bluuebunny/crossref_metadata_2025 huggingface dataset:
Variations in non-local interaction range lead to emergent chase-and-run in heterogeneous populations
Authors: Painter Kevin J. , Giunta Valeria , Potts Jonathan R. , Bernardi Sara
Published: October 2024

In a chase-and-run dynamic, the interaction between two individuals is such that one moves towards the other (the chaser), while the other moves away (the runner). Examples can be found in both interacting cells and animals. Here, we investigate the behaviours that can emerge at a population level, for a heterogeneous group that contains subpopulations of chasers and runners. We show that a wide variety of patterns can form, from stationary patterns to oscillatory and population-level chase-and-run, where the latter describes a synchronized collective movement of the two populations. We investigate the conditions under which different behaviours arise, specifically focusing on the interaction ranges: the distances over which cells or organisms can sense one another’s presence. We find that when the interaction range of the chaser is sufficiently larger than that of the runner—or when the interaction range of the chase is sufficiently larger than that of the run—population-level chase-and-run emerges in a robust manner. We discuss the results in the context of phenomena observed in cellular and ecological systems, with particular attention to the dynamics observed experimentally within populations of neural crest and placode cells.
A cryptic plastid and a novel mitochondrial plasmid in
Leucomyxa plasmidifera
gen. and sp. nov. (Ochrophyta) push the frontiers of organellar biology
Authors: Barcytė Dovilė , Jaške Karin , Pánek Tomáš , Yurchenko Tatiana , Ševčíková Tereza , Eliášová Anežka , Eliáš Marek
Published: October 2024

Complete plastid loss seems to be very rare among secondarily non-photosynthetic eukaryotes.
Leukarachnion
sp. PRA-24, an amoeboid colourless protist related to the photosynthetic algal class Synchromophyceae (Ochrophyta), is a candidate for such a case based on a previous investigation by transmission electron microscopy. Here, we characterize this organism in further detail and describe it as
Leucomyxa plasmidifera
gen. et sp. nov., additionally demonstrating it is the first known representative of a broader clade of non-photosynthetic ochrophytes. We recovered its complete plastid genome, exhibiting a reduced gene set similar to plastomes of other non-photosynthetic ochrophytes, yet being even more extreme in sequence divergence. Identification of components of the plastid protein import machinery in the
L. plasmidifera
transcriptome assembly corroborated that the organism possesses a cryptic plastid organelle. According to our bioinformatic reconstruction, the plastid contains a unique combination of biosynthetic pathways producing haem, a folate precursor and tocotrienols. As another twist to its organellar biology,
L. plasmidifera
turned out to contain an unusual long insertion in its mitogenome related to a newly discovered mitochondrial plasmid exhibiting unprecedented features in terms of its size and coding capacity. Combined, our work uncovered further striking outcomes of the evolutionary course of semiautonomous organelles in protists.
Social bonding through shared experiences: the role of emotional intensity
Authors: Chung Victor , Mennella Rocco , Pacherie Elisabeth , Grezes Julie
Published: October 2024

Sharing emotions with other individuals is a widespread phenomenon. Previous research proposed that experiencing intense and similar emotions with other individuals reinforces social bonds. However, several aspects of this phenomenon remain unclear, notably whether social bonding requires the convergence and synchronization of emotions in the group, and whether these effects generalize across positively valenced and negatively valenced emotional contexts. To address these questions, we measured subjective emotional experiences, physiological activity (cardiac, respiratory, electrodermal) and social attitudes in dyads of unacquainted individuals who watched videos in the presence of each other. We manipulated the emotional content of the videos and the type of shared attention between participants, to test for the contribution of interpersonal influence. The results revealed that intense emotions indexed by physiological arousal were associated with the emergence of reciprocal prosocial attitudes within dyads, and that this effect depended on joint attention. We did not observe the convergence and synchronization of emotions within dyads, which suggests that experiencing similar emotions was not necessary for social bonding. We discuss implications of this study for research on collective effervescence and the social consequences of shared experiences.
A distributed integral control mechanism for regulation of cholesterol concentration in the human retina
Authors: Scheepers Ronél , Levi Noa L. , Araujo Robyn P.
Published: October 2024

