bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pupil self-regulation modulates markers of cortical excitability and cortical arousal
Authors: Weijs Marieke Lieve , Missura Silvia , Potok-Szybińska Weronika , Bächinger Marc , Badii Bianca , Dominguez Manuel Carro , Wenderoth Nicole , Meissner Sarah Nadine 
Published: September 2024

AbstractThe brain’s arousal state (i.e., central arousal) is regulated by multiple neuromodulatory nuclei in the brainstem and significantly influences high-level cognitive processes. By exploiting the mechanistic connection between the locus coeruleus (LC), a key regulator of central arousal, and pupil dynamics, we recently demonstrated that participants can gain volitional control over arousal-regulating centers including the LC using a pupil-based biofeedback approach. Here, we test whether pupil-based biofeedback modulates electrophysiological markers of cortical excitability, cortical arousal, and phasic LC activity. Combining pupil-based biofeedback with single-pulse TMS, EEG recordings, and an auditory oddball task revealed three main results: pupil self-regulation significantly modulates (i) cortical excitability, (ii) the EEG spectral slope, a marker of cortical arousal, and (iii) the P300 response to target tones, an event-related potential suggested to be tightly linked to phasic LC activity. Interestingly, pupil self-regulation strength was linearly linked to the modulation of the spectral slope, suggesting a common physiological mechanism. Here, we have shown that pupil-based biofeedback modulates fundamental aspects of brain function. Whether this method could further be used to modulate these aspects in case of disturbances associated with neurological and psychiatric disorders needs to be investigated in future studies.
Impact of Acetate and Optimized Nitrate Levels on Mixotrophic Growth and Protein Dynamics inChlorella Sorokiniana
Authors: Chen Sunni , Wang Ruiqi , Kim Youn Joong , Radican Emily , Lei Yu , Cho Yongku , Xiao Zhenlei , Qiao Mingyu , Luo Yangchao 
Published: September 2024

AbstractMicroalgae are well-known for their role as sustainable bio-factories, offering a promising solution to the global food and nutrition crisis. To clarify the potential ofChlorella sorokinianaUTEX 1230 for food applications, particularly as an alternative protein source, the study employed a mixotrophic cultivation mode with sodium acetate (NaAc) as a cost-effective organic carbon (NaAc-C) source. Varying levels of NaAc-C and nitrate-sourced nitrogen were investigated, optimizing the effect of metabolic characteristics of the microalgal growth. The designed heterotrophic cultivation confirmed the ability ofC. sorokinianaUTEX 1230 to grow on NaAc-C, and then the mixotrophic cultures, when supported by both NaAc-C and CO2, exhibited superior growth performance, achieving double the biomass concentration compared to the autotrophic control. The addition of nitrogen (750 mg/L NaNO₃) facilitated the thorough metabolism of NaAc-C and enhanced photosynthetic activity indicated by a 196% increase in pigment levels, which resulted in a maximum biomass concentration of 2.82 g/L in the 150 mM NaAc-C group. A detailed analysis of nitrogen and protein concentrations over time revealed that higher nitrogen availability led to greater protein accumulation which was then degraded to support essential life activities under nitrogen starvation. Therefore, it is suggested that supplementing nitrate on the 3rdday and harvesting on the 4thday could be strategically implemented to increase protein yield from 0.17 g/L/d to 0.34 g/L/d. These findings offer theoretical guidance for further refining this microalgal strain for use as an alternative protein.
Precision not prediction: Body-ownership illusion as a consequence of online precision adaptation under Bayesian inference
Authors: Novický Filip , Meera Ajith Anil , Zeldenrust Fleur , Lanillos Pablo 
Published: September 2024

