bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stressful times in a climate crisis: how will aphids respond to more frequent drought?
Authors: Leybourne Daniel Joseph , Preedy Katharine F , Valentine Tracy A , Bos Jorunn IB , Karley Alison J 
Published: June 2020

AbstractAimAphids are abundant in natural and managed vegetation, supporting a diverse community of organisms and causing damage to agricultural crops. Using a meta-analysis approach, we aimed to advance understanding of how increased drought incidence will affect this ecologically and economically important insect group, and to characterise the underlying mechanisms.LocationGlobal.Time period1958–2020.Major taxa studiedAphids.MethodsWe used qualitative and quantitative synthesis techniques to determine whether drought stress has a negative, positive, or null effect on aphid fitness. We examined these effects in relation to 1) aphid biology, 2) the aphid-plant. species combination. We compiled two datasets: 1) a “global” dataset (n = 55 from 55 published studies) comprising one pooled effect size per study, and 2) an “expanded” dataset (n = 93) containing multiple datapoints per study, separated into different measures of aphid fitness but pooled across aphid-plant combinations. Where reported, we extracted data on the effect of drought on plant vigour, and plant tissue concentrations of nutrients and defensive compounds, to capture the potential causes of aphid responses.ResultsAcross all studies (“global” dataset), drought stress had a negative effect on aphid fitness: Hedges’ g = −0.57; 95% confidence interval (CI95) = ±0.31. The “expanded” dataset indicated that, on average, drought stress reduced aphid fecundity (g = − 0.98; CI95 = ±0.50) and increased development time (g = 1.13; CI95 = ±1.02). Furthermore, drought stress had a negative impact on plant vigour (g = −7.06; CI95 = ±2.86) and increased plant concentrations of defensive chemicals (g = 3.14; CI95 = ±3.14).Main conclusionsAphid fitness is typically reduced under drought, associated with reduced plant vigour and increased chemical defence in drought-stressed plants. We propose a conceptual model to predict drought effects on aphid fitness in relation to plant vigour and defence.
Neural Flip-Flops II: The Role of Cascaded Oscillators in Short-Term Memory, EEGs, and Epilepsy
Authors: Yoder Lane 
Published: June 2020

AbstractBy enabling many brain structures’ state changes, the explicit cascaded oscillators proposed here can generate the rhythmic neural activity found in EEGs. The function of such synchronization in information processing systems is timing error avoidance. The narrow requirement for the oscillator input pulse duration suggests a possible relationship to the abnormal electrical activity characteristic of epileptic seizures. Together, flip-flops and synchronization by oscillators suggest a resolution to the longstanding controversy of whether short-term memory depends on neurons firing persistently or in brief, coordinated bursts.The proposed cascade of oscillators consists of a ring oscillator and four toggle flip-flops connected in sequence. The novel oscillator and toggle are composed of three and six neurons, respectively. Their operation depends only on minimal properties of excitatory and inhibitory inputs.The hypothesis that cascaded oscillators produce EEG phenomena implies that the distribution of EEG frequencies is determined by just two parameters, the mean (μd) and standard deviation (σd) of the delay times of neurons that make up the initial oscillators in the cascades. For example, if μdand σdare measured in milliseconds, the boundary separating the alpha and beta frequency bands isWith 4 and 1.5 ms being the best available estimates for μdand σd, respectively, this predicted boundary value is 14.9 Hz, which is within the range of commonly cited estimates obtained empirically from EEGs. Four and 1.5 ms also accurately predict the peaks and other boundaries of the five major EEG frequency bands.Significance statementThe neuronal model proposed here implies several major aspects of electroencephalography. The matched periods of neural activity found in EEGs, and their wide distribution across the brain and across the frequency spectrum, follow from selective pressure for a biologically useful function: timing error avoidance for diverse brain functions in the trade-off between speed and accuracy. This activity can be achieved with a simple organization of synaptic connections and minimal neuron capabilities of excitation and inhibition. The multimodal distribution of EEG frequencies is an explicit function of the mean and variance of neuron delay times. The model suggests a relationship to epileptic seizures and a resolution to a short-term memory controversy. Two EEG characteristics make other models implausible.
Toll like Receptor signalling byPrevotella histicolaactivates alternative NF-κB signalling in Cystic Fibrosis bronchial epithelial cells compared toP.aeruginosa
Authors: Bertelsen A. , Elborn J.S. , Schock B.C. 
Published: June 2020

