bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA-Seq analysis and comparison of corneal epithelium in keratoconus and myopia patients
Authors: You Jingjing , Corley Susan M. , Wen Li , Hodge Chris , Höllhumer Roland , Madigan Michele C. , Wilkins Marc R. , Sutton Gerard 
Published: January 2018

AbstractKeratoconus is a common degenerative corneal disease that can lead to significant visual morbidity, and both genetic and environmental factors have been implicated in its pathogenesis. We compared the transcriptome of keratoconus and control epithelium using RNA-Seq. Epithelial tissues were obtained prior to surgery from keratoconus and myopia control patients, undergoing collagen cross-linking and photorefractive keratectomy, respectively. We identified major differences in keratoconus linked to cell-cell communication, cell signalling and cellular metabolism. The genes associated with the Hedgehog, Wnt and Notch1 signaling pathways were down-regulated in keratoconus. We also identified plasmolipin and Notch1 as being significantly reduced in keratoconus for both gene and protein expression (p < 0.05). Plasmolipin is a novel protein identified in human corneal epithelium, and has been demonstrated to have a key role in epithelial cell differentiation in other tissues. This study shows altered gene and protein expression of these three proteins in keratoconus, and further studies are clearly warranted to confirm the functional role of these proteins in the pathogenesis of keratoconus.
Engineered mesenchymal stem-cell-sheets patches prevents postoperative pancreatic leakage in a rat model
Authors: Kim Seong-Ryong , Yi Hye-Jin , Lee Yu Na , Park Ji Yoon , Hoffman Robert M. , Okano Teruo , Shim In Kyong , Kim Song Cheol 
Published: January 2018

AbstractPost-operative pancreatic fistula (POPF) following pancreatic resection is a life-threatening surgical complication. Cell sheets were prepared and harvested using temperature-responsive culture dishes and transplanted as patches to seal POPF. Two different mesenchymal stem cell (MSC) sheets were compared in terms of the preventative ability for pancreatic leakage in a rat model. Both rat adipose-derived stem cell (rADSC) and bone marrow-derived stem cell (rBMSC) sheets were transplanted. Those rADSC and rBMSC sheets are created without enzymes and thus maintained their cell-cell junctions and adhesion proteins with intact fibronectin on the basal side, as well as characteristics of MSCs. The rats with post-pancreatectomy rADSC- or rBMSC-sheet patches had significantly decreased abdominal fluid leakage compared with the control group, demonstrated by MR image analysis and measurement of the volume of abdominal fluid. Amylase level was significantly lower in the rats with rADSC-sheet and rBMSC-sheet patches compared with the control groups. The rADSC sheet patches had increased adhesive and immune-cytokine profiles (ICAM-1, L-selectin, TIMP-1), and the rBMSC sheets had reduced immune reactions compared to the control. This is first project looking at the feasibility of tissue engineering therapy using MSC-sheets as tissue patches preventing leakage of abdominal fluid caused by POPF.
Domain swapping and SMYD1 interactions with the PWWP domain of human hepatoma-derived growth factor
Authors: Chen Li-Ying , Huang Yen-Chieh , Huang Shih-Tsung , Hsieh Yin-Cheng , Guan Hong-Hsiang , Chen Nai-Chi , Chuankhayan Phimonphan , Yoshimura Masato , Tai Ming-Hong , Chen Chun-Jung 
Published: January 2018

AbstractThe human hepatoma-derived growth factor (HDGF), containing the chromatin-associated N-terminal PWWP domain capable of binding the SMYD1 promoter, participates in various cellular processes and is involved in human cancers. We report the first crystal structures of the human HDGF PWWP domain (residues 1–100) in a complex with SMYD1 of 10 bp at 2.84 Å resolution and its apo form at 3.3 Å, respectively. The structure of the apo PWWP domain comprises mainly four β-strands and two α-helices. The PWWP domain undergoes domain swapping to dramatically transform its secondary structures, altering the overall conformation from monomeric globular folding into an extended dimeric structure upon DNA binding. The flexible loop2, as a hinge loop with the partially built structure in the apo PWWP domain, notably refolds into a visible and stable α-helix in the DNA complex. The swapped PWWP domain interacts with the minor grooves of the DNA through residues Lys19, Gly22, Arg79 and Lys80 in varied ways on loops 1 and 4 of the two chains, and the structure becomes more rigid than the apo form. These novel structural findings, together with physiological and activity assays of HDGF and the PWWP domain, provide new insights into the DNA-binding mechanism of HDGF during nucleosomal functions.
Contrasting patterns of leaf trait variation among and within species during tropical dry forest succession in Costa Rica
Authors: Derroire Géraldine , Powers Jennifer S. , Hulshof Catherine M. , Cárdenas Varela Luis E. , Healey John R. 
Published: January 2018

