bluuebunny/crossref_metadata_2025_split huggingface dataset:
A modified live bat influenza A virus-based vaccine prototype provides full protection against HPAIV H5N1
Authors: Schön Jacob , Ran Wei , Gorka Marco , Schwemmle Martin , Beer Martin , Hoffmann Donata 
Published: May 2020

AbstractHighly pathogenic avian influenza viruses (HPAIVs) of subtype H5 are a major threat for poultry holdings worldwide, here especially the zoonotic Asian H5N1 viruses. These HPAIVs have caused more than 500 fatal spillover infections from poultry to humans, with a looming danger of a new pandemic by establishing human-to-human transmissions. Besides culling measures in infected farms in endemic areas, vaccination is the major tool against HPAIV. However, the mainly used inactivated preparations have several limitations, like application to the individual animal by injection and a reduced efficiency. Here we present a modified live influenza vaccine prototype, which is based on the H17N10 bat influenza virus. The new chimeric vaccine strain R65mono/H17N10 was able to provide full protection against a lethal challenge infection with HPAIV H5N1 of juvenile and subadult chickens, as well as ferrets after oronasal immunization. In addition, the H5 vaccine prototype cannot reassort with avian influenza viruses and therefore is a promising tool against HPAIV H5 infection, allowing new vaccination strategies for efficient disease control.
A data set of sea surface stereo images to resolve space-time wave fields
Authors: Guimarães Pedro Veras , Ardhuin Fabrice , Bergamasco Filippo , Leckler Fabien , Filipot Jean-François , Shim Jae-Seol , Dulov Vladimir , Benetazzo Alvise 
Published: May 2020

AbstractStereo imaging of the sea surface elevation provides unique field data to investigate the geometry and dynamics of oceanic waves. Typically, this technique allows retrieving the 4-D ocean topography (3-D space + time) at high frequency (up to 15–20 Hz) over a sea surface region of area ~104 m2. Stereo data fill the existing wide gap between sea surface elevation time-measurements, like the local observation provided by wave-buoys, and large-scale ocean observations by satellites. The analysis of stereo images provides a direct measurement of the wavefield without the need of any linear-wave theory assumption, so it is particularly interesting to investigate the nonlinearities of the surface, wave-current interaction, rogue waves, wave breaking, air-sea interaction, and potentially other processes not explored yet. In this context, this open dataset aims to provide, for the first time, valuable stereo measurements collected in different seas and wave conditions to invite the ocean-wave scientific community to continue exploring these data and to contribute to a better understanding of the nature of the sea surface dynamics.
Allosteric inhibitor of β-catenin selectively targets oncogenic Wnt signaling in colon cancer
Authors: Cheltsov Anton , Nomura Natsuko , Yenugonda Venkata M. , Roper Jatin , Mukthavaram Rajesh , Jiang Pengfei , Her Nam-Gu , Babic Ivan , Kesari Santosh , Nurmemmedov Elmar 
Published: May 2020

AbstractAbnormal regulation of β-catenin initiates an oncogenic program that serves as a main driver of many cancers. Albeit challenging, β-catenin is an attractive drug target due to its role in maintenance of cancer stem cells and potential to eliminate cancer relapse. We have identified C2, a novel β-catenin inhibitor, which is a small molecule that binds to a novel allosteric site on the surface of β-catenin. C2 selectively inhibits β-catenin, lowers its cellular load and significantly reduces viability of β-catenin-driven cancer cells. Through direct binding to β-catenin, C2 renders the target inactive that eventually activates proteasome system for its removal. Here we report a novel pharmacologic approach for selective inhibition of β-catenin via targeting a cryptic allosteric modulation site. Our findings may provide a new perspective for therapeutic targeting of β-catenin.
Digital Holographic Multimodal Cross-Sectional Fluorescence and Quantitative Phase Imaging System
Authors: Kumar Manoj , Quan Xiangyu , Awatsuji Yasuhiro , Tamada Yosuke , Matoba Osamu 
Published: May 2020

