bluuebunny/crossref_metadata_2025_split huggingface dataset:
Larval density in the invasive Drosophila suzukii: immediate and delayed effects on life-history traits
Authors: Reyes-Ramírez Alicia , Belgaidi Zaïnab , Gibert Patricia , Pommier Thomas , Siberchicot Aurélie , Mouton Laurence , Desouhant Emmanuel 
Published: October 2022

AbstractThe immediate and delayed effects of density are key in determining population dynamics, since they can positively or negatively affect the fitness of individuals. These effects have great relevance for polyphagous insects for which immature stages develop within a single site of finite feeding resources. Drosophila suzukii is a crop pest that induces severe economic losses for agricultural production, however little is known about the effects of density on its life-history traits. In the present study, we (i) investigated the egg distribution resulting from females’ egg-laying strategy and (ii) tested the immediate and delayed effects of larval density on emergence rate, development time, sex ratio of offspring, fecundity and adult size (a range of 1 to 50 larvae was used). We showed that most of fruits contain several eggs and aggregate of eggs of high density can be found in some fruits. This high density has no immediate effects on the emergence rate, but has effect on larval developmental time. This trait was involved in a trade-off with adult life-history traits: the larval development was reduced as larval density increased, but smaller and less fertile adults were produced. Our results should help to better understand the population dynamics of this species and to develop more successful control programs.
The mesoglea buffers the physico-chemical microenvironment of photosymbionts in the upside-down jellyfishCassiopeasp
Authors: Lyndby Niclas Heidelberg , Murray Margaret Caitlyn , Trampe Erik , Meibom Anders , Kühl Michael 
Published: October 2022

AbstractThe jellyfishCassiopeahas a conspicuous lifestyle, positioning itself upside-down on sediments in shallow waters thereby exposing its photosynthetic endosymbionts (Symbiodiniaceae) to light. Several studies have shown how the photosymbionts benefit the jellyfish host in terms of nutrition and O2availability, but little is known about the internal physico-chemical microenvironment ofCassiopeaduring light-dark periods. Here, we used fiber-optic sensors to investigate how light is modulated at the water-tissue interface ofCassiopeasp. and how light is scattered inside host tissue. We additionally used electrochemical and fiber-optic microsensors to investigate the dynamics of O2and pH in response to changes in the light availability in intact living specimens ofCassiopeasp.Mapping of photon scalar irradiance revealed a distinct spatial heterogeneity over different anatomical structures of the host, where oral arms and the manubrium had overall higher light availability, while shaded parts underneath the oral arms and the bell had less light available. White host pigmentation, especially in the bell tissue, showed higher light availability relative to similar bell tissue without white pigmentation. Microprofiles of scalar irradiance into white pigmented bell tissue showed intense light scattering and enhanced light penetration, while light was rapidly attenuated over the upper 0.5 mm in tissue with symbionts only.Depth profiles of O2concentration into bell tissue of intact, healthy/living jellyfish showed increasing concentration with depth into the mesoglea, with no apparent saturation point during light periods. O2was slowly depleted in the mesoglea in darkness, and O2concentration remained higher than ambient water in large (> 6 cm diameter) individuals, even after 50 min in darkness. Light-dark shifts in large medusae showed that the mesoglea slowly turns from a net sink during photoperiods into a net source of O2during darkness. In contrast, small medusae showed a more dramatic change in O2concentration, with rapid O2buildup/consumption in response to light-dark shifts; in a manner similar to corals. These effects on O2production/consumption were also reflected in moderate pH fluctuations within the mesoglea. The mesoglea thus buffers O2and pH dynamics during dark-periods.
Impact of Holocene environmental change on the evolutionary ecology of an Arctic top predator
Authors: Westbury Michael V. , Brown Stuart C. , Lorenzen Julie , O’Neill Stuart , Scott Michael B. , McCuaig Julia , Cheung Christina , Armstrong Edward , Valdes Paul J. , Samaniego Castruita Jose Alfredo , Cabrera Andrea A. , Blom Stine Keibel , Dietz Rune , Sonne Christian , Louis Marie , Galatius Anders , Fordham Damien A. , Ribeiro Sofia , Szpak Paul , Lorenzen Eline D. 
Published: October 2022

