bluuebunny/crossref_metadata_2025_split huggingface dataset:
TGF-β induced EMT and stemness characteristics are associated with epigenetic regulation in lung cancer
Authors: Kim Bit Na , Ahn Dong Hyuck , Kang Nahyeon , Yeo Chang Dong , Kim Young Kyoon , Lee Kyo Young , Kim Tae-Jung , Lee Sug Hyung , Park Mi Sun , Yim Hyeon Woo , Park Jong Y. , Park Chan Kwon , Kim Seung Joon 
Published: June 2020

AbstractTransforming growth factor-β (TGF-β) promotes tumor invasion and metastasis by inducing epithelial-mesenchymal transition (EMT). EMT is often related with acquisition of stemness characteristics. The objective of this study was to determine whether EMT and stemness characteristics induced by TGF-β might be associated with epigenetic regulation in lung cancer. A human normal lung epithelial cell line and four lung cancer cell lines were treated with TGF-β. Transcriptome analysis of BEAS-2B and A549 cells incubated with TGF-β were analyzed through next-generation sequencing (NGS). Western blotting was carried out to investigate expression levels of epithelial and mesenchymal markers. Wound healing and Matrigel invasion assay, sphere formation assay, and in vivo mice tumor model were performed to evaluate functional characteristics of EMT and stemness acquisition. To investigate whether activation of EMT and stem cell markers might be involved in epigenetic regulation of lung cancer, experiment using a DNA methyltransferase inhibitor (5-azacytidine, AZA), methylation-specific PCR (MSP) and bisulfite sequencing were performed. NGS revealed changes in expression levels of EMT markers (E-cadherin, N-cadherin, fibronectin, vimentin, slug and snail) and stem cell markers (CD44 and CD87) in both BEAS-2B and A549 cells. Functional analysis revealed increased migration, invasion, sphere formation, and tumor development in mice after TGF-β treatment. Expression of slug and CD87 genes was activated following treatment with AZA and TGF-β. MSP and bisulfite sequencing indicated DNA demethylation of slug and CD87 genes. These results suggest that TGF-β induced EMT and cancer stemness acquisition could be associated with activation of slug and CD87 gene by their promoter demethylation.
p32/C1QBP regulates OMA1-dependent proteolytic processing of OPA1 to maintain mitochondrial connectivity related to mitochondrial dysfunction and apoptosis
Authors: Noh Solhee , Phorl Sophors , Naskar Rema , Oeum Kakada , Seo Yuri , Kim Eunjung , Kweon Hee-Seok , Lee Joo-Yong 
Published: June 2020

AbstractMitochondria are dynamic organelles that undergo fusion and fission in response to various physiological and stress stimuli, which play key roles in diverse mitochondrial functions such as energy metabolism, intracellular signaling, and apoptosis. OPA1, a mitochondrial dynamin-like GTPase, is responsible for the inner membrane fusion of mitochondria, and the function of OPA1 is regulated by proteolytic cleavage in response to various metabolic stresses. Growing evidences highlighted the importance of mitochondrial adaptation in response to metabolic stimuli. Here, we demonstrated the role of p32/C1QBP in mitochondrial morphology by regulating OMA1-dependent proteolytic processing of OPA1. Genetic ablation of p32/C1QBP activates OMA1, cleaves OPA1, and leads mitochondrial fragmentation and swelling. The loss of p32/C1QBP decreased mitochondrial respiration and lipid utilization, sensitized cells to mitochondrial stress, and triggered a metabolic shift from oxidative phosphorylation to glycolysis, which were correlated with apoptosis in cancer cells and the inhibition of 3D-spheroid formation. These results suggest a unique regulation of cell physiology by mitochondria and provide a basis for a new therapeutic strategy for cancer.
miRNA–mRNA network regulation in the skeletal muscle fiber phenotype of chickens revealed by integrated analysis of miRNAome and transcriptome
Authors: Liu Yifan , Zhang Ming , Shan Yanju , Ji Gaige , Ju Xiaojun , Tu Yunjie , Sheng Zhongwei , Xie Jingfang , Zou Jianmin , Shu Jingting 
Published: June 2020

