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opencc-by-4.0Nov 2023View details →

Polymer Electrolyte Membrane Water Electrolyzer Oxygen Bubble Evolution Optical Video Recording For Deep Learning-Enhanced Characterization of Bubble Dynamics in Proton Exchange Membrane Water Electrolyzer by André Colliard-Granero, Keusra A. Gompou, Christian Rodenbücher, Kourosh Malek, Michael H. Eikerling, and Mohammad J. Eslamibidgoli

Dataset used for the training of the segmentation model employed in the work "Deep Learning-Enhanced Characterization of Bubble Dynamics in Proton Exchange Membrane Water Electrolyzer" by André Colliard-Granero, Keusra A. Gompou, Christian Rodenbücher, Kourosh Malek, Michael H. Eikerling, and Mohammad J. Eslamibidgoli. This dataset consists in 35 images and the corresponding manual annotated masks of diverse bubbly scenarios extracted from the optical video recording of a PEMWE with a transparent flow field.

dryad40/100

The evolution, complexity and diversity of models of long-term forest dynamics

1. To assess the impacts of climate change on vegetation from stand to global scales, models of forest dynamics that include tree demography are needed. Such models are now available for 50 years, but the currently existing diversity of model formulations and its evolution over time are poorly documented. This hampers systematic assessments of structural uncertainties in model-based studies. 2. We conducted a meta-analysis of 28 models, focusing on models that were used in the past five years for climate change studies. We defined 52 model attributes in five groups (basic assumptions, growth, regeneration, mortality and soil moisture) and characterized each model according to these attributes. Analyses of model complexity and diversity included hierarchical cluster analysis and redundancy analysis. 3. Model complexity evolved considerably over the past 50 years. Increases in complexity were largest for growth processes, while complexity of modelled establishment processes increased only moderately. Model diversity was lowest at the global scale, and highest at the landscape scale. We identified five distinct clusters of models, ranging from very simple models to models where specific attribute groups are rendered in a complex manner and models that feature high complexity across all attributes. 4. Most models in use today are not balanced in the level of complexity with which they represent different processes. This is the result of different model purposes, but also reflects legacies in model code, modelers' preferences, and the 'prevailing spirit of the epoch'. The lack of firm theories, laws and 'first principles' in ecology provides high degrees of freedom in model development, but also results in high responsibilities for model developers and the need for rigorous model evaluation. 5. Synthesis. The currently available model diversity is beneficial: convergence in simulations of structurally different models indicates robust projections, while convergence of similar models may convey a false sense of certainty. The existing model diversity – with the exception of global models – can be exploited for improved projections based on multiple models. We strongly recommend balanced further developments of forest models that should particularly focus on establishment and mortality processes, in order to provide robust information for decisions in ecosystem management and policymaking.

opencc-zeroAug 2022View details →

Fig. 2 in Growth dynamics and body size evolution of South American long-necked chelid turtles: A bone histology approach

Fig. 2. Stylopodial bones of chelid turtles sampled in this study, showing the position where the thin sections were obtained (gray bar) and the complete shaft section in each element. A–D. Hydromedusa tectifera Cope, 1869; Recent, La Plata, Buenos Aires province, Argentina. A. MLPR-6291, dorsal view of the left humerus (A1), cross section (A2). B. MLPR-6291, dorsal view of the left femur (B1), cross section (B2). C. MLPR-6411, dorsal view of the right humerus (C1), cross section (C2). D. MLPR-6411, dorsal view of the right femur (D1), cross section (D2). E–G. Yaminuechelys maior (Staesche, 1929); Cerro Hansen, Danian of Salamanca Formation, Chubut Province, Argentina. E. MPEFPV-599, dorsal view of the right humerus (E1), cross section (E2). F. MPEFPV-599, dorsal view of the left femur (F1), cross section (F2). G. MLP-14-9-23-1, dorsal view of the left humerus (G1), cross section (G2). Note that the expansion of the medullary region is higher in Y. maior than in H. tectifera (see discussion in the text).

Fig. 3 in Growth dynamics and body size evolution of South American long-necked chelid turtles: A bone histology approach

Fig. 3. Stylopodial bone histology of chelid turtle Yaminuechelys maior (Staesche, 1929), Cerro Hansen, Danian, Paleocene of Salamanca Formation, Chubut Province, Argentina (Bona and De la Fuente 2005). A. MPEFPV-599, humerus: dorsal (A1), dorsomedial (A2), dorsolateral (A3), and lateral (A4) areas. B. MLP-14-9-23-1, humerus: lateral (B1), dorsal (B2), medial (B3), and ventral (B4) areas. Arrowheads in A1 and B4 indicate lines of arrested growth. C. MPEFPV-599, femur: dorsal (C1), dorsolateral (C2), and ventral (C3, C4) areas. Photographs under normal light (A1, A4, B3), under polarized light (C4), under polarized light with lambda compensator (A2, A3, B1, B2, B4, C1–C3). Abbreviations: LVC, simple longitudinal vascular canals; PFB, parallel-fibered bone; RS, resorption cavities; RVC, simple radial vascular canals; SF, Sharpey's fibres.

