bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple region whole-exome sequencing reveals dramatically evolving intratumor genomic heterogeneity in esophageal squamous cell carcinoma
Authors: Cao W , Wu W , Yan M , Tian F , Ma C , Zhang Q , Li X , Han P , Liu Z , Gu J , Biddle F G 
Published: November 2015

AbstractCancer is a disease of genome instability and genomic alterations; now, genomic heterogeneity is rapidly emerging as a defining feature of cancer, both within and between tumors. Motivation for our pilot study of tumor heterogeneity in esophageal squamous cell carcinoma (ESCC) is that it is not well studied, but the highest incidences of esophageal cancers are found in China and ESCC is the most common type. We profiled the mutations and changes in copy number that were identified by whole-exome sequencing and array-based comparative genomic hybridization in multiple regions within an ESCC from two patients. The average mutational heterogeneity rate was 90% in all regions of the individual tumors in each patient; most somatic point mutations were nonsynonymous substitutions, small Indels occurred in untranslated regions of genes, and copy number alterations varied among multiple regions of a tumor. Independent Sanger sequencing technology confirmed selected gene mutations with more than 88% concordance. Phylogenetic analysis of the somatic mutation frequency demonstrated that multiple, genomically heterogeneous divergent clones evolve and co-exist within a primary ESCC and metastatic subclones result from the dispersal and adaptation of an initially non-metastatic parental clone. Therefore, a single-region sampling will not reflect the evolving architecture of a genomically heterogeneous landscape of mutations in ESCC tumors and the divergent complexity of this genomic heterogeneity among patients will complicate any promise of a simple genetic or epigenetic diagnostic signature in ESCC. We conclude that any potential for informative biomarker discovery in ESCC and targeted personalized therapies will require a deeper understanding of the functional biology of the ontogeny and phylogeny of the tumor heterogeneity.
Long-period ocean-bottom motions in the source areas of large subduction earthquakes
Authors: Nakamura Takeshi , Takenaka Hiroshi , Okamoto Taro , Ohori Michihiro , Tsuboi Seiji 
Published: November 2015

AbstractLong-period ground motions in plain and basin areas on land can cause large-scale, severe damage to structures and buildings and have been widely investigated for disaster prevention and mitigation. However, such motions in ocean-bottom areas are poorly studied because of their relative insignificance in uninhabited areas and the lack of ocean-bottom strong-motion data. Here, we report on evidence for the development of long-period (10–20 s) motions using deep ocean-bottom data. The waveforms and spectrograms demonstrate prolonged and amplified motions that are inconsistent with attenuation patterns of ground motions on land. Simulated waveforms reproducing observed ocean-bottom data demonstrate substantial contributions of thick low-velocity sediment layers to development of these motions. This development, which could affect magnitude estimates and finite fault slip modelling because of its critical period ranges on their estimations, may be common in the source areas of subduction earthquakes where thick, low-velocity sediment layers are present.
Lowering N2O emissions from soils using eucalypt biochar: the importance of redox reactions
Authors: Quin P , Joseph S , Husson O , Donne S , Mitchell D , Munroe P , Phelan D , Cowie A , Van Zwieten L 
Published: November 2015

AbstractAgricultural soils are the primary anthropogenic source of atmospheric nitrous oxide (N2O), contributing to global warming and depletion of stratospheric ozone. Biochar addition has shown potential to lower soil N2O emission, with the mechanisms remaining unclear. We incubated eucalypt biochar (550 °C) – 0, 1 and 5% (w/w) in Ferralsol at 3 water regimes (12, 39 and 54% WFPS) – in a soil column, following gamma irradiation. After N2O was injected at the base of the soil column, in the 0% biochar control 100% of expected injected N2O was released into headspace, declining to 67% in the 5% amendment. In a 100% biochar column at 6% WFPS, only 16% of the expected N2O was observed. X-ray photoelectron spectroscopy identified changes in surface functional groups suggesting interactions between N2O and the biochar surfaces. We have shown increases in -O-C = N /pyridine pyrrole/NH3, suggesting reactions between N2O and the carbon (C) matrix upon exposure to N2O. With increasing rates of biochar application, higher pH adjusted redox potentials were observed at the lower water contents. Evidence suggests that biochar has taken part in redox reactions reducing N2O to dinitrogen (N2), in addition to adsorption of N2O.
The glassy random laser: replica symmetry breaking in the intensity fluctuations of emission spectra
Authors: Antenucci Fabrizio , Crisanti Andrea , Leuzzi Luca 
Published: November 2015

