bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generative modelling of the thalamo-cortical circuit mechanisms underlying the neurophysiological effects of ketamine
Authors: Shaw Alexander D , Muthukumaraswamy Suresh D , Saxena Neeraj , Sumner Rachael L , Adams Natalie , Moran Rosalyn J , Singh Krish D 
Published: July 2019

AbstractCortical recordings of task-induced oscillations following subanaesthetic ketamine administration demonstrate alterations in amplitude, including increases at high-frequencies (gamma) and reductions at low frequencies (theta, alpha). To investigate the population-level interactions underlying these changes, we implemented a thalamo-cortical model (TCM) capable of recapitulating broadband spectral responses. Compared with an existing cortex-only 4-population model, Bayesian Model Selection preferred the TCM. The model was able to accurately and significantly recapitulate ketamine-induced reductions in alpha amplitude and increases in gamma amplitude. Parameter analysis revealed no change in receptor time-constants but significant increases in select synaptic connectivity with ketamine. Significantly increased connections included both AMPA and NMDA mediated connections from layer 2/3 superficial pyramidal cells to inhibitory interneurons and both GABAA and NMDA mediated within-population gain control of layer 5 pyramidal cells. These results support the use of extended generative models for explaining oscillatory data and provide in silico support for ketamine’s ability to alter local coupling mediated by NMDA, AMPA and GABA-A.
Realistic modeling of ephaptic fields in the human brain
Authors: Ruffini Giulio , Salvador Ricardo , Tadayon Ehsan , Sanchez-Todo Roser , Pascual-Leone Alvaro , Santarnecchi Emiliano 
Published: July 2019

AbstractSeveral decades of research suggest that weak electric fields may influence neural processing, including those induced by neuronal activity and recently proposed as substrate for a potential new cellular communication system, i.e., ephaptic transmission. Here we aim to map ephaptic activity in the human brain and explore its trajectory during aging by characterizing the macroscopic electric field generated by cortical dipoles using realistic finite element modeling. We find that modeled endogenous field magnitudes are comparable to those in measurements of weak but functionally relevant endogenous fields and to those generated by noninvasive transcranial brain stimulation, therefore possibly able to modulate neuronal activity. Then, to evaluate the role of self-generated ephaptic fields in the human cortex, we adapt an interaction approximation that considers the relative orientation of neuron and field to derive the membrane potential perturbation in pyramidal cells. Building on this, we define a simplified metric (EMOD1) that weights dipole coupling as a function of distance and relative orientation between emitter and receiver and evaluate it in a sample of 401 realistic human brain models from subjects aged 16-83. Results reveal that ephaptic modulation follows gyrification patterns in the human brain, and significantly decreases with age, with higher involvement of sensorimotor regions and medial brain structures. By providing the means for fast and direct interaction between neurons, ephaptic modulation likely contributes to the complexity of human function for cognition and behavior, and its modification across the lifespan and in response to pathology.
The Norepinephrine Metabolite DOPEGAL Confers Locus Coeruleus Tau Vulnerability and Propagation via Asparagine Endopeptidase
Authors: Kang Seong Su , Liu Xia , Ahn Eun Hee , Xiang Jie , Manfredsson Fredric P. , Yang Xifei , Luo Hongbo R. , Liles L. Cameron , Weinshenker David , Ye Keqiang 
Published: July 2019

AbstractAberrant Tau inclusions in the locus coeruleus (LC) are the earliest detectable Alzheimer’s disease (AD)-like neuropathology in the human brain; however, why LC neurons are selectively vulnerable to developing early Tau pathology and degenerating later in disease and whether the LC might seed the stereotypical spread of Tau pathology to the rest of the brain remain unclear. Here we show that 3,4-dihydroxyphenylglycolaldehyde (DOPEGAL), which is produced exclusively in noradrenergic neurons by monoamine oxidase A (MAO-A) metabolism of norepinephrine (NE), activates asparagine endopeptidase (AEP) that cleaves Tau at residue N368 into aggregation- and propagation-prone forms, thereby leading to LC degeneration and the spread of Tau pathology. DOPEGAL triggers AEP-cleaved Tau aggregationin vitroand in intact cells, resulting in LC neurotoxicity and propagation of pathology to the forebrain. Thus, our findings reveal a novel molecular mechanism underlying the selective vulnerability of LC neurons in AD.
Biased neural representation of feature-based attention in the human brain
Authors: Gong Mengyuan , Liu Taosheng 
Published: July 2019

