bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aberrantly expressed long non‐coding RNAs in air pollution‐induced congenital defects
Authors: Li Zheng , Ma Jianqing , Li Xingye , Chan Matthew T. V. , Wu William K. K. , Wu Zhanyong , Shen Jianxiong 
Published: September 2019

AbstractAir pollution has been a serious public health issue over the past few decades particularly in developing countries. Air pollution exposure during pregnancy poses potential threat to offspring as the deleterious substances might pass through placenta to alter foetal development. A growing number of studies have demonstrated that long non‐coding RNAs (lncRNAs) participate in the development of many diseases, including congenital defects. Here, we used RNA sequencing to identify differentially expressed lncRNAs in air pollution‐exposed rat embryos compared with control group. Our data suggested that 554 lncRNAs (216 up‐regulated and 338 down‐regulated) were significantly differentially expressed in the air pollution‐exposed embryos. Moreover, potential cellular functions of these deregulated lncRNAs were predicted via KEGG signal pathway/GO enrichment analyses, which suggested the possible involvements of neurological process, sensory perception of smell and the G‐protein signalling pathway. Furthermore, potential functional network of deregulated lncRNAs and their correlated mRNAs in the development of congenital spinal abnormality was established. Our data suggested that lncRNAs may play a vital role in the pathophysiology of air pollution‐exposed congenital spinal malformation.
Coordinate regulation of ELF5 and EHF at the chr11p13 CF modifier region
Authors: Swahn Hannah , Sabith Ebron Jey , Lamar Kay‐Marie , Yin Shiyi , Kerschner Jenny L. , NandyMazumdar Monali , Coppola Candice , Mendenhall Eric M. , Leir Shih‐Hsing , Harris Ann 
Published: September 2019

AbstractE74‐like factor 5 (ELF5) and ETS‐homologous factor (EHF) are epithelial selective ETS family transcription factors (TFs) encoded by genes at chr11p13, a region associated with cystic fibrosis (CF) lung disease severity. EHF controls many key processes in lung epithelial function so its regulatory mechanisms are important. Using CRISPR/Cas9 technology, we removed three key cis‐regulatory elements (CREs) from the chr11p13 region and also activated multiple open chromatin sites with CRISPRa in airway epithelial cells. Deletion of the CREs caused subtle changes in chromatin architecture and site‐specific increases in EHF and ELF5. CRISPRa had most effect on ELF5 transcription. ELF5 levels are low in airway cells but higher in LNCaP (prostate) and T47D (breast) cancer cells. ATAC‐seq in these lines revealed novel peaks of open chromatin at the 5’ end of chr11p13 associated with an expressed ELF5 gene. Furthermore, 4C‐seq assays identified direct interactions between the active ELF5 promoter and sites within the EHF locus, suggesting coordinate regulation between these TFs. ChIP‐seq for ELF5 in T47D cells revealed ELF5 occupancy within EHF introns 1 and 6, and siRNA‐mediated depletion of ELF5 enhanced EHF expression. These results define a new role for ELF5 in lung epithelial biology.
Levetiracetam treatment ameliorates LRRK2 pathological mutant phenotype
Authors: Rassu Mauro , Biosa Alice , Galioto Manuela , Fais Milena , Sini Paola , Greggio Elisa , Piccoli Giovanni , Crosio Claudia , Iaccarino Ciro 
Published: September 2019

AbstractMutations in leucine‐rich repeat kinase 2 (LRRK2) are the most common genetic cause of Parkinson's disease (PD). The LRRK2 physiological and pathological function is still debated. However, different experimental evidence based on LRRK2 cellular localization and LRRK2 protein interactors suggests that LRRK2 may be part and regulate a protein network modulating vesicle dynamics/trafficking. Interestingly, the synaptic vesicle protein SV2A is part of this protein complex. Importantly, SV2A is the binding site of the levetiracetam (LEV), a compound largely used in human therapy for epilepsy treatment. The binding of LEV to SV2A reduces the neuronal firing by the modulation of vesicle trafficking although by an unclear molecular mechanism. In this short communication, we have analysed the interaction between the LRRK2 and SV2A pathways by LEV treatment. Interestingly, LEV significantly counteracts the effect of LRRK2 G2019S pathological mutant expression in three different cellular experimental models. Our data strongly suggest that LEV treatment may have a neuroprotective effect on LRRK2 pathological mutant toxicity and that LEV repositioning could be a viable compound for PD treatment.
Resveratrol decreases CD45+CD206− subtype macrophages in LPS‐induced murine acute lung injury by SOCS3 signalling pathway
Authors: Hu Lu , Chen Zhihong , Li Liyang , Jiang Zhilong , Zhu Lei 
Published: September 2019

