bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial Competition: Roughening of an Experimental Interface
Authors: Allstadt Andrew J. , Newman Jonathan A. , Walter Jonathan A. , Korniss G. , Caraco Thomas 
Published: July 2016

AbstractLimited dispersal distance generates spatial aggregation. Intraspecific interactions are then concentrated within clusters and between-species interactions occur near cluster boundaries. Spread of a locally dispersing invader can become motion of an interface between the invading and resident species and spatial competition will produce variation in the extent of invasive advance along the interface. Kinetic roughening theory offers a framework for quantifying the development of these fluctuations, which may structure the interface as a self-affine fractal and so induce a series of temporal and spatial scaling relationships. For most clonal plants, advance should become spatially correlated along the interface and width of the interface (where invader and resident compete directly) should increase as a power function of time. Once roughening equilibrates, interface width and the relative location of the most advanced invader should each scale with interface length. We tested these predictions by letting white clover (Trifolium repens) invade ryegrass (Lolium perenne). The spatial correlation of clover growth developed as anticipated by kinetic roughening theory and both interface width and the most advanced invader’s lead scaled with front length. However, the scaling exponents differed from those predicted by recent simulation studies, likely due to clover’s growth morphology.
Experimental realization of equiangular three-state quantum key distribution
Authors: Schiavon Matteo , Vallone Giuseppe , Villoresi Paolo 
Published: July 2016

AbstractQuantum key distribution using three states in equiangular configuration combines a security threshold comparable with the one of the Bennett-Brassard 1984 protocol and a quantum bit error rate (QBER) estimation that does not need to reveal part of the key. We implement an entanglement-based version of the Renes 2004 protocol, using only passive optic elements in a linear scheme for the positive-operator valued measure (POVM), generating an asymptotic secure key rate of more than 10 kbit/s, with a mean QBER of 1.6%. We then demonstrate its security in the case of finite key and evaluate the key rate for both collective and general attacks.
Iowa Mutant Apolipoprotein A-I (ApoA-IIowa) Fibrils Target Lysosomes
Authors: Kameyama Hirokazu , Nakajima Hiroyuki , Nishitsuji Kazuchika , Mikawa Shiho , Uchimura Kenji , Kobayashi Norihiro , Okuhira Keiichiro , Saito Hiroyuki , Sakashita Naomi 
Published: July 2016

AbstractThe single amino acid mutation G26R in human apolipoprotein A-I (apoA-IIowa) is the first mutation that was associated with familial AApoA1 amyloidosis. The N-terminal fragments (amino acid residues 1–83) of apoA-I containing this mutation deposit as amyloid fibrils in patients’ tissues and organs, but the mechanisms of cellular degradation and cytotoxicity have not yet been clarified. In this study, we demonstrated degradation of apoA-IIowa fibrils via the autophagy-lysosomal pathway in human embryonic kidney 293 cells. ApoA-IIowa fibrils induced an increase in lysosomal pH and the cytosolic release of the toxic lysosomal protease cathepsin B. The mitochondrial dysfunction caused by apoA-IIowa fibrils depended on cathepsin B and was ameliorated by increasing the degradation of apoA-IIowa fibrils. Thus, although apoA-IIowa fibril transport to lysosomes and fibril degradation in lysosomes may have occurred, the presence of an excess number of apoA-IIowa fibrils, more than the lysosomes could degrade, may be detrimental to cells. Our results thus provide evidence that the target of apoA-IIowa fibrils is lysosomes and we thereby gained a novel insight into the mechanism of AApoA1 amyloidosis.
Engineering complex tissue-like microgel arrays for evaluating stem cell differentiation
Authors: Guermani Enrico , Shaki Hossein , Mohanty Soumyaranjan , Mehrali Mehdi , Arpanaei Ayyoob , Gaharwar Akhilesh K. , Dolatshahi-Pirouz Alireza 
Published: July 2016

