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  • 1
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    Pauli-limited effect in the magnetic phase diagram of FeSexTe1−x thin films (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-12-01
    Description: We present a detailed investigation on the doping dependence of the upper critical field H c 2 ( T ) of FeSe x Te 1− x thin films (0.18 ≤  x  ≤ 0.90) by measuring the electrical resistivity as a function of magnetic field. The H c 2 ( T ) curves exhibit a downturn behavior with decreasing temperature in all the samples, owing to the Pauli-limited effect (spin paramagnetic effect). The Pauli-limited effect on the upper critical field can be monotonically modulated by variation of the Se/Te composition. Our results show that Te-doping induced disorder and excess Fe atoms give rise to enhancement of the Pauli-limited effect.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 2
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    MetPP: a computational platform for comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry-based metabolomics (2013)
    Oxford University Press
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    Publication Date: 2013-07-06
    Description: Motivation: Due to the high complexity of metabolome, the comprehensive 2D gas chromatography time-of-flight mass spectrometry (GC x GC-TOF MS) is considered as a powerful analytical platform for metabolomics study. However, the applications of GC x GC-TOF MS in metabolomics are not popular owing to the lack of bioinformatics system for data analysis. Results: We developed a computational platform entitled metabolomics profiling pipeline (MetPP) for analysis of metabolomics data acquired on a GC x GC-TOF MS system. MetPP can process peak filtering and merging, retention index matching, peak list alignment, normalization, statistical significance tests and pattern recognition, using the peak lists deconvoluted from the instrument data as its input. The performance of MetPP software was tested with two sets of experimental data acquired in a spike-in experiment and a biomarker discovery experiment, respectively. MetPP not only correctly aligned the spiked-in metabolite standards from the experimental data, but also correctly recognized their concentration difference between sample groups. For analysis of the biomarker discovery data, 15 metabolites were recognized with significant concentration difference between the sample groups and these results agree with the literature results of histological analysis, demonstrating the effectiveness of applying MetPP software for disease biomarker discovery. Availability: The source code of MetPP is available at http://metaopen.sourceforge.net Contact: xiang.zhang@louisville.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 3
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    Observation of the anisotropic Dirac cone in the band dispersion of 112-structured iron-based superconductor Ca0.9La0.1FeAs2 (2016)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2016-07-30
    Description: CaFeAs 2 is a parent compound of recently discovered 112-type iron-based superconductors. It is predicted to be a staggered intercalation compound that naturally integrates both quantum spin Hall insulating and superconducting layers and an ideal system for the realization of Majorana modes. We performed a systematical angle-resolved photoemission spectroscopy and first-principles calculation study of the slightly electron-doped CaFeAs 2 . We found that the zigzag As chain of 112-type iron-based superconductors play a considerable role in the low-energy electronic structure, resulting in the characteristic Dirac-cone like band dispersion as the prediction. Our experimental results further confirm that these Dirac cones only exist around the X but not Y points in the Brillouin zone, breaking the S 4 symmetry at iron sites. Our findings present the compelling support to the theoretical prediction that the 112-type iron-based superconductors might host the topological nontrivial edge states. The slightly electron doped CaFeAs 2 would provide us a unique opportunity to realize and explore Majorana fermion physics.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 4
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    Dicer interacts with SIRT7 and regulates H3K18 deacetylation in response to DNA damaging agents (2016)
    Oxford University Press
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    Publication Date: 2016-05-06
    Description: Dicer participates in heterochromatin formation in fission yeast and plants. However, whether it has a similar role in mammals remains controversial. Here we showed that the human Dicer protein interacts with SIRT7, an NAD + -dependent H3K18Ac (acetylated lysine 18 of histone H3) deacetylase, and holds a proportion of SIRT7 in the cytoplasm. Dicer knockdown led to an increase of chromatin-associated SIRT7 and simultaneously a decrease of cytoplasmic SIRT7, while its overexpression induced SIRT7 reduction in the chromatin-associated fraction and increment in the cytoplasm. Furthermore, DNA damaging agents promoted Dicer expression, leading to decreased level of chromatin-associated SIRT7 and increased level of H3K18Ac, which can be alleviated by Dicer knockdown. Taken together with that H3K18Ac was exclusively associated with the chromatin, our findings suggest that Dicer induction by DNA damaging treatments prevents H3K18Ac deacetylation, probably by trapping more SIRT7 in the cytoplasm.