AbstractAcute lung injury/acute respiratory distress syndrome (ALI/ARDS) are life‐threatening condition in critically ill patients. Resveratrol (Res), a natural polyphenol, has therapeutic effect in animal model with ALI; however, whether Res attenuates ALI through modulation of macrophage phenotypes in the animal model remains unknown. We in this study treated LPS‐induced murine ALI with 30 mg/kg Res and observed significantly reduced severity of ALI in the Res‐treated mice 48 hours after Res treatment. Neutrophil infiltrates were significantly reduced, accompanied with lower infiltration of CD45+Siglec F− phenotype macrophages, but higher population of CD45+Siglec F+ and CD45+CD206+ alternatively activated macrophages (M2 cells) in the Res‐treated mice with ALI. In addition, the expression of IL‐1beta and CXCL15 cytokines was suppressed in the treated mice. However, Res treatment in mice with myeloid cell‐restricted SOCS3 deficiency did not significantly attenuate ALI severity and failed to increase population of both CD45+Siglec F+ and CD45+CD206+ M2 subtype macrophages in the murine ALI. Further studies in wild‐type macrophages revealed that Res treatment effectively reduced the expression of IL‐6 and CXCL15, and increased the expression of arginase‐1, SIRT1 and SOCS3. However, macrophages’ lack of SOCS3 expression were resistant to the Res‐induced suppression of IL‐6 and CXCL15 in vitro. Thus, we conclude that Res suppressed CD45+Siglec F− and CD45+CD206− M1 subtype macrophages through SOCS3 signalling in the LPS‐induced murine ALI.
Accuracy of single molecular biomarkers in saliva for the diagnosis of periodontitis: A systematic review and meta‐analysis
Authors: Arias‐Bujanda Nora , Regueira‐Iglesias Alba , Balsa‐Castro Carlos , Nibali Luigi , Donos Nikos , Tomás Inmaculada 
Published: September 2019

AbstractAimTo analyse, using a meta‐analytical approach, the diagnostic accuracy of single molecular biomarkers in saliva for the detection of periodontitis in systemically healthy subjects.Materials and MethodsArticles on molecular biomarkers in saliva providing a binary contingency table (or sensitivity and specificity values and group sample sizes) in individuals with clinically diagnosed periodontitis were considered eligible. Searches for candidate articles were conducted in six electronic databases. The methodological quality was assessed through the tool Quality Assessment of Diagnostic Studies. Meta‐analyses were performed using the Hierarchical Summary Receiver Operating Characteristic model.ResultsMeta‐analysis was possible for 5 of the 32 biomarkers studied. The highest values of sensitivity for the diagnosis of periodontitis were obtained for IL1beta (78.7%), followed by MMP8 (72.5%), IL6 and haemoglobin (72.0% for both molecules); the lowest sensitivity value was for MMP9 (70.3%). In terms of specificity estimates, MMP9 had the best result (81.5%), followed by IL1beta (78.0%) and haemoglobin (75.2%); MMP8 had the lowest specificity (70.5%).ConclusionsMMP8, MMP9, IL1beta, IL6 and Hb were salivary biomarkers with good capability to detect periodontitis in systemically healthy subjects. MMP8 and IL1beta are the most researched biomarkers in the field, both showing clinically fair effectiveness for the diagnosis of periodontitis.
Evidence for Production of Sexual Resting Cysts by the Toxic Dinoflagellate Karenia mikimotoi in Clonal Cultures and Marine Sediments
Authors: Liu Yuyang , Hu Zhangxi , Deng Yunyan , Tang Ying Zhong 
Published: September 2019