AbstractWe present a multimodal imaging system based on simple off-axis digital holography, for simultaneous recording and retrieval of cross-sectional fluorescence and quantitative phase imaging of the biological specimen. Synergism in the imaging capabilities can be achieved by incorporating two off-axis digital holographic microscopes integrated to record different information at the same time. The cross-sectional fluorescence imaging is realized by a common-path configuration of the single-shot off-axis incoherent digital holographic system. The quantitative phase imaging, on the other hand, is achieved by another off-axis coherent digital holographic microscopy operating in transmission mode. The fundamental characteristics of the proposed multimodal system are confirmed by performing various experiments on fluorescent beads and fluorescent protein-labeled living cells of the moss Physcomitrella patens lying at different axial depth positions. Furthermore, the cross-sectional live fluorescence and phase imaging of the fluorescent beads are demonstrated by the proposed multimodal system. The experimental results presented here corroborate the feasibility of the proposed system and indicate its potential in the applications to analyze the functional and structural behavior of biological cells and tissues.
Defective defence in Daphnia daughters: silver nanoparticles inhibit anti-predator defence in offspring but not in maternal Daphnia magna
Authors: Hartmann Sarah , Beasley Anna , Mozhayeva Darya , Engelhard Carsten , Witte Klaudia 
Published: May 2020

AbstractOne major environmental problem of our time are emerging contaminants in the aquatic environment. While nanoparticles exhibit attractive features such as antimicrobial properties in the case of silver nanoparticles (AgNPs), earlier studies suggest that NPs are not completely filtered out at wastewater treatment plants and may therefore be continuously introduced into the aquatic environment. Although adverse effects of AgNPs on aquatic organisms have been extensively studied, there is still a lack of knowledge on how this chemical stressor interacts with natural cues on the maternal and subsequent generation of aquatic organisms. We tested whether AgNPs (NM-300K, 14.9 ± 2.4 nm, concentration range: 2.5 µg/L – 20 µg/L) affect the kairomone-induced adaptive anti-predator defence mechanism in maternal Daphnia and their offspring. While maternal Daphnia developed typical anti-predator defence mechanisms when exposed to kairomones and AgNPs, their offspring could not develop such adaptive defensive traits. The lack of this defence mechanism in offspring could have dramatic negative consequences (e.g. reduced Daphnia population) for the entire complex food web in the aquatic ecosystem. For a realistic risk assessment, it is extremely important to test combinations of chemical stressors because aquatic organisms are exposed to several natural and artificial chemical stressors at the same time.
Direct Measurement of the Radiative Pattern of Bright and Dark Excitons and Exciton Complexes in Encapsulated Tungsten Diselenide
Authors: Schneider Lorenz Maximilian , Esdaille Shanece S. , Rhodes Daniel A. , Barmak Katayun , Hone James C. , Rahimi-Iman Arash 
Published: May 2020

AbstractThe optical properties of particularly the tungsten-based transition-metal dichalcogenides are strongly influenced by the presence of dark excitons. Recently, theoretical predictions as well as indirect experimental insights have shown that two different dark excitons exist within the light cone. While one is completely dark, the other one is only dipole forbidden out-of-plane, hence referred to as grey exciton. Here, we present angle-resolved spectroscopic data of a high-quality hexagonal-BN-encapsulated WSe2monolayer with which we directly obtain the radiation pattern of this grey exciton that deviates from that of the bright exciton and other exciton complexes obtained at cryogenic temperatures.
Effect of Fe3O4 nanoparticles on germination of seeds and concentration of elements in Helianthus annuus L. under constant magnetic field
Authors: Kornarzyński Krzysztof , Sujak Agnieszka , Czernel Grzegorz , Wiącek Dariusz 
Published: May 2020

AbstractThe aim of the study was to investigate the effect of the Fe3O4 nanoparticles (Fe-NPs) on the germination of sunflower seeds, early growth of seedlings and the concentration of selected elements in seedlings. The influence of constant magnetic fields in systems with and without Fe-NPs was investigated. Experiments were done on seeds subjected to germination under constant magnetic field (0 (control), 5, 25 and 120 mT) for 7 days in the presence of solution containing 0, 50 or 500 ppm Fe-NPs. No significant effect of Fe-NPs and the magnetic field on germination of seeds and the growth of seedlings has been demonstrated. In most cases, a decrease in germination parameters was observed. For the majority of samples the relative decrease in the concentrations of elements was demonstrated mainly for samples without Fe-NPs. Interestingly, a significant decrease in the concentrations of trivalent (including iron - Fe) and toxic elements in samples containing Fe-NPs in relation to control samples was observed. The authors suggest that in this case the binding (adsorption) of these elements in the roots and seeds of the sunflower by Fe-NPs took place. This explains the lower iron content in seedlings than in seeds prior to sowing.
Experimental Demonstration of Supervised Learning in Spiking Neural Networks with Phase-Change Memory Synapses
Authors: Nandakumar S. R. , Boybat Irem , Le Gallo Manuel , Eleftheriou Evangelos , Sebastian Abu , Rajendran Bipin 
Published: May 2020