AbstractCystic Fibrosis (CF), caused by mutations affecting theCFTRgene, is characterised by viscid secretions in multiple organ systems. CF airways contain thick mucus, creating a gradient of hypoxia, which promotes the establishment of polymicrobial infection. Such inflammation predisposes to further infection, a self-perpetuating cycle in mediated by NF-κB. Anaerobic Gram-negativePrevotellaspp. are found in sputum from healthy volunteers and CF patients and in CF lungs correlate with reduced levels of inflammation.Prevotella histicola (P.histicola)can suppress murine lung inflammation, however, no studies have examined the role ofP.histicolain modulating infection and inflammation in the CF airways. We investigated innate immune signalling and NF-kB activation in CF epithelial cells CFBE41o-in response to clinical stains ofP.histicolaandPseudomonas aeruginosa(P.aeruginosa). Toll-Like Receptor (TLR) expressing HEK-293 cells and siRNA assays for TLRs and IKKa were used to confirm signalling pathways.We show thatP.histicolainfection activated the alternative NF-kB signalling pathway in CF bronchial epithelial cells inducing HIF-1α protein. TLR5 signalling was responsible for the induction of the alternative NF-kB pathway through phosphorylation of IKKα. The induction of transcription factor HIF-1α was inversely associated with the induction of the alternative NF-kB pathway and knockdown of IKKα partially restored canonical NF-kB activation in response toP.histicola.This study demonstrates that different bacterial species in the respiratory microbiome can contribute differently to inflammation, either by activating inflammatory cascades (P.aeruginosa) or by muting the inflammatory response by modulating similar or related pathways (P.histicola). Further work is required to assess the complex interactions of the lung microbiome in response to mixed bacterial infections and their effects in people with CF.
Shared and unique brain network features predict cognition, personality and mental health in childhood
Authors: Chen Jianzhong , Tam Angela , Kebets Valeria , Orban Csaba , Ooi Leon Qi Rong , Marek Scott , Dosenbach Nico , Eickhoff Simon , Bzdok Danilo , Holmes Avram J , Thomas Yeo B.T. 
Published: June 2020

AbstractThe manner through which individual differences in brain network organization track population-level behavioral variability is a fundamental question in systems neuroscience. Recent work suggests that resting-state and task-state functional connectivity can predict specific traits at the individual level. However, the focus of most studies on single behavioral traits has come at the expense of capturing broader relationships across behaviors. Here, we utilized a large-scale dataset of 1858 typically developing children to estimate whole-brain functional network organization that is predictive of individual differences in cognition, impulsivity-related personality, and mental health during rest and task states. Predictive network features were distinct across the broad behavioral domains: cognition, personality and mental health. On the other hand, traits within each behavioral domain were predicted by highly similar network features. This is surprising given decades of research emphasizing that distinct brain networks support different mental processes. Although tasks are known to modulate the functional connectome, we found that predictive network features were similar between resting and task states. Overall, our findings reveal shared brain network features that account for individual variation within broad domains of behavior in childhood, yet are unique to different behavioral domains.
Hippocampal-Prefrontal Interactions during Spatial Decision-Making
Authors: Tavares Lucas CS , Tort Adriano BL 
Published: June 2020

