bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fiber guiding at the Dirac frequency beyond photonic bandgaps
Authors: Xie Kang , Zhang Wei , Boardman Allan D , Jiang Haiming , Hu Zhijia , Liu Yong , Xie Ming , Mao Qiuping , Hu Lei , Li Qian , Yang Tianyu , Wen Fei , Wang Erlei 
Published: June 2015

AbstractLight trapping within waveguides is a key practice of modern optics, both scientifically and technologically. Photonic crystal fibers traditionally rely on total internal reflection (index-guiding fibers) or a photonic bandgap (photonic-bandgap fibers) to achieve field confinement. Here, we report the discovery of a new light trapping within fibers by the so-called Dirac point of photonic band structures. Our analysis reveals that the Dirac point can establish suppression of radiation losses and consequently a novel guided mode for propagation in photonic crystal fibers. What is known as the Dirac point is a conical singularity of a photonic band structure where wave motion obeys the famous Dirac equation. We find the unexpected phenomenon of wave localization at this point beyond photonic bandgaps. This guiding relies on the Dirac point rather than total internal reflection or photonic bandgaps, thus providing a sort of advancement in conceptual understanding over the traditional fiber guiding. The result presented here demonstrates the discovery of a new type of photonic crystal fibers, with unique characteristics that could lead to new applications in fiber sensors and lasers. The Dirac equation is a special symbol of relativistic quantum mechanics. Because of the similarity between band structures of a solid and a photonic crystal, the discovery of the Dirac-point-induced wave trapping in photonic crystals could provide novel insights into many relativistic quantum effects of the transport phenomena of photons, phonons, and electrons.
The limits of chemosensation vary across dimensions
Authors: Bicknell Brendan A. , Dayan Peter , Goodhill Geoffrey J. 
Published: June 2015

AbstractMany biological processes rely on the ability of cells to measure local ligand concentration. However, such measurements are constrained by noise arising from diffusion and the stochastic nature of receptor–ligand interactions. It is thus critical to understand how accurately, in principle, concentration measurements can be made. Previous theoretical work has mostly investigated this in 3D under the simplifying assumption of an unbounded domain of diffusion, but many biological problems involve 2D concentration measurement in bounded domains, for which diffusion behaves quite differently. Here we present a theory of the precision of chemosensation that covers bounded domains of any dimensionality. We find that the quality of chemosensation in lower dimensions is controlled by domain size, suggesting a general principle applicable to many biological systems. Applying the theory to biological problems in 2D shows that diffusion-limited signalling is an efficient mechanism on time scales consistent with behaviour.
The transcription factor NR4A1 is essential for the development of a novel macrophage subset in the thymus
Authors: Tacke Robert , Hilgendorf Ingo , Garner Hannah , Waterborg Claire , Park Kiwon , Nowyhed Heba , Hanna Richard N. , Wu Runpei , Swirski Filip K. , Geissmann Frederic , Hedrick Catherine C. 
Published: June 2015

AbstractTissue macrophages function to maintain homeostasis and regulate immune responses. While tissue macrophages derive from one of a small number of progenitor programs, the transcriptional requirements for site-specific macrophage subset development are more complex. We have identified a new tissue macrophage subset in the thymus and have discovered that its development is dependent on transcription factor NR4A1. Functionally, we find that NR4A1-dependent macrophages are critically important for clearance of apoptotic thymocytes. These macrophages are largely reduced or absent in mice lacking NR4A1 and Nr4a1-deficient mice have impaired thymocyte engulfment and clearance. Thus, NR4A1 functions as a master transcription factor for the development of this novel thymus-specific macrophage subset.
Synthesis, characterization and observation of antisite defects in LiNiPO4 nanomaterials
Authors: Kempaiah Devaraju Murukanahally , Duc Truong Quang , Hyodo Hiroshi , Sasaki Yoshikazu , Honma Itaru 
Published: June 2015

