bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inflammation‐induced mammalian target of rapamycin signaling is essential for retina regeneration
Authors: Zhang Zhiqiang , Hou Haitao , Yu Shuguang , Zhou Cuiping , Zhang Xiaoli , Li Na , Zhang Shuqiang , Song Kaida , Lu Ying , Liu Dong , Lu Hong , Xu Hui 
Published: August 2019

AbstractUpon retina injury, Müller glia in the zebrafish retina respond by generating multipotent progenitors to repair the retina. However, the complete mechanisms underlying retina regeneration remain elusive. Here we report inflammation‐induced mammalian target of rapamycin (mTOR) signaling in the Müller glia is essential for retina regeneration in adult zebrafish. We show after a stab injury, mTOR is rapidly activated in Müller glia and later Müller glia‐derived progenitor cells (MGPCs). Importantly, mTOR is required for Müller glia dedifferentiation, as well as the proliferation of Müller glia and MGPCs. Interestingly, transient mTOR inhibition by rapamycin only reversibly suppresses MGPC proliferation, while its longer suppression by knocking down Raptor significantly inhibits the regeneration of retinal neurons. We further show mTOR promotes retina regeneration by regulating the mRNA expression of key reprogramming factors ascl1a and lin‐28a, cell cycle‐related genes and critical cytokines. Surprisingly, we identify microglia/macrophage‐mediated inflammation as an important upstream regulator of mTOR in the Müller glia and it promotes retina regeneration through mTOR. Our study not only demonstrates the important functions of mTOR but also reveals an interesting link between inflammation and the mTOR signaling during retina regeneration.
Dynamic functional connectivity states characterize NREM sleep and wakefulness
Authors: Zhou Shuqin , Zou Guangyuan , Xu Jing , Su Zihui , Zhu Huaiqiu , Zou Qihong , Gao Jia‐Hong 
Published: August 2019

AbstractAccording to recent neuroimaging studies, temporal fluctuations in functional connectivity patterns can be clustered into dynamic functional connectivity (DFC) states and correspond to fluctuations in vigilance. However, whether there consistently exist DFC states associated with wakefulness and sleep stages and what are the characteristics and electrophysiological origin of these states remain unclear. The aims of the current study were to investigate the properties of DFC in different sleep stages and to explore the relationship between the characteristics of DFC and slow‐wave activity. We collected both eyes‐closed wakefulness and sleep data from 48 healthy young volunteers with simultaneous electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) recordings. EEG data were employed as the gold standard of sleep stage scoring, and DFC states were estimated based on fMRI data. The results demonstrated that DFC states of the fMRI signals consistently corresponded to wakefulness and nonrapid eye movement sleep stages independent of the number of clusters. Furthermore, the mean dwell time of these states significantly correlated with slow‐wave activity. The inclusion or omission of regression of the global signal and the selection of parcellation schemes exerted minimal effects on the current findings. These results provide strong evidence that DFC states underlying fMRI signals match the fluctuations of vigilance and suggest a possible electrophysiological source of DFC states corresponding to vigilance states.
Downregulation of microRNA‐135b promotes atherosclerotic plaque stabilization in atherosclerotic mice by upregulating erythropoietin receptor
Authors: Wu Bo‐Wen , Liu Yu , Wu Mi‐Shan , Meng Yun‐Hui , Lu Meng , Guo Jin‐Dong , Zhou Yu‐Hui 
Published: August 2019

AbstractAtherosclerotic plaque rupture is an important pathophysiologic mechanism of acute coronary syndrome. Emerging microRNAs (miRNAs) have been implicated in the atherosclerotic plaque formation and macrophage autophagy during the development of atherosclerosis (AS). Hence, this study was conducted to explore the role microRNA‐135b (miR‐135b) in macrophages and atherosclerotic plaque in mouse models of AS. The expression of miR‐135b and erythropoietin receptor (EPOR) was altered in atherosclerotic mice to clarify their effect on inflammation, cell activities of aortic tissues, and macrophage autophagy. The obtained findings unraveled that miR‐135b was upregulated and EPOR was downregulated in atherosclerotic mice. Upregulated miR‐135b expression promoted cell apoptosis and inflammation, along with inhibited cell proliferation and decreased macrophage autophagy. Notably, miR‐135 was validated to target EPOR and activate the PI3K/Akt signaling pathway. Moreover, miR‐135b inhibition attenuated inflammation, atherosclerotic plaque development, and promoted macrophage autophagy. Besides, the effect of miR‐135b inhibition was reversed in response to EPOR silencing. Taken conjointly, the study revealed that inhibition of miR‐135b promoted macrophage autophagy and atherosclerotic plaque stabilization in atherosclerotic mice by inactivating the PI3K/Akt signaling pathway and upregulating EPOR.
Delivery of long chain C16 and C24 ceramide in HeLa cells using oxidized graphene nanoribbons
Authors: Suhrland Cassandra , Truman Jean‐Philip , Obeid Lina M. , Sitharaman Balaji 
Published: August 2019

