bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and analysis of genes associated with the synthesis of bioactive constituents in Dendrobium officinale using RNA-Seq
Authors: Shen Chenjia , Guo Hong , Chen Hailing , Shi Yujun , Meng Yijun , Lu Jiangjie , Feng Shangguo , Wang Huizhong 
Published: March 2017

AbstractDendrobium officinale L. is an important traditional herb with high commercial value in China. Several bioactive constituents, including polysaccharides and alkaloids, reportedly make major contributions toward the excellent medicinal effect of D. officinale. In this study, the contents of polysaccharides and alkaloids in various organs of D. officinale were measured and compared. We took advantage of transcriptomes from four organs to explore biological mechanisms in the organ-specific distribution of active ingredients in D. officinale. Based on Kyoto Encyclopedia of Genes and Genomes pathways, unigenes related to the enzymes involved in fructose and mannose metabolism and unigenes associated with putative upstream elements of the alkaloid biosynthetic pathway were identified. A large number of candidates, including 35 full-length glycosyltransferase genes and 49 full-length P450 genes, were also identified based on the transcriptome data, and the organ-specific expression pattern of these genes was determined. Furthermore, differential expression of all candidate genes was analyzed in two Dendrobium species, D. nobile L. and D. officinale. The data will supply important clues to exploit useful genes involved in polysaccharide and alkaloid synthesis.
RETRACTED ARTICLE: pNaKtide Attenuates Steatohepatitis and Atherosclerosis by Blocking Na/K-ATPase/ROS Amplification in C57Bl6 and ApoE Knockout Mice Fed a Western Diet
Authors: Sodhi Komal , Srikanthan Krithika , Goguet-Rubio Perrine , Nichols Alexandra , Mallick Amrita , Nawab Athar , Martin Rebecca , Shah Preeya T. , Chaudhry Muhammad , Sigdel Saroj , El-Hamdani Mehiar , Liu Jiang , Xie Zijian , Abraham Nader G. , Shapiro Joseph I. 
Published: March 2017

AbstractWe have previously reported that the α1 subunit of sodium potassium adenosine triphosphatase (Na/K-ATPase), acts as a receptor and an amplifier for reactive oxygen species, in addition to its distinct pumping function. On this background, we speculated that blockade of Na/K-ATPase-induced ROS amplification with a specific peptide, pNaKtide, might attenuate the development of steatohepatitis. To test this hypothesis, pNaKtide was administered to a murine model of NASH: the C57Bl6 mouse fed a “western” diet containing high amounts of fat and fructose. The administration of pNaKtide reduced obesity as well as hepatic steatosis, inflammation and fibrosis. Of interest, we also noted marked improvement in mitochondrial fatty acid oxidation, insulin sensitivity, dyslipidemia and aortic streaking in this mouse model. To further elucidate the effects of pNaKtide on atherosclerosis, similar studies were performed in ApoE knockout mice also exposed to the western diet. In these mice, pNaKtide not only improved steatohepatitis, dyslipidemia, and insulin sensitivity, but also ameliorated significant aortic atherosclerosis. Collectively, this study demonstrates that the Na/K-ATPase/ROS amplification loop contributes significantly to the development and progression of steatohepatitis and atherosclerosis. And furthermore, this study presents a potential treatment, the pNaKtide, for the metabolic syndrome phenotype.
Diet-induced obesity impairs spermatogenesis: a potential role for autophagy
Authors: Mu Yang , Yan Wen-jie , Yin Tai-lang , Zhang Yan , Li Jie , Yang Jing 
Published: March 2017

AbstractAutophagy is an evolutionarily conserved process that plays a crucial role in maintaining a series of cellular functions. It has been found that autophagy is closely involved in the physiological process of spermatogenesis and the regulation of sperm survival and motility. However, the role of autophagy in high-fat diet (HFD)-induced impaired spermatogenesis remains unknown. This study was designed to investigate the role of autophagy in HFD-induced spermatogenesis deficiency and employed chloroquine (CQ) to inhibit autophagy and rapamycin (RAP) to induce autophagy. 3-methyladenine (3-MA) and CQ were administered via intratesticular injection in vivo. The effects of CQ and 3-MA on the parameters of spermatozoa co-cultured with palmitic acid (PA) in vitro were also investigated. Human semen samples from obese, subfertile male patients were also collected to examine the level of autophagy. The results suggested that HFD mice subjected to CQ showed improved spermatogenesis. Inhibiting autophagy with CQ improved the decreased fertility of HFD male mice. Moreover, the in vivo and in vitro results indicated that both CQ and 3-MA could suppress the pathological changes in spermatozoa caused by HFD or PA treatment. Additionally, the excessive activation of autophagy was also observed in sperm samples from obese, subfertile male patients.
Regression of devil facial tumour disease following immunotherapy in immunised Tasmanian devils
Authors: Tovar Cesar , Pye Ruth J. , Kreiss Alexandre , Cheng Yuanyuan , Brown Gabriella K. , Darby Jocelyn , Malley Roslyn C. , Siddle Hannah V. T. , Skjødt Karsten , Kaufman Jim , Silva Anabel , Baz Morelli Adriana , Papenfuss Anthony T. , Corcoran Lynn M. , Murphy James M. , Pearse Martin J. , Belov Katherine , Lyons A. Bruce , Woods Gregory M. 
Published: March 2017

