bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preserved executive control in ageing: The role of literacy experience
Authors: Pérez Ana I. , Fotiadou Georgia , Tsimpli Ianthi 
Published: May 2022

AbstractHealthy ageing is commonly accompanied by cognitive decline affecting several domains such as executive control, whereas certain verbal skills remain relatively preserved. Interestingly, recent scientific research has shown that some intellectual activities may be linked to beneficial effects, delaying or even alleviating cognitive decline in the elderly. Thirty young (age: M = 23) and thirty old (age: M = 66) adults were assessed in executive control (switching) and literacy experience (print exposure). First, we tried to confirm whether healthy ageing was generally associated with deficits in switching by looking at mixing cost effects, to then investigate if individual differences in print exposure explained variation in that age-related mixing costs. Both accuracy and reaction times mixing cost indexes demonstrated larger cost in old (but not in young) adults when switching from local to global information. More importantly, this cost effect disappeared in old adults with higher print exposure (reaction times). Our findings suggest literacy experience accumulated across the life-span may act as a cognitive reserve proxy to prevent executive control decline.
In-situ energy budget of needle-leaves reveals shift from evaporative to ‘air cooling’ under drought
Authors: Muller Jonathan D. , Rotenberg Eyal , Tatarinov Fyodor , Oz Itay , Yakir Dan 
Published: May 2022

AbstractThe modulation of the leaf energy budget and the balance between its sensible heat (H) and latent heat (LE) fluxes is vital for vegetation functioning and survival, as it is linked to maintaining leaf temperature below the thermal threshold, an increasingly important mechanism under a drying and warming climate, when evaporative cooling is suppressed.Combining measurements and theoretical estimates using a new methodology, we obtained rare and comprehensive energy budgets of leaves on twigs under field conditions in droughted and non-droughted plots of a semi-arid pine forest with low and high evapotranspiration rates, respectively.An examination of all components of the needle-leaf energy budget indicated that under the same radiative load, leaf cooling shifts from nearly equal contributions to H and LE in non-droughted trees to almost exclusively H in droughted ones while maintaining a similar leaf temperature.This LE-to-H shift in leaves of droughted trees highlights the efficiency of the ‘air cooling’ mechanism in maintaining temperature, which can enhance the resilience of trees to drying conditions. Additionally, leaf energy budgets are a fundamental tool to help understand leaf cooling and aerodynamic resistance under field conditions, and to improve modelling of ecosystem activity and its effect on the climate system.
Differential activation of NLRP3 inflammasome by Acinetobacter baumannii strains
Authors: Li Fei-Ju , Starrs Lora , Mathur Anukriti , Ishii Hikari , Man Si Ming , Burgio Gaetan 
Published: May 2022

AbstractAcinetobacter baumannii is an emerging nosocomial, opportunistic pathogen with growing clinical significance globally. A. baumannii has an exceptional ability to rapidly develop drug resistance. It is frequently responsible for ventilator-associated pneumonia in clinical settings and inflammation resulting in severe sepsis. The inflammatory response is mediated by host pattern-recognition receptors and the inflammasomes. Inflammasome activation triggers inflammatory responses, including the secretion of the pro-inflammatory cytokines IL-1β and IL-18, the recruitment of innate immune effectors against A. baumannii infection, and the induction programmed cell death by pyroptosis. An important knowledge gap is how variation among clinical isolates affects the host’s innate response and activation of the inflammasome during A. baumannii infection. In this study, we compared nine A. baumannii strains, including clinical locally-acquired isolates, in their ability to induce activation of the inflammasome and programmed cell death pathway in primary macrophages and mice. We found a striking variability in survival outcomes of mice and bacterial dissemination in organs among three ATCC A. baumannii strains, likely due to the differences in virulence between strains. Interestingly, we found a stark contrast in activation of the NLRP3 inflammasome pathway, the non-canonical caspase-11 pathway, plasmatic secretion of the pro-inflammatory cytokines IL-1β and IL-18 between A. baumannii strains. Our study highlights the importance of utilising multiple bacterial strains and clinical isolates with differential virulence to investigate the innate immune response to A. baumannii infection.
Genetic architectures of floral pigment and patterning in hybrid monkeyflowers
Authors: Cooley Arielle M. , Schlutius Caroline , Matthews Melia , Zheng Xingyu , Thomas Daniel , Edger Patrick P. , Platts Adrian E. , LaFountain Amy , George Logan , Williams Aaron , Hundley Douglas , Yuan Yao-Wu , Twyford Alex , Puzey Joshua R. 
Published: May 2022