AbstractThe bioactive sphingolipid ceramide has many important roles in cell signaling processes, particularly in signaling programmed cell death in cancer. However, ceramide levels are often impaired in multi‐drug resistant and radiation resistant cancers due to the dysregulation of ceramide metabolism. Restoration of ceramide levels through external delivery therefore represents a potential therapeutic target for the treatment of resistant cancers. However, as a lipid, ceramide is extremely hydrophobic and requires a delivery system to enter cells. Here we report the development of a method to load significant amounts of the long chain C16 and C24 ceramides onto oxidized graphene nanoribbons (O‐GNRs) derived from carbon nanotubes. Using O‐GNRs as a delivery system for these ceramides, we were able to induce significant biological effects in HeLa cells in conjunction with C6 ceramide and ultraviolet radiation treatment. However, we found that O‐GNRs themselves exert significant biological effects and can interfere with the actions of these ceramides and ultraviolet treatment. Loading of ceramides onto O‐GNRs did not have a significant effect on the entry of the nanoparticles into cells. Despite the need for further improvement, these data represent an important first step in the development of O‐GNRs as a delivery system for long chain ceramides.
Production of 2,3‐butanediol by fermentation of enzymatic hydrolysed bagasse from agave mezcal‐waste using the native Klebsiella oxytoca UM2‐17 strain
Authors: Pasaye‐Anaya Lizbeth , Vargas‐Tah Alejandra , Martínez‐Cámara Christian , Castro‐Montoya Agustín J , Campos‐García Jesús 
Published: August 2019

AbstractBackground2,3‐butanediol is a chemical component with wide industrial applications, such as biofuels and chemical precursors. Reducing 2,3‐butanediol production costs is a high priority and recent focus has been on its biological synthesis from raw renewable materials rather than through conventional chemical procedures. In this study, a 2,3‐butanediol native bacterial producer was selected for the fermentation of Agave cupreata bagasse waste by enzymatic hydrolysation to obtain 2,3‐butanediol.ResultsThe native Klebsiella oxytoca UM2‐17 strain was selected to efficiently produce 2,3‐butanediol on synthetic mineral media. Using glucose (100 g L−1) and glucose: xylose (50 g L−1:50 g L−1) as sugar sources obtained titres of 29.36 g L−1 and 25.9 g L−1 of 2,3‐butanediol, corresponding to yields of 0.29 g g−1 and 0.26 g g−1, respectively. Agave bagasse solid waste after acid pre‐treatment was utilized to obtain enzymatic hydrolysates, obtaining liquors with glucose/xylose/arabinose at 25.8 g L−1 with efficiency of ∼52.5% sugar conversion from residual solid pre‐hydrolysed bagasse. The production of 2,3‐butanediol through batch fermentation of the enzymatic‐hydrolysate by the UM2‐17 strain showed total depletion of glucose and xylose, achieving a maximal production of 10.3 g L−1 of 2,3‐butanediol plus 0.28 g L−1 ethanol, corresponding to 2,3‐butanediol yield of 0.40 g g−1.ConclusionThe results indicate that A. cupreata bagasse waste from mezcal beverage elaboration is a sustainable bioresource for production of 2,3‐butanediol by fermentation of enzymatic bagasse‐hydrolysate using the K. oxytoca UM2‐17 strain. © 2019 Society of Chemical Industry
Central nervous system complications in adult cystinosis patients
Authors: Servais Aude , Saitovitch Ana , Hummel Aurélie , Boisgontier Jennifer , Scemla Anne , Sberro‐Soussan Rebecca , Snanoudj Renaud , Lemaitre Hervé , Legendre Christophe , Pontoizeau Clément , Antignac Corinne , Anglicheau Dany , Funalot Benoît , Boddaert Nathalie 
Published: August 2019

