bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular targets of Chinese herbs: a clinical study of hepatoma based on network pharmacology
Authors: Gao Li , Wang Xiao-dong , Niu Yang-yang , Duan Dan-dan , Yang Xue , Hao Jian , Zhu Cui-hong , Chen Dan , Wang Ke-xin , Qin Xue-mei , Wu Xiong-zhi 
Published: May 2016

AbstractTraditional Chinese medicine (TCM) has been used to treat tumors for years and has been demonstrated to be effective. However, the underlying molecular mechanisms of herbs remain unclear. This study aims to ascertain molecular targets of herbs prolonging survival time of patients with advanced hepatocellular carcinoma (HCC) based on network pharmacology, and to establish a research method for accurate treatment of TCM. The survival benefit of TCM treatment with Chinese herbal medicine (CHM) was proved by Kaplan–Meier method and Cox regression analysis among 288 patients. The correlation between herbs and survival time was performed by bivariate correlation analysis. Network pharmacology method was utilized to construct the active ingredient-target networks of herbs that were responsible for the beneficial effects against HCC. Cox regression analysis showed CHM was an independent favorable prognostic factor. The median survival time was 13 months and the 5-year overall survival rates were 2.61% in the TCM group, while there were 6 months, 0 in the non-TCM group. Correlation analysis demonstrated that 8 herbs closely associated with prognosis. Network pharmacology analysis revealed that the 8 herbs regulated multiple HCC relative genes, among which the genes affected proliferation (KRAS, AKT2, MAPK), metastasis (SRC, MMP), angiogenesis (PTGS2) and apoptosis (CASP3) etc.
Spatiotemporal profile of Map2 and microglial changes in the hippocampal CA1 region following pilocarpine-induced status epilepticus
Authors: Schartz Nicole D. , Herr Seth A. , Madsen Lauren , Butts Sarah J. , Torres Ceidy , Mendez Loyda B. , Brewster Amy L. 
Published: May 2016

AbstractStatus epilepticus (SE) triggers pathological changes to hippocampal dendrites that may promote epileptogenesis. The microtubule associated protein 2 (Map2) helps stabilize microtubules of the dendritic cytoskeleton. Recently, we reported a substantial decline in Map2 that coincided with robust microglia accumulation in the CA1 hippocampal region after an episode of SE. A spatial correlation between Map2 loss and reactive microglia was also reported in human cortex from refractory epilepsy. New evidence supports that microglia modulate dendritic structures. Thus, to identify a potential association between SE-induced Map2 and microglial changes, a spatiotemporal profile of these events is necessary. We used immunohistochemistry to determine the distribution of Map2 and the microglia marker IBA1 in the hippocampus after pilocarpine-induced SE from 4 hrs to 35 days. We found a decline in Map2 immunoreactivity in the CA1 area that reached minimal levels at 14 days post-SE and partially increased thereafter. In contrast, maximal microglia accumulation occurred in the CA1 area at 14 days post-SE. Our data indicate that SE-induced Map2 and microglial changes parallel each other’s spatiotemporal profiles. These findings may lay the foundation for future mechanistic studies to help identify potential roles for microglia in the dendritic pathology associated with SE and epilepsy.
Development of Persister-FACSeq: a method to massively parallelize quantification of persister physiology and its heterogeneity
Authors: Henry Theresa C. , Brynildsen Mark P. 
Published: May 2016

AbstractBacterial persisters are thought to underlie the relapse of chronic infections. Knowledge of persister physiology would illuminate avenues for therapeutic intervention; however, such knowledge has remained elusive because persisters have yet to be segregated from other cell types to sufficient purity. This technical hurdle has stymied progress toward understanding persistence. Here we developed Persister-FACSeq, which is a method that uses fluorescence-activated cell sorting, antibiotic tolerance assays and next generation sequencing to interrogate persister physiology and its heterogeneity. As a proof-of-concept, we used Persister-FACSeq on a library of reporters to study gene expression distributions in non-growing Escherichia coli, and found that persistence to ofloxacin is inversely correlated with the capacity of non-growing cells to synthesize protein. Since Persister-FACSeq can be applied to study persistence to any antibiotic in any environment for any bacteria that can harbor a fluorescent reporter, we anticipate that it will yield unprecedented knowledge of this detrimental phenotype.
Microgravity Induction of TRAIL Expression in Preosteoclast Cells Enhances Osteoclast Differentiation
Authors: Sambandam Yuvaraj , Baird Kelsey L. , Stroebel Maxwell , Kowal Emily , Balasubramanian Sundaravadivel , Reddy Sakamuri V. 
Published: May 2016

