bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coupling a DNA-Based Machine with Glucometer Readouts for Amplified Detection of Telomerase Activity in Cancer Cells
Authors: Wang Wenjing , Huang Shan , Li Jingjing , Rui Kai , Zhang Jian-Rong , Zhu Jun-Jie 
Published: March 2016

AbstractThe strong correlation between cancer and telomerase activity has inspired the development of new strategies to evaluate telomerase activity. Here, a personal glucose meter (PGM) system that uses DNA-based machine amplification to detect telomerase in cancer cells is reported. In this assay, telomerase elongation products are amplified in the form of another type of product by a DNA-based machine. This process can only be activated by the hybridization of the extended telomerase substrate (TS) probe and the complementary primer in the presence of telomerase. The obtained products are then transformed to glucose-related signals via a three-component assay, which enables the simple use of a PGM to indirectly quantify the telomerase activity. The proposed method realizes sensitive telomerase activity detection down to 20 HeLa cells with a significantly enhanced dynamic range. Additionally, short telomerase elongation products, such as telomerase substrate probes with two repetitive sequences, that cannot be detected using the most widely used telomeric repeat amplification protocol assay were detected.
dbPAF: an integrative database of protein phosphorylation in animals and fungi
Authors: Ullah Shahid , Lin Shaofeng , Xu Yang , Deng Wankun , Ma Lili , Zhang Ying , Liu Zexian , Xue Yu 
Published: March 2016

AbstractProtein phosphorylation is one of the most important post-translational modifications (PTMs) and regulates a broad spectrum of biological processes. Recent progresses in phosphoproteomic identifications have generated a flood of phosphorylation sites, while the integration of these sites is an urgent need. In this work, we developed a curated database of dbPAF, containing known phosphorylation sites in H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. pombe and S. cerevisiae. From the scientific literature and public databases, we totally collected and integrated 54,148 phosphoproteins with 483,001 phosphorylation sites. Multiple options were provided for accessing the data, while original references and other annotations were also present for each phosphoprotein. Based on the new data set, we computationally detected significantly over-represented sequence motifs around phosphorylation sites, predicted potential kinases that are responsible for the modification of collected phospho-sites and evolutionarily analyzed phosphorylation conservation states across different species. Besides to be largely consistent with previous reports, our results also proposed new features of phospho-regulation. Taken together, our database can be useful for further analyses of protein phosphorylation in human and other model organisms. The dbPAF database was implemented in PHP + MySQL and freely available at http://dbpaf.biocuckoo.org.
Simulated Raman correlation spectroscopy for quantifying nucleic acid-silver composites
Authors: Freeman Lindsay M. , Smolyaninov Alexei , Pang Lin , Fainman Yeshaiahu 
Published: March 2016

AbstractPlasmonic devices are of great interest due to their ability to confine light to the nanoscale level and dramatically increase the intensity of the electromagnetic field, functioning as high performance platforms for Raman signal enhancement. While Raman spectroscopy has been proposed as a tool to identify the preferential binding sites and adsorption configurations of molecules to nanoparticles, the results have been limited by the assumption that a single binding site is responsible for molecular adsorption. Here, we develop the simulated Raman correlation spectroscopy (SRCS) process to determine which binding sites of a molecule preferentially bind to a plasmonic material and in what capacity. We apply the method to the case of nucleic acids binding to silver, discovering that multiple atoms are responsible for adsorption kinetics. This method can be applied to future systems, such as to study the molecular orientation of adsorbates to films or protein conformation upon adsorption.
Structural and electronic properties of epitaxial multilayer h-BN on Ni(111) for spintronics applications
Authors: Tonkikh A. A. , Voloshina E. N. , Werner P. , Blumtritt H. , Senkovskiy B. , Güntherodt G. , Parkin S. S. P. , Dedkov Yu. S. 
Published: March 2016