AbstractThe behavior of a newly introduced overlap parameter, measuring the correlation between intensity fluctuations of waves in random media, is analyzed in different physical regimes, with varying amount of disorder and non-linearity. This order parameter allows to identify the laser transition in random media and describes its possible glassy nature in terms of emission spectra data, the only data so far accessible in random laser measurements. The theoretical analysis is performed in terms of the complex spherical spin-glass model, a statistical mechanical model describing the onset and the behavior of random lasers in open cavities. Replica Symmetry Breaking theory allows to discern different kinds of randomness in the high pumping regime, including the most complex and intriguing glassy randomness. The outcome of the theoretical study is, eventually, compared to recent intensity fluctuation overlap measurements demonstrating the validity of the theory and providing a straightforward interpretation of qualitatively different spectral behaviors in different random lasers.
P311 promotes renal fibrosis via TGFβ1/Smad signaling
Authors: Yao Zhihui , Yang Sisi , He Weifeng , Li Lian , Xu Rui , Zhang Xiaorong , Li Haisheng , Zhan Rixing , Sun Wei , Tan Jianglin , Zhou Junyi , Luo Gaoxing , Wu Jun 
Published: November 2015

AbstractP311, a gene that was identified in 1993, has been found to have diverse biological functions in processes such as cell proliferation, migration and differentiation. However, its role in fibrosis is unknown. We previously observed that P311 is highly expressed in skin hypertrophic scars. In this study, P311 over-expression was detected in a subset of tubular epithelial cells in clinical biopsy specimens of renal fibrosis; this over-expression, was found concurrent with α-smooth muscle actin (α-SMA) and transforming growth factor beta1 (TGFβ1) expression. Subsequently, these results were verified in a mouse experimental renal fibrosis model induced by unilateral ureteral obstruction. The interstitial deposition of collagen, α-SMA and TGF-β1 expression and macrophage infiltration were dramatically decreased when P311 was knocked out. Moreover, TGFβ/Smad signaling had a critical effect on the promotion of renal fibrosis by P311. In conclusion, this study demonstrate that P311 plays a key role in renal fibrosis via TGFβ1/Smad signaling, which could be a novel target for the management of renal fibrosis.
Compact Shielding of Graphene Monolayer Leads to Extraordinary SERS-Active Substrate with Large-Area Uniformity and Long-Term Stability
Authors: Liu Xiangjiang , Wang Jiajun , Wu Yichen , Fan Tianren , Xu Yang , Tang Longhua , Ying Yibin 
Published: November 2015

AbstractSurface-enhanced Raman scattering (SERS) can significantly boost the inherently weak Raman scattering signal and provide detailed structural information and binding nature of the molecules on the surface. Despite the long history of this technology, SERS has yet to become a sophisticated analytical tool in practical applications. A major obstacle is the absence of high-quality and stable SERS-active substrate. In this work, we report a monolayer graphene-shielded periodic metallic nanostructure as large-area uniform and long-term stable SERS substrate. The monolayer graphene acting as a corrosion barrier, not only greatly enhanced stability, but also endowed many new features to the substrate, such as alleviating the photo-induced damages and improving the detection sensitivity for certain analytes that are weakly adsorbed on the conventional metallic substrates. Besides, our fabrication strategy were also capable of fabricating the reproducible SERS sensing spots array, which may serve as a promising high-throughput or multi-analyte sensing platform. Taken together, the graphene-shielded SERS substrate holds great promise both in fundamental studies of the SERS effect and many practical fields.
Impacts of IOD, ENSO and ENSO Modoki on the Australian Winter Wheat Yields in Recent Decades
Authors: Yuan Chaoxia , Yamagata Toshio 
Published: November 2015