AbstractDevelopment of tissue engineering scaffolds with native-like biology and microarchitectures is a prerequisite for stem cell mediated generation of off-the-shelf-tissues. So far, the field of tissue engineering has not full-filled its grand potential of engineering such combinatorial scaffolds for engineering functional tissues. This is primarily due to the many challenges associated with finding the right microarchitectures and ECM compositions for optimal tissue regeneration. Here, we have developed a new microgel array to address this grand challenge through robotic printing of complex stem cell-laden microgel arrays. The developed microgel array platform consisted of various microgel environments that where composed of native-like cellular microarchitectures resembling vascularized and bone marrow tissue architectures. The feasibility of our array system was demonstrated through localized cell spreading and osteogenic differentiation of human mesenchymal stem cells (hMSCs) into complex tissue-like structures. In summary, we have developed a tissue-like microgel array for evaluating stem cell differentiation within complex and heterogeneous cell microenvironments. We anticipate that the developed platform will be used for high-throughput identification of combinatorial and native-like scaffolds for tissue engineering of functional organs.
Large area and deep sub-wavelength interference lithography employing odd surface plasmon modes
Authors: Liu Liqin , Luo Yunfei , Zhao Zeyu , Zhang Wei , Gao Guohan , Zeng Bo , Wang Changtao , Luo Xiangang 
Published: July 2016

AbstractIn this paper, large area and deep sub-wavelength interference patterns are realized experimentally by using odd surface plasmon modes in the metal/insulator/metal structure. Theoretical investigation shows that the odd modes possesses much higher transversal wave vector and great inhibition of tangential electric field components, facilitating surface plasmon interference fringes with high resolution and contrast in the measure of electric field intensity. Interference resist patterns with 45 nm (∼λ/8) half-pitch, 50 nm depth and area size up to 20 mm × 20 mm were obtained by using 20 nm Al/50 nm photo resist/50 nm Al films with greatly reduced surface roughness and 180 nm pitch exciting grating fabricated with conventional laser interference lithography. Much deeper resolution down to 19.5 nm is also feasible by decreasing the thickness of PR. Considering that no requirement of expensive EBL or FIB tools are employed, it provides a cost-effective way for large area and nano-scale fabrication.
Allele-specific locus binding and genome editing by CRISPR at the p16INK4a locus
Authors: Fujita Toshitsugu , Yuno Miyuki , Fujii Hodaka 
Published: July 2016

AbstractThe clustered regularly interspaced short palindromic repeats (CRISPR) system has been adopted for a wide range of biological applications including genome editing. In some cases, dissection of genome functions requires allele-specific genome editing, but the use of CRISPR for this purpose has not been studied in detail. In this study, using the p16INK4a gene in HCT116 as a model locus, we investigated whether chromatin states, such as CpG methylation, or a single-nucleotide gap form in a target site can be exploited for allele-specific locus binding and genome editing by CRISPR in vivo. First, we showed that allele-specific locus binding and genome editing could be achieved by targeting allele-specific CpG-methylated regions, which was successful for one, but not all guide RNAs. In this regard, molecular basis underlying the success remains elusive at this stage. Next, we demonstrated that an allele-specific single-nucleotide gap form could be employed for allele-specific locus binding and genome editing by CRISPR, although it was important to avoid CRISPR tolerance of a single nucleotide mismatch brought about by mismatched base skipping. Our results provide information that might be useful for applications of CRISPR in studies of allele-specific functions in the genomes.
Nearly massless Dirac fermions hosted by Sb square net in BaMnSb2
Authors: Liu Jinyu , Hu Jin , Cao Huibo , Zhu Yanglin , Chuang Alyssa , Graf D. , Adams D. J. , Radmanesh S. M. A. , Spinu L. , Chiorescu I. , Mao Zhiqiang 
Published: July 2016

AbstractLayered compounds AMnBi2 (A = Ca, Sr, Ba, or rare earth element) have been established as Dirac materials. Dirac electrons generated by the two-dimensional (2D) Bi square net in these materials are normally massive due to the presence of a spin-orbital coupling (SOC) induced gap at Dirac nodes. Here we report that the Sb square net in an isostructural compound BaMnSb2 can host nearly massless Dirac fermions. We observed strong Shubnikov-de Haas (SdH) oscillations in this material. From the analyses of the SdH oscillations, we find key signatures of Dirac fermions, including light effective mass (~0.052m0; m0, mass of free electron), high quantum mobility (1280 cm2V−1S−1) and a π Berry phase accumulated along cyclotron orbit. Compared with AMnBi2, BaMnSb2 also exhibits much more significant quasi two-dimensional (2D) electronic structure, with the out-of-plane transport showing nonmetallic conduction below 120 K and the ratio of the out-of-plane and in-plane resistivity reaching ~670. Additionally, BaMnSb2 also exhibits a G-type antiferromagnetic order below 283 K. The combination of nearly massless Dirac fermions on quasi-2D planes with a magnetic order makes BaMnSb2 an intriguing platform for seeking novel exotic phenomena of massless Dirac electrons.
Enhanced photoelectrochemical and photocatalytic behaviors of MFe2O4 (M = Ni, Co, Zn and Sr) modified TiO2 nanorod arrays
Authors: Gao Xin , Liu Xiangxuan , Zhu Zuoming , Wang Xuanjun , Xie Zheng 
Published: July 2016