AbstractHexagonal boron nitride (h-BN) is a promising material for implementation in spintronics due to a large band gap, low spin-orbit coupling, and a small lattice mismatch to graphene and to close-packed surfaces of fcc-Ni(111) and hcp-Co(0001). Epitaxial deposition of h-BN on ferromagnetic metals is aimed at small interface scattering of charge and spin carriers. We report on the controlled growth of h-BN/Ni(111) by means of molecular beam epitaxy (MBE). Structural and electronic properties of this system are investigated using cross-section transmission electron microscopy (TEM) and electron spectroscopies which confirm good agreement with the properties of bulk h-BN. The latter are also corroborated by density functional theory (DFT) calculations, revealing that the first h-BN layer at the interface to Ni is metallic. Our investigations demonstrate that MBE is a promising, versatile alternative to both the exfoliation approach and chemical vapour deposition of h-BN.
Microscopic Origin of Strain Hardening in Methane Hydrate
Authors: Jia Jihui , Liang Yunfeng , Tsuji Takeshi , Murata Sumihiko , Matsuoka Toshifumi 
Published: March 2016

AbstractIt has been reported for a long time that methane hydrate presents strain hardening, whereas the strength of normal ice weakens with increasing strain after an ultimate strength. However, the microscopic origin of these differences is not known. Here, we investigated the mechanical characteristics of methane hydrate and normal ice by compressive deformation test using molecular dynamics simulations. It is shown that methane hydrate exhibits strain hardening only if the hydrate is confined to a certain finite cross-sectional area that is normal to the compression direction. For normal ice, it does not present strain hardening under the same conditions. We show that hydrate guest methane molecules exhibit no long-distance diffusion when confined to a finite-size area. They appear to serve as non-deformable units that prevent hydrate structure failure and thus are responsible for the strain-hardening phenomenon.
Intense visible emission from ZnO/PAAX (X = H or Na) nanocomposite synthesized via a simple and scalable sol-gel method
Authors: Zhu Y. , Apostoluk A. , Gautier P. , Valette A. , Omar L. , Cornier T. , Bluet J. M. , Masenelli-Varlot K. , Daniele S. , Masenelli B. 
Published: March 2016

AbstractIntense visible nano-emitters are key objects for many technologies such as single photon source, bio-labels or energy convertors. Chalcogenide nanocrystals have ruled this domain for several decades. However, there is a demand for cheaper and less toxic materials. In this scheme, ZnO nanoparticles have appeared as potential candidates. At the nanoscale, they exhibit crystalline defects which can generate intense visible emission. However, even though photoluminescence quantum yields as high as 60% have been reported, it still remains to get quantum yield of that order of magnitude which remains stable over a long period. In this purpose, we present hybrid ZnO/polyacrylic acid (PAAH) nanocomposites, obtained from the hydrolysis of diethylzinc in presence of PAAH, exhibiting quantum yield systematically larger than 20%. By optimizing the nature and properties of the polymeric acid, the quantum yield is increased up to 70% and remains stable over months. This enhancement is explained by a model based on the hybrid type II heterostructure formed by ZnO/PAAH. The addition of PAAX (X = H or Na) during the hydrolysis of ZnEt2 represents a cost effective method to synthesize scalable amounts of highly luminescent ZnO/PAAX nanocomposites.
Room temperature continuous wave, monolithic tunable THz sources based on highly efficient mid-infrared quantum cascade lasers
Authors: Lu Quanyong , Wu Donghai , Sengupta Saumya , Slivken Steven , Razeghi Manijeh 
Published: March 2016

AbstractA compact, high power, room temperature continuous wave terahertz source emitting in a wide frequency range (ν ~ 1–5 THz) is of great importance to terahertz system development for applications in spectroscopy, communication, sensing and imaging. Here, we present a strong-coupled strain-balanced quantum cascade laser design for efficient THz generation based on intracavity difference frequency generation. Room temperature continuous wave emission at 3.41 THz with a side-mode suppression ratio of 30 dB and output power up to 14 μW is achieved with a wall-plug efficiency about one order of magnitude higher than previous demonstrations. With this highly efficient design, continuous wave, single mode THz emissions with a wide frequency tuning range of 2.06–4.35 THz and an output power up to 4.2 μW are demonstrated at room temperature from two monolithic three-section sampled grating distributed feedback-distributed Bragg reflector lasers.
Ligand-binding specificity and promiscuity of the main lignocellulolytic enzyme families as revealed by active-site architecture analysis
Authors: Tian Li , Liu Shijia , Wang Shuai , Wang Lushan 
Published: March 2016