    Keywords: Protein-protein interaction, Repair
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Radiation hardness assessment of the charge-integrating hybrid pixel detector JUNGFRAU 1.0 for photon science (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-12-25
    Description: JUNGFRAU (adJUstiNg Gain detector FoR the Aramis User station) is a two-dimensional hybrid pixel detector for photon science applications in free electron lasers, particularly SwissFEL, and synchrotron light sources. JUNGFRAU is an automatic gain switching, charge-integrating detector which covers a dynamic range of more than 10 4 photons of an energy of 12 keV with a good linearity, uniformity of response, and spatial resolving power. The JUNGFRAU 1.0 application-specific integrated circuit (ASIC) features a 256 × 256 pixel matrix of 75 × 75 μ m 2 pixels and is bump-bonded to a 320 μ m thick Si sensor. Modules of 2 × 4 chips cover an area of about 4 × 8 cm 2 . Readout rates in excess of 2 kHz enable linear count rate capabilities of 20 MHz (at 12 keV) and 50 MHz (at 5 keV). The tolerance of JUNGFRAU to radiation is a key issue to guarantee several years of operation at free electron lasers and synchrotrons. The radiation hardness of JUNGFRAU 1.0 is tested with synchrotron radiation up to 10 MGy of delivered dose. The effect of radiation-induced changes on the noise, baseline, gain, and gain switching is evaluated post-irradiation for both the ASIC and the hybridized assembly. The bare JUNGFRAU 1.0 chip can withstand doses as high as 10 MGy with minor changes to its noise and a reduction in the preamplifier gain. The hybridized assembly, in particular the sensor, is affected by the photon irradiation which mainly shows as an increase in the leakage current. Self-healing of the system is investigated during a period of 11 weeks after the delivery of the radiation dose. Annealing radiation-induced changes by bake-out at 100 °C is investigated. It is concluded that the JUNGFRAU 1.0 pixel is sufficiently radiation-hard for its envisioned applications at SwissFEL and synchrotron beam lines.
    Print ISSN: 0034-6748
    Electronic ISSN: 1089-7623
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
    Published by American Institute of Physics (AIP)
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  • 6
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    Anisotropy of iron-platinum-arsenide Ca10(PtnAs8)(Fe2−xPtxAs2)5 single crystals (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-07-10
    Description: The upper critical field H c2 anisotropy of Ca 10 (Pt n As 8 )(Fe 2− x Pt x As 2 ) 5 ( n  = 3, 4) single crystals with long FeAs interlayer distance ( d ) was studied by angular dependent resistivity measurements. A scaling of the angular dependent resistivity was realized for both single crystals using the anisotropic Ginzburg-Landau (AGL) approach with an appropriate anisotropy parameter γ . The AGL scaling parameter γ increases with decreasing temperature and reaches a value of about 10 at 0.8 T c for both single crystals. These values are much larger than those of other iron-based superconductors (FeSCs). Remarkably, the values of γ 2 show an almost linear increase with the FeAs/FeSe interlayer distance d for FeSCs. Compared to cuprates, FeSCs are less anisotropic, indicating that two dimensionality of the superconductivity is intrinsically weak.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 7
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    A novel method for discovering local spatial clusters of genomic regions with functional relationships from DNA contact maps (2016)
    Oxford University Press
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    Publication Date: 2016-06-16
    Description: Motivation: The three-dimensional structure of genomes makes it possible for genomic regions not adjacent in the primary sequence to be spatially proximal. These DNA contacts have been found to be related to various molecular activities. Previous methods for analyzing DNA contact maps obtained from Hi-C experiments have largely focused on studying individual interactions, forming spatial clusters composed of contiguous blocks of genomic locations, or classifying these clusters into general categories based on some global properties of the contact maps. Results: Here, we describe a novel computational method that can flexibly identify small clusters of spatially proximal genomic regions based on their