bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced photoelectrochemical aptasensing platform for TXNDC5 gene based on exciton energy transfer between NCQDs and TiO2 nanorods
Authors: Pang Xuehui , Wang Lin , Ma Hongmin , Zhang Yong , Pan Jihong , Chen Yao , Du Bin , Wei Qin 
Published: January 2016

AbstractThe over expression of thioredoxin domain-containing protein 5 (TXNDC5) can promote the growth of castration-resistant prostate cancer (CRPC). A novel highly sensitive photoelectrochemical (PEC) aptsensor was developed for the detection of TXNDC5 by using the nanohybrids (TiO2 NRs/NCQDs) of nitrogen-doped carbon quantum dots (NCQDs) and TiO2 nanorods as the photo-to-electron conversion medium. TiO2 NRs/NCQDs nanohybrids were prepared by controlling the experimental condition. TiO2 NRs were self-assembled to form the nanopores with good photocurrent conversion efficiency. NCQDs possessed carboxyl groups (−COOH) and amino groups (−NH2) in the preparation process. −COOH and −NH2 groups played important roles for anchoring the capture probes (5′ primer and 3′ primer) through covalent binding. The ultrasensitive and stable detection for TXNDC5 was achieved by the specific recognition between the capture probes and the targets. The fabricated aptsensor showed excellent performance with a wide linear range (0.5 fmol/L ∼ 10 nmol/L) and a low detection limit of 0.1 fmol/L. This kind of aptsensor would provide a potential application for TXNDC5.
Interferon-gamma improves impaired dentinogenic and immunosuppressive functions of irreversible pulpitis-derived human dental pulp stem cells
Authors: Sonoda Soichiro , Yamaza Haruyoshi , Ma Lan , Tanaka Yosuke , Tomoda Erika , Aijima Reona , Nonaka Kazuaki , Kukita Toshio , Shi Songtao , Nishimura Fusanori , Yamaza Takayoshi 
Published: January 2016

AbstractClinically, irreversible pulpitis is treated by the complete removal of pulp tissue followed by replacement with artificial materials. There is considered to be a high potential for autologous transplantation of human dental pulp stem cells (DPSCs) in endodontic treatment. The usefulness of DPSCs isolated from healthy teeth is limited. However, DPSCs isolated from diseased teeth with irreversible pulpitis (IP-DPSCs) are considered to be suitable for dentin/pulp regeneration. In this study, we examined the stem cell potency of IP-DPSCs. In comparison with healthy DPSCs, IP-DPSCs expressed lower colony-forming capacity, population-doubling rate, cell proliferation, multipotency, in vivo dentin regeneration and immunosuppressive activity, suggesting that intact IP-DPSCs may be inadequate for dentin/pulp regeneration. Therefore, we attempted to improve the impaired in vivo dentin regeneration and in vitro immunosuppressive functions of IP-DPSCs to enable dentin/pulp regeneration. Interferon gamma (IFN-γ) treatment enhanced in vivo dentin regeneration and in vitro T cell suppression of IP-DPSCs, whereas treatment with tumor necrosis factor alpha did not. Therefore, these findings suggest that IFN-γ may be a feasible modulator to improve the functions of impaired IP-DPSCs, suggesting that autologous transplantation of IFN-γ-accelerated IP-DPSCs might be a promising new therapeutic strategy for dentin/pulp tissue engineering in future endodontic treatment.
dbEM: A database of epigenetic modifiers curated from cancerous and normal genomes
Authors: Singh Nanda Jagpreet , Kumar Rahul , Raghava Gajendra P. S. 
Published: January 2016

AbstractWe have developed a database called dbEM (database of Epigenetic Modifiers) to maintain the genomic information of about 167 epigenetic modifiers/proteins, which are considered as potential cancer targets. In dbEM, modifiers are classified on functional basis and comprise of 48 histone methyl transferases, 33 chromatin remodelers and 31 histone demethylases. dbEM maintains the genomic information like mutations, copy number variation and gene expression in thousands of tumor samples, cancer cell lines and healthy samples. This information is obtained from public resources viz. COSMIC, CCLE and 1000-genome project. Gene essentiality data retrieved from COLT database further highlights the importance of various epigenetic proteins for cancer survival. We have also reported the sequence profiles, tertiary structures and post-translational modifications of these epigenetic proteins in cancer. It also contains information of 54 drug molecules against different epigenetic proteins. A wide range of tools have been integrated in dbEM e.g. Search, BLAST, Alignment and Profile based prediction. In our analysis, we found that epigenetic proteins DNMT3A, HDAC2, KDM6A and TET2 are highly mutated in variety of cancers. We are confident that dbEM will be very useful in cancer research particularly in the field of epigenetic proteins based cancer therapeutics. This database is available for public at URL: http://crdd.osdd.net/raghava/dbem.
Development of a luminescent G-quadruplex-selective iridium(III) complex for the label-free detection of adenosine
Authors: Lu Lihua , Zhong Hai-Jing , He Bingyong , Leung Chung-Hang , Ma Dik-Lung 
Published: January 2016

