bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Tissue Tropisms and Transstadial Transmission of aRickettsiaEndosymbiont in the Highland Midge,Culicoides impunctatus(Diptera: Ceratopogonidae)
Authors: Pilgrim Jack , Siozios Stefanos , Baylis Matthew , Hurst Gregory D. D. 
Published: June 2020

AbstractRickettsiaare a group of intracellular bacteria which can manipulate host reproduction and alter sensitivity to natural enemy attack in a diverse range of arthropods. The maintenance ofRickettsiaendosymbionts in insect populations can be achieved through both vertical and horizontal transmission routes. For example, the presence of the symbiont in the follicle cells and salivary glands ofBemisiawhiteflies allows Belli groupRickettsiatransmission via the germline and plants, respectively. However, the transmission routes of otherRickettsia, such as those in the Torix group of the genus, remain underexplored. Through fluorescencein-situhybridisation (FISH) and transmission electron microscopy (TEM) screening, this study describes the pattern of TorixRickettsiatissue tropisms in the highland midge,Culicoides impunctatus(Diptera: Ceratopogonidae). Of note is high intensity of infection of the ovarian suspensory ligament, suggestive of a novel germline targeting strategy. Additionally, localisation of the symbiont in tissues of several developmental stages suggests transstadial transmission is a major route of ensuring maintenance ofRickettsiawithinC. impunctatuspopulations. Aside from providing insights into transmission strategies,Rickettsiapresence in the fat body of larvae indicates potential host fitness and vector capacity impacts to be investigated in the future.Importance StatementMicrobial symbionts of disease vectors have garnered recent attention due to their ability to alter vectorial capacity. Their consideration as a means of arbovirus control depends on symbiont vertical transmission which leads to spread of the bacteria through a population. Previous work has identified aRickettsiasymbiont present in several vector species of biting midges (Culicoidesspp.), however, symbiont transmission strategies and host effects remain underexplored. In this study, we describe the presence ofRickettsiain the ovarian suspensory ligament and the ovarian epithelial sheath ofCulicoides impunctatus. Infection of these organs suggest the connective tissue surrounding developing eggs is important for ensuring vertical transmission of the symbiont in midges and possibly other insects. Additionally, our results indicateRickettsialocalisation in the fat body ofCulicoides impunctatus. As viruses spread by midges often replicate in the fat body, this implies possible vector competence effects to be further investigated.
Replay bursts coincide with activation of the default mode and parietal alpha network
Authors: Higgins Cameron , Liu Yunzhe , Vidaurre Diego , Kurth-Nelson Zeb , Dolan Ray , Behrens Timothy , Woolrich Mark 
Published: June 2020

AbstractOur brains at rest spontaneously replay recently acquired information, but how this process is orchestrated to avoid interference with ongoing cognition is an open question. We investigated whether replay coincided with spontaneous patterns of whole brain activity. We found, in two separate datasets, that replay sequences were packaged into transient bursts occurring selectively during activation of the default mode network (DMN) and parietal alpha network. These networks were characterized by widespread synchronized oscillations coupled to increases in ripple band power, mechanisms that coordinate information flow between disparate cortical areas. Our data show a tight correspondence between two widely studied phenomena of neural physiology and suggest the DMN may coordinate replay bursts in a manner that minimizes interference with ongoing cognition.
TheBotrytis cinereaCrh transglycosylae is a cytoplasmic effector triggering plant cell death and defense response
Authors: Bi Kai , Scalschi Loredana , Namrata Jaiswal Gupta , Frid Renana , Zhu Wenjun , Masrati Gal , Mengiste Tesfaye , Sharon Amir 
Published: June 2020

