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Article: Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes

Seeber, Peter Andreas / McEwen, Gayle / Löber, Ulrike / Förster, Daniel / Melzheimer, Joerg / Greenwood, Alex

Molecular ecology resources, 19(6):1486-1496

2019

Abstract: Determining species distributions can be extremely challenging but is crucial to ecological and conservation research. Environmental DNA (eDNA) approaches have shown particular promise in aquatic systems for several vertebrate and invertebrate species. ... ...

Institution	Leibniz-Institut für Zoo- und Wildtierforschung (Berlin)
Abstract	Determining species distributions can be extremely challenging but is crucial to ecological and conservation research. Environmental DNA (eDNA) approaches have shown particular promise in aquatic systems for several vertebrate and invertebrate species. For terrestrial animals, however, eDNA-based surveys are considerably more difficult due to the lack of or difficulty in obtaining appropriate sampling substrate. In water-limited ecosystem where terrestrial mammals are often forced to congregate at waterholes, water and sediment from shared water sources may be a suitable substrate for noninvasive eDNA approaches. We characterized mitochondrial DNA sequences from a broad range of terrestrial mammal species in two different African ecosystems (in Namibia and Tanzania) using eDNA isolated from native water, sediment and water filtered through glass fibre filters. A hybridization capture enrichment with RNA probes targeting the mitochondrial genomes of 38 mammal species representing the genera/families expected at the respective ecosystems was employed, and 16 species were identified, with a maximum mitogenome coverage of 99.8%. Conventional genus-specific PCRs were tested on environmental samples for two genera producing fewer positive results than hybridization capture enrichment. An experiment with mock samples using DNA from non-African mammals showed that baits covering 30% of nontarget mitogenomes produced 91% mitogenome coverage after capture. In the mock samples, over-representation of DNA of one species still allowed for the detection of DNA of other species that was at a 100-fold lower concentration. Hybridization capture enrichment of eDNA is therefore an effective method for monitoring terrestrial mammal species from shared water sources.
Keywords	biodiversity ; eDNA ; mitogenome ; species monitoring ; terrestrial
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article ; Online: Chimpanzees demonstrate a behavioural signature of human joint action.

Constable, Merryn D / McEwen, Emma Suvi / Knoblich, Günther / Gibson, Callum / Addison, Amanda / Nestor, Sophia / Call, Josep

Cognition

2024 Volume 246, Page(s) 105747

Abstract: The strength of human society can largely be attributed to the tendency to work together to achieve outcomes that are not possible alone. Effective social coordination benefits from mentally representing a partner's actions. Specifically, humans optimize ...

Abstract	The strength of human society can largely be attributed to the tendency to work together to achieve outcomes that are not possible alone. Effective social coordination benefits from mentally representing a partner's actions. Specifically, humans optimize social coordination by forming internal action models adapted to joint rather than individual task demands. To what extent do humans share the cognitive mechanisms that support optimal human coordination and collaboration with other species? An ecologically inspired joint handover-to-retrieve task was systematically manipulated across several experiments to assess whether joint action planning in chimpanzees reflects similar patterns to humans. Chimpanzees' chosen handover locations shifted towards the location of the experimenter's free or unobstructed hand, suggesting they represent the constraints of the joint task even though their individual half of the task was unobstructed. These findings indicate that chimpanzees and humans may share common cognitive mechanisms or predispositions that support joint action.
MeSH term(s)	Animals ; Humans ; Pan troglodytes/psychology ; Behavior, Animal ; Cooperative Behavior
Language	English
Publishing date	2024-02-26
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1499940-7
ISSN	1873-7838 ; 0010-0277
ISSN (online)	1873-7838
ISSN	0010-0277
DOI	10.1016/j.cognition.2024.105747
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Book ; Online: Differentiable and accelerated spherical harmonic and Wigner transforms

Price, Matthew A. / McEwen, Jason D.

2023

Abstract: ... g. GPUs). We also develop a hybrid automatic and manual differentiation approach so that gradients ... of Wigner $d$-functions that is both stable to high harmonic degrees and extremely parallelisable ...