AbstractSelective attention is a core cognitive function for efficient processing of information. Although it is well known that attention can modulate neural responses in many brain areas, the computational principles underlying attentional modulation remain unclear. Contrary to the prevailing view of a high-dimensional, distributed neural representation, here we show a surprisingly simple, biased neural representation for feature-based attention in a large dataset including five human fMRI studies. We found that when participants selected one feature from a compound stimulus, voxels in many cortical areas responded consistently higher to one attended feature over the other. This univariate bias was robust at the level of single brain areas and consistent across brain areas within individual subjects. Importantly, this univariate bias showed a progressively stronger magnitude along the cortical hierarchy. In frontoparietal areas, the bias was strongest and contributed largely to pattern-based decoding, whereas early visual areas lacked such a bias. These findings suggest a gradual transition from a more analog to a more abstract representation of attentional priority along the cortical hierarchy. Biased neural responses in high-level areas likely reflect a low-dimensional neural code that facilitates robust representation and simple read-out of cognitive variables.
PhyloMagnet: Fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics
Authors: Schön Max E. , Eme Laura , Ettema Thijs J.G. 
Published: July 2019

MotivationMetagenomic and metatranscriptomic sequencing analyses have become increasingly popular tools for producing massive amounts of short-read data, often used for the reconstruction of draft genomes or the detection of (active) genes in microbial communities. Unfortunately, sequence assemblies of such datasets generally remain a computationally challenging task. Frequently, researchers are only interested in a specific group of organisms or genes; yet, the assembly of multiple datasets only to identify candidate sequences for a specific question is sometimes prohibitively slow, forcing researchers to select a subset of available datasets to address their question. Here we present PhyloMagnet, a workflow to screen meta-omics datasets for taxa and genes of interest using gene-centric assembly and phylogenetic placement of sequences.ResultsUsing PhyloMagnet, we could identify up to 87% of the genera in anin vitromock community with variable abundances, while the false positive predictions per single gene tree ranged from 0% to 23%. When applied to a group of metagenomes for which a set of MAGs have been published, we could detect the majority of the taxonomic labels that the MAGs had been annotated with. In a metatranscriptomic setting the phylogenetic placement of assembled contigs corresponds to that of transcripts obtained from transcriptome assembly.AvailabilityPhyloMagnet is built using Nextflow, available atgithub.com/maxemil/PhyloMagnetand is developed and tested on Linux. It is released under the open source GNU GPL license and documentation is available atphylomagnet.readthedocs.io. Version 0.5 of PhyloMagnet was used for all benchmarks experiments.
Outwitting planarian’s antibacterial defence mechanisms:Rickettsialesbacterial trans-infection fromParamecium multimicronucleatumto planarians
Authors: Modeo Letizia , Salvetti Alessandra , Rossi Leonardo , Castelli Michele , Szokoli Franziska , Krenek Sascha , Sabaneyeva Elena , Di Giuseppe Graziano , Fokin Sergei I. , Verni Franco , Petroni Giulio 
Published: July 2019

AbstractMost of the microorganisms belonging to genera responsible for vector-borne diseases (VBD) have hematophagous arthropods as vector/reservoir. Recently, many new species of microorganisms phylogenetically related to agents of VBD were found in a variety of aquatic eukaryotic hosts, in particular, numerous new bacterial species related to the genusRickettsia(Alphaproteobacteria, Rickettsiales) were discovered in protist ciliates and other unicellular eukaryotes. Although their pathogenicity for humans and terrestrial animals is not known, these bacteria might act as etiological agents of possible VBD of aquatic organisms, with protist as vectors. In the present study, we characterized a novel strain of theRickettsia-Like Organism (RLO) endosymbiont “Candidatus(Ca.) Trichorickettsia mobilis” in the macronucleus of the ciliateParamecium multimicronucleatumthrough FluorescenceIn SituHybridization (FISH) and molecular analyses. Ultrastructural investigations on the presence of flagella confirmed previous studies on the same bacterial species. The potential trans-infection perosof this bacterium to planarians (Dugesia japonica), a widely used model system able to eliminate a wide range of bacteria pathogenic to humans and other Metazoa, was further verified. Ciliate mass cultures were set up, and trans-infection experiments were performed by adding homogenized paramecia to food of antibiotic-treated planarians, performed. Treated and non-treated (i.e. control) planarians were investigated at day 1, 3, and 7 after feeding for endosymbiont presence by means of PCR and ultrastructural analyses. Obtained results were fully concordant and suggest that this RLO endosymbiont can be transferred from ciliates to metazoans, being detected up to day 7 in treated planarian enterocytes inside and, possibly, outside phagosomes.
Current range of Agrilus planipennis Fairmaire, an alien pest of ash trees, in European Russia and Ukraine
Authors: Orlova-Bienkowskaja Marina J. , Drogvalenko Alexander N. , Zabaluev Ilya A. , Sazhnev Alexey S. , Peregudova Elena Y. , Mazurov Sergey G. , Komarov Evgenij V. , Struchaev Vitalij V. , Martynov Vladimir V. , Nikulina Tatyana V. , Bieńkowski Andrzej O. 
Published: July 2019

