bluuebunny/crossref_metadata_2025_split huggingface dataset:
Speciation and gene flow across an elevational gradient in New Guinea kingfishers
Authors: Linck Ethan , Freeman Benjamin G. , Dumbacher John P. 
Published: March 2019

AbstractClosely related species with parapatric elevational ranges are ubiquitous in tropical mountains worldwide. The gradient speciation hypothesis proposes that these series are the result of in situ ecological speciation driven by divergent selection across elevation. Direct tests of this scenario have been hampered by the difficulty inferring the geographic arrangement of populations at the time of divergence. In cichlids, sticklebacks, and Timema stick insects, support for ecological speciation driven by other selective pressures has come from demonstrating parallel speciation, where divergence proceeds independently across replicated environmental gradients. Here, we take advantage of the unique geography of the island of New Guinea to test for parallel gradient speciation in replicated populations of Syma kingfishers that show extremely subtle differentiation across elevation and between historically isolated mountain ranges. We find that currently described high elevation and low elevation species have reciprocally monophyletic gene trees and form nuclear DNA clusters, rejecting this hypothesis. However, demographic modeling suggests selection has likely maintained species boundaries in the face of gene flow following secondary contact. We compile evidence from the published literature to show that while in situ gradient speciation in labile organisms such as birds appears rare, divergent selection and post-speciation gene flow may be an underappreciated force in the origin of elevational series and tropical beta diversity along mountain slopes.
Cardiac structure and function in patients with schizophrenia taking antipsychotic drugs: an MRI study
Authors: Pillinger Toby , Osimo Emanuele F. , de Marvao Antonio , Berry Alaine , Whitehurst Thomas , Statton Ben , Quinlan Marina , Brugger Stefan , Vazir Ali , Cook Stuart A. , O’Regan Declan P. , Howes Oliver D. 
Published: March 2019

AbstractCardiovascular disease (CVD) is a major cause of excess mortality in schizophrenia. Preclinical evidence shows antipsychotics can cause myocardial fibrosis and myocardial inflammation in murine models, but it is not known if this is the case in patients. We therefore set out to determine if there is evidence of cardiac fibrosis and/or inflammation using cardiac MRI in medicated patients with schizophrenia compared with matched healthy controls. 31 participants (14 patients and 17 controls) underwent cardiac MRI assessing myocardial markers of fibrosis/inflammation, indexed by native myocardial T1 time, and cardiac structure (left ventricular (LV) mass) and function (left/right ventricular end-diastolic and end-systolic volumes, stroke volumes, and ejection fractions). Participants were physically fit, and matched for age, gender, smoking, blood pressure, BMI, HbA1c, ethnicity, and physical activity. Compared with controls, native myocardial T1 was significantly longer in patients with schizophrenia (effect size, d=0.89; p=0.02). Patients had significantly lower LV mass, and lower left/right ventricular end-diastolic and stroke volumes (effect sizes, d=0.86-1.08; all p-values <0.05). There were no significant differences in left/right end-systolic volumes and ejection fractions between groups (p>0.05). These results suggest an early diffuse fibro-inflammatory myocardial process in patients that is independent of established CVD-risk factors and could contribute to the excess cardiovascular mortality associated with schizophrenia. Future studies are required to determine if this is due to antipsychotic treatment or is intrinsic to schizophrenia.
Spectral graph theory of brain oscillations
Authors: Raj Ashish , Cai Chang , Xie Xihe , Palacios Eva , Owen Julia , Mukherjee Pratik , Nagarajan Srikantan 
Published: March 2019

AbstractThe relationship between the brain’s structural wiring and the functional patterns of neural activity is of fundamental interest in computational neuroscience. We examine a hierarchical, linear graph spectral model of brain activity at mesoscopic and macroscopic scales. The model formulation yields an elegant closed-form solution for the structure-function problem, specified by the graph spectrum of the structural connectome’s Laplacian, with simple, universal rules of dynamics specified by a minimal set of global parameters. The resulting parsimonious and analytical solution stands in contrast to complex numerical simulations of high dimensional coupled non-linear neural field models. This spectral graph model accurately predicts spatial and spectral features of neural oscillatory activity across the brain and was successful in simultaneously reproducing empirically observed spatial and spectral patterns of alpha-band (8-12 Hz) and beta-band (15-30Hz) activity estimated from source localized scalp magneto-encephalography (MEG). This spectral graph model demonstrates that certain brain oscillations are emergent properties of the graph structure of the structural connectome and provides important insights towards understanding the fundamental relationship between network topology and macroscopic whole-brain dynamics.Significance StatementThe relationship between the brain’s structural wiring and the functional patterns of neural activity is of fundamental interest in computational neuroscience. We examine a hierarchical, linear graph spectral model of brain activity at mesoscopic and macroscopic scales. The model formulation yields an elegant closed-form solution for the structure-function problem, specified by the graph spectrum of the structural connectome’s Laplacian, with simple, universal rules of dynamics specified by a minimal set of global parameters. This spectral graph model demonstrates that certain brain oscillations are emergent properties of the graph structure of the structural connectome and provides important insights towards understanding the fundamental relationship between network topology and macroscopic whole-brain dynamics.
Volumetric two-photon imaging in live cells and embryos via axially gradient excitation
Authors: Gao Yufeng , Xia Xianyuan , Yu Jia , Chen Tingai , Xu Zhili , Xiao Long , Wang Liang , Yan Fei , Du Zhuo , Chu Jun , Zheng Hairong , Li Hui , Zheng Wei 
Published: March 2019

