bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mnemonic prediction errors bias hippocampal states
Authors: Bein Oded , Duncan Katherine , Davachi Lila 
Published: August 2019

AbstractIn situations when our experience violates our predictions, it is adaptive to upregulate encoding of novel information, while down-weighting retrieval of erroneous memory predictions to promote an updated representation of the world. We asked whether mnemonic prediction errors promote distinct hippocampal processing ‘states’ by leveraging recent results showing that encoding and retrieval processes are supported by distinct patterns of connectivity, or ‘states’, across hippocampal subfields. During fMRI scanning, participants were cued to retrieve well-learned room-images and were then presented with either an image identical to the learned room or a modified version (1-4 changes). We found that CA1-entorhinal connectivity increased, and CA1-CA3 connectivity decreased, with the number of changes to the learned rooms. Further, stronger memory predictions measured in CA1 during the cue correlated with the CA1-entorhinal connectivity increase in response to violations. Our findings provide a mechanism by which mnemonic prediction errors may drive memory updating - by biasing hippocampal states.
Human Neocortical Neurosolver (HNN): A new software tool for interpreting the cellular and network origin of human MEG/EEG data
Authors: Neymotin Samuel A , Daniels Dylan S , Caldwell Blake , McDougal Robert A , Carnevale Nicholas T , Jas Mainak , Moore Christopher I , Hines Michael L , Hämäläinen Matti , Jones Stephanie R 
Published: August 2019

AbstractMagneto- and electro-encephalography (MEG/EEG) non-invasively record human brain activity with millisecond resolution providing reliable markers of healthy and disease states. Relating these macroscopic signals to underlying cellular- and circuit-level generators is a limitation that constrains using MEG/EEG to reveal novel principles of information processing or to translate findings into new therapies for neuropathology. To address this problem, we built Human Neocortical Neurosolver (HNN, https://hnn.brown.edu) software. HNN has a graphical user interface designed to help researchers and clinicians interpret the neural origins of MEG/EEG. HNN’s core is a neocortical circuit model that accounts for biophysical origins of electrical currents generating MEG/EEG. Data can be directly compared to simulated signals and parameters easily manipulated to develop/test hypotheses on a signal’s origin. Tutorials teach users to simulate commonly measured signals, including event related potentials and brain rhythms. HNN’s ability to associate signals across scales makes it a unique tool for translational neuroscience research.
A new knockdown resistance (kdr) mutation, F1534L, in the voltage-gated sodium channel ofAedes aegypti, co-occurring with F1534C, S989P and V1016G
Authors: Kushwah Raja Babu S. , Kaur Taranjeet , Dykes Cherry L. , Kumar Ravi H. , Kapoor Neera , Singh Om P. 
Published: August 2019

