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Article ; Online: Publisher Correction: A rigid body framework for multicellular modeling.

Brown, Phillip J / Green, J Edward F / Binder, Benjamin J / Osborne, James M

Nature computational science

2024 Volume 2, Issue 1, Page(s) 59

Language	English
Publishing date	2024-01-18
Publishing country	United States
Document type	Published Erratum
ISSN	2662-8457
ISSN (online)	2662-8457
DOI	10.1038/s43588-021-00188-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Optimization of an amplicon sequencing-based microsatellite panel and protocol for stock identification and kinship inference of lake trout (

Marcy-Quay, Benjamin / Wilson, Chris C / Osborne, Christopher A / Marsden, J Ellen

Ecology and evolution

2023 Volume 13, Issue 4, Page(s) e10020

Abstract: Kinship-based methods of population assessment such as close-kin mark-recapture require accurate and efficient genotyping methods capable of resolving complex relationships among kin. Inference of such relationships can be difficult using biallelic loci ... ...

Abstract	Kinship-based methods of population assessment such as close-kin mark-recapture require accurate and efficient genotyping methods capable of resolving complex relationships among kin. Inference of such relationships can be difficult using biallelic loci due to the large number of markers required to obtain the necessary power. Sequencing-based microsatellite panels offer an efficient alternative, combining high polymorphism with efficient next-generation methods. Here we construct, optimize, and test one such panel for lake trout (
Language	English
Publishing date	2023-04-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.10020
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Article: Case report: Transition from anti-CD20 therapy to inebilizumab for 14 cases of neuromyelitis optica spectrum disorder.

Osborne, Benjamin / Romanow, Gabriela / Hemphill, J Michael / Zarif, Myassar / DeAngelis, Tracy / Kaplan, Tyler / Oh, Unsong / Pinkhasov, Johnathan / Patterson, Kristina / Levy, Michael

Frontiers in neurology

2024 Volume 15, Page(s) 1352779

Abstract: Neuromyelitis optica spectrum disorder (NMOSD) is a rare autoimmune disorder of the central nervous system characterized by recurrent, disabling attacks that affect the optic nerve, spinal cord, and brain/brainstem. While rituximab, targeting CD20- ... ...

Abstract	Neuromyelitis optica spectrum disorder (NMOSD) is a rare autoimmune disorder of the central nervous system characterized by recurrent, disabling attacks that affect the optic nerve, spinal cord, and brain/brainstem. While rituximab, targeting CD20-positive B-cells, is used as an off-label therapy for NMOSD, some patients continue to exhibit breakthrough attacks and/or adverse reactions. Inebilizumab, a humanized and glycoengineered monoclonal antibody targeting CD19-positive B-cells, has been FDA approved for the treatment of NMOSD in adult patients who are anti-aquaporin-4 (AQP4) antibody positive. Given the limited real-world data on the efficacy and safety of inebilizumab, especially in those transitioning from rituximab, a retrospective chart review was conducted on 14 NMOSD patients from seven centers. Of these, 71.4% (
Language	English
Publishing date	2024-04-16
Publishing country	Switzerland
Document type	Case Reports
ZDB-ID	2564214-5
ISSN	1664-2295
ISSN	1664-2295
DOI	10.3389/fneur.2024.1352779
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Article ; Online: Spatial extent of road pollution: A national analysis.

Phillips, Benjamin B / Bullock, James M / Osborne, Juliet L / Gaston, Kevin J

The Science of the total environment

2021 Volume 773, Page(s) 145589

Abstract: Roads form vast, pervasive and growing networks across the Earth, causing negative environmental impacts that spill out into a 'road-effect zone'. Previous research has estimated the regional and global extent of these zones using arbitrary distances, ... ...

Abstract	Roads form vast, pervasive and growing networks across the Earth, causing negative environmental impacts that spill out into a 'road-effect zone'. Previous research has estimated the regional and global extent of these zones using arbitrary distances, ignoring the spatial distribution and distance-dependent attenuation of different forms of road environmental impact. With Great Britain as a study area, we used mapping of roads and realistic estimates of how pollution levels decay with distance to project the spatial distribution of road pollution. We found that 25% of land was less than 79 m from a road, 50% of land was less than 216 m and 75% of land was less than 527 m. Roadless areas were scarce, and confined almost exclusively to the uplands (mean elevation 391 m), with only ca 12% of land in Great Britain more than 1 km from roads and <4% of land more than 2.5 km from roads. Using light, noise, heavy metals, NO
Language	English
Publishing date	2021-02-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2021.145589
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Article ; Online: Conus involvement and leptomeningeal enhancement in aquaporin-4 antibody-positive neuromyelitis optica spectrum disorder: A case report.