AbstractTwo-photon microscopy(TPM) that features subcellular resolution, intrinsic optical sectioning ability, and deep penetration in sample is a powerful tool of bioimaging. However, the process of layer-by-layer scanning to form a 3D image inherently limits the volumetric imaging speed and significantly increases the phototoxicity. Here we develop a gradient TPM technique that enables rapid volumetric imaging by only acquiring two 2D images. By sequentially exciting the specimen with two axially elongated two-photon beams with complementary gradient intensities, the axial positions of fluorophores can be decoded from the intensity ratio of the paired images. We achieve an axial localization accuracy of 0.728 ± 0.657 μm, which is sufficient for rapid 3D subcellular imaging. We demonstrate the flexibility of the gradient TPM on a variety of sparsely labelled samples, including bead phantoms, mouse brain tissues, live macrophages and live nematode embryos. The results show that, compared with conventional TPM, the 3D imaging speed increases 6 folds while the photobleaching and photodamage are extremely reduced.
MiR-218: A Molecular Switch and Potential Biomarker of Susceptibility to Stress
Authors: Torres-Berrío Angélica , Nouel Dominique , Cuesta Santiago , Parise Eric M. , Restrepo-Lozano José María , Larochelle Pier , Nestler Eric J. , Flores Cecilia 
Published: March 2019

ABSTRACTLow miR-218 expression in the medial prefrontal cortex (mPFC) is a consistent trait of depression. Here we assessed whether miR-218 in the mPFC confers resilience or susceptibility to depression-like behaviors in adult mice, using the chronic social defeat stress (CSDS) model of depression. We also investigated whether stress-induced variations of miR-218 expression in the mPFC can be detected in blood. We find that downregulation of miR-218 in the mPFC increases susceptibility to a single session of social defeat, whereas overexpression of miR-218 selectively in mPFC pyramidal neurons promotes resilience to CSDS and prevents stress-induced morphological alterations to those neurons. After CSDS, susceptible mice have low levels of miR-218 in the blood as compared to control or resilient groups. We show further that up-and downregulation of miR-218 levels specifically in the mPFC correlates with miR-218 expression in blood. Our results suggest that miR-218 in the adult mPFC might function as a molecular switch that determines susceptibility versus resilience to chronic stress, and that stress-induced variations in mPFC levels of miR-218 could be detected in blood. We propose that blood expression of miR-218 might serve as potential readout of vulnerability to stress and as a proxy of mPFC function.
A Robust Model of Gated Working Memory
Authors: Strock Anthony , Hinaut Xavier , Rougier Nicolas P. 
Published: March 2019

AbstractGated working memory is defined as the capacity of holding arbitrary information at any time in order to be used at a later time. Based on electrophysiological recordings, several computational models have tackled the problem using dedicated and explicit mechanisms. We propose instead to consider an implicit mechanism based on a random recurrent neural network. We introduce a robust yet simple reservoir model of gated working memory with instantaneous updates. The model is able to store an arbitrary real value at random time over an extended period of time. The dynamics of the model is a line attractor that learns to exploit reentry and a non-linearity during the training phase using only a few representative values. A deeper study of the model shows that there is actually a large range of hyper parameters for which the results hold (number of neurons, sparsity, global weight scaling, etc.) such that any large enough population, mixing excitatory and inhibitory neurons can quickly learn to realize such gated working memory. In a nutshell, with a minimal set of hypotheses, we show that we can have a robust model of working memory. This suggests this property could be an implicit property of any random population, that can be acquired through learning. Furthermore, considering working memory to be a physically open but functionally closed system, we give account on some counter-intuitive electrophysiological recordings.
Phylogenetic inference of changes in amino acid propensities with single-position resolution
Authors: Klink Galya V. , Kalinina Olga V. , Bazykin Georgii A. 
Published: March 2019

