bluuebunny/crossref_metadata_2025_split huggingface dataset:
Invasion history ofHarmonia axyridis(Pallas, 1773) (Coleoptera: Coccinellidae) in Ecuador
Authors: Cisneros-Heredia Diego F. , Peñaherrera-Romero Emilia 
Published: June 2020

AbstractHarmonia axyridisis a ladybird extensively used around the world for biological control of agricultural pest. However, it has become invasive in several countries, producing negative ecological and socio-economic impacts. Herein, we review the invasion history of the Harlequin LadybirdHarmonia axyridis(Pallas, 1773) in Ecuador. Although first reported in Ecuador in 2012, museum specimens date back to 2004 and it is currently established across the country, especially along the Andean region. Due to its invasive nature, further studies are urgently needed to evaluate possible impacts ofH. axyridison the Ecuadorian biodiversity and agroindustry.
Hurricane-induced demographic changes in a nonhuman primate population
Authors: Morcillo Dana O. , Steiner Ulrich K. , Grayson Kristine L. , Ruiz-Lambides Angelina V. , Hernández-Pacheco Raisa 
Published: June 2020

AbstractMajor disturbance events can have large impacts on the demography and dynamics of animal populations. Hurricanes are one example of an extreme climatic event, predicted to increase in frequency due to climate change, and thus expected to be a considerable threat to population viability. However, little is understood about the underlying demographic mechanisms shaping population response following these extreme disturbances. Here, we analyze 45 years of the most comprehensive free-ranging nonhuman primate demographic dataset to determine the effects of major hurricanes on the variability and maintenance of long-term population fitness. For this, we use individual-level data to build matrix population models and perform perturbation analyses. Despite reductions in population growth rate mediated through reduced fertility, our study reveals a demographic buffering during hurricane years. As long as survival does not decrease, our study shows that hurricanes do not result in detrimental effects at the population level, demonstrating the unbalanced contribution of survival and fertility to population fitness in long-lived animal populations.
Spritz: A Proteogenomic Database Engine
Authors: Cesnik Anthony J. , Miller Rachel M. , Ibrahim Khairina , Lu Lei , Millikin Robert J. , Shortreed Michael R. , Frey Brian L. , Smith Lloyd M. 
Published: June 2020

AbstractProteoforms are the workhorses of the cell, and subtle differences between their amino acid sequence or post-translational modifications (PTMs) can change their biological function. To most effectively identify and quantify proteoforms in genetically diverse samples by mass spectrometry (MS), it is advantageous to search the MS data against a sample-specific protein database that is tailored to the sample being analyzed, in that it contains the correct amino acid sequences and relevant PTMs for that sample. To this end, we have developed Spritz (https://smith-chem-wisc.github.io/Spritz/), an open-source software tool for generating protein databases annotated with sequence variations and PTMs. We provide a simple graphical user interface (GUI) for Windows and scripts that can be run on any operating system. Spritz automatically sets up and executes approximately 20 tools, which enable construction of a proteogenomic database from only raw RNA sequencing data. Sequence variations that are discovered in RNA sequencing data upon comparison to the Ensembl reference genome are annotated on proteins in these databases, and PTM annotations are transferred from UniProt. Modifications can also be discovered and added to the database using bottom-up mass spectrometry data and global PTM discovery in MetaMorpheus. We demonstrate that such sample-specific databases allow the identification of variant peptides, modified variant peptides, and variant proteoforms by searching bottom-up and top-down proteomic data from the Jurkat human T lymphocyte cell line and demonstrate the identification of phosphorylated variant sites with phosphoproteomic data from the U2OS human osteosarcoma cell line.
Segmented K-Space Blipped-Controlled Aliasing in Parallel Imaging (Skipped-CAIPI) for High Spatiotemporal Resolution Echo Planar Imaging
Authors: Stirnberg Rüdiger , Stöcker Tony 
Published: June 2020