AbstractCrh proteins catalyze crosslinking of chitin and glucan polymers in the fugal cell wall. We revealed a novel and unexpected role ofBotrytis cinereaBcCrh1 as a cytoplasmic effector and elicitor of plant defense. During saprophytic growth the BcCrh1 protein is localized in vacuoles and ER. Upon plant infection the protein accumulates to high levels in infection cushions, it is then secreted to the apoplast and translocated into plant cells, where it induces cell death and defense responses. Two regions of 53 and 35 amino acids were found sufficient for protein uptake and cell death induction, respectively. Dimerization of BcCrh proteins was necessary for the transglycosylation activity and proper fungal development, while the monomeric proteins was sufficient for induction of cell death.Arabidopsislines expressing thebccrh1gene had reduced sensitivity toB. cinerea,demonstrating the potential use of the protein in plant immunization against necrotrophic pathogens.
The development of attentional control mechanisms in multisensory environments
Authors: Turoman Nora , Tivadar Ruxandra I. , Retsa Chrysa , Maillard Anne M. , Scerif Gaia , Matusz Pawel J. 
Published: June 2020

AbstractOutside the laboratory, people need to pay attention to relevant objects that are typically multisensory, but it remains poorly understood how the underlying neurocognitive mechanisms develop. We investigated when adult-like mechanisms controlling one’s attentional selection of visual and multisensory objects emerge across childhood. Five-, 7-, and 9-year-olds were compared with adults in their performance on a computer game-like multisensory spatial cueing task, while 129-channel EEG was simultaneously recorded. Markers of attentional control were behavioural spatial cueing effects and the N2pc ERP component (analysed traditionally and using a multivariate electrical neuroimaging framework). In behaviour, adult-like visual attentional control was present from age 7 onwards, whereas multisensory control was absent in all children groups. In EEG, multivariate analyses of the activity over the N2pc time-window revealed stable brain activity patterns in children. Adult-like visual-attentional control EEG patterns were present age 7 onwards, while multisensory control activity patterns were found in 9-year-olds (albeit behavioural measures showed no effects). By combining rigorous yet naturalistic paradigms with multivariate signal analyses, we demonstrated that visual attentional control seems to reach an adult-like state at ~7 years, before adult-like multisensory control, emerging at ~9 years. These results enrich our understanding of how attention in naturalistic settings develops.HighlightsBy age 7, children showed adult-like task-set contingent attentional capture in behaviourChildren’s behavioural data did not show evidence for attentional enhancement for multisensory objects, but 9-year-olds’ EEG topographic patterns elicited by multisensory vs. purely visual distractors differed reliablyTraditional visual attentional event-related potential (ERP) analyses, such as the N2pc, did not detect attentional enhancement for multisensory objects in adults, and visual or multisensory attention in childrenMultivariate analyses of ERPs, such as electrical neuroimaging, are more sensitive to the change of attentional control processes over development
ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways
Authors: Treveil Agatha , Bohar Balazs , Sudhakar Padhmanand , Gul Lejla , Csabai Luca , Olbei Marton , Poletti Martina , Madgwick Matthew , Andrighetti Tahila , Hautefort Isabelle , Modos Dezso , Korcsmaros Tamas 
Published: June 2020