AbstractImpacts of the Indian Ocean Dipole (IOD), two different types of El Niño/Southern Oscillation (ENSO): canonical ENSO and ENSO Modoki, on the year-to-year winter wheat yield variations in Australia have been investigated. It is found that IOD plays a dominant role in the recent three decades; the wheat yield is reduced (increased) by −28.4% (12.8%) in the positive (negative) IOD years. Although the canonical ENSO appears to be responsible for the wheat yield variations, its influences are largely counted by IOD owing to their frequent co-occurrence. In contrast, the ENSO Modoki may have its distinct impacts on the wheat yield variations, but they are much smaller compared to those of IOD. Both the observed April-May and the predicted September-November IOD indices by the SINTEX-F ocean-atmosphere coupled model initialized on April 1st just before the sowing season explain ~15% of the observed year-to-year wheat yield variances. The present study may lead to a possible scheme for predicting wheat yield variations in Australia in advance by use of simple climate mode indices.
Human Granulocyte Macrophage Colony-Stimulating Factor Enhances Antibiotic Susceptibility of Pseudomonas aeruginosa Persister Cells
Authors: Choudhary Geetika S. , Yao Xiangyu , Wang Jing , Peng Bo , Bader Rebecca A. , Ren Dacheng 
Published: November 2015

AbstractBacterial persister cells are highly tolerant to antibiotics and cause chronic infections. However, little is known about the interaction between host immune systems with this subpopulation of metabolically inactive cells and direct effects of host immune factors (in the absence of immune cells) on persister cells have not been studied. Here we report that human granulocyte macrophage-colony stimulating factor (GM-CSF) can sensitize the persister cells of Pseudomonas aeruginosa PAO1 and PDO300 to multiple antibiotics including ciprofloxacin, tobramycin, tetracycline and gentamicin. GM-CSF also sensitized the biofilm cells of P. aeruginosa PAO1 and PDO300 to tobramycin in the presence of biofilm matrix degrading enzymes. The DNA microarray and qPCR results indicated that GM-CSF induced the genes for flagellar motility and pyocin production in the persister cells, but not the normal cells of P. aeruginosa PAO1. Consistently, the supernatants from GM-CSF treated P. aeruginosa PAO1 persister cell suspensions were found cidal to the pyocin sensitive strain P. aeruginosa PAK. Collectively, these findings suggest that host immune factors and bacterial persisters may directly interact, leading to enhanced susceptibility of persister cells to antibiotics.
Isolation of exosomes by differential centrifugation: Theoretical analysis of a commonly used protocol
Authors: Livshits Mikhail A. , Khomyakova Elena , Evtushenko Evgeniy G. , Lazarev Vassili N. , Kulemin Nikolay A. , Semina Svetlana E. , Generozov Edward V. , Govorun Vadim M. 
Published: November 2015

AbstractExosomes, small (40–100 nm) extracellular membranous vesicles, attract enormous research interest because they are carriers of disease markers and a prospective delivery system for therapeutic agents. Differential centrifugation, the prevalent method of exosome isolation, frequently produces dissimilar and improper results because of the faulty practice of using a common centrifugation protocol with different rotors. Moreover, as recommended by suppliers, adjusting the centrifugation duration according to rotor K-factors does not work for “fixed-angle” rotors. For both types of rotors – “swinging bucket” and “fixed-angle” – we express the theoretically expected proportion of pelleted vesicles of a given size and the “cut-off” size of completely sedimented vesicles as dependent on the centrifugation force and duration and the sedimentation path-lengths. The proper centrifugation conditions can be selected using relatively simple theoretical estimates of the “cut-off” sizes of vesicles. Experimental verification on exosomes isolated from HT29 cell culture supernatant confirmed the main theoretical statements. Measured by the nanoparticle tracking analysis (NTA) technique, the concentration and size distribution of the vesicles after centrifugation agree with those theoretically expected. To simplify this “cut-off”-size-based adjustment of centrifugation protocol for any rotor, we developed a web-calculator.
Local structure of human hair spatially resolved by sub-micron X-ray beam
Authors: Stanić Vesna , Bettini Jefferson , Montoro Fabiano Emmanuel , Stein Aaron , Evans-Lutterodt Kenneth 
Published: November 2015