AbstractContextThe first detection of A. planipennis in European Russia was in Moscow in 2003, when it began to spread.AimTo determine the range of A. planipennis as of 2020.MethodsIn 2017-2020, our Russian-Ukrainian research team examined >7000 F. pennsylvanica trees and >2500 F. excelsior trees in 84 localities of European Russia, Ukraine and Belarus.ResultsThe current range exceeds the area of Spain and includes the Luhansk region of Ukraine and 16 regions of ER: Belgorod, Bryansk, Kaluga, Kursk, Lipetsk, Moscow, Orel, Ryazan, Smolensk, Tambov, Tula, Tver, Vladimir, Volgograd, Voronezh, and Yaroslavl. Agrilus planipennis was not detected in Belarus. The overwhelming majority of the infestations were found on F. pennsylvanica. All known cases of infestation of the native species (F. excelsior) are from artificial plantings.ConclusionAgrilus planipennis will appear in other European countries soon and damage F. pennsylvanica. Further surveys are necessary to determine whether A. planipennis infests F. excelsior in forests.
Epithelial-Mesenchymal Plasticity is regulated by inflammatory signalling networks coupled to cell morphology
Authors: Garcia Mar Arias , Yin Zheng , Roumeliotis Theodoros I. , Butera Francesca , Wang Lin , Rickman Rebecca , Choudhary Jyoti , Wong Stephen T.C. , Yuan Yinyin , Bakal Chris 
Published: July 2019

AbstractMorphology dictates how cells sense physical and soluble cues in their environment; thus contributing to fate decisions. The differentiation of epithelial cells into mesenchymal forms, or epithelial-mesenchymal plasticity (EMP), is essential for metazoan development and homeostasis. Here we show that the decision to engage EMP is coupled to cell morphology by cell-cell adhesions by microtubule and nuclear organization (MTNO). Using an integrative ‘omic approach we identify Junctional Adhesion Molecule 3 (JAM3) as a new tumour suppressor in breast cancer patients. JAM3 depletion in epithelial cells alters MTNO and causes differentiation into mesenchymal forms. Soluble TGFβ also changes MTNO, and synergizes with JAM3 depletion to promote mesenchymal morphogenesis. Through systematic proteomic analysis we show that changes in MTNO lead to the upregulation of an inflammatory signalling network where YAP/TAZ, FOXO, IKK-NFKB, and JNK pathways are active; but where insulin signalling is suppressed. The actions of the MT-motor Kinesin-1 serve to both change MTNO and promote the upregulation of the core EMP network. Critically, the upregulation of the EMP network predicts the mesenchymal state across cancers.Graphical Abstract
A geostatistical approach to estimate high resolution nocturnal bird migration densities from a weather radar network
Authors: Nussbaumer Raphaël , Benoit Lionel , Mariethoz Grégoire , Liechti Felix , Bauer Silke , Schmid Baptiste 
Published: July 2019