AbstractSkeletal muscle fibers are primarily categorized into oxidative and glycolytic fibers, and the ratios of different myofiber types are important factors in determining livestock meat quality. However, the molecular mechanism for determining muscle fiber types in chickens was hardly understood. In this study, we used RNA sequencing to systematically compare mRNA and microRNA transcriptomes of the oxidative muscle sartorius (SART) and glycolytic muscle pectoralis major (PMM) of Chinese Qingyuan partridge chickens. Among the 44,705 identified mRNAs in the two types of muscles, 3,457 exhibited significantly different expression patterns, including 2,364 up-regulated and 1,093 down-regulated mRNAs in the SART. A total of 698 chicken miRNAs were identified, including 189 novel miRNAs, among which 67 differentially expressed miRNAs containing 42 up-regulated and 25 down-regulated miRNAs in the SART were identified. Furthermore, function enrichment showed that the differentially expressed mRNAs and miRNAs were involved in energy metabolism, muscle contraction, and calcium, peroxisome proliferator-activated receptor (PPAR), insulin and adipocytokine signaling. Using miRNA-mRNA integrated analysis, we identified several candidate miRNA-gene pairs that might affect muscle fiber performance, viz, gga-miR-499-5p/SOX6 and gga-miR-196-5p/CALM1, which were supported by target validation using the dual-luciferase reporter system. This study revealed a mass of candidate genes and miRNAs involved in muscle fiber type determination, which might help understand the molecular mechanism underlying meat quality traits in chickens.
Maximum entropy approach to multivariate time series randomization
Authors: Marcaccioli Riccardo , Livan Giacomo 
Published: June 2020

AbstractNatural and social multivariate systems are commonly studied through sets of simultaneous and time-spaced measurements of the observables that drive their dynamics, i.e., through sets of time series. Typically, this is done via hypothesis testing: the statistical properties of the empirical time series are tested against those expected under a suitable null hypothesis. This is a very challenging task in complex interacting systems, where statistical stability is often poor due to lack of stationarity and ergodicity. Here, we describe an unsupervised, data-driven framework to perform hypothesis testing in such situations. This consists of a statistical mechanical approach—analogous to the configuration model for networked systems—for ensembles of time series designed to preserve, on average, some of the statistical properties observed on an empirical set of time series. We showcase its possible applications with a case study on financial portfolio selection.
Enzyme-catalysed mineralisation experiment study to solidify desert sands
Authors: Miao Linchang , Wu Linyu , Sun Xiaohao 
Published: June 2020

AbstractSandstorms are meteorological phenomena common in arid and semi-arid regions and have been recognized severe natural disasters worldwide. The key problem is how to control and mitigate sandstorm natural disasters. This research aims to mitigate their development by improving surface stability and soil water retention properties through soil mineralization. The enzymatic induced carbonate precipitation (EICP) is proposed to solidify desert sands and form a hard crust layer on the surface of desert sands. In contrast to micro-induced carbonate precipitation commonly used at room temperatures, EICP had high production efficiency and productivity at a broader temperature range (10–70 °C ±) and significantly improves material water retention properties, which was more suitable to desert environment. Results demonstrate that the enzyme-catalysed mineralisation method can be better resistance to high winds as the number of spraying times increased.
Soil as an extended composite phenotype of the microbial metagenome
Authors: Neal Andrew L. , Bacq-Labreuil Aurélie , Zhang Xiaoxian , Clark Ian M. , Coleman Kevin , Mooney Sacha J. , Ritz Karl , Crawford John W. 
Published: June 2020

AbstractWe use a unique set of terrestrial experiments to demonstrate how soil management practises result in emergence of distinct associations between physical structure and biological functions. These associations have a significant effect on the flux, resilience and efficiency of nutrient delivery to plants (including water). Physical structure, determining the air–water balance in soil as well as transport rates, is influenced by nutrient and physical interventions. Contrasting emergent soil structures exert selective pressures upon the microbiome metagenome. These selective pressures are associated with the quality of organic carbon inputs, the prevalence of anaerobic microsites and delivery of nutrients to microorganisms attached to soil surfaces. This variety results in distinctive gene assemblages characterising each state. The nature of the interactions provide evidence that soil behaves as an extended composite phenotype of the resident microbiome, responsive to the input and turnover of plant-derived organic carbon. We provide new evidence supporting the theory that soil-microbe systems are self-organising states with organic carbon acting as a critical determining parameter. This perspective leads us to propose carbon flux, rather than soil organic carbon content as the critical factor in soil systems, and we present evidence to support this view.
Parkinsonian neurotoxicants impair the anti-inflammatory response induced by IL4 in glial cells: involvement of the CD200-CD200R1 ligand-receptor pair
Authors: Rabaneda-Lombarte Neus , Blasco-Agell Lucas , Serratosa Joan , Ferigle Laura , Saura Josep , Solà Carme 
Published: June 2020