AbstractModified TiO2 nanomaterials are considered to be promising in energy conversion and ferrites modification may be one of the most efficient modifications. In this research, various ferrites, incorporated with various cations (MFe2O4, M = Ni, Co, Zn and Sr), are utilized to modify the well aligned TiO2 nanorod arrays (NRAs), which is synthesized by hydrothermal method. It is found that all MFe2O4/TiO2 NRAs show obvious red shift into the visible light region compared with the TiO2 NRAs. In particular, NiFe2O4 modification is demonstrated to be the best way to enhance the photoelectrochemical and photocatalytic activity of TiO2 NRAs. Furthermore, the separation and transfer of charge carriers after MFe2O4 modification are clarified by electrochemical impedance spectroscopy measurements. Finally, the underlying mechanism accounting for the enhanced photocatalytic activity of MFe2O4/TiO2 NRAs is proposed. Through comparison among different transition metals modified TiO2 with the same synthesis process and under the same evaluating condition, this work may provide new insight in designing modified TiO2 nanomaterials as visible light active photocatalysts.
Magnetic Resonance Imaging of Phosphocreatine and Determination of BOLD Kinetics in Lower Extremity Muscles using a Dual-Frequency Coil Array
Authors: Brown Ryan , Khegai Oleksandr , Parasoglou Prodromos 
Published: July 2016

AbstractMagnetic resonance imaging (MRI) provides the unique ability to study metabolic and microvasculature functions in skeletal muscle using phosphorus and proton measurements. However, the low sensitivity of these techniques can make it difficult to capture dynamic muscle activity due to the temporal resolution required for kinetic measurements during and after exercise tasks. Here, we report the design of a dual-nuclei coil array that enables proton and phosphorus MRI of the human lower extremities with high spatial and temporal resolution. We developed an array with whole-volume coverage of the calf and a phosphorus signal-to-noise ratio of more than double that of a birdcage coil in the gastrocnemius muscles. This enabled the local assessment of phosphocreatine recovery kinetics following a plantar flexion exercise using an efficient sampling scheme with a 6 s temporal resolution. The integrated proton array demonstrated image quality approximately equal to that of a clinical state-of-the-art knee coil, which enabled fat quantification and dynamic blood oxygen level-dependent measurements that reflect microvasculature function. The developed array and time-efficient pulse sequences were combined to create a localized assessment of calf metabolism using phosphorus measurements and vasculature function using proton measurements, which could provide new insights into muscle function.
Molecular developmental mechanism in polypterid fish provides insight into the origin of vertebrate lungs
Authors: Tatsumi Norifumi , Kobayashi Ritsuko , Yano Tohru , Noda Masatsugu , Fujimura Koji , Okada Norihiro , Okabe Masataka 
Published: July 2016

AbstractThe lung is an important organ for air breathing in tetrapods and originated well before the terrestrialization of vertebrates. Therefore, to better understand lung evolution, we investigated lung development in the extant basal actinopterygian fish Senegal bichir (Polypterus senegalus). First, we histologically confirmed that lung development in this species is very similar to that of tetrapods. We also found that the mesenchymal expression patterns of three genes that are known to play important roles in early lung development in tetrapods (Fgf10, Tbx4 and Tbx5) were quite similar to those of tetrapods. Moreover, we found a Tbx4 core lung mesenchyme-specific enhancer (C-LME) in the genomes of bichir and coelacanth (Latimeria chalumnae) and experimentally confirmed that these were functional in tetrapods. These findings provide the first molecular evidence that the developmental program for lung was already established in the common ancestor of actinopterygians and sarcopterygians.
Consecutive Reaction to Construct Hierarchical Nanocrystalline CuS “Branch” with Tunable Catalysis Properties
Authors: Zhang Xiangdan , Yang Feifei , Cui Shizhong , Wei Wutao , Chen Weihua , Mi Liwei 
Published: July 2016

