bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling Three‐Dimensional Wave Propagation in Anelastic Models With Surface Topography by the Optimal Strong Stability Preserving Runge‐Kutta Method
Authors: Wang Nian , Li Jiahang , Borisov Dmitry , Gharti Hom Nath , Shen Yang , Zhang Wei , Savage Brian 
Published: December 2018

AbstractAccurate and efficient forward modeling methods are important for simulation of seismic wave propagation in 3D realistic Earth models and crucial for high‐resolution full waveform inversion. In the presence of attenuation, wavefield simulation could be inaccurate or unstable over time if not well treated, indicating the importance of the implementation of a strong stability preserving time discretization scheme. In this study, to solve the anelastic wave equation, we choose the optimal strong stability preserving Runge‐Kutta (SSPRK) method for the temporal discretization and apply the fourth‐order MacCormack scheme for the spatial discretization. We approximate the rheological behaviors of the Earth by using the generalized Maxwell body model and use an optimization procedure to calculate the anelastic coefficients determined by the Q(ω) law. This optimization constrains positivity of the anelastic coefficients and ensures the decay of total energy with time, resulting in a stable viscoelastic system even in the presence of strong attenuation. Moreover, we perform theoretical and numerical analyses of the SSPRK method, including the stability criteria and the numerical dispersion. Compared with the traditional fourth‐order Runge‐Kutta method, the SSPRK has a larger stability condition number and can better suppress numerical dispersion. We use the complex‐frequency‐shifted perfectly matched layer for the absorbing boundary conditions based on the auxiliary difference equation and employ the traction image method for the free‐surface boundary condition on curvilinear grids representing the surface topography. Finally, we perform several numerical experiments to demonstrate the accuracy of our anelastic modeling in the presence of surface topography.
Solution-processed intermediate-band solar cells with lead sulfide quantum dots and lead halide perovskites
Authors: Hosokawa Hiroji , Tamaki Ryo , Sawada Takuya , Okonogi Akinori , Sato Haruyuki , Ogomi Yuhei , Hayase Shuzi , Okada Yoshitaka , Yano Toshihiro 
Published: December 2018

AbstractThe intermediate-band solar cell (IBSC) with quantum dots and a bulk semiconductor matrix has potential for high power conversion efficiency, exceeding the Shockley-Queisser limit. However, the IBSCs reported to date have been fabricated only by dry process and their efficiencies are limited, because their photo-absorption layers have low particle density of quantum dots, defects due to lattice strain, and low bandgap energy of bulk semiconductors. Here we present solution-processed IBSCs containing photo-absorption layers where lead sulfide quantum dots are densely dispersed in methylammonium lead bromide perovskite matrices with a high bandgap energy of 2.3 eV under undistorted conditions. We confirm that the present IBSCs exhibit two-step photon absorption via intermediate-band at room temperature by inter-subband photocurrent spectroscopy.
The signaling axis atypical protein kinase C λ/ι-Satb2 mediates leukemic transformation of B-cell progenitors
Authors: Nayak R. C. , Hegde S. , Althoff M. J. , Wellendorf A. M. , Mohmoud F. , Perentesis J. , Reina-Campos M. , Reynaud D. , Zheng Y. , Diaz-Meco M. T. , Moscat J. , Cancelas J. A. 
Published: December 2018

AbstractEpigenetically regulated transcriptional plasticity has been proposed as a mechanism of differentiation arrest and resistance to therapy. BCR-ABL leukemias result from leukemic stem cell/progenitor transformation and represent an opportunity to identify epigenetic progress contributing to lineage leukemogenesis. Primary human and murine BCR-ABL+ leukemic progenitors have increased activation of Cdc42 and the downstream atypical protein kinase C (aPKC). While the isoform aPKCζ behaves as a leukemic suppressor, aPKCλ/ι is critically required for oncogenic progenitor proliferation, survival, and B-cell differentiation arrest, but not for normal B-cell lineage differentiation. In vitro and in vivo B-cell transformation by BCR-ABL requires the downregulation of key genes in the B-cell differentiation program through an aPKC λ/ι-Erk dependent Etv5/Satb2 chromatin repressive signaling complex. Genetic or pharmacological targeting of aPKC impairs human oncogenic addicted leukemias. Therefore, the aPKCλ/ι-SATB2 signaling cascade is required for leukemic BCR-ABL+ B-cell progenitor transformation and is amenable to non-tyrosine kinase inhibition.
Lattice engineering enables definition of molecular features allowing for potent small-molecule inhibition of HIV-1 entry
Authors: Lai Yen-Ting , Wang Tao , O’Dell Sijy , Louder Mark K. , Schön Arne , Cheung Crystal S. F. , Chuang Gwo-Yu , Druz Aliaksandr , Lin Bob , McKee Krisha , Peng Dongjun , Yang Yongping , Zhang Baoshan , Herschhorn Alon , Sodroski Joseph , Bailer Robert T. , Doria-Rose Nicole A. , Mascola John R. , Langley David R. , Kwong Peter D. 
Published: December 2018

