bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection of suitable reference genes for qRT-PCR normalisation under different experimental conditions in Eucommia ulmoides Oliv
Authors: Ye Jing , Jin Cang-Fu , Li Nan , Liu Min-Hao , Fei Zhao-Xue , Dong Li-Zheng , Li Long , Li Zhou-Qi 
Published: October 2018

AbstractNormalisation of data, by choosing the appropriate reference genes, is fundamental for obtaining reliable results in quantitative real-time PCR (qPCR). This study evaluated the expression stability of 11 candidate reference genes with different varieties, developmental periods, tissues, and abiotic stresses by using four statistical algorithms: geNorm, NormFinder, BestKeeper, and RefFinder. The results indicated that ubiquitin-conjugating enzyme S (UBC) and ubiquitin-conjugating enzyme E2 (UBC E2) could be used as reference genes for different E. ulmoides varieties and tissues, UBC and histone H4 (HIS4) for different developmental periods, beta-tubulin (TUB) and UBC for cold treatment, ubiquitin extension protein (UBA80) and HIS4 for drought treatment, and ubiquitin-60S ribosomal protein L40 (UBA52) and UBC E2 for salinity treatment. UBC and UBC E2 for the group “Natural growth” and “Total”, UBA80 and UBC for the group “Abiotic stresses”. To validate the suitability of the selected reference genes in this study, mevalonate kinase (MK), phenylalanine ammonia-lyase (PAL), and 4-coumarate-CoA ligase (4CL) gene expression patterns were analysed. When the most unstable reference genes were used for normalisation, the expression patterns had significant biases compared with the optimum reference gene combinations. These results will be beneficial for more accurate quantification of gene expression levels in E. ulmoides.
Effects of coumaphos and imidacloprid on honey bee (Hymenoptera: Apidae) lifespan and antioxidant gene regulations in laboratory experiments
Authors: Gregorc Ales , Alburaki Mohamed , Rinderer Nicholas , Sampson Blair , Knight Patricia R. , Karim Shahid , Adamczyk John 
Published: October 2018

AbstractThe main objective of this study was to test comparatively the effects of two common insecticides on honey bee Apis mellifera worker’s lifespan, food consumption, mortality, and expression of antioxidant genes. Newly emerged worker bees were exposed to organophosphate insecticide coumaphos, a neonicotinoid imidacloprid, and their mixtures. Toxicity tests were conducted along with bee midgut immunohistological TUNEL analyses. RT-qPCR assessed the regulation of 10 bee antioxidant genes linked to pesticide toxicity. We tested coumaphos at 92,600 ppb concentration, in combination with 5 and 20 ppb imidacloprid. Coumaphos induced significantly higher bee mortality, which was associated with down regulation of catalase compared to coumaphos and imidacloprid (5/20 ppb) mixtures, whereas, both imidacloprid concentrations independently had no effect on bee mortality. Mixture of coumaphos and imidacloprid reduced daily bee consumption of a control food patty to 10 mg from a coumaphos intake of 14.3 mg and 18.4 and 13.7 mg for imidacloprid (5 and 20) ppb, respectively. While coumaphos and imidacloprid mixtures induced down-regulation of antioxidant genes with noticeable midgut tissue damage, imidacloprid induced intensive gene up-regulations with less midgut apoptosis.
Overlapping motifs on the herpes viral proteins ICP27 and ORF57 mediate interactions with the mRNA export adaptors ALYREF and UIF
Authors: Tunnicliffe Richard B. , Tian Xiaochen , Storer Joanna , Sandri-Goldin Rozanne M. , Golovanov Alexander P. 
Published: October 2018

