bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic functional brain networks underlying the temporal inertia of negative emotions
Authors: Gaviria Julian , Rey Gwladys , Bolton Thomas , Van De Ville Dimitri , Vuilleumier Patrik 
Published: March 2021

AbstractAffective inertia represents the lasting impact of transient emotions at one time point on affective state at a subsequent time point. Here we describe the neural underpinnings of inertia following negative emotions elicited by sad events in movies. Using a co-activation pattern analysis of dynamic functional connectivity, we examined the temporal expression and reciprocal interactions among brain-wide networks during movies and subsequent resting periods. Our findings revealed distinctive spatiotemporal expression of visual (VIS), default mode (DMN), central executive (CEN), and frontoparietal control (FPCN) networks both in negative movies and in rest periods following these movies. We also identified different reciprocal relationships among these networks, in transitions from movie to rest. While FPCN and DMN expression increased during and after negative movies, respectively, FPCN occurrences during the movie predicted lower DMN and higher CEN expression during subsequent rest after neutral movies, but this relationship was reversed after the elicitation of negative emotions. Changes in FPCN and DMN activity correlated with more negative subjective affect. These findings provide new insights into the transient interactions of intrinsic brain networks underpinning the inertia of negative emotions. More specifically, they describe a major role of FPCN in emotion elicitation processes, with prolonged impact on DMN activity in subsequent rest, presumably involved in emotion regulation and restoration of homeostatic balance after negative events.HighlightsModulations of dynamic functional brain connectivity are associated to the temporal inertia of negative emotions.Functional co-activations patterns (CAPs) during emotional episodes predict changes in spontaneous brain dynamics during subsequent resting state.Classical “task-rest” anticorrelations in network activity are reversed by negative emotions.
Time-course RNASeq ofCamponotus floridanusforager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor
Authors: Das Biplabendu , de Bekker Charissa 
Published: March 2021

AbstractBackgroundCircadian clocks allow organisms to anticipate daily fluctuations in their environment by driving rhythms in physiology and behavior. Inter-organismal differences in daily rhythms, called chronotypes, exist and can shift with age. In ants, age, caste-related behavior and chronotype appear to be linked. “Around-the-clock” active nurse ants are usually younger and, with age, transition into rhythmically active foragers. Moreover, ants can shift between these behavioral castes depending on social context. We investigated how changes in daily gene expression could be contributing to such behavioral plasticity inCamponotus floridanuscarpenter ants by combining time-course behavioral assays and RNA-Sequencing of forager and nurse brains.ResultsWe found that nurse brains have three times fewer 24h oscillating genes than foragers. However, several hundred genes that oscillated every 24h in forager brains showed robust 8h oscillations in nurses, including the core clock genesPeriodandShaggy. These differentially rhythmic genes consisted of several components of the circadian entrainment pathway, and showed enrichments for functions related to metabolism, cellular communication and protein modification. We additionally found thatVitellogenin, known to regulate division of labor in social insects, showed robust 24h oscillations in nurse brains but not in foragers. Furthermore, the protein products of several genes that were differentially expressed between the two ant castes were previously found in the trophallactic fluid ofC. floridanus. This suggests a putative role for trophallaxis in regulating behavioral division of labor through caste-specific gene expression.ConclusionWe provide a first look at the chronobiological differences in gene expression between forager and nurse ant brains. This endeavor allowed us to identify putative molecular mechanisms underlying plastic timekeeping. Several components of the ant circadian clock and its output can seemingly oscillate at different harmonics of the circadian rhythm. We propose that such chronobiological plasticity has evolved to allow for distinct regulatory networks that underlie behavioral castes, while supporting swift caste transitions in response to colony demands. Behavioral division of labor is common among social insects. The links between chronobiological and behavioral plasticity that we found inC. floridanus, thus, likely represent a more general phenomenon that warrants further investigation.
Paternal obesity results in placental hypoxia and sex-specific impairments in placental vascularization and offspring metabolic function
Authors: Jazwiec Patrycja A. , Patterson Violet S. , Ribeiro Tatiane A. , Yeo Erica , Kennedy Katherine M. , Mathias Paulo C.F. , Petrik Jim J. , Sloboda Deborah M. 
Published: March 2021