Tight homeostatic control of cholesterol concentration within the complex tissue microenvironment of the retina is the hallmark of a healthy eye. By contrast, dysregulation of biochemical mechanisms governing retinal cholesterol homeostasis likely contributes to the aetiology and progression of age-related macular degeneration (AMD). While the signalling mechanisms maintaining cellular cholesterol homeostasis are well-studied, a systems-level description of molecular interactions regulating cholesterol balance within the human retina remains elusive. Here, we provide a comprehensive overview of all currently-known molecular-level interactions involved in cholesterol regulation across the major compartments of the human retina, encompassing the retinal pigment epithelium (RPE), photoreceptor cell layer, Müller cell layer and Bruch’s membrane. We develop a comprehensive chemical reaction network (CRN) of these interactions, involving 71 molecular species, partitioned into 10 independent subnetworks. These subnetworks collectively ensure robust homeostasis of 14 forms of cholesterol across distinct retinal cellular compartments. We provide mathematical evidence that three independent antithetic integral feedback controllers tightly regulate ER cholesterol in retinal cells, with additional independent mechanisms extending this regulation to other forms of cholesterol throughout the retina. Our novel mathematical model of retinal cholesterol regulation provides a framework for understanding the mechanisms of cholesterol dysregulation in diseased eyes and for exploring potential therapeutic strategies.
Documenting research in simulation science to enhance understanding for reusability
Authors: Hermann Sibylle , Fehr Jörg
Published: October 2024

One goal of Open Science is to promote reusability, which requires understanding and documentation. Reusability spans a spectrum from the straightforward reuse of existing materials to the extraction and adaptation of specific elements, depending on the maturity of the reused research and the research context. Beyond knowledge, understanding is crucial for enabling reusability. Simply reading an article is often insufficient; thus, publishing the underlying data and software is recommended. While the FAIR principles (Findable, Accessible, Interoperable, Reusable) facilitate the discovery and legal reuse of data and software through metadata, they fall short of promoting comprehensive understanding. By applying insights from the epistemology of simulation to computational mechanics research cases, we tested our hypothesis that the simulation process involves critical components beyond software and data that are essential to understand for reuse. Our findings indicate that reusability in these cases predominantly involves adjusting existing methodologies—a combination of different process steps from an epistemological perspective. Therefore, it is imperative to document not only learned knowledge but also the decisions regarding adjustments, assumptions and applications that concern the entire simulation process. Documentation is vital for understanding and herby enabling true reusability in scientific research, aligning with philosophical considerations of transparency and the nature of scientific knowledge.
Modelling COVID-19 mutant dynamics: understanding the interplay between viral evolution and disease transmission dynamics
Authors: Saldaña Fernando , Stollenwerk Nico , Aguiar Maíra
Published: October 2024

Understanding virus mutations is critical for shaping public health interventions. These mutations lead to complex multi-strain dynamics often under-represented in models. Aiming to understand the factors influencing variants’ fitness and evolution, we explore several scenarios of virus spreading to gain qualitative insight into the factors dictating which variants ultimately predominate at the population level. To this end, we propose a two-strain stochastic model that accounts for asymptomatic transmission, mutations and the possibility of disease import. We find that variants with milder symptoms are likely to spread faster than those with severe symptoms. This is because severe variants can prompt affected individuals to seek medical help earlier, potentially leading to quicker identification and isolation of cases. However, milder or asymptomatic cases may spread more widely, making it harder to control the spread. Therefore, increased transmissibility of milder variants can still result in higher hospitalizations and fatalities due to widespread infection. The proposed model highlights the interplay between viral evolution and transmission dynamics. Offering a nuanced view of factors influencing variant spread, the model provides a foundation for further investigation into mitigating strategies and public health interventions.
Milk metabolite composition of a semi-captive population of Asian elephants
Authors: Galante Laura , Franco dos Santos Diogo João , Mikkonen Elisabeth , Horak Jeannie , Stijepic Zorica , Demmelmair Hans , Vielhauer Andrea , Koletzko Berthold , Zaw Htet Thi , Htut Win , Lummaa Virpi , Lahdenperä Mirkka
Published: October 2024

Lack of maternal milk commonly leads to Asian elephant calves’ death in captivity. Currently, available supplements seem inefficient. Hence, we aimed at characterizing the composition of Asian elephant milk to provide information on calves’ nutritional needs. Seventy milk samples from 22 Asian elephants living in semi-captivity in their natural environment in Myanmar were collected. Samples were analysed through various techniques including liquid chromatography tandem mass spectrometry, gas chromatography-flame ionization detector, and bicinchoninic acid assay to determine total protein content and various metabolites. Associations with lactation stage (months postpartum) were investigated through repeated measure mixed models. We identified 160 compounds: 22 amino acids, 12 organic acids of the tricarboxylic acid cycle, 27 fatty acids, 15 acyl-carnitines and 84 phospholipids. The milk contained substantial amounts of free glutamate (median: 1727.9, interquartile range (IQR): 1278.4 µmol l
−1
) and free glycine (2541.7, IQR: 1704.1 µmol l
−1
). The fatty acid profile was mostly constituted by saturated fatty acids, particularly capric acid (40.1, IQR: 67.3 g l
−1
). Milk samples also contained high amounts of carnitines, phospholipids and organic acids. The wide array of metabolites identified and quantified, some of which present high concentrations in the milk from this species as opposed to other species, suggests underpinning physiological functions that might be crucial for the survival of Asian elephant calves.
Immune challenge affects risk sensitivity and locomotion in mosquitofish (
Gambusia holbrooki
)
Authors: Encel Stella A. , Ward Ashley J. W.
Published: October 2024