AbstractThe Arctic is among the most climatically sensitive environments on Earth, and the disappearance of multiyear sea-ice in the Arctic Ocean is predicted within decades. As apex predators, polar bears are sentinel species for addressing the impact of environmental variability on Arctic marine ecosystems. By integrating genomics, isotopic analysis, morphometrics, and ecological modelling, we investigate how Holocene environmental changes affected the evolutionary ecology of polar bears around Greenland. We show that throughout the last ∼11,000 years, Greenlandic polar bears have been heavily influenced by changes in sea-surface temperature (SST) and sea-ice cover. Most notable are major reductions in effective population size at the beginning of the Holocene and during the Holocene Thermal Maximum ∼6 kya, which coincide with increases in annual mean SST, reduction in sea-ice covers, declines in suitable habitat, and shifts in suitable habitat northwards. Furthermore, we show how individuals sampled from west and east Greenland are genetically, morphologically, and ecologically distinct. We find bears sampled in west Greenland to be larger, more genetically diverse and have diets dominated by ringed seals, whereas bears from east Greenland are smaller and less diverse with more varied diets, putatively driven by regional biotic differences. Taken together, we provide novel insights into the vulnerability of polar bears to environmental change, and how the Arctic marine ecosystem plays a vital role in shaping the evolutionary and ecological trajectories of its inhabitants.TeaserMultivariate investigations of the environment’s role in the evolutionary ecology of Greenlandic polar bears.
Toward an Over-parameterized Direct-Fit Model of Visual Perception
Authors: Li Xin 
Published: October 2022

AbstractIn this paper, we revisit the problem of computational modeling of simple and complex cells for an over-parameterized and direct-fit model of visual perception. Unlike conventional wisdom, we highlight the difference in parallel and sequential binding mechanisms between simple and complex cells. A new proposal for abstracting them into space partitioning and composition is developed as the foundation of our new hierarchical construction. Our construction can be interpreted as a product topology-based generalization of the existing k-d tree, making it suitable for brute-force direct-fit in a high-dimensional space. The constructed model has been applied to several classical experiments in neuroscience and psychology. We provide an anti-sparse coding interpretation of the constructed vision model and show how it leads to a dynamic programming (DP)-like approximate nearest-neighbor search based on 𝓁∞-optimization. We also briefly discuss two possible implementations based on asymmetrical (decoder matters more) auto-encoder and spiking neural networks (SNN), respectively.
Development of Enterovirus anti-viral agents that target the viral 2C protein
Authors: Kejriwal Rishabh , Evans Tristan , Calabrese Joshua , Swistak Lea , Alexandrescu Lauren , Cohen Michelle , Rahman Nahian , Henriksen Niel , Dash Radha Charan , Hadden M. Kyle , Stonehouse Nicola J. , Rowlands David J. , Kingston Natalie J. , Hartnoll Madeline , Dobson Samuel J. , White Simon J. 
Published: October 2022

AbstractThe enterovirus (EV) genus includes a number of important human and animal pathogens. EV-A71, EV-D68, poliovirus (PV), and coxsackievirus (CV) outbreaks have affected millions worldwide causing a range of upper respiratory, skin, neuromuscular diseases, including acute flaccid myelitis, and hand-foot-and-mouth disease. There are no FDA-approved anti-viral therapeutics for these enteroviruses. In this study, we describe novel broad spectrum anti-viral compounds targeting the conserved non-structural viral protein 2C that have low micro-molar to nanomolar IC50 values. The selection of resistant mutants resulted in amino acid substitutions in the viral capsid protein, implying a role for 2C in capsid assembly, as has been seen in PV. The assembly and encapsidation stages of the viral life cycle are not fully understood and the inhibitors reported here could be useful probes in understanding these processes.
Mucins shed from the laminated layer in cystic echinococcosis are captured by Kupffer cells via the lectin receptor Clec4F
Authors: Barrios Anabella A. , Mouhape Camila , Schreiber Leonard , Zhang Linyun , Nell Juliane , Suárez-Martins Mariana , Schlapp Geraldine , Meikle María Noel , Mulet Ana Paula , Hsu Tsui-Ling , Hsieh Shie-Liang , Mourglia-Ettlin Gustavo , González Carlos , Crispo Martina , Barth Thomas F. E. , Casaravilla Cecilia , Jenkins Stephen J. , Díaz Álvaro 
Published: October 2022