AbstractHumans can experience body-ownership of new (external) body parts, for instance, via visuotactile stimulation. While there are models that capture the influence of such body illusions in body localization and recalibration, the computational mechanism that drives the experience of body-ownership of external limbs is still not well understood and under discussion. Here, we describe a mathematical model of this phenomenon via uncertainty minimization. Using the Rubber Hand Illusion (RHI) as a proxy, we show that to properly estimate one’s arm position, an agent infers the least uncertain world model that explains the observed reality through online adaptation of the signals’ relevance, i.e., the precision parameters (inverse variance of the prediction error signal). Our computational model describes that the illusion is triggered when the sensory precision quickly adapts to account for the increase of sensory noise during the physical stimulation of the rubber hand due to the real hand occlusion. This adaptation produces a change in the uncertainty of the body position estimates yielding to a switch of the perceived reality: the ‘rubber hand is the agent’s hand’ becomes the most plausible model (i.e., it has the least posterior uncertainty). Overall, our theoretical account, along with the numerical simulations provided, suggests that while the perceptual drifts in body localization may be driven by prediction error minimization, body-ownership illusions are a consequence of estimating the signals precision, i.e. the uncertainty associated with the prediction error.Author summaryUnderstanding how body illusions occur is critical for comprehending body perception and embodiment. These illusions may hide powerful mechanisms of the brain and the body to handle uncertainty and conflicts in the sensory input and to adapt to body changes and world interactions. For instance, in less than one minute of visuotactile stimulation humans can experience body-ownership experiences of fake body parts or even experience that a different body is their own. Here, we present a possible explanation, through computational modeling, of why humans suddenly perceive a fake body part as their own. The proposed underlying process is the tracking of the uncertainty associated with the error between the predicted signals and the current sensory input. Our model describes that while the effect of body mislocalization during body illusions may be driven by prediction error minimization, body ownership illusions are triggered by uncertainty resolution.
Changes in flexibility but not in compactness underlie the thermal adaptation of prokaryotic adenylate kinases
Authors: Kontopoulos Dimitrios - Georgios , Patmanidis Ilias , Barraclough Timothy G. , Pawar Samraat 
Published: September 2024

AbstractUnderstanding the structural changes that enable enzymes to remain active in extreme thermal conditions is of broad scientific interest for both fundamental and applied biological research. Three key mechanisms that underlie the thermal adaptation of enzymes are modifications in structural flexibility, compactness, and the contacts formed among amino acids. However, most previous studies on these topics have been limited to small sample sizes or a narrow taxonomic focus, and the importance of these factors to thermal adaptation remains poorly understood. In this study, we combined molecular dynamics simulations and phylogenetic comparative analyses to thoroughly analyse the structural factors underlying thermal adaptation in adenylate kinase—a key enzyme involved in cellular energy balance and homeostasis—across 70 prokaryotic species. We detect systematic increases in the flexibility of the enzyme with temperature, both across and within species. In contrast, structural compactness appears to be almost completely independent of temperature. Finally, we uncover a remarkable diversity in the number and types of amino acid contacts observed in different adenylate kinases that cannot be explained solely by temperature. Our results suggest that there are multiple paths toward the adaptation of prokaryotic adenylate kinases to extreme thermal environments and that these paths are generally accessible through changes in flexibility.Lay summaryThe structure of a given enzyme can vary considerably among species, reflecting local environmental conditions to an extent. To this day, we do not have a clear picture of the impacts of the thermal environment on enzyme structure. To fill this gap, we performed a structural comparison of the enzyme adenylate kinase (ADK) from 70 species of bacteria and archaea. We find that rises in temperature tend to increase the flexibility of the enzyme. However, at any given temperature, ADKs from cold environments tend to be more flexible than those from hot environments. In contrast, the compactness of the enzyme did not vary consistently with temperature. Finally, we found that the pattern of amino acid contacts can vary dramatically across ADKs of different species, in a manner that cannot be predicted by temperature alone. Overall, our study shows that there are multiple ways to evolve an enzyme structure that can tolerate extreme temperatures, with a key constraint being maintaining sufficient flexibility at temperatures typically experienced by each species.
Inferring long-term and short-term determinants of genetic diversity in honey bees: Beekeeping impact and conservation strategies
Authors: Leroy Thibault , Faux Pierre , Basso Benjamin , Eynard Sonia , Wragg David , Vignal Alain 
Published: September 2024