AbstractFitness conferred by the same allele may differ between genotypes, and these differences shape variation and evolution. Changes in amino acid propensities at protein sites over the course of evolution have been inferred from sequence alignments statistically, but the existing methods are data-intensive and aggregate multiple sites. Here, we develop an approach to detect individual amino acids that confer different fitness in different groups of species from combined sequence and phylogenetic data. Using the fact that the probability of a substitution to an amino acid depends on its fitness, our method looks for amino acids such that substitutions to them occur more frequently in one group of lineages than in another. We validate our method using simulated evolution of a protein site under different scenarios and show that it has high specificity for a wide range of assumptions regarding the underlying changes in selection, while its sensitivity differs between scenarios. We apply our method to the env gene of two HIV-1 subtypes, A and B, and to the HA gene of two influenza A subtypes, H1 and H3, and show that the inferred fitness changes are consistent with the fitness differences observed in deep mutational scanning experiments. We find that changes in relative fitness of different amino acid variants within a site do not always trigger episodes of positive selection and therefore may not result in an overall increase in the frequency of substitutions, but can still be detected from changes in relative frequencies of different substitutions.Author summaryWhich amino acids are acceptable at a certain protein site can change with time. In viruses, for example, this can be due to changes in mechanisms of drug resistance and immune escape in the course of evolution. Here, we develop a method for detecting such changes from how evolutionary events are distributed over an evolutionary tree. Informally, we infer that a certain amino acid is favored in a certain group of lineages if substitutions giving rise to it repeatedly occur in the evolution of this group, and disfavored if such substitutions are rare. In surface proteins of HIV-1 and influenza A, we find that changes in preferences detected with d-test match those observed in deep mutational scanning experiments. Our purely bioinformatic approach allows inference of changes in selection between lineages from sequences alone, shedding light on the functional differences between strains or species even in the absence of any structural or functional data.
Hippo pathway effectors YAP1/TAZ induce a EWS-FLI1-opposing gene signature and associate with disease progression in Ewing Sarcoma
Authors: Rodríguez-Núñez Pablo , Romero-Pérez Laura , Amaral Ana T. , Puerto-Camacho Pilar , Jordán Carmen , Marcilla David , Grunewald Thomas G. P. , de Alava Enrique , Díaz-Martín Juan 
Published: March 2019

AbstractYAP1 and TAZ (WWTR1) oncoproteins are the final transducers of Hippo tumor suppressor pathway. Deregulation of the pathway leads to YAP1/TAZ activation fostering tumorigenesis in multiple malignant tumor types, including sarcoma. However, oncogenic mutations within the core components of the Hippo pathway are uncommon. Ewing Sarcoma (EwS), a pediatric cancer with low mutation rate, is characterized by a canonical fusion involvingEWSR1gene, andFLI1as the most common partner. The fusion protein is a potent driver of oncogenesis but secondary alterations are scarce, and little is known about other biological factors that determine the risk of relapse or progression. We have observed YAP1/TAZ expression and transcriptional activity in EwS cell lines. Analyses of 55 primary human EwS samples revealed that high YAP1/TAZ expression was associated with progression of the disease and predicted poorer outcome.We did not observe recurrent SNV or copy number gains/losses in Hippo pathway-related loci. However, differential CpG methylation ofRASSF1locus -a regulator of Hippo pathway- was observed in EwS cell lines compared with mesenchymal stem cells, the putative cell of origin of EwS. Hypermethylation ofRASSF1correlated with the transcriptional silencing of the tumor suppressor isoformRASFF1A, and transcriptional activation of the protumorigenic isoformRASSF1Cpromoting YAP1/TAZ activation. Knockdown of YAP1/TAZ decreased proliferation and invasion abilities of EwS cells, and revealed that YAP1/TAZ transcription activity is inversely correlated with the EWS-FLI1 transcriptional signature. This transcriptional antagonism could be partly explained by EWS-FLI1-mediated transcriptional repression of TAZ. Thus, YAP1/TAZ may override the transcriptional program induced by the fusion protein, contributing to the phenotypic plasticity determined by dynamic fluctuation of the fusion protein, a recently proposed model for disease dissemination in EwS.
Childhood socio-economic disadvantage predicts reduced myelin growth across adolescence and young adulthood
Authors: Ziegler Gabriel , Moutoussis Michael , Hauser Tobias U. , Fearon Pasco , Bullmore Edward T. , Goodyer Ian M. , Fonagy Peter , Jones Peter B. ,   NSPN Consortium, Lindenberger Ulman , Dolan Raymond J. 
Published: March 2019