AbstractCystic echinococcosis is caused by the larval stages (hydatids) of cestode parasites belonging to the species clusterEchinococcus granulosus sensu lato, withE. granulosus sensu strictobeing the main infecting species. Hydatids are bladder-like structures that attain large sizes within various internal organs of livestock ungulates and humans. Hydatids are protected by the massive acellular laminated layer (LL), composed mainly by mucins. Parasite growth requires LL turnover, and abundant LL-derived particles are found at infection sites in infected humans, raising the question of how LL materials are dealt with by the hosts. In this article, we show thatE. granulosus sensu strictoLL mucins injected into mice are taken up by Kupffer cells, the liver macrophages exposed to the vascular space. This uptake is largely dependent on the intact mucin glycans and on Clec4F, a C-type lectin receptor which in rodents is selectively expressed in Kupffer cells. This uptake mechanism operates on mucins injected both in soluble form i.v. and in particulate form i.p. In mice harbouring intraperitoneal infections by the same species, LL mucins were found essentially only at the infection site and in the liver, where they were taken up by Kupffer cells via Clec4F. Therefore, shed LL materials circulate in the host and Kupffer cells can act as a sink for these materials even when the parasite grows in sites other than the liver.
Escalation of alcohol intake is associated with regionally decreased insular cortex activity but not associated with changes in taste quality
Authors: Mukherjee A , Paladino MS , McSain SL , Gilles-Thomas EA , Lichte DD , Camadine RD , Willock S , Sontate K , Honeycutt SC , Loney GC 
Published: October 2022

AbstractBackgroundIntermittent access to ethanol (EtOH) drives persistent escalation of intake and rapid transition from moderate to compulsive-like drinking. Intermittent EtOH drinking may facilitate escalation in part by altering aversion-sensitive neural substrates, such as the insular cortex (IC), thus driving greater approach toward stimuli previously treated as aversive.MethodsWe conducted a series of experiments in rats to examine behavioral and neural responses associated with escalation of EtOH intake. First, taste reactivity analyses quantified the degree that intermittent brief-access ethanol exposure (BAEE) alters sensitivity to the aversive properties of EtOH. Next, we determined whether pharmacological IC inhibition facilitated EtOH escalation. Finally, given that IC is primary gustatory cortex, we employed psychophysical paradigms to assess whether escalation of EtOH intake induced changes in EtOH taste. These paradigms measured changes in sensitivity to the intensity of EtOH taste and whether escalation shifts the salient taste quality of EtOH by measuring the degree that the taste of EtOH generalized to a sucrose-like (‘sweet’) or quinine-like (‘bitter’) percept.ResultsWe found a near complete loss of aversive oromotor responses in EtOH-exposed relative to -naïve rats. Additionally, we observed significantly reduced expression of EtOH-induced c-Fosexpression in the posterior IC in exposed rats relative to naïve rats. Inhibition of the IC resulted in a modest, but statistically reliable increase in acceptance of higher EtOH concentrations in naïve rats. Finally, we found no evidence of changes in the psychophysical assessment of the taste of EtOH in exposed, relative to naïve, rats.ConclusionsOur results demonstrate that neural activity within the IC adapts following escalation of EtOH intake in a manner that correlates with reduced sensitivity to the aversive hedonic properties of EtOH. These data further establish that IC may be driving exposure-induced escalations in EtOH intake and directly contributing to development of compulsive-like EtOH drinking.
Towards Greater Neuroimaging Classification Transparency via the Integration of Explainability Methods and Confidence Estimation Approaches
Authors: Ellis Charles A. , Miller Robyn L. , Calhoun Vince D. 
Published: October 2022

AbstractThe field of neuroimaging has increasingly sought to develop artificial intelligence-based models for neurological and neuropsychiatric disorder automated diagnosis and clinical decision support. However, if these models are to be implemented in a clinical setting, transparency will be vital. Two aspects of transparency are (1) confidence estimation and (2) explainability. Confidence estimation approaches indicate confidence in individual predictions. Explainability methods give insight into the importance of features to model predictions. In this study, we integrate confidence estimation and explainability approaches for the first time. We demonstrate their viability for schizophrenia diagnosis using resting state functional magnetic resonance imaging (rs-fMRI) dynamic functional network connectivity (dFNC) data. We compare two confidence estimation approaches: Monte Carlo dropout (MCD) and MC batch normalization (MCBN). We combine them with two gradient-based explainability approaches, saliency and layer-wise relevance propagation (LRP), and examine their effects upon explanations. We find that MCD often adversely affects model gradients, making it ill-suited for integration with gradient-based explainability methods. In contrast, MCBN does not affect model gradients. Additionally, we find many participant-level differences between regular explanations and the distributions of explanations for combined explainability and confidence estimation approaches. This suggests that a similar confidence estimation approach used in a clinical context with explanations only output for the regular model would likely not yield adequate explanations. We hope that our findings will provide a starting point for the integration of the two fields, provide useful guidance for future studies, and accelerate the development of transparent neuroimaging clinical decision support systems.
Intracellular reactive oxygen species (intraROS)-aided localized cell death contributing to immune responses against wheat powdery mildew pathogen
Authors: Li Yinghui , Roychowdhury Rajib , Govta Liubov , Jaiwar Samidha , Wei Zhen-Zhen , Shams Imad , Fahima Tzion 
Published: October 2022

