bluuebunny/crossref_metadata_2025_split huggingface dataset:
Empathizing associates with mean diffusivity
Authors: Takeuchi Hikaru , Taki Yasuyuki , Nouchi Rui , Yokoyama Ryoichi , Kotozaki Yuka , Nakagawa Seishu , Sekiguchi Atsushi , Iizuka Kunio , Yamamoto Yuki , Hanawa Sugiko , Araki Tsuyoshi , Miyauchi Carlos Makoto , Sakaki Kohei , Sassa Yuko , Nozawa Takayuki , Ikeda Shigeyuki , Yokota Susumu , Daniele Magistro , Kawashima Ryuta 
Published: June 2019

AbstractEmpathizing is defined as “the drive to identify another’s mental states and to respond to these with an appropriate emotion” and systemizing is defined as “the drive to the drive to analyze and construct rule-based systems”. While mean diffusivity (MD) has been robustly associated with several cognitive traits and disorders related with empathizing and systemizing, its direct correlation with empathizing and systemizing remains to be investigated. We undertook voxel-by-voxel investigations of regional MD to discover microstructural correlates of empathizing, systemizing, and the discrepancy between them (D score: systemizing − empathizing). Whole-brain analyses of covariance revealed that across both sexes, empathizing was positively correlated with MD of (a) an anatomical cluster that primarily spreads in the areas in and adjacent to the left dorsolateral prefrontal cortex, left anterior to the middle cingulate cortex, and left insula and (b) an anatomical cluster of the left postcentral gyrus and left rolandic operculum. The former overlaps with positive MD correlates of cooperativeness. The D score and systemizing did not show significant correlations. In conclusion, while increased MD has generally been associated with reduced neural tissues and possibly area function, higher empathizing and cooperativeness were commonly reflected by greater MD values in areas (a) that mainly overlap with areas that play a key role in emotional salience and empathy. In addition, higher empathizing was correlated with greater MD values in areas (b) that play a key role in the mirror neuron system.
Combating viral contaminants in CHO cells by engineering innate immunity
Authors: Chiang Austin W. T. , Li Shangzhong , Kellman Benjamin P. , Chattopadhyay Gouri , Zhang Yaqin , Kuo Chih-Chung , Gutierrez Jahir M. , Ghazi Faezeh , Schmeisser Hana , Ménard Patrice , Bjørn Sara Petersen , Voldborg Bjørn G. , Rosenberg Amy S. , Puig Montserrat , Lewis Nathan E. 
Published: June 2019

AbstractViral contamination in biopharmaceutical manufacturing can lead to shortages in the supply of critical therapeutics. To facilitate the protection of bioprocesses, we explored the basis for the susceptibility of CHO cells to RNA virus infection. Upon infection with certain ssRNA and dsRNA viruses, CHO cells fail to generate a significant interferon (IFN) response. Nonetheless, the downstream machinery for generating IFN responses and its antiviral activity is intact in these cells: treatment of cells with exogenously-added type I IFN or poly I:C prior to infection limited the cytopathic effect from Vesicular stomatitis virus (VSV), Encephalomyocarditis virus (EMCV), and Reovirus-3 virus (Reo-3) in a STAT1-dependent manner. To harness the intrinsic antiviral mechanism, we used RNA-Seq to identify two upstream repressors of STAT1: Gfi1 and Trim24. By knocking out these genes, the engineered CHO cells exhibited activation of cellular immune responses and increased resistance to the RNA viruses tested. Thus, omics-guided engineering of mammalian cell culture can be deployed to increase safety in biotherapeutic protein production among many other biomedical applications.
Effects of geometry on large-scale tube-shear exfoliation of graphite to multilayer graphene and nanographite in water
Authors: Blomquist Nicklas , Alimadadi Majid , Hummelgård Magnus , Dahlström Christina , Olsen Martin , Olin Håkan 
Published: June 2019