AbstractThe SARS-CoV-2 pandemic of 2020 has mobilised scientists around the globe to research all aspects of the coronavirus virus and its infection. For fruitful and rapid investigation of viral pathomechanisms, a collaborative and interdisciplinary approach is required. Therefore, we have developed ViralLink: a systems biology workflow which reconstructs and analyses networks representing the effect of viruses on intracellular signalling. These networks trace the flow of signal from intracellular viral proteins through their human binding proteins and downstream signalling pathways, ending with transcription factors regulating genes differentially expressed upon viral exposure. In this way, the workflow provides a mechanistic insight from previously identified knowledge of virally infected cells. By default, the workflow is set up to analyse the intracellular effects of SARS-CoV-2, requiring only transcriptomics counts data as input from the user: thus, encouraging and enabling rapid multidisciplinary research. However, the wide-ranging applicability and modularity of the workflow facilitates customisation of viral context,a prioriinteractions and analysis methods. Through a case study of SARS-CoV-2 infected bronchial/tracheal epithelial cells, we evidence the functionality of the workflow and its ability to identify key pathways and proteins in the cellular response to infection. The application of ViralLink to different viral infections in a cell-type specific manner using different available transcriptomics datasets will uncover key mechanisms in viral pathogenesis. The workflow is available on GitHub (https://github.com/korcsmarosgroup/ViralLink) in an easily accessible Python wrapper script, or as customisable modular R and Python scripts.Author summaryCollaborative and multidisciplinary science provides increased value for experimental datasets and speeds the process of discovery. Such ways of working are especially important at present due to the urgency of the SARS-CoV-2 pandemic. Here, we present a systems biology workflow which models the effect of viral proteins on the infected host cell, to aid collaborative and multidisciplinary research. Through integration of gene expression datasets with context-specific and context-agnostic molecular interaction datasets, the workflow can be easily applied to different datasets as they are made available. Application to diverse SARS-CoV-2 datasets will increase our understanding of the mechanistic details of the infection at a cell type specific level, aid drug target discovery and help explain the variety of clinical manifestations of the infection.
Automated video-based heart rate tracking for the anesthetized and behaving monkey
Authors: Froesel Mathilda , Goudard Quentin , Hauser Marc , Gacoin Maëva , Ben Hamed Suliann 
Published: June 2020

AbstractBackgroundHeart rate is extremely valuable in the study of complex behaviours and their physiological correlates in non-human primates. However, collecting this information is often challenging, involving either invasive implants or tedious behavioural training.New MethodIn the present study, we implement a Eulerian Video Magnification (EVM) heart tracking method in the macaque monkey combined with wavelet transform. This is based on a measure of image to image fluctuations in skin reflectance due to changes in blood influx.ResultsWe show a strong temporal coherence and amplitude match between EVM-based heart tracking and ground truth ECG, from both color (RGB) and infrared (IR) videos, in anesthetized macaques, to a level comparable to what can be achieved in humans. We further show that this method allows to identify consistent heart rate changes following the presentation of conspecific emotional voices or faces.Comparison with Existing Method(s)Eulerian Video Magnification (EVM) is used to extract heart rate in humans but has never been applied to non-human primates. Video photoplethysmography allows to extract awake macaques heart rate from RGB videos. In contrast, our method allows to extract awake macaques heart rate from both RGB and IR videos and is particularly resilient to the head motion that can be observed in awake behaving monkeys.ConclusionsOverall, we believe that this method can be generalized as a tool to track heart rate of the awake behaving monkey, for ethological, behavioural, neuroscience or welfare purposes.HighlightsHeart rate varies during complex non-human primate (NHP) behaviour and cognition.We apply Eulerian Video Magnification to track NHP heart rate (EVM-HR).EVM-HR can be used with RGB & IR videos, and anesthetized or awake NHPs.NHP EVM-HR vary with emotional content of presented stimuli.EVM-HR is of interest to ethology, behavioural, neuroscience & welfare purposes.
Dissecting the impact of metabolic environment on three common cancer cell phenotypes
Authors: Kochanowski Karl , Sander Timur , Link Hannes , Chang Jeremy , Altschuler Steven , Wu Lani 
Published: June 2020

AbstractThe impact of different metabolic environments on cancer cell behavior is poorly understood. Here, we systematically altered nutrient composition of cell culture media and examined the impact on three phenotypes—drug-treatment survival, cell migration, and lactate overflow—that are frequently studied in cancer cells. These perturbations across diverse metabolic environments revealed simple relationships between cell growth rate and drug-treatment survival or migration. In contrast, lactate overflow was highly sensitive to changes in sugar availability but largely insensitive to changes in amino acid availability, regardless of the growth rate. Further investigation suggested that the degree of lactate overflow across metabolic environments is largely determined by the cells’ ability to maintain high rates of sugar uptake. This study enabled us to elucidate quantitative relationships between metabolic environment and cancer cell phenotypes, which echo empirical growth laws discovered to govern analogous phenotypes in microbes.
Cultural Evolution of Genetic Heritability
Authors: Uchiyama Ryutaro , Spicer Rachel , Muthukrishna Michael 
Published: June 2020