AbstractNew CuS nanocrystals with a 3D hierarchical branched structure are successfully synthesized through in situ consecutive reaction method with copper foam as template. The formation mechanism of the 3D hierarchical branched structure obtained from the secondary reaction is investigated by adjusting the reaction time. The morphology of CuS nanosheet arrays with the 3D hierarchical branched structure is changed through Cu2+ exchange. In this method, the copper foam reacted completely, and the as-synthesized CuS@Cu9S5 nanocrystals are firmly grown on the surface of the 3D framework. This tunable morphology significantly influence the physical and chemical properties, particularly catalytic performance, of the materials. The as-obtained material of Cu@CuS-2 with the 3D hierarchical branched structure as catalyst for methylene blue degradation exhibits good catalytic performance than that of the material of Cu@CuS with 2D nanosheets in dark environment. Furthermore, the cation exchange between Cu and Cu2+ indicates that Cu2+ in wastewater could be absorbed by Cu@CuS-2 with the 3D hierarchical branched structure. The exchanged resultant of CuS@Cu9S5 retains its capability to degrade organic dyes. This in situ consecutive reaction method may have a significant impact on controlling the crystal growth direction of inorganic material.
Local noise in a diffusive conductor
Authors: Tikhonov E. S. , Shovkun D. V. , Ercolani D. , Rossella F. , Rocci M. , Sorba L. , Roddaro S. , Khrapai V. S. 
Published: July 2016

AbstractThe control and measurement of local non-equilibrium configurations is of utmost importance in applications on energy harvesting, thermoelectrics and heat management in nano-electronics. This challenging task can be achieved with the help of various local probes, prominent examples including superconducting or quantum dot based tunnel junctions, classical and quantum resistors, and Raman thermography. Beyond time-averaged properties, valuable information can also be gained from spontaneous fluctuations of current (noise). From these perspective, however, a fundamental constraint is set by current conservation, which makes noise a characteristic of the whole conductor, rather than some part of it. Here we demonstrate how to remove this obstacle and pick up a local noise temperature of a current biased diffusive conductor with the help of a miniature noise probe. This approach is virtually noninvasive for the electronic energy distributions and extends primary local measurements towards strongly non-equilibrium regimes.
A Decentralized Approach to the Formulation of Hypotheses: A Hierarchical Structural Model for a Prion Self-Assembled System
Authors: Wang Mingyang , Zhang Feifei , Song Chao , Shi Pengfei , Zhu Jin 
Published: July 2016

AbstractInnovation in hypotheses is a key transformative driver for scientific development. The conventional centralized hypothesis formulation approach, where a dominant hypothesis is typically derived from a primary phenomenon, can, inevitably, impose restriction on the range of conceivable experiments and legitimate hypotheses, and ultimately impede understanding of the system of interest. We report herein the proposal of a decentralized approach for the formulation of hypotheses, through initial preconception-free phenomenon accumulation and subsequent reticular logical reasoning processes. The two-step approach can provide an unbiased, panoramic view of the system and as such should enable the generation of a set of more coherent and therefore plausible hypotheses. As a proof-of-concept demonstration of the utility of this open-ended approach, a hierarchical model has been developed for a prion self-assembled system, allowing insight into hitherto elusive static and dynamic features associated with this intriguing structure.
Citrobacter freundii carrying blaKPC-2 and blaNDM-1: characterization by whole genome sequencing
Authors: Wu Wenjing , Espedido Björn , Feng Yu , Zong Zhiyong 
Published: July 2016

AbstractA carbapenem-resistant Citrobacter freundii strain WCHCF65 was recovered from hospital sewage and was characterized by genome sequencing and conjugation experiments. The strain carried nine genes encoding β-lactamases including two carbapenemase genes, blaNDM-1 and blaKPC-2. blaNDM-1 was carried on an IncX3 plasmid, which was identical to a plasmid found in a local Escherichia coli, suggesting interspecies horizontal transfer. blaKPC-2 was bracketed by two copies of insertion sequence ISKpn19, which could form a composite transposon with the potential to mobilize blaKPC-2, on a new type of plasmid. The coexistence of blaNDM-1 and blaKPC-2 conferred higher levels of resistance to carbapenems compared with blaNDM-1 or blaKPC-2 alone. The coexistence of these carbapenemase genes, on two different plasmids, in one strain may allow new genetic platforms to be generated to mediate their spread.
Polymorphisms in TCF7L2 gene are associated with gestational diabetes mellitus in Chinese Han population
Authors: Ye Dan , Fei Yang , Ling Qi , Xu Weiwei , Zhang Zhe , Shu Jing , Li Chengjiang , Dong Fengqin 
Published: July 2016