AbstractDiverse entry inhibitors targeting the gp120 subunit of the HIV-1 envelope (Env) trimer have been developed including BMS-626529, also called temsavir, a prodrug version of which is currently in phase III clinical trials. Here we report the characterization of a panel of small-molecule inhibitors including BMS-818251, which we show to be >10-fold more potent than temsavir on a cross-clade panel of 208-HIV-1 strains, as well as the engineering of a crystal lattice to enable structure determination of the interaction between these inhibitors and the HIV-1 Env trimer at higher resolution. By altering crystallization lattice chaperones, we identify a lattice with both improved diffraction and robust co-crystallization of HIV-1 Env trimers from different clades complexed to entry inhibitors with a range of binding affinities. The improved diffraction reveals BMS-818251 to utilize functional groups that interact with gp120 residues from the conserved β20-β21 hairpin to improve potency.
Three-dimensional monolithic integration in flexible printed organic transistors
Authors: Kwon Jimin , Takeda Yasunori , Shiwaku Rei , Tokito Shizuo , Cho Kilwon , Jung Sungjune 
Published: December 2018

AbstractDirect printing of thin-film transistors has enormous potential for ubiquitous and lightweight wearable electronic applications. However, advances in printed integrated circuits remain very rare. Here we present a three-dimensional (3D) integration approach to achieve technology scaling in printed transistor density, analogous to Moore’s law driven by lithography, as well as enhancing device performance. To provide a proof of principle for the approach, we demonstrate the scalable 3D integration of dual-gate organic transistors on plastic foil by printing with high yield, uniformity, and year-long stability. In addition, the 3D stacking of three complementary transistors enables us to propose a programmable 3D logic array as a new route to design printed flexible digital circuitry essential for the emerging applications. The 3D monolithic integration strategy demonstrated here is applicable to other emerging printable materials, such as carbon nanotubes, oxide semiconductors and 2D semiconducting materials.
Planetary-scale streak structure reproduced in high-resolution simulations of the Venus atmosphere with a low-stability layer
Authors: Kashimura Hiroki , Sugimoto Norihiko , Takagi Masahiro , Matsuda Yoshihisa , Ohfuchi Wataru , Enomoto Takeshi , Nakajima Kensuke , Ishiwatari Masaki , Sato Takao M. , Hashimoto George L. , Satoh Takehiko , Takahashi Yoshiyuki O. , Hayashi Yoshi-Yuki 
Published: December 2018

AbstractCloud patterns are important clues for revealing the atmospheric circulation of Venus. Recently, a planetary-scale streak structure has been discovered in middle- and lower-cloud images of Venus’ night-side taken by IR2, the 2-μm camera, on board the Akatsuki orbiter. However, its formation mechanism has not been investigated. Here we succeed, for the first time, in reproducing the patterns of the observed streak structure, as regions of strong downward flows that develop in high-resolution global simulations of the Venus atmosphere. The streaks are formed in both hemispheres with equatorial symmetry, which is caused by equatorial Rossby-like and Kelvin-like waves with zonal wavenumber one. The low-stability layer that has been suggested by past observations is essential for reproducing the streak structure. The streaks of downward flow result from the interaction of the meridionally tilted phase lines of the Rossby-like waves and the characteristics of baroclinic instability produced around the low-stability layer.
Ultrasensitive detection of miRNA with an antimonene-based surface plasmon resonance sensor
Authors: Xue Tianyu , Liang Weiyuan , Li Yawen , Sun Yuanhui , Xiang Yuanjiang , Zhang Yupeng , Dai Zhigao , Duo Yanhong , Wu Leiming , Qi Kun , Shivananju Bannur Nanjunda , Zhang Lijun , Cui Xiaoqiang , Zhang Han , Bao Qiaoliang 
Published: December 2018