The immune system is crucial in responding to disease-causing pathogens. However, immune responses may also cause stereotypical changes in behaviour known as sickness behaviours, which often include reduced activity. Sickness behaviours are thought to have an important role in conserving energy required to support the immune response; however, little is known about how they manifest over time or in relation to risk, particularly in fishes. Here, we induced an immune response in mosquitofish (
Gambusia holbrooki
) by inoculating them with
Escherichia coli
lipopolysaccharide (LPS). We subsequently tested batches of fish at 24 h intervals and examined: locomotory behaviour, tendency to use a refuge and fast-start response immediately following a threat stimulus (measured as peak acceleration). Control and LPS-treated fish behaved similarly on days 1, 3 and 4. However, 2 days post-inoculation, LPS fish swam more slowly and spent more time in the refuge than control fish, although no difference in post-threat peak acceleration was found. Our findings suggest that sickness behaviours peak roughly 2 days following exposure to LPS and are relatively short-lived. Specifically, immune-challenged individuals exhibit reduced locomotion and exploratory behaviour, becoming more risk averse overall while still retaining the ability to respond acutely to a threat stimulus.
Using the basic reproduction ratio to quantify transmission and identify data gaps for epizootic haemorrhagic disease virus
Authors: Gubbins Simon
Published: October 2024

Epizootic haemorrhagic disease virus (EHDV) is an arbovirus transmitted by
Culicoides
biting midges that has recently emerged in Europe. Here, the basic reproduction ratio (
R
0
) was used to quantify the transmission of EHDV and its dependence on temperature for cattle and deer. Using data from the published literature the parameters needed to calculate
R
0
were estimated with Bayesian methods to incorporate uncertainty in the calculations. The Sobol method of sensitivity analysis was used to determine the parameters having the greatest influence on
R
0
and, hence, to identify important data gaps. Depending on the strain, the maximum
R
0
for EHDV varied from 0.7 to 2.5 in cattle and 1.3 to 4.3 in deer. The maximum
R
0
occurred at temperatures between 22 and 25°C, while the lowest temperature at which
R
0
exceeded one was between 16 and 20°C. The sensitivity analysis identified the threshold temperature for virus replication, the probability of transmission from host to vector and the vector- to- host ratio as the most important parameters influencing
R
0
. Furthermore, there are only limited data on EHDV in European deer species and on transmission in wildlife and at the livestock/wildlife interface. These data gaps should be the focus of future research.
Evolution of concentration distribution and removal of a solute in magnetohydrodynamics channel flow: effects of buoyancy-driven force and induced magnetic field
Authors: Saha Gourab , Poddar Nanda , Mondal Kajal Kumar , Wang Ping
Published: October 2024

The dispersion of reactive solutes in various flow geometries has significant implications for ecological and environmental applications. Researchers such as Poddar
et al
. (Poddar
et al
. 2021
Proc. R. Soc. A
477
, 20200830 (doi:
10.1098/rspa.2020.0830
) and Dhar
et al
. (Dhar
et al
. 2021
Phys. Fluids.
33
, 083609) have extensively studied solute transport in magnetohydrodynamics (MHD) channel flow, focusing on the applied magnetic field. However, the impact of the induced magnetic field on solute dispersion between two parallel plates remains poorly understood. This article presents an analytical investigation using Mei’s multi-scale homogenization approach to examine the effects of the Hartmann number, Grashof number and absorption parameter on the multi-dimensional concentration distribution and removal efficiency of a reactive solute in MHD laminar channel flow. The findings provide insights into concentration behaviour, such as the decrease in the Taylor transport coefficient with an increase in the induced magnetic field. These insights have practical implications for improving sewage and wastewater treatment by effectively separating desired particles from contaminants, contributing to advancements in environmental purification techniques.
Local gaps in three-dimensional periodic media
Authors: Godin Yuri A. , Vainberg Boris
Published: October 2024

The propagation of acoustic waves in a medium with a periodic array of small inclusions of arbitrary shape is considered. The inclusion size

a

is much smaller than the array period. We show that global gaps do not exist if

a

is small enough. We introduce and study the concept of local gaps, which depends on the choice of the wave vector

k

. We analytically determine the location of local gaps for the Dirichlet and transmission problems.
On the asymptotic analysis of pulsating planar Poiseuille flow instabilities
Authors: Andriano G. , Passaggia P. -Y. , Caillol C. , Higelin P. , Harambat F. , Houille S.
Published: October 2024

The linear stability analysis of a pulsating flow between parallel plates at finite amplitudes and different frequencies demonstrates the presence of instability with a different nature to that initially reported in earlier studies at

W
o
<
25

. The time-dependent stability problem is formulated using a Floquet expansion of the perturbation and solved in a matrix approach. At higher pulsation frequencies (i.e.

