bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection, Characterization and Application of Artificial DNA Aptamer Containing Appended Bases with Sub-nanomolar Affinity for a Salivary Biomarker
Authors: Minagawa Hirotaka , Onodera Kentaro , Fujita Hiroto , Sakamoto Taiichi , Akitomi Joe , Kaneko Naoto , Shiratori Ikuo , Kuwahara Masayasu , Horii Katsunori , Waga Iwao 
Published: March 2017

AbstractWe have attained a chemically modified DNA aptamer against salivary α-amylase (sAA), which attracts researchers’ attention as a useful biomarker for assessing human psychobiological and social behavioural processes, although high affinity aptamers have not been isolated from a random natural DNA library to date. For the selection, we used the base-appended base (BAB) modification, that is, a modified-base DNA library containing (E)-5-(2-(N-(2-(N6-adeninyl)ethyl))carbamylvinyl)-uracil in place of thymine. After eight rounds of selection, a 75 mer aptamer, AMYm1, which binds to sAA with extremely high affinity (Kd < 1 nM), was isolated. Furthermore, we have successfully determined the 36-mer minimum fragment, AMYm1-3, which retains target binding activity comparable to the full-length AMYm1, by surface plasmon resonance assays. Nuclear magnetic resonance spectral analysis indicated that the minimum fragment forms a specific stable conformation, whereas the predicted secondary structures were suggested to be disordered forms. Thus, DNA libraries with BAB-modifications can achieve more diverse conformations for fitness to various targets compared with natural DNA libraries, which is an important advantage for aptamer development. Furthermore, using AMYm1, a capillary gel electrophoresis assay and lateral flow assay with human saliva were conducted, and its feasibility was demonstrated.
REST is a crucial regulator for acquiring EMT-like and stemness phenotypes in hormone-refractory prostate cancer
Authors: Chang Yi-Ting , Lin Tzu-Ping , Campbell Mel , Pan Chin-Chen , Lee Shu-Hui , Lee Hsin-Chen , Yang Muh-Hwa , Kung Hsing-Jien , Chang Pei-Ching 
Published: March 2017

AbstractCastration-resistance prostate cancer (CRPC), also known as hormone-refractory prostate cancer (HRPC), requires immediate attention since it is not only resistant to androgen ablation, chemo- and radiotherapy, but also highly metastatic. Increasing evidence suggests that enrichment of neuroendocrine (NE) cells is associated with CRPC. Here, combined RNA-seq and ChIP-seq analysis reveals that REST is involved in epithelial-mesenchymal transition (EMT) and stemness acquisition in NE differentiated prostate cancer (PCa) cells via direct transcriptional repression of Twist1 and CD44. Specifically we show that short-term knockdown of REST induces NE differentiation of LNCaP cells. Long-term REST knockdown enhanced the expression of Twist1 and CD44, cell migration and sphere formation. Overexpression of REST in hormone-refractory CWR22Rv1 PCa cells significantly reduces Twist1 and CD44 expression, cell migration and sphere formation. Collectively, our study uncovers REST in regulating EMT and stemness properties of NE PCa cells and suggests that REST is a potential therapeutic target for CRPC.
Chitosan-coated mesoporous MIL-100(Fe) nanoparticles as improved bio-compatible oral nanocarriers
Authors: Hidalgo T. , Giménez-Marqués M. , Bellido E. , Avila J. , Asensio M. C. , Salles F. , Lozano M. V. , Guillevic M. , Simón-Vázquez R. , González-Fernández A. , Serre C. , Alonso M. J. , Horcajada P. 
Published: March 2017

AbstractNanometric biocompatible Metal-Organic Frameworks (nanoMOFs) are promising candidates for drug delivery. Up to now, most studies have targeted the intravenous route, related to pain and severe complications; whereas nanoMOFs for oral administration, a commonly used non-invasive and simpler route, remains however unexplored. We propose here the biofriendly preparation of a suitable oral nanocarrier based on the benchmarked biocompatible mesoporous iron(III) trimesate nanoparticles coated with the bioadhesive polysaccharide chitosan (CS). This method does not hamper the textural/structural properties and the sorption/release abilities of the nanoMOFs upon surface engineering. The interaction between the CS and the nanoparticles has been characterized through a combination of high resolution soft X-ray absorption and computing simulation, while the positive impact of the coating on the colloidal and chemical stability under oral simulated conditions is here demonstrated. Finally, the intestinal barrier bypass capability and biocompatibility of CS-coated nanoMOF have been assessed in vitro, leading to an increased intestinal permeability with respect to the non-coated material, maintaining an optimal biocompatibility. In conclusion, the preservation of the interesting physicochemical features of the CS-coated nanoMOF and their adapted colloidal stability and progressive biodegradation, together with their improved intestinal barrier bypass, make these nanoparticles a promising oral nanocarrier.
Scale effect of slip boundary condition at solid–liquid interface
Authors: Nagayama Gyoko , Matsumoto Takenori , Fukushima Kohei , Tsuruta Takaharu 
Published: March 2017