AbstractIndustrially scalable methods for the production of graphene and other nanographites are needed to achieve cost-efficient commercial products. At present, there are several available routes for the production of these materials but few allow large-scale manufacturing and environmentally friendly low-cost solvents are rarely used. We have previously demonstrated a scalable and low-cost industrial route to produce nanographites by tube-shearing in water suspensions. However, for a deeper understanding of the exfoliation mechanism, how and where the actual exfoliation occurs must be known. This study investigates the effect of shear zone geometry, straight and helical coil tubes, on this system based on both numerical simulation and experimental data. The results show that the helical coil tube achieves a more efficient exfoliation with smaller and thinner flakes than the straight version. Furthermore, only the local wall shear stress in the turbulent flow is sufficient for exfoliation since the laminar flow contribution is well below the needed range, indicating that exfoliation occurs at the tube walls. This explains the exfoliation mechanism of water-based tube-shear exfoliation, which is needed to achieve scaling to industrial levels of few-layer graphene with known and consequent quality.
Live yeast in juvenile diet induces species-specific effects on Drosophila adult behaviour and fitness
Authors: Murgier Juliette , Everaerts Claude , Farine Jean-Pierre , Ferveur Jean-François 
Published: June 2019

AbstractThe presence and the amount of specific yeasts in the diet of saprophagous insects such as Drosophila can affect their development and fitness. However, the impact of different yeast species in the juvenile diet has rarely been investigated. Here, we measured the behavioural and fitness effects of three live yeasts (Saccharomyces cerevisiae = SC; Hanseniaspora uvarum = HU; Metschnikowia pulcherrima = MP) added to the diet of Drosophila melanogaster larvae. Beside these live yeast species naturally found in natural Drosophila populations or in their food sources, we tested the inactivated “drySC” yeast widely used in Drosophila research laboratories. All flies were transferred to drySC medium immediately after adult emergence, and several life traits and behaviours were measured. These four yeast diets had different effects on pre-imaginal development: HU-rich diet tended to shorten the “egg-to-pupa” period of development while MP-rich diet induced higher larval lethality compared to other diets. Pre- and postzygotic reproduction-related characters (copulatory ability, fecundity, cuticular pheromones) varied according to juvenile diet and sex. Juvenile diet also changed adult food choice preference and longevity. These results indicate that specific yeast species present in natural food sources and ingested by larvae can affect their adult characters crucial for fitness.
High frequency GPS bursts and path-level analysis reveal linear feature tracking by red foxes
Authors: Bischof Richard , Gjevestad Jon Glenn Omholt , Ordiz Andrés , Eldegard Katrine , Milleret Cyril 
Published: June 2019

AbstractThere is a need to quantify and better understand how wildlife interact with linear features, as these are integral elements of most landscapes. One potentially important aspect is linear feature tracking (LFT), yet studies rarely succeed in directly revealing or quantifying this behavior. In a proof-of-concept study, we employed short-term intensive GPS monitoring of red foxes (Vulpes vulpes) in a multiple-use landscape in southern Norway. Using periodic bursts of high frequency GPS position fixes, we performed modified path selection analyses to estimate the propensity of foxes to track natural and man-made linear features (roads, forest edges, and streams) once they are encountered. Foxes in our study tracked primarily forest edges and roads. Forty-three percent of bursts that encountered any linear feature resulted in LFT. LFT, although prominent, was manifested as a short-lived behavior, with overall median times to linear feature abandonment around two minutes. Movement speeds were highest along roads, perhaps due to greater ease of travel or higher perceived risk. In the highly heterogeneous habitats that characterize human-dominated landscapes, LFT may be manifested at such a fine spatio-temporal scale that it would remain hidden during telemetry studies employing conventional position fix frequencies. The approach described here may aid others studying spatial behaviors that are manifested over very short durations, yet are biologically significant.
Probing the effect(s) of the microwaves’ electromagnetic fields in enzymatic reactions
Authors: Horikoshi Satoshi , Nakamura Kota , Yashiro Mikio , Kadomatsu Kanae , Serpone Nick 
Published: June 2019