ABSTRACTPaternal obesity predisposes offspring to metabolic dysfunction, but the underlying mechanisms remain unclear. We investigated whether paternal obesity-induced offspring metabolic dysfunction is associated with placental endoplasmic reticulum (ER) stress and impaired vascular development. We determined whether offspring glucose intolerance is fueled by ER stress-mediated changes in fetal hepatic development. Furthermore, we also determined whether paternal obesity may indirectly affectin uterodevelopment by disrupting maternal metabolic adaptations to pregnancy. Male mice fed a standard chow diet (CON; 17% kcal fat) or high fat diet (PHF; 60% kcal fat) for 8-10 weeks were time-mated with control female mice to generate pregnancies and offspring. Glucose tolerance in pregnant females was evaluated at mid-gestation (embryonic day (E) 14.5) and term gestation (E18.5). At E14.5 and E18.5, fetal liver and placentae were collected, and markers of hypoxia, angiogenesis, endocrine function, and macronutrient transport, and unfolded protein response (UPR) regulators were evaluated to assess ER stress. Young adult offspring glucose tolerance and metabolic parameters were assessed at ∼60 days of age. Paternal obesity did not alter maternal glucose tolerance or placental lactogen in pregnancy but did induce placental hypoxia, ER stress, and altered placental angiogenesis. This effect was most pronounced in placentae associated with female fetuses. Consistent with this, paternal obesity also activated the ATF6 and PERK branches of the UPR in fetal liver and altered hepatic expression of gluconeogenic factors at E18.5. Adult offspring of obese fathers showed glucose intolerance and impaired whole-body energy metabolism, particularly in female offspring. Thus, paternal obesity programs sex-specific adverse placental structural and functional adaptations and alters fetal hepatic development via ER stress-induced pathways. These changes likely underpin metabolic deficits in adult offspring.Summary SentencePaternal obesity alters placental vascular structures and is associated with sex-specific compromises in glucose tolerance and metabolism in young offspring
Data-driven speciation tree prior for better species divergence times in calibration-poor molecular phylogenies
Authors: Tao Qiqing , Barba-Montoya Jose , Kumar Sudhir 
Published: March 2021

AbstractMotivationPrecise time calibrations needed to estimate ages of species divergence are not always available due to fossil records’ incompleteness. Consequently, clock calibrations available for Bayesian dating analyses can be few and diffused, i.e., phylogenies are calibration-poor, impeding reliable inference of the timetree of life. We examined the role of speciation birth-death tree prior on Bayesian node age estimates in calibration-poor phylogenies and tested the usefulness of an informative, data-driven tree prior to enhancing the accuracy and precision of estimated times.ResultsWe present a simple method to estimate parameters of the birth-death tree prior from the molecular phylogeny for use in Bayesian dating analyses. The use of a data-driven birth-death (ddBD) tree prior leads to improvement in Bayesian node age estimates for calibration-poor phylogenies. We show that the ddBD tree prior, along with only a few well-constrained calibrations, can produce excellent node ages and credibility intervals, whereas the use of an uninformative, uniform (flat) tree prior may require more calibrations. Relaxed clock dating with ddBD tree prior also produced better results than a flat tree prior when using diffused node calibrations. We also suggest using ddBD tree priors to improve the detection of outliers and influential calibrations in cross-validation analyses.ConclusionEmpirical Bayesian dating analyses with ddBD tree priors enable more accurate and precise node age estimates for calibration-poor phylogenies. Our results have practical applications because the ddBD tree prior reduces the number of well-constrained calibrations necessary to obtain reliable node age estimates. This would help address key impediments in building the grand timetree of life, revealing the process of speciation, and elucidating the dynamics of biological diversification.AvailabilityAn R module for computing the ddBD tree prior, simulated datasets, and empirical datasets are available athttps://github.com/cathyqqtao/ddBD-tree-prior.
Tissue-specific mRNA profiling of theBrassica napus-Sclerotinia sclerotioruminteraction uncovers novel regulators of plant immunity
Authors: Walker Philip L. , Girard Ian J. , Giesbrecht Shayna , Whyard Steve , Fernando W.G. Dilantha , de Kievit Teresa R. , Belmonte Mark F. 
Published: March 2021

AbstractWhite mold inBrassica napus(canola) is caused by the fungal pathogenSclerotinia sclerotiorumand is responsible for significant losses in crop yield across the globe. With advances in high-throughput transcriptomics, our understanding of theB. napusdefense response toS. sclerotiorumis becoming clearer; however, the response of individual tissue layers directly at the site of infection has yet to be explored. Using laser microdissection coupled with RNA sequencing, we profiled the epidermis, mesophyll and vascular leaf tissue layers in response toS. sclerotiorum. This strategy increases the number of genes detected compared to whole-leaf assessments and provides unprecedented information on tissue-specific gene expression networks in response to pathogen attack. Our findings provide novel insight into the conserved and specific roles of ontogenetically distinct leaf tissue layers in response to infection. Using bioinformatics tools, we identified several defense genes that might coordinate plant immunity responses shared across different tissue layers within the leaf. These genes were functionally characterized by challenging T-DNA insertion lines of Arabidopsis with necrotrophic, hemi-biotrophic, and biotrophic pathogens, ultimately converging on the PR5-like RECEPTOR KINASE (PRK5). Together, these data provide insight on the complexity of theB. napusdefense response directly at the site of infection.HighlightLaser microdissection coupled RNA sequencing of theB. napus–S. sclerotioruminteraction identifies candidate genes predicted to guide plant immunity against pathogen attack.
Anatomy of unfolding: The site-specific fold stability of Yfh1 measured by 2D NMR
Authors: Puglisi Rita , Karunanithy Gogulan , Hansen D. Flemming , Pastore Annalisa , Temussi Piero Andrea 
Published: March 2021