AbstractHuman hair has three main regions, the medulla, the cortex and the cuticle. An existing model for the cortex suggests that the α-keratin- based intermediate filaments (IFs) align with the hair’s axis, but are orientationally disordered in-plane. We found that there is a new region in the cortex near the cuticle’s boundary in which the IFs are aligned with the hair’s axis, but additionally, they are orientationally ordered in-plane due to the presence of the cuticle/hair boundary. Further into the cortex, the IF arrangement becomes disordered, eventually losing all in-plane orientation. We also find that in the cuticle, a key diffraction feature is absent, indicating the presence of the β-keratin rather than that of the α-keratin phase. This is direct structural evidence that the cuticle contains β-keratin sheets. This work highlights the importance of using a sub-micron x-ray beam to unravel the structures of poorly ordered, multi-phase systems.
Confirmation of co-denitrification in grazed grassland
Authors: Selbie Diana R. , Lanigan Gary J. , Laughlin Ronald J. , Di Hong J. , Moir James L. , Cameron Keith C. , Clough Tim J. , Watson Catherine J. , Grant James , Somers Cathal , Richards Karl G. 
Published: November 2015

AbstractPasture-based livestock systems are often associated with losses of reactive forms of nitrogen (N) to the environment. Research has focused on losses to air and water due to the health, economic and environmental impacts of reactive N. Di-nitrogen (N2) emissions are still poorly characterized, both in terms of the processes involved and their magnitude, due to financial and methodological constraints. Relatively few studies have focused on quantifying N2 losses in vivo and fewer still have examined the relative contribution of the different N2 emission processes, particularly in grazed pastures. We used a combination of a high 15N isotopic enrichment of applied N with a high precision of determination of 15N isotopic enrichment by isotope-ratio mass spectrometry to measure N2 emissions in the field. We report that 55.8 g N m−2 (95%, CI 38 to 77 g m−2) was emitted as N2 by the process of co-denitrification in pastoral soils over 123 days following urine deposition (100 g N m−2), compared to only 1.1 g N m−2 (0.4 to 2.8 g m−2) from denitrification. This study provides strong evidence for co-denitrification as a major N2 production pathway, which has significant implications for understanding the N budgets of pastoral ecosystems.
Electric-field-assisted formation of an interfacial double-donor molecule in silicon nano-transistors
Authors: Samanta Arup , Moraru Daniel , Mizuno Takeshi , Tabe Michiharu 
Published: November 2015

AbstractControl of coupling of dopant atoms in silicon nanostructures is a fundamental challenge for dopant-based applications. However, it is difficult to find systems of only a few dopants that can be directly addressed and, therefore, experimental demonstration has not yet been obtained. In this work, we identify pairs of donor atoms in the nano-channel of a silicon field-effect transistor and demonstrate merging of the donor-induced potential wells at the interface by applying vertical electric field. This system can be described as an interfacial double-donor molecule. Single-electron tunneling current is used to probe the modification of the potential well. When merging occurs at the interface, the gate capacitance of the potential well suddenly increases, leading to an abrupt shift of the tunneling current peak to lower gate voltages. This is due to the decrease of the system’s charging energy, as confirmed by Coulomb blockade simulations. These results represent the first experimental observation of electric-field-assisted formation of an interfacial double-donor molecule, opening a pathway for designing functional devices using multiple coupled dopant atoms.
Fragmented mitochondrial genomes in two suborders of parasitic lice of eutherian mammals (Anoplura and Rhynchophthirina, Insecta)
Authors: Shao Renfu , Barker Stephen C , Li Hu , Song Simon , Poudel Shreekanta , Su Yuan 
Published: November 2015

AbstractParasitic lice (order Phthiraptera) infest birds and mammals. The typical animal mitochondrial (mt) genome organization, which consists of a single chromosome with 37 genes, was found in chewing lice in the suborders Amblycera and Ischnocera. The sucking lice (suborder Anoplura) known, however, have fragmented mt genomes with 9–20 minichromosomes. We sequenced the mt genome of the elephant louse, Haematomyzus elephantis – the first species of chewing lice investigated from the suborder Rhynchophthirina. We identified 33 mt genes in the elephant louse, which were on 10 minichromosomes. Each minichromosome is 3.5–4.2 kb in size and has 2–6 genes. Phylogenetic analyses of mt genome sequences confirm that the elephant louse is more closely related to sucking lice than to the chewing lice in the Amblycera and Ischnocera. Our results indicate that mt genome fragmentation is shared by the suborders Anoplura and Rhynchophthirina. Nine of the 10 mt minichromosomes of the elephant louse differ from those of the sucking lice (Anoplura) known in gene content and gene arrangement, indicating that distinct mt karyotypes have evolved in Anoplura and Rhynchophthirina since they diverged ~92 million years ago.
Dopant morphology as the factor limiting graphene conductivity
Authors: Hofmann Mario , Hsieh Ya-Ping , Chang Kai-Wen , Tsai He-Guang , Chen Tzung-Te 
Published: November 2015

