bluuebunny/crossref_metadata_2025_split huggingface dataset:
Auxin Response Factors promote organogenesis by chromatin-mediated repression of the pluripotency gene SHOOTMERISTEMLESS
Authors: Chung Yuhee , Zhu Yang , Wu Miin-Feng , Simonini Sara , Kuhn Andre , Armenta-Medina Alma , Jin Run , Østergaard Lars , Gillmor C. Stewart , Wagner Doris 
Published: February 2019

AbstractSpecification of new organs from transit amplifying cells is critical for higher eukaryote development. In plants, a central stem cell pool maintained by the pluripotency factor SHOOTMERISTEMLESS (STM), is surrounded by transit amplifying cells competent to respond to auxin hormone maxima by giving rise to new organs. Auxin triggers flower initiation through Auxin Response Factor (ARF) MONOPTEROS (MP) and recruitment of chromatin remodelers to activate genes promoting floral fate. The contribution of gene repression to reproductive primordium initiation is poorly understood. Here we show that downregulation of the STM pluripotency gene promotes initiation of flowers and uncover the mechanism for STM silencing. The ARFs ETTIN (ETT) and ARF4 promote organogenesis at the reproductive shoot apex in parallel with MP via histone-deacetylation mediated transcriptional silencing of STM. ETT and ARF4 directly repress STM, while MP acts indirectly, through its target FILAMENTOUS FLOWER (FIL). Our data suggest that – as in animals- downregulation of the pluripotency program is important for organogenesis in plants.
Multi-band mass enhancement towards critical doping in a pnictide superconductor
Authors: Moir Camilla Margaret , Riggs Scott Chandler , Galvis Jose Augusto , Lian Xiujun , Giraldo-Gallo Paula , Chu Jiun-Haw , Walmsley Philip , Fisher Ian Randal , Shekhter Arkady , Boebinger Gregory Scott 
Published: February 2019

AbstractNear critical doping, high-temperature superconductors exhibit multiple anomalies associated with enhanced electronic correlations and quantum criticality. Quasiparticle mass enhancement approaching optimal doping has been reported in quantum oscillation measurements in both cuprate and pnictide superconductors. Although the data are suggestive of enhanced interactions, the microscopic theory of quantum oscillation measurements near a quantum critical point is not yet firmly established. It is therefore desirable to have a direct thermodynamic measurement of quasiparticle mass. Here we report high-magnetic field measurements of heat capacity in the doped pnictide superconductor BaFe2(As1−xPx)2. We observe saturation of the specific heat at high magnetic field in a broad doping range above optimal doping which enables a direct determination of the electronic density of states recovered when superconductivity is suppressed. Our measurements find a strong total mass enhancement in the Fermi pockets that superconduct. This mass enhancement extrapolates to a mass divergence at a critical doping of x = 0.28.
Association of IL1RAP-related genetic variation with cerebrospinal fluid concentration of Alzheimer-associated tau protein
Authors: Zettergren Anna , Höglund Kina , Kern Silke , Thorvaldsson Valgeir , Johan Skoog Msc , Hansson Oskar , Andreasen Niels , Bogdanovic Nenad , Blennow Kaj , Skoog Ingmar , Zetterberg Henrik 
Published: February 2019

AbstractA possible involvement of the gene IL1RAP (interleukin-1 receptor-associated protein) in the pathogenesis of Alzheimer’s disease (AD) has been suggested in GWASs of cerebrospinal fluid (CSF) tau levels and longitudinal change in brain amyloid burden. The aim of this study was to examine previously implicated genetic markers in and near IL1RAP in relation to AD risk, CSF tau and Aβ biomarkers, as well as cognitive decline, in a case (AD)-control study and an age homogenous population-based cohort. Genotyping of IL1RAP-related single nucleotide polymorphisms (SNPs), selected based on previous GWAS results, was performed. 3446 individuals (1154 AD cases and 2292 controls) were included in the analyses of AD risk, 1400 individuals (cognitively normal = 747, AD = 653) in the CSF biomarker analyses, and 861 individuals in the analyses of cognitive decline. We found no relation between IL1RAP-related SNPs and AD risk. However, CSF total-tau and phospho-tau were associated with the SNP rs9877502 (p = 6 × 10−3 and p = 5 × 10−4). Further, nominal associations (p = 0.03–0.05) were found between three other SNPs and CSF biomarker levels, or levels of cognitive performance and decline in a sub-sample from the general population. These results support previous studies suggesting an association of IL1RAP with disease intensity of AD.
Comparative transcriptome analysis reveals differentially expressed genes related to the tissue-specific accumulation of anthocyanins in pericarp and aleurone layer for maize
Authors: Li Tingchun , Zhang Wei , Yang Huaying , Dong Qing , Ren Jie , Fan Honghong , Zhang Xin , Zhou Yingbing 
Published: February 2019

AbstractPurple corn is a rich source of anthocyanins. In the experiment, two anthocyanins-enriched purple corn lines Ha0414 and Ha6130 were identified. The anthocyanins were respectively accumulated in the pericarp of Ha0414 and the aleurone layer of Ha6130 with different composition and content. Transcriptome analysis of the two tissues in both lines identified 16 and 14 differentially expressed genes belonging to anthocyanin metabolism pathway in pericarp and the aleurone layer, individually. Of these genes, two genes encoding 2-oxoglutarate (2OG) and Fe (II)-dependent oxygenase superfamily proteins, and one gene annotated as UDP-glycosyltransferase superfamily protein exhibited increased transcript abundance in both the colored pericarp and aleurone layer. Otherwise, one gene annotated as flavonoid 3′, 5′-hydroxylase, and another gene encoding flavonoid 3′-monooxygenase displayed increased transcript abundance in the aleurone layer of Ha6130. Moreover, 36 transcription factors were identified with increased transcript abundance in the pericarp of Ha0414, such as bHLH transcription factors, WRKY transcription factors, and HB transcription factors. And 79 transcription factors were isolated with an increased expression level in the aleurone layer of Ha6130, including MYB transcription factors, MYB-related transcription factors, and bHLH transcription factors. These genes expression may result in the tissue-specific accumulation of anthocyanins in pericarp and aleurone layer.
The effect of prebiotic fortified infant formulas on microbiota composition and dynamics in early life
Authors: Borewicz Klaudyna , Suarez-Diez Maria , Hechler Christine , Beijers Roseriet , de Weerth Carolina , Arts Ilja , Penders John , Thijs Carel , Nauta Arjen , Lindner Cordula , Van Leusen Ellen , Vaughan Elaine E. , Smidt Hauke 
Published: February 2019

AbstractGastrointestinal (GI) microbiota composition differs between breastfed and formula-fed infants. Today’s infant formulas are often fortified with prebiotics to better mimic properties of human milk with respect to its effect on GI microbiota composition and function. We used Illumina HiSeq sequencing of PCR-amplified 16S rRNA gene fragments to investigate the composition of faecal microbiota in 2–12 week old infants receiving either breastmilk, infant formulas fortified with prebiotics, or mixed feeding. We compared these results with results from infants fed traditional formulas used in the Netherlands in 2002–2003, which contained no added prebiotics. We showed that today’s formulas supplemented with either scGOS (0.24–0.50 g/100 ml) or scGOS and lcFOS (at a 9:1 ratio; total 0.6 g/100 ml) had a strong bifidogenic effect as compared to traditional formulas, and they also resulted in altered patterns of microbial colonisation within the developing infant gastrointestinal tract. We identified three microbial states (or developmental stages) in the first 12 weeks of life, with a gradual transition pattern towards a bifidobacteria dominated state. In infants receiving only fortified formulas, this transition towards the bifidobacteria dominated state was accelerated, whereas in infants receiving mixed feeding the transition was delayed, as compared to exclusively breastfed infants.
Cooling of atoms using an optical frequency comb
Authors: Šantić N. , Buhin D. , Kovačić D. , Krešić I. , Aumiler D. , Ban T. 
Published: February 2019

AbstractWe report on laser cooling of neutral rubidium atoms by using a single mode of a frequency comb. Cooling is achieved on a dipole-allowed transition at 780 nm in a one-dimensional retro-reflected beam geometry. Temperatures are measured using standard time-of-flight imaging. We show the dependence of the temperature on the cooling time, intensity and detuning of the frequency comb. The lowest temperature achieved is approximately equal to the Doppler temperature and is limited by the intensity of the comb mode driving the cooling transition. Additionally, we verify the analogy between frequency comb and continuous-wave laser cooling. Our work is a step towards laser cooling of atoms with strong cycling transitions in the vacuum ultraviolet, such as hydrogen, deuterium and antihydrogen, where generation of continuous-wave laser light is limited by current laser technology. Achieving efficient cooling at these wavelengths would significantly improve the precision of optical frequency standards, enable measurements of fundamental constants with unprecedented accuracy, improve tests of charge, parity, and time reversal symmetry, and open the way to achieving quantum degeneracy width new atomic species.
Microvascular flow dictates the compromise between spatial resolution and acquisition time in Ultrasound Localization Microscopy
Authors: Hingot Vincent , Errico Claudia , Heiles Baptiste , Rahal Line , Tanter Mickael , Couture Olivier 
Published: February 2019

AbstractMedical ultrasound is a widely used diagnostic imaging technique for tissues and blood vessels. However, its spatial resolution is limited to a sub-millimeter scale. Ultrasound Localization Microscopy was recently introduced to overcome this limit and relies on subwavelength localization and tracking of microbubbles injected in the blood circulation. Yet, as microbubbles follow blood flow, long acquisition time are required to detect them in the smallest vessels, leading to long reconstruction of the microvasculature. The objective of this work is to understand how blood flow limits acquisition time. We studied the reconstruction of a coronal slice of a rat’s brain during a continuous microbubble injection close to clinical concentrations. After acquiring 192000 frames over 4 minutes, we find that the biggest vessels can be reconstructed in seconds but that it would take tens of minutes to map the entire capillary network. Moreover, the appropriate characterization of flow profiles based on microbubble velocity within vessels is bound by even more stringent temporal limitations. As we use simple blood flow models to characterize its impact on reconstruction time, we foresee that these results and methods can be adapted to determine adequate microbubble injections and acquisition times in clinical and preclinical practice.
Soluble Graphene Nanosheets for the Sunlight-Induced Photodegradation of the Mixture of Dyes and its Environmental Assessment
Authors: Gunture  , Singh Anupriya , Bhati Anshu , Khare Prateek , Tripathi Kumud Malika , Sonkar Sumit Kumar 
Published: February 2019

AbstractCurrently, the air and water pollutions are presenting the most serious global concerns. Despite the well known tremendous efforts, it could be a promising sustainability if the black carbon (BC) soot can be utilized for the practical and sustainable applications. For this, the almost complete aqueous phase photodegradation of the three well-known organic pollutant dyes as crystal violet (CV); rhodamine B (RhB); methylene blue (MB) and their mixture (CV + RhB + MB), by using water-soluble graphene nanosheets (wsGNS) isolated from the BC soot under the influence of natural sunlight is described. The plausible mechanism behind the photocatalytic degradation of dyes and their mixture has been critically analyzed via the trapping of active species and structural analysis of photodegraded products. The impact of diverse interfering ions like Ca2+, Fe3+, SO42−, HPO42−, NO3−, and Cl− on the photodegradation efficiency of wsGNS was also investigated. Importantly, the environmental assessment of the whole process has been evaluated towards the growth of wheat plants using the treated wastewater. The initial studies for the fifteen days confirmed that growth of wheat plants was almost the same in the photodegraded wastewater as being noticed in the control sample, while in case of dyes contaminated water it showed the retarded growth. Using the natural sunlight, the overall sustainability of the presented work holds the potential for the utilization of pollutant soot in real-practical applications related to the wastewater remediation and further the practical uses of treated water.
Synthesis and Rational design of Europium and Lithium Doped Sodium Zinc Molybdate with Red Emission for Optical Imaging
Authors: Jain Neha , Paroha Ruchi , Singh Rajan K. , Mishra Siddhartha K. , Chaurasiya Shivendra K. , Singh R. A. , Singh Jai 
Published: February 2019

AbstractHighly efficient fluorescent and biocompatible europium doped sodium zinc molybdate (NZMOE) nanoprobes were successfully synthesized via Polyol method. Non-radiative defect centres get reduced with Li+ co-doping in NZMOE nanoprobes. XRD spectra and Rietveld refinement confirmed successful incorporation of lithium ion and crystallinity was also improved with Li+ co-doping. The shape of phosphor is rod shaped, as determined by TEM. Significant enhancement in photoluminescence intensity was observed with 266, 395 and 465 nm excitations. Profound red emission was recorded for 5 at% Li+ co-doped NZMOE nanoprobes with 266 nm excitation. It shows high asymmetry ratio (~15), color purity (94.90%) and good quantum efficiency (~70%). Judd Ofelt parameters have been calculated to measure intensity parameters and radiative transition rates. In order to measure biocompatibility of the nanoprobes, cytotoxicity assays were performed with HePG2 cells. The fluorescence emitted from phosphor material treated HePG2 cells was also measured by Laser Scanning Confocal Microscopy. The bright red fluorescence in HePG2 cells treated with very low concentration (20 μg/ml) of phosphor material indicates that it could be a promising phosphor for biological detection or bio-imaging.
The glial sodium-potassium-2-chloride cotransporter is required for synaptic transmission in the Drosophila visual system
Authors: Stenesen Drew , Moehlman Andrew T. , Schellinger Jeffrey N. , Rodan Aylin R. , Krämer Helmut 
Published: February 2019

AbstractThe Drosophila Ncc69 gene encodes a Na+-K+-2Cl−-cotransporter (NKCC) that is critical for regulating intra- and extracellular ionic conditions in different tissues. Here, we show that the Ncc69 transporter is necessary for fly vision and that its expression is required non-autonomously in glia to maintain visual synaptic transmission. Flies mutant for Ncc69 exhibit normal photoreceptor depolarization in response to a light pulse but lack the ON and OFF-transients characteristic of postsynaptic responses of lamina neurons, indicating a failure in synaptic transmission. We also find that synaptic transmission requires the Ncc69 regulatory kinases WNK and Fray in glia. The ERG phenotype is associated with a defect in the recycling of the histamine neurotransmitter. Ncc69 mutants exhibit higher levels of the transport metabolite carcinine in lamina cartridges, with its accumulation most intense in the extracellular space. Our work reveals a novel role of glial NKCC transporters in synaptic transmission, possibly through regulating extracellular ionic conditions.
Identification and characterization of a factor Va-binding site on human prothrombin fragment 2
Authors: Friedmann Alexander P. , Koutychenko Anatoli , Wu Chengliang , Fredenburgh James C. , Weitz Jeffrey I. , Gross Peter L. , Xu Ping , Ni Feng , Kim Paul Y. 
Published: February 2019

AbstractThe fragment 2 domain (F2) of prothrombin and its interaction with factor (F) Va is known to contribute significantly to prothrombinase-catalyzed activation of prothrombin. The extent to which the F2-FVa interaction affects the overall thrombin generation, however, is uncertain. To study this interaction, nuclear magnetic resonance spectroscopy of recombinant F2 was used to identify seven residues within F2 that are significantly responsive to FVa binding. The functional role of this region in interacting with FVa during prothrombin activation was verified by the FVa-dependent inhibition of thrombin generation using peptides that mimic the same region of F2. Because six of the seven residues were within a 9-residue span, these were mutated to generate a prothrombin derivative (PT6). These mutations led to a decreased affinity for FVa as determined by surface plasmon resonance. When thrombin generation by an array of FXa containing prothrombinase components was monitored, a 54% decrease in thrombin generation was observed with PT6 compared with the wild-type, only when FVa was present. The functional significance of the specific low-affinity binding between F2 and FVa is discussed within the context of a dynamic model of molecular interactions between prothrombin and FVa engaging multiple contact sites.
Inheritance of Susceptibility to Malignant Blood Disorders
Authors: Jønsson Viggo , Awan Haneef , Jones Neil D. , Johannesen Tom B. , Steig Bjarni á , Andosdottir Gudrid , Tjønnfjord Geir E. 
Published: February 2019

AbstractMalignant blood disorders depend on heritable susceptibility genes and occur in familial aggregations. We suggest a model of transgenerational segregation of the susceptibility genes based on the study of malignant blood disorders in Norwegian and Danish families with unrelated parents, and in the inbred Faroese population with related parents. This model, consisting of parental genomic imprinting and mother-son microchimerism, can explain the male predominance in most of the diseases, the predominance of affected parent-offspring when parents are not related, and the different modes of segregation in males and females. The model displays a specific pattern in the distribution of affected relatives for each diagnosis, viz. a characteristic distribution in the pedigrees of family members with malignant blood disorder related to the proband. Three such patterns, each reflecting a specific transgenerational passage, were identified: (1) alterations in the number of affected relatives in paternal lines alone, e.g. in patterns for probands with multiple myeloma; (2) alterations in the number of affected relatives in both paternal and maternal lines for probands with chronic lymphocytic leukemia; and (3) no alterations in the numbers of male and female affected relatives in the parental lines, e.g. for probands with some types of malignant lymphoma.
Accelerating Neutron Tomography experiments through Artificial Neural Network based reconstruction
Authors: Micieli Davide , Minniti Triestino , Evans Llion Marc , Gorini Giuseppe 
Published: February 2019

AbstractNeutron Tomography (NT) is a non-destructive technique to investigate the inner structure of a wide range of objects and, in some cases, provides valuable results in comparison to the more common X-ray imaging techniques. However, NT is time consuming and scanning a set of similar objects during a beamtime leads to data redundancy and long acquisition times. Nowadays NT is unfeasible for quality checking study of large quantities of similar objects. One way to decrease the total scan time is to reduce the number of projections. Analytical reconstruction methods are very fast but under this condition generate streaking artifacts in the reconstructed images. Iterative algorithms generally provide better reconstruction for limited data problems, but at the expense of longer reconstruction time. In this study, we propose the recently introduced Neural Network Filtered Back-Projection (NN-FBP) method to optimize the time usage in NT experiments. Simulated and real neutron data were used to assess the performance of the NN-FBP method as a function of the number of projections. For the first time a machine learning based algorithm is applied and tested for NT image reconstruction problem. We demonstrate that the NN-FBP method can reliably reduce acquisition and reconstruction times and it outperforms conventional reconstruction methods used in NT, providing high image quality for limited datasets.
Effect of deuterium irradiation on graphite boronized in the NSTX-U tokamak
Authors: Bedoya F. , Allain J. P. , Dominguez-Gutierrez F. J. , Krstic P. S. 
Published: February 2019

AbstractBoronization has been used in the National Spherical Torus-Upgrade (NSTX-U) as first wall conditioning technique. The technique decreased the oxygen impurities in the plasma and the O% on the Plasma Facing Components (PFC) as measured with an in-vacuo probe. Samples were extracted from tiles removed from the tokamak for post-mortem and controlled studies. Ex-vessel low energy and fluence D2+ and Ar+ irradiations were characterized in-situ to elucidate surface evolution of a cored graphite sample with an intrinsic concentration of boron from a tokamak environment. In addition, quadrupole mass spectrometer measurements of emitted D-containing species during irradiation, indicate potential retention of D by the boronized graphite interface and correlated back to the surface chemistry evolution. Classical Molecular Dynamics (CMD) simulations were used to investigate the chemistry of the B-C-O-D system. The results suggest that boron coatings retain oxygen by forming oxidized boron states in the presence of deuterium plasmas and corroborate empirical findings. A four times increase in the O% of the boron coatings was observed following in-situ deuterium exposures, in contrast with a reduction of equal magnitude observed after Ar irradiations. These results illustrate the complex chemistry driven by energetic ions at the edge of tokamaks plasmas on the PFCs.
Effect of chain flexibility on cell adhesion: Semi-flexible model-based analysis of cell adhesion to hydrogels
Authors: Lee Jooyoung , Song Boa , Subbiah Ramesh , Chung Justin J. , Choi U Hyeok , Park Kwideok , Kim Sang-Heon , Oh Seung Ja 
Published: February 2019

AbstractHydrogels have been developed and applied to various biomedical applications due to their biocompatibility. However, understanding of modulation between cells to hydrogel interface is still unclear, and parameters to explain the interaction are not sophisticated enough. In this report, we studied the effect of polymer chain flexibility on cell adhesion to various hydrogel constructs of collagen and fibrin gels. Specifically, novel method of semi-flexible model-based analysis confirmed that chain flexibility mediated microstructure of the hydrogels is a critical factor for cell adhesion on their surfaces. The proposed analysis showed possibility of more accurate prediction of biocompatibility of hydrogels, and it should be considered as one of the important criteria for polymer design and selections for enhancing both biocompatibility and biofunctionality.