bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human outperform mouse Purkinje cells in dendritic complexity and computational capacity
Authors: Masoli Stefano , Sanchez-Ponce Diana , Vrieler Nora , Abu-Haya Karin , Lerner Vitaly , Shahar Tal , Nedelescu Hermina , Rizza Martina Francesca , Benavides-Piccione Ruth , DeFelipe Javier , Yarom Yosef , Munoz Alberto , D’Angelo Egidio 
Published: March 2023

ABSTRACTPurkinje cells (PC) of the cerebellum are amongst the largest neurons of the brain and have been extensively investigated in rodents. However, their morphological and physiological properties in humans are still poorly understood. Here, we have taken advantage of high-resolution morphological reconstructions and of unique electrophysiological recordings of human PCsex vivoto generate computational models and estimate computational capacity. An inter-species comparison showed that human PCs had similar fractal structure but were bigger than mouse PCs. Consequently, given a similar spine density (2/μm), human PCs hosted about 5 times more dendritic spines. Moreover, human had higher dendritic complexity than mouse PCs and usually emitted 2-3 main dendritic trunks instead than 1. Intrinsic electroresponsiveness was similar in the two species but model simulations revealed that the dendrites generated ~6.5 times (n=51 vs. n=8) more combinations of independent input patterns in human than mouse PCs leading to an exponential 2nincrease in Shannon information. Thus, while during evolution human PCs maintained similar patterns of spike discharge as in rodents, they developed more complex dendrites enhancing computational capacity up to the limit of 10 billion times.
Behavioral, neural and ultrastructural alterations in a graded-dose 6-OHDA mouse model of early-stage Parkinson’s disease
Authors: Slézia Andrea , Hegedüs Panna , Rusina Evgeniia , Lengyel Katalin , Solari Nicola , Kaszas Attila , Balázsfi Diána , Botzanowski Boris , Acerbo Emma , Missey Florian , Williamson Adam , Hangya Balázs 
Published: March 2023

AbstractStudying animal models furthers our understanding of Parkinson’s disease (PD) pathophysiology by providing tools to investigate detailed molecular, cellular and circuit functions. Different versions of the neurotoxin-based 6-hydroxydopamine (6-OHDA) model of PD have been widely used in rats. However, these models typically assess the result of extensive and definitive dopaminergic lesions that reflect a late stage of PD, leading to a paucity of studies and a consequential gap of knowledge regarding initial stages, in which early interventions would be possible. Additionally, the better availability of genetic tools increasingly shifts the focus of research from rats to mice, but few mouse PD models are available yet. To address these, we characterize here the behavioral, neuronal and ultrastructural features of a graded-dose unilateral, single-injection, striatal 6-OHDA model in mice, focusing on early-stage changes within the first two weeks of lesion induction. We observed early onset, dose-dependent impairments of overall locomotion without substantial deterioration of motor coordination. In accordance, histological evaluation demonstrated a partial, dose-dependent loss of dopaminergic neurons of substantia nigra pars compacta (SNc). Furthermore, electron microscopic analysis revealed degenerative ultrastructural changes in SNc dopaminergic neurons. Our results show that mild ultrastructural and cellular degradation of dopaminergic neurons of the SNc can lead to certain motor deficits shortly after unilateral striatal lesions, suggesting that a unilateral dose-dependent intrastriatal 6-OHDA lesion protocol can serve as a successful model of the early stages of Parkinson’s disease in mice.Highlights-Unilateral striatal 6-OHDA injection caused an early onset dose-dependent behavioral deficit in mice-Behavioral deficit manifested as mild impairment of locomotion and locomotive movement initialization-Behavioral changes were accompanied by moderate, dose-dependent loss of SNc dopaminergic neurons-Behavioral changes were paralleled by ultrastructural alterations of SNc dopaminergic neurons
A new diatom-based multimetric index to assess lake ecological status
Authors: Tison-Rosebery J. , Boutry S. , Bertrin V. , Leboucher T. , Morin S. 
Published: March 2023

