bluuebunny/crossref_metadata_2025 huggingface dataset:
Hypertonic lactate infusion reduces vasopressor requirement and biomarkers of brain and cardiac injury after experimental cardiac arrest
Authors: Annoni Filippo , Su Fuhong , Peluso Lorenzo , Lisi Ilaria , Caruso Enrico , Pischiutta Francesca , Gouvea Bogossian Elisa , Garcia Bruno , Njimi Hassane , Vincent Jean-Louis , Gaspard Nicolas , Ferlini Lorenzo , Creteur Jacques , Zanier Elisa R , Taccone Fabio Silvio
Published: March 2023

Introduction

Prognosis after resuscitated cardiac arrest (CA) remains poor with high morbidity and mortality due to extensive cardiac and brain injuries and the lack of effective treatments. Hypertonic sodium lactate (HSL) could be beneficial after CA by buffering severe metabolic acidosis, increasing brain perfusion and cardiac performance, reducing cerebral swelling, and serving as alternative energetic cellular substrate. The aim of this study was therefore to test the effects of HSL infusion on brain and cardiac injury in an experimental model of CA.

Methods

After a 10-min electrically induced CA followed by 5 min of cardiopulmonary resuscitation maneuvers, adult swine (n=35) were randomly assigned to receive either balanced crystalloids (controls, n=11) or HSL infusion, either starting during cardiopulmonary resuscitation (CPR, Intra-arrest, n=12) or after return of spontaneous circulation (Post-ROSC, n=11) for the following 12 hours. In all animals, extensive multimodal neurological and cardiovascular monitoring was implemented. All animals were treated with target temperature management at 34°C.

Results

34 out of 35 (97.1%) animals achieved ROSC and one animal in the Intra-arrest group deceased before completing the observation period. Arterial pH, lactate, sodium concentrations and plasma osmolarity were higher in treated animals then in controls (p<0.001), while potassium concentrations were lower (p=0.004). HSL infusion either Intra-arrest or Post-ROSC improved hemodynamic compared to controls, as shown by reduced vasopressors need to maintain mean arterial pressure target above 65 mmHg (p=0.005 for interaction; p=0.01 for groups). Moreover, plasmatic troponin-I levels and glial fibrillary acid protein (GFAP) concentrations were lower in treated groups at several time-points than in controls.

Conclusions

In this experimental CA model, HSL infusion was associated with reduced vasopressor requirements and decreased plasmatic levels of biomarkers of cardiac and cerebral injury.
A temporal hierarchy of object processing in human visual cortex
Authors: Xu Rui , Zhou Wenjing , Xu Xin , Ling Zhipei , Liu Hesheng , Hong Bo
Published: March 2023

Our brain constructs increasingly sophisticated representations along the ventral visual pathway to support object recognition. To understand how these representations unfold over time, we recorded human intracranial electroencephalography responses to 120 object images at five consecutive stages of the ventral pathway from V1 to occipitotemporal areas. Using representational similarity analysis, we confirmed that response patterns were more strongly driven by low-order stimulus properties at early stages and high-order category information at late stages, respectively. Interestingly, response patterns also became less stimulus-driven and more categorical at all stages over time, from ∼100 to 200 ms post-stimulus. During this period, we found significant noise correlation between single-trial response patterns across stages, indicating tight inter-areal coupling. Thus, multi-areal recurrent processes may be essential in building high-order object representations.
Synaptic changes in pallidostriatal circuits observed in parkinsonian model triggers abnormal beta synchrony with accurate spatio-temporal properties across the basal ganglia
Authors: Azizpour Lindi Shiva , Mallet Nicolas P. , Leblois Arthur
Published: March 2023