AbstractBackgroundAedes aegyptiis a primary vector of dengue, chikungunya and zika infections in India. In the absence of specific drugs or safe and effective vaccines for these infections, their control relies mainly on vector control measures. The emergence of insecticide resistance in vectors, especially against pyrethroids, is a serious threat to the insecticide-based vector control programme. This study reports the presence of multiple knockdown resistance (kdr) mutations present in anAe. aegyptipopulation from Bengaluru (India), including a new mutation F1534L.MethodsAedes aegypticollected from Bengaluru were subjected to insecticide susceptibility tests with DDT, deltamethrin and permethrin. The DNA sequencing of partial domain II, III and IV of the voltage-gated sodium channel (VGSC) was performed to screenkdrmutations present in the population and PCR-based assays were developed for their detection. Genotyping ofkdrmutations was done using PCR-based assays, allelic frequencies were determined, and tests of genetic association ofkdrmutations with the insecticide resistance phenotype were performed.ResultsTheAe. aegyptipopulation were resistant to DDT, deltamethrin and permethrin. The DNA sequencing of the VGSC revealed the presence of fourkdrmutations, i.e., S989P and V1016G in domain II and two alternativekdrmutations F1534C and F1534L in domain III. Allele-specific PCR assays (ASPCR) were developed for the detection ofkdrmutations S989P and V1016G and an existing PCR-RFLP based strategy was modified for the genotyping of all three knownkdrmutations in domain III (F1534L, F1534C and T1520I). Genotyping ofAe. aegyptisamples collected between October 2014 and April 2015 revealed a moderate frequency of S989P/V1016G (18.27%) and F1534L (17.48%), a relatively high frequency of F1534C (50.61%) and absence of T1520I in the population. Mutations S989P and V1016G were in complete linkage disequilibrium in this population while they were in linkage equilibrium withkdrmutations F1534C and F1534L. The alleles F1534C and F1534L are genetically associated with permethrin resistance.ConclusionsA newkdrmutation, F1534L, was found in anAe. aegyptipopulation from Bengaluru (India), co-occurring with the other three mutations S989P, V1016G and F1534C. The findings of a new mutation and development of PCR-based diagnostics have implications for insecticide resistance management. Monitoring of F1534L-kdrin other populations and studies on their functional role in altering neuro-sensitivity is warranted.
Genomic sequencing ofPhyllosticta citriasianaprovide insight into its conservation and diversification with closely relatedPhyllostictaspecies associated with citrus
Authors: Wang Mingshuang , Liu Bei , Ruan Ruoxin , Zeng Yibing , Luo Jinshui , Li Hongye 
Published: August 2019

AbstractPhyllosticta citriasianais the causal agent of the pomelo tan spot. Here, we presented the ~34Mb genome ofP. citriasiana.The genome is organized in 92 contigs, encompassing 9202 predicted genes. Comparative genomic analyses with other twoPhyllostictaspecies (P. citricarpaandP. capitalensis) associated with citrus was conducted to understand their evolutionary conservation and diversification. Pairwise genome alignments revealed that these species are highly syntenic. All species encode similar numbers of CAZymes and secreted proteins. However, the molecular functions of the secretome showed that each species contains some enzymes with distinct activities. ThreePhyllostictaspecies shared a core set of 7261 protein families.P. capitalensishad the largest set of orphan genes (2040), in complete contrast to that ofP. citriasiana(371) andP. citricarpa(262). Most of the orphan genes were functionally unknown, but they contain a certain number of species-specific secreted proteins. A total of 23 secondary metabolites (SM) biosynthesis clusters were identified in the threePhyllostictaspecies, 21 of them are highly conserved among these species while the remaining 2 showed whole cluster gain and loss polymorphisms or gene content polymorphisms. Taken together, our study reveals insights into the genetic mechanisms of host adaptation ofPhyllostictaspecies associated with citrus and paves the way to identify effectors that function in infection of citrus plants.
Social interactions drive efficient foraging and income equality in groups of fish
Authors: Harpaz Roy , Schneidman Elad 
Published: August 2019

AbstractThe social interactions underlying group foraging and their benefits have been mostly studied using mechanistic models replicating qualitative features of group behavior, and focused on a single resource or a few clustered ones. Here, we tracked groups of freely foraging adult zebrafish with spatially dispersed food items and found that fish perform stereotypical maneuvers when consuming food, which attract neighboring fish. We then present a mathematical model, based oninferredfunctional interactions between fish, which accurately describes individual and group foraging of real fish. We show that these interactions allow fish to combine individual and social information to achieve near-optimal foraging efficiency and promote income equality within groups. We further show that the interactions that would maximize efficiency in these social foraging models depend on group size, but not on food distribution - suggesting that fish may adaptively pick the subgroup of neighbors they “listen to” to determine their own behavior.Impact statementAnalysis and modeling of group behavior of adult zebrafish shows that a specialized social interaction mechanism increases foraging efficiency and equality within groups, under a variety of environmental conditions.
Adapting the Eysenck Personality Questionnaire-Revised Neuroticism scale for use in epidemiologic studies: A psychometric evaluation using item response theory in the UK Biobank
Authors: Bauermeister Sarah , Pflanz Chris Patrick , Gallacher John 
Published: August 2019