AbstractRapid advances in microelectromechanical systems have stimulated the development of compact devices, which require effective cooling technologies (e.g., microchannel cooling). However, the inconsistencies between experimental and classical theoretical predictions for the liquid flow in microchannel remain unclarified. Given the larger surface/volume ratio of microchannel, the surface effects increase as channel scale decreases. Here we show the scale effect of the boundary condition at the solid–liquid interface on single-phase convective heat transfer characteristics in microchannels. We demonstrate that the deviation from classical theory with a reduction in hydraulic diameters is due to the breakdown of the continuum solid–liquid boundary condition. The forced convective heat transfer characteristics of single-phase laminar flow in a parallel-plate microchannel are investigated. Using the theoretical Poiseuille and Nusselt numbers derived under the slip boundary condition at the solid–liquid interface, we estimate the slip length and thermal slip length at the interface.
High-frequency torsional Alfvén waves as an energy source for coronal heating
Authors: Srivastava Abhishek Kumar , Shetye Juie , Murawski Krzysztof , Doyle John Gerard , Stangalini Marco , Scullion Eamon , Ray Tom , Wójcik Dariusz Patryk , Dwivedi Bhola N. 
Published: March 2017

AbstractThe existence of the Sun’s hot atmosphere and the solar wind acceleration continues to be an outstanding problem in solar-astrophysics. Although magnetohydrodynamic (MHD) modes and dissipation of magnetic energy contribute to heating and the mass cycle of the solar atmosphere, yet direct evidence of such processes often generates debate. Ground-based 1-m Swedish Solar Telescope (SST)/CRISP, Hα 6562.8 Å observations reveal, for the first time, the ubiquitous presence of high frequency (~12–42 mHz) torsional motions in thin spicular-type structures in the chromosphere. We detect numerous oscillating flux tubes on 10 June 2014 between 07:17 UT to 08:08 UT in a quiet-Sun field-of-view of 60” × 60” (1” = 725 km). Stringent numerical model shows that these observations resemble torsional Alfvén waves associated with high frequency drivers which contain a huge amount of energy (~105 W m−2) in the chromosphere. Even after partial reflection from the transition region, a significant amount of energy (~103 W m−2) is transferred onto the overlying corona. We find that oscillating tubes serve as substantial sources of Alfvén wave generation that provide sufficient Poynting flux not only to heat the corona but also to originate the supersonic solar wind.
Yield Optimisation of Hepatitis B Virus Core Particles in E. coli Expression System for Drug Delivery Applications
Authors: Bin Mohamed Suffian Izzat Fahimuddin , Garcia-Maya Mitla , Brown Paul , Bui Tam , Nishimura Yuya , Palermo Amir Rafiq Bin Mohammad Johari , Ogino Chiaki , Kondo Akihiko , Al-Jamal Khuloud T. 
Published: March 2017

AbstractAnE. coliexpression system offers a mean for rapid, high yield and economical production of Hepatitis B Virus core (HBc) particles. However, high-level production of HBc particles in bacteria is demanding and optimisation of HBc particle yield fromE. coliis required to improve laboratory-scale productivity for further drug delivery applications. Production steps involve bacterial culture, protein isolation, denaturation, purification and finally protein assembly. In this study, we describe a modifiedE. colibased method for purifying HBc particles and compare the results with those obtained using a conventional purification method. HBc particle morphology was confirmed by Atomic Force Microscopy (AFM). Protein specificity and secondary structure were confirmed by Western Blot and Circular Dichroism (CD), respectively. The modified method produced ~3-fold higher yield and greater purity of wild type HBc particles than the conventional method. Our results demonstrated that the modified method produce a better yield and purity of HBc particles in anE. coli-expression system, which are fully characterised and suitable to be used for drug delivery applications.
A Predictive Structural Model of the Primate Connectome
Authors: Beul Sarah F. , Barbas Helen , Hilgetag Claus C. 
Published: March 2017