Abstract	Many areas of science and engineering encounter data defined on spherical manifolds. Modelling and analysis of spherical data often necessitates spherical harmonic transforms, at high degrees, and increasingly requires efficient computation of gradients for machine learning or other differentiable programming tasks. We develop novel algorithmic structures for accelerated and differentiable computation of generalised Fourier transforms on the sphere $\mathbb{S}^2$ and rotation group $\text{SO}(3)$, i.e. spherical harmonic and Wigner transforms, respectively. We present a recursive algorithm for the calculation of Wigner $d$-functions that is both stable to high harmonic degrees and extremely parallelisable. By tightly coupling this with separable spherical transforms, we obtain algorithms that exhibit an extremely parallelisable structure that is well-suited for the high throughput computing of modern hardware accelerators (e.g. GPUs). We also develop a hybrid automatic and manual differentiation approach so that gradients can be computed efficiently. Our algorithms are implemented within the JAX differentiable programming framework in the S2FFT software code. Numerous samplings of the sphere are supported, including equiangular and HEALPix sampling. Computational errors are at the order of machine precision for spherical samplings that admit a sampling theorem. When benchmarked against alternative C codes we observe up to a 400-fold acceleration. Furthermore, when distributing over multiple GPUs we achieve very close to optimal linear scaling with increasing number of GPUs due to the highly parallelised and balanced nature of our algorithms. Provided access to sufficiently many GPUs our transforms thus exhibit an unprecedented effective linear time complexity. Comment: 30 pages, 7 figures, code available at https://github.com/astro-informatics/s2fft
Keywords	Physics - Computational Physics ; Astrophysics - Instrumentation and Methods for Astrophysics ; Computer Science - Machine Learning
Subject code	006
Publishing date	2023-11-24
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The dynamic nature of refugee children's resilience: a cohort study of Syrian refugees in Lebanon.

Popham, C M / McEwen, F S / Karam, E / Fayyad, J / Karam, G / Saab, D / Moghames, P / Pluess, M

Epidemiology and psychiatric sciences

2022 Volume 31, Page(s) e41

Abstract: Aims: Children's responses to war and displacement are varied; many struggle, while others appear resilient. However, research into these outcomes disproportionately focuses on cross-sectional data in high-income countries. We aimed to (1) investigate ... ...

Abstract	Aims: Children's responses to war and displacement are varied; many struggle, while others appear resilient. However, research into these outcomes disproportionately focuses on cross-sectional data in high-income countries. We aimed to (1) investigate change in resilience across two timepoints in a highly vulnerable sample of Syrian refugee children in Lebanon, and (2) explore predictors of their mental health problems across time. Methods: In total, 982 Syrian child-caregiver dyads living in refugee settlements in Lebanon completed questionnaires via interview at baseline and follow-up one year later. We categorised children into groups based on their risk for mental health problems across both timepoints (stable high risk/SHR, deteriorating, improving, stable low risk) according to locally validated cut-offs on measures of post-traumatic stress disorder (PTSD), depression and behavioural problems. Analyses of covariance identified how the groups differed on a range of individual and socio-environmental predictors, followed up by cross-lagged panel models (CLPMs) to investigate the directionality of the relationships between significantly related predictors and symptoms. Results: The sample showed a meaningful amount of change in mental health symptoms from baseline to follow-up. Over half (56.3%) of children met SHR criteria and 10.3% deteriorated over time, but almost one-quarter (24.2%) showed meaningful improvement, and 9.2% were consistently at low risk for mental health problems at both timepoints. Several predictors differentiated the groups, particularly social measures. According to CLPMs, maternal acceptance ( Conclusions: Our results show risk and resilience are dynamic, and the family environment plays a key role in children's response to war and displacement. Conversely, children also have a significant impact on the family environment and caregiver's own mental health. Interventions to promote resilience in refugee children should therefore consider family-wide mechanisms.
MeSH term(s)	Cohort Studies ; Cross-Sectional Studies ; Humans ; Lebanon/epidemiology ; Refugees/psychology ; Stress Disorders, Post-Traumatic/psychology ; Syria
Language	English
Publishing date	2022-06-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2607964-1
ISSN	2045-7979 ; 2045-7960
ISSN (online)	2045-7979
ISSN	2045-7960
DOI	10.1017/S2045796022000191
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Article: Combined Video Laryngoscope and Fiberoptic Nasal Intubation.

Nedrud, Stacey M / Baasch, Douglas G / Cabral, John D / McEwen, Daniel S / Dasika, Jayanth

Cureus

2021 Volume 13, Issue 11, Page(s) e19482

Abstract: Techniques for facilitating nasal intubation and reducing associated airway trauma are well documented in the literature. This case series describes an additional technique that combines the use of the video laryngoscope and fiberoptic bronchoscope for ... ...

Abstract	Techniques for facilitating nasal intubation and reducing associated airway trauma are well documented in the literature. This case series describes an additional technique that combines the use of the video laryngoscope and fiberoptic bronchoscope for intubation. Rather than first starting with the fiberoptic bronchoscope, an endotracheal tube is passed through the nasopharynx and lined up with the glottis using video laryngoscopy. Subsequently, the fiberoptic bronchoscope is used only to guide the endotracheal tube through the glottis. The two perspectives simultaneously provide enhanced guidance to the operator, which can, in turn, reduce the burden of fiberoptic navigation through blood, secretions, and/or altered airway anatomy. Additionally, our report demonstrates that this procedure can be used as a rescue measure when Magill forceps are unsuccessful.
Language	English
Publishing date	2021-11-11
Publishing country	United States
Document type	Case Reports
ZDB-ID	2747273-5
ISSN	2168-8184
ISSN	2168-8184
DOI	10.7759/cureus.19482
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Article ; Online: Clinical adaptations for advanced career emergency physicians: an approach to support practice transition.