AbstractExposure to pesticides such as rotenone is a risk factor for Parkinson’s disease. Dopaminergic neurons are especially sensitive to the toxicity of compounds that inhibit the mitochondrial respiratory chain such as rotenone and 1-methyl-4-phenylpyridinium (MPP+). However, there is scarce information on their effects on glia. To evaluate whether these neurotoxicants affect the immune response of glia, primary mouse mixed glial and microglial cultures were treated with interleukin (IL) 4 in the absence and presence of MPP+ or rotenone. Using qRTPCR or western blot, we determined the expression of anti-inflammatory markers, the CD200R1 microglial receptor and its ligand CD200, and genes regulating glycolysis and oxidative metabolism. ATP and lactate levels were additionally determined as an index of cell metabolism. Microglial phagocytosis was also evaluated. MPP+ and rotenone clearly abrogated the IL4-induced expression of anti-inflammatory markers in mixed glial cultures. CD200 and CD200R1 expression and microglia phagocytosis were also affected by the neurotoxicants. Changes in the mRNA expression of the molecules regulating glycolysis and oxidative metabolism, as well as in ATP levels and lactate release suggested that metabolic reprogramming in response to MPP+ and rotenone differs between microglial and mixed glial cultures. These findings support the hypothesis that parkinsonian neurotoxicants may impair brain immune response altering glial cell metabolism.
Beta-nerve growth factor stimulates spontaneous electrical activity of in vitro embryonic mouse GnRH neurons through a P75 mediated-mechanism
Authors: Pinet-Charvet Caroline , Fleurot Renaud , Derouin-Tochon Flavie , de Graaf Simon , Druart Xavier , Tsikis Guillaume , Taragnat Catherine , Teixeira-Gomes Ana-Paula , Labas Valérie , Moreau Thierry , Cayla Xavier , Duittoz Anne H 
Published: June 2020

AbstractThe control of ovulation helps guarantee the success of reproduction and as such, contributes to the fitness of a species. In mammals, two types of ovulation are observed: induced and spontaneous ovulation. Recent work on camelids, that are induced ovulators, highlighted the role of a factor present in seminal plasma, beta Nerve Growth Factor (β-NGF), as the factor that triggers ovulation in a GnRH dependent manner. In the present work, we characterized alpaca β-NGF (aβ-NGF) and its 3D structure and compared it with human recombinant β-NGF (hβ-NGF). We showed that the β-NGF enriched fraction of alpaca semen and the human recombinant protein, both stimulated spontaneous electrical activity of primary GnRH neurons derived from mouse embryonic olfactory placodes. This effect was dose-dependent and mediated by p75 receptor signaling. P75 receptors were found expressed in vitro by olfactory ensheathing cells (OEC) in close association with GnRH neurons and in vivo by tanycytes in close vicinity to GnRH fibers in adult mouse. Altogether, these results suggested that β-NGF induced ovulation through an increase in GnRH secretion provoked by a glial dependent P75 mediated mechanism.
Effects of novel non-thermal atmospheric plasma treatment of titanium on physical and biological improvements and in vivo osseointegration in rats
Authors: Zheng Zheng , Ao Xiaogang , Xie Peng , Wu Jie , Dong Yuqing , Yu Deping , Wang Jian , Zhu Zhimin , Xu Hockin H. K. , Chen Wenchuan 
Published: June 2020