AbstractThis paper examines the effects that electromagnetic fields from microwave radiation have in enzymatic reactions. Hydrolysis of proteins in beef (in vivo case) and casein (in vitro case) by the papain enzyme, a major industrial enzyme, is used herein as a model reaction to assess, under highly controlled conditions, the various parameters of microwave radiation (electric field, magnetic field, pulsed microwave irradiation, continuous microwave irradiation) as they might influence these in vivo and in vitro enzymatic reactions. The effect(s) of the microwaves’ electromagnetic fields was clearly evidenced in the in vivo case, contrary to the in vitro case where no such effect was observed, likely due to the nature of the hydrolysis reaction and to the autolysis (self-digestion) of the papain enzyme. Additionally, the effect of pulsed versus continuous microwave irradiation was further assessed by examining the catalase-assisted decomposition of hydrogen peroxide.
Nucleation in confinement generates long-range repulsion between rough calcite surfaces
Authors: Dziadkowiec Joanna , Zareeipolgardani Bahareh , Dysthe Dag Kristian , Røyne Anja 
Published: June 2019

AbstractFluid-induced alteration of rocks and mineral-based materials often starts at confined mineral interfaces where nm-thick water films can persist even at high overburden pressures and at low vapor pressures. These films enable transport of reactants and affect forces acting between mineral surfaces. However, the feedback between the surface forces and reactivity of confined solids is not fully understood. We used the surface forces apparatus (SFA) to follow surface reactivity in confinement and measure nm-range forces between two rough calcite surfaces in NaCl, CaCl2, or MgCl2 solutions with ionic strength of 0.01, 0.1 or 1 M. We observed long-range repulsion that could not be explained by changes in calcite surface roughness, surface damage, or by electrostatic or hydration repulsion, but was correlated with precipitation events which started at µm-thick separations. We observed a submicron-sized precipitate that formed in the confined solution. This liquid-like viscous precipitate did not undergo any spontaneous ripening into larger crystals, which suggested that confinement prevented its dehydration. Nucleation was significantly postponed in the presence of Mg2+. The long-range repulsion generated by nucleation between confined mineral surfaces can have a crucial influence on evolution of the microstructure and therefore the macroscopic strength of rocks and materials.
Down regulation of p-coumarate 3-hydroxylase in petunia uniquely alters the profile of emitted floral volatiles
Authors: Kim Joo Young , Swanson Robert T. , Alvarez Maria I. , Johnson Timothy S. , Cho Keun H. , Clark David G. , Colquhoun Thomas A. 
Published: June 2019

AbstractPetunia × hybrida cv ‘Mitchell Diploid’ floral volatile benzenoid/phenylpropanoid (FVBP) biosynthesis ultimately produces floral volatiles derived sequentially from phenylalanine, cinnamic acid, and p-coumaric acid. In an attempt to better understand biochemical steps after p-coumaric acid production, we cloned and characterized three petunia transcripts with high similarity to p-coumarate 3-hydroxylase (C3H), hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyl transferase (HCT), and caffeoyl shikimate esterase (CSE). Transcript accumulation of PhC3H and PhHCT was highest in flower limb tissue during open flower stages. PhCSE transcript accumulation was also highest in flower limb tissue, but it was detected earlier at initial flower opening with a bell-shaped distribution pattern. Down regulation of endogenous PhC3H transcript resulted in altered transcript accumulation of many other FVBP network transcripts, a reduction in floral volatiles, and the emission of a novel floral volatile. Down regulation of PhHCT transcript did not have as large of an effect on floral volatiles as was observed for PhC3H down regulation, but eugenol and isoeugenol emissions were significantly reduced on the downstream floral volatiles. Together these results indicate that PhC3H is involved in FVBP biosynthesis and the reduction of PhC3H transcript influences FVBP metabolism at the network level. Additional research is required to illustrate PhHCT and PhCSE functions of petunia.
Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen
Authors: Bedre Renesh , Irigoyen Sonia , Schaker Patricia D. C. , Monteiro-Vitorello Claudia B. , Da Silva Jorge A. , Mandadi Kranthi K. 
Published: June 2019