AbstractBiomass can be converted into sugars by a series of lignocellulolytic enzymes, which belong to the glycoside hydrolase (GH) families summarized in CAZy databases. Here, using a structural bioinformatics method, we analyzed the active site architecture of the main lignocellulolytic enzyme families. The aromatic amino acids Trp/Tyr and polar amino acids Glu/Asp/Asn/Gln/Arg occurred at higher frequencies in the active site architecture than in the whole enzyme structure. And the number of potential subsites was significantly different among different families. In the cellulase and xylanase families, the conserved amino acids in the active site architecture were mostly found at the −2 to +1 subsites, while in β-glucosidase they were mainly concentrated at the −1 subsite. Families with more conserved binding amino acid residues displayed strong selectivity for their ligands, while those with fewer conserved binding amino acid residues often exhibited promiscuity when recognizing ligands. Enzymes with different activities also tended to bind different hydroxyl oxygen atoms on the ligand. These results may help us to better understand the common and unique structural bases of enzyme-ligand recognition from different families and provide a theoretical basis for the functional evolution and rational design of major lignocellulolytic enzymes.
Tailoring superradiance to design artificial quantum systems
Authors: Longo Paolo , Keitel Christoph H. , Evers Jörg 
Published: March 2016

AbstractCooperative phenomena arising due to the coupling of individual atoms via the radiation field are a cornerstone of modern quantum and optical physics. Recent experiments on x-ray quantum optics added a new twist to this line of research by exploiting superradiance in order to construct artificial quantum systems. However, so far, systematic approaches to deliberately design superradiance properties are lacking, impeding the desired implementation of more advanced quantum optical schemes. Here, we develop an analytical framework for the engineering of single-photon superradiance in extended media applicable across the entire electromagnetic spectrum, and show how it can be used to tailor the properties of an artificial quantum system. This “reverse engineering” of superradiance not only provides an avenue towards non-linear and quantum mechanical phenomena at x-ray energies, but also leads to a unified view on and a better understanding of superradiance across different physical systems.
The BDNF Val66Met polymorphism is associated with the functional connectivity dynamics of pain modulatory systems in primary dysmenorrhea
Authors: Wei Shyh-Yuh , Chao Hsiang-Tai , Tu Cheng-Hao , Lin Ming-Wei , Li Wei-Chi , Low Intan , Shen Horng-Der , Chen Li-Fen , Hsieh Jen-Chuen 
Published: March 2016

AbstractPrimary dysmenorrhea (PDM), menstrual pain without an organic cause, is a prevailing problem in women of reproductive age. We previously reported alterations of structure and functional connectivity (FC) in the periaqueductal gray (PAG) of PDM subjects. Given that the brain derived neurotrophic factor (BDNF) acts as a pain modulator within the PAG and the BDNF Val66Met polymorphism contributes towards susceptibility to PDM, the present study of imaging genetics set out to investigate the influence of, firstly, the BDNF Val66Met single nucleotide polymorphism and, secondly, the genotype-pain interplays on the descending pain modulatory systems in the context of PAG-seeded FC patterning. Fifty-six subjects with PDM and 60 controls participated in the current study of resting-state functional magnetic resonance imaging (fMRI) during the menstruation and peri-ovulatory phases; in parallel, blood samples were taken for genotyping. Our findings indicate that the BDNF Val66Met polymorphism is associated with the diverse functional expressions of the descending pain modulatory systems. Furthermore, PAG FC patterns in pain-free controls are altered in women with PDM in a genotype-specific manner. Such resilient brain dynamics may underpin the individual differences and shed light on the vulnerability for chronic pain disorders of PDM subjects.
Structural insights and in vitro reconstitution of membrane targeting and activation of human PI4KB by the ACBD3 protein
Authors: Klima Martin , Tóth Dániel J. , Hexnerova Rozalie , Baumlova Adriana , Chalupska Dominika , Tykvart Jan , Rezabkova Lenka , Sengupta Nivedita , Man Petr , Dubankova Anna , Humpolickova Jana , Nencka Radim , Veverka Vaclav , Balla Tamas , Boura Evzen 
Published: March 2016