Fig. 4 in Growth dynamics and body size evolution of South American long-necked chelid turtles: A bone histology approach

Fig. 4. Stylopodial bone histology of chelid turtle Hydromedusa tectifera Cope, 1869; Recent, La Plata, Buenos Aires province, Argentina. A. MLPR-6474, humerus: dorsolateral (A1) and ventral (A2) areas. B. MLPR-6474, femur: ventral (B1) and dorsal (B2) areas. C. MLPR-6291, humerus: dorsal (C1) and ventral (C2) areas. D. MLPR-6291, femur: lateral (D1) and ventrolateral (D2) areas; annuli, yellow A; zones, green Z. E. MLPR-6411, humerus: dorsal (E1) and ventral (E2) areas. F. MLPR-6411, femur: lateral areas (F1, F2). Arrowheads in E2 and F2 indicate lines of arrested growth. Photographs under normal light (B1, B2, D1, E1, F2), under polarized light (E2), under polarized light with lambda compensator (A1, A2, C1, C2, D2, F1). Abbreviations: LVC, simple longitudinal vascular canals; PFB, parallel-fibered bone; RS, resorption cavities; SF, Sharpey's fibers.

Fig. 1 in Growth dynamics and body size evolution of South American long-necked chelid turtles: A bone histology approach

Fig. 1. Size distribution of chelid turtles represented in two different phylogenetic hypotheses from Maniel et al. (2018). Both topologies recover two alternative hypotheses (orange): the monophyly of the South American chelid clade (A) and the monophyly of the of the long necked chelid turtles (B) see Maniel et al. 2018, for more information). Grey, species smaller than 20 cm; green, 20–60 cm; blue and bold, larger than 60 cm. The size is based on the carapace length.

FIGURE 3 in Reassessing the causal connection between satDNA dynamics and chromosomal evolution in Ctenomys (Rodentia, Ctenomyidae): Unveiling the overlooked importance of the Y chromosome

FIGURE 3 Ancestral RPCS copy number reconstruction. RPCS copy number was mapped along the mtDNA phylogeny using the phytools function anc.ML, for males and females of the Ctenomys Corrientes group separately. The projection of the reconstruction onto the edges of the tree was made with the function contMap. RPCS copy number is expressed as thousands of copies. The scale of the tree is expressed in substitutions per site. Letters A–D correspond to the four main clades of the group.

FIGURE 2 in Reassessing the causal connection between satDNA dynamics and chromosomal evolution in Ctenomys (Rodentia, Ctenomyidae): Unveiling the overlooked importance of the Y chromosome

FIGURE 2 Geographic distribution of mean RPCS copy number. The Corrientes group lineages are surrounded by dashed lines. Locality numbers are: 1 – San Alonso, 2 – Loreto, 3 – Contreras_Cué, 4 – Estancia La Tacuarita, 5 – Saladas Sur, 6 – Saladas, 7 – Santa Rosa, 8 – San Roque, 9 – Estancia San Luis, 10 – Pago Alegre, 11 – Mbarigüí, 12 – Paraje Angostura, 13 – Goya, 14 – Chavarría, 15 – Colonia 3 de abril, 16 – Rincón de Ambrosio.

FIGURE 1 in Reassessing the causal connection between satDNA dynamics and chromosomal evolution in Ctenomys (Rodentia, Ctenomyidae): Unveiling the overlooked importance of the Y chromosome

FIGURE 1 Differences in RPCS copy number in males and females. Scatter plot showing differences in RPCS copy numbers between males and females of the Ctenomys Corrientes group, expressed as thousands of copies. Clades A-D correspond to the four different clades of the phylogeny (figs 3 and 4). A smoothing function was applied with the package ggplot2.

FIGURE 4 in Reassessing the causal connection between satDNA dynamics and chromosomal evolution in Ctenomys (Rodentia, Ctenomyidae): Unveiling the overlooked importance of the Y chromosome

FIGURE 4 Ancestral reconstruction of diploid numbers (2n) and main RPCS reductions and amplifications in the Ctenomys Corrientes group. Ancestral diploid numbers were inferred with the ChromEvol model implemented in RevBayes, over the mtDNA Bayesian phylogeny of the Corrientes group. Numbers in internal nodes/ terminals represent inferred/observed 2n. Colored circles depict 2n (size) and posterior probability of the inferred value (color). Red and green branches depict significant reductions and amplifications in diploid numbers, respectively. Smaller equal-sized black circles show well-supported nodes (posterior probability> 0.75). Black arrowheads denote a marked increase/decrease in RPCS copy numbers (inferred from females). The scale bar is expressed in substitutions per site.

Figure 1 in Life history dynamics and biogeography of a nudibranch with contrasting developmental modes: A hypothesis for the evolution of larval types

Figure 1. Map of the lower Gulf of Maine with the distribution of Dendronotus frondosus and Dendronotus sp. from subtidal and intertidal habitats near the coasts of Maine (ME) and New Hampshire (NH), USA and New Brunswick (NB) and Nova Scotia (NS), Canada. See Table I to reference site numbers and Cartesian coordinates. Sites for seasonal monitoring of hydroid and nudibranch abundance include York (2), West Quoddy Head (12) and Eastport (13), Maine.