ABSTRACTHybridization generates inter-genomic interactions, which may result in unique traits not seen in either parent species. Here we explore the genetic basis of both carotenoid and anthocyanin floral pigmentation in hybrids between monkeyflower speciesMimulus cupreusandM. luteusvar.variegatus. Mimulus cupreushas abundant yellow carotenoid pigmentation in its petal lobes, whileM. l. variegatushas a derived reduction in carotenoid intensity. Thus, as expected, carotenoid intensity segregates in an F2 hybrid population. More surprisingly, both species appear to have petal lobes solidly and identically covered in magenta anthocyanin pigment (which, when overlaid on the bright yellow carotenoid background, leads to an orange color inM. cupreus), yet F1 and F2 hybrids exhibit novel and complex spatial patterns of anthocyanin spotting. A rare yellow morph ofM. cupreus, which lacks petal anthocyanins, also generates spatially patterned offspring when hybridized withM. l. variegatus. We use this cross, together with newly developed high-quality genome assembly ofM. l. luteusand image analysis tools, to investigate the genetic architecture of color and pattern variation in an F2 hybrid population. We report a single QTL, containing theBeta-carotene hydroxylase(BCH) gene, associated with the non-patterned carotenoid reduction inM. l. variegatus. HPLC shows that relative beta-carotene abundance differs between dark yellow and light yellow petals, supporting a causal role forBCH. The presence versus absence of petal lobe anthocyanin segregates in a 3:1 ratio, and we report (as expected) an associated QTL encompassing the anthocyanin activatorMYB5a/NEGANwhich has previously been shown to be both necessary and sufficient to activate petal lobe anthocyanins inM. l. variegatus. Anthocyanin patterning was more complex, with seven QTLs associated with five quantitative patterning traits on the upper petals; 11 on the lower petals; and three qualitative whole-flower patterning traits. Although power was too limited to effectively test for epistatic interactions in this cross, the QTLs provide candidate genomic regions for further investigating the molecular mechanisms of spatially complex floral color patterning, and multiple candidate genes are identified including anthocyanin activators and an anthocyanin repressor.
The effect of external lateral stabilization on ankle moment control during steady-state walking
Authors: van Leeuwen A.M. , van Dieën J.H. , Bruijn S.M. 
Published: May 2022

AbstractExternal lateral stabilization can help identify stability control mechanisms during steady-state walking. The degree of step-by-step foot placement control and step width are known to decrease when walking with external lateral stabilization. Here, we investigated the effect of external lateral stabilization on ankle moment control in healthy participants. Ankle moment control complements foot placement, by allowing a corrective center-of-pressure shift once the foot has been placed. This is reflected by a model predicting this center-of-pressure shift based on the preceding foot placement error. Here, the absolute explained variance accounted for by this model decreased when walking with external lateral stabilization. In other words, we found a reduction in the contribution of step-by-step ankle moment control to mediolateral gait stability when externally stabilized. Concurrently, foot placement error and the average center-of-pressure shift remained unchanged.
Long-term population decline of a genetically homogenous continental-wide top Arctic predator
Authors: Gousy-Leblanc Marianne , Therrien Jean-François , Broquet Thomas , Rioux Delphine , Curt-Grand-Gaudin Nadine , Tissot Nathalie , Tissot Sophie , Szabo Ildiko , Wilson Laurie , Evans Jack T. , Bowes Victoria , Gauthier Gilles , Wiebe Karen L. , Yannic Glenn , Lecomte Nicolas 
Published: May 2022