AbstractDevil facial tumour disease (DFTD) is a transmissible cancer devastating the Tasmanian devil (Sarcophilus harrisii) population. The cancer cell is the ‘infectious’ agent transmitted as an allograft by biting. Animals usually die within a few months with no evidence of antibody or immune cell responses against the DFTD allograft. This lack of anti-tumour immunity is attributed to an absence of cell surface major histocompatibility complex (MHC)-I molecule expression. While the endangerment of the devil population precludes experimentation on large experimental groups, those examined in our study indicated that immunisation and immunotherapy with DFTD cells expressing surface MHC-I corresponded with effective anti-tumour responses. Tumour engraftment did not occur in one of the five immunised Tasmanian devils, and regression followed therapy of experimentally induced DFTD tumours in three Tasmanian devils. Regression correlated with immune cell infiltration and antibody responses against DFTD cells. These data support the concept that immunisation of devils with DFTD cancer cells can successfully induce humoral responses against DFTD and trigger immune-mediated regression of established tumours. Our findings support the feasibility of a protective DFTD vaccine and ultimately the preservation of the species.
Conditional Survival Analysis of Patients With Locally Advanced Laryngeal Cancer: Construction of a Dynamic Risk Model and Clinical Nomogram
Authors:   Multidisciplinary Larynx Cancer Working Group, Sheu Tommy , Vock David M. , Mohamed Abdallah S. R. , Gross Neil , Mulcahy Collin , Zafereo Mark , Gunn G. Brandon , Garden Adam S. , Sevak Parag , Phan Jack , Lewin Jan S. , Frank Steven J. , Beadle Beth M. , Morrison William H. , Lai Stephen Y. , Hutcheson Katherine , Marai G. Elisabeta , Canahuate Guadalupe M. , Kies Merrill , El-Naggar Adel , Weber Randal S. , Rosenthal David I. , Fuller Clifton D. 
Published: March 2017

AbstractConditional survival (CS), the survival beyond a pre-defined time interval, can identify periods of higher mortality risk for patients with locally advanced laryngeal cancer who face treatment-related toxicity and comorbidities related to alcohol and smoking in the survivorship setting. Using Weibull regression modeling, we analyzed retrospectively abstracted data from 638 records of patients who received radiation to identify prognostic factors for overall survival (OS) and recurrence free survival (RFS) for the first 3 years of survival and for OS conditional upon 3 years of survival. The CS was iteratively calculated, stratifying on variables that were statistically significant on multivariate regression. Predictive nomograms were generated. The median total follow up time was 175 months. The 3- and 6- year actuarial overall survival (OS) was 68% (95% confidence interval [CI] 65–72%) and 49% (CI 45–53%). The 3-year conditional overall survival (COS) at 3 years was 72% (CI 65–74%). Black patients had worse COS over time. Nodal disease was significantly associated with recurrence, but after 3 years, the 3-year conditional RFS converged for all nodal groups. In conclusion, the CS analysis in this patient cohort identified subgroups and time intervals that may represent opportunities for intervention.
Portable Infrared Laser Spectroscopy for On-site Mycotoxin Analysis
Authors: Sieger Markus , Kos Gregor , Sulyok Michael , Godejohann Matthias , Krska Rudolf , Mizaikoff Boris 
Published: March 2017