Safadi, Amy Li / Myers, Cory J / Hu, Nancy N / Osborne, Benjamin

Multiple sclerosis and related disorders

2021 Volume 52, Page(s) 103011

Abstract: There are a variety of clinical phenotypes and radiological features that continue to make a diagnosis of neuromyelitis optica spectrum disorder (NMOSD) challenging. We present an atypical case of an adult woman who presented with flaccid paralysis of ... ...

Abstract	There are a variety of clinical phenotypes and radiological features that continue to make a diagnosis of neuromyelitis optica spectrum disorder (NMOSD) challenging. We present an atypical case of an adult woman who presented with flaccid paralysis of all extremities with unusual neuroimaging features, including extensive enhancing lesions in the upper cervical cord and conus medullaris with associated leptomeningeal enhancement. She was ultimately found to have AQP4 antibody-positive NMOSD. We discuss the factors that complicated a timely diagnosis, including her atypical radiographic features and an initially negative cell-based assay for myelin oligodendrocyte glycoprotein (MOG) and aquaporin-4 (AQP4) antibodies. Despite the rarity of conus medullaris involvement or leptomeningeal enhancement in AQP4 antibody-positive NMOSD, it is important to maintain a high level of clinical suspicion to avoid diagnostic and therapeutic delays. Though cell-based assays have high sensitivities, testing should be repeated on negative values in these scenarios.
MeSH term(s)	Adult ; Animals ; Aquaporin 4 ; Autoantibodies ; Conus Snail ; Female ; Humans ; Myelin-Oligodendrocyte Glycoprotein ; Neuromyelitis Optica
Chemical Substances	Aquaporin 4 ; Autoantibodies ; Myelin-Oligodendrocyte Glycoprotein
Language	English
Publishing date	2021-05-07
Publishing country	Netherlands
Document type	Case Reports ; Letter
ZDB-ID	2645330-7
ISSN	2211-0356 ; 2211-0348
ISSN (online)	2211-0356
ISSN	2211-0348
DOI	10.1016/j.msard.2021.103011
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Article ; Online: A rigid body framework for multicellular modeling.

Brown, Phillip J / Green, J Edward F / Binder, Benjamin J / Osborne, James M

Nature computational science

2021 Volume 1, Issue 11, Page(s) 754–766

Abstract: Off-lattice models are a well-established approach in multicellular modeling, where cells are represented as points that are free to move in space. The representation of cells as point objects is useful in a wide range of settings, particularly when ... ...

Abstract	Off-lattice models are a well-established approach in multicellular modeling, where cells are represented as points that are free to move in space. The representation of cells as point objects is useful in a wide range of settings, particularly when large populations are involved; however, a purely point-based representation is not naturally equipped to deal with objects that have length, such as cell boundaries or external membranes. Here we introduce an off-lattice modeling framework that exploits rigid body mechanics to represent objects using a collection of conjoined one-dimensional edges in a viscosity-dominated system. This framework can be used to represent cells as free moving polygons, to allow epithelial layers to smoothly interact with themselves, to model rod-shaped cells such as bacteria and to robustly represent membranes. We demonstrate that this approach offers solutions to the problems that limit the scope of current off-lattice multicellular models.
Language	English
Publishing date	2021-11-25
Publishing country	United States
Document type	Journal Article
ISSN	2662-8457
ISSN (online)	2662-8457
DOI	10.1038/s43588-021-00154-4
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Article ; Online: Meta-analysis prediction intervals are under reported in sport and exercise medicine.

Borg, David N / Impellizzeri, Franco M / Borg, Samantha J / Hutchins, Kate P / Stewart, Ian B / Jones, Tamara / Baguley, Brenton J / Orssatto, Lucas B R / Bach, Aaron J E / Osborne, John O / McMaster, Benjamin S / Buhmann, Robert L / Bon, Joshua J / Barnett, Adrian G

Scandinavian journal of medicine & science in sports

2024 Volume 34, Issue 3, Page(s) e14603

Abstract: Aim: Prediction intervals are a useful measure of uncertainty for meta-analyses that capture the likely effect size of a new (similar) study based on the included studies. In comparison, confidence intervals reflect the uncertainty around the point ... ...