AbstractThe hippocampus has been linked to memory encoding and spatial navigation, while the prefrontal cortex is associated with cognitive functions such as decision-making. These regions are hypothesized to communicate in tasks that demand both spatial navigation and decision-making processes. However, the electrophysiological signatures underlying this communication remain to be better elucidated. To investigate the dynamics of the hippocampal-prefrontal interactions, we have analyzed their local field potentials and spiking activity recorded from rats performing an odor-cued spatial alternation task in an 8-shaped maze. We found that the phase coherence of theta peaked around the choice point area of the maze. Moreover, Granger causality revealed a hippocampus->prefrontal cortex directionality of information flow at theta frequency, peaking at starting areas of the maze, and on the reverse direction at delta frequency, peaking near the turn onset. Additionally, the patterns of phase-amplitude cross-frequency coupling within and between the regions also showed spatial selectivity, and a new method revealed that hippocampal theta and prefrontal delta modulated not only gamma amplitude but also inter-regional gamma synchrony. Lastly, we found that the theta rhythm dynamically modulated neurons in both regions, with the highest modulation at the choice area; interestingly, prefrontal cortex neurons were more strongly modulated by the hippocampal theta rhythm than by their local field rhythm. In all, our results reveal maximum electrophysiological interactions between the hippocampus and the prefrontal cortex near the decision-making period of the spatial alternation task. These results corroborate the hypothesis that a dynamic interplay between these regions takes place during spatial decisions.
Evaluation of origin of driving force for loop formation in a chromatin fiber
Authors: Yokota Hiroshi , Tachikawa Masashi 
Published: June 2020

AbstractChromosome condensation results from the formation of consecutive chromatin loops in which excluded volume interactions lead to chromosome stiffness. Formation of chromatin loops requires energy, but the source of such energy remains controversial. Here, we quantified the energy balance during chromatin loop formation by calculating the free energies of unlooped and looped chromatins using a lattice model of polymer chains. We tested two hypothetical energy sources: thermal fluctuation and ATP hydrolysis. We evaluated the free energy difference of the chain loop model without accounting for excluded volume interactions (phantom loop model), and integrated those interactions by employing the mean-field theory (interacting loop model), where we introduced the parameter of excluded volume interaction within a single loopvex. Using our strategy, we confirmed that loop-growth efficiency calculated by the phantom loop model is too high to explain the experimental data. Comparing loop-growth efficiencies for each energy source, and using the interacting loop model, we found that excluded volume interaction is essential for chromatin’s resistance to looping, regardless of the energy source. We predict that the quantitative measurement ofvexdetermines which energy source is more plausible.Author summaryBefore mitosis, the chromatin fibers of eukaryotic cells fold into consecutive loop structures and condense into rod-like chromosomes. Chromosome stiffness results from the interaction of the excluded volume between chromatin loops. The driving force of loop formation and growth is still controversial, despite the many efforts undertaken to clarify it. Two possible origins can be considered: the energy provided by thermal fluctuations or the energy gained from ATP hydrolysis. To discuss the validity of each, we constructed a theoretical model of chromatin loop formation that includes excluded volume interactions. Using this model, we calculated the free energy difference before and after chromatin loop formation, which corresponds to the energy that fuels chromatin looping. By comparing the results for each energy source, we conclude that the spatial distribution of chromatin loops should be relatively wide, given the large excluded volume interaction within a single loop, irrespective of which energy source is valid. Moreover, our results imply that intra-loop interactions are key to determine the driving force of chromatin loop formation.
Transgenerational fitness effects of lifespan extension by dietary restriction inCaenorhabditis elegans
Authors: Ivimey-Cook Edward R. , Sales Kris , Carlsson Hanne , Immler Simone , Chapman Tracey , Maklakov Alexei A. 
Published: June 2020

AbstractDietary restriction increases lifespan in a broad variety of organisms and improves health in humans. However, long-term transgenerational consequences of dietary interventions are poorly understood. Here we investigated the effect of dietary restriction by temporary fasting (TF) on mortality risk, age-specific reproduction and fitness across three generations of descendants inC. elegans. We show that while TF robustly reduces mortality risk and improves late-life reproduction in the parental generation (P0), it has a wide range of both positive and deleterious effects on future generations (F1-F3). Remarkably, great-grandparental exposure to TF in early-life reduces fitness and increases mortality risk of F3descendants to such an extent that TF no longer promotes a lifespan extension. These findings reveal that transgenerational trade-offs accompany the instant benefits of dietary restriction underscoring the need to consider fitness of future generations in pursuit of healthy ageing.
Consistent marine biogeographic boundaries across the tree of life despite centuries of human impacts
Authors: Holman Luke E. , de Bruyn Mark , Creer Simon , Carvalho Gary , Robidart Julie , Rius Marc 
Published: June 2020