ABSTRACTReactive oxygen species (ROS) and hypersensitive response (HR) mediated cell death have long been known to play critical roles in plant immunity to pathogens. Wheat powdery mildew caused byBlumeria graminisf. sp.tritici(Bgt) is a destructive wheat pathogen. Here, we report a quantitative analysis of the proportion of infected cells with local apoplastic ROS (apoROS) versus intracellular ROS (intraROS) accumulation in various wheat accessions that carry different disease resistance genes (R genes), at a series of time points post-infection. The proportion of apoROS accumulation was 70-80% of the infected wheat cells detected in both compatible and incompatible host-pathogen interactions. However, intensive intraROS accumulation followed by localized cell death responses were detected in 11-15% of the infected wheat cells, mainly in wheat lines that carried nucleotide-binding leucine-rich repeat (NLR) R genes (e.g.Pm3F, Pm41, TdPm60, MIIW72, Pm69). The lines that carry unconventional R genes,Pm24(Wheat Tandem Kinase 3) andpm42(a recessive R gene), showed very less intraROS responses, while 11% ofPm24line infected epidermis cells still showed HR cell death, suggesting that different resistance pathways are activated there. Here, we also demonstrated that ROS could not act as a strong systemic signal for inducing high resistance toBgtin wheat, although it induced the expression of pathogenesis-related (PR)genes. These results provide new insights on the contribution of intraROS and localized cell death to immune responses against wheat powdery mildew.
A single amino acid change drives left- right asymmetry in Bilateria
Authors: Truchado-García Marta , Perry Kimberly J. , Cavodeassi Florencia , Kenny Nathan J. , Henry Jonathan Q. , Grande Cristina 
Published: October 2022

ABSTRACTAsymmetries are essential for proper organization and function of organ systems. Genetic studies in deuterostomes have shown signaling through the Nodal/Smad2 pathway plays a key, conserved role in the establishment of body asymmetries. While Nodal signaling is required for the establishment of left-right asymmetry (LRA) across bilaterian species, little is known about the regulation of Nodal signaling in spiralians. Here, we identified orthologs of the egf-cfc gene, a master regulator of the Nodal pathway in vertebrates, in several invertebrate species, the first evidence of its presence in non-deuterostomes. Our functional experiments indicate that despite being present, egf-cfc does not play a role in the establishment LRA in gastropods. However, experiments in zebrafish suggest that a single amino acid mutation in the egf-cfc gene in the deuterostome common ancestor was the necessary step in inducing a gain-of-function in LRA regulation. This study shows that that the egf-cfc gene likely appeared in the bilaterian stem lineage, before being adopted as a master mechanism to regulate the Nodal pathway and the establishment of LRA in deuterostomes.
Improving polygenic risk prediction in admixed populations by explicitly modeling ancestral-specific effects via GAUDI
Authors: Sun Quan , Rowland Bryce T. , Chen Jiawen , Mikhaylova Anna V. , Avery Christy , Peters Ulrike , Lundin Jessica , Matise Tara , Buyske Steve , Tao Ran , Mathias Rasika A. , Reiner Alexander P. , Auer Paul L. , Cox Nancy J. , Kooperberg Charles , Thornton Timothy A. , Raffield Laura M. , Li Yun 
Published: October 2022

AbstractPolygenic risk scores (PRS) have shown successes in clinics, but most PRS methods have focused only on individuals with one primary continental ancestry, thus poorly accommodating recently-admixed individuals. Here, we develop GAUDI, a novel penalized-regression-based method specifically designed for admixed individuals by explicitly modeling ancestry-specific effects and jointly estimating ancestry-shared effects. We demonstrate marked advantages of GAUDI over other methods through comprehensive simulation and real data analyses.
Elevated L1 expression in ataxia telangiectasia likely explained by an RNA-seq batch effect
Authors: Faulkner Geoffrey J. 
Published: October 2022