AbstractBees are vital pollinators in natural and agricultural landscapes around the globe, playing a key role in maintaining flowering plant biodiversity and ensuring food security. Among the honey bee species, the Western honey bee (Apis mellifera) is particularly significant, not only for its extensive crop pollination services but also for producing economically valuable products such as honey. Here, we analyzed whole-genome sequence data from fourApisspecies to explore how honey bee evolution has shaped current diversity patterns. Using Approximate Bayesian Computation, we first reconstructed the demographic history ofA. melliferain Europe, finding support for postglacial secondary contacts, therefore predating human-mediated transfers linked to modern beekeeping. However, our analysis of recent demographic changes then reveals significant bottlenecks due to beekeeping practices, which have notably affected genetic diversity. Black honey bee populations from conservatories, particularly those on islands, exhibit considerable genetic loss, raising concerns about the long-term effectiveness of current conservation strategies. Additionally, we observed a high degree of conservation in the genomic landscapes of nucleotide diversity across the four species, despite a divergence gradient spanning over 15 million years, consistent with a long-term conservation of the recombination landscapes. Taken together, our results provide the most comprehensive assessment of diversity patterns in honey bees to date and offer insights into the optimal management of resources to ensure the long-term persistence of honey bees and their invaluable pollination services.
Loss or redistribution? A better way of estimating regional changes in animal distribution and numbers caused by increased human activities
Authors: Mercker Moritz , Peschko Verena , Borkenhagen Kai , Markones Nele , Schwemmer Henriette , Dierschke Volker , Garthe Stefan 
Published: September 2024

AbstractA differentiated understanding of how regional human activities affect the spatial distribution and numbers of animals within specific areas of interest is of great ecological importance. Estimating these effects from empirical data is challenging however, because human activities can affect animals in qualitatively different ways and on different spatial and temporal scales. In addition, spatio-temporal animal abundance is frequently influenced by factors intrinsic and extrinsic to the area of interest, potentially confounding impact studies, e.g., based on trends.In this study, we synergistically combined regression and mechanistic modelling to separate these different influences. We first used partial differential equations to simulate various potential animal redistribution patterns affected by regional human activities. We then selected appropriate patterns as predictors in regression-based species distribution models, together with additional anthropogenic and natural covariates. The simultaneous consideration of large-scale (number-conserving) animal reorganisation, their regional loss or gain, and the influence of additional environmental covariates eventually allowed the generation of qualitative and quantitative estimates and predictions of human-induced changes.We exemplarily applied our approach to investigate the current and future impact of increasing offshore wind farm (OWF) implementation in the German North Sea on common murres (Uria aalge) during autumn. OWFs constructed up to 2019 reduced common murre numbers in German waters by 18.3%. If the planned OWF priority and reservation areas outlined in the German Marine Spatial Plan are implemented, the predicted loss would increase to 77.7%. Notably, these predictions did not include additional anthropogenic activities or further plans for OWF installation, which could together lead to the almost complete disappearance of common murres from the German North Sea.By directly comparing predicted animal numbers and distributions in hypothetical scenarios with and without human pressures, the presented method allows us to measure and predict the effects of human activities on regional trends and large-scale reorganisation. This in turn helps us to quantify and predict the impact of planned human activities on wildlife, including in the context of the current rapid expansion of alternative energies.
The spatial reference frame of history-driven distractor suppression and target enhancement
Authors: Ilksoy Yayla A. , van Moorselaar Dirk , Los Sander A. , Theeuwes Jan 
Published: September 2024