AbstractMicroRNA exhibits differential expression levels in cancer and can affect cellular transformation, carcinogenesis and metastasis. Although fluorescence techniques using dye molecule labels have been studied, label-free molecular-level quantification of miRNA is extremely challenging. We developed a surface plasmon resonance sensor based on two-dimensional nanomaterial of antimonene for the specific label-free detection of clinically relevant biomarkers such as miRNA-21 and miRNA-155. First-principles energetic calculations reveal that antimonene has substantially stronger interaction with ssDNA than the graphene that has been previously used in DNA molecule sensing, due to thanking for more delocalized 5s/5p orbitals in antimonene. The detection limit can reach 10 aM, which is 2.3–10,000 times higher than those of existing miRNA sensors. The combination of not-attempted-before exotic sensing material and SPR architecture represents an approach to unlocking the ultrasensitive detection of miRNA and DNA and provides a promising avenue for the early diagnosis, staging, and monitoring of cancer.
Retrotranspositional landscape of Asian rice revealed by 3000 genomes
Authors: Carpentier Marie-Christine , Manfroi Ernandes , Wei Fu-Jin , Wu Hshin-Ping , Lasserre Eric , Llauro Christel , Debladis Emilie , Akakpo Roland , Hsing Yue-Ie , Panaud Olivier 
Published: December 2018

AbstractThe recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events.
Transition from source- to stress-controlled plasticity in nanotwinned materials below a softening temperature
Authors: Taheri Mousavi Seyedeh Mohadeseh , Zhou Haofei , Zou Guijin , Gao Huajian 
Published: December 2018

AbstractNanotwinned materials have been widely studied as a promising class of nanostructured materials that exhibit an exceptional combination of high strength, good ductility, large fracture toughness, remarkable fatigue resistance, and creep stability. Recently, an apparent controversy has emerged with respect to how the strength of nanotwinned materials varies as the twin thickness is reduced. While a transition from hardening to softening was observed in nanotwinned Cu when the twin thickness is reduced below a critical value, continuous hardening was reported in nanotwinned ceramics and nanotwinned diamond. Here, by conducting atomistic simulations and developing a theoretical modeling of nanotwinned Pd and Cu systems, we discovered that there exists a softening temperature, below which the material hardens continuously as the twin thickness is reduced (as in nanotwinned ceramics and diamond), while above which the strength first increases and then decreases, exhibiting a maximum strength and a hardening to softening transition at a critical twin thickness (as in nanotwinned Cu). This important phenomenon has been attributed to a transition from source- to stress-controlled plasticity below the softening temperature, and suggests that different hardening behaviors may exist even in the same nanotwinned material depending on the temperature and that at a given temperature, different materials could exhibit different hardening behaviors depending on their softening temperature.
The role of decomposition reactions in assessing first-principles predictions of solid stability
Authors: Bartel Christopher J. , Weimer Alan W. , Lany Stephan , Musgrave Charles B. , Holder Aaron M. 
Published: December 2018

AbstractThe performance of density functional theory approximations for predicting materials thermodynamics is typically assessed by comparing calculated and experimentally determined enthalpies of formation from elemental phases, ΔHf. However, a compound competes thermodynamically with both other compounds and their constituent elemental forms, and thus, the enthalpies of the decomposition reactions to these competing phases, ΔHd, determine thermodynamic stability. We evaluated the phase diagrams for 56,791 compounds to classify decomposition reactions into three types: 1. those that produce elemental phases, 2. those that produce compounds, and 3. those that produce both. This analysis shows that the decomposition into elemental forms is rarely the competing reaction that determines compound stability and that approximately two-thirds of decomposition reactions involve no elemental phases. Using experimentally reported formation enthalpies for 1012 solid compounds, we assess the accuracy of the generalized gradient approximation (GGA) (PBE) and meta-GGA (SCAN) density functionals for predicting compound stability. For 646 decomposition reactions that are not trivially the formation reaction, PBE (mean absolute difference between theory and experiment (MAD) = 70 meV/atom) and SCAN (MAD = 59 meV/atom) perform similarly, and commonly employed correction schemes using fitted elemental reference energies make only a negligible improvement (~2 meV/atom). Furthermore, for 231 reactions involving only compounds (Type 2), the agreement between SCAN, PBE, and experiment is within ~35 meV/atom and is thus comparable to the magnitude of experimental uncertainty.
Evolution of the low-temperature Fermi surface of superconducting FeSe1−xSx across a nematic phase transition
Authors: Coldea Amalia I. , Blake Samuel F. , Kasahara Shigeru , Haghighirad Amir A. , Watson Matthew D. , Knafo William , Choi Eun Sang , McCollam Alix , Reiss Pascal , Yamashita Takuya , Bruma Mara , Speller Susannah C. , Matsuda Yuji , Wolf Thomas , Shibauchi Takasada , Schofield Andrew J. 
Published: December 2018

