What drives team learning: core conditions and paths

Pinheiro, Margarida M.; Rebelo, Teresa; Lourenço, Paulo Renato; Dimas, Isabel Dórdio

doi:10.1108/jwl-06-2022-0079

Cited by 8 publications

(8 citation statements)

References 73 publications

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“…Outside of the phylogenetics ecosystem, phytools also presently depends on or imports from a number of other R packages including clusterGeneration ( Qiu & Joe, 2023 ), coda ( Plummer et al, 2006 ), combinat ( Chasalow, 2012 ), doParallel ( Microsoft Corporation & Weston, 2022a ), expm ( Maechler, Dutang & Goulet, 2023 ), foreach ( Microsoft Corporation & Weston, 2022b ), maps ( Becker et al, 2022a ), MASS ( Venables & Ripley, 2002 ), mnormt ( Azzalini & Genz, 2022 ), nlme ( Pinheiro & Bates, 2000 ; Pinheiro, Bates & R Core Team, 2022 ), numDeriv ( Gilbert & Varadhan, 2019 ), optimParallel ( Gerber & Furrer, 2019 ; Lemon, 2006 ), and scatterplot3d ( Ligges & Mächler, 2003 ), although dependency relationships are dynamic as packages evolve and may change.…”

Section: Relationship Of Phytools To Other Packagesmentioning

confidence: 99%

phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things)

Revell

2024

PeerJ

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Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution, diversification dynamics, biogeography, community ecology, and a wide range of other phenomena or processes. Over the past ten years or so, the phytools R package has grown to become an important research tool for phylogenetic comparative analysis. phytools is a diverse contributed R library now consisting of hundreds of different functions covering a variety of methods and purposes in phylogenetic biology. As of the time of writing, phytools included functionality for fitting models of trait evolution, for reconstructing ancestral states, for studying diversification on trees, and for visualizing phylogenies, comparative data, and fitted models, as well numerous other tasks related to phylogenetic biology. Here, I describe some significant features of and recent updates to phytools, while also illustrating several popular workflows of the phytools computational software.

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Section: Relationship Of Phytools To Other Packagesmentioning

confidence: 99%

phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things)

Revell

2024

PeerJ

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“…We used this approach to construct a maximal random effects structure model as preconized in the literature as more generalizable ( Barr et al, 2013 ). The model was estimated by restricted maximum likelihood using the lme function of the nlme package ( Pinheiro et al, 2023 ) with an unstructured covariance matrix.…”

Section: Methodsmentioning

confidence: 99%

Dysfunctional hippocampal-prefrontal network underlies a multidimensional neuropsychiatric phenotype following early-life seizure

Ruggiero,

Marques,

Rossignoli

et al. 2024

eLife

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Brain disturbances during development can have a lasting impact on neural function and behavior. Seizures during this critical period are linked to significant long-term consequences such as neurodevelopmental disorders, cognitive impairments, and psychiatric symptoms, resulting in a complex spectrum of multimorbidity. The hippocampus-prefrontal cortex (HPC-PFC) circuit emerges as a potential common link between such disorders. However, the mechanisms underlying these outcomes and how they relate to specific behavioral alterations are unclear. We hypothesized that specific dysfunctions of hippocampal-cortical communication due to early-life seizure would be associated with distinct behavioral alterations observed in adulthood. Here, we performed a multilevel study to investigate behavioral, electrophysiological, histopathological, and neurochemical long-term consequences of early-life Status epilepticus in male rats. We show that adult animals submitted to early-life seizure (ELS) present working memory impairments and sensorimotor disturbances, such as hyperlocomotion, poor sensorimotor gating, and sensitivity to psychostimulants despite not exhibiting neuronal loss. Surprisingly, cognitive deficits were linked to an aberrant increase in the HPC-PFC long-term potentiation (LTP) in a U-shaped manner, while sensorimotor alterations were associated with heightened neuroinflammation, as verified by glial fibrillary acidic protein (GFAP) expression, and altered dopamine neurotransmission. Furthermore, ELS rats displayed impaired HPC-PFC theta-gamma coordination and an abnormal brain state during active behavior resembling rapid eye movement (REM) sleep oscillatory dynamics. Our results point to impaired HPC-PFC functional connectivity as a possible pathophysiological mechanism by which ELS can cause cognitive deficits and psychiatric-like manifestations even without neuronal loss, bearing translational implications for understanding the spectrum of multidimensional developmental disorders linked to early-life seizures.

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“…Data were analysed in R v.4.2.2 [22], and one-way repeated measures ANOVA was performed using the nlme (v.3.1-160) package [23] to test for any statistical differences between values for tidal volume, breathing frequency, metabolic rate, WCR, and OEE. Data are shown as means ± s.e.m unless otherwise stated.…”

Section: Methodsmentioning

confidence: 99%

Oxygen extraction efficiency of the tidally-ventilated rectal gills of dragonfly nymphs

Lee,

Matthews

2024

Proc. R. Soc. B.

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Dragonfly nymphs breathe water using tidal ventilation, a highly unusual strategy in water-breathing animals owing to the high viscosity, density and low oxygen (O 2 ) concentration of water. This study examines how well these insects extract O 2 from the surrounding water during progressive hypoxia. Nymphs were attached to a custom-designed respiro-spirometer to simultaneously measure tidal volume, ventilation frequency and metabolic rate. Oxygen extraction efficiencies (OEE) were calculated across four partial pressure of oxygen (pO 2 ) treatments, from normoxia to severe hypoxia. While there was no significant change in tidal volume, ventilation frequency increased significantly from 9.4 ± 1.2 breaths per minute (BPM) at 21.3 kPa to 35.6 ± 2.9 BPM at 5.3 kPa. Metabolic rate increased significantly from 1.4 ± 0.3 µl O 2 min −1 at 21.3 kPa to 2.1 ± 0.4 µl O 2 min −1 at 16.0 kPa, but then returned to normoxic levels as O 2 levels declined further. OEE of nymphs was 40.1 ± 6.1% at 21.3 kPa, and did not change significantly during hypoxia. Comparison to literature shows that nymphs maintain their OEE during hypoxia unlike other aquatic tidal-breathers and some unidirectional breathers. This result, and numerical models simulating experimental conditions, indicate that nymphs maintain these extraction efficiencies by increasing gill conductance and/or lowering internal pO 2 to maintain a sufficient diffusion gradient across their respiratory surface.

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What drives team learning: core conditions and paths

Cited by 8 publications

References 73 publications

phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things)

phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things)

Dysfunctional hippocampal-prefrontal network underlies a multidimensional neuropsychiatric phenotype following early-life seizure

Oxygen extraction efficiency of the tidally-ventilated rectal gills of dragonfly nymphs

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