local contact patterns. Using simulated data that highly resemble Hi-C data obtained from real genome structures, we demonstrate that our method identifies spatial clusters that are more compact than methods previously used for clustering genomic regions based on DNA contact maps. The clusters identified by our method enable us to confirm functionally related genomic regions previously reported to be spatially proximal in different species. We further show that each genomic region can be assigned a numeric affinity value that indicates its degree of participation in each local cluster, and these affinity values correlate quantitatively with DNase I hypersensitivity, gene expression, super enhancer activities and replication timing in a cell type specific manner. We also show that these cluster affinity values can precisely define boundaries of reported topologically associating domains, and further define local sub-domains within each domain. Availability and implementation: The source code of BNMF and tutorials on how to use the software to extract local clusters from contact maps are available at http://yiplab.cse.cuhk.edu.hk/bnmf/ . Contact: kevinyip@cse.cuhk.edu.hk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 8
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    Large linear magnetoresistance in a transition-metal stannide β-RhSn4 (2016)
    American Institute of Physics (AIP)
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    Publication Date: 2016-09-20
    Description: Materials exhibiting large magnetoresistance may not only be of fundamental research interest, but also can lead to wide-ranging applications in magnetic sensors and switches. Here we demonstrate a large linear-in-field magnetoresistance, Δ ρ / ρ reaching as high as ∼600% at 2 K under a 9 T field, in the tetragonal phase of a transition-metal stannide β -RhSn 4 . Detailed analyses show that its magnetic responses are overall inconsistent with the classical model based on the multiple electron scattering by mobility fluctuations in an inhomogenous conductor, but rather in line with the quantum effects due to the presence of Dirac-like dispersions in the electronic structure. Our results may help guiding the future quest for quantum magnetoresistive materials into the family of stannides, similar to the role played by PtSn 4 with topological node arcs.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 9
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    Synthesizing skyrmion bound pairs in Fe-Gd thin films (2016)
    American Institute of Physics (AIP)
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    Publication Date: 2016-07-12
    Description: We show that properly engineered amorphous Fe-Gd alloy thin films with perpendicular magnetic anisotropy exhibit bound pairs of like-polarity, opposite helicity skyrmions at room temperature. Magnetic mirror symmetry planes present in the stripe phase, instead of chiral exchange, determine the internal skyrmion structure and the net achirality of the skyrmion phase. Our study shows that stripe domain engineering in amorphous alloy thin films may enable the creation of skyrmion phases with technologically desirable properties.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 10
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    Hybrid improper ferroelectricity in Ruddlesden-Popper Ca3(Ti,Mn)2O7 ceramics (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-05-20
    Description: The hybrid improper ferroelectricity (HIF) has been proposed as a promising way to create multiferroic materials with strong magnetoelectric coupling by the first-principle calculation, and the experimental evidences of HIF in Ruddlesden-Poper Ca 3 (Ti 1− x Mn x ) 2 O 7 ( x  = 0, 0.05, 0.1, and 0.15) ceramics have been shown in the present work. The room temperature ferroelectric hysteresis loops are observed in these ceramics, and a polar orthorhombic structure with two oxygen tilting modes has been confirmed by the X-ray powder diffraction. A first-order phase transition around 1100 K in Ca 3 Ti 2 O 7 was evidenced, and the temperatures of phase transitions decrease linearly with increasing of the contents of Mn 4+ ions. Based on the result of first-principle calculations, the polarization should be reversed by switching through the mediated Amam phase in Ca 3 Ti 2 O 7 ceramics.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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