bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathogen community composition and co-infection patterns in a wild community of rodents
Authors: Abbate Jessica L. , Galan Maxime , Razzauti Maria , Sironen Tarja , Voutilainen Liina , Henttonen Heikki , Gasqui Patrick , Cosson Jean-François , Charbonnel Nathalie 
Published: February 2020

AbstractRodents are major reservoirs of pathogens that can cause disease in humans and livestock. It is therefore important to know what pathogens naturally circulate in rodent populations, and to understand the factors that may influence their distribution in the wild. Here, we describe the occurrence and distribution patterns of a range of endemic and zoonotic pathogens circulating among rodent communities in northern France. The community sample consisted of 713 rodents, including 11 host species from diverse habitats. Rodents were screened for virus exposure (hantaviruses, cowpox virus, Lymphocytic choriomeningitis virus, Tick-borne encephalitis virus) using antibody assays. Bacterial communities were characterized using 16S rRNA amplicon sequencing of splenic samples. Multiple correspondence (MCA), multiple regression and association screening (SCN) analyses were used to determine the degree to which extrinsic factors (study year and site; host habitat, species, sex and age class) contributed to pathogen community structure, and to identify patterns of associations between pathogens within hosts. We found a rich diversity of bacterial genera, with 36 known or suspected to be pathogenic. We revealed that host species is the most important determinant of pathogen community composition, and that hosts that share habitats can have very different pathogen communities. Pathogen diversity and co-infection rates also vary among host species. Aggregation of pathogens responsible for zoonotic diseases suggests that some rodent species may be more important for transmission risk than others. Moreover, we detected positive associations between several pathogens, includingBartonella,Mycoplasmaspecies, Cowpox virus (CPXV) and hantaviruses, and these patterns were generally specific to particular host species. Altogether, our results suggest that host and pathogen specificity is the most important driver of pathogen community structure, and that interspecific pathogen-pathogen associations also depend on host species.
SpliceViNCI: Visualizing the splicing of non-canonical introns through recurrent neural networks
Authors: Dutta Aparajita , Singh Kusum Kumari , Anand Ashish 
Published: February 2020

AbstractMost of the current computational models for splice junction prediction are based on the identification of canonical splice junctions. However, it is observed that the junctions lacking the consensus dimersGTandAGalso undergo splicing. Identification of such splice junctions, called the non-canonical splice junctions, is also essentially important for a comprehensive understanding of the splicing phenomenon. This work focuses on the identification of non-canonical splice junctions through the application of a bidirectional long short-term memory (BLSTM) network. Furthermore, we apply a back-propagation based (integrated gradient) and a perturbation based (occlusion) visualization techniques to extract the non-canonical splicing features learned by the model. The features obtained are validated with the existing knowledge from the literature. Integrated gradient extracts features that comprise contiguous nucleotides, whereas occlusion extracts features that are individual nucleotides distributed across the sequence.
Septins coordinate cell wall integrity and lipid metabolism in a sphingolipid-dependent process
Authors: Mela Alexander , Momany Michelle 
Published: February 2020

AbstractDuring normal development and response to environmental stress, fungi must coordinate synthesis of the cell wall and plasma membrane. Septins, small cytoskeletal GTPases, colocalize with membrane sterol-rich regions and facilitate recruitment of cell wall synthases during dynamic wall remodeling. In this study we show that null mutants missing anAspergillus nidulanscore septin present in hexamers and octamers (ΔaspAcdc11, ΔaspBcdc3, or ΔaspCcdc12) are sensitive to multiple cell wall-disturbing agents known to activate the cell wall integrity MAPK pathway and that this sensitivity can be remediated by osmotic support. The null mutant missing the octamer-exclusive core septin (ΔaspDcdc10) showed similar osmotic-remedial sensitivity, but only to a single cell wall-disturbing agent and the null mutant missing the noncore septin (ΔaspE) showed very mild osmotic-remedial sensitivity to a different single agent. Representative core septin null mutants showed changes in cell wall polysaccharide composition, organization, and chitin synthase localization. Double mutant analysis withΔmpkAsuggested core septins interact with the cell wall integrity pathway. Null mutants missing any of the five septins were resistant to ergosterol-disrupting agents. The ΔaspAcdc11, ΔaspBcdc3, and ΔaspCcdc12mutants showed increased sensitivity to sphingolipid-disrupting agents that was remediated by addition of exogenous phytosphingosine. Representative core septins were mislocalized after treatment with sphingolipid-disrupting agents, but not after treatment with ergosterol-disrupting agents. When challenged with both sphingolipid-disturbing and cell wall-disturbing agents in combination, remediation of the lipid defect restored proper growth to ΔaspAcdc11, ΔaspBcdc3, and ΔaspCcdc12, but remediation of the cell wall defect did not. Our data suggest that the core hexamer and octamer septins are involved in cell wall integrity signaling with the noncore septin playing a minor role; that all five septins are involved in monitoring ergosterol metabolism; that the hexamer septins are required for sphingolipid metabolism; and that septins require sphingolipids to coordinate the cell wall integrity response.
Structural variation in hippocampal dentations among healthy young adults
Authors: ten Hove Julia , Poppenk Jordan 
Published: February 2020