AbstractAnatomical connectivity imposes strong constraints on brain function, but there is no general agreement about principles that govern its organization. Based on extensive quantitative data, we tested the power of three factors to predict connections of the primate cerebral cortex: architectonic similarity (structural model), spatial proximity (distance model) and thickness similarity (thickness model). Architectonic similarity showed the strongest and most consistent influence on connection features. This parameter was strongly associated with the presence or absence of inter-areal connections and when integrated with spatial distance, the factor allowed predicting the existence of projections with very high accuracy. Moreover, architectonic similarity was strongly related to the laminar pattern of projection origins, and the absolute number of cortical connections of an area. By contrast, cortical thickness similarity and distance were not systematically related to connection features. These findings suggest that cortical architecture provides a general organizing principle for connections in the primate brain, providing further support for the well-corroborated structural model.
Cell Type-Specific Epigenomic Analysis Reveals a Uniquely Closed Chromatin Architecture in Mouse Rod Photoreceptors
Authors: Hughes Andrew E. O. , Enright Jennifer M. , Myers Connie A. , Shen Susan Q. , Corbo Joseph C. 
Published: March 2017

AbstractRod photoreceptors are specialized neurons that mediate vision in dim light and are the predominant photoreceptor type in nocturnal mammals. The rods of nocturnal mammals are unique among vertebrate cell types in having an ‘inverted’ nuclear architecture, with a dense mass of heterochromatin in the center of the nucleus rather than dispersed clumps at the periphery. To test if this unique nuclear architecture is correlated with a unique epigenomic landscape, we performed ATAC-seq on mouse rods and their most closely related cell type, cone photoreceptors. We find that thousands of loci are selectively closed in rods relative to cones as well as >60 additional cell types. Furthermore, we find that the open chromatin profile of photoreceptors lacking the rod master regulator Nrl is nearly indistinguishable from that of native cones, indicating that Nrl is required for selective chromatin closure in rods. Finally, we identified distinct enrichments of transcription factor binding sites in rods and cones, revealing key differences in the cis-regulatory grammar of these cell types. Taken together, these data provide insight into the development and maintenance of photoreceptor identity, and highlight rods as an attractive system for studying the relationship between nuclear organization and local changes in gene regulation.
Myofibroblast differentiation and its functional properties are inhibited by nicotine and e-cigarette via mitochondrial OXPHOS complex III
Authors: Lei Wei , Lerner Chad , Sundar Isaac K. , Rahman Irfan 
Published: March 2017

AbstractNicotine is the major stimulant in tobacco products including e-cigarettes. Fibroblast to myofibroblast differentiation is a key process during wound healing and is dysregulated in lung diseases. The role of nicotine and e-cigarette derived nicotine on cellular functions including profibrotic response and other functional aspects is not known. We hypothesized that nicotine and e-cigarettes affect myofibroblast differentiation, gel contraction, and wound healing via mitochondria stress through nicotinic receptor-dependent mechanisms. To test the hypothesis, we exposed human lung fibroblasts with various doses of nicotine and e-cigarette condensate and determined myofibroblast differentiation, mitochondrial oxidative phosphorylation (OXPHOS), wound healing, and gel contraction at different time points. We found that both nicotine and e-cigarette inhibit myofibroblast differentiation as shown by smooth muscle actin and collagen type I, alpha 1 abundance. Nicotine and e-cigarette inhibited OXPHOS complex III accompanied by increased MitoROS, and this effect was augmented by complex III inhibitor antimycin A. These mitochondrial associated effects by nicotine resulted in inhibition of myofibroblast differentiation. These effects were associated with inhibition of wound healing and gel contraction suggesting that nicotine is responsible for dysregulated repair during injurious responses. Thus, our data suggest that nicotine causes dysregulated repair by inhibition of myofibroblast differentiation via OXPHOS pathway.
Effects of RET, NRG1 and NRG3 Polymorphisms in a Chinese Population with Hirschsprung Disease
Authors: Yang Dehua , Yang Jun , Li Shuai , Jiang Meng , Cao Guoqing , Yang Li , Zhang Xi , Zhou Ying , Li Kang , Tang Shao-tao 
Published: March 2017

