bluuebunny/crossref_metadata_2025_split huggingface dataset:
Annexin-A1 promotes RIG-I-dependent signaling and apoptosis via regulation of the IRF3–IFNAR–STAT1–IFIT1 pathway in A549 lung epithelial cells
Authors: Yap Gracemary L. R. , Sachaphibulkij Karishma , Foo Sok Lin , Cui Jianzhou , Fairhurst Anna-Marie , Lim Lina H. K. 
Published: June 2020

AbstractWithin the last century, millions of lives have been lost to the four major Influenza pandemics. These influenza pandemics were all caused by Influenza Type A viruses (IAV) through their ability to undergo antigenic drifts and shifts. A greater understanding of IAV and host–pathogen interactions is required to develop effective therapeutics against future outbreaks. Annexin A1 (ANXA1) is a phospholipid binding, calcium-dependent protein known to play essential roles in multiple cellular functions including inflammation, proliferation, migration, and apoptosis. ANXA1 was previously shown to enhance apoptosis after IAV infection. The current study explores the role of ANXA1 in IAV infection of A549 lung epithelial cells further in the context of RIG-I-dependent signaling using A549 and Crispr/Cas9 ANXA1 deleted (A549∆ANXA1) cells. ANXA1 was found to enhance the expression of a cytoplasmic RNA sensor, RIG-I basally and post-infection. RIG-I activation by 5′ppp-RNA in A549 lung epithelial cell induces apoptotic cell death, which is inhibited when ANXA1 is deleted, and reversed when ANXA1 is re-expressed. RIG-I activation by 5′ppp-RNA stimulates the production of IFNβ from lung epithelial cells to the same extent as monocytic cells, albeit very late after infection at 48–72 h, through IRF3 and STAT1 activation. ANXA1 deletion delays the phosphorylation of IRF3 and STAT1, leading to lower expression of interferon-stimulated genes, such as IFIT1, and silencing IFIT1 inhibited RIG-I-induced cell death. In all, these results suggest that ANXA1 plays a regulatory role in RIG-I signaling and cell death in A549 lung epithelial cells.
Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly
Authors: Ren Xianwen , Zhong Guojie , Zhang Qiming , Zhang Lei , Sun Yujie , Zhang Zemin 
Published: June 2020

AbstractSingle-cell RNA sequencing (scRNA-seq) has revolutionized transcriptomic studies by providing unprecedented cellular and molecular throughputs, but spatial information of individual cells is lost during tissue dissociation. While imaging-based technologies such as in situ sequencing show great promise, technical difficulties currently limit their wide usage. Here we hypothesize that cellular spatial organization is inherently encoded by cell identity and can be reconstructed, at least in part, by ligand-receptor interactions, and we present CSOmap, a computational tool to infer cellular interaction de novo from scRNA-seq. We show that CSOmap can successfully recapitulate the spatial organization of multiple organs of human and mouse including tumor microenvironments for multiple cancers in pseudo-space, and reveal molecular determinants of cellular interactions. Further, CSOmap readily simulates perturbation of genes or cell types to gain novel biological insights, especially into how immune cells interact in the tumor microenvironment. CSOmap can be a widely applicable tool to interrogate cellular organizations based on scRNA-seq data for various tissues in diverse systems.
Experimental exchange of grins between quantum Cheshire cats
Authors: Liu Zheng-Hao , Pan Wei-Wei , Xu Xiao-Ye , Yang Mu , Zhou Jie , Luo Ze-Yu , Sun Kai , Chen Jing-Ling , Xu Jin-Shi , Li Chuan-Feng , Guo Guang-Can 
Published: June 2020

AbstractIntuition suggests that an object should carry all of its physical properties. However, a quantum object may not act in such a manner—it can temporarily leave some of its physical properties where it never appears. This phenomenon is known as the quantum Cheshire cat effect. It has been proposed that a quantum object can even permanently discard a physical property and obtain a new one it did not initially have. Here, we observe this effect experimentally by casting non-unitary imaginary-time evolution on a photonic cluster state to extract weak values, which reveals the counterintuitive phenomenon that two photons exchange their spins without classically meeting each other. A phenomenon presenting only in the quantum realm, our results are in stark contrast with the perception of inseparability between objects and properties, and shed new light on comprehension of the ontology of observables.
The influence of the brittle-ductile transition zone on aftershock and foreshock occurrence
Authors: Petrillo Giuseppe , Lippiello Eugenio , Landes François P. , Rosso Alberto 
Published: June 2020