AbstractThe TREX complex mediates the passage of bulk cellular mRNA export to the nuclear export factor TAP/NXF1 via the export adaptors ALYREF or UIF, which appear to act in a redundant manner. TREX complex recruitment to nascent RNA is coupled with 5′ capping, splicing and polyadenylation. Therefore to facilitate expression from their intronless genes, herpes viruses have evolved a mechanism to circumvent these cellular controls. Central to this process is a protein from the conserved ICP27 family, which binds viral transcripts and cellular TREX complex components including ALYREF. Here we have identified a novel interaction between HSV-1 ICP27 and an N-terminal domain of UIF in vivo, and used NMR spectroscopy to locate the UIF binding site within an intrinsically disordered region of ICP27. We also characterized the interaction sites of the ICP27 homolog ORF57 from KSHV with UIF and ALYREF using NMR, revealing previously unidentified binding motifs. In both ORF57 and ICP27 the interaction sites for ALYREF and UIF partially overlap, suggestive of mutually exclusive binding. The data provide a map of the binding sites responsible for promoting herpes virus mRNA export, enabling future studies to accurately probe these interactions and reveal the functional consequences for UIF and ALYREF redundancy.
Functional analysis of polyketide synthase genes in the biocontrol fungus Clonostachys rosea
Authors: Fatema Umma , Broberg Anders , Jensen Dan Funck , Karlsson Magnus , Dubey Mukesh 
Published: October 2018

AbstractClonostachys rosea is a mycoparasitic fungus used for biological control of plant diseases. Its genome contains 31 genes putatively encoding for polyketide synthases (PKSs), 75% of which are arranged in biosynthetic gene clusters. Gene expression analysis during C. rosea interactions with the fungal plant pathogens Botrytis cinerea and Fusarium graminearum showed common and species-specific induction of PKS genes. Our data showed a culture media dependent correlation between PKS gene expression and degree of antagonism in C. rosea. The pks22 and pks29 genes were highly induced during fungal-fungal interactions but not during pigmentation, and gene deletion studies revealed that PKS29 was required for full antagonism against B. cinerea, and for biocontrol of fusarium foot rot on barley. Metabolite analysis revealed that Δpks29 strains has a 50% reduced production (P = 0.001) of an unknown polyketide with molecular formula C15H28O3, while Δpks22 strains lost the ability to produce four previously unknown polyketides named Clonorosein A-D. Clonorosein A and B were purified, their structures determined, and showed strong antifungal activity against B. cinerea and F. graminearum. These results show that PKS22 is required for production of antifungal polyketide Clonorosein A-D, and demonstrate the role of PKS29 in antagonism and biocontrol of fungal plant diseases.
Persistent platelet activation and apoptosis in virologically suppressed HIV-infected individuals
Authors: Mesquita Emersom C. , Hottz Eugenio D. , Amancio Rodrigo T. , Carneiro Alan B. , Palhinha Lohanna , Coelho Lara E. , Grinsztejn Beatriz , Zimmerman Guy A. , Rondina Matthew T. , Weyrich Andrew S. , Bozza Patrícia T. , Bozza Fernando A. 
Published: October 2018

AbstractCardiovascular diseases and thrombotic events became major clinical problems in the combined antiretroviral therapy (cART) era. Although the precise mechanisms behind these clinical problems have not been fully elucidated, a persistent pro-inflammatory state plays a central role. As platelets play important roles on both, thrombus formation and inflammatory/immune response, we aimed at investigating platelet function in HIV-infected subjects virologically controlled through cART. We evaluate parameters of activation, mitochondrial function and activation of apoptosis pathways in platelets from 30 HIV-infected individuals under stable cART and 36 healthy volunteers. Despite viral control achieved through cART, HIV-infected individuals exhibited increased platelet activation as indicated by P-selectin expression and platelet spreading when adhered on fibrinogen-coated surfaces. Platelets from HIV-infected subjects also exhibited mitochondrial dysfunction and activation of apoptosis pathways. Finally, thrombin stimuli induced lower levels of P-selectin translocation and RANTES secretion, but not TXA2 synthesis, in platelets from HIV-infected individuals compared to control; and labeling of platelet alpha granules showed reduced granule content in platelets from HIV-infected individuals when compared to healthy subjects. In summary, platelets derived from HIV-infected individuals under stable cART exhibit a phenotype of increased activation, activation of the intrinsic pathway of apoptosis and undermined granule secretion in response to thrombin.
Stress-induced changes in social dominance are scaled by AMPA-type glutamate receptor phosphorylation in the medial prefrontal cortex
Authors: Park Min-Jung , Seo Bo Am , Lee Boyoung , Shin Hee-Sup , Kang Myoung-Goo 
Published: October 2018