AbstractEutrophication impairs lake ecosystems at a global scale. In this context, as benthic microalgae are well-established warnings for a large range of stressors, particularly nutrient enrichment, the Water Framework Directive required the development of diatom-based methods to monitor lake eutrophication.Here, we present the diatom-based index we developed for French lakes, named IBDL. Data were collected in 93 lakes from 2015 to 2020. A challenge arose from the discontinuous pressure gradient of our dataset, especially the low number of nutrient-impacted lakes. To analyze the data we opted for the so-called “Threshold Indicator Taxa ANalysis” method, which makes it possible to determine a list of “alert taxa”. We obtained a multimetric index based on different pressure gradients (Kjeldahl nitrogen, suspended matter, biological oxygen demand and total phosphorous).The IBDL proved to be particularly relevant as it has a twofold interest: an excellent relationship with total phosphorus and possible application to any lake metatype. Its complementarity with macrophyte-based indices moreover justifies the use of at least two primary producer components for lake ecological status classification.
Leaf metabolic traits reveal hidden dimensions of plant form and function
Authors: Walker Tom W. N. , Schrodt Franziska , Allard Pierre-Marie , Defossez Emmanuel , Jassey Vincent E. J. , Schuman Meredith C. , Alexander Jake M. , Baines Oliver , Baldy Virginie , Bardgett Richard D. , Capdevila Pol , Coley Phyllis D. , van Dam Nicole M. , David Bruno , Descombes Patrice , Endara Maria-Jose , Fernandez Catherine , Forrister Dale , Gargallo-Garriga Albert , Gauser Gaёtan , Marr Sue , Neumann Steffen , Pellissier Loïc , Peters Kristian , Rasmann Sergio , Roessner Ute , Salguero-Gómez Roberto , Sardans Jordi , Weckwerth Wolfram , Wolfender Jean-Luc , Peñuelas Josep 
Published: March 2023

SummaryThe plant metabolome encompasses the biochemical mechanisms through which evolutionary and ecological processes shape plant form and function1,2. However, while the metabolome should thus be an important component of plant life-history variation3, we know little about how it varies across the plant kingdom. Here, we use the plant functional trait concept4– a powerful framework for describing plant form and function5–7– to interpret leaf metabolome variation among 457 tropical and 339 temperate plant species. Distilling metabolite chemistry into five discriminant metabolic functional traits reveals that plants vary along two major axes of leaf metabolic specialization – a leaf chemical defense spectrum and an expression of leaf longevity. These axes are qualitatively consistent for tropical and temperate species, with many trait combinations being viable. However, axes of leaf metabolic specialization vary orthogonally to life-history strategies described by widely used functional traits5–7, while being at least equally important to them. Our findings question classical trait6and plant defense8theory that predicts relationships between the leaf chemical phenotype, plant productivity, and pace of life. Moreover, we show that metabolic functional traits describe unique dimensions of plant life-history variation that are complementary to, and independent from, those captured by existing plant functional traits.
Diet quality alters the consequences of gradual phenotypic plasticity for individual performance
Authors: Van Baelen Marine , Bec Alexandre , Sperfeld Erik , Frizot Nathan , Koussoroplis Apostolos-Manuel 
Published: March 2023

AbstractOrganisms exhibit reversible physiological adjustments as a response to rapidly changing environments. Yet, such plasticity of the phenotype is gradual and may lag behind the environmental fluctuations, thereby affecting the long-term average performance of the organisms. By supplying energy and essential compounds for optimal tissue building, food determines the range of possible phenotypic changes and potentially the rate at which they occur. Here, we assess how differences in the dietary supply of essential lipids modulate the phenotypic plasticity of an ectotherm facing thermal fluctuations. We use three phytoplankton strains to create a gradient of polyunsaturated fatty acids and sterols supply forDaphnia magnaunder constant and fluctuating temperatures. We used three different fluctuation periodicities to unravel the temporal dynamics of gradual plasticity and its long-term consequences onD. magnaperformance measured as juvenile somatic growth rate. In agreement with gradual plasticity theory, we show that inD.magna, fluctuation periodicity determines the differential between observed growth rates and those expected from constant conditions. Most importantly, we show that diet modulates both the size and the direction of the growth rate differential. Overall, we demonstrate that the nutritional context is essential for predicting ectotherm consumers’ performance in fluctuating thermal environments.
Branching responses to pruning in cocoa
Authors: Tosto Ambra , Evers Jochem B. , Anten Niels P. R. , Zuidema Pieter A. 
Published: March 2023