AbstractEvidence indicates that astronauts experience significant bone loss in space. We previously showed that simulated microgravity (μXg) using the NASA developed rotary cell culture system (RCCS) enhanced bone resorbing osteoclast (OCL) differentiation. However, the mechanism by which μXg increases OCL formation is unclear. RANK/RANKL signaling pathway is critical for OCL differentiation. Tumor necrosis factor-related apoptosis inducing ligand (TRAIL) has been shown to increase osteoclastogenesis. We hypothesize that TRAIL may play an important role in μXg enhanced OCL differentiation. In this study, we identified by RT profiler PCR array screening that μXg induces high levels of TRAIL expression in murine preosteoclast cells in the absence of RANKL stimulation compared to ground based (Xg) cultures. We further identified that μXg elevated the adaptor protein TRAF-6 and fusion genes OC-STAMP and DC-STAMP expression in preosteoclast cells. Interestingly, neutralizing antibody against TRAIL significantly reduced μXg induced OCL formation. We further identified that over-expression of pTRAIL in RAW 264.7 cells enhanced OCL differentiation. These results indicate that TRAIL signaling plays an important role in the μXg increased OCL differentiation. Therefore, inhibition of TRAIL expression could be an effective countermeasure for μXg induced bone loss.
Tissue factor is induced by interleukin-33 in human endothelial cells: a new link between coagulation and inflammation
Authors: Stojkovic Stefan , Kaun Christoph , Basilio Jose , Rauscher Sabine , Hell Lena , Krychtiuk Konstantin A. , Bonstingl Cornelia , de Martin Rainer , Gröger Marion , Ay Cihan , Holnthoner Wolfgang , Eppel Wolfgang , Neumayer Christoph , Huk Ihor , Huber Kurt , Demyanets Svitlana , Wojta Johann 
Published: May 2016

AbstractTissue factor (TF) is the primary trigger of coagulation. Elevated levels of TF are found in atherosclerotic plaques and TF leads to thrombus formation when released upon plaque rupture. Interleukin (IL)-33 was previously shown to induce angiogenesis and inflammatory activation of endothelial cells (ECs). Here, we investigated the impact of IL-33 on TF in human ECs, as a possible new link between inflammation and coagulation. IL-33 induced TF mRNA and protein in human umbilical vein ECs and coronary artery ECs. IL-33-induced TF expression was ST2- and NF-κB-dependent, but IL-1-independent. IL-33 also increased cell surface TF activity in ECs and TF activity in ECs-derived microparticles. IL-33-treated ECs reduced coagulation time of whole blood and plasma but not of factor VII-deficient plasma. In human carotid atherosclerotic plaques (n = 57), TF mRNA positively correlated with IL-33 mRNA expression (r = 0.691, p < 0.001). In this tissue, IL-33 and TF protein was detected in ECs and smooth muscle cells by immunofluorescence. Furthermore, IL-33 and TF protein co-localized at the site of clot formation within microvessels in plaques of patients with symptomatic carotid stenosis. Through induction of TF in ECs, IL-33 could enhance their thrombotic capacity and thereby might impact on thrombus formation in the setting of atherosclerosis.
Exposure to Melan-A/MART-126-35 tumor epitope specific CD8+T cells reveals immune escape by affecting the ubiquitin-proteasome system (UPS)
Authors: Ebstein Frédéric , Keller Martin , Paschen Annette , Walden Peter , Seeger Michael , Bürger Elke , Krüger Elke , Schadendorf Dirk , Kloetzel Peter-M. , Seifert Ulrike 
Published: May 2016