AbstractThe establishment and maintenance of social dominance are critical for social stability and the survival and health of individual animals. Stress lead to depression and a decrease in the social status of depressed persons is a risk factor for suicide. Therefore, we explored the mechanistic and behavioral links among stress, depression, and social dominance and found that mice subjected to chronic restraint stress (CRS), an animal model of stress-induced depression, showed decreased social dominance as measured by a dominance tube test. Importantly, this submissive behavior was occluded by the antidepressant, fluoxetine, a selective serotonin reuptake inhibitor. It is known that social dominance is controlled by synaptic efficacy in the medial prefrontal cortex (mPFC) and that AMPA-type glutamate receptor (AMPA-R) is a key molecule for synaptic efficacy. We found that the phosphorylation on AMPA-R was bidirectionally changed by CRS and fluoxetine in the mPFC of mice with CRS. Moreover, we found a strong correlation between social dominance and AMPA-R phosphorylation that regulates synaptic efficacy by modulating the synaptic targeting of AMPA-R. Our correlational analysis of the behavior and biochemistry of the CRS model suggests that AMPA-R phosphorylation in the mPFC may serve as a biomarker of social dominance related to stress.
Uncovering association networks through an eQTL analysis involving human miRNAs and lincRNAs
Authors: Branco Paulo R. , de Araújo Gilderlanio S. , Barrera Júnior , Suarez-Kurtz Guilherme , de Souza Sandro José 
Published: October 2018

AbstractNon-coding RNAs (ncRNA) have an essential role in the complex landscape of human genetic regulatory networks. One area that is poorly explored is the effect of genetic variations on the interaction between ncRNA and their targets. By integrating a significant amount of public data, the present study cataloged the vast landscape of the regulatory effect of microRNAs (miRNA) and long intergenic noncoding RNAs (lincRNA) in the human genome. An expression quantitative trait loci (eQTL) analysis was used to identify genetic variants associated with miRNA and lincRNA and whose genotypes affect gene expression. Association networks were built for eQTL associated to traits of clinical and/or pharmacological relevance.
Tumor DNA-dependent protein kinase catalytic subunit expression is associated with hepatitis B surface antigen status and tumor progression in patients with hepatocellular carcinoma
Authors: Shimizu Takayuki , Aoki Taku , Mori Shozo , Iso Yukihiro , Kato Masato , Ishizuka Mitsuru , Kubota Keiichi 
Published: October 2018

AbstractThe DNA-dependent protein kinase catalytic subunit (DNA-PKcs), which plays an important role in the DNA damage response, has been reported to be associated with tumor progression in various carcinomas. However, the clinical significance of DNA-PKcs in hepatocellular carcinoma (HCC) patients remains unclear. In the present study, we determined the tumor expression of DNA-PKcs in 104 resected HCC specimens by immunohistochemistry. The DNA-PKcs expression was scored as follows; 0, negative staining; 1, staining of nuclei at the tumor edge; 2, staining of the nuclei deep within the tumor and/or the tumor cytoplasm. The relationships between tumor expression of DNA-PKcs and the clinical characteristics and patient outcomes were investigated. Among the 104 HCCs, the distribution of staining for DNA-PKcs was as follows: 32 tumors were assigned a score of 0, 27 tumors were assigned a score of 1, and 45 tumors were assigned a score of 2. Statistical analyses revealed that tumor DNA-PKcs expression was significantly associated with the HBs antigen (HBsAg) status, presence/absence of portal vein invasion, size of the largest tumor nodule (<3.0 cm/>3.0, cm), and the serum alpha-fetoprotein level. Significant differences in the overall survival and recurrence-free survival were observed between patients showing (staining score 1 or 2) and not showing (staining score 0) tumor DNA-PKcs expression (P = 0.049 and P = 0.045, respectively). Our results suggest that tumor expression of DNA-PKcs is associated with tumor progression, HBsAg status and the postoperative outcomes in patients with HCC.
Simultaneous evaluation of anti-EGFR-induced tumour and adverse skin effects in a microfluidic human 3D co-culture model
Authors: Hübner Juliane , Raschke Marian , Rütschle Isabel , Gräßle Sarah , Hasenberg Tobias , Schirrmann Kerstin , Lorenz Alexandra , Schnurre Susanne , Lauster Roland , Maschmeyer Ilka , Steger-Hartmann Thomas , Marx Uwe 
Published: October 2018