AbstractLittle is known about hippocampus dentations – or “bumps” on the inferior surface of the hippocampus – and whether they hold functional significance. Empirical work on these features is beginning to emerge, but no study has yet been conducted in which their spatial positions are demarcated, and their putative role in individual differences in memory is based on a single small study. We gathered ultra-high resolution isotropic MTL scans from young-adult sample and performed such measurements. On the long axis, we found smaller and denser dentations moving towards the hippocampus’ posterior extent. Although other reports have distinguished the functional characteristics of anterior and posterior hippocampal dentations, we found hardly any were actually localized in the hippocampal head, with half of participants featuring no anterior dentations at all. We also observed more numerous dentations in the left hemisphere than right, and found this asymmetry tracked right-hand dominance. All dentations lay specifically within in the CA1 subfield, which was thicker at dentations – protruding below standard lower boundary of the hippocampus – as well as larger in participants with more dentations, suggesting dentations reflect CA1 growth rather than mere folding. Finally, we observed an association between dentations and visual source memory, but not recognition memory. The current report is the first to characterize the spatial properties of this intriguing neuroanatomical feature, which requires the direct spatial labeling of dentations. Further to better characterizing this intriguing neuroanatomical feature, we provide some confirmatory evidence for a link to episodic memory, although we found evidence for this link to be less overwhelming than initially reported.
Genome Wide Association Study of Resistance to PstS2 and Warrior Races of Stripe (Yellow) Rust in Bread Wheat Landraces
Authors: Tehseen Muhammad Massub , Tonk Fatma Aykut , Tosun Muzaffer , Amri Ahmed , Sansaloni Carolina P. , Kurtulus Ezgi , Yazbek Mariana , Al-Sham’aa Khaled , Ozseven Izzet , Safdar Luqman Bin , Shehadeh Ali , Nazari Kumarse 
Published: February 2020

ABSTRACTStripe rust, caused byPuccinia striiformisWestend. f. sp.triticiis a major threat to wheat production worldwide. The breakdown in resistance of certain major genes and new emerging aggressive races of stripe rusts are causing serious concerns in all main wheat growing areas of the world. To search for new sources of resistance genes and associated QTL for effective utilization in future breeding programs an association mapping panel comprising of 600 bread wheat landraces collected from eight different countries conserved at ICARDA gene bank were evaluated for seedling and adult plant resistance againstPstS2andWarriorraces of stripe rust at the Regional Cereal Rust Research Center (RCRRC), Izmir, Turkey during 2016, 2018 and 2019. A set of 25,169 informative SNP markers covering the whole genome were used to examine the population structure, linkage disequilibrium and marker-trait associations in the association mapping panel. The genome-wide association study (GWAS) was carried out using a Mixed Linear Model (MLM). We identified 47 SNP markers at 19 genomic regions with significant SNP-trait associations for both seedling and adult plant stage resistance, the threshold of significance for all SNP-trait associations was determined by the false discovery rate (q) ≤ 0.05. Three genomic regions (QYr.1D_APR, QYr.3A_seedlingandQYr.7D_seedling) identified in this study are far away from any previously reportedYrgene or QTL hence, tagging novel genomic regions. TheIn-silicoanalysis of the novel QTL regions identified candidate resistance genes encoding proteins putative to plants disease resistance and defense mechanism.
Dynamics of coherent activity between cortical areas defines a two-stage process of selective attention
Authors: Levichkina E. , Kermani M. , Saalmann Y.B. , Vidyasagar T.R. 
Published: February 2020