AbstractA coordinated response to environmental drivers amongst individual functional traits is central to the plant strategy concept. However, whether the trait co-ordination observed at the global scale occurs at other ecological scales (especially within species) remains an open question. Here, for sapling communities of two tropical dry forest types in Costa Rica, we show large differences amongst traits in the relative contribution of species turnover and intraspecific variation to their directional changes in response to environmental changes along a successional gradient. We studied the response of functional traits associated with the leaf economics spectrum and drought tolerance using intensive sampling to analyse inter- and intra-specific responses to environmental changes and ontogeny. Although the overall functional composition of the sapling communities changed during succession more through species turnover than through intraspecific trait variation, their relative contributions differed greatly amongst traits. For instance, community mean specific leaf area changed mostly due to intraspecific variation. Traits of the leaf economics spectrum showed decoupled responses to environmental drivers and ontogeny. These findings emphasise how divergent ecological mechanisms combine to cause great differences in changes of individual functional traits over environmental gradients and ecological scales.
Enhanced YAP expression leads to EGFR TKI resistance in lung adenocarcinomas
Authors: Lee Ting-Fang , Tseng Yu-Chi , Nguyen Phung Anh , Li Yu-Chuan , Ho Chao-Chi , Wu Cheng-Wen 
Published: January 2018

AbstractEpidermal growth factor receptor (EGFR) mutation is prevalently expressed in lung adenocarcinoma cases and acts as one of the major driving oncogenes. EGFR tyrosine kinase inhibitors (TKIs) have been used in patients with EGFR-mutant as an effective targeted therapy in lung adenocarcinoma, but drug resistance and tumor recurrence inevitably occurs. Recently, Yes-associate protein (YAP) has been reported to promote multiple cancer cell properties, such as promoting cell proliferation, epithelial-mesenchymal transition and drug resistance. This study investigated the roles of YAP in TKI-resistant lung adenocarcinoma. In TKI-sensitive cells, enhanced YAP expression leads to TKI resistant. Also, upregulated YAP expression and activation were detected in long-term TKI-induced resistant cells. With reduced YAP expression using shRNA or YAP inhibitors, TKI-resistant cells become TKI-sensitive. reduced xenograft tumor size in nude mice and Moreover, combined EGFR TKI and a YAP inhibitor, statin, prolonged survival among lung cancer patients analyzed by Taiwan National Health Insurance Research database. These observations revealed the importance of YAP in promoting TKI-resistance and combined YAP inhibition can be a potential therapy delaying the occurrence of TKI-resistance in lung adenocarcinoma.
MicroRNA-7 mediates cross-talk between metabolic signaling pathways in the liver
Authors: Singaravelu Ragunath , Quan Curtis , Powdrill Megan H. , Shaw Tyler A. , Srinivasan Prashanth , Lyn Rodney K. , Alonzi Rhea C. , Jones Daniel M. , Filip Roxana , Russell Rodney S. , Pezacki John P. 
Published: January 2018

AbstractMicroRNAs (miRNAs) have emerged as critical regulators of cellular metabolism. To characterise miRNAs crucial to the maintenance of hepatic lipid homeostasis, we examined the overlap between the miRNA signature associated with inhibition of peroxisome proliferator activated receptor-α (PPAR-α) signaling, a pathway regulating fatty acid metabolism, and the miRNA profile associated with 25-hydroxycholesterol treatment, an oxysterol regulator of sterol regulatory element binding protein (SREBP) and liver X receptor (LXR) signaling. Using this strategy, we identified microRNA-7 (miR-7) as a PPAR-α regulated miRNA, which activates SREBP signaling and promotes hepatocellular lipid accumulation. This is mediated, in part, by suppression of the negative regulator of SREBP signaling: ERLIN2. miR-7 also regulates genes associated with PPAR signaling and sterol metabolism, including liver X receptor β (LXR-β), a transcriptional regulator of sterol synthesis, efflux, and excretion. Collectively, our findings highlight miR-7 as a novel mediator of cross-talk between PPAR, SREBP, and LXR signaling pathways in the liver.
Novel haemodialysis (HD) treatment employing molecular hydrogen (H2)-enriched dialysis solution improves prognosis of chronic dialysis patients: A prospective observational study
Authors: Nakayama Masaaki , Itami Noritomo , Suzuki Hodaka , Hamada Hiromi , Yamamoto Ryo , Tsunoda Kazumasa , Osaka Naoyuki , Nakano Hirofumi , Maruyama Yukio , Kabayama Shigeru , Nakazawa Ryoichi , Miyazaki Mariko , Ito Sadayoshi 
Published: January 2018