W
o
>
30

), pulsation amplitudes and sufficiently large Reynolds numbers, the time-dependent baseflow displays multiple inflexion points throughout the entire duration of the pulsation. A scaling analysis of the temporal growth rate reveals that the instability is of inviscid type and scales with

R

e

−
1

. Freezing the time-dependent baseflow for a particular set of parameters, the growth rate is simultaneously controlled by viscosity solely acting on the perturbation, and the pulsating frequency coupling the harmonics. In the asymptotic limit (

R
e
→
+
∞

), we demonstrate that the temporal problem simplifies to a set of steady stability analyses dependent on the phase of the pulsation. In particular, we show that in this limit, Rayleigh and Fjørtoft’s criteria for instability become valid again, that sub-harmonic periodic orbits can be used to estimate the inviscid growth rate and match with the asymptotic values predicted from the viscous stability analysis.
Snap-through eversion of axisymmetric shells under contact indentation
Authors: Huang Weicheng , Liu Zhaowei , Liu Mingchao , Hsia K. Jimmy
Published: October 2024

In this paper, we systematically investigate the stability of an axisymmetric shell and the snap-through eversion induced by indentation through a discrete numerical approach. To capture the intricate interplay between the geometric and boundary nonlinearities during contact actuation, we employ the discrete axisymmetric shell model accompanied by the incremental potential formulation for our analysis. Our results reveal that the indentation response of a spherical shell can be classified into three groups, i.e. monotonous, monostable and bistable behaviours, whose boundaries can be characterized by a simple scaling law. We further discover that, for bistable shells, the snap-through eversion happens at a critical state where the configurations are universal, which is independent of the indenter size and can be captured by a simple geometric model. One interesting prediction of our model is that, with increasing indenter size, the contact state between the shell and indenter changes from conformal contact to partial separation, which is validated by a finite element method simulation. Our findings may provide explanations for some biophysical phenomena (e.g. cell fusion) and can also guide optimal designs of intelligent structures (e.g. soft actuators and soft robots).
Bending-neutral deformations of minimal surfaces
Authors: Sonnet André M. , Virga Epifanio G.
Published: October 2024

Minimal surfaces are ubiquitous in nature. Here, they are considered as geometric objects that bear a deformation content. By refining the resolution of the surface deformation gradient afforded by the polar decomposition theorem, we identify a
bending
content and a class of deformations that leave it unchanged. These are the
bending-neutral
deformations, fully characterized by an integrability condition; they preserve normals. We prove that: (i) every minimal surface is transformed into a minimal surface by a bending-neutral deformation; (ii) given two minimal surfaces with the same system of normals, there is a bending-neutral deformation that maps one into the other; and (iii)
all
minimal surfaces have indeed a
universal
bending content.
Dynamic multi-dose vaccination with initial immunity on higher-order networks
Authors: Qian Yinuo , Zhao Dawei , Xia Chengyi , Özer Mahmut , Perc Matjaž
Published: October 2024

Vaccination remains crucial during pandemics for combating disease spread. We here propose a two-layer model for multi-dose vaccination policy, considering vaccine hesitancy, initial immunity, as well as media-driven information dissemination concerning vaccine strategy selection. Moreover, we consider collective opinions through social networks with higher-order interactions. We perform numerical simulations to analyse variations in vaccination strategies. We further compare obtained outcomes with the exploration of real data on vaccination behaviours. Our research indicates that information dissemination can regulate vaccination, and that models accounting for individual immunity align more closely with real-world scenarios. Furthermore, we find that considering vaccination decisions from neighbouring agents is crucial under multi-dose policies for the facilitation of faster vaccination diffusion.
Models of animal coalitions and their implications for human evolution
Authors: Ihara Yasuo
Published: October 2024

Social interaction is a prime driver for the evolution of animal behaviour. Dyadic interaction, in particular, has been the focus of intensive research on the evolution of mutualistic, altruistic, selfish or spiteful behaviours. Meanwhile, triadic interaction has been the minimal framework for the study of animal coalition as observed in some species of primates, as well as in carnivores and cetaceans, where two or more individuals act jointly against a third party in a competitive context. Previous mathematical models of animal coalition have either failed to explain the observed diversity in the configuration of coalition or presumed fine-tuned decision-making that may be unrealistic for non-human animals. To approach these issues, the present study develops a new model that is fairly simple, but still able to account for the observed diversity in animal coalitions. Analysis of the model specifies key parameters affecting the predicted types of coalition: the nature of the benefit being contested, the cost-to-benefit ratio associated with fighting and the synergistic effect in coalition formation. Additionally, the model is used to evaluate the social selection hypothesis, which claims that coalition formation induced social selection favouring reduced aggression and lower fighting abilities during human evolution.
Female reproductive tract microbiota varies with MHC profile
Authors: Leclaire Sarah , Bandekar Mandar , Rowe Melissah , Ritari Jarmo , Jokiniemi Annalaura , Partanen Jukka , Allinen Pia , Kuusipalo Liisa , Kekäläinen Jukka
Published: October 2024