Figure 5 in Life history dynamics and biogeography of a nudibranch with contrasting developmental modes: A hypothesis for the evolution of larval types

Figure 5. Summary of the larval dispersal potential of Dendronotus frondosus and Dendronotus sp. in laboratory cultures at 10°C (Sisson 2002b, 2004). The ''egg-to-juvenile'' period lasts from spawn deposition through larval settlement and metamorphosis.

Figure 3 in Life history dynamics and biogeography of a nudibranch with contrasting developmental modes: A hypothesis for the evolution of larval types

Figure 3. Abundance of spawn masses deposited by Dendronotus spp. at: (a) York, Maine, (b) Eastport, Maine and (c) the intertidal site at West Quoddy Head, Lubec, Maine.

Figure 4 in Life history dynamics and biogeography of a nudibranch with contrasting developmental modes: A hypothesis for the evolution of larval types

Figure 4. Weekly mean (¡SD), minimum and maximum water temperature (in °C) at the subtidal sampling sites in York and Eastport, Maine.

opencc-by-4.0Sep 2021View details →

Dataset for Evolution of Cooperation in Costly Institutions: Red Queen and Black Queen Dynamics in Heterogenous Public Goods

This dataset contains the Matlab codes used in "Evolution of Cooperation in Costly Institutions: Red Queen and Black Queen Dynamics in Heterogenous Public Goods". The zip file contains Matlab codes used in simulation and numerical solutions of the replicator dynamics. The zip file "Figures" contains the Matlab code and data used to produce figures in this study.

opencc-by-4.0Nov 2022View details →

dataset for bioRxiv preprint titled 'Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease'

This data supports the Figures in the preprint titled Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease working abstract The HIV-1 protease is one of several common key targets of combination drug therapies for human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS).  During the progression of the disease, some individual patients acquire -drug resistance due to mutational hotspots on the viral proteins targeted by combination drug therapies.  It has recently been discovered that drug-resistant mutations accumulate on the ‘flap region’ of the HIV-1 protease,  which is a critical dynamic region involved in non-specific polypeptide binding  during invasion and infection of the host cell.  In this study, we utilize machine learning assisted comparative molecular dynamics, conducted at single amino acid site resolution, to investigate the dynamic changes that occur during functional dimerization and polypeptide binding of the main protease. We use a multi-agent machine learning model to identify conserved dynamics of the HIV-1 main protease that are preserved across simian and feline protease orthologs (SIV and FIV).  We also investigate changes in dynamics due to common drug-resistant mutations in many patients. We find that a key functional site in the flap region, a solvent-exposed isoleucine (ILE50) and surrounding sites that control flap dynamics is often targeted by drug-resistance mutations, likely leading to malfunctional molecular dynamics affecting the overall flexibility of the flap region. We conclude that better long term patient outcomes may be achieved by designing drugs that target protease regions which are less dependent upon single sites with large functional binding effects.

dryad40/100

The evolution of dynamic and flexible courtship displays that reveal individual quality

Abstract Sexual selection is a major force shaping morphological and behavioral diversity. Existing theory focuses on courtship display traits such as morphological ornaments whose costs and benefits are assumed be to fixed across individuals' lifetimes. In contrast, empirically observed displays are often inherently dynamic, as vividly illustrated by the acrobatic dances, loud vocalizations, and vigorous motor displays involved in courtship behavior across a broad range of taxa. One empirically observed form of display flexibility occurs when signalers adjust their courtship investment based on the number of rival signalers. The predictions of established sexual selection theory cannot readily be extended to such displays because display expression varies between courtship events, such that any given display may not reliably reflect signaler quality. We thus lack an understanding of how dynamic displays coevolve with sexual preferences and how signalers should tactically adjust their display investment across multiple courtship opportunities. To address these questions, we extended an established model of the coevolution of a female sexual preference and a male display trait to allow for flexible, dynamic displays. We find that such a display can coevolve with a sexual preference away from their naturally selected optima, though display intensity is a weaker signal of male quality than for non-flexible displays. Furthermore, we find that males evolve to decrease their display investment when displaying alongside more rivals. This research represents a first step towards generalizing the findings of sexual selection theory to account for the ubiquitous dynamism of animal courtship. Significance statement Animal courtship displays are typically costly for survival: songs attract predators; dances are exhausting; extravagant plumage is cumbersome. Because of the trade-off between mating benefits and survival costs, displaying individuals often vary their displays across time, courting more intensely when the potential benefit is higher or the cost is lower. Despite the ubiquity of such adjustment in nature, existing theory cannot account for how this flexibility might affect the coevolution of displays with sexual preferences, nor for the patterns of tactical display adjustment that might result, because those models treat displays as static, with fixed costs and benefits. Generalizing a well-studied model of sexual selection, we find that a static display and a flexible display can evolve under similar conditions. Our model predicts that courtship should be less intense when more competitors are present.

opencc-zeroFeb 2023View details →