The toxic dinoflagellate Karenia mikimotoi has been well‐known for causing large‐scale and dense harmful algal blooms (HABs) in coastal waters worldwide and serious economic loss in aquaculture and fisheries and other adverse effects on marine ecosystems. Whether K. mikimotoi forms resting cysts has been a puzzling issue regarding to the mechanisms of bloom initiation and geographic expansion of this species. We provide morphological and molecular confirmation of sexually produced thin‐walled resting cysts by K. mikimotoi based on observations of laboratory cultures and their direct detection in marine sediments. Light and scanning electron microscopy evidences for sexual reproduction include attraction and pairing of gametes, gamete fusion, formation of planozygote and thin‐walled cyst, and the documentation of the thin‐walled cyst germination processes. Evidence for cysts in marine sediments was in three aspects: positive PCR detection of cysts using species‐specific primers in the DNA extracted from whole sediments; fluorescence in situ hybridization detection of cysts using FISH probes; and single‐cell PCR sequencing for cysts positively labeled with FISH probes. The existence of sexually produced, thin‐walled resting cysts by K. mikimotoi provides a possible mechanism accounting for the initiation of annually recurring blooms at certain regions and global expansion of the species during the past decades.
RNA‐Seq of in planta‐expressed Magnaporthe oryzae genes identifies MoSVP as a highly expressed gene required for pathogenicity at the initial stage of infection
Authors: Shimizu Motoki , Nakano Yuki , Hirabuchi Akiko , Yoshino Kae , Kobayashi Michie , Yamamoto Kosuke , Terauchi Ryohei , Saitoh Hiromasa 
Published: September 2019

SummaryThe ascomycete fungus Magnaporthe oryzae is a hemibiotrophic pathogen that causes rice blast disease. Magnaporthe oryzae infects rice leaves, stems and panicles, and induces severe reductions in yield. Effector proteins secreted by M. oryzae in planta are thought to be involved its virulence activity. Here, using RNA‐sequencing (RNA‐Seq), we generated transcriptome data for M. oryzae isolate Ina168 during the initial stages of infection. We prepared samples from conidia (the inoculum) and from peeled epidermal cotyledon tissue of susceptible barley Hordeum vulgare ‘Nigrate’ at 12, 24, 36 and 48 hours post‐inoculation (hpi). We also generated a draft genome sequence of M. oryzae isolate Ina168 and used it as a reference for mapping the RNA‐Seq reads. Gene expression profiling across all stages of M. oryzae infection revealed 1728 putative secreted effector protein genes. We selected seven such genes that were strongly up‐regulated at 12 hpi and down‐regulated at 24 or 36 hpi and performed gene knockout analysis to determine their roles in pathogenicity. Knockout of MoSVP, encoding a small putative secreted protein with a hydrophobic surface binding protein A domain, resulted in a reduction in pathogenicity, suggesting that MoSVP is a novel virulence effector of M. oryzae.
Clinical features and outcomes of community‐acquired late‐onset sepsis: Focusing on group B Streptococcus and Escherichia coli
Authors: Yun Ki Wook , Park Sun Hyung , Cho Eun Young , Lee Hyunju 
Published: September 2019

AbstractBackgroundGroup B Streptococcus (GBS) and Escherichia coli are leading causes of late‐onset sepsis (LOS) and bacterial meningitis in neonates and infants. This study aimed to describe clinical characteristics and outcomes of community‐acquired (CA) LOS caused by GBS and E. coli.MethodsA retrospective observational study was performed in three university hospitals in Korea. All infants aged <90 days who were diagnosed with GBS or E coli CA‐LOS from 2011 to 2017 were enrolled. Data on the clinical characteristics and outcomes of GBS and E. coli CA‐LOS were compared.ResultsForty GBS and 43 E. coli CA‐LOS cases were identified, which mostly (82/83) included term or near‐term infants. Meningitis was identified in 54.1% of GBS CA‐LOS cases and in 30.3% of E. coli CA‐LOS cases, and 88.4% of E. coli CA‐LOS cases involved urosepsis. Ten percent each of GBS and non‐uropathogenic E. coli (non‐UPEC) meningitis cases and all uropathogenic E. coli (UPEC) meningitis cases were diagnosed by pleocytosis without bacterial growth in the cerebrospinal fluid (CSF). Patients with non‐culture‐proven meningitis had lower CSF pleocytosis and protein levels and higher CSF/serum glucose ratios than patients with culture‐proven meningitis (P < 0.05 for all). One patient died of CA‐LOS, which was accompanied by meningitis with extended‐spectrum β‐lactamase‐producing non‐UPEC. Neurological complications developed in 22.5% of GBS CA‐LOS cases and in 2.3% of E. coli CA‐LOS cases.ConclusionsNeurological complications were frequently observed in GBS CA‐LOS cases, although no mortality was observed. Escherichia coli CA‐LOS generally developed as urosepsis, which caused non‐culture‐proven meningitis and had a favorable outcome.
A Dual Emissive Coumarin–urea Derivative with an Electron‐withdrawing Substituent in the Presence of Acetate Anion
Authors: Shinoda Tomoyuki , Nishimura Yoshinobu , Arai Tatsuo 
Published: September 2019