Numerous studies have shown that a healthy reproductive tract microbiota is crucial for successful reproduction and that its composition is influenced by various environmental and host factors. However, it is not known whether the reproductive microbiota is also shaped by the major histocompatibility complex (MHC), a family of genes essential to differentiate ‘self’ from ‘non-self’ peptides to initiate an adaptive immune response. We tested the association between the follicular fluid microbiome and MHC genes in 27 women. Women with higher MHC diversity had a higher microbiome diversity, characterized by bacteria commonly associated with vaginal dysbiosis. Women with similar MHC genes were also similar in their microbiome composition, indicating that MHC composition may be a key factor in determining the bacterial assemblage in the reproductive tract. Finally, the composition of the follicular fluid microbiome was similar to the vaginal microbiome, suggesting that numerous bacteria of the vagina are true inhabitants of the follicular fluid or that vaginal microbiota contaminated the follicular fluid microbiota during transvaginal collection. Collectively, our results demonstrate the importance of host genetic factors in shaping women's reproductive microbiota and they open the door for further research on the role of microbiota in mediating MHC-related variation in reproductive success.
The evolution of gestation length in eutherian mammals
Authors: Danis Thodoris , Rokas Antonis
Published: October 2024

Eutherian mammals exhibit considerable variation in their gestation lengths, which has traditionally been linked to variation in other traits, including body mass and lifespan. To understand how gestation length variation, including its association with body mass and lifespan variation, changed over mammalian evolution, we conducted phylogeny-informed analyses of 845 representative extant species. We found that gestation length substantially differed in both whether and how strongly it was associated with body mass and lifespan across mammals. For example, gestation length was not associated with lifespan or body mass in Chiroptera and Cetacea but was strongly associated only with body mass in Carnivora. We also identified 52 evolutionary shifts in gestation length variation across the mammal phylogeny and 14 shifts when we jointly considered variation of all three traits; six shifts were shared. Notably, two of these shifts, both positive, occurred at the roots of Cetacea and Pinnipedia, respectively, coinciding with the transition of these clades to the marine environment, whereas a negative shift occurred at the root of Chiroptera, coinciding with the evolution of flight in this clade. These results suggest that the relationship between gestation length and the two other traits has varied substantially across mammalian phylogeny.
Tree growth rate-mediated trade-off between drought resistance and recovery in the Northern Hemisphere
Authors: Tao Wenjing , He Jiang , Smith Nicholas G. , Yang Hongjun , Liu Jinchun , Chen Lei , Tao Jianping , Luo Weixue
Published: October 2024

The frequency and severity of drought events have increased with climate warming. This poses a significant threat to tree growth and survival worldwide. However, the underlying mechanism of tree growth responses to drought across diverse geographic regions and species remains inconclusive. Here, we used 2808 tree ring width chronologies of 32 species from 1951 to 2020 to examine the relationships between growth rates and resistance and recovery of trees in response to drought in the Northern Hemisphere. We found that trees with fast growth rates exhibited lower drought resistance but higher drought recovery compared to those with slow growth rates, which was further corroborated by the trade-off between resistance and recovery in response to variations in leaf photosynthetic traits. The difference in growth rates also well explained the large variability in the drought resistance and recovery for different geographic regions, as well as for species from different clades and successional stages. Our study provides a conclusive and uniform perspective that tree growth rate regulates drought resistance and recovery, shedding light on the diverse strategies employed by tree species in response to drought stress in the Northern Hemisphere.
Mating receptivity mediated by endosymbiont interactions in a haplodiploid thrips species
Authors: Tourani Amir H. , Katlav Alihan , Cook James M. , Riegler Markus
Published: October 2024

Many arthropods carry maternally inherited endosymbionts that cause cytoplasmic incompatibility (CI), manifested as embryonic mortality in matings of infected males with uninfected females. Infected females, however, do not suffer this cost. Therefore, in populations with mixed endosymbiont infections, selection is expected to favour mechanisms that enable hosts to avoid or mitigate CI. This may include changes in mating behaviour, such as reduced female receptivity to mating and/or remating when approached by incompatible males. Here, we investigated mating behavioural traits in haplodiploid thrips naturally associated with two CI-inducing endosymbionts,
Cardinium
and
Wolbachia
. Compared with females with both endosymbionts, those with only
Cardinium
showed reduced receptivity to males carrying both. However, surprisingly, females without endosymbionts were not less receptive to incompatible males. Furthermore, in contrast to females without endosymbionts, females with
Cardinium
were far less likely to remate with incompatible than compatible males irrespective of the compatibility type of the first mating. Our results suggest that endosymbiont-specific sexual selection processes occur, whereby females carrying only
Cardinium
recognize
Wolbachia
in coinfected males to avoid CI. This may hinder a CI-driven
Wolbachia
spread. Endosymbiont-mediated mating behaviours may be crucial for the dynamics of CI-inducing endosymbionts and their application in pest management strategies.
Experimental elevated temperature affects bumblebee foraging and flight speed
Authors: Gérard Maxence , Gardelin Erika , Lehmann Philipp , Roberts Kevin T. , Sepúlveda-Rodríguez Guadalupe , Sisquella Clara , Baird Emily
Published: October 2024