AbstractMost techniques allow detection of protein unfolding either by following the behaviour of single reporters or as an averaged all-or-none process. We recently added 2D NMR spectroscopy to the well-established techniques able to obtain information on the process of unfolding using resonances of residues in the hydrophobic core of a protein. Here, we questioned whether an analysis of the individual stability curves from each resonance could provide additional site-specific information. We used the Yfh1 protein that has the unique feature to undergo both cold and heat denaturation at temperatures above water freezing at low ionic strength. We show that stability curves inconsistent with the average NMR curve from hydrophobic core residues mainly comprise exposed outliers that do nevertheless provide precious information. By monitoring both cold and heat denaturation of individual residues we gain knowledge on the process of cold denaturation and convincingly demonstrate that the two unfolding processes are intrinsically different.
A machine-learning algorithm correctly classifies cortical evoked potentials from both natural retinal stimulation and electrical stimulation of the optic nerve
Authors: Gaillet Vivien , Zollinger Elodie Geneviève , Ghezzi Diego 
Published: March 2021

AbstractObjectiveOptic nerve’s intraneural stimulation is an emerging neuroprosthetic approach to provide artificial vision to totally blind patients. An open question is the possibility to evoke individual non-overlapping phosphenes via selective intraneural optic nerve stimulation. To begin answering this question, first, we aim at showing in preclinical experiments with animals that each intraneural electrode could evoke a distinguishable activity pattern in the primary visual cortex.ApproachWe performed both patterned visual stimulation and patterned electrical stimulation in healthy rabbits while recording evoked cortical activity with an electrocorticogram array in the primary visual cortex. Electrical stimulation was delivered to the optic nerve with the intraneural array OpticSELINE. We used a support vector machine algorithm paired to a linear regression model to classify cortical responses originating from visual stimuli located in different portions of the visual field and electrical stimuli from the different electrodes of the OpticSELINE.Main resultsCortical activity induced by visual and electrical stimulation could be classified with nearly 100% accuracy relative to the specific location in the visual field or electrode in the array from which it originated. For visual stimulation, the accuracy increased with the separation of the stimuli and reached 100% for separation higher than 7 degrees. For electrical stimulation, at low current amplitudes, the accuracy increased with the distance between electrodes, while at higher current amplitudes, the accuracy was nearly 100% already for the shortest separation.SignificanceOptic nerve’s intraneural stimulation with the OpticSELINE induced discernible cortical activity patterns. These results represent a leap forward for intraneural optic nerve stimulation towards artificial vision.
The strange role of brain lesion size in cognitive neuropsychology
Authors: Sperber Christoph 
Published: March 2021

AbstractThe size of brain lesions is a variable that is frequently considered in cognitive neuropsychology. In particular, lesion-deficit inference studies often control for lesion size, and the association of lesion size with post-stroke cognitive deficits and its predictive value are studied. In the present article, the role of lesion size in cognitive deficits and its computational or design-wise consideration is discussed and questioned. First, I argue that the commonly discussed role or effect of lesion size in cognitive deficits eludes us. A generally valid understanding of the causal relation of lesion size, lesion location, and cognitive deficits is unachievable. Second, founded on the theory of covariate control, I argue that lesion size control is no valid covariate control. Instead, it is identified as a procedure with only situational benefits, which is supported by empirical data. This theoretical background is used to suggest possible research practices in lesion-deficit inference, post-stroke outcome prediction, and behavioural studies. Last, control for lesion size is put into a bigger methodological and also historical context – it is identified to relate to a long-known association problem in neuropsychology, which was previously discussed from the perspectives of a mislocalisation in lesion-deficit mapping and the symptom complex approach.Highlights-Lesion size is a factor that is often considered or controlled in neuropsychology-No general causal relation between lesion size, lesion location and deficit exists-Lesion size in brain mapping, outcome prediction and behavioural study is discussed-Lesion size control is no valid covariate control-Practical suggestions and guidelines how to consider lesion size are provided
Pathogenesis-related protein 1 (PR-1) genes in soybean: genome-wide identification, structural analysis and expression profiling under multiple biotic and abiotic stresses
Authors: Almeida-Silva Fabricio , Venancio Thiago M. 
Published: March 2021