AbstractThe RET proto-oncogene was identified as a major locus involved in Hirschsprung disease (HSCR). A genome-wide association study (GWAS) and whole exome sequencing identified NRG1 and NRG3 as additional HSCR susceptibility loci. We investigated the effects of RET (rs2506030 and rs2435357), NRG1 (rs2439302, rs16879552 and rs7835688) and NRG3 (rs10748842, rs10883866 and rs6584400) polymorphisms in a Chinese population with HSCR. We assessed single nucleotide polymorphisms (SNPs) in the RET, NRG1 and NRG3 genes in a cohort of 362 sporadic HSCR patients and 1,448 normal controls using a TaqMan genotyping assay. Significant associations were found between HSCR risk and rs2506030, rs2435357, rs2439302 and rs7835688 (odds ratio [OR] 1.64, P = 1.72E-06; 2.97, P = 5.15E-33; 1.84, P = 9.36E-11; and 1.93, P = 1.88E-12, respectively). Two locus analyses of SNPs indicated increased disease risks of HSCR between NRG1 rs2439302 and RET rs2435357 or rs2506030. RET rs2506030 (GG genotype) and rs2435357 (TT genotype), in combination with NRG1 rs2439302 (GG genotype), were strongly associated with the highest risk of HSCR (OR = 56.53, P = 4.50E-07) compared with the two loci or a single SNP of either RET or NRG1. Our results support the association between genetic variation of RET and NRG1 and susceptibility to HSCR in the Chinese population.
Deriving Flood-Mediated Connectivity between River Channels and Floodplains: Data-Driven Approaches
Authors: Zhao Tongtiegang , Shao Quanxi , Zhang Yongyong 
Published: March 2017

AbstractThe flood-mediated connectivity between river channels and floodplains plays a fundamental role in flood hazard mapping and exerts profound ecological effects. The classic nearest neighbor search (NNS) fails to derive this connectivity because of spatial heterogeneity and continuity. We develop two novel data-driven connectivity-deriving approaches, namely, progressive nearest neighbor search (PNNS) and progressive iterative nearest neighbor search (PiNNS). These approaches are illustrated through a case study in Northern Australia. First, PNNS and PiNNS are employed to identify flood pathways on floodplains through forward tracking. That is, progressive search is performed to associate newly inundated cells in each time step to previously inundated cells. In particular, iterations in PiNNS ensure that the connectivity is continuous – the connection between any two cells along the pathway is built through intermediate inundated cells. Second, inundated floodplain cells are collectively connected to river channel cells through backward tracing. Certain river channel sections are identified to connect to a large number of inundated floodplain cells. That is, the floodwater from these sections causes widespread floodplain inundation. Our proposed approaches take advantage of spatial–temporal data. They can be applied to achieve connectivity from hydro-dynamic and remote sensing data and assist in river basin planning and management.
Human eyelid adipose tissue-derived Schwann cells promote regeneration of a transected sciatic nerve
Authors: Wang Gangyang , Cao Lingling , Wang Yang , Hua Yingqi , Cai Zhengdong , Chen Jun , Chen Lulu , Jin Yuqing , Niu Lina , Shen Hua , Lu Yan , Shen Zunli 
Published: March 2017

AbstractSchwann cells (SCs) can promote the regeneration of injured peripheral nerves while the clinical application is limited by donor site complications and the inability to generate an ample amount of cells. In this study, we have isolated human eyelid adipose-derived Schwann cells (hE-SCs) from human eyelid adipose tissue and identified the cell phenotype and function. Using immunofluorescence and H & E staining, we detected subtle nerve fibers and SCs in human eyelid adipose tissue. Immunofluorescence staining indicated that hE-SCs expressed glial markers, such as S100, p75NTR GFAP, Sox10 and Krox20. To explore whether hE-SCs promote the regeneration of injured peripheral nervesin vivo,a Balb/c-nu mice model was used in the study, and mice were randomly assigned to five groups: Matrigel; hE-SCs/P0; hE-SCs/P2; hE-FLCs/P2; and Autograft. After 12 weeks, functional and histological assessments of the regenerated nerves showed that sciatic nerve defect was more effectively repaired in the hE-SCs/P2 group which achieved 66.1 ± 6.5% purity, than the other three groups and recovered to similar level to the Autograft group. These results indicated that hE-SCs can promote the regeneration of injured peripheral nerve and the abundant, easily accessible supply of adipose tissue might be a promising source of SCs for peripheral nerve repair.
Personalized chemotherapy selection for breast cancer using gene expression profiles
Authors: Yu Kaixian , Sang Qing-Xiang Amy , Lung Pei-Yau , Tan Winston , Lively Ty , Sheffield Cedric , Bou-Dargham Mayassa J. , Liu Jun S. , Zhang Jinfeng 
Published: March 2017