AbstractQuantifying nocturnal bird migration at high resolution is essential for (1) understanding the phenology of migration and its drivers, (2) identifying critical spatio-temporal protection zones for migratory birds, and (3) assessing the risk of collision with man-made structures.We propose a tailored geostatistical model to interpolate migration intensity monitored by a network of weather radars. The model is applied to data collected in autumn 2016 from 69 European weather radars. To cross-validate the model, we compared our results with independent measurements of two bird radars.Our model estimated bird densities at high resolution (0.2°latitude-longitude, 15min) and assessed the associated uncertainty. Within the area covered by the radar network, we estimated that around 120 million birds were simultaneously in flight [10-90 quantiles: 107-134]. Local estimations can be easily visualized and retrieved from a dedicated interactive website:birdmigrationmap.vogelwarte.ch.This proof-of-concept study demonstrates that a network of weather radar is able to quantify bird migration at high resolution and accuracy. The model presented has the ability to monitor population of migratory birds at scales ranging from regional to continental in space and daily to yearly in time. Near-real-time estimation should soon be possible with an update of the infrastructure and processing software.
mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation
Authors: Werner Johannes , Geron Augustin , Kerssemakers Jules , Matallana-Surget Sabine 
Published: July 2019

AbstractMetaproteomics allows to decipher the structure and functionality of microbial communities. Despite its rapid development, crucial steps such as the creation of standardized protein search databases and reliable protein annotation remain challenging. To overcome those critical steps, we developed a new program named mPies (metaProteomics in environmental sciences). mPies allows the creation of protein databases derived from assembled or unassembled metagenomes, and/or public repositories based on taxon IDs, gene or protein names. For the first time, mPies facilitates the automatization of reliable taxonomic and functional consensus annotations at the protein group level, minimizing the well-known protein inference issue which is commonly encountered in metaproteomics. mPies’ workflow is highly customizable with regards to input data, workflow steps, and parameter adjustment. mPies is implemented in Python 3/Snakemake and freely available on GitHub: https://github.com/johanneswerner/mPies/.
Kinetic study of the expression of genes related to hepatic steatosis, global intermediate metabolism and cellular stress during overfeeding in mule ducks
Authors: Pioche Tracy , Skiba Fabien , Bernadet Marie-Dominique , Seiliez Iban , Massimino William , Houssier Marianne , Tavernier Annabelle , Ricaud Karine , Davail Stéphane , Skiba-Cassy Sandrine , Gontier Karine 
Published: July 2019

ABSTRACTInduced by overfeeding, hepatic steatosis is a reversible process exploited for “foie gras” production. To better understand the mechanisms underlying this non-pathological phenomenon, we analysed the physiological responses of the mule duck to cope with 22 carbohydrate meals. A kinetic analysis of intermediate metabolism and cell protection mechanisms was performed during overfeeding. As expected, dietary carbohydrates are up taken mainly by the liver (chrebp, glut1/2/8) and converted into lipids (acox, scd1, acsl1, fas, dgat2). Our study showed an activation of cholesterol biosynthetic pathway with significant correlations between plasma cholesterol, expression of key genes (hmgcr, soat1) and liver weight. Results revealed an activation of insulin and amino acid cell signalling pathway suggesting that ducks boost insulin sensitivity to raise glucose uptake and useviaglycolysis and lipogenesis. Expression ofcpt1a, acad, hadhsuggested an induction of beta-oxidation probably to remove part of newly synthesized lipids and avoid lipotoxicity. Cellular stress analysis revealed an upregulation of autophagy-related gene expression (atg8, atg9, sqstm1) in contrast with an induction ofcyp2e1suggesting that autophagy could be suppressed.Lamp2aandplin2enhanced, conflicting with the idea of an inhibition of lipophagy.Hsbp1overexpression indicated that mechanisms are carried out during overfeeding to limit cellular stress and apoptosis to prevent the switch to pathological state.Atf4andasnsoverexpression reflects the nutritional imbalance during overfeeding. These results permitted to highlight the mechanisms enabling mule ducks to efficiently handle the huge starch overload and reveal potential biomarker candidates of hepatic steatosis as plasma cholesterol for liver weight.
Non-ohmic tissue conduction in cardiac electrophysiology: upscaling the non-linear voltage-dependent conductance of gap junctions
Authors: Hurtado Daniel E. , Jilberto Javiera , Panasenko Grigory 
Published: July 2019