AbstractStructural studies of high voltage cathode materials are necessary to understand their chemistry to improve the electrochemical performance for applications in lithium ion batteries. LiNiPO4 nanorods and nanoplates are synthesized via a one pot synthesis using supercritical fluid process at 450 oC for 10 min. The X-ray diffraction (XRD) analysis confirmed that LiNiPO4 phase is well crystallized, phase purity supported by energy dispersive spectroscopy (EDS) and elemental mapping by scanning electron transmission electron microscopy (STEM). For the first time, we have carried out direct visualization of atom-by-atom structural observation of LiNiPO4 nanomaterials using high-angle annular dark-field (HAADF) and annular bright-field (ABF) scanning transmission electron microscopy (STEM) analysis. The Rietveld refinement analysis was performed to find out the percentage of antisite defects presents in LiNiPO4 nanoplates and about 11% of antisite defects were found. Here, we provide the direct evidence for the presence of Ni atoms in Li sites and Li in Ni sites as an antisite defects are provided for understanding of electrochemical behavior of high voltage Li ion battery cathode materials.
Prediction models and risk assessment for silicosis using a retrospective cohort study among workers exposed to silica in China
Authors: Tse Lap Ah , Dai Juncheng , Chen Minghui , Liu Yuewei , Zhang Hao , Wong Tze Wai , Leung Chi Chiu , Kromhout Hans , Meijer Evert , Liu Su , Wang Feng , Yu Ignatius Tak-sun , Shen Hongbing , Chen Weihong 
Published: June 2015

AbstractThis study aims to develop a prognostic risk prediction model for the development of silicosis among workers exposed to silica dust in China. The prediction model was performed by using retrospective cohort of 3,492 workers exposed to silica in an iron ore, with 33 years of follow-up. We developed a risk score system using a linear combination of the predictors weighted by the LASSO penalized Cox regression coefficients. The model’s predictive accuracy was evaluated using time-dependent ROC curves. Six predictors were selected into the final prediction model (age at entry of the cohort, mean concentration of respirable silica, net years of dust exposure, smoking, illiteracy and no. of jobs). We classified workers into three risk groups according to the quartile (Q1, Q3) of risk score; 203 (23.28%) incident silicosis cases were derived from the high risk group (risk score ≥ 5.91), whilst only 4 (0.46%) cases were from the low risk group (risk score < 3.97). The score system was regarded as accurate given the range of AUCs (83–96%). This study developed a unique score system with a good internal validity, which provides scientific guidance to the clinicians to identify high-risk workers, thus has important cost efficient implications.
Transcriptomic and proteomic analysis of pre-diapause and non-diapause eggs of migratory locust, Locusta migratoria L. (Orthoptera: Acridoidea)
Authors: Tu Xiongbing , Wang Jie , Hao Kun , Whitman Douglas W. , Fan Yaoli , Cao Guangchun , Zhang Zehua 
Published: June 2015

AbstractLow temperature induces diapause in locusts. However, the physiological processes and initiation mechanism of diapause are not well understood. To understand the molecular basis of diapause, ‘omics’ analyses were performed to examine the differences between diapause and non-diapause eggs at both transcriptional and translational levels. Results indicated that a total of 62,241 mRNAs and 212 proteins were differentially expressed. Among them, 116 transcripts had concurrent transcription and translation profiles. Up-regulated genes related to diapause included glutathiones-S-transferase et al. and down-regulated genes including juvenile hormone esterase-like protein et al. KEGG analysis mapped 7,243 and 99 differentially expressed genes and proteins, to 83 and 25 pathways, respectively. Correlation enriched pathways indicated that there were nine identical pathways related to diapause. Gene Ontology analysis placed these genes and proteins into three categories and a higher proportion of genes related to metabolism was up-regulated than down-regulated. Furthermore, three up-regulated pathways were linked to cryoprotection. This study demonstrates the applicability of high-throughput omics tools to identify molecules linked to diapause in the locust. In addition, it reveals cellular metabolism in diapause eggs is more active than in non-diapause eggs and up-regulated enzymes may play roles in cryoprotection and storing energy for diapause and post-diapause stages.
Evolution of an Enzyme from a Noncatalytic Nucleic Acid Sequence
Authors: Gysbers Rachel , Tram Kha , Gu Jimmy , Li Yingfu 
Published: June 2015