AbstractSpiking neural networks (SNN) are computational models inspired by the brain’s ability to naturally encode and process information in the time domain. The added temporal dimension is believed to render them more computationally efficient than the conventional artificial neural networks, though their full computational capabilities are yet to be explored. Recently, in-memory computing architectures based on non-volatile memory crossbar arrays have shown great promise to implement parallel computations in artificial and spiking neural networks. In this work, we evaluate the feasibility to realize high-performance event-driven in-situ supervised learning systems using nanoscale and stochastic analog memory synapses. For the first time, the potential of analog memory synapses to generate precisely timed spikes in SNNs is experimentally demonstrated. The experiment targets applications which directly integrates spike encoded signals generated from bio-mimetic sensors with in-memory computing based learning systems to generate precisely timed control signal spikes for neuromorphic actuators. More than 170,000 phase-change memory (PCM) based synapses from our prototype chip were trained based on an event-driven learning rule, to generate spike patterns with more than 85% of the spikes within a 25 ms tolerance interval in a 1250 ms long spike pattern. We observe that the accuracy is mainly limited by the imprecision related to device programming and temporal drift of conductance values. We show that an array level scaling scheme can significantly improve the retention of the trained SNN states in the presence of conductance drift in the PCM. Combining the computational potential of supervised SNNs with the parallel compute power of in-memory computing, this work paves the way for next-generation of efficient brain-inspired systems.
Multi-photon attenuation-compensated light-sheet fluorescence microscopy
Authors: Veettikazhy Madhu , Nylk Jonathan , Gasparoli Federico , Escobet-Montalbán Adrià , Hansen Anders Kragh , Marti Dominik , Andersen Peter Eskil , Dholakia Kishan 
Published: May 2020

AbstractAttenuation of optical fields owing to scattering and absorption limits the penetration depth for imaging. Whilst aberration correction may be used, this is difficult to implement over a large field-of-view in heterogeneous tissue. Attenuation-compensation allows tailoring of the maximum lobe of a propagation-invariant light field and promises an increase in depth penetration for imaging. Here we show this promising approach may be implemented in multi-photon (two-photon) light-sheet fluorescence microscopy and, furthermore, can be achieved in a facile manner utilizing a graded neutral density filter, circumventing the need for complex beam shaping apparatus. A “gold standard” system utilizing a spatial light modulator for beam shaping is used to benchmark our implementation. The approach will open up enhanced depth penetration in light-sheet imaging to a wide range of end users.
Study of a classification algorithm for AIEC identification in geographically distinct E. coli strains
Authors: Camprubí-Font Carla , Bustamante Paula , Vidal Roberto M. , O’Brien Claire L. , Barnich Nicolas , Martinez-Medina Margarita 
Published: May 2020

AbstractAdherent-invasive Escherichia coli (AIEC) have been extensively implicated in Crohn’s disease pathogenesis. Currently, AIEC is identified phenotypically, since no molecular marker specific for AIEC exists. An algorithm based on single nucleotide polymorphisms was previously presented as a potential molecular tool to classify AIEC/non-AIEC, with 84% accuracy on a collection of 50 strains isolated in Girona (Spain). Herein, our aim was to determine the accuracy of the tool using AIEC/non-AIEC isolates from different geographical origins and extraintestinal pathogenic E. coli (ExPEC) strains. The accuracy of the tool was significantly reduced (61%) when external AIEC/non-AIEC strains from France, Chile, Mallorca (Spain) and Australia (82 AIEC, 57 non-AIEC and 45 ExPEC strains in total) were included. However, the inclusion of only the ExPEC strains showed that the tool was fairly accurate at differentiating these two close pathotypes (84.6% sensitivity; 79% accuracy). Moreover, the accuracy was still high (81%) for those AIEC/non-AIEC strains isolated from Girona and Mallorca (N = 63); two collections obtained from independent studies but geographically close. Our findings indicate that the presented tool is not universal since it would be only applicable for strains from similar geographic origin and demonstrates the need to include strains from different origins to validate such tools.
Impact of Sub-Retinal Fluid on the Long-Term Incidence of Macular Atrophy in Neovascular Age-related Macular Degeneration under Treat & Extend Anti-Vascular Endothelial Growth Factor Inhibitors
Authors: Siedlecki Jakob , Fischer Cheryl , Schworm Benedikt , Kreutzer Thomas C. , Luft Nikolaus , Kortuem Karsten U. , Schumann Ricarda G. , Wolf Armin , Priglinger Siegfried G. 
Published: May 2020