AbstractSocio-economic disadvantage (SED) increases exposure to life stressors. Animal research suggests early life stressors affect later neurodevelopment, including myelin developmental growth. To determine whether human childhood SED affects myelination in adolescence and early adulthood we measured the developmental increase of a sensitive myelin marker, magnetization transfer (MT), in a longitudinal study. Childhood SED was associated with globally reduced MT, as well as slower intra-cortical MT increase in widespread sensory-motor, cingulate, insular and prefrontal areas and subcortical areas. Parental education partially accounted for the SED effects on MT increase, while positive parenting provided a partial protection against the impact of SED. Thus, early socio-economic disadvantage, a vulnerability factor for a range of ill-health outcomes, is a risk factor for aberrant myelin growth during a critical developmental period that is associated with a high risk of psychiatric disorder.
Automated quantification of synaptic boutons reveals their 3D distribution in the honey bee mushroom body
Authors: Cabirol Amélie , Haase Albrecht 
Published: March 2019

AbstractSynaptic boutons are highly plastic structures undergoing experience-dependent changes in their number, volume, and shape. Their plasticity has been intensively studied in the insect mushroom bodies by manually counting the number of boutons in small regions of interest and extrapolating this number to the volume of the mushroom body neuropil.Here we extend this analysis to the synaptic bouton distribution within a larger subregion of the mushroom body olfactory neuropil of honey bees (Apis mellifera). This required the development of an automated method combining two-photon imaging with advanced image post-processing and multiple threshold segmentation. The method was first validated in subregions of the mushroom body olfactory and visual neuropils. Further analyses in the olfactory neuropil suggested that previous studies overestimated the number of synaptic boutons. As a reason for that, we identified boundaries effects in the small volume samples. The application of the automated analysis to larger volumes of the mushroom body olfactory neuropil revealed a corrected average density of synaptic boutons and, for the first time, their 3D spatial distribution. This distribution exhibited a considerable heterogeneity.This additional information on the synaptic bouton distribution provides the basis for future studies on brain development, symmetry, and plasticity.
Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers
Authors: Darolti Iulia , Wright Alison E. , Sandkam Benjamin A. , Morris Jake , Bloch Natasha I. , Farré Marta , Fuller Rebecca C. , Bourne Godfrey R. , Larkin Denis M. , Breden Felix , Mank Judith E. 
Published: March 2019

ABSTRACTOnce recombination is halted between the X and Y chromosome, sex chromosomes begin to differentiate and transition to heteromorphism. While there is a remarkable variation across clades in the degree of sex chromosome divergence, far less is known about variation in sex chromosome differentiation within clades. Here, we combined whole genome and transcriptome sequencing data to characterise the structure and conservation of sex chromosome systems across Poeciliidae, the livebearing clade that includes guppies. We found that thePoecilia reticulataXY system is much older than previously thought, being shared not only with its sister species,Poecilia wingei, but also withPoecilia picta, which diverged 30 mya. Despite the shared ancestry, we uncovered an extreme heterogeneity across these species in the proportion of the sex chromosome with suppressed recombination, and the degree of Y chromosome decay. The sex chromosomes inP. reticulataare largely homomorphic, with recombination persisting over a substantial fraction. However, the sex chromosomes inP. pictaare completely non-recombining and strikingly heteromorphic. ln addition to being highly divergent, the sex chromosome system inP. pictaincludes a neo-sex chromosome, the result of a fusion between the ancestral sex chromosome and part of chromosome 7. Remarkably, the profound degradation of the ancestral Y chromosome inP. pictais counterbalanced by the evolution of complete dosage compensation in this species, the first such documented case in teleost fish. Our results offer important insight into the initial stages of sex chromosome evolution and dosage compensation.
Single-molecule genome assembly of the BasketWillow, Salix viminalis, reveals earliest stages of sex chromosome expansion
Authors: Almeida Pedro , Proux-Wera Estelle , Churcher Allison , Soler Lucile , Dainat Jacques , Pucholt Pascal , Nordlund Jessica , Martin Tom , Rönnberg-Wästljung Ann Christine , Nystedt Björn , Berlin Sofia , Mank Judith E. 
Published: March 2019

AbstractSex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes and this leads to a range of non-adaptive modifications causing the gradual degeneration and gene loss on the sex-limited chromosome. However, because studies on sex chromosomes have primarily focused on old and highly differentiated sex chromosomes, the causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear. Here, we use long- and short-read single molecule sequencing approaches to assemble and annotate a draft genome of the basket willow,Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W divergence, largely the result of the accumulation of single nucleotide polymorphisms in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although a few genes present on the Z have already been lost from the W. Furthermore, we use multiple lines of evidence to test for inversions, which have long been assumed to halt recombination between the sex chromosomes. Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation.