bluuebunny/crossref_metadata_2025_split huggingface dataset:
A social-ecological framework for analyzing and designing integrated crop–livestock systems from farm to territory levels
Authors: Moraine Marc , Duru Michel , Therond Olivier 
Published: January 2016

AbstractIntegrated crop–livestock systems are often considered a promising way to address agricultural sustainability issues. Many authors claim that complementarities and synergies between crops and livestock can improve nutrient cycling and delivery of ecosystem services (ES) in agricultural systems. They have analyzed effects of interactions at the farm level and affirmed the potential advantage of developing crop–livestock interactions at the territory level. However, potential benefits of developing synergies beyond the farm level have not been clearly identified. Thus, we developed a conceptual framework that can be used to analyze, design and perform integrated assessment of crop–livestock systems at the territory level. To address crop–livestock interaction issues, we define it as a social-ecological system called the territorial crop–livestock system (TCLS). The ecological system is represented as three interacting components, crops, grasslands and animals, allowing description of various land uses and their potential effects on nutrient cycling and ES. The social system, represented as farmers interacting with natural-resource managers and agro-food chain actors, determines land use and the nature and intensity of ES delivered. We highlight the importance of coordination and learning among actors to support implementation of complex adaptive systems such as TCLSs. We illustrate the expressive power of our conceptual framework through development of a generic typology of crop–livestock systems. Then we show how our conceptual framework can be used as an intermediary object with stakeholders in participatory design approaches. We illustrate this process by representing four archetypal TCLSs. We provide an example of the design approach implemented in Southwestern France to address severe recurrent water shortages, which includes analysis of land use in the current crop–livestock system and the associated key metabolic and ES issues, identification of options for change and multi-criteria analysis of these options. We conclude that this framework shows great potential to support development of sustainable farming systems at the territory level.
Shaping the nonlinear near field
Authors: Wolf Daniela , Schumacher Thorsten , Lippitz Markus 
Published: January 2016

AbstractLight scattering at plasmonic nanoparticles and their assemblies has led to a wealth of applications in metamaterials and nano-optics. Although shaping of fields around nanostructures is widely studied, the influence of the field inside the nanostructures is often overlooked. The linear field distribution inside the structure taken to the third power causes third-harmonic generation, a nonlinear optical response of matter. Here we demonstrate by a far field Fourier imaging method how this simple fact can be used to shape complex fields around a single particle alone. We employ this scheme to switch the third-harmonic emission from a single point source to two spatially separated but coherent sources, as in Young’s double-slit assembly. We envision applications as diverse as coherently feeding antenna arrays and optical spectroscopy of spatially extended electronic states.
Endogenous IL-6 of mesenchymal stem cell improves behavioral outcome of hypoxic-ischemic brain damage neonatal rats by supressing apoptosis in astrocyte
Authors: Gu Yan , He Mulan , Zhou Xiaoqin , Liu Jinngjing , Hou Nali , Bin Tan , Zhang Yun , Li Tingyu , Chen Jie 
Published: January 2016

AbstractMesenchymal stem cell (MSC) transplantation reduces the neurological impairment caused by hypoxic-ischemic brain damage (HIBD) via immunomodulation. In the current study, we found that MSC transplantation improved learning and memory function and enhanced long-term potentiation in neonatal rats subjected to HIBD and the amount of IL-6 released from MSCs was far greater than that of other cytokines. However, the neuroprotective effect of MSCs infected with siIL-6-transduced recombinant lentivirus (siIL-6 MSCs) was significantly weakened in the behavioural tests and electrophysiological analysis. Meanwhile, the hippocampal IL-6 levels were decreased following siIL-6 MSC transplantation. In vitro, the levels of IL-6 release and the levels of IL-6R and STAT3 expression were increased in both primary neurons and astrocytes subjected to oxygen and glucose deprivation (OGD) following MSCs co-culture. The anti-apoptotic protein Bcl-2 was upregulated and the pro-apoptotic protein Bax was downregulated in OGD-injured astrocytes co-cultured with MSCs. However, the siIL-6 MSCs suppressed ratio of Bcl-2/Bax in the injured astrocytes and induced apoptosis number of the injured astrocytes. Taken together, these data suggest that the neuroprotective effect of MSC transplantation in neonatal HIBD rats is partly mediated by IL-6 to enhance anti-apoptosis of injured astrocytes via the IL-6/STAT3 signaling pathway.
Two-dimensional Topological Crystalline Insulator Phase in Sb/Bi Planar Honeycomb with Tunable Dirac Gap
Authors: Hsu Chia-Hsiu , Huang Zhi-Quan , Crisostomo Christian P. , Yao Liang-Zi , Chuang Feng-Chuan , Liu Yu-Tzu , Wang Baokai , Hsu Chuang-Han , Lee Chi-Cheng , Lin Hsin , Bansil Arun 
Published: January 2016