Excessive oscillatory activity across basal ganglia (BG) nuclei in theβfrequencies (12–30Hz) is a hallmark of Parkinson’s disease (PD). While the link between oscillations and symptoms remains debated, exaggeratedβoscillations constitute an important biomarker for therapeutic effectiveness in PD. The neuronal mechanisms ofβ-oscillation generation however remain unknown. Many existing models rely on a central role of the subthalamic nucleus (STN) or cortical inputs to BG. Contrarily, neural recordings and optogenetic manipulations in normal and parkinsonian rats recently highlighted the central role of the external pallidum (GPe) in abnormalβoscillations, while showing that the integrity of STN or motor cortex is not required. Here, we evaluate the mechanisms for the generation of abnormalβoscillations in a BG network model where neuronal and synaptic time constants, connectivity, and firing rate distributions are strongly constrained by experimental data. Guided by a mean-field approach, we show in a spiking neural network that several BG sub-circuits can drive oscillations. Strong recurrent STN-GPe connections or collateral intra-GPe connections drive gamma oscillations (>40Hz), whereas strong pallidostriatal loops drive low-β(10-15Hz) oscillations. We show that pathophysiological strengthening of striatal and pallidal synapses following dopamine depletion leads to the emergence of synchronized oscillatory activity in the mid-βrange with spike-phase relationships between BG neuronal populations in-line with experiments. Furthermore, inhibition of GPe, contrary to STN, abolishes oscillations. Our modeling study uncovers the neural mechanisms underlying PDβoscillations and may thereby guide the future development of therapeutic strategies.

Significance statement

In Parkinson’s disease, neural activity in subcortical nuclei called the basal ganglia displays abnormal oscillatory synchronization that constitutes an important biomarker for therapeutic effectiveness. The neural mechanisms for the generation of these oscillations remain unknown. Here, in a theoretical neuronal network model strongly constrained by anatomical and physiological data, we show that specific circuit modifications in basal ganglia connectivity during Parkinson’s disease lead to the emergence of synchronized oscillatory activity in the network with properties that strongly agree with available experimental evidence. This and future theoretical investigations of the neural mechanisms underlying abnormal neuronal activity in Parkinson’s disease are necessary to guide the future development of therapeutic strategies to ameliorate symptoms.
A multi-omics genome-and-transcriptome single-cell atlas of human preimplantation embryogenesis reveals the cellular and molecular impact of chromosome instability
Authors: Gallardo Elia Fernandez , Sifrim Alejandro , Chappell Joel , Demeulemeester Jonas , Herrmann Jennifer Clara , Vermotte Robin , Kerremans Alison , Van der Haegen Michiel , Herck Jens Van , Vanuytven Sebastiaan , Vandereyken Katy , Macaulay Iain C. , Vermeesch Joris Robert , Peeraer Karen , Debrock Sophie , Pasque Vincent , Voet Thierry
Published: March 2023

The frequent acquisition of genomic abnormalities in human preimplantation embryos is a leading cause of pregnancy loss, but does not necessarily prohibit healthy offspring. However, the impact of genomic abnormalities on cellular states and development of the early human embryo remains largely unclear. Here, we characterise aneuploidy and reconstruct gene regulatory networks in human preimplantation embryos, and investigate gene expression and developmental perturbations instigated by aneuploidy using single-cell genome-and-transcriptome sequencing (G&T-seq). At the genomic level, we show that acquired numerical and structural chromosomal aberrations are frequent across all stages of early embryogenesis and in all cell lineages. At the transcriptome level, we identify regulators of cell identity and uncover a network of 248 transcription factors from 10 major gene regulatory modules that characterise the distinct lineages of human preimplantation embryos. By integrating single-cell DNA-with RNA-information, we unveil how expression levels are affected by losses or gains of the corresponding genes in embryonic cells across human preimplantation development, as well as how copy-number aberrant transcription factor genes perturb the expression of their cognate target genes in euploid regions. Furthermore, we reveal a majority of aneuploid cells show a developmental delay and reduced fitness, indicating cell competition within the mosaic diploid-aneuploid embryo, which may contribute to selection against aneuploid cells and the birth of healthy offspring from mosaic diploid-aneuploid embryos. In summary, our multi-modal analyses provide unprecedented insights into early human embryo development.
Short-term transcutaneous vagus nerve stimulation increases pupil size but does not affect EEG alpha power: a replication
Authors: Lloyd Beth , Wurm Franz , de Kleijn Roy , Nieuwenhuis Sander
Published: March 2023

Background

Transcutaneous auricular vagus nerve stimulation (taVNS) is a promising brain stimulation method for the treatment of pharmaco-resistant epilepsy and depression. Its clinical efficacy is thought to depend on taVNS-induced activation of the locus coeruleus. However, unlike for invasive VNS, there is little evidence for an effect of taVNS on noradrenergic activity.

Objective

We attempted to replicate recently published findings by Sharon et al. (2021), showing that short bursts of taVNS transiently increased pupil size and decreased EEG alpha power, two correlates of central noradrenergic activity.