AbstractAntibody therapies targeting the epithelial growth factor receptor (EGFR) are being increasingly applied in cancer therapy. However, increased tumour containment correlates proportionally with the severity of well-known adverse events in skin. The prediction of the latter is not currently possible in conventional in vitro systems and limited in existing laboratory animal models. Here we established a repeated dose “safficacy” test assay for the simultaneous generation of safety and efficacy data. Therefore, a commercially available multi-organ chip platform connecting two organ culture compartments was adapted for the microfluidic co-culture of human H292 lung cancer microtissues and human full-thickness skin equivalents. Repeated dose treatment of the anti-EGFR-antibody cetuximab showed an increased pro-apoptotic related gene expression in the tumour microtissues. Simultaneously, proliferative keratinocytes in the basal layer of the skin microtissues were eliminated, demonstrating crucial inhibitory effects on the physiological skin cell turnover. Furthermore, antibody exposure modulated the release of CXCL8 and CXCL10, reflecting the pattern changes seen in antibody-treated patients. The combination of a metastatic tumour environment with a miniaturized healthy organotypic human skin equivalent make this “safficacy” assay an ideal tool for evaluation of the therapeutic index of EGFR inhibitors and other promising oncology candidates.
Losing half the conductive area hardly impacts the water status of mature trees
Authors: Dietrich Lars , Hoch Günter , Kahmen Ansgar , Körner Christian 
Published: October 2018

AbstractThe water status of transpiring tree crowns depends on a hydraulic continuum from the soil matrix around roots to the sub-stomatal cavity of leaves, with a multitude of hydraulic resistances along this path. Although the stem xylem path may not be the most critical of these resistances, it had been suggested that a >50% interruption of that path by drought-stress-induced embolization (air filling) of conduits is critical for tree survival. Here we show that cutting the sapwood of mature, 35 m tall trees in half hardly affects crown water status and transpiration. Counter expectation, this first adult tree sapwood interception experiment revealed that shoot water potential in the canopy (assessed by using a 45 m canopy crane) either remained unaffected (spruce) or became less negative (beech), associated with small reductions in leaf diffusive conductance for water vapour. We conclude that the stem xylem of these trees has a large overcapacity and the tree hydraulics debate requires a critical re-visitation.
Towards epitaxial graphene p-n junctions as electrically programmable quantum resistance standards
Authors: Hu Jiuning , Rigosi Albert F. , Kruskopf Mattias , Yang Yanfei , Wu Bi-Yi , Tian Jifa , Panna Alireza R. , Lee Hsin-Yen , Payagala Shamith U. , Jones George R. , Kraft Marlin E. , Jarrett Dean G. , Watanabe Kenji , Taniguchi Takashi , Elmquist Randolph E. , Newell David B. 
Published: October 2018

AbstractWe report the fabrication and measurement of top gated epitaxial graphene p-n junctions where exfoliated hexagonal boron nitride (h-BN) is used as the gate dielectric. The four-terminal longitudinal resistance across a single junction is well quantized at the von Klitzing constant $${{\boldsymbol{R}}}_{{\boldsymbol{K}}}$$

R

K

with a relative uncertainty of 10−7. After the exploration of numerous parameter spaces, we summarize the conditions upon which these devices could function as potential resistance standards. Furthermore, we offer designs of programmable electrical resistance standards over six orders of magnitude by using external gating.
Molecular signalling towards mitochondrial breakdown is enhanced in skeletal muscle of patients with chronic obstructive pulmonary disease (COPD)
Authors: Leermakers P. A. , Schols A. M. W. J. , Kneppers A. E. M. , Kelders M. C. J. M. , de Theije C. C. , Lainscak M. , Gosker H. R. 
Published: October 2018