AbstractNeuroticism has been described as a broad and pervasive personality dimension or ‘heterogeneous’ trait measuring components of mood instability, such as worry; anxiety; irritability; moodiness; self-consciousness and sadness. Consistent with depression and anxiety-related disorders, increased neuroticism places an individual vulnerable for other unipolar and bipolar mood disorders and therefore highly relevant in epidemiologic research. However, the measurement of neuroticism remains a challenge. We aimed to adapt the 12-item Eysenck Personality Questionnaire-Revised Neuroticism (EPQ-RN) scale for use in epidemiologic studies by identifying psychometrically efficient items using item response theory. The 12-item EPQ-RN scale was evaluated by estimating an IRT model on data from 401,527 UK Biobank participants aged 39 to 73 years (M= 56.41 years;SD= 8.06), 53.68% female. The IRT model yielded two item characteristics: item discrimination, an indicator of how well an item differentiates between respondents, and item difficulty, an indicator of the amount of the latent construct (neuroticism) needed to endorse an item. The EPQ-RN exhibited psychometric inefficiency with poor discrimination at extremes of the scale range. High and low scores are relatively poorly represented and uninformative suggesting that high neuroticism scores derived from the scale are a function of cumulative mid-range values. Following systematic item deletion, a 3-item scale was found to have high levels of discrimination, but offered a narrow range of difficulty i.e. was not sensitive to low levels of neuroticism. A 7-item scale was found to be most informative; providing high levels of discrimination across the range of neuroticism scores.
A new lineage of segmented RNA viruses infecting animals
Authors: Obbard Darren J. , Shi Mang , Roberts Katherine E. , Longdon Ben , Dennis Alice B. 
Published: August 2019

AbstractMetagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.
m6A methylation potentiates cytosolic dsDNA recognition in a sequence-specific manner
Authors: Balzarolo Melania , Engels Sander , de Jong Anja J. , Franke Katka , van den Berg Timo K. , Janssen Edith M. , van Steensel Bas , Wolkers Monika C. 
Published: August 2019

AbstractNucleic acid sensing through pattern recognition receptors is critical for immune recognition of microbial infections. Microbial DNA is frequently methylated at the N6 position of adenines (m6A), a modification that is rare in mammalian host DNA. We show that m6A-methylation of 5’-GATC-3’ motifs augments the immunogenicity of double stranded (ds)DNA in macrophages and dendritic cells. Transfection with m6A-methylated DNA increased the expression of the activation markers CD69 and CD86, and of Ifnβ, iNos and Cxcl10 mRNA. Recognition of m6A DNA occurs independently of TLR and RIG-I signaling but requires STING, a key mediator of cytosolic DNA sensing. Intriguingly, the response to m6A DNA is sequence-specific. m6A is immunostimulatory in some motifs, but immunosuppressive in others, a feature that is conserved between mouse and human. In conclusion, epigenetic alterations of bacterial DNA are differentially perceived by innate cells, a feature that could potentially be used for the design of immune-modulating therapeutics.
Partitioning plant spectral diversity into alpha and beta components
Authors: Laliberté Etienne , Schweiger Anna K. , Legendre Pierre 
Published: August 2019

ABSTRACTPlant spectral diversity — how plants differentially interact with solar radiation — is an integrator of plant chemical, structural, and taxonomic diversity that can be remotely sensed. We propose to measure spectral diversity as spectral variance, which allows the partitioning of the spectral diversity of a region, called spectral gamma (γ) diversity, into additive alpha (α; within communities) and beta (β; among communities) components. Our method calculates the contributions of individual bands or spectral features to spectral γ-, β-, and α-diversity, as well as the contributions of individual plant communities to spectral diversity. We present two case studies illustrating how our approach can identify “hotspots” of spectral α-diversity within a region, and discover spectrally unique areas that contribute strongly to β-diversity. Partitioning spectral diversity and mapping its spatial components has many applications for conservation since high local diversity and distinctiveness in composition are two key criteria used to determine the ecological value of ecosystems.
LIN28B-PDZ Binding Kinase Signaling Promotes Neuroblastoma Metastasis
Authors: Chen Dongdong , Cox Julie , Annam Jayabhargav , Weingart Melanie , Essien Grace , Rathi Komal S. , Rokita Jo Lynne , Khurana Priya , Cuya Selma M. , Bosse Kristopher R. , Pilgrim Adeiye , Li Daisy , Maris John M. , Schnepp Robert W. 
Published: August 2019