ABSTRACTAnalysing a visual scene requires the brain to briefly keep in memory potentially relevant parts and then direct attention to their locations for detailed processing. To reveal the neuronal basis of the underlying working memory and top-down attention processes, we trained macaques to match two patterns presented with a delay between them. As the above processes are likely to require communication between brain regions, and the parietal cortex is involved in spatial attention, we simultaneously recorded neuronal activities from the interconnected parietal and middle temporal areas. We found that mnemonic information about the first pattern was retained in coherent oscillating activity between the areas in high-frequency bands, followed by coherent activity in low-frequency bands that mediate top-down attention on the relevant location.ONE SENTENCE SUMMARYGamma coherence allows retaining object features in a saliency map while lower frequency coherence facilitates attention.
SAR1 paralogs differ biochemically in assembly of the COPII coat
Authors: Melville David B. , Studer Sean , Schekman Randy 
Published: February 2020

ABSTRACTCOPII-coated vesicles are the primary mediators of vesicular traffic from the ER to the Golgi apparatus. SAR1 is a small GTPase, which, upon GTP binding, recruits the other COPII proteins to the ER membrane. In mammals, there are two SAR1 paralogs which genetic data suggest may have distinct physiological roles, e.g. in lipoprotein secretion for SAR1B. We identified two clusters of amino acids that have conserved, paralog-specific sequences. One cluster is adjacent to the SAR1 GTP-binding pocket and alters the kinetics of GTP exchange. The other cluster is adjacent to the binding site of COPII components SEC31 and SEC23. We found that the latter cluster confers a SEC23A binding preference to SAR1B over SAR1A. In contrast to SAR1B, SAR1A is prone to oligomerize on a membrane surface. Importantly, in relation to its physiological function, SAR1B, but not SAR1A, can compensate for loss of SAR1B in lipoprotein secretion. The SEC31/SEC23-binding site-adjacent divergent cluster is critical for this function. These data identify the novel paralog-specific function for SAR1B, and provide insights into the mechanisms of large cargo secretion and COPII related diseases.
Vezatin is required for the retrograde axonal transport of endosomes inDrosophilaand zebrafish
Authors: Spinner Michael A. , Pinter Katherine , Drerup Catherine M. , Herman Tory G. 
Published: February 2020

ABSTRACTActive transport of organelles within axons is critical for neuronal health. Retrograde axonal transport, in particular, relays neurotrophic signals received by axon terminals to the nucleus and circulates new material amongen passantsynapses. The single retrograde motor, cytoplasmic dynein, is linked to diverse cargos by adaptors that promote dynein motility. Here we identify Vezatin as a new, cargo-specific regulator of retrograde axonal transport. Loss-of-function mutations in theDrosophila vezatin-like(vezl) gene prevent signaling endosomes containing activated BMP receptors from initiating transport out of motor neuron terminal boutons.vezlloss also decreases the transport of endosomes and dense core vesicles (DCVs) within axon shafts. While vertebrate Vezatin (Vezt) has not previously been implicated in axonal transport, we show thatveztloss in zebrafish impairs the retrograde movement of late endosomes, causing their accumulation in axon terminals. Our work establishes a new, conserved, cargo-specific role for Vezatin proteins in axonal transport.
Quantifying ecoacoustic activity in the Amazon rainforest through Information Theory quantifiers
Authors: Colonna Juan G. , Carvalho José Reginaldo H. , Rosso Osvaldo A. 
Published: February 2020

AbstractAutomatic monitoring of biodiversity by acoustic sensors has become an indispensable tool to assess environmental stress at an early stage. Due to the difficulty in recognizing the Amazon’s high acoustic diversity and the large amounts of raw audio data recorded by the sensors, the labeling and manual inspection of this data is not feasible.Therefore, we propose an ecoacoustic index that allows us to quantify the complexity of an audio segment and correlate this measure with the biodiversity of the soundscape. The approach uses unsupervised methods to avoid the problem of labeling each species individually. The proposed index, named the Ecoacoustic Global Complexity Index (EGCI), makes use of Entropy, Divergence and Statistical Complexity. A distinguishing feature of this index is the mapping of each audio segment, including those of varied lenghts, as a single point in a 2D-plane, supporting us in understanding the ecoacoustic dynamics of the rainforest. The main results show a regularity in the ecoacoustic richness of a floodplain, considering different temporal granularities, be it between hours of the day or between consecutive days of the monitoring program. We observed that this regularity does a good job of characterizing the soundscape of the environmental protection area of Mamirauá, in the Amazon, differentiating between species richness and environmental phenomena.
MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection
Authors: Luu Phuc-Loi , Ong Phuc-Thinh , Loc Tran Thai Huu , Lam Dilys , Pidsley Ruth , Stirzaker Clare , Clark Susan J. 
Published: February 2020