AbstractA panel of six luminescent iridium(III) complexes were synthesized and evaluated for their ability to act as G-quadruplex-selective probes. The novel iridium(III) complex 1 was found to be highly selective for G-quadruplex DNA and was employed for the construction of a label-free G-quadruplex-based adenosine detection assay in aqueous solution. Two different detection strategies were investigated for adenosine detection and the results showed that initial addition of adenosine to the adenosine aptamer gave superior results. The assay exhibited a linear response for adenosine in the concentration range of 5 to 120 μM (R2 = 0.992) and the limit of detection for adenosine was 5 μM. Moreover, this assay was highly selective for adenosine over other nucleosides and exhibited potential use for biological sample analysis.
Isolation of highly enriched primary human microglia for functional studies
Authors: Rustenhoven Justin , Park Thomas I-H , Schweder Patrick , Scotter John , Correia Jason , Smith Amy M. , Gibbons Hannah M. , Oldfield Robyn L. , Bergin Peter S. , Mee Edward W. , Faull Richard L. M. , Curtis Maurice A. , Scott Graham E. , Dragunow Mike 
Published: January 2016

AbstractMicroglia, the resident macrophages of the central nervous system play vital roles in brain homeostasis through clearance of pathogenic material. Microglia are also implicated in neurological disorders through uncontrolled activation and inflammatory responses. To date, the vast majority of microglial studies have been performed using rodent models. Human microglia differ from rodent counterparts in several aspects including their response to pharmacological substances and their inflammatory secretions. Such differences highlight the need for studies on primary adult human brain microglia and methods to isolate them are therefore required. Our procedure generates microglial cultures of >95% purity from both biopsy and autopsy human brain tissue using a very simple media-based culture procedure that takes advantage of the adherent properties of these cells. Microglia obtained in this manner can be utilised for research within a week. Isolated microglia demonstrate phagocytic ability and respond to inflammatory stimuli and their purity makes them suitable for numerous other forms of in vitro studies, including secretome and transcriptome analysis. Furthermore, this protocol allows for the simultaneous isolation of neural precursor cells during the microglial isolation procedure. As human brain tissue is such a precious and valuable resource the simultaneous isolation of multiple cell types is highly beneficial.
Evidencing the existence of exciting half-metallicity in two-dimensional TiCl3 and VCl3 sheets
Authors: Zhou Yungang , Lu Haifeng , Zu Xiaotao , Gao Fei 
Published: January 2016

AbstractHalf-metallicity combined with wide half-metallic gap, unique ferromagnetic character and high Curie temperature has become a key driving force to develop next-generation spintronic devices. In previous studies, such half-metallicity always occurred under certain manipulation. Here, we, via examining a series of two-dimensional transition-metal trichlorides, evidenced that TiCl3 and VCl3 sheets could display exciting half-metallicity without involving any external modification. Calculated half-metallic band-gaps for TiCl3 and VCl3 sheets are about 0.60 and 1.10 eV, respectively. Magnetic coupled calculation shows that both sheets favor the ferromagnetic order with a substantial collective character. Estimated Curie temperatures can be up to 376 and 425 K for TiCl3 and VCl3 sheets, respectively. All of these results successfully disclose two new promising two-dimensional half-metallic materials toward the application of next-generation paper-like spintronic devices.
Ion-beam assisted laser fabrication of sensing plasmonic nanostructures
Authors: Kuchmizhak Aleksandr , Gurbatov Stanislav , Vitrik Oleg , Kulchin Yuri , Milichko Valentin , Makarov Sergey , Kudryashov Sergey 
Published: January 2016