AbstractRecent studies have revealed unique biological characteristics of molecular hydrogen (H2) as an anti-inflammatory agent. We developed a novel haemodialysis (E-HD) system delivering an H2 (30–80 ppb)-enriched dialysis solution by water electrolysis, and conducted a non-randomized, non-blinded, prospective observational study exploring its clinical impact. Prevalent chronic HD patients were allocated to either the E-HD (n = 161) group or the conventional HD (C-HD: n = 148) group, and received the respective HD treatments during the study. The primary endpoint was a composite of all-cause mortality and development of non-lethal cardio-cerebrovascular events (cardiac disease, apoplexy, and leg amputation due to peripheral artery disease). During the 3.28-year mean observation period, there were no differences in dialysis parameters between the two groups; however, post-dialysis hypertension was ameliorated with significant reductions in antihypertensive agents in the E-HD patients. There were 91 events (50 in the C-HD group and 41 in the E-HD group). Multivariate analysis of the Cox proportional hazards model revealed E-HD as an independent significant factor for the primary endpoint (hazard ratio 0.59; [95% confidence interval: 0.38–0.92]) after adjusting for confounding factors (age, cardiovascular disease history, serum albumin, and C-reactive protein). HD applying an H2-dissolved HD solution could improve the prognosis of chronic HD patients.
Innate IFN-γ ameliorates experimental autoimmune encephalomyelitis and promotes myeloid expansion and PDL-1 expression
Authors: White Madeleine P. J. , Webster Gill , Leonard Faith , La Flamme Anne Camille 
Published: January 2018

AbstractThe innate immune system plays a central role in the immune-mediated pathology of multiple sclerosis, and is a therapeutic target for progressive disease. Recently, it has been demonstrated that MIS416, a novel immunomodulatory microparticle that activates NOD-2 and TLR-9-signaling, has disease-modifying activity in multiple sclerosis models. This activity is dependent on innate IFN-γ; however, the precise immune regulatory mechanisms amplified by MIS416 have not previously been determined. Using the experimental autoimmune encephalomyelitis model, MIS416 treatment was associated with IFN-γ–dependant expansion of Treg number and increased suppressive function; however, these cells did not account for disease reduction. Additionally, MIS416 treatment stimulated increased nitric oxide production that was IFN-γ–dependant but dispensable for protection. Finally, MIS416-mediated protection was shown to correlate with IFN-γ–dependant expansion of PDL-1-expressing peripheral myeloid cells, a subset of which was found to be selectively recruited to the brain. This central nervous system trafficking was independent of neuro-inflammatory signals as it occurred in MIS416-treated healthy mice. Together, these findings provide insight into regulatory myeloid cell activities amplified by MIS416-mediated NOD-2 and TLR-9 signalling and highlight the potential importance of these cells in accessing the brain where they may act locally and contribute to the control of neuroinflammation.
Mathematical model of salt cavern leaching for gas storage in high-insoluble salt formations
Authors: Li Jinlong , Shi Xilin , Yang Chunhe , Li Yinping , Wang Tongtao , Ma Hongling 
Published: January 2018

AbstractA mathematical model is established to predict the salt cavern development during leaching in high-insoluble salt formations. The salt-brine mass transfer rate is introduced, and the effects of the insoluble sediments on the development of the cavern are included. Considering the salt mass conservation in the cavern, the couple equations of the cavern shape, brine concentration and brine velocity are derived. According to the falling and accumulating rules of the insoluble particles, the governing equations of the insoluble sediments are deduced. A computer program using VC++ language is developed to obtain the numerical solution of these equations. To verify the proposed model, the leaching processes of two salt caverns of Jintan underground gas storage are simulated by the program, using the actual geological and technological parameters. The same simulation is performed by the current mainstream leaching software in China. The simulation results of the two programs are compared with the available field data. It shows that the proposed software is more accurate on the shape prediction of the cavern bottom and roof, which demonstrates the reliability and applicability of the model.
Perception during double-step saccades
Authors: Zimmermann E. , Morrone M. C. , Binda P. 
Published: January 2018