AbstractPurposeA segmented k-space blipped-CAIPI (skipped-CAIPI) sampling strategy for echo planar imaging (EPI) is proposed, which allows for a flexible choice of EPI factor and phase encode bandwidth independent of the controlled aliasing (CAIPIRINHA) pattern.Theory and MethodsWith previously proposed approaches, exactly two EPI trajectories were possible given a specific CAIPIRINHA pattern: either with slice gradient blips (blipped-CAIPI), or following a shot-selective approach (higher resolution). Recently, interleaved multi-shot segmentation along shot-selective CAIPI trajectories has been applied for high-resolution anatomical imaging. For more flexibility and a broader range of applications, we propose segmentation along any blipped-CAIPI trajectory. Thus, all EPI factors and phase encode bandwidths available with traditional segmented EPI can be combined with controlled aliasing.ResultsTemporal signal-to-noise ratios of moderate-to-high-resolution time series acquisitions at varying undersampling factors demonstrate beneficial sampling alternatives to blipped-CAIPI or shot-selective CAIPI. Rapid high-resolution scans furthermore demonstrate SNR-efficient and motion-robust structural imaging with almost arbitrary EPI factor and minimal noise penalty.ConclusionsSkipped-CAIPI sampling increases protocol flexibility for high spatiotemporal resolution EPI. In terms of signal-to-noise ratio and efficiency, high-resolution functional or structural scans benefit vastly from a free choice of the CAIPIRINHA pattern. Even at moderate resolutions, the independence of sampling pattern, echo time and image matrix size is valuable for optimized functional protocol design. Although demonstrated with 3D-EPI, skipped-CAIPI is also applicable with simultaneous multislice EPI.
Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria
Authors: Klassen Leeann , Reintjes Greta , Tingley Jeffrey P. , Jones Darryl R. , Hehemann Jan-Hendrik , Smith Adam D. , Schwinghamer Timothy D. , Arnosti Carol , Jin Long , Alexander Trevor W. , Amundsen Carolyn , Thomas Dallas , Amann Rudolf , McAllister Tim A. , Abbott D. Wade 
Published: June 2020

AbstractGut microbiomes have vast catabolic potential and are essential to host health and nutrition. An in-depth understanding of the metabolic pathways in these ecosystems will enable us to design treatments (i.e. prebiotics) that influence microbiome structure and enhance host physiology. Currently, the investigation of metabolic pathways relies on inferences derived from metagenomics orin vitrocultivations, however, novel approaches targeting specific cell physiologies can illuminate the functional potential encoded within microbial (meta)genomes to accurately assess metabolic abilities. Here, we present a multi-faceted study using complimentary next-generation physiology and ‘omics’ approaches to characterize the microbial adaptation to a prebiotic in the rumen ecosystem. Using fluorescently labeled polysaccharides, we identified bacteria that actively metabolize a glycan prebiotic in the rumen microbiomeex vivo. Subsequently, we characterized strain-level variability in carbohydrate utilization systems and predict metabolic strategies of isolated bovine-adapted strains ofBacteroides thetaiotaomicronusing comparative whole genome sequencing, RNA-Seq, and carbohydrate-active enzyme fingerprinting.
Integrating remote sensing and jurisdictional observation networks to improve the resolution of ecological management
Authors: Townsend Philip A. , Clare John , Liu Nanfeng , Stenglein Jennifer L. , Anhalt-Depies Christine , Van Deelen Timothy R. , Gilbert Neil A. , Singh Aditya , Martin Karl J. , Zuckerberg Benjamin 
Published: June 2020