AbstractPhosphatidylinositol 4-kinase beta (PI4KB) is one of four human PI4K enzymes that generate phosphatidylinositol 4-phosphate (PI4P), a minor but essential regulatory lipid found in all eukaryotic cells. To convert their lipid substrates, PI4Ks must be recruited to the correct membrane compartment. PI4KB is critical for the maintenance of the Golgi and trans Golgi network (TGN) PI4P pools, however, the actual targeting mechanism of PI4KB to the Golgi and TGN membranes is unknown. Here, we present an NMR structure of the complex of PI4KB and its interacting partner, Golgi adaptor protein acyl-coenzyme A binding domain containing protein 3 (ACBD3). We show that ACBD3 is capable of recruiting PI4KB to membranes both in vitro and in vivo and that membrane recruitment of PI4KB by ACBD3 increases its enzymatic activity and that the ACBD3:PI4KB complex formation is essential for proper function of the Golgi.
Resolving the spin reorientation and crystal-field transitions in TmFeO3 with terahertz transient
Authors: Zhang Kailin , Xu Kai , Liu Xiumei , Zhang Zeyu , Jin Zuanming , Lin Xian , Li Bo , Cao Shixun , Ma Guohong 
Published: March 2016

AbstractRare earth orthoferrites (RFeO3) exhibit abundant physical properties such as, weak macroscopic magnetization, spin reorientation transition and magneto-optical effect, especially the terahertz magnetic response, have received lots of attention in recent years. In this work, quasi-ferromagnetic (FM) and quasi-antiferromagnetic (AFM) modes arising from Fe sublattice of TmFeO3 single crystal are characterized in a temperature range from 40 to 300 K, by using terahertz time-domain spectroscopy (THz-TDS). The magnetic anisotropy constants in ac-plane are estimated according to the temperature-dependent resonant frequencies of both FM and AFM modes. Here, we further observe the broad-band absorptions centered ~0.52, ~0.61 and ~1.15 THz below 110 K, which are reasonably assigned to a series of crystal-field transitions (R modes) of ground multiplets (6H3) of Tm3+ ions. Specially, our finding reveals that the spin reorientation transition at a temperature interval from 93 to 85 K is driven by magnetic anisotropy, however, which plays negligible role on the electronic transitions of Tm ions in the absence of applied magnetic fields.
Tetrapod-like pelvic girdle in a walking cavefish
Authors: Flammang Brooke E. , Suvarnaraksha Apinun , Markiewicz Julie , Soares Daphne 
Published: March 2016

AbstractFishes have adapted a number of different behaviors to move out of the water, but none have been described as being able to walk on land with a tetrapod-like gait. Here we show that the blind cavefish Cryptotora thamicola walks and climbs waterfalls with a salamander-like diagonal-couplets lateral sequence gait and has evolved a robust pelvic girdle that shares morphological features associated with terrestrial vertebrates. In all other fishes, the pelvic bones are suspended in a muscular sling or loosely attached to the pectoral girdle anteriorly. In contrast, the pelvic girdle of Cryptotora is a large, broad puboischiadic plate that is joined to the iliac process of a hypertrophied sacral rib; fusion of these bones in tetrapods creates an acetabulum. The vertebral column in the sacral area has large anterior and posterior zygapophyses, transverse processes and broad neural spines, all of which are associated with terrestrial organisms. The diagonal-couplet lateral sequence gait was accomplished by rotation of the pectoral and pelvic girdles creating a standing wave of the axial body. These findings are significant because they represent the first example of behavioural and morphological adaptation in an extant fish that converges on the tetrapodal walking behaviour and morphology.
Dynamin II is required for 17β-estradiol signaling and autophagy-based ERα degradation
Authors: Totta Pierangela , Busonero Claudia , Leone Stefano , Marino Maria , Acconcia Filippo 
Published: March 2016

Abstract17β-estradiol (E2) regulates diverse physiological effects, including cell proliferation, by binding to estrogen receptor α (ERα). ERα is both a transcription factor that drives E2-sensitive gene expression and an extra-nuclear localized receptor that triggers the activation of diverse kinase cascades. While E2 triggers cell proliferation, it also induces ERα degradation in a typical hormone-dependent feedback loop. Although ERα breakdown proceeds through the 26S proteasome, a role for lysosomes and for some endocytic proteins in controlling ERα degradation has been reported. Here, we studied the role of the endocytic protein dynamin II in E2-dependent ERα signaling and degradation. The results indicate that dynamin II siRNA-mediated knock-down partially prevents E2-induced ERα degradation through the inhibition of an autophagy-based pathway and impairs E2-induced cell proliferation signaling. Altogether, these data demonstrate that dynamin II is required for the E2:ERα signaling of physiological functions and uncovers a role for autophagy in the control of ERα turnover.
Far-field radially polarized focal spot from plasmonic spiral structure combined with central aperture antenna
Authors: Mao Lei , Ren Yuan , Lu Yonghua , Lei Xinrui , Jiang Kang , Li Kuanguo , Wang Yong , Cui Chenjing , Wen Xiaolei , Wang Pei 
Published: March 2016