AbstractHow the visual system achieves perceptual stability across saccadic eye movements is a long-standing question in neuroscience. It has been proposed that an efference copy informs vision about upcoming saccades, and this might lead to shifting spatial coordinates and suppressing image motion. Here we ask whether these two aspects of visual stability are interdependent or may be dissociated under special conditions. We study a memory-guided double-step saccade task, where two saccades are executed in quick succession. Previous studies have led to the hypothesis that in this paradigm the two saccades are planned in parallel, with a single efference copy signal generated at the start of the double-step sequence, i.e. before the first saccade. In line with this hypothesis, we find that visual stability is impaired during the second saccade, which is consistent with (accurate) efference copy information being unavailable during the second saccade. However, we find that saccadic suppression is normal during the second saccade. Thus, the second saccade of a double-step sequence instantiates a dissociation between visual stability and saccadic suppression: stability is impaired even though suppression is strong.
A model of human lung fibrogenesis for the assessment of anti-fibrotic strategies in idiopathic pulmonary fibrosis
Authors: Roach Katy M. , Sutcliffe Amanda , Matthews Laura , Elliott Gill , Newby Chris , Amrani Yassine , Bradding Peter 
Published: January 2018

AbstractIdiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease with limited therapeutic options. KCa3.1 ion channels play a critical role in TGFβ1-dependent pro-fibrotic responses in human lung myofibroblasts. We aimed to develop a human lung parenchymal model of fibrogenesis and test the efficacy of the selective KCa3.1 blocker senicapoc. 2 mm3 pieces of human lung parenchyma were cultured for 7 days in DMEM ± TGFβ1 (10 ng/ml) and pro-fibrotic pathways examined by RT-PCR, immunohistochemistry and collagen secretion. Following 7 days of culture with TGFβ1, 41 IPF- and fibrosis-associated genes were significantly upregulated. Immunohistochemical staining demonstrated increased expression of ECM proteins and fibroblast-specific protein after TGFβ1-stimulation. Collagen secretion was significantly increased following TGFβ1-stimulation. These pro-fibrotic responses were attenuated by senicapoc, but not by dexamethasone. This 7 day ex vivo model of human lung fibrogenesis recapitulates pro-fibrotic events evident in IPF and is sensitive to KCa3.1 channel inhibition. By maintaining the complex cell-cell and cell-matrix interactions of human tissue, and removing cross-species heterogeneity, this model may better predict drug efficacy in clinical trials and accelerate drug development in IPF. KCa3.1 channels are a promising target for the treatment of IPF.
N-domain of angiotensin-converting enzyme hydrolyzes human and rat amyloid-β(1-16) peptides as arginine specific endopeptidase potentially enhancing risk of Alzheimer’s disease
Authors: Kugaevskaya Elena V. , Veselovsky Alexander V. , Indeykina Maria I. , Solovyeva Nina I. , Zharkova Maria S. , Popov Igor A. , Nikolaev Eugene N. , Mantsyzov Alexey B. , Makarov Alexander A. , Kozin Sergey A. 
Published: January 2018

AbstractAlzheimer’s disease (AD) is a multifactorial neurodegenerative disorder. Amyloid-β (Aβ) aggregation is likely to be the major cause of AD. In contrast to humans and other mammals, that share the same Aβ sequence, rats and mice are invulnerable to AD-like neurodegenerative pathologies, and Aβ of these rodents (ratAβ) has three amino acid substitutions in the metal-binding domain 1-16 (MBD). Angiotensin-converting enzyme (ACE) cleaves Aβ-derived peptide substrates, however, there are contradictions concerning the localization of the cleavage sites within Aβ and the roles of each of the two ACE catalytically active domains in the hydrolysis. In the current study by using mass spectrometry and molecular modelling we have tested a set of peptides corresponding to MBDs of Aβ and ratAβ to get insights on the interactions between ACE and these Aβ species. It has been shown that the N-domain of ACE (N-ACE) acts as an arginine specific endopeptidase on the Aβ and ratAβ MBDs with C-amidated termini, thus assuming that full-length Aβ and ratAβ can be hydrolyzed by N-ACE in the same endopeptidase mode. Taken together with the recent data on the molecular mechanism of zinc-dependent oligomerization of Aβ, our results suggest a modulating role of N-ACE in AD pathogenesis.
Site-specific randomization of the endogenous genome by a regulatable CRISPR-Cas9 piggyBac system in human cells
Authors: Ishida Kentaro , Xu Huaigeng , Sasakawa Noriko , Lung Mandy Siu Yu , Kudryashev Julia Alexandra , Gee Peter , Hotta Akitsu 
Published: January 2018