AbstractEfficient processing of target antigens by the ubiquitin-proteasome-system (UPS) is essential for treatment of cancers by T cell therapies. However, immune escape due to altered expression of IFN-γ-inducible components of the antigen presentation machinery and consequent inefficient processing of HLA-dependent tumor epitopes can be one important reason for failure of such therapies. Here, we show that short-term co-culture of Melan-A/MART-1 tumor antigen-expressing melanoma cells with Melan-A/MART-126-35-specific cytotoxic T lymphocytes (CTL) led to resistance against CTL-induced lysis because of impaired Melan-A/MART-126-35 epitope processing. Interestingly, deregulation of p97/VCP expression, which is an IFN-γ-independent component of the UPS and part of the ER-dependent protein degradation pathway (ERAD), was found to be essentially involved in the observed immune escape. In support, our data demonstrate that re-expression of p97/VCP in Melan-A/MART-126-35 CTL-resistant melanoma cells completely restored immune recognition by Melan-A/MART-126-35 CTL. In conclusion, our experiments show that impaired expression of IFN-γ-independent components of the UPS can exert rapid immune evasion of tumor cells and suggest that tumor antigens processed by distinct UPS degradation pathways should be simultaneously targeted in T cell therapies to restrict the likelihood of immune evasion due to impaired antigen processing.
Whole Genome Re-Sequencing Identifies a Quantitative Trait Locus Repressing Carbon Reserve Accumulation during Optimal Growth in Chlamydomonas reinhardtii
Authors: Goold Hugh Douglas , Nguyen Hoa Mai , Kong Fantao , Beyly-Adriano Audrey , Légeret Bertrand , Billon Emmanuelle , Cuiné Stéphan , Beisson Fred , Peltier Gilles , Li-Beisson Yonghua 
Published: May 2016

AbstractMicroalgae have emerged as a promising source for biofuel production. Massive oil and starch accumulation in microalgae is possible, but occurs mostly when biomass growth is impaired. The molecular networks underlying the negative correlation between growth and reserve formation are not known. Thus isolation of strains capable of accumulating carbon reserves during optimal growth would be highly desirable. To this end, we screened an insertional mutant library of Chlamydomonas reinhardtii for alterations in oil content. A mutant accumulating five times more oil and twice more starch than wild-type during optimal growth was isolated and named constitutive oil accumulator 1 (coa1). Growth in photobioreactors under highly controlled conditions revealed that the increase in oil and starch content in coa1 was dependent on light intensity. Genetic analysis and DNA hybridization pointed to a single insertional event responsible for the phenotype. Whole genome re-sequencing identified in coa1 a >200 kb deletion on chromosome 14 containing 41 genes. This study demonstrates that, 1), the generation of algal strains accumulating higher reserve amount without compromising biomass accumulation is feasible; 2), light is an important parameter in phenotypic analysis; and 3), a chromosomal region (Quantitative Trait Locus) acts as suppressor of carbon reserve accumulation during optimal growth.
CPEB1 restrains proliferation of Glioblastoma cells through the regulation of p27Kip1 mRNA translation
Authors: Galardi Silvia , Petretich Massimo , Pinna Guillaume , D’Amico Silvia , Loreni Fabrizio , Michienzi Alessandro , Groisman Irina , Ciafrè Silvia Anna 
Published: May 2016

AbstractThe cytoplasmic element binding protein 1 (CPEB1) regulates many important biological processes ranging from cell cycle control to learning and memory formation, by controlling mRNA translation efficiency via 3′ untranslated regions (3′UTR). In the present study, we show that CPEB1 is significantly downregulated in human Glioblastoma Multiforme (GBM) tissues and that the restoration of its expression impairs glioma cell lines growth. We demonstrate that CPEB1 promotes the expression of the cell cycle inhibitor p27Kip1 by specifically targeting its 3′UTR, and competes with miR-221/222 binding at an overlapping site in the 3′UTR, thus impairing miR-221/222 inhibitory activity. Upon binding to p27Kip1 3′UTR, CPEB1 promotes elongation of poly-A tail and the subsequent translation of p27Kip1 mRNA. This leads to higher levels of p27Kip1 in the cell, in turn significantly inhibiting cell proliferation, and confers to CPEB1 a potential value as a tumor suppressor in Glioblastoma.
Gold@silver bimetal nanoparticles/pyramidal silicon 3D substrate with high reproducibility for high-performance SERS
Authors: Zhang Chao , Jiang Shou Zhen , Yang Cheng , Li Chong Hui , Huo Yan Yan , Liu Xiao Yun , Liu Ai Hua , Wei Qin , Gao Sai Sai , Gao Xing Guo , Man Bao Yuan 
Published: May 2016