ABSTRACTPlant pathogenesis-related (PR) proteins are a large group of proteins, classified in 17 families, that are induced by pathological conditions. Here, we characterized the soybean PR-1 (GmPR-1) gene repertoire at the sequence, structural and expression levels. We found 24 GmPR-1 genes, clustered in two phylogenetic groups. GmPR-1 genes are under strong purifying selection, particularly those that emerged by tandem duplications. GmPR-1 promoter regions are abundant in cis-regulatory elements associated with major stress-related transcription factor families, namely WRKY, ERF, HD-Zip, C2H2, NAC, and GATA. We observed that 23 GmPR-1 genes are induced by stress conditions or exclusively expressed upon stress. We explored 1972 transcriptome samples, including 26 stress conditions, revealing that most GmPR-1 genes are differentially expressed in a plethora of biotic and abiotic stresses. Our findings highlight stress-responsive GmPR-1 genes with potential biotechnological applications, such as the development of transgenic lines with increased resistance to biotic and abiotic stresses.
Quantitative detection of SARS-CoV-2 B.1.1.7 variant in wastewater by allele-specific RT-qPCR
Authors: Lee Wei Lin , McElroy Kyle A , Armas Federica , Imakaev Maxim , Gu Xiaoqiong , Duvallet Claire , Chandra Franciscus , Chen Hongjie , Leifels Mats , Mendola Samuel , Floyd-O’Sullivan Róisín , Powell Morgan M , Wilson Shane T , Wu Fuqing , Xiao Amy , Moniz Katya , Ghaeli Newsha , Matus Mariana , Thompson Janelle , Alm Eric J 
Published: March 2021

ABSTRACTWastewater-based epidemiology (WBE) has emerged as a critical public health tool in tracking the SARS-CoV-2 epidemic. Monitoring SARS-CoV-2 variants of concern in wastewater has to-date relied on genomic sequencing, which lacks sensitivity necessary to detect low variant abundances in diluted and mixed wastewater samples. Here, we develop and present an open-source method based on allele specific RT-qPCR (AS RT-qPCR) that detects and quantifies the B.1.1.7 variant, targeting spike protein mutations at three independent genomic loci highly predictive of B.1.1.7 (HV69/70del, Y144del, and A570D). Our assays can reliably detect and quantify low levels of B.1.1.7 with low cross-reactivity, and at variant proportions between 0.1% and 1% in a background of mixed SARS-CoV-2. Applying our method to wastewater samples from the United States, we track B.1.1.7 occurrence over time in 19 communities. AS RT-qPCR results align with clinical trends, and summation of B.1.1.7 and wild-type sequences quantified by our assays strongly correlate with SARS-CoV-2 levels indicated by the US CDC N1/N2 assay. This work paves the path for rapid inexpensive surveillance of B.1.1.7 and other SARS-CoV-2 variants in wastewater.
Delayed dosing of minocycline plus N-acetylcysteine reduces neurodegeneration in distal brain regions and restores spatial memory after experimental traumatic brain injury
Authors: Whitney Kristen , Nikulina Elena , Rahman Syed N. , Alexis Alisia , Bergold Peter J. 
Published: March 2021

AbstractMultiple drugs to treat traumatic brain injury (TBI) have failed clinical trials. Most drugs lose efficacy as the time interval increases between injury and treatment onset. Insufficient therapeutic time window is a major reason underlying failure in clinical trials. Few drugs have been developed with therapeutic time windows sufficiently long enough to treat TBI because little is known about which brain functions can be targeted if therapy is delayed hours to days after injury. We identified multiple injury parameters that are improved by first initiating treatment with the drug combination minocycline (MINO) plus N-acetylcysteine (NAC) at 72 hours after injury (MN72) in a mouse closed head injury (CHI) experimental TBI model. CHI produces spatial memory deficits resulting in impaired performance on Barnes maze, hippocampal neuronal loss, and bilateral damage to hippocampal neurons, dendrites, spines and synapses. MN72 treatment restores Barnes maze acquisition and retention, protects against hippocampal neuronal loss, limits damage to dendrites, spines and synapses, and accelerates recovery of microtubule associated protein 2 (MAP2) expression, a key protein in maintaining proper dendritic architecture and synapse density. These data show that in addition to the structural integrity of the dendritic arbor, spine and synapse density can be successfully targeted with drugs first dosed days after injury. Retention of substantial drug efficacy even when first dosed 72 hours after injury makes MINO plus NAC a promising candidate to treat clinical TBI.