolus.

Tartakoff, Alan / DiMario, Patrick / Hurt, Eduard / McStay, Brian / Panse, Vikram Govind / Tollervey, David

Genes & development

2022 Volume 36, Issue 13-14, Page(s) 765–769

Abstract: The nucleolus is best known for housing the highly ordered assembly line that produces ribosomal subunits. The >100 ribosome assembly factors in the nucleolus are thought to cycle between two states: an operative state (when integrated into subunit ... ...

Abstract	The nucleolus is best known for housing the highly ordered assembly line that produces ribosomal subunits. The >100 ribosome assembly factors in the nucleolus are thought to cycle between two states: an operative state (when integrated into subunit assembly intermediates) and a latent state (upon release from intermediates). Although it has become commonplace to refer to the nucleolus as "being a multilayered condensate," and this may be accurate for latent factors, there is little reason to think that such assertions pertain to the operative state of assembly factors.
MeSH term(s)	Cell Nucleolus ; RNA, Ribosomal
Chemical Substances	RNA, Ribosomal
Language	English
Publishing date	2022-10-20
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural
ZDB-ID	806684-x
ISSN	1549-5477 ; 0890-9369
ISSN (online)	1549-5477
ISSN	0890-9369
DOI	10.1101/gad.349748.122
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Article ; Online: Increased luminal area of large conducting airways in patients with COVID-19 and post-acute sequelae of COVID-19 A retrospective case-control study

Zaremba, Solomiia / Miller, Alex J. / Ovrom, Erik A. / Senefeld, Jonathon W. / Wiggins, Chad C. / Dominelli, Paolo B. / Ganesh, Ravindra / Hurt, Ryan T. / Bartholmai, Brian J. / Welch, Brian T. / Ripoll, Juan G. / Joyner, Michael J. / Ramsook, Andrew H.

medRxiv

Abstract: Background Coronavirus disease 2019 (COVID–19) is associated with enlarged luminal areas of large conducting airways. In 10—30% of patients with acute COVID–19 infection, symptoms persist for more than 4 weeks (referred to as post–acute sequelae of COVID– ...

Abstract	Background Coronavirus disease 2019 (COVID–19) is associated with enlarged luminal areas of large conducting airways. In 10—30% of patients with acute COVID–19 infection, symptoms persist for more than 4 weeks (referred to as post–acute sequelae of COVID–19, or PASC), and it is unknown if airway changes are associated with this persistence. Thus, we aim to investigate if luminal area of large conducting airways is different between PASC and COVID–19 patients, and healthy controls. Methods In this retrospective case–control study seventy–five patients with PASC (48 females) were age–, height–, and sex–matched to 75 individuals with COVID-19 and 75 healthy controls. Using three–dimensional digital reconstruction from computed tomography imaging, we measured luminal areas of seven conducting airways, including trachea, right and left main bronchi, bronchus intermediate, right and left upper lobe, and left lower lobe bronchi. Findings Airway luminal areas between COVID–19 and PASC groups were not different (p>0.66). There were no group differences in airway luminal area (PASC vs control) for trachea and right main bronchus. However, in the remaining five airways, airway luminal areas were 12% to 39% larger among PASC patients compared to controls (p<0.05). Interpretation Patients diagnosed with COVID–19 and PASC have greater airway luminal area in most large conducting airways compared to healthy controls. No differences in luminal area between patients with COVID–19 and PASC suggest persistence of changes or insufficient time for complete reversal of changes. Funding National Heart, Lung, and Blood Institute (F32HL154320 to JWS; 5R35HL139854 to MJJ); Postdoctoral Fellowship from the Natural Sciences and Engineering Research Council of Canada (AHR).
Keywords	covid19
Language	English
Publishing date	2024-03-02
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2024.02.29.24303556
Database	COVID19

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Article ; Online: Deep Learning Localization of Pneumonia ; 2019 Coronavirus (COVID-19) Outbreak

Hurt, Brian / Kligerman, Seth / Hsiao, Albert

Journal of Thoracic Imaging

2020 Volume 35, Issue 3, Page(s) W87–W89

Keywords	Pulmonary and Respiratory Medicine ; Radiology Nuclear Medicine and imaging ; covid19
Language	English
Publisher	Ovid Technologies (Wolters Kluwer Health)
Publishing country	us
Document type	Article ; Online
ZDB-ID	632900-7
ISSN	1536-0237 ; 0883-5993
ISSN (online)	1536-0237
ISSN	0883-5993
DOI	10.1097/rti.0000000000000512
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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