AbstractSimple high-performance, two-stage hybrid technique was developed for fabrication of different plasmonic nanostructures, including nanorods, nanorings, as well as more complex structures on glass substrates. In this technique, a thin noble-metal film on a dielectric substrate is irradiated by a single tightly focused nanosecond laser pulse and then the modified region is slowly polished by an accelerated argon ion (Ar+) beam. As a result, each nanosecond laser pulse locally modifies the initial metal film through initiation of fast melting and subsequent hydrodynamic processes, while the following Ar+-ion polishing removes the rest of the film, revealing the hidden topography features and fabricating separate plasmonic structures on the glass substrate. We demonstrate that the shape and lateral size of the resulting functional plasmonic nanostructures depend on the laser pulse energy and metal film thickness, while subsequent Ar+-ion polishing enables to vary height of the resulting nanostructures. Plasmonic properties of the fabricated nanostructures were characterized by dark-field micro-spectroscopy, Raman and photoluminescence measurements performed on single nanofeatures, as well as by supporting numerical calculations of the related electromagnetic near-fields and Purcell factors. The developed simple two-stage technique represents a new step towards direct large-scale laser-induced fabrication of highly ordered arrays of complex plasmonic nanostructures.
Squalene epoxidase is a bona fide oncogene by amplification with clinical relevance in breast cancer
Authors: Brown David N. , Caffa Irene , Cirmena Gabriella , Piras Daniela , Garuti Anna , Gallo Maurizio , Alberti Saverio , Nencioni Alessio , Ballestrero Alberto , Zoppoli Gabriele 
Published: January 2016

AbstractSQLEencodes squalene epoxidase, a key enzyme in cholesterol synthesis.SQLEhas sporadically been reported among copy-number driven transcripts in multi-omics cancer projects. Yet, its functional relevance has never been subjected to systematic analyses. Here, we assessed the correlation ofSQLEcopy number (CN) and gene expression (GE) across multiple cancer types, focusing on the clinico-pathological associations in breast cancer (BC). We then investigated whether any biological effect of SQLE inhibition could be observed in BC cell line models. Breast, ovarian and colorectal cancers showed the highest CN driven GE among 8,783 cases from 22 cancer types, with BC presenting the strongest one.SQLEoverexpression was more prevalent in aggressive BC and was an independent prognostic factor of unfavorable outcome. Through SQLE pharmacological inhibition and silencing in a panel of BC cell lines portraying the diversity ofSQLECN and GE, we demonstrated that SQLE inhibition resulted in a copy-dosage correlated decrease in cell viability and in a noticeable increase in replication time, only in lines with detectableSQLEtranscript. Altogether, our results pinpointSQLEas abona fidemetabolic oncogene by amplification and as a therapeutic target in BC. These findings could have implications in other cancer types.
Adiponectin-derived active peptide ADP355 exerts anti-inflammatory and anti-fibrotic activities in thioacetamide-induced liver injury
Authors: Wang Huafeng , Zhang Huan , Zhang Zimu , Huang Biao , Cheng Xixi , Wang Dan , la Gahu Zha , Xue Zhenyi , Da Yurong , Li Daiqing , Yao Zhi , Gao Fei , Xu Aimin , Zhang Rongxin 
Published: January 2016

AbstractAdiponectin is an adipocyte-derived circulating protein with beneficial effects on injured livers. Adiponectin-deficient (adipo(−/−)) mice develop enhanced liver fibrosis, suggesting that adiponectin could be a therapeutic target for liver injury. In the present study, we investigated the protective role of ADP355, an adiponectin-based active short peptide, in thioacetamide (TAA)-induced acute injury and chronic liver fibrosis in mice. ADP355 remarkably reduced TAA-induced necroinflammation and liver fibrosis. ADP355 treatment increased liver glycogen, decreased serum alanine transaminase and alkaline phosphatase activity and promoted body weight gain, hyper-proliferation and hypo-apoptosis. In addition, ADP355 administration suppressed the TAA-induced activation of hepatic stellate cells and macrophages in the liver. These were associated with the inactivation of TGF-β1/SMAD2 signaling and the promotion of AMPK and STAT3 signaling. Sensitivity of adipo(−/−) mice to chronic liver injury was decreased with ADP355. In conclusion, ADP355 could mimic adiponectin’s action and may be suitable for the preclinical or clinical therapy of chronic liver injury.
Identification and developmental expression profiling of putative alkaloid biosynthetic genes in Corydalis yanhusuo bulbs
Authors: Liao Dengqun , Wang Pengfei , Jia Chan , Sun Peng , Qi Jianjun , Zhou Lili , Li Xian’en 
Published: January 2016