AbstractWe investigated the fluorescent properties, including the excited‐state intermolecular proton transfer, of urea derivatives comprising a coumarin ring, which is a widely used fluorophore. We prepared two different coumarin–urea derivatives, 6CU and 7CU, which bear a urea‐based substituent at the 6 and 7 positions of a coumarin ring, respectively. In the presence of the acetate ion, 7CU showed additional tautomer fluorescence emission with respect to 6CU, indicating that tautomer formation depends on the positions of the urea‐based substituent on the coumarin ring. Thus, the resonance structures of urea derivatives might play an important role in the behavior of dual fluorescence, which is an important phenomenon applicable to photochemical anion sensing. Moreover, in order to further improve the fluorescence properties of the mentioned derivatives, a CF3 group was introduced in a phenyl ring opposite to a coumarin ring. The fluorescence quantum yield of 7CUCF3 thus synthesized was 65 times as large as that of 7CU, an observation that renders 7CUCF3 a suitable anion sensor candidate. The results of this study will contribute to the development of new molecular designs for highly fluorescent sensing.
GmMAX2–D14 and –KAI interaction‐mediated SL and KAR signaling play essential roles in soybean root nodulation
Authors: Ahmad Muhammad Zulfiqar , Rehman Naveed ur , Yu Shuwei , Zhou Yuanze , Haq Basir ul , Wang Junjie , Li Penghui , Zeng Zhixiong , Zhao Jian 
Published: September 2019

SummaryDespite of important functions of strigolactones (SLs) and karrikins (KARs) in plant development, plant–parasite and plant–fungi interactions, their roles in soybean–rhizobia interaction remain elusive. SL/KAR signaling genes GmMAX2a, GmD14s, and GmKAIs are activated by rhizobia infection. GmMAX2a restored atmax2 root hair defects and soybean root hairs were changed in GmMAX2a overexpression (GmMAX2a‐OE) or knockdown (GmMAX2a‐KD) mutants. GmMAX2a‐KD gave fewer, whereas GmMAX2a‐OE produced more nodules than GUS hairy roots. Mutation of GmMAX2a in its KD or OE transgenic hairy roots affected the rhizobia infection‐induced increases in early nodulation gene expression. Both mutant hairy roots also displayed the altered auxin, jasmonate and abscisic acid levels, as further verified by transcriptomic analyses of their synthetic genes. Overexpression of an auxin synthetic gene GmYUC2a also affected SL and KAR signaling genes. GmMAX2a physically interacted with SL/KAR receptors GmD14s, GmKAIs, and GmD14Ls with different binding affinities, depending on variations in the critical amino acids, forming active D14/KAI‐SCFMAX2 complexes. The knockdown mutant roots of the nodule‐specifically expressing GmKAIs and GmD14Ls gave fewer nodules, with altered expression of several early nodulation genes. The expression levels of GmKAIs, and GmD14Ls were markedly changed in GmMAX2a mutant roots, so did their target repressor genes GmD53s and GmSMAX1s. Thus, SL and KAR signaling were involved in soybean–rhizobia interaction and nodulation partly through interactions with hormones, and this may explain the different effects of MXA2 orthologs on legume determinate and indeterminate nodulation. The study provides fresh insights into the roles of GmMAX2‐mediated SL/KAR signaling in soybean root hair and nodule formation.
A New Class of Uniform Continuous Higher-Order Sliding Mode Controllers
Authors: Kamal Shyam , Ramesh Kumar P. , Chalanga Asif , Goyal Jitendra Kumar , Bandyopadhyay Bijnan , Fridman L. 
Published: September 2019