AbstractThe mechanism by which enzymes arose from both abiotic and biological worlds remains an unsolved natural mystery. We postulate that an enzyme can emerge from any sequence of any functional polymer under permissive evolutionary conditions. To support this premise, we have arbitrarily chosen a 50-nucleotide DNA fragment encoding for the Bos taurus (cattle) albumin mRNA and subjected it to test-tube evolution to derive a catalytic DNA (DNAzyme) with RNA-cleavage activity. After only a few weeks, a DNAzyme with significant catalytic activity has surfaced. Sequence comparison reveals that seven nucleotides are responsible for the conversion of the noncatalytic sequence into the enzyme. Deep sequencing analysis of DNA pools along the evolution trajectory has identified individual mutations as the progressive drivers of the molecular evolution. Our findings demonstrate that an enzyme can indeed arise from a sequence of a functional polymer via permissive molecular evolution, a mechanism that may have been exploited by nature for the creation of the enormous repertoire of enzymes in the biological world today.
The lysophosphatidic acid receptor LPA4 regulates hematopoiesis-supporting activity of bone marrow stromal cells
Authors: Igarashi Hidemitsu , Akahoshi Noriyuki , Ohto-Nakanishi Takayo , Yasuda Daisuke , Ishii Satoshi 
Published: June 2015

AbstractLysophosphatidic acid (LPA) is a pleiotropic lipid mediator that acts through G protein-coupled receptors (LPA1-6). Although several biological roles of LPA4are becoming apparent, its role in hematopoiesis has remained unknown. Here, we show a novel regulatory role for LPA4in hematopoiesis.Lpar4 mRNA was predominantly expressed in mouse bone marrow (BM) PDGFRα+stromal cells, known as the components of the hematopoietic stem/progenitor cell (HSPC) niche. Compared with wild-type mice, LPA4-deficient mice had reduced HSPC numbers in the BM and spleen and were hypersusceptible to myelosuppression, most likely due to impairments in HSPC recovery and stem cell factor production in the BM. Analysis of reciprocal BM chimeras (LPA4-deficient BM into wild-type recipients andvice versa) indicated that stromal cells likely account for these phenotypes. Consistently, LPA4-deficient BM stromal cells showed downregulated mRNA expression of stem cell factor and tenascin-cin vitro. Taken together, these results suggest a critical and novel role for the LPA/LPA4axis in regulating BM stromal cells.
Large-area soft-imprinted nanowire networks as light trapping transparent conductors
Authors: van de Groep Jorik , Gupta Dhritiman , Verschuuren Marc A. , M. Wienk Martijn , Janssen Rene A. J. , Polman Albert 
Published: June 2015

AbstractUsing soft-imprint nanolithography, we demonstrate large-area application of engineered two-dimensional polarization-independent networks of silver nanowires as transparent conducting electrodes. These networks have high optical transmittance, low electrical sheet resistance and at the same time function as a photonic light-trapping structure enhancing optical absorption in the absorber layer of thin-film solar cells. We study the influence of nanowire width and pitch on the network transmittance and sheet resistance and demonstrate improved performance compared to ITO. Next, we use P3HT-PCBM organic solar cells as a model system to show the realization of nanowire network based functional devices. Using angle-resolved external quantum efficiency measurements, we demonstrate engineered light trapping by coupling to guided modes in the thin absorber layer of the solar cell. Concurrent to the direct observation of controlled light trapping we observe a reduction in photocurrent as a result of increased reflection and parasitic absorption losses; such losses can be minimized by re-optimization of the NW network geometry. Together, these results demonstrate how engineered 2D NW networks can serve as multifunctional structures that unify the functions of a transparent conductor and a light trapping structure. These results are generic and can be applied to any type of optoelectronic device.
Quantitative assessment of single-cell whole genome amplification methods for detecting copy number variation using hippocampal neurons
Authors: Ning Luwen , Li Zhoufang , Wang Guan , Hu Wen , Hou Qingming , Tong Yin , Zhang Meng , Chen Yao , Qin Li , Chen Xiaoping , Man Heng-Ye , Liu Pinghua , He Jiankui 
Published: June 2015