AbstractAlternative splicing (AS) promotes transcriptome and proteome diversity during growth, development, and stress responses in eukaryotes. Genome-wide studies of AS in sugarcane (Saccharum spp.) are lacking, mainly due to the absence of a high-quality sequenced reference genome, sugarcane’s large, complex genome, and the variable chromosome numbers and polyploidy of sugarcane cultivars. Here, we analyzed changes in the sugarcane isoform-level transcriptome and AS landscape during infection with the smut fungus (Sporisorium scitamineum) using a hybrid approach involving Sorghum bicolor reference-based and Trinity de novo mapping tools. In total, this analysis detected 16,039 and 15,379 transcripts (≥2 FPKM) at 5 and 200 days after infection, respectively. A conservative estimate of isoform-level expression suggested that approximately 5,000 (14%) sugarcane genes undergo AS. Differential expression analysis of the alternatively spliced genes in healthy and smut-infected sugarcane revealed 896 AS events modulated at different stages of infection. Gene family and gene ontology functional enrichment analysis of the differentially spliced genes revealed overrepresentation of functional categories related to the cell wall, defense, and redox homeostasis pathways. Our study provides novel insight into the AS landscape of sugarcane during smut disease interactions.
Structural Model of the ETR1 Ethylene Receptor Transmembrane Sensor Domain
Authors: Schott-Verdugo Stephan , Müller Lena , Classen Elisa , Gohlke Holger , Groth Georg 
Published: June 2019

AbstractThe structure, mechanism of action and copper stoichiometry of the transmembrane sensor domain of the plant ethylene receptor ETR1 and homologs have remained elusive, hampering the understanding on how the perception of the plant hormone ethylene is transformed into a downstream signal. We generated the first structural model of the transmembrane sensor domain of ETR1 by integrating ab initio structure prediction and coevolutionary information. To refine and independently validate the model, we determined protein-related copper stoichiometries on purified receptor preparations and explored the helix arrangement by tryptophan scanning mutagenesis. All-atom molecular dynamics simulations of the dimeric model reveal how ethylene can bind proximal to the copper ions in the receptor, illustrating the initial stages of the ethylene perception process.
Divergent behavioural responses of gypsy moth (Lymantria dispar) caterpillars from three different subspecies to potential host trees
Authors: Clavijo McCormick Andrea , Arrigo Luca , Eggenberger Helen , Mescher Mark C. , De Moraes Consuelo M. 
Published: June 2019

AbstractAlmost all previous work on host-plant selection by insect herbivores has focused on adult behaviour; however, immature life stages can also play an active role in host discrimination. The important forest pest Lymantria dispar (gypsy moth) has three recognised subspecies: the European, Asian, and Japanese gypsy moth. Unlike the other two subspecies, the European subspecies is characterised by a loss of female flight ability, which might impose a selective pressure on larvae to actively engage in host-plant selection. We therefore explored the interactions of early-instar larvae from laboratory colonies of each subspecies with four potential hosts of differing quality: oak, beech, maple, and pine—measuring larval survival and performance, feeding preferences, responses to host-derived odour cues, and the propensity to disperse from hosts via ballooning. Compared to larvae from the Asian and Japanese subspecies, larvae from the (American-originated) European gypsy moth colony exhibited (i) significantly lower survival on the poorest quality host (pine), (ii) an ability to discriminate among hosts via olfactory cues; and (iii) higher propensity to disperse from sub-optimal hosts. These results are consistent with the hypothesis that larvae from flightless female European Gypsy moth subspecies play a more active role in host-plant selection.
Land use and land cover change effect on surface temperature over Eastern India
Authors: Gogoi Partha Pratim , Vinoj V. , Swain D. , Roberts G. , Dash J. , Tripathy S. 
Published: June 2019

AbstractLand use and land cover (LULC) change has been shown to have significant effect on climate through various pathways that modulate land surface temperature and rainfall. However, few studies have illustrated such a link over the Indian region using observations. Through a combination of ground, satellite remote sensing and reanalysis products, we investigate the recent changes to land surface temperature in the Eastern state of Odisha between 1981 and 2010 and assess its relation to LULC. Our analysis reveals that the mean temperature of the state has increased by ~0.3 °C during the past three decades with the most accelerated warming (~0.9 °C) occurring during the recent decade (2001 to 2010). Our study shows that 25 to 50% of this observed overall warming is associated with LULC. Further we observe that the spatial pattern of LULC changes matches well with the independently estimated warming associated with LULC suggesting a physical association between them. This study also reveals that the largest changes are linked to changing vegetation cover as evidenced by changes to both LULC classes and normalized difference vegetation index (NDVI). Our study shows that the state has undergone an LULC induced warming which accounts for a quarter of the overall temperature rise since 2001. With the expected expansion of urban landscape and concomitant increase in anthropogenic activities along with changing cropping patterns, LULC linked changes to surface temperature and hence regional climate feedback over this region necessitates additional investigations.
A Hybrid Gene Selection Method Based on ReliefF and Ant Colony Optimization Algorithm for Tumor Classification
Authors: Sun Lin , Kong Xianglin , Xu Jiucheng , Xue Zhan’ao , Zhai Ruibing , Zhang Shiguang 
Published: June 2019