AbstractSub-retinal fluid (SRF) has been discussed as a protective factor against macular atrophy in eyes with neovascular age-related macular degeneration (nAMD).To gauge the impact of SRF on macular atrophy, a database of 310 nAMD eyes was screened for eyes manifesting an SRF-only phenotype under treat & extend anti-VEGF treatment, defined as nAMD expressing CNV exudation beyond the three monthly anti-VEGF loading doses by SRF only without any signs of exudative intra-retinal fluid (IRF) for ≥3 years. Incidence of macular atrophy and treatment responses were evaluated on multimodal imaging, including optical coherence tomography (OCT), blue autofluorescence (BAF) and near-infrared (NIR) confocal scanning laser ophthalmoscopy and fluorescence and indocyanine green angiography (FAG/ICGA). In total, 27 eyes (8.7%) of 26 patients with a mean follow-up of 4.2 ± 0.9 (3–5) years met the inclusion criteria. Mean age was 72 ± 6 (range: 61–86) years. The SRF only phenotype was seen from baseline in 14 eyes (52%), and in 13 eyes (48%) after a mean 1.0 ± 1.3 (1–3) injections. In years 1 to 5, mean 7.5, 5.9, 6.1, 6.1 and 7.0 anti-VEGF injections were given (p = 0.33). Cumulative macular atrophy incidence was 11.5% at year 1, 15.4% throughout years 2 to 4, and 22.4% at year 5. In conclusion, eyes manifesting activity by SRF only in treat & extend anti-VEGF regimen for nAMD seem to exhibit rather low rates of macular atrophy during long-term follow-up. SRF might be an indicator of a more benign form of nAMD.
Novel clostridial lineages recovered from metagenomes of a hot oil reservoir
Authors: Christman Glenn D. , León-Zayas Rosa I. , Zhao Rui , Summers Zarath M. , Biddle Jennifer F. 
Published: May 2020

AbstractOil reservoirs have been shown to house numerous microbial lineages that differ based on the in-situ pH, salinity and temperature of the subsurface environment. Lineages of Firmicutes, including Clostridiales, have been frequently detected in oil reservoirs, but are typically not considered impactful or relevant due to their spore-forming nature. Here we show, using metagenomics, a high temperature oil reservoir of marine salinity contains a microbial population that is predominantly from within the Order Clostridiales. These organisms form an oil-reservoir specific clade based on the phylogenies of both 16S rRNA genes and ribosomal proteins, which we propose to name UPetromonas tenebris, meaning they are single-celled organisms from dark rocks. Metagenome-assembled genomes (MAGs) of these Petromonas sp. were obtained and used to determine that these populations, while capable of spore-formation, were also likely replicating in situ in the reservoir. We compared these MAGs to closely related genomes and show that these subsurface Clostridiales differ, from the surface derived genomes, showing signatures of the ability to degrade plant-related compounds, whereas subsurface genomes only show the ability to process simple sugars. The estimation of in-situ replication from genomic data suggest that UPetromonas tenebris lineages are functional in-situ and may be specifically adapted to inhabit oil reservoirs.
Antidepressants during and after Menopausal Transition: A Systematic Review and Meta-Analysis
Authors: Wu Ching-Kuan , Tseng Ping-Tao , Wu Ming-Kung , Li Dian-Jeng , Chen Tien-Yu , Kuo Fu-Chen , Stubbs Brendon , Carvalho Andre F. , Chen Yen-Wen , Lin Pao-Yen , Cheng Yu-Shian , Sun Cheuk-Kwan 
Published: May 2020