AbstractWe predict planar Sb/Bi honeycomb to harbor a two-dimensional (2D) topological crystalline insulator (TCI) phase based on first-principles computations. Although buckled Sb and Bi honeycombs support 2D topological insulator (TI) phases, their structure becomes planar under tensile strain. The planar Sb/Bi honeycomb structure restores the mirror symmetry and is shown to exhibit non-zero mirror Chern numbers, indicating that the system can host topologically protected edge states. Our computations show that the electronic spectrum of a planar Sb/Bi nanoribbon with armchair or zigzag edges contains two Dirac cones within the band gap and an even number of edge bands crossing the Fermi level. Lattice constant of the planar Sb honeycomb is found to nearly match that of hexagonal-BN. The Sb nanoribbon on hexagonal-BN exhibits gapped edge states, which we show to be tunable by an out-of-the-plane electric field, providing controllable gating of edge state important for device applications.
A Search for Blood Biomarkers for Autism: Peptoids
Authors: Zaman Sayed , Yazdani Umar , Deng Yan , Li Wenhao , Gadad Bharathi S. , Hynan Linda , Karp David , Roatch Nichole , Schutte Claire , Nathan Marti C. , Hewitson Laura , German Dwight C. 
Published: January 2016

AbstractAutism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impairments in social interaction and communication and restricted, repetitive patterns of behavior. In order to identify individuals with ASD and initiate interventions at the earliest possible age, biomarkers for the disorder are desirable. Research findings have identified widespread changes in the immune system in children with autism, at both systemic and cellular levels. In an attempt to find candidate antibody biomarkers for ASD, highly complex libraries of peptoids (oligo-N-substituted glycines) were screened for compounds that preferentially bind IgG from boys with ASD over typically developing (TD) boys. Unexpectedly, many peptoids were identified that preferentially bound IgG from TD boys. One of these peptoids was studied further and found to bind significantly higher levels (>2-fold) of the IgG1 subtype in serum from TD boys (n = 60) compared to ASD boys (n = 74), as well as compared to older adult males (n = 53). Together these data suggest that ASD boys have reduced levels (>50%) of an IgG1 antibody, which resembles the level found normally with advanced age. In this discovery study, the ASD1 peptoid was 66% accurate in predicting ASD.
Regulation of Asymmetric Division by Atypical Protein Kinase C Influences Early Specification of CD8+ T Lymphocyte Fates
Authors: Metz Patrick J. , Lopez Justine , Kim Stephanie H. , Akimoto Kazunori , Ohno Shigeo , Chang John T. 
Published: January 2016

AbstractNaïve CD8+ T lymphocytes responding to microbial pathogens give rise to effector T cells that provide acute defense and memory T cells that provide long-lived immunity. Upon activation, CD8+ T lymphocytes can undergo asymmetric division, unequally distributing factors to the nascent daughter cells that influence their eventual fate towards the effector or memory lineages. Individual loss of either atypical protein kinase C (aPKC) isoform, PKCζ or PKCλ/ι, partially impairs asymmetric divisions and increases CD8+ T lymphocyte differentiation toward a long-lived effector fate at the expense of memory T cell formation. Here, we show that deletion of both aPKC isoforms resulted in a deficit in asymmetric divisions, increasing the proportion of daughter cells that inherit high amounts of effector fate-associated molecules, IL-2Rα, T-bet, IFNγR and interferon regulatory factor 4 (IRF4). However, unlike CD8+ T cells deficient in only one aPKC isoform, complete loss of aPKC unexpectedly increased CD8+ T cell differentiation toward a short-lived, terminal effector fate, as evidenced by increased rates of apoptosis and decreased expression of Eomes and Bcl2 early during the immune response. Together, these results provide evidence for an important role for asymmetric division in CD8+ T lymphocyte fate specification by regulating the balance between effector and memory precursors at the initiation of the adaptive immune response.
Wnt9a deficiency discloses a repressive role of Tcf7l2 on endocrine differentiation in the embryonic pancreas
Authors: Pujadas G. , Cervantes S. , Tutusaus A. , Ejarque M. , Sanchez L. , García A. , Esteban Y. , Fargas L. , Alsina B. , Hartmann C. , Gomis R. , Gasa R. 
Published: January 2016

AbstractTranscriptional and signaling networks establish complex cross-regulatory interactions that drive cellular differentiation during development. Using microarrays we identified the gene encoding the ligand Wnt9a as a candidate target of Neurogenin3, a basic helix-loop-helix transcription factor that functions as a master regulator of pancreatic endocrine differentiation. Here we show that Wnt9a is expressed in the embryonic pancreas and that its deficiency enhances activation of the endocrine transcriptional program and increases the number of endocrine cells at birth. We identify the gene encoding the endocrine transcription factor Nkx2-2 as one of the most upregulated genes in Wnt9a-ablated pancreases and associate its activation to reduced expression of the Wnt effector Tcf7l2. Accordingly, in vitro studies confirm that Tcf7l2 represses activation of Nkx2-2 by Neurogenin3 and inhibits Nkx2-2 expression in differentiated β-cells. Further, we report that Tcf7l2 protein levels decline upon initiation of endocrine differentiation in vivo, disclosing the downregulation of this factor in the developing endocrine compartment. These findings highlight the notion that modulation of signalling cues by lineage-promoting factors is pivotal for controlling differentiation programs.
Focal Adhesion Kinase Regulates Fibroblast Migration via Integrin beta-1 and Plays a Central Role in Fibrosis
Authors: Zhao Xue-Ke , Cheng Yiju , Liang Cheng Ming , Yu Lei , Mu Mao , Li Hong , Liu Yang , Zhang Baofang , Yao Yumei , Guo Hui , Wang Rong , Zhang Quan 
Published: January 2016

AbstractLung fibrosis is a major medical problem for the aging population worldwide. Fibroblast migration plays an important role in fibrosis. Focal Adhesion Kinase (FAK) senses the extracellular stimuli and initiates signaling cascades that promote cell migration. This study first examined the dose and time responses of FAK activation in human lung fibroblasts treated with platelet derived growth factor BB (PDGF-BB). The data indicate that FAK is directly recruited by integrin β1 and the subsequent FAK activation is required for fibroblast migration on fibronectin. In addition, the study has identified that α5β1 and α4β1 are the major integrins for FAK-mediated fibroblast migration on fibronect. In contrast, integrins αvβ3, αvβ6 and αvβ8 play a minor but distinct role in fibroblast migration on fibronectin. FAK inhibitor significantly reduces PDGF-BB stimulated fibroblast migration. Importantly, FAK inhibitor protects bleomycin-induced lung fibrosis in mice. FAK inhibitor blocks FAK activation and significantly reduces signaling cascade of fibroblast migration in bleomycin-challenged mice. Furthermore, FAK inhibitor decreases lung fibrotic score, collagen accumulation, fibronectin production and myofibroblast differentiation in in bleomycin-challenged mice. These data demonstrate that FAK mediates fibroblast migration mainly via integrin β1. Furthermore, the findings suggest that targeting FAK signaling is an effective therapeutic strategy against fibrosis.
Angle Insensitive Color Filters in Transmission Covering the Visible Region
Authors: Mao Kening , Shen Weidong , Yang Chenying , Fang Xu , Yuan Wenjia , Zhang Yueguang , Liu Xu 
Published: January 2016

AbstractAngle insensitive color filter based on Metal-SiOx-Metal structure is proposed in this paper, which can keep the same perceived transmitted color when the incidence angle changes from 0° to 60°, especially for p-polarization light. Various silicon oxide films deposited by reaction magnetron sputtering with a tunable refractive index from 1.97 to 3.84 is introduced to meet the strict angle insensitive resonance conditions. The angle resolved spectral filtering for both p-polarization light and s-polarization light are quite well, which can be attributed to the different physical origins for the high angular tolerance for two polarizations. Finally, the effect of SiOx absorption and Ag thickness on the peak transmittance are analyzed.
Benchmarking Deep Networks for Predicting Residue-Specific Quality of Individual Protein Models in CASP11
Authors: Liu Tong , Wang Yiheng , Eickholt Jesse , Wang Zheng 
Published: January 2016

AbstractQuality assessment of a protein model is to predict the absolute or relative quality of a protein model using computational methods before the native structure is available. Single-model methods only need one model as input and can predict the absolute residue-specific quality of an individual model. Here, we have developed four novel single-model methods (Wang_deep_1, Wang_deep_2, Wang_deep_3 and Wang_SVM) based on stacked denoising autoencoders (SdAs) and support vector machines (SVMs). We evaluated these four methods along with six other methods participating in CASP11 at the global and local levels using Pearson’s correlation coefficients and ROC analysis. As for residue-specific quality assessment, our four methods achieved better performance than most of the six other CASP11 methods in distinguishing the reliably modeled residues from the unreliable measured by ROC analysis; and our SdA-based method Wang_deep_1 has achieved the highest accuracy, 0.77, compared to SVM-based methods and our ensemble of an SVM and SdAs. However, we found that Wang_deep_2 and Wang_deep_3, both based on an ensemble of multiple SdAs and an SVM, performed slightly better than Wang_deep_1 in terms of ROC analysis, indicating that integrating an SVM with deep networks works well in terms of certain measurements.
Reproducibility of Intra- and Inter-scanner Measurements of Liver Fat Using Complex Confounder-corrected Chemical Shift Encoded MRI at 3.0 Tesla
Authors: Wu Bing , Han Wei , Li Zhenhong , Zhao Yonghua , Ge Mingmei , Guo Xueqing , Wu Xinhuai 
Published: January 2016

AbstractThe purpose of this study was to prospectively evaluate the reproducibility of the proton density fat-fraction (PDFF) of the liver using the IDEAL algorithm, a quantitative confounder-corrected chemical-shift-encoded MRI method. Data were obtained from 15 volunteers on four different days. The first and the third examinations were conducted on scanner one with one-week intervals, while the second and the fourth tests were performed on scanner two with same time interval. For each test, two MR scans were performed, one before and one after a meal. Regions-of-interest measurements were manually calculated to estimate the PDFF in the right and left lobes on the PDFF images. Reproducibility was measured using the intra-class correlation coefficient (ICC). The ICCs of the PDFF in the right and left lobes were 0.935 and 0.878, respectively. The intra-scanner ICCs of the right lobe before and after a meal or at a one-week interval were 0.924 and 0.953, respectively. The inter-scanner ICCs of PDFF the next day and at a one-week interval were 0.920 and 0.864, respectively. The PDFF of liver derived from IDEAL demonstrated high intra- and inter-scanner measurement reproducibility. The PDFF of the right lobe before a meal was more reproducible than after-meal measurements.
Matrix-Assisted Plasma Atomization Emission Spectrometry for Surface Sampling Elemental Analysis
Authors: Yuan Xin , Zhan Xuefang , Li Xuemei , Zhao Zhongjun , Duan Yixiang 
Published: January 2016

AbstractAn innovative technology has been developed involving a simple and sensitive optical spectrometric method termed matrix-assisted plasma atomization emission spectrometry (MAPAES) for surface sampling elemental analysis using a piece of filter paper (FP) for sample introduction. MAPAES was carried out by direct interaction of the plasma tail plume with the matrix surface. The FP absorbs energy from the plasma source and releases combustion heating to the analytes originally present on its surface, thus to promote the atomization and excitation process. The matrix-assisted plasma atomization excitation phenomenon was observed for multiple elements. The FP matrix served as the partial energy producer and also the sample substrate to adsorb sample solution. Qualitative and quantitative determinations of metal ions were achieved by atomic emission measurements for elements Ba, Cu, Eu, In, Mn, Ni, Rh and Y. The detection limits were down to pg level with linear correlation coefficients better than 0.99. The proposed MAPAES provides a new way for atomic spectrometry which offers advantages of fast analysis speed, little sample consumption, less sample pretreatment, small size and cost-effective.
Thermally triggered phononic gaps in liquids at THz scale
Authors: Bolmatov Dima , Zhernenkov Mikhail , Zav’yalov Dmitry , Stoupin Stanislav , Cunsolo Alessandro , Cai Yong Q. 
Published: January 2016