Global warming threatens wild bees and their interaction with plants. While earlier studies have highlighted the negative effects of elevated temperatures on bee–plant interactions, we still lack knowledge about how they impact the foraging behaviours that are central to bee pollination activities. To address this knowledge gap, we investigated how ambient temperature affected the foraging behaviours of the bumblebee
Bombus terrestris
. We allowed the bumblebees to forage freely on artificial flowers in two climate-controlled rooms set at 24°C and 32°C. The colonies were alternated between the two temperatures every week. We recorded the flower visitation rate, flight speed, total foraging time and number of foraging trips. In addition, we measured flight metabolic rate across a range of temperatures to assess its potential as an underlying mechanism. In comparison to 24°C, at 32°C, flower visitation time decreased while flower visitation rate and flight speed increased. This is consistent with the reduction in flight metabolic rate recorded between these temperatures. At 32°C, the number of trips made by each worker decreased, suggesting that, despite the reduced energetic cost, flight in elevated temperatures may be stressful. Our results suggest that elevated temperatures affect bumblebee foraging behaviour and that this would likely disrupt plant–insect interactions.
Constructing stability: optimal learning in noisy ecological niches
Authors: Lee Edward D. , Flack Jessica C. , Krakauer David C.
Published: October 2024

Organisms can learn in response to environmental inputs as well as actively modify their environments through niche construction on slower evolutionary time scales. How quickly should an organism respond to a changing environment, and when possible, should organisms adjust the time scale of environmental change? We formulate these questions using a model of learning costs that considers optimal time scales of both memory and environment. We derive a general, sublinear scaling law for optimal memory as a function of environmental persistence. This encapsulates a trade-off between remembering and forgetting. We place learning strategies within a niche construction dynamics in a game theoretic setting. Niche construction is found to reduce or stabilize environmental volatility when learned environmental resources can be monopolized. When learned resources are shared, niche destructors evolve to degrade the shared environment. We integrate these results into a metabolic scaling framework in order to derive learning strategies as a function of body size.
Exploring genetic signatures of zoonotic influenza A virus at the swine-human interface with phylogenetic and ancestral sequence reconstruction
Authors: Anker K.M. , Ciucani M.M. , Nissen J.N. , Anderson T.K. , Pedersen A.G. , Trebbien R.
Published: October 2024

Influenza A viruses (IAVs) in swine have zoonotic potential and pose a continuous threat of causing human pandemics, as demonstrated by the H1N1 pandemic in 2009. Despite increased genomic surveillance, we have limited knowledge of the IAV evolutionary dynamics leading to such zoonotic events and no clear understanding of genetic markers associated with interspecies transmission of IAV between humans and swine. To explore this, we analyzed a comprehensive publicly available whole genome dataset of human and swine IAV sequences. We conducted phylogenetic analyses and inference of ancestral host and sequence states for each IAV segment and mapped inferred mutations that were associated with transmission within and between swine and human hosts. We developed a custom python library to combine information from host and ancestral sequence annotated trees and applied statistical models to identify genetic markers associated with intra- or interspecies transmissions between swine and humans. This included analyzing mutation rates and the selective pressures acting on the viral proteins following intra- and interspecies transmissions and using a scalable, gradient-boosted decision tree machine learning approach to predict key amino acid positions critical for different transmission types. Our analyses indicated complex mutational patterns within and across viral proteins, but also suggested that specific protein regions and amino acid positions of especially several of the internal gene segments were more important for interspecies transmission. Our findings identify potential genetic signatures across the IAV proteins associated with host adaptation and zoonotic potential, offering valuable markers for early-warning genomic surveillance systems to enhance animal health and minimize the potential for zoonotic transmission of IAV.
Shared Genetic and Regulatory Mechanisms in Acute Myeloid Leukaemia and Blast Crisis Chronic Myeloid Leukaemia
Authors: Basu Sulagna , Pandey Rakesh
Published: October 2024