AbstractA novel and efficient surface enhanced Raman scattering (SERS) substrate has been presented based on Gold@silver/pyramidal silicon 3D substrate (Au@Ag/3D-Si). By combining the SERS activity of Ag, the chemical stability of Au and the large field enhancement of 3D-Si, the Au@Ag/3D-Si substrate possesses perfect sensitivity, homogeneity, reproducibility and chemical stability. Using R6G as probe molecule, the SERS results imply that the Au@Ag/3D-Si substrate is superior to the 3D-Si, Ag/3D-Si and Au/3D-Si substrate. We also confirmed these excellent behaviors in theory via a commercial COMSOL software. The corresponding experimental and theoretical results indicate that our proposed Au@Ag/3D-Si substrate is expected to develop new opportunities for label-free SERS detections in biological sensors, biomedical diagnostics and food safety.
Ginsenoside Rg1 promotes osteogenic differentiation of rBMSCs and healing of rat tibial fractures through regulation of GR-dependent BMP-2/SMAD signaling
Authors: Gu Yanqing , Zhou Jinchun , Wang Qin , Fan Weimin , Yin Guoyong 
Published: May 2016

AbstractFracture healing is closely related to the number and activity of bone marrow mesenchymal stem cells (BMSCs) near the fracture site. The present study was to investigate the effect of Rg1 on osteogenic differentiation of cultured BMSCs and related mechanisms and on the fracture healing in a fracture model.In vitroexperiments showed that Rg1 promoted the proliferation and osteogenic differentiation of BMSCs. Western blot analyses demonstrated that Rg1 promoted osteogenic differentiation of BMSCs through the glucocorticoid receptor (GR)-dependent BMP-2/Smad signaling pathway.In vivo, X-ray examination showed that callus growth in rats treated with Rg1 was substantially faster than that in control rats after fracture. The results of H&E and Safranin-O/Fast Green staining revealed that, compared with controls, rats in the Rg1 treatment group had a significantly higher proportion of trabecular bone but a much lower proportion of fibers and cartilage components inside the callus. Micro-CT suggested that bone mineral density (BMD), percent bone volume (BV/TV), trabecular number (Tb.N) and trabecular thickness (Tb.Th) were significantly increased in the treatment group, whereas trabecular separation (Tb.Sp) was significantly reduced. Thus, Rg1 promotes osteogenic differentiation by activating the GR/BMP-2 signaling pathway, enhances bone calcification and ultimately accelerates the fracture healing in rats.
Employing Synergetic Effect of Doping and Thin Film Coating to Boost the Performance of Lithium-Ion Battery Cathode Particles
Authors: Patel Rajankumar L. , Jiang Ying-Bing , Choudhury Amitava , Liang Xinhua 
Published: May 2016

AbstractAtomic layer deposition (ALD) has evolved as an important technique to coat conformal protective thin films on cathode and anode particles of lithium ion batteries to enhance their electrochemical performance. Coating a conformal, conductive and optimal ultrathin film on cathode particles has significantly increased the capacity retention and cycle life as demonstrated in our previous work. In this work, we have unearthed the synergetic effect of electrochemically active iron oxide films coating and partial doping of iron on LiMn1.5Ni0.5O4 (LMNO) particles. The ionic Fe penetrates into the lattice structure of LMNO during the ALD process. After the structural defects were saturated, the iron started participating in formation of ultrathin oxide films on LMNO particle surface. Owing to the conductive nature of iron oxide films, with an optimal film thickness of ~0.6 nm, the initial capacity improved by ~25% at room temperature and by ~26% at an elevated temperature of 55 °C at a 1C cycling rate. The synergy of doping of LMNO with iron combined with the conductive and protective nature of the optimal iron oxide film led to a high capacity retention (~93% at room temperature and ~91% at 55 °C) even after 1,000 cycles at a 1C cycling rate.
Cascading failures in coupled networks with both inner-dependency and inter-dependency links
Authors: Liu Run-Ran , Li Ming , Jia Chun-Xiao , Wang Bing-Hong 
Published: May 2016

AbstractWe study the percolation in coupled networks with both inner-dependency and inter-dependency links, where the inner- and inter-dependency links represent the dependencies between nodes in the same or different networks, respectively. We find that when most of dependency links are inner- or inter-ones, the coupled networks system is fragile and makes a discontinuous percolation transition. However, when the numbers of two types of dependency links are close to each other, the system is robust and makes a continuous percolation transition. This indicates that the high density of dependency links could not always lead to a discontinuous percolation transition as the previous studies. More interestingly, although the robustness of the system can be optimized by adjusting the ratio of the two types of dependency links, there exists a critical average degree of the networks for coupled random networks, below which the crossover of the two types of percolation transitions disappears, and the system will always demonstrate a discontinuous percolation transition. We also develop an approach to analyze this model, which is agreement with the simulation results well.
A pseudouridylation switch in rRNA is implicated in ribosome function during the life cycle of Trypanosoma brucei
Authors: Chikne Vaibhav , Doniger Tirza , Rajan K. Shanmugha , Bartok Osnat , Eliaz Dror , Cohen-Chalamish Smadar , Tschudi Christian , Unger Ron , Hashem Yaser , Kadener Sebastian , Michaeli Shulamit 
Published: May 2016