AbstractThe world around us is inherently structured and often repetitive. Research has shown that we can implicitly learn to prioritize relevant objects and locations while filtering out distracting information, creating an integrated priority map for attention allocation. The current study examines whether these attentional biases are tied to environment-dependent (allocentric) or viewpoint-dependent (egocentric) coordinates. The search display consisted of six stimuli that were surrounded by a wheel and square frame. In two experiments, either a distractor or a target appeared more frequently in one location, leading to the suppression or enhancement of that location, respectively. Learning blocks were followed by test blocks, where the surrounding frame rotated, creating egocentric-matching and allocentric-matching locations. These experiments showed that both target and distractor learning relied on an egocentric reference frame only. In follow-up experiments, the likely target and distractor location rotated dynamically with the frame during learning. This revealed that participants can learn to enhance a likely target location in an object-centered, allocentric manner. We hypothesized that while space-based learning feeds into a priority map reliant on an egocentric reference frame, object-based learning allows for implicit prioritization of subparts of objects independent of their spatial orientation.Public significance statementAttention is shaped by past experiences, guiding us to suppress locations likely to contain distractors while enhancing locations likely to contain relevant information. This study explores how these attentional biases behave when the search environment is viewed from different perspectives. Do these biases persist relative to our viewpoint, or do they remain stable within the environment? The findings reveal that implicitly suppressed and enhanced locations are tied to viewpoint-dependent coordinates. However, attentional biases can also be formed in an object-centered manner, where a likely target location within an object is prioritized, irrespective of the orientation of that object.
MHC heterozygosity may increase subordinate but not alpha male siring success in white-faced capuchin monkeys (Cebus imitator)
Authors: Buckner Janet C. , Jack Katharine M. , Buehler Margaret , Melin Amanda D. , Schoof Valérie A. M. , Wikberg Eva C. , Hernandez Saul Cheves , Fedigan Linda M. , Lynch Jessica W. 
Published: September 2024

AbstractThe genes of the major histocompatibility complex (MHC) are vital to vertebrate immunity and may influence mate choice in several species. The extent to which the MHC influences female mate choice in primates remains poorly understood, and studies of MHC-based mate choice in platyrrhines are especially rare. White-faced capuchin monkeys (Cebus imitator) reside in multimale-multifemale groups where alpha males sire most of the offspring. In this study, we investigated the roles of social dominance, relatedness, and MHC genotypes in determining which mating pairs produced offspring in wild white-faced capuchins in the Sector Santa Rosa (SSR), Área de Conservación Guanacaste, Costa Rica. We find that males in this population do not differ significantly in MHC metrics based on their social status or siring success. Using mixed conditional logit models and generalized linear models, we find that alpha males that are distantly related to reproducing females are significantly more likely to sire offspring while MHC metrics do not predict the probability of siring offspring, or becoming an alpha male. However, we do find some evidence that subordinate males heterozygous at MHC loci sire significantly more offspring than homozygous subordinates. Further, one-sided binomial simulations reveal that offspring are more frequently heterozygous at MHC loci than expected given the gene pool. We conclude that in this population with limited genomic variation, females may preferentially mate with MHC-diverse subordinate males when related to the alpha, leading to increased probabilities of MHC-diverse offspring.
Probability of outbreaks of forest insects in Europe: a generic model calibrated on six forest insect profiles
Authors: Collot Dorian , Robinet Christelle 
Published: September 2024

AbstractInsect pests are one of the major threats to forests. Although invasive species cause more and more impacts, native species could also generate temporary very high damages. The population dynamics of insects relies on several factors, going from weather to stand conditions. Due to global change, insects could face conditions they have never encountered before, leading to unusual population outbreaks. Forest managers need to consider these possible emerging pests but predicting insect outbreaks is still very challenging. In this context, we have developed a mathematical model at the crossroad of statistical and mechanistic models to describe the likelihood of outbreaks for a set of 6 insect profiles: bark beetles, longhorn beetles, tortrix moth, other moths, aphids, and Hymenoptera. This model describes the probability of occurrence of an outbreak at a given time and at a given area, based on several conditions. It has been built and parametrized on the most documented orders of European forest pests. Parametrization for these species’ profiles can be used as a baseline to explore the risk of outbreaks for closely related pest species. We provide an illustration of the model application for the oak processionary moth,Thaumetopoea processionea, which reach epidemic levels in north-western Europe. This generic outbreak model is particularly performant to point out some years or areas as unlikely for an outbreak, and thus targets correctly factors that inhibit outbreaks. It is still at an exploratory level and should be further improved for an operational use in forest stand surveillance and management.
British Version of the Iowa Test of Consonant Perception
Authors: Guo Xiaoxuan , Benzaquén Ester , Holmes Emma , Choi Inyong , McMurray Bob , Bamiou Doris-Eva , Berger Joel I , Griffiths Timothy D 
Published: September 2024