AbstractFor the DNA microarray datasets, tumor classification based on gene expression profiles has drawn great attention, and gene selection plays a significant role in improving the classification performance of microarray data. In this study, an effective hybrid gene selection method based on ReliefF and Ant colony optimization (ACO) algorithm for tumor classification is proposed. First, for the ReliefF algorithm, the average distance among k nearest or k non-nearest neighbor samples are introduced to estimate the difference among samples, based on which the distances between the samples in the same class or the different classes are defined, and then it can more effectively evaluate the weight values of genes for samples. To obtain the stable results in emergencies, a distance coefficient is developed to construct a new formula of updating weight coefficient of genes to further reduce the instability during calculations. When decreasing the distance between the same samples and increasing the distance between the different samples, the weight division is more obvious. Thus, the ReliefF algorithm can be improved to reduce the initial dimensionality of gene expression datasets and obtain a candidate gene subset. Second, a new pruning rule is designed to reduce dimensionality and obtain a new candidate subset with the smaller number of genes. The probability formula of the next point in the path selected by the ants is presented to highlight the closeness of the correlation relationship between the reaction variables. To increase the pheromone concentration of important genes, a new phenotype updating formula of the ACO algorithm is adopted to prevent the pheromone left by the ants that are overwhelmed with time, and then the weight coefficients of the genes are applied here to eliminate the interference of difference data as much as possible. It follows that the improved ACO algorithm has the ability of the strong positive feedback, which quickly converges to an optimal solution through the accumulation and the updating of pheromone. Finally, by combining the improved ReliefF algorithm and the improved ACO method, a hybrid filter-wrapper-based gene selection algorithm called as RFACO-GS is proposed. The experimental results under several public gene expression datasets demonstrate that the proposed method is very effective, which can significantly reduce the dimensionality of gene expression datasets, and select the most relevant genes with high classification accuracy.
Complement Receptor 1 availability on red blood cell surface modulates Plasmodium vivax invasion of human reticulocytes
Authors: Prajapati Surendra Kumar , Borlon Céline , Rovira-Vallbona Eduard , Gruszczyk Jakub , Menant Sebastien , Tham Wai-Hong , Kattenberg Johanna Helena , Villasis Elizabeth , De Meulenaere Katlijn , Gamboa Dionicia , Vinetz Joseph , Fujita Ricardo , Xuan Xa Nguyen , Urbano Ferreira Marcelo , Niño Carlos H. , Patarroyo Manuel A. , Spanakos Gregory , Kestens Luc , Abbeele Jan Van Den , Rosanas-Urgell Anna 
Published: June 2019

AbstractPlasmodium vivaxparasites preferentially invade reticulocyte cells in a multistep process that is still poorly understood. In this study, we usedex vivoinvasion assays and population genetic analyses to investigate the involvement of complement receptor 1 (CR1) inP.vivaxinvasion. First, we observed thatP.vivaxinvasion of reticulocytes was consistently reduced when CR1 surface expression was reduced through enzymatic cleavage, in the presence of naturally low-CR1-expressing cells compared with high-CR1-expressing cells, and with the addition of soluble CR1, a known inhibitor ofP.falciparuminvasion. Immuno-precipitation experiments withP.vivaxReticulocyte Binding Proteins showed no evidence of complex formation. In addition, analysis of CR1 genetic data for worldwide human populations with different exposure to malaria parasites show significantly higher frequency of CR1 alleles associated with low receptor expression on the surface of RBCs and higher linkage disequilibrium in human populations exposed toP.vivaxmalaria compared with unexposed populations. These results are consistent with a positive selection of low-CR1-expressing alleles in vivax-endemic areas. Collectively, our findings demonstrate that CR1 availability on the surface of RBCs modulatesP.vivaxinvasion. The identification of new molecular interactions is crucial to guiding the rational development of new therapeutic interventions against vivax malaria.