AbstractThe emergence of citizen science, passive sensors (e.g., trail cameras and acoustic monitoring), and satellite remote sensing have enabled biological data to be collected at unprecedented spatial and temporal scales. There is growing interest in networking these datastreams to expedite the collection and synthesis of environmental and biological data to improve broad-scale ecological monitoring, but there are no examples of such networks being developed to directly inform decision-making by managing agencies. Here, we present the implementation of one such jurisdictional observation network (JON), Snapshot Wisconsin (SW), that links satellite remote sensing (RS) with a volunteer-based trail camera network to generate new insights into wildlife distributions and improve their management by the state agency. SW relies on citizen scientists to deploy trail cameras across the state and classify images of wildlife. As of early 2020 SW comprises nearly 1800 volunteers hosting >2100 active cameras recording >37 million images across a sampling effort of >2000 combined trap-years at >3300 distinct camera locations. We use a set of case studies to demonstrate the potential power of a JON to monitor wildlife with unprecedented combinations of spatial, temporal, and biological resolution and extent. Specifically, we demonstrate that SW markedly improves the spatial and temporal resolution with which black bear distributions can be monitored or forecast, in turn improving the resolution of decision-making. Enhancing the biological resolution of monitoring (e.g., monitoring the distribution of species traits or behaviors) may provide new insights into population drivers, such as the connection between vegetation productivity and white-tailed deer foraging behaviors. Enhanced taxonomic extent provided by trail cameras and other passive sensor networks provide managers new information for a wide range of species and communities that are not otherwise monitored. Our cases further show that JONs synergize existing monitoring practices by serving as a complementary and independent line of evidence or as a tool to enhance the extent and precision of existing models through integrated modeling approaches. SW and other JONS are a powerful new tool for agencies to better achieve their missions and reshape the nature of environmental decision-making.
Mineral density differences between femoral cortical bone and trabecular bone are not explained by turnover rate alone
Authors: Lerebours Chloé , Weinkamer Richard , Roschger Andreas , Buenzli Pascal R. 
Published: June 2020

AbstractBone mineral density distributions (BMDDs) are a measurable property of bone tissues that depends strongly on bone remodelling and mineralisation processes. These processes can vary significantly in health and disease and across skeletal sites, so there is high interest in analysing these processes from experimental BMDDs. Here, we propose a rigorous hypothesis-testing approach based on a mathematical model of mineral heterogeneity in bone due to remodelling and mineralisation, to help explain differences observed between the BMDD of human femoral cortical bone and the BMDD of human trabecular bone. Recent BMDD measurements show that femoral cortical bone possesses a higher bone mineral density, but a similar mineral heterogeneity around the mean compared to trabecular bone. By combining this data with the mathematical model, we are able to test whether this difference in BMDD can be explained by (i) differences in turnover rate; (ii) differences in osteoclast resorption behaviour; and (iii) differences in mineralisation kinetics between the two bone types. We find that accounting only for differences in turnover rate is inconsistent with the fact that both BMDDs have a similar spread around the mean, and that accounting for differences in osteoclast resorption behaviour leads to biologically inconsistent bone remodelling patterns. We conclude that the kinetics of mineral accumulation in bone matrix must therefore be different in femoral cortical bone and trabecular bone. Although both cortical and trabecular bone are made up of lamellar bone, the different mineralisation kinetics in the two types of bone point towards more profound structural differences than usually assumed.
Total workflows of the single-molecule imaging analysis in living cells: a tutorial guidance to the measurement of the drug effects on a GPCR
Authors: Yanagawa Masataka , Sako Yasushi 
Published: June 2020

AbstractSingle-molecule imaging (SMI) is a powerful method to measure the dynamics of membrane proteins on the cell membrane. The single-molecule tracking (SMT) analysis provides information about the diffusion dynamics, the oligomer size distribution, and the particle density change. The affinity and on/off-rate of a protein—protein interaction can be estimated from the dual-color SMI analysis. However, it is difficult for trainees to determine quantitative information from the SMI movies. The present protocol guides the detailed workflows to measure the drug-activated dynamics of a G protein-coupled receptor (GPCR) and metabotropic glutamate receptor 3 (mGluR3), by using the total internal reflection fluorescence microscopy (TIRFM). This tutorial guidance comprises an open-source software named smDynamicsAnalyzer, with which one can easily analyze the SMT dataset by just following the workflows after building a designated folder structure (https://github.com/masataka-yanagawa/IgorPro8-smDynamicsAnalyzer).
SARS-CoV-2 placental infection and inflammation leading to fetal distress and neonatal multi-organ failure in an asymptomatic woman
Authors: Schoenmakers Sam , Snijder Pauline , Verdijk Robert M. , Kuiken Thijs , Kamphuis Sylvia S.M. , Koopman Laurens P. , Krasemann Thomas B. , Rousian Melek , Broekhuizen Michelle , Steegers Eric A.P. , Koopmans Marion P.G. , Fraaij Pieter L.A. , Reiss Irwin K.M. 
Published: June 2020