AbstractA recent study (Takahashi et al., Neuron, 2022) concluded LINE-1 (L1) retrotransposon activation drives cerebellar ataxia and neurodegeneration. This position was based on L1 upregulation in ataxia telangiectasia (AT) patient cerebellum samples, as measured by RNA-seq, and observation of ataxia and neurodegeneration in mice where cerebellar L1 expression was induced via dCas9-CRISPR. Here, a re-analysis of the RNA-seq data, which were obtained by rRNA depletion rather than polyA+ selection, revealed a high fraction (38.4%) of intronic reads. Significantly (p=0.034) more intronic reads were present in the AT data than the matched controls. This finding provides an alternative and robust explanation for a key result reported by Takahashi et al.: intronic L1 sequences are abundant in pre-mRNAs, and more pre-mRNAs were retained in the AT libraries. This apparent batch effect deserves further examination, as claims of L1-mediated pathogenesis could shape future efforts to treat AT by trying to attenuate L1 activity.
Early cellular mechanism of type I interferon-driven susceptibility to tuberculosis
Authors: Kotov Dmitri I. , Lee Ophelia V. , Fattinger Stefan A. , Langner Charlotte , Guillen Jaresley V. , Peters Joshua M. , Moon Andres , Burd Eileen M. , Witt Kristen C. , Stetson Daniel B. , Jaye David L. , Bryson Bryan D. , Vance Russell E. 
Published: October 2022

SummaryMycobacterium tuberculosis(Mtb) causes 1.6 million deaths annually. Active tuberculosis correlates with a neutrophil-driven type I interferon (IFN) signature, but the cellular mechanisms underlying tuberculosis pathogenesis remain poorly understood. We found interstitial macrophages (IMs) and plasmacytoid dendritic cells (pDCs) are dominant producers of type I IFN duringMtbinfection in mice and non-human primates, and pDCs localize near humanMtbgranulomas. Depletion of pDCs reducesMtbburdens, implicating pDCs in tuberculosis pathogenesis. During IFN-driven disease, we observe abundant DNA-containing neutrophil extracellular traps (NETs) known to activate pDCs. Cell type-specific disruption of the type I IFN receptor suggests IFNs act on IMs to inhibitMtbcontrol. Single cell RNA-seq indicates type I IFN-responsive cells are defective in their response to IFNγ, a cytokine critical forMtbcontrol. We propose pDC-derived type I IFNs act on IMs to drive bacterial replication, further neutrophil recruitment, and active tuberculosis disease.
Dopamine signaling regulates predator-driven changes inCaenorhabditis elegans’egg laying behavior
Authors: Pribadi Amy , Rieger Michael A. , Rosales Kaila , Reddy Kirthi C. , Chalasani Sreekanth H. 
Published: October 2022

AbstractPrey respond to predators by altering their behavior to optimize their own fitness and survival. Specifically, prey are known to avoid predator-occupied territories to reduce their risk of harm or injury to themselves and their progeny. We probe the interactions betweenCaenorhabditis elegansand its naturally cohabiting predatorPristionchus uniformisto reveal the pathways driving changes in prey behavior. WhileC. elegansprefers to lay its eggs on a bacteria food lawn, the presence of a predator inside a lawn inducesC. elegansto lays more eggs away from that lawn. We confirm that this change in egg laying is in response to bites from predators, rather than to predatory secretions. Moreover, predator-exposed prey continue to lay their eggs away from the dense lawn even after the predator is removed, indicating a form of learning. Next, we find that mutants in dopamine synthesis significantly reduce egg laying behavior off the lawn in both predator-free and predator-inhabited lawns, which we can rescue by transgenic complementation or supplementation with exogenous dopamine. Moreover, we find that dopamine is likely released from multiple dopaminergic neurons and requires combinations of both D1-(DOP-1), and D2-like (DOP-2 and DOP-3) dopamine receptors to alter predator-induced egg laying behavior, whereas other combinations modify baseline levels of egg laying behavior. Together, we show that dopamine signaling can alter both predator-free and predator-induced foraging strategies, implying a role for this pathway in defensive behaviors.