Acute Myeloid Leukemia (AML) and Blast Crisis Chronic Myeloid Leukemia (BC CML) share several clinical characteristics, including the accumulation of immature myeloid cells and disrupted hematopoiesis. Despite the similarities, the two diseases exhibit different genetic profiles, contributing to distinct disease progressions and therapeutic outcomes. In this study, we perform a comparative analysis using bioinformatics and systems biology approaches to explore shared and unique mutational signatures, transcriptional networks, and molecular regulators in AML and BC CML. Our analysis identifies 29 genes common to both diseases, which are involved in key biological processes such as cell proliferation, cell death regulation, and transcriptional control. A subsequent pathway enrichment highlights common pathways, including the PI3K-AKT signaling and cytokine-mediated signaling, that may contribute to disease progression and resistance to therapy. Additionally, we construct a protein-protein interaction network and a transcription factor-miRNA coregulatory network, revealing key hub genes such as TP53, RUNX1, and BCL2. These genes could be potential shared therapeutic targets for treating AML and BC CML. Therefore, our analysis offers insights into the molecular underpinnings of these aggressive hematological malignancies.
Label-Free Optical Biopsy Reveals Biomolecular and Morphological Features of Diabetic Kidney Tissue in 2D and 3D
Authors: Fung Anthony A. , Li Zhi , Boote Craig , Markov Petar , Jain Sanjay , Shi Lingyan
Published: October 2024

Kidney disease, the ninth leading cause of death in the United States, has one of the poorest diagnostic efficiencies of only 10%1. Conventional diagnostic methods often rely on light microscopy analysis of 2D fixed tissue sections with limited molecular insight compared to omics studies. Targeting multiple features in a biopsy using molecular or chemical reagents can enhance molecular phenotyping but are limited by overlap of their spatial and chromatic properties, variations in quality of the products, limited multimodal nature and need additional tissue processing. To overcome these limitations and increase the breadth of molecular information available from tissue without an impact on routine diagnostic workup, we implemented label-free imaging modalities including stimulated Raman scattering (SRS) microscopy, second harmonic generation (SHG), and two photon fluorescence (TPF) into a single microscopy setup. We visualized and identified morphological, structural, lipidomic, and metabolic biomarkers of control and diabetic human kidney biopsy samples in 2D and 3D at a subcellular resolution. The label-free biomarkers, including collagen fiber morphology, mesangial-glomerular fractional volume, lipid saturation, redox status, and relative lipid and protein concentrations in the form of Stimulated Raman Histology (SRH), illustrate distinct features in kidney disease tissues not previously appreciated. The same tissue section can be used for routine diagnostic work up thus enhancing the power of cliniopathological insights obtainable without compromising already limited tissue. The additional multimodal biomarkers and metrics are broadly applicable and deepen our understanding of the progression of kidney diseases by integrating lipidomic, fibrotic, and metabolic data.

Abstract Figure

Graphical Abstract

Label-free indicators of diabetic nephropathies.
Ultra-fast physics-based modeling of the elephant trunk
Authors: Kaczmarski Bartosz , Moulton Derek E. , Goriely Zéphyr , Goriely Alain , Kuhl Ellen
Published: October 2024

With more than 90,000 muscle fascicles, the elephant trunk is a complex biological structure and the largest known muscular hydrostat. It achieves an unprecedented control through intricately orchestrated contractions of a wide variety of muscle architectures. Fascinated by the elephant trunk’s unique performance, scientists of all disciplines are studying its anatomy, function, and mechanics, and use it as an inspiration for biomimetic soft robots. Yet, to date, there is no precise mapping between microstructural muscular activity and macrostructural trunk motion, and our understanding of the elephant trunk remains incomplete. Specifically, no model of the elephant trunk employs formal physics-based arguments that account for its complex muscular architecture, while preserving low computational cost, to enable fast screening of its configuration space. Here we create a reduced-order model of the elephant trunk that can–within a fraction of a second– predict the trunk’s motion as a result of its muscular activity. To ensure reliable results in the finite deformation regime, we integrate first principles of continuum mechanics and the theory of morphoelasticity for fibrillar activation. We employ dimensional reduction to represent the trunk as an active slender structure, which results in closed-form expressions for its curvatures and extension as functions of muscle activation and anatomy. We create a high-resolution digital representation of the trunk from magnetic resonance images to quantify the effects of different muscle groups. We propose a general solution method for the inverse motion problem and apply it to extract the muscular activations of three representative trunk motions: picking a fruit; lifting a log; and lifting a log asymmetrically. For each task, we identify key features in the muscle activation profiles. Our results suggest that, upon reaching maximum contraction in select muscle groups, the elephant trunk autonomously reorganizes muscle activation to perform specific tasks. Our study provides a complete quantitative characterization of the fundamental science behind elephant trunk biomechanics, with potential applications in the material science of flexible structures, the design of soft robots, and the creation of flexible prosthesis and assist devices.
Menstrual Cycle Phase-Based Interval Training Yields Distinct Muscle Changes in Female Athletes
Authors: Kissow Julie , Jacobsen Kamine J. , Jessen Søren , Thomsen Laura B. , Quesada Júlia P. , Bangsbo Jens , Deshmukh Atul S. , Hostrup Morten
Published: October 2024