AbstractMycotoxins are toxic secondary metabolites of fungi that spoil food, and severely impact human health (e.g., causing cancer). Therefore, the rapid determination of mycotoxin contamination including deoxynivalenol and aflatoxin B1 in food and feed samples is of prime interest for commodity importers and processors. While chromatography-based techniques are well established in laboratory environments, only very few (i.e., mostly immunochemical) techniques exist enabling direct on-site analysis for traders and manufacturers. In this study, we present MYCOSPEC - an innovative approach for spectroscopic mycotoxin contamination analysis at EU regulatory limits for the first time utilizing mid-infrared tunable quantum cascade laser (QCL) spectroscopy. This analysis technique facilitates on-site mycotoxin analysis by combining QCL technology with GaAs/AlGaAs thin-film waveguides. Multivariate data mining strategies (i.e., principal component analysis) enabled the classification of deoxynivalenol-contaminated maize and wheat samples, and of aflatoxin B1 affected peanuts at EU regulatory limits of 1250 μg kg−1 and 8 μg kg−1, respectively.
Bioinspired lignocellulosic films to understand the mechanical properties of lignified plant cell walls at nanoscale
Authors: Muraille L. , Aguié-Béghin V. , Chabbert B. , Molinari M. 
Published: March 2017

AbstractThe physicochemical properties of plant fibres are determined by the fibre morphology and structural features of the cell wall, which is composed of three main layers that differ in chemical composition and architecture. This composition and hierarchical structure are responsible for many of the mechanical properties that are desirable for industrial applications. As interactions between the lignocellulosic polymers at the molecular level are the main factor governing the final cohesion and mechanical properties of plant fibres, atomic force microscopy (AFM) is well suited for the observation and measurement of their physical properties at nanoscale levels. Given the complexity of plant cell walls, we have developed a strategy based on lignocellulosic assemblies with increasing complexity to understand the influence of the different polymers on the nanomechanical properties. Measurements of the indentation moduli performed on one type of lignified cell wall compared with those performed on the corresponding lignocellulosic films clearly show the importance of the lignin in the mechanical properties of cell walls. Through this strategy, we envision a wide application of bioinspired systems in future studies of the physical properties of fibres.
Selective targeting of HDAC1/2 elicits anticancer effects through Gli1 acetylation in preclinical models of SHH Medulloblastoma
Authors: Coni Sonia , Mancuso Anna Barbara , Di Magno Laura , Sdruscia Giulia , Manni Simona , Serrao Silvia Maria , Rotili Dante , Spiombi Eleonora , Bufalieri Francesca , Petroni Marialaura , Kusio-Kobialka Monika , De Smaele Enrico , Ferretti Elisabetta , Capalbo Carlo , Mai Antonello , Niewiadomski Pawel , Screpanti Isabella , Di Marcotullio Lucia , Canettieri Gianluca 
Published: March 2017

AbstractSHH Medulloblastoma (SHH-MB) is a pediatric brain tumor characterized by an inappropriate activation of the developmental Hedgehog (Hh) signaling. SHH-MB patients treated with the FDA-approved vismodegib, an Hh inhibitor that targets the transmembrane activator Smoothened (Smo), have shown the rapid development of drug resistance and tumor relapse due to novel Smo mutations. Moreover, a subset of patients did not respond to vismodegib because mutations were localized downstream of Smo. Thus, targeting downstream Hh components is now considered a preferable approach. We show here that selective inhibition of the downstream Hh effectors HDAC1 and HDAC2 robustly counteracts SHH-MB growth in mouse models. These two deacetylases are upregulated in tumor and their knockdown inhibits Hh signaling and decreases tumor growth. We demonstrate that mocetinostat (MGCD0103), a selective HDAC1/HDAC2 inhibitor, is a potent Hh inhibitor and that its effect is linked to Gli1 acetylation at K518. Of note, we demonstrate that administration of mocetinostat to mouse models of SHH-MB drastically reduces tumor growth, by reducing proliferation and increasing apoptosis of tumor cells and prolongs mouse survival rate. Collectively, these data demonstrate the preclinical efficacy of targeting the downstream HDAC1/2-Gli1 acetylation in the treatment of SHH-MB.
A decade of global volcanic SO2 emissions measured from space
Authors: Carn S. A. , Fioletov V. E. , McLinden C. A. , Li C. , Krotkov N. A. 
Published: March 2017