AbstractAftershock occurrence is characterized by scaling behaviors with quite universal exponents. At the same time, deviations from universality have been proposed as a tool to discriminate aftershocks from foreshocks. Here we show that the change in rheological behavior of the crust, from velocity weakening to velocity strengthening, represents a viable mechanism to explain statistical features of both aftershocks and foreshocks. More precisely, we present a model of the seismic fault described as a velocity weakening elastic layer coupled to a velocity strengthening visco-elastic layer. We show that the statistical properties of aftershocks in instrumental catalogs are recovered at a quantitative level, quite independently of the value of model parameters. We also find that large earthquakes are often anticipated by a preparatory phase characterized by the occurrence of foreshocks. Their magnitude distribution is significantly flatter than the aftershock one, in agreement with recent results for forecasting tools based on foreshocks.
An Erg-driven transcriptional program controls B cell lymphopoiesis
Authors: Ng Ashley P. , Coughlan Hannah D. , Hediyeh-zadeh Soroor , Behrens Kira , Johanson Timothy M. , Low Michael Sze Yuan , Bell Charles C. , Gilan Omer , Chan Yih-Chih , Kueh Andrew J. , Boudier Thomas , Feltham Rebecca , Gabrielyan Anna , DiRago Ladina , Hyland Craig D. , Ierino Helen , Mifsud Sandra , Viney Elizabeth , Willson Tracy , Dawson Mark A. , Allan Rhys S. , Herold Marco J. , Rogers Kelly , Tarlinton David M. , Smyth Gordon K. , Davis Melissa J. , Nutt Stephen L. , Alexander Warren S. 
Published: June 2020

AbstractB lymphoid development is initiated by the differentiation of hematopoietic stem cells into lineage committed progenitors, ultimately generating mature B cells. This highly regulated process generates clonal immunological diversity via recombination of immunoglobulin V, D and J gene segments. While several transcription factors that control B cell development and V(D)J recombination have been defined, how these processes are initiated and coordinated into a precise regulatory network remains poorly understood. Here, we show that the transcription factor ETS Related Gene (Erg) is essential for early B lymphoid differentiation. Erg initiates a transcriptional network involving the B cell lineage defining genes, Ebf1 and Pax5, which directly promotes expression of key genes involved in V(D)J recombination and formation of the B cell receptor. Complementation of Erg deficiency with a productively rearranged immunoglobulin gene rescued B lineage development, demonstrating that Erg is an essential and stage-specific regulator of the gene regulatory network controlling B lymphopoiesis.
Bio-inspired vertebral design for scalable and flexible perovskite solar cells
Authors: Meng Xiangchuan , Cai Zheren , Zhang Yanyan , Hu Xiaotian , Xing Zhi , Huang Zengqi , Huang Zhandong , Cui Yongjie , Hu Ting , Su Meng , Liao Xunfan , Zhang Lin , Wang Fuyi , Song Yanlin , Chen Yiwang 
Published: June 2020

AbstractThe translation of unparalleled efficiency from the lab-scale devices to practical-scale flexible modules affords a huge performance loss for flexible perovskite solar cells (PSCs). The degradation is attributed to the brittleness and discrepancy of perovskite crystal growth upon different substrates. Inspired by robust crystallization and flexible structure of vertebrae, herein, we employ a conductive and glued polymer between indium tin oxide and perovskite layers, which simultaneously facilitates oriented crystallization of perovskite and sticks the devices. With the results of experimental characterizations and theoretical simulations, this bionic interface layer accurately controls the crystallization and acts as an adhesive. The flexible PSCs achieve the power conversion efficiencies of 19.87% and 17.55% at effective areas of 1.01 cm2 and 31.20 cm2 respectively, retaining over 85% of original efficiency after 7000 narrow bending cycles with negligible angular dependence. Finally, the modules are assembled into a wearable solar-power source, enabling the upscaling of flexible electronics.
A self-sustaining endocytic-based loop promotes breast cancer plasticity leading to aggressiveness and pro-metastatic behavior
Authors: Schiano Lomoriello Irene , Giangreco Giovanni , Iavarone Claudia , Tordonato Chiara , Caldieri Giusi , Serio Gaetana , Confalonieri Stefano , Freddi Stefano , Bianchi Fabrizio , Pirroni Stefania , Bertalot Giovanni , Viale Giuseppe , Disalvatore Davide , Tosoni Daniela , Malabarba Maria Grazia , Disanza Andrea , Scita Giorgio , Pece Salvatore , Pilcher Brian K. , Vecchi Manuela , Sigismund Sara , Di Fiore Pier Paolo 
Published: June 2020