ABSTRACTGenetic analysis can provide valuable information for conservation programs by unraveling the demographic trajectory of populations, by estimating effective population size, or by inferring genetic differentiation between populations. Here, we investigated the genetic differentiation within the Snowy Owl (Bubo scandiacus), a species identified as vulnerable by the IUCN, to (i) quantify connectivity among wintering areas, (ii) to evaluate current genetic diversity and effective population size and (iii) to infer changes in the historical effective population size changes from the last millennia to the recent past. The Snowy Owl, a highly mobile top predator, breeds across the Arctic tundra which is a region especially sensitive to current climate change. Using SNP-based analyses on Snowy Owls sampled across the North American nonbreeding range, we found an absence of genetic differentiation among individuals located up to 4,650 km apart. Our results suggest high genetic intermixing and effective dispersal at the continental scale despite documented philopatry to nonbreeding sites in winter. Reconstructing the population demographic indicated that North American Snowy Owls have been steadily declining since the Last Glacial Maximum ca 20,000 years ago and concurrently with global increases in temperature. Conservation programs should now consider North American Snowy Owls as a single, genetically homogenous continental-wide population which is most likely sensitive to the long-term global warming occurring since the Last Glacial Maximum.
Discordant effects of resource limitation on host survival and systemic pathogen growth in Drosophila-bacteria infection models: resistance vs. tolerance
Authors: Basu Aabeer , Singh Aparajita , Sehgal Suhaas , Madaan Tanvi , Prasad Nagaraj Guru 
Published: May 2022

ABSTRACTIn the experiments presented here, we explore the effect of resource limitation, in form of starvation (which leads to decrease in accessible resources and depletion of reserves) and sexual activity (which leads to reallocation of resources from somatic defence towards reproduction), on immune function of female Drosophila melanogaster flies. We infected females with five bacterial pathogens and measured their post-infection survival when subjected to either starvation or sexual activity (mating). Additionally, we measured within host pathogen levels in case of three of these pathogens. Based on previous literature, we predicted that both modes of resource limitation will increase post-infection mortality, but only sexual activity will lead to increase of pathogen load (because of compromised immune function), while starvation will either not affect or reduce pathogen loads (because of reduced availability of resources for the pathogen to proliferate within the host). Our results indicate that both starvation and sexual activity can lead to increased within-host pathogen levels, in addition to increased post-infection mortality, but in a pathogen-specific manner.
ChemPert: mapping between chemical perturbation and transcriptional response for non-cancer cells
Authors: Zheng Menglin , Okawa Satoshi , Bravo Miren , Chen Fei , Martínez-Chantar María-Luz , del Sol Antonio 
Published: May 2022

AbstractPrior knowledge of perturbation data can significantly assist in inferring the relationship between chemical perturbations and their specific transcriptional response. However, current databases mostly contain cancer cell lines, which are unsuitable for the aforementioned inference in non-cancer cells. Here we present ChemPert (https://chempert.uni.lu/), a database consisting of 82270 transcriptional signatures across 167 non-cancer cell types, enabling more accurate predictions of perturbation responses and drugs compared to cancer databases in non-cancer cells. In particular, ChemPert correctly predicted drug effects for treating non-alcoholic steatohepatitis and novel drugs for osteoarthritis. Overall, ChemPert provides a valuable resource for drug discovery in non-cancer diseases.
Correcting gradient-based interpretations of deep neural networks for genomics
Authors: Majdandzic Antonio , Rajesh Chandana , Koo Peter K. 
Published: May 2022

ABSTRACTPost-hoc attribution methods are widely applied to provide insights into patterns learned by deep neural networks (DNNs). Despite their success in regulatory genomics, DNNs can learn arbitrary functions outside the probabilistic simplex that defines one-hot encoded DNA. This introduces a random gradient component that manifests as noise in attribution scores. Here we demonstrate the pervasiveness of off-simplex gradient noise for genomic DNNs and introduce a statistical correction that is effective at improving the interpretability of attribution methods.
Phylogenomics provides insights into the evolution of cactophily and host plant shifts inDrosophila
Authors: Moreyra Nicolás Nahuel , Almeida Francisca Cunha , Allan Carson , Frankel Nicolás , Matzkin Luciano Matías , Hasson Esteban 
Published: May 2022