AbstractAlkaloids in bulbs ofCorydalis(C.)yanhusuoare the major pharmacologically active compounds in treatment of blood vessel diseases, tumors and various pains. However, due to the absence of gene sequences inC. yanhusuo, the genes involved in alkaloid biosynthesis and their expression during bulb development remain unknown. We therefore established the first transcriptome database ofC. yanhusuovia Illumina mRNA-Sequencing of a RNA composite sample collected at Bulb initiation (Day 0), early enlargement (Day 10) and maturation (Day 30). 25,013,630 clean 90 bp paired-end reads werede novoassembled into 47,081 unigenes with an average length of 489 bp, among which 30,868 unigenes (65.56%) were annotated in four protein databases. Of 526 putative unigenes involved in biosynthesis o f various alkaloids, 187 were identified as the candidate genes involved in the biosynthesis of benzylisoquinoline alkaloids (BIAs), the only alkaloid type reported inC. yanhusuountill now. BIAs biosynthetic genes were highly upregulated in the overall pathway during bulb development. Identification of alkaloid biosynthetic genes inC. yanhusuoprovide insights on pathways and molecular regulation of alkaloid biosynthesis, to initiate metabolic engineering in order to improve the yield of interesting alkaloids and to identify potentially new alkaloids predicted from the transcriptomic information.
Direct measurement of nonlocal entanglement of two-qubit spin quantum states
Authors: Cheng Liu-Yong , Yang Guo-Hui , Guo Qi , Wang Hong-Fu , Zhang Shou 
Published: January 2016

AbstractWe propose efficient schemes of direct concurrence measurement for two-qubit spin and photon-polarization entangled states via the interaction between single-photon pulses and nitrogen-vacancy (NV) centers in diamond embedded in optical microcavities. For different entangled-state types, diversified quantum devices and operations are designed accordingly. The initial unknown entangled states are possessed by two spatially separated participants and nonlocal spin (polarization) entanglement can be measured with the aid of detection probabilities of photon (NV center) states. This non-demolition entanglement measurement manner makes initial entangled particle-pair avoid complete annihilation but evolve into corresponding maximally entangled states. Moreover, joint inter-qubit operation or global qubit readout is not required for the presented schemes and the final analyses inform favorable performance under the current parameters conditions in laboratory. The unique advantages of spin qubits assure our schemes wide potential applications in spin-based solid quantum information and computation.
Comprehensive Structural Characterization of the Bacterial Homospermidine Synthase–an Essential Enzyme of the Polyamine Metabolism
Authors: Krossa Sebastian , Faust Annette , Ober Dietrich , Scheidig Axel J. 
Published: January 2016

AbstractThe highly conserved bacterial homospermidine synthase (HSS) is a key enzyme of the polyamine metabolism of many proteobacteria including pathogenic strains such as Legionella pneumophila and Pseudomonas aeruginosa; The unique usage of NAD(H) as a prosthetic group is a common feature of bacterial HSS, eukaryotic HSS and deoxyhypusine synthase (DHS). The structure of the bacterial enzyme does not possess a lysine residue in the active center and thus does not form an enzyme-substrate Schiff base intermediate as observed for the DHS. In contrast to the DHS the active site is not formed by the interface of two subunits but resides within one subunit of the bacterial HSS. Crystal structures of Blastochloris viridis HSS (BvHSS) reveal two distinct substrate binding sites, one of which is highly specific for putrescine. BvHSS features a side pocket in the direct vicinity of the active site formed by conserved amino acids and a potential substrate discrimination, guiding and sensing mechanism. The proposed reaction steps for the catalysis of BvHSS emphasize cation-π interaction through a conserved Trp residue as a key stabilizer of high energetic transition states.
Magnetic MoS2 pizzas and sandwiches with Mnn (n = 1–4) cluster toppings and fillings: A first-principles investigation
Authors: Zhang Meng , Huang Zhongjia , Wang Xiao , Zhang Hongyu , Li Taohai , Wu Zhaolong , Luo Youhua , Cao Wei 
Published: January 2016