AbstractGap junctions are key mediators of the intercellular communication in cardiac tissue, and their function is vital to sustain normal cardiac electrical activity. Conduction through gap junctions strongly depends on the hemichannel arrangement and transjunctional voltage, rendering the intercellular conductance highly non-Ohmic. Despite this marked non-linear behavior, current tissue-level models of cardiac conduction are rooted on the assumption that gap-junctions conductance is constant (Ohmic), which results in inaccurate predictions of electrical propagation, particularly in the low junctional-coupling regime observed under pathological conditions. In this work, we present a novel non-Ohmic multiscale (NOM) model of cardiac conduction that is suitable for tissue-level simulations. Using non-linear homogenization theory, we develop a conductivity model that seamlessly upscales the voltage-dependent conductance of gap junctions, without the need of explicitly modeling gap junctions. The NOM model allows for the simulation of electrical propagation in tissue-level cardiac domains that accurately resemble that of cell-based microscopic models for a wide range of junctional coupling scenarios, recovering key conduction features at a fraction of the computational complexity. A unique feature of the NOM model is the possibility of upscaling the response of non-symmetric gap-junction conductance distributions, which result in conduction velocities that strongly depend on the direction of propagation, thus allowing to model the normal and retrograde conduction observed in certain regions of the heart. We envision that the NOM model will enable organ-level simulations that are informed by sub- and inter-cellular mechanisms, delivering an accurate and predictive in-silico tool for understanding the heart function.Author summaryThe heart relies on the propagation of electrical impulses that are mediated gap junctions, whose conduction properties vary depending on the transjunctional voltage. Despite this non-linear feature, current mathematical models assume that cardiac tissue behaves like an Ohmic (linear) material, thus delivering inaccurate results when simulated in a computer. Here we present a novel mathematical multiscale model that explicitly includes the non-Ohmic response of gap junctions in its predictions. Our results show that the proposed model recovers important conduction features modulated by gap junctions at a fraction of the computational complexity. This contribution represents an important step towards constructing computer models of a whole heart that can predict organ-level behavior in reasonable computing times.
New Geographies of Residential Capitalism: Financialization of the Turkish Housing Market Since the Early 2000s
Authors: Erol Isil 
Published: July 2019

AbstractThe post‐2001 financial crisis era in Turkey gave rise to twin booms in housing construction and credit markets, both of which suffered from the subsequent debt crisis. The financial transformation of the economy in conjunction with state‐led urban legislation reform had significant effects on the housing market in terms of commodification of housing, countrywide construction activities and substantial increases in household debt and construction company loans. The changing role and function of the state as a direct provider of housing can be regarded as actually existing neoliberalism providing favourable conditions for financialization, as it ushered in the commodification of housing. The Turkish government, together with the government‐backed housing agency, metropolitan municipalities and publicly owned real‐estate investment company, has been active in nationwide housing construction and urban regeneration projects. This article argues that there is a lack of synchrony between the commodification of housing and the financialization of the household sector owing to the institutional setting of the mortgage system and structural macroeconomic problems. Rather, housing commodification has been accompanied by the financialization of the corporate sector through a steep rise in the external debt burden of construction companies.
Legal Technologies of Primitive Accumulation: Judicial Robbery and Dispossession‐by‐Restitution in Warsaw
Authors: Kusiak Joanna 
Published: July 2019

AbstractAmong the ‘extra‐economic means’ that facilitate primitive accumulation, or accumulation by dispossession, the law plays a prominent role. But works on neoliberal urban restructuring rarely engage with concrete legal technologies. Analysing judicial property restitution (‘reprivatization’) in Warsaw, this article grasps the machine of accumulation by dispossession at a moment of faltering and exposes the distinctive legal technologies behind its troubleshooting. It makes three contributions to critical urban studies. First, it demonstrates how judicial systems can steal political conflicts that obstruct the cycle of accumulation by dispossession. It thus introduces the notion of ‘judicial robbery’, a non‐legislated expropriation of common property through judicial engineering that simultaneously deprives the public of political agency. Second, it shows that seemingly neutral legal technicalities, usually sheltered from political debate, can become a key locus of urban politics. Third, it examines the agency, scope and spatial patterns of ‘dispossession by restitution’, the term I use for a locally specific form of accumulation by dispossession in Warsaw. Lastly, I raise the question of political struggle against primitive accumulation. Is the judicial robbery reversible? If we can reclaim property, can we also reclaim political conflicts that have been stolen by the law?