ABSTRACTBehavioral genetics and cultural evolution have both revolutionized our understanding of human behavior, but largely independently of each other. Here we reconcile these two fields using a dual inheritance approach, which offers a more nuanced understanding of the interaction between genes and culture, and a resolution to several long-standing puzzles. For example, by neglecting how human environments are extensively shaped by cultural dynamics, behavioral genetic approaches systematically inflate heritability estimates and thereby overestimate the genetic basis of human behavior. A WEIRD (Western, educated, industrialized, rich, democratic) gene problem obscures this inflation. Considering both genetic and cultural evolutionary forces, heritability scores become less a property of a trait and more a moving target that responds to cultural and social changes. Ignoring cultural evolutionary forces leads to an over-simplified model of gene-to-phenotype causality. When cumulative culture functionally overlaps with genes, genetic effects become masked, or even reversed, and the causal effect of an identified gene is confounded with features of the cultural environment, specific to a particular society at a particular time. This framework helps explain why it is easier to discover genes for deficiencies than genes for abilities. With this framework, we predict the ways in which heritability should differ between societies, between socioeconomic levels within some societies but not others, and over the life course. An integrated cultural evolutionary behavioral genetics cuts through the nature–nurture debate and elucidates controversial topics such as general intelligence.
Gene Regulatory Network Inference as Relaxed Graph Matching
Authors: Weighill Deborah , Guebila Marouen Ben , Lopes-Ramos Camila , Glass Kimberly , Quackenbush John , Platig John , Burkholz Rebekka 
Published: June 2020

AbstractGene regulatory network inference is instrumental to the discovery of genetic mechanisms driving diverse diseases, including cancer. Here, we present a theoretical framework for PANDA, an established method for gene regulatory network inference. PANDA is based on iterative message passing updates that resemble the gradient descent of an optimization problem, OTTER, which can be interpreted as relaxed inexact graph matching between a gene-gene co-expression and a protein-protein interaction matrix. The solutions of OTTER can be derived explicitly and inspire an alternative spectral algorithm, for which we can provide network recovery guarantees. We compare different solution approaches of OTTER to other inference methods using three biological data sets, which we make publicly available to offer a new application venue for relaxed graph matching in gene regulatory network inference. We find that using modern gradient descent methods with superior convergence properties solving OTTER outperforms state-of-the-art gene regulatory network inference methods in predicting binding of transcription factors to regulatory regions.
Phylogeographic structure of the dunes sagebrush lizard, an endemic habitat specialist
Authors: Chan Lauren M. , Painter Charles W. , Hill Michael T. , Hibbitts Toby J. , Leavitt Daniel J. , Ryberg Wade A. , Walkup Danielle , Fitzgerald Lee A. 
Published: June 2020

AbstractPhylogeographic divergence and population genetic diversity within species reflect the impacts of habitat connectivity, demographics, and landscape level processes in both the recent and distant past. Characterizing patterns of differentiation across the geographic range of a species provides insight on the roles of organismal and environmental traits, on evolutionary divergence, and future population persistence. This is particularly true of habitat specialists where habitat availability and resource dependence may result in pronounced genetic structure as well as increased population vulnerability. We use DNA sequence data as well as microsatellite genotypes to estimate range-wide phylogeographic divergence, historical population connectivity, and historical demographics in an endemic habitat specialist, the dunes sagebrush lizard (Sceloporus arenicolus). This species is found exclusively in dune blowouts and patches of open sand within the shinnery oak-sand dune ecosystem of southeastern New Mexico and adjacent Texas. We find evidence of phylogeographic structure consistent with breaks and constrictions in suitable habitat at the range-wide scale. In addition, we find support for a dynamic and variable evolutionary history across the range ofS. arenicolus. Populations in the Monahans Sandhills have deeply divergent lineages consistent with long-term demographic stability. In contrast, populations in the Mescalero Sands are not highly differentiated, though we do find evidence of demographic expansion in some regions and relative demographic stability in others. Phylogeographic history and population genetic differentiation in this species has been shaped by the configuration of habitat patches within a geologically complex and historically dynamic landscape. Our findings identify regions as genetically distinctive conservation units as well as underscore the genetic and demographic history of different lineages ofS. arenicolus.
FlyBrainLab: Accelerating the Discovery of the Functional Logic of theDrosophilaBrain in the Connectomic/Synaptomic Era
Authors: Lazar Aurel A. , Liu Tingkai , Turkcan Mehmet Kerem , Zhou Yiyin 
Published: June 2020