AbstractThe subversion of endocytic routes leads to malignant transformation and has been implicated in human cancers. However, there is scarce evidence for genetic alterations of endocytic proteins as causative in high incidence human cancers. Here, we report that Epsin 3 (EPN3) is an oncogene with prognostic and therapeutic relevance in breast cancer. Mechanistically, EPN3 drives breast tumorigenesis by increasing E-cadherin endocytosis, followed by the activation of a β-catenin/TCF4-dependent partial epithelial-to-mesenchymal transition (EMT), followed by the establishment of a TGFβ-dependent autocrine loop that sustains EMT. EPN3-induced partial EMT is instrumental for the transition from in situ to invasive breast carcinoma, and, accordingly, high EPN3 levels are detected at the invasive front of human breast cancers and independently predict metastatic rather than loco-regional recurrence. Thus, we uncover an endocytic-based mechanism able to generate TGFβ-dependent regulatory loops conferring cellular plasticity and invasive behavior.
Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry
Authors: Reim Alexander , Ackermann Roland , Font-Mateu Jofre , Kammel Robert , Beato Miguel , Nolte Stefan , Mann Matthias , Russmann Christoph , Wierer Michael 
Published: June 2020

AbstractTranscription factors (TFs) regulate target genes by specific interactions with DNA sequences. Detecting and understanding these interactions at the molecular level is of fundamental importance in biological and clinical contexts. Crosslinking mass spectrometry is a powerful tool to assist the structure prediction of protein complexes but has been limited to the study of protein-protein and protein-RNA interactions. Here, we present a femtosecond laser-induced crosslinking mass spectrometry (fliX-MS) workflow, which allows the mapping of protein-DNA contacts at single nucleotide and up to single amino acid resolution. Applied to recombinant histone octamers, NF1, and TBP in complex with DNA, our method is highly specific for the mapping of DNA binding domains. Identified crosslinks are in close agreement with previous biochemical data on DNA binding and mostly fit known complex structures. Applying fliX-MS to cells identifies several bona fide crosslinks on DNA binding domains, paving the way for future large scale ex vivo experiments.
Anapole mediated giant photothermal nonlinearity in nanostructured silicon
Authors: Zhang Tianyue , Che Ying , Chen Kai , Xu Jian , Xu Yi , Wen Te , Lu Guowei , Liu Xiaowei , Wang Bin , Xu Xiaoxuan , Duh Yi-Shiou , Tang Yu-Lung , Han Jing , Cao Yaoyu , Guan Bai-Ou , Chu Shi-Wei , Li Xiangping 
Published: June 2020

AbstractFeatured with a plethora of electric and magnetic Mie resonances, high index dielectric nanostructures offer a versatile platform to concentrate light-matter interactions at the nanoscale. By integrating unique features of far-field scattering control and near-field concentration from radiationless anapole states, here, we demonstrate a giant photothermal nonlinearity in single subwavelength-sized silicon nanodisks. The nanoscale energy concentration and consequent near-field enhancements mediated by the anapole mode yield a reversible nonlinear scattering with a large modulation depth and a broad dynamic range, unveiling a record-high nonlinear index change up to 0.5 at mild incident light intensities on the order of MW/cm2. The observed photothermal nonlinearity showcases three orders of magnitude enhancement compared with that of unstructured bulk silicon, as well as nearly one order of magnitude higher than that through the radiative electric dipolar mode. Such nonlinear scattering can empower distinctive point spread functions in confocal reflectance imaging, offering the potential for far-field localization of nanostructured Si with an accuracy approaching 40 nm. Our findings shed new light on active silicon photonics based on optical anapoles.
Neural stem cell delivery via porous collagen scaffolds promotes neuronal differentiation and locomotion recovery in spinal cord injury
Authors: Kourgiantaki Alexandra , Tzeranis Dimitrios S. , Karali Kanelina , Georgelou Konstantina , Bampoula Efstathia , Psilodimitrakopoulos Sotirios , Yannas Ioannis V. , Stratakis Emmanuel , Sidiropoulou Kyriaki , Charalampopoulos Ioannis , Gravanis Achille 
Published: June 2020