Abstract
This paper proposes a new class of uniform continuous higher-order sliding mode algorithm (UCHOSMA) for the arbitrary relative degree systems. The proposed methodology is a combination of two controllers where one of the components is a uniform super-twisting control which acts as the disturbance compensator and the second part gives the uniform finite time convergence for the disturbance free system. This algorithm provides uniform finite time convergence of the output and its higher derivatives using an absolutely continuous control signal and thus alleviating the chattering phenomenon. The attractive feature of the proposed controller is that irrespective of the different initial conditions, the control is able to bring the states of the system to the equilibrium point uniformly in finite time. The effectiveness of the proposed controller has been demonstrated with both simulation and experimental results.
Design, Optimization, and Analysis of Supersonic Radial Turbines
Authors: Inhestern Lukas Benjamin , Braun James , Paniagua Guillermo , Serrano Cruz José Ramón 
Published: September 2019

Abstract
New compact engine architectures such as pressure gain combustion require ad hoc turbomachinery to ensure an adequate range of operation with high performance. A critical factor for supersonic turbines is to ensure the starting of the flow passages, which limits the flow turning and airfoil thickness. Radial outflow turbines inherently increase the cross section along the flow path, which holds great potential for high turning of supersonic flow with a low stage number and guarantees a compact design. First, the preliminary design space is described. Afterward a differential evolution multi-objective optimization with 12 geometrical design parameters is deducted. With the design tool autoblade 10.1, 768 geometries were generated and hub, shroud, and blade camber line were designed by means of Bezier curves. Outlet radius, passage height, and axial location of the outlet were design variables as well. Structured meshes with around 3.7 × 106 cells per passage were generated. Steady three-dimensional (3D) Reynolds-averaged Navier–Stokes (RANS) simulations, enclosed by the k-omega shear stress transport turbulence model were solved by the commercial solver CFD++. The geometry was optimized toward low entropy and high-power output. To prove the functionality of the new turbine concept and optimization, a full wheel unsteady RANS simulation of the optimized geometry exposed to a nozzled rotating detonation combustor (RDC) has been performed and the advantageous flow patterns of the optimization were also observed during transient operation.
Mechanistic Study of Fines Migration in Porous Media Using Lattice Boltzmann Method Coupled With Rigid Body Physics Engine
Authors: Vasheghani Farahani Mehrdad , Foroughi Sajjad , Norouzi Sevda , Jamshidi Saeid 
Published: September 2019

AbstractThis paper presents a pore-scale model proposed for numerical simulation of fines migration in porous media. The model simulates the behavior of spherical particles with different radii in flow by coupling lattice Boltzmann method (LBM) as a computational fluid dynamics (CFD) solver for the simulation of the fluid flow with a rigid body physics engine responsible for the simulation of the particulate transports. To achieve this, the basic LBM algorithm was extended to treat the curved particle boundaries, and a fluid-particle force interaction was implemented in order to account for the exerted force acting on the particles by the fluid and subsequent particulate movements. The accuracy and reliability of the proposed numerical model were successfully validated by simulating Poiseuille flow and Stokes flow and comparing the simulation results with those of the analytical solution. Thereafter, it was employed to simulate the migration of fine particles through synthetic 2D porous media. The simulation results were also presented to investigate the influence of fines migration on the porosity and permeability of the medium, and more interestingly on the hydraulic tortuosity as a criterion for changes in preferential flow path. As will be shown, the developed numerical method is able to successfully capture major retention mechanisms responsible for fines migration associated formation damage including external cake formation by the large particles, internal cake formation by the small particles, pore plugging, and surface deposition. This work provides a framework for further investigations regarding pore-scale phenomena associated with fines migration in the porous media.
Optimal Power Tracking of DFIG-Based Wind Turbine Using MOGWO-Based Fractional-Order Sliding Mode Controller
Authors: Darvish Falehi Ali 
Published: September 2019

AbstractThe doubly fed induction generator (DFIG)-based wind turbine as a nonlinear, compound, and multivariable time-varying system encompasses several uncertainties especially unfamiliar disturbances and unmodeled dynamics. The design of a high-performance and reliable controller for this system is regarded as a complex task. In this paper, an effective and roust fractional-order sliding mode controller (FOSMC) has been designed to accurately regulate the active and reactive power of DFIG. FOSMC has overcome the system uncertainties and abated the chattering amplitude. Since tuning the FOSMC is a challenging assignment, the application of a multi-objective optimization algorithm can efficiently and precisely solve the design problem. In this regard, non-dominated sorting multi-objective gray wolf optimizer (MOGWO) is taken into account to optimally adjust the FOSMC. In a word, the simulation results have definitively validated robustness of MOGWO-based FOSMC in order to accurately track DFIG's active and reactive power.