AbstractOver millennia, ecological and evolutionary mechanisms have shaped macroecological distributions across the tree of life. Research describing patterns of regional and global biogeography has traditionally focussed on the study of conspicuous species. Consequently, there is limited understanding of cross-phyla biogeographic structuring, and an escalating need to understand the macroecology of both microscopic and macroscopic organisms. Here we used environmental DNA (eDNA) metabarcoding to explore the biodiversity of marine metazoans, micro-eukaryotes and prokaryotes along an extensive and highly heterogeneous coastline. Our results showed remarkably consistent biogeographic structure across the kingdoms of life, which were underpinned by environmental and anthropogenic influence. Additionally, metazoan communities displayed biographic patterns that suggest regional biotic homogenisation of conspicuous species. Against the backdrop of global pervasive anthropogenic environmental change, our work highlights the importance of considering multiple domains of life to understand the maintenance and drivers of marine biodiversity across broad taxonomic, ecological and geographical scales.
Wolbachia-conferredantiviral protection is determined by developmental temperature
Authors: Chrostek Ewa , Martins Nelson , Marialva Marta S , Teixeira Luis 
Published: June 2020

AbstractWolbachiais a maternally transmitted bacterium widespread in arthropods and filarial nematodes, and confers strong antiviral protection inDrosophila melanogasterand other insects.Wolbachia-transinfectedAedes aegyptiare currently being deployed to fight transmission of dengue and Zika viruses. However, the mechanism of antiviral protection and factors influencing it are still not fully understood. Here we show that temperature modulatesWolbachia-conferred protection inDrosophila melanogaster. Temperature after infection directly impactsDrosophilaC virus replication and modulatesWolbachiaprotection. At higher temperatures virus proliferates more and is more lethal, whileWolbachiaconfers lower protection. Strikingly, host developmental temperature is a determinant ofWolbachia-conferred antiviral protection. While there is a strong protection when flies are raised from egg to adult at 25°C, the protection is highly reduced or completely abolished when flies develop at 18°C. However,Wolbachia-induced changes during development are not sufficient to limit virus-induced mortality, asWolbachiais still required to be present in adults at the time of infection. This developmental effect is general, since it was present in different host genotypes,Wolbachiavariants and upon infection with different viruses. Overall, we show thatWolbachia-conferred antiviral protection is temperature dependent, being present or absent depending on the environmental conditions. This interaction likely impactsWolbachia-host interactions in nature and, as a result, frequencies of host and symbionts in different climates. Dependence ofWolbachia-mediated pathogen blocking on developmental temperature could be used to dissect the mechanistic bases of protection and should be considered by programmes deployingWolbachiaas an antiviral agent in the field.Significance StatementInsects are often infected with beneficial intracellular bacteria. The bacteriumWolbachiacan protect insects from pathogenic viruses. This effect can be used to prevent transmission of dengue and Zika viruses byWolbachia-infected mosquitoes. To deployWolbachiain the field successfully and understand the biology of insects in the wild we need to discover which factors affectWolbachia-conferred antiviral protection. Here we show that the temperature in which insects develop from eggs to adults can determine presence or absence of antiviral protection. The environment, therefore, influences this insect-bacterium interaction. Our work may help to provide insights into the mechanism of viral blocking byWolbachiaand inform programs usingWolbachiain mosquito-borne disease control.
Comparative transcriptome analyses reveal genes associated with SARS-CoV-2 infection of human lung epithelial cells
Authors: Chandrashekar Darshan S. , Manne Upender , Varambally Sooryanarayana 
Published: June 2020