AbstractSingle-cell genomic analysis has grown rapidly in recent years and finds widespread applications in various fields of biology, including cancer biology, development, immunology, pre-implantation genetic diagnosis and neurobiology. To date, the amplification bias, amplification uniformity and reproducibility of the three major single cell whole genome amplification methods (GenomePlex WGA4, MDA and MALBAC) have not been systematically investigated using mammalian cells. In this study, we amplified genomic DNA from individual hippocampal neurons using three single-cell DNA amplification methods and sequenced them at shallow depth. We then systematically evaluated the GC-bias, reproducibility and copy number variations among individual neurons. Our results showed that single-cell genome sequencing results obtained from the MALBAC and WGA4 methods are highly reproducible and have a high success rate. The MALBAC displays significant biases towards high GC content. We then attempted to correct the GC bias issue by developing a bioinformatics pipeline, which allows us to call CNVs in single cell sequencing data and chromosome level and sub-chromosomal level CNVs among individual neurons can be detected. We also proposed a metric to determine the CNV detection limits. Overall, MALBAC and WGA4 have better performance than MDA in detecting CNVs.
The peculiarity of the metal-ceramic interface
Authors: Zhang Zaoli , Long Yao , Cazottes S. , Daniel R. , Mitterer C. , Dehm G. 
Published: June 2015

AbstractImportant properties of materials are strongly influenced or controlled by the presence of solid interfaces, i.e. from the atomic arrangement in a region which is a few atomic spacing wide. Using the quantitative analysis of atom column positions enabled by CS-corrected transmission electron microscopy and theoretical calculations, atom behaviors at and adjacent to the interface was carefully explored. A regular variation of Cu interplanar spacing at a representative metal-ceramic interface was experimentally revealed, i.e. Cu-MgO (001). We also found the periodic fluctuations of the Cu and Mg atomic positions triggered by the interfacial geometrical misfit dislocations, which are partially verified by theoretical calculations using empirical potential approach. Direct measurements of the bond length of Cu-O at the coherent regions of the interface showed close correspondence with theoretical results. By successively imaging of geometrical misfit dislocations at different crystallographic directions, the strain fields around the interfacial geometrical misfit dislocation are quantitatively demonstrated at a nearly three-dimensional view. A quantitative evaluation between the measured and calculated strain fields using simplified model around the geometrical misfit dislocation is shown.
MAP3K3 expression in tumor cells and tumor-infiltrating lymphocytes is correlated with favorable patient survival in lung cancer
Authors: He Yanli , Wang Lihui , Liu Weijun , Zhong Jinjie , Bai Shengbin , Wang Zhuwen , Thomas Dafydd G. , Lin Jules , Reddy Rishindra M. , Ramnath Nithya , Carrott Philip W. , Lynch William R. , Orringer Mark B. , Chang Andrew C. , Beer David G. , Chen Guoan 
Published: June 2015

AbstractMAP3K3 is involved in both the immune response and in tumor progression. Its potential biological role in vitro in lung cancer cell lines and the association of mRNA/protein expression patterns with clinical outcome of primary lung tumors were investigated in this study. Silencing MAP3K3 using siRNA in lung cancer cell lines resulted in decreased cell proliferation, migration and invasion. These effects were associated with down-regulation of the JNK, p38, AKT and GSK3β pathways as determined using phospho-protein and gene expression array analyses. However, MAP3K3 mRNA and protein overexpression in primary lung tumors correlated significantly with favorable patient survival. Gene cluster and pathway analyses of primary tumor datasets indicated that genes positively-correlated with MAP3K3 are significantly involved in immune response rather than the cell cycle regulators observed using in vitro analyses. These results indicate that although MAP3K3 overexpression has an oncogenic role in vitro, in primary lung adenocarcinomas it correlates with an active immune response in the tumor environment that correlates with improved patient survival. MAP3K3 may potentially not only serve as diagnostic/prognostic markers for patients with lung cancer but also provide an indicator for future investigations into immunomodulatory therapies for lung cancer.
Multiple levels of linguistic and paralinguistic features contribute to voice recognition
Authors: Mary Zarate Jean , Tian Xing , Woods Kevin J. P. , Poeppel David 
Published: June 2015