ABSTRACTNeuroblastoma is an aggressive pediatric malignancy of the neural crest with suboptimal cure rates and a striking predilection for widespread metastases, underscoring the need to identify novel therapeutic vulnerabilities. We recently identified the RNA binding protein LIN28B as a driver in high-risk neuroblastoma and demonstrated it promotes oncogenic cell proliferation by coordinating a RAN-Aurora kinase A network. Here, we demonstrate that LIN28B influences another key hallmark of cancer, metastatic dissemination. Using a murine xenograft model of neuroblastoma dissemination, we show that LIN28B promotes metastasis. We demonstrate that this is in part due to the effects of LIN28B on self-renewal and migration, providing an understanding of how LIN28B shapes the metastatic phenotype. Our studies reveal that the let-7 family, which LIN28B inhibits, opposes the effects of LIN28B. Next, we identify PDZ Binding Kinase (PBK) as a novel LIN28B target. PBK is a serine/threonine kinase that promotes the proliferation and self-renewal of neural stem cells and serves as an oncogenic driver in multiple aggressive malignancies. We demonstrate that PBK is both a novel direct target of let-7 and that MYCN regulates PBK expression, thus elucidating two oncogenic drivers that converge on PBK. Functionally, PBK promotes self-renewal and migration, phenocopying LIN28B. Taken together, our findings define a role for LIN28B in neuroblastoma metastasis and define the targetable kinase PBK as a potential novel vulnerability in metastatic neuroblastoma.
Site-specific ubiquitination of the E3 ligase HOIP regulates cell death and immune signaling
Authors: Fennell Lilian M. , Deszcz Luiza , Schleiffer Alexander , Mechtler Karl , Kavirayani Anoop , Ikeda Fumiyo 
Published: August 2019

AbstractHOIP, the catalytic component of the Linear Ubiquitin chain Assembly Complex (LUBAC), is a critical regulator of inflammation. However, how HOIP itself is regulated to control inflammatory responses is unclear. Here, we discover that site-specific ubiquitination of K784 within HOIP promotes Tumour Necrosis Factor (TNF)-induced inflammatory signalling by controlling TNF Receptor complex I (TNFR1) formation. A HOIP K784R mutant is catalytically active but shows reduced induction of an NF-κB reporter relative to wild type HOIP. HOIP K784 is evolutionarily conserved, equivalent to HOIP K778 in mice. We generated HoipK778R/K778R knockin mice, which show no overt developmental phenotypes; however, in response to TNF, HoipK778R/K778R mouse embryonic fibroblasts display suppressed NF-κB activation and increased sensitivity to apoptosis. On the other hand, HOIP K778R enhances the TNF-induced formation of TNFR complex II, and an interaction between TNFR complex II and LUBAC. Loss of the LUBAC component SHARPIN leads to embryonic lethality in HoipK778R/K778R mice, which is rescued by knockout of TNFR1. We propose that site-specific ubiquitination of HOIP regulates a LUBAC-dependent switch between survival and apoptosis in TNF-signalling.
In vivo characterisation of endogenous cardiovascular extracellular vesicles in larval and adult zebrafish
Authors: Scott Aaron , Ballesteros Lorena Sueiro , Bradshaw Marston , Power Ann , Lorriman James , Love John , Paul Danielle , Herman Andrew , Emanueli Costanza , Richardson Rebecca J. 
Published: August 2019