AbstractTo assess the therapeutic benefits of antidepressants in depressive women during and after menopausal transition, PubMed, Cochrane Library, EMBASE and Science Direct were systematically searched from inception to February 1, 2020 for randomized controlled trials examining antidepressants compared to placebo. Primary outcome was change in depressive symptom severity, while secondary outcomes were rates of response/remission rates and dropout/discontinuation due to adverse events. Seven trials involving 1,676 participants (mean age = 52.6 years) showed significant improvement in depressive symptoms (k = 7, Hedges’ g = 0.44, 95% confidence interval (CI) = 0.32 to 0.57, p < 0.001) relative to that in controls. Furthermore, response (k = 3, odds ratio (OR) = 2.53, 95% CI = 1.24 to 5.15, p = 0.01) and remission (k = 3, OR = 1.84, 95% CI = 1.32 to 2.57, p < 0.001) rates were significantly higher in antidepressant-treated groups compared to those with controls. Although dropout rates did not differ between antidepressant and control groups (k = 6, OR = 0.93, 95% CI = 0.70 to 1.26, p = 0.68), the rate of discontinuation due to adverse events was significantly higher in antidepressant-treated groups (k = 6, OR = 0.55, 95% CI = 0.35 to 0.86, p = 0.01). Subgroup analysis indicated that antidepressants were also efficacious for depressive symptoms in those without diagnosis of MDD. The results demonstrated that antidepressants were efficacious for women with depressive syndromes during and after menopausal transition but associated with a higher risk of discontinuation due to adverse events.
An Automated Segmentation Pipeline for Intratumoural Regions in Animal Xenografts Using Machine Learning and Saturation Transfer MRI
Authors: Lam Wilfred W. , Oakden Wendy , Karami Elham , Koletar Margaret M. , Murray Leedan , Liu Stanley K. , Sadeghi-Naini Ali , Stanisz Greg J. 
Published: May 2020

AbstractSaturation transfer MRI can be useful in the characterization of different tumour types. It is sensitive to tumour metabolism, microstructure, and microenvironment. This study aimed to use saturation transfer to differentiate between intratumoural regions, demarcate tumour boundaries, and reduce data acquisition times by identifying the imaging scheme with the most impact on segmentation accuracy. Saturation transfer-weighted images were acquired over a wide range of saturation amplitudes and frequency offsets along with T1 and T2 maps for 34 tumour xenografts in mice. Independent component analysis and Gaussian mixture modelling were used to segment the images and identify intratumoural regions. Comparison between the segmented regions and histopathology indicated five distinct clusters: three corresponding to intratumoural regions (active tumour, necrosis/apoptosis, and blood/edema) and two extratumoural (muscle and a mix of muscle and connective tissue). The fraction of tumour voxels segmented as necrosis/apoptosis quantitatively matched those calculated from TUNEL histopathological assays. An optimal protocol was identified providing reasonable qualitative agreement between MRI and histopathology and consisting of T1 and T2 maps and 22 magnetization transfer (MT)-weighted images. A three-image subset was identified that resulted in a greater than 90% match in positive and negative predictive value of tumour voxels compared to those found using the entire 24-image dataset. The proposed algorithm can potentially be used to develop a robust intratumoural segmentation method.
Modelling and synthesis of Magnéli Phases in ordered titanium oxide nanotubes with preserved morphology
Authors: Malik Hammad , Sarkar Sayan , Mohanty Swomitra , Carlson Krista 
Published: May 2020

AbstractThe presence of Magnéli phases in titanium oxide nanotubes (NTs) can open up frontiers in many applications owing to their electrical and optical properties. Synthesis of NTs with Magnéli phases have posed a challenge due to the degradation and loss of morphology in NTs upon high-temperature treatments (>600 °C) in a reducing environment. This study reports on the synthesis of anodically formed NTs containing Magnéli phases through a double annealing route: oxygen (O2) annealing followed by annealing in 2% hydrogen with a nitrogen balance (2%H2-N2). The nucleation, growth, and transformation of anodized amorphous NTs into crystalline phases was investigated. The NTs obtained through this route were highly ordered and composed of mixed phases of anatase, rutile, and the Magnéli phase (Ti4O7). Experimental results from scanning electron microscopy (SEM), X-ray diffraction (XRD), scanning transmission electron microscopy (S/TEM), and Raman spectroscopy were combined with first principle calculations to develop an understanding of the sequential phase transformations during annealing. A predictive model was developed using density functional theory (DFT) to potentially predict the titanium oxides formed and their stability with reference to the mole fraction of oxygen. The change in the density of states (DOS), band structure, optical properties, and stability of phases are also discussed using DFT simulations. The combination of experimental characterization and modelling helped to understand the nucleation of anatase and rutile and the reorganization of these phases to form Magnéli phases on the anodized amorphous NTs through annealing treatment.