AbstractManipulation of a vector micro-beam with an optical antenna has significant potentials for nano-optical technology applications including bio-optics, optical fabrication and quantum information processing. We have designed and demonstrated a central aperture antenna within an Archimedean spiral that extracts the bonding plasmonic field from a surface to produce a new vector focal spot in far-field. The properties of this vector focal field are revealed by confocal microscopy and theoretical simulations. The pattern, polarization and phase of the focal field are determined by the incident light and by the chirality of the Archimedean spiral. For incident light with right-handed circular polarization, the left-handed spiral (one-order chirality) outputs a micro-radially polarized focal field. Our results reveal the relationship between the near-field and far-field distributions of the plasmonic spiral structure and the structure has the potential to lead to advances in diverse applications such as plasmonic lenses, near-field angular momentum detection and optical tweezers.
Artificial neural network‐based modelling of compensated multi‐crystalline solar‐grade silicon under wide temperature variations
Authors: Patra Jagdish Chandra , Modanese Chiara , Acciarri Maurizio 
Published: March 2016

In recent years, multi‐crystalline solar grade silicon (mc‐SoG‐Si), instead of expensive electronic‐grade Si, is being considered in photovoltaic industry for production of solar modules. These materials usually contain a comparable amount of acceptors (e.g. boron) and donors (e.g. phosphorus) and are therefore called compensated mc‐SoG‐Si. The electrical parameters, e.g. majority carrier mobility (μ), majority carrier density (p) and resistivity (ρ), of compensated mc‐SoG‐Si which affect performance of the solar cells vary non‐linearly with temperature due to several complex mechanisms. In this study, the authors propose artificial neural network (ANN)‐based models to predict the three electrical parameters of mc‐SoG‐Si material. Using a limited amount of measurement data, the authors have shown that the ANN‐based models can predict the three electrical parameters of a given sample over a wide temperature range of 70–400 K and a specific range of compensation ratio. The authors have shown with extensive simulated results that these models can predict the three parameters with a maximum error of ±10%.
Hierarchical porous ZnMn2O4 derived from cotton substance as high‐performance lithium ion battery anode
Authors: Zhao Chenhao , Shen Ye , Qiu Sheng'en , Hu Zhibiao , Liu Kaiyu 
Published: March 2016

Hierarchical porous ZnMn2O4 has been prepared by an initial cotton template and subsequent calcination route. The as‐prepared hierarchical porous ZnMn2O4 composed of numerous nanoparticles well inherit the fibre‐like structure of cotton, and these nanoparticles have a size of ∼20–50 nm. The N2 adsorption–desorption test indicates this ZnMn2O4 has a Brunauer–Emmett–Teller surface area of ∼16.7084 m2 g−1 and average pore size of ∼27.0 nm. As lithium ion battery anodes, the ZnMn2O4 can deliver a discharge capacity of 674.9 mAh g−1 after 200 cycles at current density of 200 mA g−1. Even at 1000 mA g−1, this ZnMn2O4 still shows a stable discharge capacity of 541.5 mAh g−1. These promising electrochemical performances may be attributed to its unique hierarchical porous structure which helps to accelerate the ions transportation and elevate the structure stability.
Stalk cell differentiation without polyketides in the cellular slime mold
Authors: Sato Yukie G , Suarez Teresa , Saito Tamao 
Published: March 2016

Abstract
Polyketides induce prestalk cell differentiation in Dictyostelium. In the double-knockout mutant of the SteelyA and B polyketide synthases, most of the pstA cells—the major part of the prestalk cells—are lost, and we show by whole mount in situ hybridization that expression of prestalk genes is also reduced. Treatment of the double-knockout mutant with the PKS inhibitor cerulenin gave a further reduction, but some pstA cells still remained in the tip region, suggesting the existence of a polyketide-independent subtype of pstA cells. The double-knockout mutant and cerulenin-treated parental Ax2 cells form fruiting bodies with fragile, single-cell layered stalks after cerulenin treatment. Our results indicate that most pstA cells are induced by polyketides, but the pstA cells at the very tip of the slug are induced in some other way. In addition, a fruiting body with a single-cell layered, vacuolated stalk can form without polyketides.