Methods

Following the original study, we used a single-blind, sham-controlled, randomized cross-over design. We applied short-term (3.4 s) taVNS in healthy human volunteers (n=29), while collecting resting-state pupil-size and EEG data. To analyze the data, we used scripts provided by Sharon and colleagues.

Results

Consistent with Sharon et al. (2021), pupil dilation was significantly larger during taVNS than during sham stimulation (p= .009; Bayes factor supporting the difference = 7.45). However, we failed to replicate the effect of taVNS on EEG alpha power (p= .37); the data were four times more likely under the null hypothesis (BF10= 0.28).

Conclusion

Our findings support the effectiveness of short-term taVNS in inducing transient pupil dilation, a correlate of phasic noradrenergic activity. However, we failed to replicate the recent finding by Sharon et al. (2021) that taVNS attenuates EEG alpha activity. Overall, this study highlights the need for continued research on the neural mechanisms underlying taVNS efficacy and its potential as a treatment option for pharmaco-resistant conditions. It also highlights the need for direct replications of influential taVNS studies.
Spatial transcriptomic analysis of virtual prostate biopsy reveals confounding effect of heterogeneity on genomic signature scoring
Authors: Figiel Sandy , Yin Wencheng , Doultsinos Dimitrios , Erickson Andrew , Poulose Ninu , Singh Reema , Magnussen Anette , Anbarasan Thineskrishna , Teague Renuka , He Mengxiao , Lundeberg Joakim , Loda Massimo , Verrill Clare , Colling Richard , Gill Pelvender S. , Bryant Richard J. , Hamdy Freddie C. , Woodcock Dan J. , Mills Ian G. , Cussenot Olivier , Lamb Alastair D.
Published: March 2023

Genetic signatures have added a molecular dimension to prognostics and therapeutic decision-making. However, tumour heterogeneity in prostate cancer and current sampling methods could confound accurate assessment. Based on previously published spatial transcriptomic data from multifocal prostate cancer, we created virtual biopsy models that mimic conventional biopsy placement and core size. We then analysed the gene expression of different prognostic signatures (OncotypeDx®, Decipher®, Prostadiag®) using a step-wise approach increasing resolution from pseudo-bulk analysis of the whole biopsy, to differentiation by tissue subtype (benign, stroma, tumour), followed by distinct tumour grade and finally clonal resolution. The gene expression profile of virtual tumour biopsies revealed clear differences between grade groups and tumour clones, compared to a benign control, which were not reflected in bulk analyses. This suggests that bulk analyses of whole biopsies or tumour-only areas, as used in clinical practice, may provide an inaccurate assessment of gene profiles. The type of tissue, the grade of the tumour and the clonal composition all influence the gene expression in a biopsy. Clinical decision making based on biopsy genomics should be made with caution while we await more precise targeting and cost-effective spatial analyses.

Patient summary

Prostate cancers are very variable, including within a single tumour. Current genetic scoring systems, which are sometimes used to make decisions for how to treat patients with prostate cancer, are based on sampling methods which do not reflect these variations. We found, using state-of-the-art spatial genetic technology to simulate accurate assessment of variation in biopsies, that the current approaches miss important details which could negatively impact clinical decisions.

Take home message

Virtual biopsies from spatial transcriptomic analysis of a whole prostate reveal that current genomic risk scores potentially deliver misleading results as they are based on bulk analysis of prostate biopsies and ignore tumour heterogeneity.
Infinite Physical Monkey: Do Deep Learning Methods Really Perform Better in Conformation Generation?
Authors: Zhang Haotian , Zhang Jintu , Zhao Huifeng , Jiang Dejun , Deng Yafeng
Published: March 2023