AbstractLittle is known about the long‐term progression of adult nephropathic cystinosis patients. Our objective was to study central nervous system complications in cystinosis patients in the era of early cysteamine treatment, using advanced neuroimaging techniques. Neurological examination and multimodal brain 3 Tesla MRI were performed in 21 adult cystinosis patients, including 18 infantile cystinosis patients, 20 controls matched for age and renal function, and 12 healthy controls. Differences in gray matter volume and rest cerebral blood flow (CBF) using arterial spin labeling sequence were investigated using whole‐brain voxel‐based approach. Median age was 33.8 years (18.7‐65.8). Seven patients (38.9%) presented with at least one central nervous system clinical abnormality: two (11.1%) with seizures, three (16.7%) with memory defects, five (27.8%) with cognitive defect, and one (5.5%) with stroke‐like episode. These patients had a worse compliance to treatment (compliance score 2 vs 1, P = .03) and received a lower median cysteamine dose (0.9 g/day vs 2.1 g/day, P = .02). Among patients with infantile cystinosis, 13 (72.2%) showed cortical atrophy, which was absent in controls, but it was not correlated with symptoms. Cystinosis patients showed a significant gray matter decrease in the middle frontal gyrus compared with healthy controls and a significant negative correlation between the cystine blood level and rest CBF was observed in the right superior frontal gyrus, a region associated with executive function. Compliance to cysteamine treatment is a major concern in these adult patients and could have an impact on the development of neurological and cognitive complications.
Study on the spectrum‐effect relationship of the xanthine oxidase inhibitory activity of Ligustrum lucidum
Authors: Gao Sai , Chen Huaguo , Zhou Xin 
Published: August 2019

AbstractTo evaluate the xanthine oxidase inhibitory activity of the chemical constituents of Ligustrum lucidum in vitro, the spectrum‐effect relationship was investigated. The high‐performance liquid chromatography fingerprint was established by ultraviolet spectrophotometry, and the xanthine oxidase inhibitory activity was tested in vitro by a high‐throughput screening method. Cluster analysis, principal component analysis, gray correlation analysis, and partial least squares regression were used to explore the spectrum‐effect relationships. Sixty batches of Ligustrum lucidum were collected from 16 provinces for testing. The results revealed differences among the batches of medicinal materials, and the similarity score was between 0.635 and 0.968. Thirty‐three characteristic peaks (1–33) were calibrated by fingerprint evaluation software for traditional Chinese medicine. The spectrum‐effect relationship study further revealed that the contents of peaks 1, 2, 4, 5, 6, 7, 14, 17, 25, 28, 31, and 33, which are potentially critical ingredients for quality control of Ligustrum lucidum fruit, were highly correlated with the inhibition of xanthine oxidase activity.
Numerical experiments on a hybrid WENO5 filter for shock‐capturing
Authors: Mahmoodi Darian Hossein , Bozorgpour Reza , Shafaee Maziar 
Published: August 2019

AbstractIn the present paper, a hybrid filter is introduced for high accurate numerical simulation of shock‐containing flows. The fourth‐order compact finite difference scheme is used for the spatial discretization and the third‐order Runge–Kutta scheme is used for the time integration. After each time‐step, the hybrid filter is applied on the results. The filter is composed of a linear sixth‐order filter and the dissipative part of a fifth‐order weighted essentially nonoscillatory scheme (WENO5). The classic WENO5 scheme and the WENO5 scheme with adaptive order (WENO5‐AO) are used to form the hybrid filter. Using a shock‐detecting sensor, the hybrid filter reduces to the linear sixth‐order filter in smooth regions for damping high frequency waves and reduces to the WENO5 filter at shocks in order to eliminate unwanted oscillations produced by the nondissipative spatial discretization method. The filter performance and accuracy of the results are examined through several test cases including the advection, Euler and Navier–Stokes equations. The results are compared with that of a hybrid second‐order filter and also that of the WENO5 and WENO5‐AO schemes.
Convergence of a positive nonlinear control volume finite element scheme for an anisotropic seawater intrusion model with sharp interfaces
Authors: Ait Hammou Oulhaj Ahmed , Maltese David 
Published: August 2019