AbstractBackgroundMultiplex bisulphite PCR sequencing is a convenient and scalable method to comprehensively profile DNA methylation at selected loci. The method is useful for validation of methylation biomarker panels on large clinical cohorts, as it can be applied to DNA isolated from fresh tissue, archival formalin fixed paraffin embedded tissue (FFPET) or circulating cell free DNA in plasma. However, successful clinical implementation of DNA methylation biomarkers for disease detection using multiplex bisulphite PCR sequencing, requires user-friendly sample analysis methods and a diversity of visualisation options, which are not met by current tools.ResultsWe have developed a computational pipeline with an interactive graphical interface, calledMethPanel, in order to rapidly analyse multiplex bisulphite PCR sequencing data.MethPanelcomprises a complete analysis workflow from genomic alignment to DNA methylation calling and supports an unlimited number of PCR amplicons and input samples. Moreover,MethPaneloffers important and unique features, such as calculation of a polymorphism score and bisulphite PCR bias correction capabilities.MethPanelis designed so that the methylation data from all samples can be run in parallel on either a personal computer or a high performance computer. The outputs are also automatically forwarded to a shinyApp for convenient display, visualisation and sharing data with collaborators and clinicians. Importantly the data is centralised in one location, which aids storage management.Availability and ImplementationMethPanelis freely available athttps://github.com/thinhong/MethPanelConclusionMethPanelprovides a novel parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation marker panels for disease detection.
A Software Toolkit for TMS Electric-Field Modeling with Boundary Element Fast Multipole Method: An Efficient MATLAB Implementation
Authors: Makarov Sergey N. , Wartman William A. , Daneshzand Mohammad , Fujimoto Kyoko , Raij Tommi , Nummenmaa Aapo 
Published: February 2020

AbstractBackgroundTranscranial magnetic stimulation (TMS) is currently the only non-invasive neurostimulation modality that enables painless and safe supra-threshold stimulation by employing electromagnetic induction to efficiently penetrate the skull. Accurate, fast, and high resolution modeling of the electric fields (E-fields) may significantly improve individualized targeting and dosing of TMS and therefore enhance the efficiency of existing clinical protocols as well as help establish new application domains.ObjectiveTo present and disseminate our TMS modeling software toolkit, including several new algorithmic developments, and to apply this software to realistic TMS modeling scenarios given a high-resolution model of the human head including cortical geometry and an accurate coil model.MethodThe recently developed charge-based boundary element fast multipole method (BEM-FMM) is employed as an alternative to the 1st order finite element method (FEM) most commonly used today. The BEM-FMM approach provides high accuracy and unconstrained field resolution close to and across cortical interfaces. Here, the previously proposed BEM-FMM algorithm has been improved in several novel ways.Results and ConclusionsThe improvements resulted in a threefold increase in computational speed while maintaining the same solution accuracy. The computational code based on the MATLAB®platform is made available to all interested researchers, along with a coil model repository and examples to create custom coils, head model repository, and supporting documentation. The presented software toolkit may be useful for post-hoc analyses of navigated TMS data using high-resolution subject-specific head models as well as accurate and fast modeling for the purposes of TMS coil/hardware development.
Combinatorial effect of miR-486-5p & miR-22-3p mimics thrombopoietin’s impact on hematopoietic stem & progenitor cells
Authors: Kao Chen-Yuan , Jiang Jinlin , Papoutsakis Eleftherios T. 
Published: February 2020