AbstractThe branching pattern of a tree determines the efficiency of light interception and carbon assimilation. Pruning can modify the branching pattern, as a result of changes in physiological and environmental conditions, and ultimately pruning can have major effects on yield. For one of the major tropical tree crops, cocoa (Theobroma cacao), very little is known about branching response to pruning. To address this knowledge gap we performed a pruning experiment on young cocoa trees in Côte d’Ivoire.We applied five treatments: two heading treatments (the removal of the terminal apex or 66% of a branch) and two thinning treatments (the removal of 1 or 2 primary branches) and one unpruned control. The branching pattern of the primary branches was described by the number, position, and length of lateral branches right after pruning, and the same observations were repeated after a cycle of leaf production. The probability of branching and the length of lateral branches along a primary branch, in pruned and unpruned conditions, was analyzed using generalized mixed effect models.In unpruned conditions, the probability of branch presence was higher towards the middle of the primary branches and lower at the extremes. Branch length decreased going from the base to the tip of a primary branch. After one cycle of leaf production, new branches emerged preferentially on the distal section of a branch, but probability of branch emergence was reduced by the presence of other lateral branches. Pruning increased the probability of branch emergence mostly towards the tip of a branch, with heavy heading having the strongest effect. By contrast, heavy thinning increased branch emergence also toward the base of the branch.Our results can be applied to improve formation pruning, as this may trigger branching in different part of the crown, depending on the form of pruning. Our study also assists the development of three-dimensional tree models that could further our understanding of the impact of pruning on cocoa growth and productivity.
Visual environment of rearing sites affects larval response to perceived risk
Authors: Fouilloux Chloe A. , Stynoski Jennifer L. , Yovanovich Carola A. M. , Rojas Bibiana 
Published: March 2023

AbstractTurbidity challenges the visual performance of aquatic animals. During development, environments with limited visibility may affect the fine-tuning of visual systems and thus the perception of, and response to, risk. While turbidity has frequently been used to characterise permanent aquatic habitats, it has been an overlooked feature of ephemeral ones.Here, we use the natural diversity of ephemeral rearing sites (phytotelmata) in which the tadpoles of two poison frog species are deposited and confined until metamorphosis to explore the relationship between environments with limited visibility and response to perceived risk.We sampled wild tadpoles ofDendrobates tinctorius, a rearing-site generalist with facultatively cannibalistic tadpoles, andOophaga(formerlyDendrobates)pumilio, a small-phytotelm specialist dependent on maternal food-provisioning, to investigate how the visual environment in rearing sites influences tadpole behaviour. We hypothesised that turbid rearing conditions negatively impact both species’ ability to perceive risk, decreasing response strength to predatory visual stimuli. Using experimental arenas, we measured tadpole activity and space first on a black and white background, and then on either black or white backgrounds where tadpoles were exposed to visual stimuli of (potentially cannibalistic) conspecifics or potential predators.When placed in a novel arena, the effects of rearing environment onD. tinctoriustadpoles were clear: tadpoles from darker pools were less active than tadpoles from brighter pools, and did not respond to either visual stimuli, whereas tadpoles from brighter pools swam more when paired with conspecifics versus odonate larvae, suggesting that tadpoles can visually discriminate between predators. ForO. pumilio, tadpoles were more active on experimental backgrounds that more closely matched the luminosity of their rearing sites, but their responses to the two visual stimuli did not differ.Larval specialisation associated with species-specific microhabitat use may underlie the observed responses to visual stimuli, which has implications for the stability of species interactions and trophic dynamics in pool communities. Together, our findings demonstrate that light availability of wild larval rearing conditions influences the perception of risk in novel contexts, and provide insight into how visually guided animals may respond to sudden environmental disturbances.
LeishMANIAdb: a comparative resource forLeishmaniaproteins
Authors: Tusnády Gábor E. , Zeke András , Kálmán Zsófia E. , Fatoux Marie , Ricard-Blum Sylvie , Gibson Toby J. , Dobson Laszlo 
Published: March 2023