AbstractNeural stem cell (NSC) grafts have demonstrated significant effects in animal models of spinal cord injury (SCI), yet their clinical translation remains challenging. Significant evidence suggests that the supporting matrix of NSC grafts has a crucial role in regulating NSC effects. Here we demonstrate that grafts based on porous collagen-based scaffolds (PCSs), similar to biomaterials utilized clinically in induced regeneration, can deliver and protect embryonic NSCs at SCI sites, leading to significant improvement in locomotion recovery in an experimental mouse SCI model, so that 12 weeks post-injury locomotion performance of implanted animals does not statistically differ from that of uninjured control animals. NSC-seeded PCS grafts can modulate key processes required to induce regeneration in SCI lesions including enhancing NSC neuronal differentiation and functional integration in vivo, enabling robust axonal elongation, and reducing astrogliosis. Our findings suggest that the efficacy and translational potential of emerging NSC-based SCI therapies could be enhanced by delivering NSC via scaffolds derived from well-characterized clinically proven PCS.
A unique approach to monitor stress in coral exposed to emerging pollutants
Authors: Stien Didier , Suzuki Marcelino , Rodrigues Alice M. S. , Yvin Marion , Clergeaud Fanny , Thorel Evane , Lebaron Philippe 
Published: June 2020

AbstractMetabolomic profiling of the hexacoral Pocillopora damicornis exposed to solar filters revealed a metabolomic signature of stress in this coral. It was demonstrated that the concentration of the known steroid (3β, 5α, 8α) -5, 8-epidioxy- ergosta- 6, 24(28) - dien- 3- ol (14) increased in response to octocrylene (OC) and ethylhexyl salicylate (ES) at 50 µg/L. Based on the overall coral response, we hypothesize that steroid 14 mediates coral response to stress. OC also specifically altered mitochondrial function at this concentration and above, while ES triggered a stress/inflammatory response at 300 µg/L and above as witnessed by the significant increases in the concentrations of polyunsaturated fatty acids, lysophosphatidylcholines and lysophosphatidylethanolamines. Benzophenone-3 increased the concentration of compound 14 at 2 mg/L, while the concentration of stress marker remained unchanged upon exposition to the other solar filters tested. Also, our results seemed to refute earlier suggestions that platelet-activating factor is involved in the coral inflammatory response.
A Neural Network Approach to Quantify Blood Flow from Retinal OCT Intensity Time-Series Measurements
Authors: Braaf Boy , Donner Sabine , Uribe-Patarroyo Néstor , Bouma Brett E. , Vakoc Benjamin J. 
Published: June 2020

AbstractMany diseases of the eye are associated with alterations in the retinal vasculature that are possibly preceded by undetected changes in blood flow. In this work, a robust blood flow quantification framework is presented based on optical coherence tomography (OCT) angiography imaging and deep learning. The analysis used a forward signal model to simulate OCT blood flow data for training of a neural network (NN). The NN was combined with pre- and post-processing steps to create an analysis framework for measuring flow rates from individual blood vessels. The framework’s accuracy was validated using both blood flow phantoms and human subject imaging, and across flow speed, vessel angle, hematocrit levels, and signal-to-noise ratio. The reported flow rate of the calibrated NN framework was measured to be largely independent of vessel angle, hematocrit levels, and measurement signal-to-noise ratio. In vivo retinal flow rate measurements were self-consistent across vascular branch points, and approximately followed a predicted power-law dependence on the vessel diameter. The presented OCT-based NN flow rate estimation framework addresses the need for a robust, deployable, and label-free quantitative retinal blood flow mapping technique.
Assessment of cerebral autoregulation indices – a modelling perspective
Authors: Liu Xiuyun , Czosnyka Marek , Donnelly Joseph , Cardim Danilo , Cabeleira Manuel , Lalou Despina Aphroditi , Hu Xiao , Hutchinson Peter J. , Smielewski Peter 
Published: June 2020