AbstractVoice or speaker recognition is critical in a wide variety of social contexts. In this study, we investigated the contributions of acoustic, phonological, lexical and semantic information toward voice recognition. Native English speaking participants were trained to recognize five speakers in five conditions: non-speech, Mandarin, German, pseudo-English and English. We showed that voice recognition significantly improved as more information became available, from purely acoustic features in non-speech to additional phonological information varying in familiarity. Moreover, we found that the recognition performance is transferable between training and testing in phonologically familiar conditions (German, pseudo-English and English), but not in unfamiliar (Mandarin) or non-speech conditions. These results provide evidence suggesting that bottom-up acoustic analysis and top-down influence from phonological processing collaboratively govern voice recognition.
Single Fluorescence Channel-based Multiplex Detection of Avian Influenza Virus by Quantitative PCR with Intercalating Dye
Authors: Ahrberg Christian D. , Manz Andreas , Neuzil Pavel 
Published: June 2015

AbstractSince its invention in 1985 the polymerase chain reaction (PCR) has become a well-established method for amplification and detection of segments of double-stranded DNA. Incorporation of fluorogenic probe or DNA intercalating dyes (such as SYBR Green) into the PCR mixture allowed real-time reaction monitoring and extraction of quantitative information (qPCR). Probes with different excitation spectra enable multiplex qPCR of several DNA segments using multi-channel optical detection systems. Here we show multiplex qPCR using an economical EvaGreen-based system with single optical channel detection. Previously reported non quantitative multiplex real-time PCR techniques based on intercalating dyes were conducted once the PCR is completed by performing melting curve analysis (MCA). The technique presented in this paper is both qualitative and quantitative as it provides information about the presence of multiple DNA strands as well as the number of starting copies in the tested sample. Besides important internal control, multiplex qPCR also allows detecting concentrations of more than one DNA strand within the same sample. Detection of the avian influenza virus H7N9 by PCR is a well established method. Multiplex qPCR greatly enhances its specificity as it is capable of distinguishing both haemagglutinin (HA) and neuraminidase (NA) genes as well as their ratio.
Interfacial reaction control and its mechanism of AlN epitaxial films grown on Si(111) substrates by pulsed laser deposition
Authors: Wang Wenliang , Yang Weijia , Liu Zuolian , Wang Haiyan , Wen Lei , Li Guoqiang 
Published: June 2015

AbstractHigh-quality AlN epitaxial films have been grown on Si substrates by pulsed laser deposition (PLD) by effective control of the interfacial reactions between AlN films and Si substrates. The surface morphology, crystalline quality and interfacial property of as-grown AlN/Si hetero-interfaces obtained by PLD have been systemically studied. It is found that the amorphous SiAlN interfacial layer is formed during high temperature growth, which is ascribed to the serious interfacial reactions between Si atoms diffused from the substrates and the AlN plasmas produced by the pulsed laser when ablating the AlN target during the high temperature growth. On the contrary, abrupt and sharp AlN/Si hetero-interfaces can be achieved by effectively controlling the interfacial reactions at suitable growth temperature. The mechanisms for the evolution of interfacial layer from the amorphous SiAlN layer to the abrupt and sharp AlN/Si hetero-interfaces by PLD are hence proposed. This work of obtaining the abrupt interfaces and the flat surfaces for AlN films grown by PLD is of paramount importance for the application of high-quality AlN-based devices on Si substrates.
Impairment of Caloric Function After Cochlear Implantation
Authors: Kuang Heide , Haversat Heather H. , Michaelides Elias M. 
Published: June 2015

Purpose
This article seeks to review current literature on caloric function following cochlear implantation while analyzing any correlations of caloric function changes with vestibular symptoms.

Method
This article is a systematic review of evidence-based literature. English language articles published between 1980 and 2014 that presented some form of caloric data from cochlear implant (CI) patients and that did not solely analyze overlapping data from a previous study were reviewed. Twenty-five articles met these criteria.

Results
Of the 439 individuals tested, 37% of patients demonstrated reduced maximum slow-phase velocity, and 34% had onset of caloric asymmetry post-CI.

Conclusions
This review article found that cochlear implantation can affect caloric responses but is variable. When counseling patients preoperatively, possible effects of CI on labyrinthine function should be discussed.