AbstractThe global flux of sulfur dioxide (SO2) emitted by passive volcanic degassing is a key parameter that constrains the fluxes of other volcanic gases (including carbon dioxide, CO2) and toxic trace metals (e.g., mercury). It is also a required input for atmospheric chemistry and climate models, since it impacts the tropospheric burden of sulfate aerosol, a major climate-forcing species. Despite its significance, an inventory of passive volcanic degassing is very difficult to produce, due largely to the patchy spatial and temporal coverage of ground-based SO2 measurements. We report here the first volcanic SO2 emissions inventory derived from global, coincident satellite measurements, made by the Ozone Monitoring Instrument (OMI) on NASA’s Aura satellite in 2005–2015. The OMI measurements permit estimation of SO2 emissions from over 90 volcanoes, including new constraints on fluxes from Indonesia, Papua New Guinea, the Aleutian Islands, the Kuril Islands and Kamchatka. On average over the past decade, the volcanic SO2 sources consistently detected from space have discharged a total of ~63 kt/day SO2 during passive degassing, or ~23 ± 2 Tg/yr. We find that ~30% of the sources show significant decadal trends in SO2 emissions, with positive trends observed at multiple volcanoes in some regions including Vanuatu, southern Japan, Peru and Chile.
A potential regulatory network underlying distinct fate commitment of myogenic and adipogenic cells in skeletal muscle
Authors: Sun Wenjuan , He Ting , Qin Chunfu , Qiu Kai , Zhang Xin , Luo Yanhong , Li Defa , Yin Jingdong 
Published: March 2017

AbstractMechanism controlling myo-adipogenic balance in skeletal muscle is of great significance for human skeletal muscle dysfunction and myopathies as well as livestock meat quality. In the present study, two cell subpopulations with particular potency of adipogenic or myogenic differentiation were isolated from neonatal porcine longissimus dorsi using the preplate method to detect mechanisms underlying distinct fate commitment of myogenic and adipogenic cells in skeletal muscle. Both cells share a common surface expression profile of CD29+CD31−CD34−CD90+CD105+, verifying their mesenchymal origin. A total of 448 differentially expressed genes (DEGs) (FDR < 0.05 and |log2 FC| ≥ 1) between two distinct cells were identified via RNA-seq, including 358 up-regulated and 90 down-regulated genes in myogenic cells compared with adipogenic cells. The results of functional annotation and enrichment showed that 42 DEGs were implicated in cell differentiation, among them PDGFRα, ITGA3, ITGB6, MLCK and MLC acted as hubs between environment information processing and cellular process, indicating that the interaction of the two categories exerts an important role in distinct fate commitment of myogenic and adipogenic cells. Particularly, we are first to show that up-regulation of intracellular Ca2+-MLCK and Rho-DMPK, and subsequently elevated MLC, may contribute to the distinct commitment of myogenic and adipogenic lineages via mediating cytoskeleton dynamics.
Computational On-Chip Imaging of Nanoparticles and Biomolecules using Ultraviolet Light
Authors: Daloglu Mustafa Ugur , Ray Aniruddha , Gorocs Zoltan , Xiong Matthew , Malik Ravinder , Bitan Gal , McLeod Euan , Ozcan Aydogan 
Published: March 2017

AbstractSignificant progress in characterization of nanoparticles and biomolecules was enabled by the development of advanced imaging equipment with extreme spatial-resolution and sensitivity. To perform some of these analyses outside of well-resourced laboratories, it is necessary to create robust and cost-effective alternatives to existing high-end laboratory-bound imaging and sensing equipment. Towards this aim, we have designed a holographic on-chip microscope operating at an ultraviolet illumination wavelength (UV) of 266 nm. The increased forward scattering from nanoscale objects at this short wavelength has enabled us to detect individual sub-30 nm nanoparticles over a large field-of-view of >16 mm2 using an on-chip imaging platform, where the sample is placed at ≤0.5 mm away from the active area of an opto-electronic sensor-array, without any lenses in between. The strong absorption of this UV wavelength by biomolecules including nucleic acids and proteins has further enabled high-contrast imaging of nanoscopic aggregates of biomolecules, e.g., of enzyme Cu/Zn-superoxide dismutase, abnormal aggregation of which is linked to amyotrophic lateral sclerosis (ALS) - a fatal neurodegenerative disease. This UV-based wide-field computational imaging platform could be valuable for numerous applications in biomedical sciences and environmental monitoring, including disease diagnostics, viral load measurements as well as air- and water-quality assessment.
Epitaxially grown BaM hexaferrite films having uniaxial axis in the film plane for self-biased devices
Authors: Zhang Xiaozhi , Meng Siqin , Song Dongsheng , Zhang Yao , Yue Zhenxing , Harris Vincent G. 
Published: March 2017