AbstractVarious methodologies to assess cerebral autoregulation (CA) have been developed, including model - based methods (e.g. autoregulation index, ARI), correlation coefficient - based methods (e.g. mean flow index, Mx), and frequency domain - based methods (e.g. transfer function analysis, TF). Our understanding of relationships among CA indices remains limited, partly due to disagreement of different studies by using real physiological signals, which introduce confounding factors. The influence of exogenous noise on CA parameters needs further investigation. Using a set of artificial cerebral blood flow velocities (CBFV) generated from a well-known CA model, this study aims to cross-validate the relationship among CA indices in a more controlled environment. Real arterial blood pressure (ABP) measurements from 34 traumatic brain injury patients were applied to create artificial CBFVs. Each ABP recording was used to create 10 CBFVs corresponding to 10 CA levels (ARI from 0 to 9). Mx, TF phase, gain and coherence in low frequency (LF) and very low frequency (VLF) were calculated. The influence of exogenous noise was investigated by adding three levels of colored noise to the artificial CBFVs. The result showed a significant negative relationship between Mx and ARI (r = −0.95, p < 0.001), and it became almost purely linear when ARI is between 3 to 6. For transfer function parameters, ARI positively related with phase (r = 0.99 at VLF and 0.93 at LF, p < 0.001) and negatively related with gain_VLF(r = −0.98, p < 0.001). Exogenous noise changed the actual values of the CA parameters and increased the standard deviation. Our results show that different methods can lead to poor correlation between some of the autoregulation parameters even under well controlled situations, undisturbed by unknown confounding factors. They also highlighted the importance of exogenous noise, showing that even the same CA value might correspond to different CA levels under different ‘noise’ conditions.
Single-Walled Carbon Nanotube Supported PtNi Nanoparticles
(PtNi@SWCNT) Catalyzed Oxidation of Benzyl Alcohols to the Benzaldehyde Derivatives in
Oxygen Atmosphere
Authors: Göksu Haydar , Cellat Kemal , Şen Fatih 
Published: June 2020

AbstractThis study reports a developed process which is a general and facile
method for the oxidation of benzyl alcohol (BnOH) compounds to the benzaldehyde (BA)
derivatives, under mild conditions. The oxidation of BnOH species catalyzed by
PtNi@SWCNT in toluene (3 ml) at 80 °C under a continuous stream of
O2. Single wall carbon nanotube supported PtNi
(PtNi@SWCNT) nanoparticles were synthesized using a single-step modified reduction
process. The characterization of PtNi@SWCNT nanocatalyst was performed by
transmission electron microscope (TEM), X-ray diffraction (XRD), X-ray Photoelectron
Spectroscopy (XPS), and elemental analysis by ICP-OES. A variety of BnOH compounds
were oxidized by the PtNi@SWCNT catalyst and all the expected oxidation products
were obtained in high efficiency in 2 hours of reaction time. TLC was used to
monitoring the reaction progress, and the products were identified by1H/13C-NMR
analysis.
Isolation and propagation of leptospires at 37 °C directly from the mammalian host
Authors: Hornsby Richard L. , Alt David P. , Nally Jarlath E. 
Published: June 2020

AbstractThe causative agent of leptospirosis includes multiple serovars and species of pathogenic leptospires that are excreted via urine from reservoir hosts of infection. Primary isolation takes weeks to months, and is limited to semi-solid media at 28–30 °C. Here we present an alternative media formulation, HAN, compared to commercially available EMJH and the more specialized T80/40/LH media formulations, in semi-solid and liquid compositions, for the primary isolation of two diverse species and serovars of pathogenic leptospires directly from host kidney tissue. All three media types supported the isolation and propagation ofL.interrogansserovar Copenhageni strain IC:20:001 in semi-solid media at 29 °C. However, only HAN and T80/40/LH supported the growth ofL.borgpeterseniiserovar Hardjo strain HB15B203 at 29 °C. In addition, HAN supported primary isolation at 37 °C. Both T80/40/LH and HAN supported primary isolation of strain IC:20:001 in liquid media at 29 °C but only HAN supported growth of strain HB15B203 in liquid media, at both 29 and 37 °C. HAN media supports the primary isolation of fastidious pathogenic leptospires directly from infected host tissue at either 29 or 37 °C: this formulation represents a more defined media for the continued optimization of growth factors required to support the primary isolation of the large and diverse range of species and serovars within the genusLeptospiracirculating within domestic and wild animal populations.