AbstractLoss of skeletal muscle mitochondrial oxidative capacity is well-established in patients with COPD, but the role of mitochondrial breakdown herein is largely unexplored. Currently, we studied if mitochondrial breakdown signalling is increased in skeletal muscle of COPD patients and associates with the loss of mitochondrial content, and whether it is affected in patients with iron deficiency (ID) or systemic inflammation. Therefore, mitophagy, autophagy, mitochondrial dynamics and content markers were analysed in vastus lateralis biopsies of COPD patients (N = 95, FEV1% predicted: 39.0 [31.0–53.6]) and healthy controls (N = 15, FEV1% predicted: 112.8 [107.5–125.5]). Sub-analyses were performed on patients stratified by ID or C-reactive protein (CRP). Compared with controls, COPD patients had lower muscle mitochondrial content, higher BNIP3L and lower FUNDC1 protein, and higher Parkin protein and gene-expression. BNIP3L and Parkin protein levels inversely correlated with mtDNA/gDNA ratio and FEV1% predicted. ID-COPD patients had lower BNIP3L protein and higher BNIP3 gene-expression, while high CRP patients had higher BNIP3 and autophagy-related protein levels. In conclusion, our data indicates that mitochondrial breakdown signalling is increased in skeletal muscle of COPD patients, and is related to disease severity and loss of mitochondrial content. Moreover, systemic inflammation is associated with higher BNIP3 and autophagy-related protein levels.
Shockwave phenomena in an inhibited gas‐to‐liquid hydrocarbon transformer oil under lightning impulse voltages
Authors: Lu Wu , Li Feng , Gao Yuan , Zhao Wenbin 
Published: October 2018

Gas‐to‐liquid (GTL) transformer oil is increasingly considered as an alternative to conventional mineral oils, due to its consistent performance, high purity and essentially free of sulphur. This high interest has led to growing research attention on streamer and breakdown performance of GTL oil. A large effort has been made to characterise the streamer phenomena of GTL oil. However, the secondary effect of shockwaves, which are produced synchronously with the propagation of streamers, is not well studied. Shockwave phenomena in a GTL oil under standard lightning impulse voltages were studied using a 10 mm point‐plane gap and the Schlieren photograph technology. Shockwave propagation velocity and shape were measured in order to quantitatively describe the pressure profiles inside the streamer channels.
Pumped energy storage system technology and its AC–DC interface topology, modelling and control analysis: a review
Authors: Bitew Girmaw Teshager , Han Minxiao , Mekonnen Sifrash A. , Patrobers Simiyu , Khan Zmarrak W. , Tuan Luu K. 
Published: October 2018

Pumped‐storage hydropower plants can contribute to a better integration of intermittent renewable energy and to balance generation and demand in real time by providing rapid response generation. The utilisation of variable‐speed pump‐turbine units with a doubly fed induction machine is being progressively applied due to its overall efficiency and high level of operating flexibility. This study presents state‐of‐the‐art pumped energy storage system technology and its AC–DC interface topology, modelling, simulation and control analysis. It also provides information on the existing global capacities, technological development, topologies and control strategies of the pumped‐storage system. This report also outlines the analysis of dynamic performances of the system. It also attempts to recommend the future works in this area. This study concludes that pumped storage is the most suitable technology for small autonomous island grids and massive energy storage, where the energy efficiency of pumped storage varies in practice. Around the world, the size of the pumped‐storage plant mostly lies in the range of a small size to 3060 MW. The back‐to‐back voltage source converter topology is mostly conducted due to its significant features. Due to its imperative features, the vector control strategy is widely used. The pumped‐storage plant is dedicated to power management and stability regulation of grid and isolated power systems.
Power conditioning system control strategy for cascaded H‐bridge converter battery energy storage system
Authors: Hasabelrasul Hashim , Yan Xiangwu , Gadalla Abuzaid Saeed 
Published: October 2018

Large capability for a cascaded H‐bridge converter battery energy storage system is one of the effective tools to solve the grid‐connection problem of renewable energy resource such as large‐scale wind farm. The power conditioning system (PCS) control strategy is used proportional‐resonant regulator to implement the control with decoupled current control for instantaneous power. The balancing control of the state of charge (SOC) is divided into individual balancing control between bridges is implemented by means of the proportional controller and cluster control between three phases is based on the zero‐sequence‐voltage injection. The system designed in high‐power medium voltage 6.6 kV combining 30 LiFePO4 (lithium iron phosphate) battery units with cascaded H‐bridge multilevel inverter. The simulation results of SOC balancing control was carried out. As a result, a steady‐state error of PCS can be smaller and three‐phase output power balancing has been achieved, thus, a system simulation model has verified the effectiveness of control strategy. The waveforms of PCS in quadrant operation show voltage and current at active power 1 MW.