AbstractRandomized mutagenesis at an endogenous chromosomal locus is a promising approach for protein engineering, functional assessment of regulatory elements, and modeling genetic variations. In mammalian cells, however, it is challenging to perform site-specific single-nucleotide substitution with single-stranded oligodeoxynucleotide (ssODN) donor templates due to insufficient homologous recombination and the infeasibility of positive selection. Here, we developed a DNA transposon based CRISPR-Cas9 regulated transcription and nuclear shuttling (CRONUS) system that enables the stable transduction of CRISPR-Cas9/sgRNA in broad cell types, but avoids undesired genome cleavage in the absence two chemical inducing molecules. Highly efficient single nucleotide alterations induced randomization of desired codons (up to 4 codons) at a defined genomic locus in various human cell lines, including human iPS cells. Thus, CRONUS provides a novel platform for modeling diseases and genetic variations.
Evaluation of in vivo digital root reconstruction based on anatomical characteristics of the periodontal ligament using cone beam computed tomography
Authors: Wang Chenxin , Liu Yi , Wang Siwei , Wang Yong , Zhao Yijiao 
Published: January 2018

AbstractThis study’s aim was to develop and validate an approach to automatically extract and reconstruct three-dimensional (3D) digital root models from in vivo teeth based on the anatomical characteristics of the periodontal ligament using cone beam computed tomography (CBCT) data. Prior to undergoing dental extractions for orthodontic purposes, the CBCT data of each study participant were collected and imported into Mimics software to reconstruct 3D in vivo digital root models (test models). Twenty roots of 17 teeth extracted from the study’s participants were scanned using a dental scanner to obtain 3D in vitro digital root models (reference models). The 3D morphological deviation between the reference and test models was compared; the 3D size of the bucco-lingual, mesio-distal, and root length dimensions were calculated. This approach achieved an average 3D morphological deviation of 0.21 mm, and the average size error in the bucco-lingual, mesio-distal, and root length dimensions were −0.35 mm, −0.17 mm, and 0.47 mm, respectively. This new automatic extraction approach rapidly and accurately reconstructs 3D in vivo root models with detailed morphological information, and has the potential to improve diagnostic and treatment work flow in orthodontic clinics, as well as in other areas of dentistry.
Ultraviolet-B enhances the resistance of multiple plant species to lepidopteran insect herbivory through the jasmonic acid pathway
Authors: Qi Jinfeng , Zhang Mou , Lu Chengkai , Hettenhausen Christian , Tan Qing , Cao Guoyan , Zhu Xudong , Wu Guoxing , Wu Jianqiang 
Published: January 2018

AbstractLand plants protect themselves from ultraviolet-B (UV-B) by accumulating UV-absorbing metabolites, which may also function as anti-insect toxins. Previous studies have shown that UV-B enhances the resistance of different plant species to pierce-sucking pests; however, whether and how UV-B influences plant defense against chewing caterpillars are not well understood. Here we show that UV-B treatment increased Spodoptera litura herbivory-induced jasmonic acid (JA) production in Arabidopsis and thereby Arabidopsis exhibited elevated resistance to S. litura. Using mutants impaired in the biosynthesis of JA and the defensive metabolites glucosinolates (GSs), we show that the UV-B-induced resistance to S. litura is dependent on the JA-regulated GSs and an unidentified anti-insect metabolite(s). Similarly, UV-B treatment also enhanced the levels of JA-isoleucine conjugate and defense-related secondary metabolites in tobacco, rice, and maize after these plants were treated with simulated herbivory of lepidopteran insects; consistently, these plants showed elevated resistance to insect larvae. Using transgenic plants impaired in JA biosynthesis or signaling, we further demonstrate that the UV-B-enhanced defense responses also require the JA pathway in tobacco and rice. Our findings reveal a likely conserved JA-dependent mechanism by which UV-B enhances plant defense against lepidopteran insects.