AbstractUnderstanding the molecular mechanism of SARS-CoV-2 infection (the cause of COVID-19) is a scientific priority for 2020. Various research groups are working toward development of vaccines and drugs, and many have published genomic and transcriptomic data related to this viral infection. The power inherent in publicly available data can be demonstrated via comparative transcriptome analyses. In the current study, we collected high-throughput gene expression data related to human lung epithelial cells infected with SARS-CoV-2 or other respiratory viruses (SARS, H1N1, rhinovirus, avian influenza, and Dhori) and compared the effect of these viruses on the human transcriptome. The analyses identified fifteen genes specifically expressed in cells transfected with SARS-CoV-2; these includedCSF2(colony-stimulating factor 2) andS100A8andS100A9(calcium-binding proteins), all of which are involved in lung/respiratory disorders. The analyses showed that genes involved in the Type1 interferon signaling pathway and the apoptosis process are commonly altered by infection of SARS-CoV-2 and influenza viruses. Furthermore, results of protein-protein interaction analyses were consistent with a functional role of CSF2 in COVID-19 disease. In conclusion, our analysis has revealed cellular genes associated with SARS-CoV-2 infection of the human lung epithelium; these are potential therapeutic targets.
Synthesis of higher order feature codes through stimulus-specific supra-linear summation
Authors: Lyall Evan H. , Mossing Daniel P. , Pluta Scott R. , Dudai Amir , Adesnik Hillel 
Published: June 2020

AbstractHow cortical circuits build representations of complex objects is poorly understood. The massive dimensional expansion from the thalamus to the primary sensory cortex may enable sparse, comprehensive representations of higher order features to facilitate object identification. To generate such a code, cortical neurons must integrate broadly over space, yet simultaneously obtain sharp tuning to specific stimulus features. The logic of cortical integration that may synthesize such a sparse, high dimensional code for complex features is not known. To address this question, we probed the integration and population coding of higher order stimuli in the somatosensory and visual cortices of awake mice using two-photon calcium imaging across cortical layers. We found that somatosensory and visual cortical neurons sum highly specific combinations of sensory inputs supra-linearly, but integrate other inputs sub-linearly, leading to selective responses to higher order features. This integrative process generates a sparse, but comprehensive code for complex stimuli from the earliest stages of cortical processing. These results from multiple sensory modalities imply that input-specific supra-linear summation may represent a widespread cortical mechanism for the synthesis of higher order feature codes. This new mechanism may explain how the brain exploits the thalamocortical expansion of dimensionality to encode arbitrary complex features of sensory stimuli.
Intestinal receptor of SARS-CoV-2 in inflamed IBD tissue is downregulated by HNF4A in ileum and upregulated by interferon regulating factors in colon
Authors: Verstockt Bram , Verstockt Sare , Rahiman Saeed Abdu , Ke Bo-jun , Arnauts Kaline , Cleynen Isabelle , Sabino João , Ferrante Marc , Matteoli Gianluca , Vermeire Séverine 
Published: June 2020

ABSTRACTPatients with IBD are considered immunosuppressed, but do not seem more vulnerable for COVID-19. Nevertheless, intestinal inflammation has shown an important risk factor for SARS-CoV-2 infection and prognosis. Therefore, we investigated the effect of intestinal inflammation on the viral intestinal entry mechanisms, includingACE2, in IBD.We collected (un)inflamed mucosal biopsies from CD (n=193) and UC (n=158) patients, and 51 matched non-IBD controls for RNA sequencing, differential gene expression and co-expression analysis. Organoids from UC patients were subjected to an inflammatory mix and processed for RNA sequencing. Transmural ileal biopsies were processed for single-cell (sc) sequencing. Publicly available colonic sc-RNA sequencing data, and microarrays from tissue pre/post anti-TNF therapy, were analyzed.In inflamed CD ileum,ACE2was significantly decreased compared to control ileum (p=4.6E-07), whereas colonicACE2expression was higher in inflamed colon of CD/UC compared to control (p=8.3E-03; p=1.9E-03). Sc-RNA sequencing confirmed thisACE2dysregulation, and exclusive epithelialACE2expression. Network analyses highlightedHNF4Aas key regulator of ilealACE2, while pro-inflammatory cytokines and interferon regulating factors regulated colonicACE2.Inflammatory stimuli upregulatedACE2in UC organoids (p=1.7E-02), not in non-IBD controls (p=9.1E-01). Anti-TNF therapy restored colonicACE2dysregulation in responders.Intestinal inflammation alters SARS-CoV-2 coreceptors in the intestine, with opposing effects in ileum and colon.HNF4A, an IBD susceptibility gene, is an important upstream regulator ofACE2in ileum, whereas interferon signaling dominates in colon. Our data support the importance of adequate control of IBD in order to reduce risk of (complicated) COVID-19.