AbstractIn recent years, a wealth ofDrosophilaneuroscience data have become available. These include cell type, connectome and synaptome datasets for both the larva and adult fly. To facilitate integration across data modalities and to accelerate the understanding of the functional logic of the fly brain, we developed an interactive computing environment called FlyBrainLab.FlyBrainLab is uniquely positioned to accelerate the discovery of the functional logic of theDrosophilabrain. Its interactiveopen sourcearchitecture seamlessly integrates and brings together computational models with neuroanatomical, neurogenetic and electrophysiological data, changing the organization of neuroscientific fly brain data from a group of seemingly disparate databases, arrays and tables, to a well structured data and executable circuit repository.The FlyBrainLab User Interface supports a highly intuitive and automated work-flow that streamlines the 3D exploration and visualization of fly brain circuits, and the interactive exploration of the functional logic of executable circuits created directly from the explored and visualized fly brain data. Furthermore, efficient comparisons of circuit models are supported, across models developed by different researchers, across different developmental stages of the fruit fly and across different datasets.The FlyBrainLab Utility Libraries help untangle the graph structure of neural circuits from raw connectome and synaptome data. The Circuit Libraries facilitate the exploration of neural circuits of the neuropils of the central complex and, the development and implementation of models of the adult and larva fruit fly early olfactory systems.Seeking to transcend the limitations of the connectome, FlyBrainLab provides additional libraries for molecular transduction arising in sensory coding in vision and olfaction. Together with sensory neuron activity data, these libraries serve as entry points for discovering circuit function in the sensory systems of the fruit fly brain. They also enable the biological validation of developed executable circuits within the same platform.
Dopa decarboxylase is a genetic hub of parental control over offspring behavior
Authors: Bonthuis Paul J. , Steinwand Susan , Huang Wei-Chao , Stacher Hörndli Cornelia N. , Emery Jared , Kravitz Stephanie , Ferris Elliott , Gregg Christopher 
Published: June 2020

SUMMARYDopa decarboxylase (DDC) regulates the synthesis of monoaminergic neurotransmitters and is linked to psychiatric and metabolic disorders.Ddcexhibits complex genomic imprinting effects that have not been functionally studied. Here, we investigate different noncanonical imprinting effects at the cellular level with a focus onDdc. Using allele-specific reporter mice, we foundDdcexhibits dominant expression of the maternal allele in subpopulations of cells in 14 of 52 brain regions, and dominant paternal or maternal allele expression in adrenal cell subpopulations. Maternal versus paternalDdcallele null mutations differentially affect offspring social, foraging and exploratory behaviors. Machine learning analyses of naturalistic foraging inDdc−/+and+/−offspring uncovered finite behavioral sequences controlled by the maternal versus paternalDdcalleles. Additionally, parentalDdcgenotype is revealed to affect behavior independent of offspring genotype. Thus,Ddcis a hub of maternal and paternal influence on behavior that mediates diverse imprinting and parental effects.HIGHLIGHTSDopa decarboxylase (Ddc) allelic expression resolved at the cellular levelCells differentially express maternal versus paternalDdcallelesMaternal and paternalDdcalleles control distinct behavioral sequencesParentalDdcgenotype affects offspring independent of mutation transmissioneTOCAllelic reporter mice and machine learning analyses reveal dopa decarboxylase is affected by diverse imprinting and parental effects that shape finite behavioral sequences in sons and daughters.