AbstractIn this paper we present inelastic X-ray scattering experiments in a diamond anvil cell and molecular dynamic simulations to investigate the behavior of phononic excitations in liquid Ar. The spectra calculated using molecular dynamics were found to be in a good agreement with the experimental data. Furthermore, we observe that, upon temperature increases, a low-frequency transverse phononic gap emerges while high-frequency propagating modes become evanescent at the THz scale. The effect of strong localization of a longitudinal phononic mode in the supercritical phase is observed for the first time. The evidence for the high-frequency transverse phononic gap due to the transition from an oscillatory to a ballistic dynamic regimes of motion is presented and supported by molecular dynamics simulations. This transition takes place across the Frenkel line thermodynamic limit which demarcates compressed liquid and non-compressed fluid domains on the phase diagram and is supported by calculations within the Green-Kubo phenomenological formalism. These results are crucial to advance the development of novel terahertz thermal devices, phononic lenses, mirrors and other THz metamaterials.
Mapping of Low-Frequency Raman Modes in CVD-Grown Transition Metal Dichalcogenides: Layer Number, Stacking Orientation and Resonant Effects
Authors: O’Brien Maria , McEvoy Niall , Hanlon Damien , Hallam Toby , Coleman Jonathan N. , Duesberg Georg S. 
Published: January 2016

AbstractLayered inorganic materials, such as the transition metal dichalcogenides (TMDs), have attracted much attention due to their exceptional electronic and optical properties. Reliable synthesis and characterization of these materials must be developed if these properties are to be exploited. Herein, we present low-frequency Raman analysis of MoS2, MoSe2, WSe2 and WS2 grown by chemical vapour deposition (CVD). Raman spectra are acquired over large areas allowing changes in the position and intensity of the shear and layer-breathing modes to be visualized in maps. This allows detailed characterization of mono- and few-layered TMDs which is complementary to well-established (high-frequency) Raman and photoluminescence spectroscopy. This study presents a major stepping stone in fundamental understanding of layered materials as mapping the low-frequency modes allows the quality, symmetry, stacking configuration and layer number of 2D materials to be probed over large areas. In addition, we report on anomalous resonance effects in the low-frequency region of the WS2 Raman spectrum.
Alterations of the volatile metabolome in mouse models of Alzheimer’s disease
Authors: Kimball Bruce A. , Wilson Donald A. , Wesson Daniel W. 
Published: January 2016

AbstractIn the present study, we tested whether the volatile metabolome was altered by mutations of the Alzheimer’s disease (AD)-implicated amyloid precursor protein gene (APP) and comprehensively examined urinary volatiles that may potentially serve as candidate biomarkers of AD. Establishing additional biomarkers in screening populations for AD will provide enhanced diagnostic specificity and will be critical in evaluating disease-modifying therapies. Having strong evidence of gross changes in the volatile metabolome of one line ofAPPmice, we utilized three unique mouse lines which over-express human mutations of theAPPgene and their respective non-transgenic litter-mates (NTg). Head-space gas chromatography/mass spectrometry (GC/MS) of urinary volatiles uncovered several aberrant chromatographic peak responses. We later employed linear discrimination analysis and found that the GC/MS peak responses provide accurate (>84%) genotype classification of urinary samples. These initial data in animal models show that mutantAPPgene expression entails a uniquely identifiable urinary odor, which if uncovered in clinical AD populations, may serve as an additional biomarker for the disease.
Effect of topical rebamipide on conjunctival goblet cell recovery after vitrectomy
Authors: Kato Kumiko , Takashima Yuko , Matsunaga Koichi , Sugimoto Masahiko , Matsubara Hisashi , Hirano Koji , Kondo Mineo 
Published: January 2016

AbstractIn vitro and in vivo experiments have shown that topical rebamipide will increase the number of goblet cells in the bulbar conjunctiva. The purpose of this study was to determine whether topical rebamipide will enhance the recovery of conjunctival goblet cells that were damaged during vitrectomy. Forty patients who underwent vitrectomy surgery were studied. The 40 patients consisted of 20 with diabetes mellitus (DM) and 20 patients without DM. They were randomized in a 1:1 ratio into groups that were treated or not treated with topical 2% rebamipide after the surgery. Impression cytology was performed at the end of surgery and at 14 days after the surgery. The mean goblet cell density of each specimen was determined by averaging the total number of goblet cells obtained from three consecutive high magnification microscopic images. In patients without DM, the mean goblet cell density at 14 days after the vitrectomy was significantly higher in eyes with topical rebemipide than in eyes without rebemipide (P < 0.01). In patients with DM, a similar tendency was observed but the difference was not significant (P = 0.09). These results suggest that topical rebamipide can be helpful in patients with globlet cell damage that occur during and after vitrectomy.