AbstractLeishmaniasis is a detrimental disease causing serious changes in quality of life and some forms lead to death. The disease is spread by the parasiteLeishmaniatransmitted by sandfly vectors and their primary hosts are vertebrates including humans. The pathogen penetrates host cells and secretes proteins (the secretome) to repurpose cells for pathogen growth and to alter cell signaling via host-pathogen Protein-Protein Interactions (PPIs). Here we present LeishMANIAdb, a database specifically designed to investigate howLeishmaniavirulence factors may interfere with host proteins. Since the secretomes of differentLeishmaniaspecies are only partially characterized, we collected various experimental evidence and used computational predictions to identifyLeishmaniasecreted proteins to generate a user-friendly unified web resource allowing users to access all information available on experimental and predicted secretomes. In addition, we manually annotated host-pathogen interactions of 211 proteins, and the localization/function of 3764 transmembrane (TM) proteins of differentLeishmaniaspecies. We also enriched all proteins with automatic structural and functional predictions that can provide new insights in the molecular mechanisms of infection. Our database, available athttps://leishmaniadb.ttk.humay provide novel insights intoLeishmaniahost-pathogen interactions and help to identify new therapeutic targets for this neglected disease.
Postural and muscular effects of upper-limb movements on voicing
Authors: Pouw Wim , Burchardt Lara S. , Selen Luc 
Published: March 2023

ABSTRACTVoice production can be a whole-body affair: Upper limb movements physically impact the voice in steady-state vocalization, speaking, and singing. This is supposedly due to biomechanical impulses on the chest-wall, affecting subglottal pressure. Unveiling such biomechanics is important, as humans gesture with their hands in a synchronized way with speaking. Here we assess biomechanical interactions between arm movements and the voice, by measurement of key (respiratory-related) muscles with electromyography (EMG) during different types of upper limb movement while measuring the bodys center of mass. We show that gesture-related muscle activations scale with positive peaks in the voices amplitude. Some of these muscles also strongly associate with changes in the center mass, confirming that gesture-vocal coupling partly arises due to posture-related muscle activity. If replicated, these results suggest an evolutionary ancient gesture-vocal connection at the level of biomechanics. These preliminary results will support a pre-registration of analyses for a larger-scale confirmatory study.
Evidence that common arbuscular mycorrhizal network alleviates phosphate shortage in interconnected walnut sapling and maize plants
Authors: Mortier Emma , Mounier Arnaud , Kreplak Jonathan , Martin-Laurent Fabrice , Recorbet Ghislaine , Lamotte Olivier 
Published: March 2023

AbstractUnder agroforestry practices, inter-specific facilitation between tree rows and cultivated alleys occurs when plants increase the growth of their neighbours especially under nutrient limitation. Due to a coarse roots architecture limiting soil inorganic phosphate (Pi) uptake, walnut trees (Juglansspp.) exhibit dependency on soil-borne symbiotic arbuscular mycorrhizal fungi that extend extra-radical hyphae beyond the root Pi depletion zone. To investigate the benefits of mycorrhizal walnuts in alley cropping, we experimentally simulated an agroforestry system in which walnut rootstocks RX1 (J. regiaxJ. microcarpa) were connected or not by a common mycelial network (CMN) to maize plants grown under two contrasting Pi levels. Mycorrhizal colonization parameters showed that the inoculum reservoir formed by inoculated walnut donor saplings allowed the mycorrhization of maize recipient roots. Relative to non-mycorrhizal plants and whatever the Pi supply, CMN enabled walnut saplings to access maize Pi fertilization residues according to significant increases in biomass, stem diameter and expression ofJrPHT1;1andJrPHT1;2, two mycorrhiza-inducible phosphate transporter candidates here identified by phylogenic inference of orthologs. In the lowest Pi supply, stem height, leaf Pi concentration and biomass of RX1 were significantly higher than in non-mycorrhizal controls, showing that mycorrhizal connections between walnut and maize roots alleviated Pi deficiency in the mycorrhizal RX1 donor plant. Under Pi limitation, maize recipient plants also benefited from mycorrhization relative to controls, as inferred from larger stem diameter and height, biomass, leaf number, N content and Pi concentration. Mycorrhization-induced Pi uptake generated a higher carbon cost for donor walnut plants than for maize plants by increasing walnut plant photosynthesis to provide the AM fungus with carbon assimilate. Here we show for the first time that CMN alleviates Pi deficiency in co-cultivated walnut and maize plants, and may therefore contribute to limit the use of chemical P fertilizers in agroforestry systems.
Sherlock - A flexible, low-resource tool for processing camera-trapping images
Authors: Penn Matthew J. , Miles Verity , Astley Kelly L. , Ham Cally , Woodroffe Rosie , Rowcliffe Marcus , Donnelly Christl A. 
Published: March 2023