AbstractTitanium (Ti) has achieved extensive applications due to its excellent biocompatibility and mechanical properties. Plasma can enhance surface hydrophilia of Ti with decreased carbon contamination. The traditional conditions using a single gas plasma was for longer treatment time and more prone to being contaminated. We designed and developed novel and universal apparatus and methods with a special clamping device of non-thermal atmospheric plasma (NTAP) treatment using mixed gas for Ti surface activation. We systematically and quantitatively investigated the effective effects of NTAP-Ti. The surface water contact angle decreased by 100%, the carbon content decreased by 80% and oxygen content increased by 50% in the novel NTAP-Ti surfaces. NTAP treatment accelerated the attachment, spread, proliferation, osteogenic differentiation and mineralization of MC3T3-E1 mouse preosteoblasts in vitro. The percentage of bone-to-implant contact increased by 25–40%, and the osteoclasts and bone resorption were suppressed by 50% in NTAP-Ti in vivo. In conclusion, NTAP-Ti substantially enhanced the physical and biological effects and integration with bone. The novel and universal apparatus and methods with a special clamping device using gas mixtures are promising for implant activation by swiftly and effectively changing the Ti surface to a hydrophilic one to enhance dental and orthopedic applications.
Zebrafish (Danio rerio) physiological and behavioural responses to insect-based diets: a multidisciplinary approach
Authors: Zarantoniello Matteo , Randazzo Basilio , Gioacchini Giorgia , Truzzi Cristina , Giorgini Elisabetta , Riolo Paola , Gioia Giorgia , Bertolucci Cristiano , Osimani Andrea , Cardinaletti Gloriana , Lucon-Xiccato Tyrone , Milanović Vesna , Annibaldi Anna , Tulli Francesca , Notarstefano Valentina , Ruschioni Sara , Clementi Francesca , Olivotto Ike 
Published: June 2020

AbstractBlack Soldier Fly (BSF) meal is considered as an alternative, emerging and sustainable ingredient for aquafeed production. However, results on fish physiological responses are still fragmentary and often controversial, while no studies are available on fish behavior in response to these new diets. The present work represents the first comprehensive multidisciplinary study aimed to investigate zebrafish physiological and behavioural responses to BSF-based diets. Five experimental diets characterized by increasing inclusion levels (0, 25, 50, 75 and 100% respect to fish meal) of full fat BSF prepupae meal were tested during a 2-months feeding trial. Prepupae were cultured on coffee silverskin growth substrate enriched with a 10%Schizochytriumsp. to improve insects’ fatty acids profile. The responses of zebrafish were assayed through biometric, histological, gas chromatographic, microbiological, spectroscopic, molecular and behavioural analyses. Results evidenced that BSF-based diets affected fish fatty acid composition, while behavioural tests did not show differences among groups. Specifically, a 50% BSF inclusion level diet represented the best compromise between ingredient sustainability and proper fish growth and welfare. Fish fed with higher BSF inclusions (75 and 100%) showed hepatic steatosis, microbiota modification, higher lipid content, fatty acid modification and higher expression of immune response markers.
Cardiomyocyte-specific deletion of GCN5L1 in mice restricts mitochondrial protein hyperacetylation in response to a high fat diet
Authors: Thapa Dharendra , Manning Janet R. , Stoner Michael W. , Zhang Manling , Xie Bingxian , Scott Iain 
Published: June 2020

AbstractMitochondrial lysine acetylation regulates several metabolic pathways in cardiac cells. The current study investigated whether GCN5L1-mediated lysine acetylation regulates cardiac mitochondrial metabolic proteins in response to a high fat diet (HFD). GCN5L1 cardiac-specific knockout (cKO) mice showed significantly reduced mitochondrial protein acetylation following a HFD relative to wildtype (WT) mice. GCN5L1 cKO mice did not display any decrease in ex vivo cardiac workload in response to a HFD. In contrast, ex vivo cardiac function in HFD-fed WT mice dropped ~ 50% relative to low fat diet (LFD) fed controls. The acetylation status of electron transport chain Complex I protein NDUFB8 was significantly increased in WT mice fed a HFD, but remained unchanged in GCN5L1 cKO mice relative to LFD controls. Finally, we observed that inhibitory acetylation of superoxide dismutase 2 (SOD2) at K122 was increased in WT (but not cKO mice) on a HFD. This correlated with significantly increased cardiac lipid peroxidation in HFD-fed WT mice relative to GCN5L1 cKO animals under the same conditions. We conclude that increased GCN5L1 expression in response to a HFD promotes increased lysine acetylation, and that this may play a role in the development of reactive oxygen species (ROS) damage caused by nutrient excess.
Pathogenic role of human C-reactive protein in diabetic retinopathy
Authors: Qiu Fangfang , Ma Xiang , Shin Young-Hwa , Chen Jianglei , Chen Qian , Zhou Kelu , Wu Wenjing , Liang Wentao , Wu Yalin , Song Qing , Ma Jian-Xing 
Published: June 2020