AbstractCactophilic species of theDrosophila buzzatiicluster (repletagroup) comprise an excellent model group to investigate genomic changes underlying adaptation to extreme climate conditions and host plants. In particular, these species offer a subject to study the transition from chemically simpler breeding sites (like prickly pears of the genusOpuntia) to chemically more complex hosts (columnar cacti). Here, we report four highly contiguous genome assemblies of three species of thebuzzatiicluster. Based on this genomic data and inferred phylogenetic relationships, we identified candidate taxonomically restricted genes (TRGs) likely involved in the evolution of cactophily and cactus host specialization in internal branches of the subgenusDrosophila. Functional enrichment analyses of TRGs within thebuzzatiicluster identified genes involved in detoxification, water preservation, immune system response, anatomical structure development, and morphogenesis. In contrast, processes that regulate responses to stress, as well as the metabolism of nitrogen compounds, transport, and secretion were found in the set of species that are columnar cacti dwellers. These findings are in line with the hypothesis that those genomic innovations brought about instrumental mechanisms underlying adaptation in a group of species that speciated in the arid regions of South America.
Distinct Effects of the Male-Killing BacteriaWolbachiaandSpiroplasmaand a Partiti-Like Virus in the Tea Pest Moth,Homona magnanima
Authors: Arai Hiroshi , Takamatsu Takumi , Lin Shiou-Ruei , Mizutani Tetsuya , Omatsu Tsutomu , Katayama Yukie , Nakai Madoka , Kunimi Yasuhisa , Inoue Maki N. 
Published: May 2022

ABSTRACTMale killing, the phenomenon of male death during development, is considered to be one of the advantageous strategies exerted by maternally transmitted microbes. Male killing has attracted interest in the fields of evolutionary biology and ecology for decades; however, little is known about its mechanism and origin. Here, we characterized and compared the effects of three distinct male killers,Wolbachia(Alphaproteobacteria),Spiroplasma(Mollicutes), and Osugoroshi virus (OGV) (Partitiviridae) in the tea pest mothHomona magnanima(Lepidoptera, Tortricidae). Regardless of the genetic sex (male: ZZ; female: ZW), female specific splice variants of the doublesex gene (dsx), a downstream regulator of the sex-determining gene cascade, was expressed inH. magnanimaharbored either male-killingWolbachiaorSpiroplasma. However, OGV and non-male-killingWolbachiadid not alterdsxsplicing. RNA sequencing and quantitative PCR assays demonstrated that male-killingWolbachiaimpaired the host’s dosage compensation system by altering the global gene expression of the Z chromosome (corresponding toBombyx morichromosome 1 and 15) in males, whereasSpiroplasmadid not affect dosage compensation. In contrast, the partiti-like virus OGVs did not affect sex-determination cascades or dosage compensation systems. Besides, male killers distinctly altered host gene expression and metabolomes associated with physiology, morphology, and diverse metabolic pathways. Moreover,WolbachiaandSpiroplasmainfections triggered abnormal apoptosis only in male embryos. These findings suggest that distantly related microbes employ distinct machineries to kill identical host males, which have been acquired through independent evolutionary processes.ImportanceMale-killing caused by diverse microbes has attracted substantial attention. However, it remains unclear how such male killers have evolved similar phenotypes, in part because male-killing mechanisms have been studied using different insect models. Here, by comparing three phylogenetically distinct male killers,Wolbachia, Spiroplasma, and a partiti-like virus, in an identical host, we provide evidence that microbes can affect male viability through distinct machinery, demonstrating distinct evolutionary scenarios for microbes to acquire make-killing ability. These findings provide insight into new directions for studying microbe–host interactions.
Evolution is not uniform along protein sequences
Authors: Bricout Raphaël , Weil Dominique , Stroebel David , Genovesio Auguste , Crollius Hugues Roest 
Published: May 2022