AbstractChoosing the optimal chemotherapy regimen is still an unmet medical need for breast cancer patients. In this study, we reanalyzed data from seven independent data sets with totally 1079 breast cancer patients. The patients were treated with three different types of commonly used neoadjuvant chemotherapies: anthracycline alone, anthracycline plus paclitaxel, and anthracycline plus docetaxel. We developed random forest models with variable selection using both genetic and clinical variables to predict the response of a patient using pCR (pathological complete response) as the measure of response. The models were then used to reassign an optimal regimen to each patient to maximize the chance of pCR. An independent validation was performed where each independent study was left out during model building and later used for validation. The expected pCR rates of our method are significantly higher than the rates of the best treatments for all the seven independent studies. A validation study on 21 breast cancer cell lines showed that our prediction agrees with their drug-sensitivity profiles. In conclusion, the new strategy, called PRES (Personalized REgimen Selection), may significantly increase response rates for breast cancer patients, especially those with HER2 and ER negative tumors, who will receive one of the widely-accepted chemotherapy regimens.
Family-based case-control study of homotopic connectivity in first-episode, drug-naive schizophrenia at rest
Authors: Guo Wenbin , Liu Feng , Chen Jindong , Wu Renrong , Li Lehua , Zhang Zhikun , Zhao Jingping 
Published: March 2017

AbstractFamily-based case-control design is rarely used but powerful to reduce the confounding effects of environmental factors on schizophrenia. Twenty-eight first-episode, drug-naive patients with schizophrenia, 28 family-based controls (FBC), and 40 healthy controls (HC) underwent resting-state functional MRI. Voxel-mirrored homotopic connectivity (VMHC), receiver operating characteristic curve (ROC), and support vector machine (SVM) were used to process the data. Compared with the FBC, the patients showed lower VMHC in the precuneus, fusiform gyrus/cerebellum lobule VI, and lingual gyrus/cerebellum lobule VI. The patients exhibited lower VMHC in the precuneus relative to the HC. ROC analysis exhibited that the VMHC values in these brain regions might not be ideal biomarkers to distinguish the patients from the FBC/HC. However, SVM analysis indicated that a combination of VMHC values in the precuneus and lingual gyrus/cerebellum lobule VI might be used as a potential biomarker to distinguish the patients from the FBC with a sensitivity of 96.43%, a specificity of 89.29%, and an accuracy of 92.86%. Results suggested that patients with schizophrenia have decreased homotopic connectivity in the motor and low level sensory processing regions. Neuroimaging studies can adopt family-based case-control design as a viable option to reduce the confounding effects of environmental factors on schizophrenia.
Formation of the 2015 Shenzhen landslide as observed by SAR shape-from-shading
Authors: Wang Chisheng , Li Qingquan , Zhu Jiasong , Gao Wei , Shan Xinjian , Song Jun , Ding Xiaoli 
Published: March 2017

AbstractThe time-series topography change of a landfill site before its failure has rarely been surveyed in detail. However, this information is important for both landfill management and early warning of landslides. Here, we take the 2015 Shenzhen landslide as an example, and we use the radar shape-from-shading (SFS) technique to retrieve time-series digital elevation models of the landfill. The results suggest that the total filling volume reached 4,074,300 m3 in the one and a half years before the landslide, while 2,817,400 m3 slid down in the accident. Meanwhile, the landfill rate in most areas exceeded 2 m/month, which is the empirical upper threshold in landfill engineering. Using topography captured on December 12, 2015, the slope safety analysis gives a factor of safety of 0.932, suggesting that this slope was already hazardous before the landslide. We conclude that the synthetic aperture radar (SAR) SFS technique has the potential to contribute to landfill failure monitoring.