AbstractIntroductionIn general SARS-CoV-2-infection during pregnancy is not considered to be an increased risk for severe maternal outcomes, but has been associated with an increased risk for fetal distress. So far, there is no direct evidence of intrauterine vertical transmission and the mechanisms leading to the adverse outcomes are not well understoodResultsAn asymptomatic pregnant woman with preterm fetal distress during the COVID19 pandemic was included. We obtained multiple maternal, placental and neonatal swabs, which showed a median viral load in maternal blood, urine, oropharynx, fornix posterior over a period of 6 days was 5.0 log copies /mL. The maternal side of the placenta had a viral load of 4.42 log copies /mL, while the fetal side had 7.15 log copies /mL. Maternal breast milk, feces and all neonatal samples tested negative. Serology of immunoglobulins against SARS-CoV-2 was tested positive in maternal blood, but negative in umbilical cord and neonatal blood. Pathological examination of the placenta included immunohistochemical investigation against SARS-CoV-2 antigen expression in combination with SARS-CoV-2 RNA in situ hybridization and transmission electron microscopy. It showed the presence of SARS-CoV-2 particles with generalized inflammation characterized by histiocytic intervillositis with diffuse perivillous fibrin depositions with damage to the syncytiotrophoblasts.DiscussionPlacental infection by SARS-CoV-2 lead to fibrin depositions hampering fetal-maternal gas exchange most likely resulted in fetal distress necessitating a premature emergency caesarean section. Postpartum, the neonate showed a clinical presentation resembling a pediatric inflammatory multisystem syndrome including coronary artery ectasia, most likely associated with SARS-CoV-2 (PIMS-TS) for which admittance and care on the Neonatal Intensive Care unit (NICU) was required, despite being negative for SARS-CoV-2. This highlights the need for awareness of adverse fetal and neonatal outcomes during the current COVID-19 pandemic, especially considering that the majority of pregnant women appear asymptomatic.
Image-based modelling of inhaler deposition during respiratory exacerbation
Authors: Williams Josh , Kolehmainen Jari , Cunningham Steve , Ozel Ali , Wolfram Uwe 
Published: June 2020

AbstractFor many of the one billion sufferers of respiratory diseases worldwide, managing their disease with inhalers improves their ability to breathe. Poor disease management and rising pollution can trigger exacerbations which require urgent relief. Higher drug deposition in the throat instead of the lungs limits the impact on patient symptoms. To optimise delivery to the lung, patient-specific computational studies of aerosol inhalation can be used. How-ever in many studies, inhalation modelling does not represent an exacerbation, where the patient’s breath is much faster and shorter. Here we compare differences in deposition of inhaler particles (10, 4 µm) in the airways of a healthy male, female lung cancer and child cystic fibrosis patient. We aimed to evaluate deposition differences during an exacerbation compared to healthy breathing with image-based healthy and diseased patient models. We found that the ratio of drug in the lower to upper lobes was 35% larger during healthy breathing than an exacerbation. For smaller particles the upper airway deposition was similar in all patients, but local deposition hotspots differed in size, location and intensity. Our results identify that image-based airways must be used in respiratory modelling. Various inhalation profiles should be tested for optimal prediction of inhaler deposition.HighlightsRegional and local drug deposition was modelled in three patients during normal, sinusoidal inhalation and an exacerbation.Local drug deposition changes with airway shape and inhalation profile, even when regional deposition is similar.Image-based models were combined with highly-resolved particle tracking including particle contact and cohesion.Fluid model validated by comparing gas velocity field with in vitro experiments.
Hydroxychloroquine inhibits trained immunity – implications for COVID-19
Authors: Rother Nils , Yanginlar Cansu , Lindeboom Rik G.H. , Bekkering Siroon , van Leent Mandy M.T. , Buijsers Baranca , Jonkman Inge , de Graaf Mark , Baltissen Marijke , Lamers Lieke A. , Riksen Niels P. , Fayad Zahi A. , Mulder Willem J.M. , Hilbrands Luuk B. , Joosten Leo A.B. , Netea Mihai G. , Vermeulen Michiel , van der Vlag Johan , Duivenvoorden Raphaël 
Published: June 2020