AbstractThe Iowa Test of Consonant Perception (ITCP) is a single-word closed-set speech- in-noise test with well-balanced phonetic features that provides a reliable testing option for real-world listening.Objectives.The current study aimed to establish a UK version of the test (B-ITCP) based on the British received pronunciation.Design.We conducted a validity test with 46 participants using the B-ITCP test, a sentence-in- noise test, and audiogram.Results.The B-ITCP demonstrated excellent test-retest reliability, cross-talker validity, and good convergent validity, consistent with the US results.Conclusions.These findings suggest that B-ITCP is a reliable measure of speech-in-noise perception, to facilitate comparative or combined studies in USA and UK. All materials (application and scripts) to run or construct the B-ITCP and ITCP are freely available online.
Identification of small molecule enhancers of NK cell tumoricidal activity via a tumor microenvironment-mimicking co-culture assay
Authors: Binici Aylin , Hennes Elisabeth , Koska Sandra , Niemann Jens , Reich Alisa , Pfaff Christiane , Sievers Sonja , Kahnt Astrid S. , Thomas Dominique , Ziegler Slava , Watzl Carsten , Waldmann Herbert 
Published: September 2024

SummaryThe tumor microenvironment (TME) is a pro-cancerous niche harboring immunosuppressive factors that are secreted by cancer cells and the surrounding cancer-supportive tissue, such as kynurenine, prostaglandin E2 and transforming growth factor β (TGFβ). These factors dampen the activity of cytotoxic lymphocytes like natural killer (NK) cells, allowing evasion of immune cell-mediated killing. To identify small molecules that counteract the immunosuppressive effect of the TME and restore NK cell-mediated cytotoxicity, we developed a phenotypic co-culture assay of cancer cells and primary lymphocytes suitable for medium-throughput screening. We discovered small molecules that restore NK cell-mediated cytotoxicity through diverse mechanisms. The potent TGFβ type I receptor (TGFβR-1) inhibitor, RepSox, stood out as superior to other TGFβR-1 inhibitors due to its ability to abolish the effects of both inhibitory factors used in our setup. This mode of action goes beyond TGFβR-1 inhibition and is related to the simultaneous abrogation of cyclooxygenase 1 (COX1) activity.
Myosin XVA isoforms participate in the mechanotransduction-dependent remodeling of the actin cytoskeleton in auditory stereocilia
Authors: López-Porras Ana I. , Kruse Ava M. , McClendon Mark T. , Vélez-Ortega A Catalina 
Published: September 2024

AbstractAuditory hair cells form precise and sensitive staircase-like actin protrusions known as stereocilia. These specialized microvilli detect deflections induced by sound through the activation of mechano-electrical transduction (MET) channels located at their tips. At rest, a small MET channel current results in a constant calcium influx, which regulates the morphology of the actin cytoskeleton in the shorter ‘transducing’ stereocilia. However, the molecular mechanisms involved in this novel type of activity-driven plasticity in the stereocilium cytoskeleton are currently unknown. Here, we tested the contribution of myosin XVA (MYO15A) isoforms. We used electron microscopy to evaluate morphological changes in the cytoskeleton of auditory hair cell stereocilia after the pharmacological blockage of resting MET currents in cochlear explants from mice that lacked one or all isoforms of MYO15A. Hair cells lacking functional MYO15A isoforms did not exhibit MET-dependent remodeling in their stereocilia cytoskeleton. In contrast, hair cells that only lack the long isoform of MYO15A exhibited increased MET-dependent stereocilia remodeling, including remodeling in stereocilia from the tallest ‘non-transducing’ row of the bundle. We conclude that MYO15A isoforms not only enable but also fine-tune the MET-dependent remodeling of the actin cytoskeleton in transducing stereocilia and contribute to the stability of the tallest row.