1AbstractThe use of camera traps to study wildlife has increased markedly in the last two decades. Camera surveys typically produce large datasets which require processing to isolate images containing the species of interest. This is time consuming and costly, particularly if there are many empty images that can result from false triggers. Computer vision technology can assist with data processing, but existing artificial intelligence algorithms are limited by the requirement of a training dataset, which itself can be challenging to acquire. Furthermore, deep-learning methods often require powerful hardware and proficient coding skills.We present Sherlock, a novel algorithm that can reduce the time required to process camera trap data by removing a large number of unwanted images. The code is adaptable, simple to use and requires minimal processing power.We tested Sherlock on 240 596 camera trap images collected from 46 cameras placed in a range of habitats on farms in Cornwall, UK, and set the parameters to find European badgers (Meles meles). The algorithm correctly classified 91.9% of badger images and removed 49.3% of the unwanted ‘empty’ images. When testing model parameters, we found that faster processing times were achieved by reducing both the number of sampled pixels and ’bouncing’ attempts (the number of paths explored to identify a disturbance), with minimal implications for model sensitivity and specificity. When Sherlock was tested on two sites which contained no livestock in their images, its performance greatly improved and it removed 92.3% of the empty images.Though further refinements may improve its performance, Sherlock is currently an accessible, simple and useful tool for processing camera trap data.
High within-tree leaf trait variation and its response to species diversity and soil nutrients
Authors: Davrinche Andréa , Bittner Anna , Bruelheide Helge , Albert Georg , Harpole W. Stanley , Haider Sylvia 
Published: March 2023

AbstractLeaf functional traits provide important insights into plants’ responses to different environments. Leaf traits have been increasingly studied within-species in the last decade, following the growing realisation that neglecting the intra-specific scale can result in misreading plants’ response to environmental change. However, while likely to lead to similar pitfalls, within-individual leaf traits are under-researched despite being the scale at which elementary interactions shape ecosystem processes.To address this critical lack of understanding at the local scale, we assessed leaf trait variation in a large biodiversity-ecosystem functioning experiment in subtropical China. We used optical spectroscopy to determine nine morphological and biochemical traits of >5800 leaves from 414 trees representing 14 species. We evaluated the relative importance of the intra-individual level for total leaf trait variation, and the interacting effect of two trait variation’s drivers, soil nutrient availability, and a local species richness gradient.Comparing the amount of trait variation at the between-species, between-individuals and intra-individual levels, we found that intra-individual variation accounted on average for >25% of total trait variation. Additionally, intra-individual variation was the most prominent component of intra-specific variation. We found partial support for positive effects of soil nutrient availability and species diversity on intra-individual trait variation, and a strong interdependence of both effects. Contrary to the amplifying effects we expected, trait variation increased with soil nutrient availability at intermediate diversity, but decreased at low and high diversity.Our findings quantify the relevance of intra-individual level for leaf trait variation, and expose a complex interaction between its drivers. In particular, interactive effects of soil nutrient availability and local species diversity on trait variation suggest responses ranging from alleviating competition to enhancing complementarity. Taken together, our work highlights the importance of integrating an intra-individual perspective to understand trait-based mechanisms in biodiversity-ecosystem functioning relationships.