ABSTRACTSARS-CoV-2 infection can cause severe disease for which currently no specific therapy is available. The use of hydroxychloroquine to prevent or treat SARS-CoV-2 infection is controversial and its mode of action poorly understood. We demonstrate that hydroxychloroquine inhibits trained immunity at the functional and epigenetic level and is accompanied by profound changes in the cellular lipidome as well as reduced expression of interferon-stimulated genes. Trained immunity comprises a functional adaptation induced by epigenetic reprogramming which facilitates the anti-viral innate immune response. Our findings therefore suggest that hydroxychloroquine may not have a beneficial effect on the anti-viral immune response to SARS-CoV-2.
Motivation and Cognitive Abilities as Mediators between Polygenic Scores and Psychopathology in Children
Authors: Pat Narun , Riglin Lucy , Anney Richard , Wang Yue , Barch Deanna M. , Thapar Anita , Stringaris Argyris 
Published: June 2020

AbstractObjectiveFundamental questions in biological psychiatry concern the mechanisms that mediate between genetic liability and psychiatric symptoms. Genetic liability for many common psychiatric disorders often confers transdiagnostic risk to develop a wide variety of psychopathological symptoms through yet unknown pathways. We examine the psychological and cognitive pathways that might mediate the relationship between genetic liability (indexed by polygenic scores; PS) and broad psychopathology (indexed by p factor and its underlying dimensions).MethodWe first identified which of the common psychiatric PSs (major depressive disorder [MDD], attention-deficit/hyperactivity disorder [ADHD], anxiety, bipolar, schizophrenia, autism) were associated with p factor. We then focused on three pathways: punishment sensitivity (reflected by behavioral inhibition system; BIS), reward sensitivity (reflected by behavioral activation system; BAS) and cognitive abilities (reflected by g factor based on 10 neurocognitive tasks). We applied structural equation modeling on the Adolescent Brain Cognitive Development (ABCD) dataset (n=4,814; 2,263 female children; 9-10 years old).ResultsMDD and ADHD PSs were associated with p factor. The association between MDD PS and psychopathology was partially mediated by punishment sensitivity and cognitive abilities: proportion mediated= 22.35%. Conversely, the influence of ADHD PS on psychopathology was partially mediated by reward sensitivity and cognitive abilities: proportion mediated=30.04%. The mediating role of punishment sensitivity was specific to the emotional/internalizing. This mediating role of both reward sensitivity and cognitive abilities was focusing on the behavioral/externalizing and neurodevelopmental dimensions of psychopathology.ConclusionWe provide a better understanding of how genetic risks for MDD and ADHD confer risks for psychopathology and suggest potential prevention/intervention targets for children at-risk.
An Assessment of Bayesian Model-Averaged Logistic Regression for Intensive-Care Prognosis
Authors: Dybowski Richard 
Published: June 2020

SUMMARYLogistic regression is the standard method for developing prognostic models for intensive care, but this approach does not take into account the uncertainty in the model selected and the uncertainty in its regression coefficients. This weakness can be addressed by adopting a Bayesian model-averaged approach to logistic regression; however, with respect to the dataset used for our study, we found maximum likelihood to be as effective as the more elaborate Bayesian approach, and an implementation of model averaging did not improve performance. Nevertheless, the Bayesian approach has the theoretical advantage that it can exploit prior knowledge about regression coefficient and model probabilities.