AbstractMegakaryocytes shed and release submicron size microparticles (MkMPs), the most abundant microparticle in circulation. We have previously reported that MkMPs target peripheral-blood CD34+hematopoietic stem/progenitor cells (HSPCs) to induce megakaryocytic differentiation and proliferation, and that small RNAs delivered to HSPCs via MkMPs play an important role in the development of this phenotype. Here, using single-molecule real-time (SMRT) RNA sequencing (RNAseq), we identify the top seven most abundant microRNAs (miRs) in MkMPs as potential candidates in mediating the effect of MkMPs on HSPCs. Using miR mimics, we demonstrate that among the seven most abundant miRs, two, miR-486-5p and miR-22-3p, are able to drive the Mk differentiation of HSPCs in the absence of thrombopoietin (TPO). The effect of these two miRs is comparable to the TPO- or MkMP-induced megakaryocytic differentiation of HSPCs, thus suggesting that these two miRs are responsible for this MkMP-induced phenotype. To probe the signaling through which MkMPs might enable this phenotype, we used kinase inhibitors of potential signaling pathways engaged in megakaryocytic differentiation. Our data suggest that MkMP-induced Mk differentiation of HSPCs is enabled through JNK and PI3K/Akt/mTOR signaling. Our data show that MkMPs activate Akt and mTOR phosphorylation. Furthermore, MkMPs downregulate PTEN expression, a direct target of miR-486-5p and a negative regulator of PI3K/Akt signaling, via JNK signaling. Taken together, our data provide a mechanistic understanding of the biological effect of MkMPs in inducing megakaryocytic differentiation of HSPCs, which, as was previously suggested, is a phenotype of potential physiological significance in stress megakaryopoiesis.Key PointsmiR-486-5p and miR-22-3p drive megakaryocytic differentiation in the absence of thrombopoietin.Megakaryocytic microparticles trigger megakaryocytic differentiation of CD34+cells through JNK and PI3K/Akt/mTOR signaling.Visual Abstract
Major discrepancy between factual antibiotic resistance and consumption in South of France: analysis of 539,037 bacterial strains
Authors: Diallo Ousmane Oumou , Baron Sophie Alexandra , Dubourg Gregory , Chaudet Hervé , Halfon Philippe , Camiade Sabine , Comte Béatrice , Joubert Stéphanie , François Arnaud , Seyral Philippe , Parisot François , Casalta Jean-Paul , Ruimy Raymond , Maruejouls Christophe , Achiardy Jean-Christophe , Burignat Sophie , Carvajal Joseph , Delaunay Edouard , Meyer Sandra , Levy Pierre-Yves , Roussellier Patricia , Brunet Patrick , Bosi Claude , Stolidi Philippe , Arzouni Jean-Pierre , Gay Gisele , Hance Pierre , Colson Philippe , Raoult Didier , Rolain Jean-Marc 
Published: February 2020

AbstractIntroductionThe burden of antibiotic resistance is currently estimated by mathematical modeling, without real count of resistance to key antibiotics. Here we report the real rate of resistance to key antibiotics in bacteria isolated from humans during a 5 years period in a large area in southeast in France.MethodsWe conducted a retrospective study on antibiotic susceptibility of 539,107 clinical strains isolated from hospital and private laboratories in south of France area from January 2014 to January 2019. The resistance rate to key antibiotics as well as the proportion of bacteria classified as Difficult-to-Treat (DTR) were determined and compared with the Mann-Whitney U test, the χ2 test or the Fisher’s exact test.ResultsAmong 539,037 isolates, we did not observe any significant increase or decrease in resistance to key antibiotics for 5 years, (oxacillin resistance inStaphylococcus aureus, carbapenem resistance in enterobacteria andPseudomonas aeruginosaand 3rdgeneration cephalosporin resistance inEscherichia coliandKlebsiella pneumoniae). However, we observed a significant decrease in imipenem resistance forAcinetobacter baumanniifrom 2014 to 2018 (24.19% to 12.27%; p=0.005) and a significant increase of ceftriaxone resistance inKlebsiella pneumoniae(9.9% to 24,03%; p=0.001) andEnterobacter cloacae(24,05% to 42,05%; p=0.004). Of these 539,037 isolates, 1,604 (0.3%) had a DTR phenotype.ConclusionOver a 5-year period, we did not observe a burden of AR in our region despite a high rate of antibiotic consumption in our country. These results highlight the need for implementation of real-time AR surveillance systems which use factual data.