AbstractBarium hexaferrite (BaM) films with in-plane c-axis orientation are promising and technically important materials for self-biased magnetic microwave devices. In this work, highly oriented BaM films with different thickness and an in-plane easy axis (c-axis) of magnetization were grown on a-plane "Equation missing" single-crystal sapphire substrates by direct current magnetron sputtering. A procedure involving seed layers, layer-by-layer annealing was adopted to reduce the substrate-induced strains and allow for the growth of thick (~3.44 μm) films. The epitaxial growth of the BaM film on sapphire was revealed by high-resolution transmission electron microscopy with dislocations being observed at the film-substrate interface. The orientation was also verified by X-ray diffraction and more notably, polarized Raman scattering. The magnetic properties and ferromagnetic resonant frequencies were experimentally characterized by a vibrating sample magnetometry and a frequency-swept ferromagnetic resonant flip-chip technique, respectively. The micron-thick BaM films exhibited a large remanence ratio of 0.92 along in-plane easy axis and a small one of 0.09 for the in-plane hard axis loop measurement. The FMR frequency was 50.3 GHz at zero field and reached 57.9 GHz under a magnetic field of 3 kOe, indicating that the epitaxial BaM films with strong self-biased behaviors have good electromagnetic properties in millimeter-wave range.
Variability in statin-induced changes in gene expression profiles of pancreatic cancer
Authors: Gbelcová Helena , Rimpelová Silvie , Ruml Tomáš , Fenclová Marie , Kosek Vítek , Hajšlová Jana , Strnad Hynek , Kolář Michal , Vítek Libor 
Published: March 2017

AbstractStatins, besides being powerful cholesterol-lowering drugs, also exert potent anti-proliferative activities. However, their anti-cancer efficacy differs among the individual statins. Thus, the aim of this study was to identify the biological pathways affected by individual statins in an in vitro model of human pancreatic cancer. The study was performed on a human pancreatic cancer cell line MiaPaCa-2, exposed to all commercially available statins (12 μM, 24 h exposure). DNA microarray analysis was used to determine changes in the gene expression of treated cells. Intracellular concentrations of individual statins were measured by UPLC (ultra performance liquid chromatography)-HRMS (high resolution mass spectrometer). Large differences in the gene transcription profiles of pancreatic cancer cells exposed to various statins were observed; cerivastatin, pitavastatin, and simvastatin being the most efficient modulators of expression of genes involved namely in the mevalonate pathway, cell cycle regulation, DNA replication, apoptosis and cytoskeleton signaling. Marked differences in the intracellular concentrations of individual statins in pancreatic cancer cells were found (>11 times lower concentration of rosuvastatin compared to lovastatin), which may contribute to inter-individual variability in their anti-cancer effects. In conclusion, individual statins exert different gene expression modulating effects in treated pancreatic cancer cells. These effects may be partially caused by large differences in their bioavailability. We report large differences in gene transcription profiles of pancreatic cancer cells exposed to various statins. These data correlate to some extent with the intracellular concentrations of statins, and may explain the inter-individual variability in the anti-cancer effects of statins.
The acute airway inflammation induced by PM2.5 exposure and the treatment of essential oils in Balb/c mice
Authors: Wang Hetong , Song Laiyu , Ju Wenhui , Wang Xuguang , Dong Lu , Zhang Yining , Ya Ping , Yang Chun , Li Fasheng 
Published: March 2017

AbstractPM2.5 is the main particulate air pollutant whose aerodynamic diameter is less than 2.5 micron. The inflammation of various respiratory diseases are associated with PM2.5 inhalation. Pro-inflammatory cytokine IL-1β generated from effected cells usually plays a crucial role in many kinds of lung inflammatory reactions. The exacerbation of Th immune responses are identified in some PM2.5 related diseases. To elucidate the underlying mechanism of PM2.5-induced acute lung inflammation, we exposed Balb/c mice to PM2.5 intratracheally and established a mice model. Acute lung inflammation and increased IL-1β expression was observed after PM2.5 instillation. Regulatory factors of IL-1β (TLR4/MyD88 signaling pathway and NLRP3 inflammasome) participated in this lung inflammatory response as well. Treatment with compound essential oils (CEOs) substantially attenuated PM2.5-induced acute lung inflammation. The decreased IL-1β and Th immune responses after CEOs treatment were significant. PM2.5 may increase the secretion of IL-1β through TLR4/MyD88 and NLRP3 pathway resulting in murine airway inflammation. CEOs could attenuate the lung inflammation by reducing IL-1β and Th immune responses in this model. This study describes a potentially important mechanism of PM2.5-induced acute lung inflammation and that may bring about novel therapies for the inflammatory diseases associated with PM2.5 inhalation.