Abstract	Aim: Prediction intervals are a useful measure of uncertainty for meta-analyses that capture the likely effect size of a new (similar) study based on the included studies. In comparison, confidence intervals reflect the uncertainty around the point estimate but provide an incomplete summary of the underlying heterogeneity in the meta-analysis. This study aimed to estimate (i) the proportion of meta-analysis studies that report a prediction interval in sports medicine; and (ii) the proportion of studies with a discrepancy between the reported confidence interval and a calculated prediction interval. Methods: We screened, at random, 1500 meta-analysis studies published between 2012 and 2022 in highly ranked sports medicine and medical journals. Articles that used a random effect meta-analysis model were included in the study. We randomly selected one meta-analysis from each article to extract data from, which included the number of estimates, the pooled effect, and the confidence and prediction interval. Results: Of the 1500 articles screened, 866 (514 from sports medicine) used a random effect model. The probability of a prediction interval being reported in sports medicine was 1.7% (95% CI = 0.9%, 3.3%). In medicine the probability was 3.9% (95% CI = 2.4%, 6.6%). A prediction interval was able to be calculated for 220 sports medicine studies. For 60% of these studies, there was a discrepancy in study findings between the reported confidence interval and the calculated prediction interval. Prediction intervals were 3.4 times wider than confidence intervals. Conclusion: Very few meta-analyses report prediction intervals and hence are prone to missing the impact of between-study heterogeneity on the overall conclusions. The widespread misinterpretation of random effect meta-analyses could mean that potentially harmful treatments, or those lacking a sufficient evidence base, are being used in practice. Authors, reviewers, and editors should be aware of the importance of prediction intervals.
MeSH term(s)	Humans ; Exercise ; Probability ; Sports ; Uncertainty ; Meta-Analysis as Topic
Language	English
Publishing date	2024-03-15
Publishing country	Denmark
Document type	Journal Article
ZDB-ID	1077418-x
ISSN	1600-0838 ; 0905-7188
ISSN (online)	1600-0838
ISSN	0905-7188
DOI	10.1111/sms.14603
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Article: The Prevalence of Integument Injuries and Associated Risk Factors Among Canadian Turkeys.

Leishman, Emily M / van Staaveren, Nienke / Osborne, Vern R / Wood, Benjamin J / Baes, Christine F / Harlander-Matauschek, Alexandra

Frontiers in veterinary science

2022 Volume 8, Page(s) 757776

Abstract: Injurious pecking can cause a wide range of damage and is an important welfare and economic issue in turkey production. Aggressive pecking typically targets the head/neck (HN) area, and feather pecking typically targets the back/tail (BT) area; injuries ... ...

Abstract	Injurious pecking can cause a wide range of damage and is an important welfare and economic issue in turkey production. Aggressive pecking typically targets the head/neck (HN) area, and feather pecking typically targets the back/tail (BT) area; injuries in these separate areas could be used as a proxy for the level of aggressive and feather pecking in a flock. The objective of this study was to identify risk factors for integument injuries in Canadian turkey flocks. A survey containing a questionnaire about housing and management practices and a scoring guide was distributed to 500 turkey farmers across Canada. The farmer scored pecking injuries in two different body areas (HN and BT) on a 0-2 scale on a subset of birds within each flock. Multivariable logistic regression modeling was used to identify factors associated with the presence of HN and BT injuries. The prevalence of birds with integument injuries ranged widely between the flock subsets (HN = 0-40%, BT = 0-97%), however the mean prevalence was low (HN = 6%, BT = 10%). The presence of injuries for logistic regression was defined as flocks with an injury prevalence greater than the median level of injury prevalence in the dataset (3.3% HN and 6.6% BT). The final logistic regression model for HN injuries contained five variables: flock sex, flock age, number of daily inspections, number of different people during inspections, and picking up birds during inspections (N = 62, pR
Language	English
Publishing date	2022-01-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2834243-4
ISSN	2297-1769
ISSN	2297-1769
DOI	10.3389/fvets.2021.757776
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Article ; Online: The Prevalence of Integument Injuries and Associated Risk Factors Among Canadian Turkeys