Advances in mass-spectrometry(MS)-based technologies have leveraged our understanding of skeletal muscle responsiveness to exercise in humans. However, there is a lack of such data in females, particularly pertaining to female athletes and menstrual cycle phase-based sprint interval training(SIT) despite its efficacy and popularity. Here, we present a comprehensive proteomic analysis of skeletal muscle adaptations to high-frequency SIT during different menstrual cycle phases in female athletes. We randomized 49 eumenorrheic females to either high-frequency SIT in the follicular(FB) or luteal phase(LB) over one menstrual cycle comprising eight sessions of 6×30-s all-out efforts. Twenty-five completed the intervention with verified cycles. MS-based proteomics revealed notable differences in muscle adaptations to phase-based SIT. LB suppressed mitochondrial pathways of the tricarboxylic acid cycle and electron transport chain while enriching ribosomal complexes. Conversely, FB enriched filament organization and skeletal system development. Mitochondrial repression during LB was linked to reduced V̇O2max, whereas exercise capacity improved in FB only. Our findings show that synching high-frequency SIT with menstrual cycle phases induces distinct muscle adaptations and affects phenotype in eumenorrheic female athletes.
External Validation of Predictive Models for Diagnosis, Management and Severity of Pediatric Appendicitis
Authors: Marcinkevičs Ričards , Sokol Kacper , Paulraj Akhil , Hilbert Melinda A. , Rimili Vivien , Wellmann Sven , Knorr Christian , Reingruber Bertram , Vogt Julia E. , Wolfertstetter Patricia Reis
Published: October 2024

Background

Appendicitis is a common condition among children and adolescents. Machine learning models can offer much-needed tools for improved diagnosis, severity assessment and management guidance for pediatric appendicitis. However, to be adopted in practice, such systems must be reliable, safe and robust across various medical contexts, e.g., hospitals with distinct clinical practices and patient populations.

Methods

We performed external validation of models predicting the diagnosis, management and severity of pediatric appendicitis. Trained on a cohort of 430 patients admitted to the Children’s Hospital St. Hedwig (Regensburg, Germany), the models were validated on an independent cohort of 301 patients from the Florence-Nightingale-Hospital (Düsseldorf, Germany). The data included demographic, clinical, scoring, laboratory and ultrasound parameters. In addition, we explored the benefits of model retraining and inspected variable importance.

Results

The distributions of most parameters differed between the datasets. Consequently, we saw a decrease in predictive performance for diagnosis, management and severity across most metrics. After retraining with a portion of external data, we observed gains in performance, which, nonetheless, remained lower than in the original study. Notably, the most important variables were consistent across the datasets.

Conclusions

While the performance of transferred models was satisfactory, it remained lower than on the original data. This study demonstrates challenges in transferring models between hospitals, especially when clinical practice and demographics differ or in the presence of externalities such as pandemics. We also highlight the limitations of retraining as a potential remedy since it could not restore predictive performance to the initial level.
Leukocytes use endothelial membrane tunnels to extravasate the vasculature
Authors: van der Meer Werner J. , van Steen Abraham C.I. , Mahlandt Eike , Rolas Loïc , Wang Haitao , Arts Janine J.G. , Kempers Lanette , Grönloh Max L.B. , Schoon Rianne M. , Driessen Amber , van Rijssel Jos , Klaassen Ingeborg , Schlingemann Reinier O. , Manavski Yosif , Hoogenboezem Mark , Boon Reinier A. , Khuon Satya , Wait Eric , Heddleston John , Chew Teng-Leong , Nolte Martijn A. , Nourshargh Sussan , Goedhart Joachim , van Buul Jaap D.
Published: October 2024

Upon inflammation, leukocytes extravasate through endothelial cells. When they extravasate in a paracellular manner, it is generally accepted that neighbouring endothelial cells physically disconnect to open cell-cell junctions, allowing leukocytes to cross. When carefully examining endothelial junctions, we found a partial membrane overlap of endothelial cells beyond VE-cadherin distribution. These overlaps are regulated by actin polymerization and, although marked by, do not require PECAM-1, nor VE-cadherin. Neutrophils prefer wider membrane overlaps as exit sites. Detailed 3D analysis of endothelial membrane dynamics during paracellular neutrophil transmigration in real-time, at high spatiotemporal resolution using resonant confocal and lattice light-sheet imaging, revealed that overlapping endothelial membranes form a tunnel during neutrophil transmigration. These tunnels are formed by the neutrophil lifting the membrane of the upper endothelial cell while indenting and crawling over the membrane of the underlying endothelial cell. Our work shows that endothelial cells do not simply retract upon passage of neutrophils but provide membrane tunnels, allowing neutrophils to extravasate. This discovery defines the 3D multicellular architecture in which the paracellular transmigration of neutrophils occurs.