AbstractWe study a sharp interface model in the context of seawater intrusion in an anisotropic unconfined aquifer. It is a degenerate parabolic system with cross‐diffusion modeling the flow of fresh and saltwater. We study a nonlinear control volume finite element scheme. This scheme ensures the nonnegativity of the discrete solution without any restriction on the transmissibility coefficients. Moreover, it also provides a control on the entropy. The existence of a discrete solution and the convergence of this scheme are obtained, based on nonlinear stability results.
Confined crystallization morphology of poly(ϵ‐caprolactone) block within poly(ϵ‐caprolactone)–poly(l‐lactide) copolymers
Authors: Han Weiqiang , Li Shaojie , Liao Xia , He Bin , Yang Qi , Li Guangxian 
Published: August 2019

AbstractThe confined crystallization of poly(ϵ‐caprolactone) (PCL) block in poly(ϵ‐caprolactone)–poly(l‐lactide) (PCL‐PLLA) copolymers was investigated using differential scanning calorimetry, polarized optical microscopy, scanning electronic microscopy and atomic force microscopy. To study the effect of crystallization and molecular chain motion state of PLLA blocks in PCL‐PLLA copolymers on PCL crystallization morphology, high‐temperature annealing (180 °C) and low‐temperature annealing (80 °C) were applied to treat the samples. It was found that the crystallization morphology of PCL block in PCL‐PLLA copolymers is not only related to the ratio of block components, but also related to the thermal history. After annealing PCL‐PLLA copolymers at 180 °C, the molten PCL blocks are rejected from the front of PLLA crystal growth into the amorphous regions, which will lead to PCL and PLLA blocks exhibiting obvious fractionated crystallization and forming various morphologies depending on the length of PLLA segment. On the contrary, PCL blocks more easily form banded spherulites after PCL‐PLLA copolymers are annealed at 80 °C because the preexisting PLLA crystal template and the dangling amorphous PLLA chains on PCL segments more easily cause unequal stresses at opposite fold surfaces of PCL lamellae during the growth process. Also, it was found that the growth rate of banded spherulites is less than that of classical spherulites and the growth rate of banded spherulites decreases with decreasing band spacing. © 2019 Society of Chemical Industry
Quantitative Proteomic Analysis of Simian Primary Hepatocytes Reveals Candidate Molecular Markers for Permissiveness to Relapsing Malaria Plasmodium cynomolgi
Authors: Dembele Laurent , Gupta Devendra Kumar , Dutta Bamaprasad , Chua Adeline C. Y. , Sze Siu Kwan , Bifani Pablo 
Published: August 2019

AbstractA major obstacle impeding malaria research is the lack of an in vitro system capable of supporting infection through the entire liver stage cycle of the parasite, including that of the dormant forms known as hypnozoites. Primary hepatocytes lose their liver specific functions in long‐term in vitro culture. The malaria parasite Plasmodium initiates infection in hepatocyte. This corresponds to the first step of clinically silent infection and development of malaria parasite Plasmodium in the liver. Thus, the liver stage is an ideal target for development of novel antimalarial interventions and vaccines. However, drug discovery against Plasmodium liver stage is severely hampered by the poor understanding of host–parasite interactions during the liver stage infection and development. In this study, tandem mass tag labeling based quantitative proteomic analysis is performed in simian primary hepatocytes cultured in three different systems of susceptibility to Plasmodium infection. The results display potential candidate molecular markers, including asialoglycoprotein receptor, apolipoproteins, squalene synthase, and scavenger receptor B1 (SR‐BI) that facilitate productive infection and full development in relapsing Plasmodium species. The identification of these candidate proteins required for constructive infection and development of hepatic malaria liver stages paves the way to explore them as therapeutic targets.
Template‐based modeling by ClusPro in CASP13 and the potential for using co‐evolutionary information in docking
Authors: Porter Kathryn A. , Padhorny Dzmitry , Desta Israel , Ignatov Mikhail , Beglov Dmitri , Kotelnikov Sergei , Sun Zhuyezi , Alekseenko Andrey , Anishchenko Ivan , Cong Qian , Ovchinnikov Sergey , Baker David , Vajda Sandor , Kozakov Dima 
Published: August 2019