Emily M. Leishman / Nienke van Staaveren / Vern R. Osborne / Benjamin J. Wood / Christine F. Baes / Alexandra Harlander-Matauschek

Frontiers in Veterinary Science, Vol

2022 Volume 8

Abstract	Injurious pecking can cause a wide range of damage and is an important welfare and economic issue in turkey production. Aggressive pecking typically targets the head/neck (HN) area, and feather pecking typically targets the back/tail (BT) area; injuries in these separate areas could be used as a proxy for the level of aggressive and feather pecking in a flock. The objective of this study was to identify risk factors for integument injuries in Canadian turkey flocks. A survey containing a questionnaire about housing and management practices and a scoring guide was distributed to 500 turkey farmers across Canada. The farmer scored pecking injuries in two different body areas (HN and BT) on a 0–2 scale on a subset of birds within each flock. Multivariable logistic regression modeling was used to identify factors associated with the presence of HN and BT injuries. The prevalence of birds with integument injuries ranged widely between the flock subsets (HN = 0–40%, BT = 0–97%), however the mean prevalence was low (HN = 6%, BT = 10%). The presence of injuries for logistic regression was defined as flocks with an injury prevalence greater than the median level of injury prevalence in the dataset (3.3% HN and 6.6% BT). The final logistic regression model for HN injuries contained five variables: flock sex, flock age, number of daily inspections, number of different people during inspections, and picking up birds during inspections (N = 62, pR2 = 0.23, α = 0.05). The final logistic regression model for BT injuries contained six variables: flock sex, flock age, litter depth, litter condition, inspection duration, and use of hospital pens for sick/injured birds (N = 59, pR2 = 0.29, α = 0.05). Flock age, and to a lesser extent, sex was associated with both types of injuries. From a management perspective, aggressive pecking injuries appear to be influenced by variables related to human interaction, namely during inspections. On the other hand, the presence of feather pecking injuries, was associated with litter condition ...
Keywords	animal welfare ; injurious pecking damage ; management ; Meleagris gallopavo ; stockmanship ; survey ; Veterinary medicine ; SF600-1100
Subject code	630
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Spatial extent of road pollution: A national analysis

Phillips, Benjamin B / Bullock, James M / Osborne, Juliet L / Gaston, Kevin J

Science of the total environment. 2021 June 15, v. 773

2021

Abstract: Roads form vast, pervasive and growing networks across the Earth, causing negative environmental impacts that spill out into a ‘road-effect zone’. Previous research has estimated the regional and global extent of these zones using arbitrary distances, ... ...

Abstract	Roads form vast, pervasive and growing networks across the Earth, causing negative environmental impacts that spill out into a ‘road-effect zone’. Previous research has estimated the regional and global extent of these zones using arbitrary distances, ignoring the spatial distribution and distance-dependent attenuation of different forms of road environmental impact. With Great Britain as a study area, we used mapping of roads and realistic estimates of how pollution levels decay with distance to project the spatial distribution of road pollution.We found that 25% of land was less than 79 m from a road, 50% of land was less than 216 m and 75% of land was less than 527 m. Roadless areas were scarce, and confined almost exclusively to the uplands (mean elevation 391 m), with only ca 12% of land in Great Britain more than 1 km from roads and <4% of land more than 2.5 km from roads. Using light, noise, heavy metals, NO₂, and particulate matter PM₂.₅ and PM₁₀ as examples, we estimate that roads have a zone of influence that extends across >70% of the land area. Potentially less than 6% of land escapes any impact, resulting in nearly ubiquitously elevated pollution levels. Generalising from this, we find that, whilst the greatest levels of road pollution are relatively localised around the busiest roads, low levels of road pollution (which may be ecologically significant) are pervasive.Our findings demonstrate the importance of incorporating greater realism into road-effect zones and considering the ubiquity of road pollution in global environmental issues. We used Great Britain as a study area, but the findings likely apply to other densely populated regions at present, and to many additional regions in the future due to the predicted rapid expansion of the global road network.
Keywords	environment ; environmental impact ; particulates ; pollution ; roads ; Great Britain
Language	English
Dates of publication	2021-0615
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2021.145589
Database	NAL-Catalogue (AGRICOLA)

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