AbstractThe inorganic layered crystal (ILC) MoS2 in low dimensions is considered as one of the most promising and efficient semiconductors. To enable the magnetism and keep intrinsic crystal structures, we carried out a first-principles study of the magnetic and semiconductive monolayer MoS2 adsorbed with the Mnn (n = 1–4) clusters and bilayer MoS2 intercalated with the same clusters. Geometric optimizations of the Mnn@MoS2 systems show the complexes prefer to have Mnn@MoS2(M) pizza and Mnn@MoS2(B) sandwich forms in the mono- and bi-layered cases, respectively. Introductions of the clusters will enhance complex stabilities, while bonds and charge transfers are found between external Mn clusters and the S atoms in the hosts. The pizzas have medium magnetic moments of 3, 6, 9, 4 μB and sandwiches of 3, 2, 3, 2 μB following the manganese numbers. The pizzas and sandwiches are semiconductors, but with narrower bandgaps compared to their corresponding pristine hosts. Direct bandgaps were found in the Mnn@MoS2(M) (n = 1,4) pizzas and excitingly in the Mn1@MoS2(B) sandwich. Combining functional clusters to the layered hosts, the present work shows a novel material manipulation strategy to boost semiconductive ILCs applications in magnetics.
Auranofin-loaded nanoparticles as a new therapeutic tool to fight streptococcal infections
Authors: Díez-Martínez Roberto , García-Fernández Esther , Manzano Miguel , Martínez Ángel , Domenech Mirian , Vallet-Regí María , García Pedro 
Published: January 2016

AbstractDrug-loaded nanoparticles (NPs) can improve infection treatment by ensuring drug concentration at the right place within the therapeutic window. Poly(lactic-co-glycolic acid) (PLGA) NPs are able to enhance drug localization in target site and to sustainably release the entrapped molecule, reducing the secondary effects caused by systemic antibiotic administration. We have loaded auranofin, a gold compound traditionally used for treatment of rheumatoid arthritis, into PLGA NPs and their efficiency as antibacterial agent against two Gram-positive pathogens, Streptococcus pneumoniae and Streptococcus pyogenes was evaluated. Auranofin-PLGA NPs showed a strong bactericidal effect as cultures of multiresistant pneumococcal strains were practically sterilized after 6 h of treatment with such auranofin-NPs at 0.25 μM. Moreover, this potent bactericidal effect was also observed in S. pneumoniae and S. pyogenes biofilms, where the same concentration of auranofin-NPs was capable of decreasing the bacterial population about 4 logs more than free auranofin. These results were validated using a zebrafish embryo model demonstrating that treatment with auranofin loaded into NPs achieved a noticeable survival against pneumococcal infections. All these approaches displayed a clear superiority of loaded auranofin PLGA nanocarriers compared to free administration of the drug, which supports their potential application for the treatment of streptococcal infections.
On-chip integratable all-optical quantizer using strong cross-phase modulation in a silicon-organic hybrid slot waveguide
Authors: Kang Zhe , Yuan Jinhui , Zhang Xianting , Sang Xinzhu , Wang Kuiru , Wu Qiang , Yan Binbin , Li Feng , Zhou Xian , Zhong Kangping , Zhou Guiyao , Yu Chongxiu , Farrell Gerald , Lu Chao , Yaw Tam Hwa , Wai P. K. A. 
Published: January 2016

AbstractHigh performance all-optical quantizer based on silicon waveguide is believed to have significant applications in photonic integratable optical communication links, optical interconnection networks and real-time signal processing systems. In this paper, we propose an integratable all-optical quantizer for on-chip and low power consumption all-optical analog-to-digital converters. The quantization is realized by the strong cross-phase modulation and interference in a silicon-organic hybrid (SOH) slot waveguide based Mach-Zehnder interferometer. By carefully designing the dimension of the SOH waveguide, large nonlinear coefficients up to 16,000 and 18,069 W−1/m for the pump and probe signals can be obtained respectively, along with a low pulse walk-off parameter of 66.7 fs/mm and all-normal dispersion in the wavelength regime considered. Simulation results show that the phase shift of the probe signal can reach 8π at a low pump pulse peak power of 206 mW and propagation length of 5 mm such that a 4-bit all-optical quantizer can be realized. The corresponding signal-to-noise ratio is 23.42 dB and effective number of bit is 3.89-bit.