AbstractAmino acids evolve at different speeds within protein sequences, because their functional and structural roles are different. However, the position of an amino-acid within the sequence is not known to influence this evolutionary speed. Here we discovered that amino-acid evolve almost twice faster at protein termini than in their centre, hinting at a strong topological bias along the sequence length. We further show that the distribution of functional domains and of solvent-accessible residues in proteins readily explain how functional constrains are weaker at their termini, leading to the observed excess of amino-acid substitutions. Finally, we show that methods inferring sites under positive selection are strongly biased towards protein termini, suggesting that they may confound positive selection with weak negative selection. These results suggest that accounting for positional information should improve evolutionary models.
Tree diversity and density affect damage caused by the invasive pest Cameraria ohridella in urban areas
Authors: Stemmelen Alex , Jactel Hervé , Castagneyrol Bastien 
Published: May 2022

AbstractInvasive, non-native invasive pests pose a growing threat to urban trees and the services they provide to urban residents. With the reluctance to use chemical insecticides in cities, environmentally friendly methods of pest management are needed. Tree diversity is known to affect insect herbivory in forest, with higher tree species diversity leading to lower level of damage. However, the validity of those findings for a non-native insect in an urban environment remains to be demonstrated.We monitored 54 horse chestnut trees attacked by the invasive horse chestnut leafminer Cameraria ohridella in the city of Bordeaux, France. We analyzed the effects of neighboring tree diversity and density on the abundance, damage and parasitism rate of these leafminers.We showed that the abundance and damage of C. ohridella significantly increased with higher local tree canopy cover. We found that the parasitism rate of C. ohridella increased with the species diversity of neighboring trees. However, this increase in parasitism rate was not associated with a decrease in leaf area damaged.Our results pave the way for the management of exotic insect pests in cities based on the manipulation of spatial distribution and species diversity of urban trees.
Uncovering Additional Predictors of Urothelial Carcinoma from Voided Urothelial Cell Clusters Through a Deep Learning Based Image Preprocessing Technique
Authors: Levy Joshua J. , Liu Xiaoying , Marotti Jonathan D. , Kerr Darcy A. , Gutmann Edward J. , Glass Ryan E. , Dodge Caroline P. , Suriawinata Arief A. , Vaickus Louis J. 
Published: May 2022

AbstractUrine cytology is commonly used as a screening test for high grade urothelial carcinoma for patients with risk factors or hematuria and is an essential step in longitudinal monitoring of patients with a prior bladder cancer history. However, the semi-subjective nature of current reporting systems for urine cytology (e.g., The Paris System) can hamper reproducibility. For instance, the incorporation of urothelial cell clusters into the classification schema is still an item of debate and perplexity amongst expert cytopathologists, as several previous works have disputed their diagnostic relevance. Recently, several machine learning and morphometric algorithms have been proposed to provide quantitative descriptors of urine cytology specimens in an effort to reduce subjectivity and include automated assessments of cell clusters. However, it remains unclear how these computer algorithms interpret/analyze cell clusters. In this work, we have developed an automated preprocessing tool for urothelial cell cluster assessment that divides urothelial cell clusters into meaningful components for downstream assessment (i.e., population-based studies, workflow automation). Results indicate that cell cluster atypia (i.e., defined by whether the cell cluster harbored multiple atypical cells, thresholded by a minimum number of cells), cell border overlap and smoothness, and total number of clusters are important markers of specimen atypia when considering assessment of urothelial cell clusters. Markers established through techniques to separate cell clusters may have wider applicability for the design and implementation of machine learning approaches for urine cytology assessment.
An automated approach to quantify chemotaxis index in Caenorhabditis nematodes
Authors: Crombie Timothy A. , Chikuturudzi Chido , Cook Daniel E. , Andersen Erik C. 
Published: May 2022

AbstractChemotaxis assays are used extensively to study behavioral responses of Caenorhabditis nematodes to environmental cues. These assays result in a chemotaxis index (CI) that denotes the behavioral response of a population of nematodes to a particular compound and can range from 1 (maximum attraction) to −1 (maximum avoidance). Traditional chemotaxis assays have low throughput because researchers must manually setup experimental populations and score CIs. Here, we describe an automated methodology that increases throughput by using liquid-handling robots to setup experimental populations and a custom image analysis package, ct, to automate the scoring of CIs from plate images.