Abstract
Purpose: Elevated blood levels of C-reactive protein (CRP) are associated with both type 1 and type 2 diabetes and diabetic complications, such as diabetic retinopathy (DR). However, its pathogenic role in DR remains unknown. The present study aims to investigate the potential role of CRP in DR pathogenesis and explore its underlying mechanism.
Materials and methods: Human CRP transgenic (hCRP-Tg) rats were employed for streptozotocin (STZ)-induced diabetic and oxygen-induced retinopathy (OIR) models. The retina function was monitored by electroretinography (ERG) and retinal thickness was measured by optical coherence tomography (OCT). TUNEL and cell death ELISA were performed to measure the apoptosis. Oxidative stress was detected by the measurement of reactive oxygen species (ROS) in cells and 3-Nitrotyrosine staining in tissue sections.
Results: In non-diabetic condition, hCRP-Tg with elevated hCRP levels in the retinas demonstrated declined ERG responses and decreased retinal thickness. In STZ-induced diabetic condition, overexpression of hCRP deteriorated retinal neurodegeneration as shown by ERG and apoptosis assays. hCRP also exacerbated retinal leukostasis and acellular capillary formation induced by diabetes. In the OIR model, overexpression of hCRP exacerbated retinal neovascularization (NV). In retinal cell lines, hCRP treatment induced cell death and over-production of ROS. Furthermore, hCRP-induced overexpression of pro-inflammatory, pro-oxidative, and pro-angiogenic factors was associated with up-regulation of CD32 and the NF-κB signaling in the retinas.
Conclusions: Elevated hCRP levels play a pathogenic role in DR. Targeting the hCRP-CD32-NF-κB pathway may represent a novel therapeutic strategy for DR.
IOTA: a 1.7‐TOP/J inference processor for binary convolutional neural networks with 4.7 K LUTs in a tiny FPGA
Authors: Kim T. , Shin J. , Choi K. 
Published: June 2020

This Letter presents an efficient inference processor for binary convolutional neural networks in an FPGA that has tight limitation of the available hardware resources. The proposed processor, named inference processor in a tiny FPGA (IOTA), incorporates the dual block‐processing cores, which process each constituent block of a network cooperatively skipping redundant operations. Implemented in Intel®MAX®10, IOTA achieves the energy efficiency of 1.7 TOP/J with the resource usage of just 4.7 K lookup table (LUT) and 384Kbit BRAMs, where a single binary operation has been counted by 1 OP. A fully‐integrated inference system has been developed to demonstrate the functionality of IOTA. It can infer the classes of 172.85 images per joule for the CIFAR‐10 classification task.
The abundance of S- and Si-bearing molecules in O-rich circumstellar envelopes of AGB stars
Authors: Massalkhi S. , Agúndez M. , Cernicharo J. , Velilla-Prieto L. 
Published: June 2020

Aims.We aim to determine the abundances of SiO, CS, SiS, SO, and SO2in a large sample of oxygen-rich asymptotic giant branch (AGB) envelopes covering a wide range of mass loss rates to investigate the potential role that these molecules could play in the formation of dust in these environments.Methods.We surveyed a sample of 30 oxygen-rich AGB stars in theλ2 mm band using the IRAM 30m telescope. We performed excitation and radiative transfer calculations based on the large velocity gradient method to model the observed lines of the molecules and to derive their fractional abundances in the observed envelopes.Results.We detected SiO in all 30 targeted envelopes, as well as CS, SiS, SO, and SO2in 18, 13, 26, and 19 sources, respectively. Remarkably, SiS is not detected in any envelope with a mass loss rate below 10−6M⊙yr−1, whereas it is detected in all envelopes with mass loss rates above that threshold. From a comparison with a previous, similar study on C-rich sources, it becomes evident that the fractional abundances of CS and SiS show a marked differentiation between C-rich and O-rich sources, being two orders of magnitude and one order of magnitude more abundant in C-rich sources, respectively, while the fractional abundance of SiO turns out to be insensitive to the C/O ratio. The abundance of SiO in O-rich envelopes behaves similarly to C-rich sources, that is, the denser the envelope the lower its abundance. A similar trend, albeit less clear than for SiO, is observed for SO in O-rich sources.Conclusions.The marked dependence of CS and SiS abundances on the C/O ratio indicates that these two molecules form more efficiently in C- than O-rich envelopes. The decline in the abundance of SiO with increasing envelope density and the tentative one for SO indicate that SiO and possibly SO act as gas-phase precursors of dust in circumstellar envelopes around O-rich AGB stars.