Conformation Generation is a fundamental problem in drug discovery and cheminformatics. And organic molecule conformation generation, particularly in vacuum and protein pocket environments, is most relevant to drug design. Recently, with the development of geometric neural networks, the data-driven schemes have been successfully applied in this field, both for molecular conformation generation (in vacuum) and binding pose generation (in protein pocket). The former beats the traditional ETKDG method, while the latter achieves similar accuracy compared with the widely used molecular docking software. Although these methods have shown promising results, some researchers have recently questioned whether deep learning (DL) methods perform better in molecular conformation generation via a parameter-free method. To our surprise, what they have designed is some kind analogous to the famous infinite monkey theorem, the monkeys that are even equipped with physics education. To discuss the feasibility of their proving, we constructed a real infinite stochastic monkey for molecular conformation generation, showing that even with a more stochastic sampler for geometry generation, the coverage of the benchmark QM-computed conformations are higher than those of most DL-based methods. By extending their physical monkey algorithm for binding pose prediction, we also discover that the successful docking rate also achieves near-best performance among existing DL-based docking models. Thus, though their conclusions are right, their proof process needs more concern.
Comparative Genomics of Firmicutes reveals probable adaptations for xylose fermentation in Thermoanaerobacterium saccharolyticum
Authors: Fiamenghi Mateus B. , Prodonoff Juliana S. , Borelli Guilherme , Carazzolle Marcelo F. , Pereira Gonçalo A. G. , José Juliana
Published: March 2023

Second-generation (2G) ethanol is one potential biofuel that could be used to achieve the goal of reducing greenhouse gas emissions. Many challenges still need to be overcome for the feasibility of this technology, most of them related to consumption of xylose, a pentose sugar not easily metabolized by industrial microorganisms. Thus, exploring genes, pathways and other organisms that can ferment xylose is a strategy implemented to solve industrial bottlenecks.Thermoanaerobacterium saccharolyticum(T. sac) is an organism from the firmicutes phylum, capable of naturally fermenting compounds of industrial interest, such as xylan and xylose. Understanding evolutionary adaptations may help not only to solidify this bacterium as a potential substitute to the yeastSaccharomyces cerevisiaein industry, but also bring novel genes and information that can be used for yeast, enhance its fermenting capabilities, and increase production of current bio-platforms. This study presents a deep evolutionary study of members of the firmicutes clade, focusing on adaptations that may be related to overall fermentation metabolism, especially for xylose fermentation. One highlight is the finding of positive selection on a xylose binding protein of the xylFGH operon, close to the annotated sugar binding site, with this protein already being found to be expressed in xylose fermenting conditions in a previous study. Results from this study can serve as basis for searching for candidate genes to use in industrial strains or to improveT. sacas a new microbial cell factory, which may help to solve current problems found in the biofuels industry.
Continuous assembly required: perpetual species turnover in two trophic level ecosystems
Authors: Spaak Jurg W. , Adler Peter B. , Ellner Stephen P.
Published: March 2023

Community assembly is often treated as deterministic, converging on one or at most a few possible stable endpoints. However, in nature we typically observe continuous change in community composition, which is often ascribed to environmental change. But continuous changes in community composition can also arise in deterministic, time-invariant community models, especially food web models. Our goal was to determine why some models produce continuous assembly and others do not. We investigated a simple two trophic-level community model to show that continuous assembly is driven by the relative niche width of the trophic levels. If predators have a larger niche width than prey, community assembly converges to a stable equilibrium. Conversely, if predators have a smaller niche width than prey, then community composition never stabilizes. Evidence that food webs need not reach a stable equilibrium has important implications, as many ecological theories of community ecology based on equilibria may be difficult to apply to such food webs.
ancIBD - Screening for identity by descent segments in human ancient DNA
Authors: Ringbauer Harald , Huang Yilei , Akbari Ali , Mallick Swapan , Patterson Nick , Reich David
Published: March 2023