Abu-Laban, Riyad B / Rose, Nicholas G W / Migneault, David / Fukushima, Erin / Walker, Kerry E / McEwen, Jill

CJEM

2023 Volume 25, Issue 12, Page(s) 931–934

MeSH term(s)	Humans ; Surveys and Questionnaires ; Physicians ; Career Choice
Language	English
Publishing date	2023-09-22
Publishing country	England
Document type	Editorial
ISSN	1481-8043
ISSN (online)	1481-8043
DOI	10.1007/s43678-023-00591-2
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Book ; Online: Scattering Networks on the Sphere for Scalable and Rotationally Equivariant Spherical CNNs

McEwen, Jason D. / Wallis, Christopher G. R. / Mavor-Parker, Augustine N.

2021

Abstract: Convolutional neural networks (CNNs) constructed natively on the sphere have been developed recently and shown to be highly effective for the analysis of spherical data. While an efficient framework has been formulated, spherical CNNs are nevertheless ... ...

Abstract	Convolutional neural networks (CNNs) constructed natively on the sphere have been developed recently and shown to be highly effective for the analysis of spherical data. While an efficient framework has been formulated, spherical CNNs are nevertheless highly computationally demanding; typically they cannot scale beyond spherical signals of thousands of pixels. We develop scattering networks constructed natively on the sphere that provide a powerful representational space for spherical data. Spherical scattering networks are computationally scalable and exhibit rotational equivariance, while their representational space is invariant to isometries and provides efficient and stable signal representations. By integrating scattering networks as an additional type of layer in the generalized spherical CNN framework, we show how they can be leveraged to scale spherical CNNs to the high-resolution data typical of many practical applications, with spherical signals of many tens of megapixels and beyond. Comment: 16 pages, 5 figures
Keywords	Computer Science - Computer Vision and Pattern Recognition ; Astrophysics - Instrumentation and Methods for Astrophysics ; Computer Science - Machine Learning ; Electrical Engineering and Systems Science - Image and Video Processing
Subject code	004 ; 006
Publishing date	2021-02-04
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Exercise Predicts a Good Night's Sleep: Preliminary Findings from a UCLA Study of First-Episode Schizophrenia.

Subotnik, Kenneth L / McEwen, Sarah C / Ventura, Joseph / Turner, Luana Rene / Sturdevant, Yurika / Niess, Trudy L / Casaus, Laurie R / Distler, Margaret G / Zito, Michael F / Hellemann, Gerhard S / Nguyen, Clara D / Nuechterlein, Keith H

Behavioral sciences (Basel, Switzerland)

2023 Volume 13, Issue 2

Abstract: Background: Physical exercise can improve sleep quality in the general population. Understanding the negative impact of poor sleep quality on multiple domains of functioning among persons with schizophrenia is a new frontier of exploration. It is also ... ...

Abstract	Background: Physical exercise can improve sleep quality in the general population. Understanding the negative impact of poor sleep quality on multiple domains of functioning among persons with schizophrenia is a new frontier of exploration. It is also imperative to investigate non-pharmacologic methods to improve sleep quality as these approaches may not carry the side effect burdens associated with medication. Objective: We examined the relationship between regular physical exercise and sleep quality among participants in an intervention consisting of both cognitive training and exercise. Methods: Participants (N = 48) were schizophrenia patients who had a first psychotic episode within two years of study entry. Participants received 4 h/week of internet-based cognitive training and an aerobic exercise program over a 6-month period. Sleep was assessed with the Pittsburgh Sleep Quality Index at baseline and six months later. Results: During the 3 months prior to the 6-month follow-up sleep assessment, participants completed an average of 12.6 group exercise sessions and an average of 12.9 individual at-home exercise sessions. A significant relationship between the number of exercise sessions and global sleep quality was seen at month six, r = -0.44, df = 39, Conclusion: We demonstrated that a group of young adults with schizophrenia can be engaged in a regular exercise program, even during the tumultuous early course of the disorder. The number of exercise sessions in which they participated was associated with better sleep quality at six months and pre-postintervention improvement in sleep quality. Key message: Improved sleep quality appears to be a benefit of regular exercise among individuals with serious mental illness.
Language	English
Publishing date	2023-01-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2651997-5
ISSN	2076-328X
ISSN	2076-328X
DOI	10.3390/bs13020088
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Article ; Online: Multi-model order spatially constrained ICA reveals highly replicable group differences and consistent predictive results from resting data: A large N fMRI schizophrenia study.