AbstractObjectiveExtracellular vesicles (EVs) facilitate molecular transport across extracellular space, allowing local and systemic signalling during homeostasis and in disease. Extensive studies have described functional roles for EV populations, including during cardiovascular disease, but the in vivo characterisation of endogenously produced EVs is still in its infancy. Due to their genetic tractability and opportunities for live imaging, zebrafish represent an ideal but under-used model to investigate endogenous EVs. The overall aim of this study was to establish a transgenic zebrafish model to allow the in vivo identification, tracking and extraction of endogenous EVs produced by different cell types.Approach and ResultsUsing a membrane-tethered fluorophore reporter system, we show that EVs can be fluorescently labelled in larval and adult zebrafish and demonstrate that multiple cell types including endothelial cells and cardiomyocytes actively produce EVs in vivo. Cell-type specific EVs can be tracked by high spatiotemporal resolution light-sheet live imaging and modified flow cytometry methods allow these EVs to be further evaluated. Importantly, we demonstrate the utility of this model by showing that cardiomyocytes, endothelial cells and macrophages exchange EVs in the adult heart and that ischaemic injury models dynamically alter EV production.ConclusionsWe have developed a powerful in vivo zebrafish model for the investigation of endogenous EVs in all aspects of cardiovascular biology and pathology. A cell membrane fluorophore labelling approach allows cell type-specific tracing of EV origin without bias towards the expression of individual protein markers and will allow detailed future examination of their function.
The temporal structure of the inner retina at a single glance
Authors: Zhao Zhijian , Klindt David , Chagas André Maia , Szatko Klaudia P. , Rogerson Luke , Protti Dario A. , Behrens Christian , Dalkara Deniz , Schubert Timm , Bethge Matthias , Franke Katrin , Berens Philipp , Ecker Alexander , Euler Thomas 
Published: August 2019

AbstractThe retina decomposes visual stimuli into parallel channels that encode different features of the visual environment. Central to this computation is the synaptic processing in a dense and thick layer of neuropil, the so-called inner plexiform layer (IPL). Here, different types of bipolar cells stratifying at distinct depths relay the excitatory feedforward drive from photoreceptors to amacrine and ganglion cells. Current experimental techniques for studying processing in the IPL do not allow imaging the entire IPL simultaneously in the intact tissue. Here, we extend a two-photon microscope with an electrically tunable lens allowing us to obtain optical vertical slices of the IPL, which provide a complete picture of the response diversity of bipolar cells at a “single glance”. The nature of these axial recordings additionally allowed us to isolate and investigate batch effects, i.e. inter-experimental variations resulting in systematic differences in response speed. As a proof of principle, we developed a simple model that disentangles biological from experimental causes of variability, and allowed us to recover the characteristic gradient of response speeds across the IPL with higher precision than before. Our new framework will make it possible to study the computations performed in the central synaptic layer of the retina more efficiently.
Women in control and tax compliance
Authors: Damayanti Theresia Woro , Supramono Supramono 
Published: August 2019

PurposeThe study aims to empirically analyze the effects of the presence of female top managers and owners on corporate tax compliance.Design/methodology/approachData for analysis were sourced from the World Bank Enterprise Surveys that involved 23,178 private firms in 98 countries. The surveys used a stratified random sampling method by using three criteria, namely, firm size, business sector and geographic region, within each country. Further, data are analyzed using the ordinal logistic regression and supported by the marginal effect analysis.FindingsThe results show that the presence of female top managers and owners is a significant factor that underlies the firm-level tax compliance difference when firms exhibit relatively lower compliance.Practical implicationsAlthough this study shows that the determinants of corporate tax compliance are very complex, there are also crucial roles of top managers and owners' gender. This study advises firms to use the gender equality strategy to generate the best human capital, especially in their top management levels. Besides, this study can be helpful in designing policies that facilitate women to reach top managerial levels or to own businesses as an alternative method to enhance tax compliance for developing countries that fail to generate optimal corporate income tax revenues.Originality/valueTo the best of the authors’ knowledge, no previous studies examine the effects of the presence of female top managers and business owners on firms’ tax compliance policies. This study contributes to extend the understanding of the important role of women in corporate strategic decision-making, especially in taxation policies in various developing countries.