AbstractGraphene’s low intrinsic carrier concentration necessitates extrinsic doping to enhance its conductivity and improve its performance for application as electrodes or transparent conductors. Despite this importance limited knowledge of the doping process at application-relevant conditions exists. Employing in-situ carrier transport and Raman characterization of different dopants, we here explore the fundamental mechanisms limiting the effectiveness of doping at different doping levels. Three distinct transport regimes for increasing dopant concentration could be identified. First the agglomeration of dopants into clusters provides a route to increase the graphene conductivity through formation of ordered scatterers. As the cluster grows, the charge transfer efficiency between graphene and additional dopants decreases due to emerging polarization effects. Finally, large dopant clusters hinder the carrier motion and cause percolative transport that leads to an unexpected change of the Hall effect. The presented results help identifying the range of beneficial doping density and guide the choice of suitable dopants for graphene’s future applications.
Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement
Authors: De Vega Jose J. , Ayling Sarah , Hegarty Matthew , Kudrna Dave , Goicoechea Jose L. , Ergon Åshild , Rognli Odd A. , Jones Charlotte , Swain Martin , Geurts Rene , Lang Chunting , Mayer Klaus F. X. , Rössner Stephan , Yates Steven , Webb Kathleen J. , Donnison Iain S. , Oldroyd Giles E. D. , Wing Rod A. , Caccamo Mario , Powell Wayne , Abberton Michael T. , Skøt Leif 
Published: November 2015

AbstractRed clover (Trifolium pratense L.) is a globally significant forage legume in pastoral livestock farming systems. It is an attractive component of grassland farming, because of its high yield and protein content, nutritional value and ability to fix atmospheric nitrogen. Enhancing its role further in sustainable agriculture requires genetic improvement of persistency, disease resistance and tolerance to grazing. To help address these challenges, we have assembled a chromosome-scale reference genome for red clover. We observed large blocks of conserved synteny with Medicago truncatula and estimated that the two species diverged ~23 million years ago. Among the 40,868 annotated genes, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition. Genotyping by sequencing of a synthetic population of 86 genotypes show that the number of markers required for genomics-based breeding approaches is tractable, making red clover a suitable candidate for association studies and genomic selection.
Electrospun interconnected Fe-N/C nanofiber networks as efficient electrocatalysts for oxygen reduction reaction in acidic media
Authors: Wu Nan , Wang Yingde , Lei Yongpeng , Wang Bing , Han Cheng , Gou Yanzi , Shi Qi , Fang Dong 
Published: November 2015

AbstractOne-dimensional electrospun nanofibers have emerged as a potential candidate for high-performance oxygen reduction reaction (ORR) catalysts. However, contact resistance among the neighbouring nanofibers hinders the electron transport. Here, we report the preparation of interconnected Fe-N/C nanofiber networks (Fe-N/C NNs) with low electrical resistanceviaelectrospinning followed by maturing and pyrolysis. The Fe-N/C NNs show excellent ORR activity with onset and half-wave potential of 55 and 108 mV less than those of Pt/C catalyst in 0.5 M H2SO4. Intriguingly, the resulting Fe-N/C NNs exhibit 34% higher peak current density and superior durability than generic Fe-N/C ones with similar microstructure and chemical compositions. Additionally, it also displays much better durability and methanol tolerance than Pt/C catalyst. The higher electroactivity is mainly due to the more effective electron transport between the interconnected nanofibers. Thus, our findings provide a novel insight into the design of functional electrospun nanofibers for the application in energy storage and conversion fields.