AbstractAs a participant in the joint CASP13‐CAPRI46 assessment, the ClusPro server debuted its new template‐based modeling functionality. The addition of this feature, called ClusPro TBM, was motivated by the previous CASP‐CAPRI assessments and by the proven ability of template‐based methods to produce higher‐quality models, provided templates are available. In prior assessments, ClusPro submissions consisted of models that were produced via free docking of pre‐generated homology models. This method was successful in terms of the number of acceptable predictions across targets; however, analysis of results showed that purely template‐based methods produced a substantially higher number of medium‐quality models for targets for which there were good templates available. The addition of template‐based modeling has expanded ClusPro's ability to produce higher accuracy predictions, primarily for homomeric but also for some heteromeric targets. Here we review the newest additions to the ClusPro web server and discuss examples of CASP‐CAPRI targets that continue to drive further development. We also describe ongoing work not yet implemented in the server. This includes the development of methods to improve template‐based models and the use of co‐evolutionary information for data‐assisted free docking.
A strategy of rapidly screening out herbicidal chemicals from Eucalyptus essential oils
Authors: Li Aoxin , Wu Hanwen , Feng Yuanjiao , Deng Siyu , Hou Aijiao , Che Fenfang , Liu Yuanyuan , Geng Qianqian , Ni Hanwen , Wei Yun 
Published: August 2019

AbstractBACKGROUNDTo enhance discovering efficiency of new herbicidal compounds, a strategy for rapidly screening out strongly herbicidal chemical components from natural resources is necessary.RESULTSSeventeen essential oils selected from 14 Eucalyptus species and hybrids were evaluated for their herbicidal activities on annual ryegrass. A feasible strategy was established for rapidly pinpointing the chemicals contributing to strong herbicidal activities without the process of isolation and purification of individual compounds. This strategy was based on gas chromatography–mass spectrometry (GC–MS) coupled with principal component analysis (PCA) and verified by the bioassay results using several individual compounds. Two strong herbicidal compounds trans‐pinocarveol and α‐terpineol were screened out using the strategy. The strong herbicidal activity of trans‐pinocarveol was discovered for the first time.CONCLUSIONThe established strategy of screening herbicidal compounds from natural resources is simple, feasible and reliable. © 2019 Society of Chemical Industry
A comparative study of dynamic adsorption of anionic synthetic and nanocellulose-based surfactant in Malaysian reservoir
Authors: Ayoub Muhammad , Mohyaldinn Mysara Eissa , Mahmood Syed Mohammad , Aqsha Aqsha , Jufar Shiferaw Regassa , Farrukh Sarah , Inayat Farrukh , Shamsuddin Muhammad Rashid 
Published: August 2019

AbstractThis project is aimed at studying the applicability of nanocellulose-based surfactant as a sustainable surfactant for enhanced oil recovery process (EOR) in Malaysia. Abundant biomass waste from palm oil industry in Malaysia is hard to be disposed of. Therefore, potential application of biomass in chemical EOR is an attractive alternative to minimize these problems. For this study, nanocellulose is synthesized from oil palm empty fruit bunch (OPEFB) and undergoes chemical modification for it to act like a surfactant. All methods and techniques in synthesizing nanocellulose and preparing nanocellulose-based surfactant are made inhouse. While waiting for the material preparation, adsorption study is carried out by using anionic synthetic surfactant. Characterization result shows the nanocellulose undergoes chemical modification successfully. The IFT results for the nanocellulose-based surfactants are also in a good and acceptable range, but there are some limitations in using nanocellulose-synthesized surfactant. The average particle size of nanocellulose is 283.5 µm which is larger than size of the reservoir pore throat. Dynamic adsorption cannot be performed as the large particle size of nanocellulose might plug the porous domains. Therefore, it is recommended to further improve the method of synthesizing nanocellulose from OPEFB because the nanocellulose-based surfactant is expected to have potential of lower adsorption in porous media once it becomes nanosized and due to its advantages such as being of lower cost and environmental friendly compared to other commercial surfactants.