AbstractThis study aimed to investigate the possible association between diabetes susceptibility gene transcription factor 7-like 2 (TCF7L2) and gestational diabetes mellitus (GDM) in a Chinese Han population. A total of 556 GDM patients and 500 Non-GDM were included. Eighteen single nucleotide polymorphisms (SNPs) were evaluated. Fifteen tag SNPs were selected from HapMap CHB database with a minor allele frequency of >0.2 and r2of >0.8. Three additional SNPs were also chosen because these SNPs are associated with type 2 diabetes in East Asians.TCF7L2rs290487, rs6585194, and rs7094463 polymorphisms were found to be significantly associated with GDM. In multivariate analysis, rs290487 genetic variation (OR = 2.686 per each C allele,P = 0.002), pre-BMI > 24 kg/m2(OR = 1.592,P = 0.018), age > 25 years (OR = 1.780,P = 0.012) and LDL-C > 3.6 mmol/L (OR = 2.034, P = 0.009) were identified as independent risk factors of GDM, rs7094463 genetic variation (OR = 0.429 per each G allele,P = 0.005) was identified as independent protect factor of GDM. This finding suggests thatTCF7L2rs290487, and rs7094463 were a potential clinical value for the prediction of GDM.
Facultative parthenogenesis in the Ryukyu drywood termite Neotermes koshunensis
Authors: Kobayashi Kazuya , Miyaguni Yasushi 
Published: July 2016

AbstractParthenogenesis is a relatively rare reproductive mode in nature compared to sex. In social insects, the evolution of parthenogenesis has a notable impact on their life histories. Some termites with parthenogenetic ability produce numerous non-dispersing supplementary queens asexually, whereas other castes are produced via sexual reproduction. This asexual queen succession (AQS) system is adaptive because hundreds of the asexual queens improve the reproductive potential of the colony and maintain the genetic diversity within the colony. However, the evolutionary process of the AQS system remains unclear because parthenogenetic species without this system are unknown. Here, we report facultative parthenogenesis in the drywood termiteNeotermes koshunensis. Although the eggs produced by females isolated from males hatched, the hatching rate of those eggs was lower than that of the eggs produced by females kept with males. These parthenogenetic offspring inherited only the maternal alleles and showed high homozygosity, which indicates that the mechanism of ploidy restoration is terminal fusion. A previous study showed that most colonies of this species have a single queen or orphan; thus, the AQS system has not evolved despite their parthenogenetic ability. Further investigations ofN. koshunensiswill reveal how parthenogenesis evolved and its role in the insect societies.
Exome-based Variant Detection in Core Promoters
Authors: Kim Yeong C. , Cui Jian , Luo Jiangtao , Xiao Fengxia , Downs Bradley , Wang San Ming 
Published: July 2016

AbstractCore promoter controls the initiation of transcription. Core promoter sequence change can disrupt transcriptional regulation, lead to impairment of gene expression and ultimately diseases. Therefore, comprehensive characterization of core promoters is essential to understand normal and abnormal gene expression in biomedical studies. Here we report the development of EVDC (Exome-based Variant Detection in Core promoters) method for genome-scale analysis of core-promoter sequence variation. This method is based on the fact that exome sequences contain the sequences not only from coding exons but also from non-coding region including core promoters generated by random fragmentation in exome sequencing process. Using exome data from three cell types of CD4+ T cells, CD19+ B cells and neutrophils of a single individual, we characterized the features of core promoter-mapped exome sequences, and analysed core-promoter variation in this individual genome. We also compared the core promoters between YRI (Yoruba in Ibadan, Nigeria) and the CEU (Utah residents of European decedent) populations using the exome data generated by the 1000 Genome project, and observed much higher variation in YRI population than in CEU population. Our study demonstrates that the EVDC method provides a simple but powerful means for genome-wile de novo characterization of core promoter sequence variation.