AbstractThe protozoan parasite Trypanosoma brucei, which causes devastating diseases in humans and animals in sub-Saharan Africa, undergoes a complex life cycle between the mammalian host and the blood-feeding tsetse fly vector. However, little is known about how the parasite performs most molecular functions in such different environments. Here, we provide evidence for the intriguing possibility that pseudouridylation of rRNA plays an important role in the capacity of the parasite to transit between the insect midgut and the mammalian bloodstream. Briefly, we mapped pseudouridines (Ψ) on rRNA by Ψ-seq in procyclic form (PCF) and bloodstream form (BSF) trypanosomes. We detected 68 Ψs on rRNA, which are guided by H/ACA small nucleolar RNAs (snoRNA). The small RNome of both life cycle stages was determined by HiSeq and 83 H/ACAs were identified. We observed an elevation of 21 Ψs modifications in BSF as a result of increased levels of the guiding snoRNAs. Overexpression of snoRNAs guiding modification on H69 provided a slight growth advantage to PCF parasites at 30 °C. Interestingly, these modifications are predicted to significantly alter the secondary structure of the large subunit (LSU) rRNA suggesting that hypermodified positions may contribute to the adaption of ribosome function during cycling between the two hosts.
Co-spread of metal and antibiotic resistance within ST3-IncHI2 plasmids from E. coli isolates of food-producing animals
Authors: Fang Liangxing , Li Xingping , Li Liang , Li Shumin , Liao Xiaoping , Sun Jian , Liu Yahong 
Published: May 2016

AbstractConcerns have been raised in recent years regarding co-selection for antibiotic resistance among bacteria exposed to heavy metals, particularly copper and zinc, used as growth promoters for some livestock species. In this study, 25 IncHI2 plasmids harboring oqxAB (20/25)/blaCTX-M (18/25) were found with sizes ranging from ∼260 to ∼350 kb and 22 belonged to the ST3-IncHI2 group. In addition to blaCTX-M and oqxAB, pcoA-E (5/25) and silE-P (5/25), as well as aac(6′)-Ib-cr (18/25), floR (16/25), rmtB (6/25), qnrS1(3/25) and fosA3 (2/25), were also identified on these IncHI2 plasmids. The plasmids carried pco and sil contributed to increasing in the MICs of CuSO4 and AgNO3. The genetic context surrounding the two operons was well conserved except some variations within the pco operon. The ~32 kb region containing the two operons identified in the IncHI2 plasmids was also found in chromosomes of different Enterobacteriaceae species. Further, phylogenetic analysis of this structure showed that Tn7-like transposon might play an important role in cross-genus transfer of the sil and pco operons among Enterobacteriaceae. In conclusion, co-existence of the pco and sil operons, and oqxAB/blaCTX-M as well as other antibiotic resistance genes on IncHI2 plasmids may promote the development of multidrug-resistant bacteria.
Determining the Origin of Half-bandgap-voltage Electroluminescence in Bifunctional Rubrene/C60 Devices
Authors: Chen Qiusong , Jia Weiyao , Chen Lixiang , Yuan De , Zou Yue , Xiong Zuhong 
Published: May 2016

AbstractLowering the driving voltage of organic light-emitting diodes (OLEDs) is an important approach to reduce their energy consumption. We have fabricated a series of bifunctional devices (OLEDs and photovoltaics) using rubrene and fullerene (C60) as the active layer, in which the electroluminescence threshold voltage(~1.1 V) was half the value of the bandgap of rubrene. Magneto-electroluminescence (MEL) response of planner heterojunction diodes exhibited a small increase in response to a low magnetic field strength (<20 mT); however, a very large decay was observed at a high magnetic field strength (>20 mT). When a hole-transport layer with a low mobility was included in these devices, the MEL response reversed in shape and simultaneously, the EL threshold voltage became larger than the bandgap voltage. When bulk heterojunction device was examined, the amplitude of MEL curves presented an anomalous voltage-dependence. Following an analysis of the MEL responses of these devices, we proposed that the EL of half-bandgap-voltage device originated from bimolecular triplet-triplet annihilation in the rubrene film, rather than from singlet excitons that formed via an interface auger recombination. This work provides critical insight into the mechanisms of OLED emission and will help advance the applications of bifunctional devices.