Long DNA sequences shared between two individuals, known as Identical by descent (IBD) segments, are a powerful signal for identifying close and distant biological relatives because they only arise when the pair shares a recent common ancestor. Existing methods to call IBD segments between present-day genomes cannot be straightforwardly applied to ancient DNA data (aDNA) due to typically low coverage and high genotyping error rates. We present ancIBD, a method to identify IBD segments for human aDNA data implemented as a Python package. Our approach is based on a Hidden Markov Model, using as input genotype probabilities imputed based on a modern reference panel of genomic variation. Through simulation and downsampling experiments, we demonstrate that ancIBD robustly identifies IBD segments longer than 8 centimorgan for aDNA data with at least either 0.25x average whole-genome sequencing (WGS) coverage depth or at least 1x average depth for in-solution enrichment experiments targeting a widely used aDNA SNP set (‘1240k’). This application range allows us to screen a substantial fraction of the aDNA record for IBD segments and we showcase two downstream applications. First, leveraging the fact that biological relatives up to the sixth degree are expected to share multiple long IBD segments, we identify relatives between 10,156 ancient Eurasian individuals and document evidence of long-distance migration, for example by identifying a pair of two approximately fifth-degree relatives who were buried 1410km apart in Central Asia 5000 years ago. Second, by applying ancIBD, we reveal new details regarding the spread of ancestry related to Steppe pastoralists into Europe starting 5000 years ago. We find that the first individuals in Central and Northern Europe carrying high amounts of Steppe-ancestry, associated with the Corded Ware culture, share high rates of long IBD (12-25 cM) with Yamnaya herders of the Pontic-Caspian steppe, signaling a strong bottleneck and a recent biological connection on the order of only few hundred years, providing evidence that the Yamnaya themselves are a main source of Steppe ancestry in Corded Ware people. We also detect elevated sharing of long IBD segments between Corded Ware individuals and people associated with the Globular Amphora culture (GAC) from Poland and Ukraine, who were Copper Age farmers not yet carrying Steppe-like ancestry. These IBD links appear for all Corded Ware groups in our analysis, indicating that individuals related to GAC contexts must have had a major demographic impact early on in the genetic admixtures giving rise to various Corded Ware groups across Europe. These results show that detecting IBD segments in aDNA can generate new insights both on a small scale, relevant to understanding the life stories of people, and on the macroscale, relevant to large-scale cultural-historical events.
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

Purkinje 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

Studying 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

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Unilateral striatal 6-OHDA injection caused an early onset dose-dependent behavioral deficit in mice

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Behavioral deficit manifested as mild impairment of locomotion and locomotive movement initialization

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Behavioral changes were accompanied by moderate, dose-dependent loss of SNc dopaminergic neurons

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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

Eutrophication 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

The 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

Organisms 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

The 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

Turbidity 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

Leishmaniasis 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

Voice 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

Under 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

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The 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

Leaf 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.
How often are male mosquitoes attracted to humans?
Authors: Paris Véronique , Hardy Christopher , Hoffmann Ary A. , Ross Perran A.
Published: March 2023

Many mosquito species live close to humans where females feed on human blood. While male mosquitoes do not feed on blood, it has long been recognized that males of some species can be attracted to human hosts. To investigate the frequency of male mosquito attraction to humans, we conducted a literature review and human-baited field trials, as well as laboratory experiments involving males and females of three common Aedes species. Our literature review indicated that male attraction to humans is limited to a small number of species, including Ae. aegypti and Ae. albopictus. In our human-baited field collections, only 4 out of 13 species captured included males. In laboratory experiments, we found that male Ae. notoscriptus and Ae. vigilax showed no attraction to humans, while male Ae. aegypti exhibited persistent attraction for up to 30 minutes. Both male and female Ae. aegypti displayed similar preferences for different human subjects, suggesting that male Ae. aegypti respond to similar cues as females. Additionally, we found that mosquito repellents applied to human skin effectively repelled male mosquitoes. These findings shed light on mosquito behaviour and have implications for mosquito control programs, particularly those involving the release or monitoring of the male mosquito population.
Connectional axis of individual functional variability: Patterns, structural correlates, and relevance for development and cognition
Authors: Yang Hang , Wu Guowei , Li Yaoxin , Xu Xiaoyu , Cong Jing , Xu Haoshu , Ma Yiyao , Li Yang , Chen Runsen , Pines Adam , Xu Ting , Sydnor Valerie Jill , Satterthwaite Theodore D. , Cui Zaixu
Published: March 2023

The human cerebral cortex exhibits intricate interareal functional synchronization at the macroscale, with substantial individual variability in these functional connections. However, the spatial organization of functional connectivity (FC) variability across the human connectome edges and its significance in cognitive development remain unclear. Here, we identified a connectional axis in the edge-level FC variability. The variability declined continuously along this axis from within-network to between-network connections, and from the edges linking association networks to those linking the sensorimotor and association networks. This connectional axis of functional variability is associated with spatial pattern of structural connectivity variability. Moreover, the connectional variability axis evolves in youth with an increasing flatter axis slope. We also observed that the slope of connectional variability axis was positively related to the performance in the higher-order cognition. Together, our results reveal a connectional axis in functional variability that is linked with structural connectome variability, refines during development, and is relevant to cognition.