Meng, Xing / Iraji, Armin / Fu, Zening / Kochunov, Peter / Belger, Aysenil / Ford, Judy M / McEwen, Sara / Mathalon, Daniel H / Mueller, Bryon A / Pearlson, Godfrey / Potkin, Steven G / Preda, Adrian / Turner, Jessica / van Erp, Theo G M / Sui, Jing / Calhoun, Vince D

NeuroImage. Clinical

2023 Volume 38, Page(s) 103434

Abstract: Brain functional networks identified from resting functional magnetic resonance imaging (fMRI) data have the potential to reveal biomarkers for brain disorders, but studies of complex mental illnesses such as schizophrenia (SZ) often yield mixed results ... ...

Abstract	Brain functional networks identified from resting functional magnetic resonance imaging (fMRI) data have the potential to reveal biomarkers for brain disorders, but studies of complex mental illnesses such as schizophrenia (SZ) often yield mixed results across replication studies. This is likely due in part to the complexity of the disorder, the short data acquisition time, and the limited ability of the approaches for brain imaging data mining. Therefore, the use of analytic approaches which can both capture individual variability while offering comparability across analyses is highly preferred. Fully blind data-driven approaches such as independent component analysis (ICA) are hard to compare across studies, and approaches that use fixed atlas-based regions can have limited sensitivity to individual sensitivity. By contrast, spatially constrained ICA (scICA) provides a hybrid, fully automated solution that can incorporate spatial network priors while also adapting to new subjects. However, scICA has thus far only been used with a single spatial scale (ICA dimensionality, i.e., ICA model order). In this work, we present an approach using multi-objective optimization scICA with reference algorithm (MOO-ICAR) to extract subject-specific intrinsic connectivity networks (ICNs) from fMRI data at multiple spatial scales, which also enables us to study interactions across spatial scales. We evaluate this approach using a large N (N > 1,600) study of schizophrenia divided into separate validation and replication sets. A multi-scale ICN template was estimated and labeled, then used as input into scICA which was computed on an individual subject level. We then performed a subsequent analysis of multiscale functional network connectivity (msFNC) to evaluate the patient data, including group differences and classification. Results showed highly consistent group differences in msFNC in regions including cerebellum, thalamus, and motor/auditory networks. Importantly, multiple msFNC pairs linking different spatial scales were implicated. The classification model built on the msFNC features obtained up to 85% F1 score, 83% precision, and 88% recall, indicating the strength of the proposed framework in detecting group differences between schizophrenia and the control group. Finally, we evaluated the relationship of the identified patterns to positive symptoms and found consistent results across datasets. The results verified the robustness of our framework in evaluating brain functional connectivity of schizophrenia at multiple spatial scales, implicated consistent and replicable brain networks, and highlighted a promising approach for leveraging resting fMRI data for brain biomarker development.
MeSH term(s)	Humans ; Schizophrenia/diagnostic imaging ; Magnetic Resonance Imaging/methods ; Brain Mapping/methods ; Brain/diagnostic imaging ; Cerebellum ; Biomarkers
Chemical Substances	Biomarkers
Language	English
Publishing date	2023-05-17
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2701571-3
ISSN	2213-1582 ; 2213-1582
ISSN (online)	2213-1582
ISSN	2213-1582
DOI	10.1016/j.nicl.2023.103434
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Article: Chemical data evaluation: general considerations and approaches for IUPAC projects and the chemistry community (IUPAC Technical Report).

Shaw, David G / Bruno, Ian / Chalk, Stuart / Hefter, Glenn / Hibbert, D Brynn / Hutchinson, Robin A / Magalhães, M Clara F / Magee, Joseph / McEwen, Leah R / Rumble, John / Russell, Gregory T / Waghorne, Earle / Walczyk, Thomas / Wallington, Timothy J

Pure and applied chemistry. Chimie pure et appliquee

2023 Volume 95, Issue 10

Abstract: The International Union of Pure and Applied Chemistry (IUPAC) has a long tradition of supporting the compilation of chemical data and their evaluation through direct projects, nomenclature and terminology work, and partnerships with international ... ...

Abstract	The International Union of Pure and Applied Chemistry (IUPAC) has a long tradition of supporting the compilation of chemical data and their evaluation through direct projects, nomenclature and terminology work, and partnerships with international scientific bodies, government agencies and other organizations. The IUPAC Interdivisional Subcommittee on Critical Evaluation of Data (ISCED) has been established to provide guidance on issues related to the evaluation of chemical data. In this first report we define the general principles of the evaluation of scientific data and describe best practices and approaches to data evaluation in chemistry.
Language	English
Publishing date	2023-11-15
Publishing country	England
Document type	Journal Article
ZDB-ID	1514-3
ISSN	0033-4545
ISSN	0033-4545
DOI	10.1515/pac-2022-0802
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