AbstractThe existence of a nematic phase transition in iron-chalcogenide superconductors poses an intriguing question about its impact on superconductivity. To understand the nature of this unique quantum phase transition, it is essential to study how the electronic structure changes across this transition at low temperatures. Here, we investigate the evolution of the Fermi surfaces and electronic interactions across the nematic phase transition of FeSe1−xSx using Shubnikov-de Haas oscillations in high magnetic fields up to 45 T in the low temperature regime down to 0.4 K. Most of the Fermi surfaces of FeSe1−xSx monotonically increase in size except for a prominent low frequency oscillation associated with a small, but highly mobile band, which disappears at the nematic phase boundary near x ~ 0.17, indicative of a topological Lifshitz transition. The quasiparticle masses are larger inside the nematic phase, indicative of a strongly correlated state, but they become suppressed outside it. The experimentally observed changes in the Fermi surface topology, together with the varying degree of electronic correlations, will change the balance of electronic interactions in the multi-band system FeSe1−xSx and promote different kz-dependent superconducting pairing channels inside and outside the nematic phase.
Utility of the JAX Clinical Knowledgebase in capture and assessment of complex genomic cancer data
Authors: Patterson Sara E. , Statz Cara M. , Yin Taofei , Mockus Susan M. 
Published: December 2018

AbstractCancer genomic data is continually growing in complexity, necessitating improved methods for data capture and analysis. Tumors often contain multiple therapeutically relevant alterations, and co-occurring alterations may have a different influence on therapeutic response compared to if those alterations were present alone. One clinically important example of this is the existence of a resistance conferring alteration in combination with a therapeutic sensitizing mutation. The JAX Clinical Knowledgebase (JAX-CKB) (https://ckb.jax.org/) has incorporated the concept of the complex molecular profile, which enables association of therapeutic efficacy data with multiple genomic alterations simultaneously. This provides a mechanism for rapid and accurate assessment of complex cancer-related data, potentially aiding in streamlined clinical decision making. Using the JAX-CKB, we demonstrate the utility of associating data with complex profiles comprising ALK fusions with another variant, which have differing impacts on sensitivity to various ALK inhibitors depending on context.
Conventional analysis of movement on non-flat surfaces like the plasma membrane makes Brownian motion appear anomalous
Authors: Adler Jeremy , Sintorn Ida-Maria , Strand Robin , Parmryd Ingela 
Published: December 2018

AbstractCells are neither flat nor smooth, which has serious implications for prevailing plasma membrane models and cellular processes like cell signalling, adhesion and molecular clustering. Using probability distributions from diffusion simulations, we demonstrate that 2D and 3D Euclidean distance measurements substantially underestimate diffusion on non-flat surfaces. Intuitively, the shortest within surface distance (SWSD), the geodesic distance, should reduce this problem. The SWSD is accurate for foldable surfaces but, although it outperforms 2D and 3D Euclidean measurements, it still underestimates movement on deformed surfaces. We demonstrate that the reason behind the underestimation is that topographical features themselves can produce both super- and subdiffusion, i.e. the appearance of anomalous diffusion. Differentiating between topography-induced and genuine anomalous diffusion requires characterising the surface by simulating Brownian motion on high-resolution cell surface images and a comparison with the experimental data.
Hepatocyte growth factor activator inhibitor-2 stabilizes Epcam and maintains epithelial organization in the mouse intestine
Authors: Kawaguchi Makiko , Yamamoto Koji , Takeda Naoki , Fukushima Tsuyoshi , Yamashita Fumiki , Sato Katsuaki , Kitamura Kenichiro , Hippo Yoshitaka , Janetka James W. , Kataoka Hiroaki 
Published: December 2018

AbstractMutations in SPINT2 encoding the epithelial serine protease inhibitor hepatocyte growth factor activator inhibitor-2 (HAI-2) are associated with congenital tufting enteropathy. However, the functions of HAI-2 in vivo are poorly understood. Here we used tamoxifen-induced Cre-LoxP recombination in mice to ablate Spint2. Mice lacking Spint2 died within 6 days after initiating tamoxifen treatment and showed severe epithelial damage in the whole intestinal tracts, and, to a lesser extent, the extrahepatic bile duct. The intestinal epithelium showed enhanced exfoliation, villous atrophy, enterocyte tufts and elongated crypts. Organoid crypt culture indicated that Spint2 ablation induced Epcam cleavage with decreased claudin-7 levels and resulted in organoid rupture. These organoid changes could be rescued by addition of serine protease inhibitors aprotinin, camostat mesilate and matriptase-selective α-ketobenzothiazole as well as by co-deletion of Prss8, encoding the serine protease prostasin. These results indicate that HAI-2 is an essential cellular inhibitor for maintaining intestinal epithelium architecture.
A scientometric review of genome-wide association studies
Authors: Mills Melinda C. , Rahal Charles 
Published: December 2018

AbstractThis scientometric review of genome-wide association studies (GWAS) from 2005 to 2018 (3639 studies; 3508 traits) reveals extraordinary increases in sample sizes, rates of discovery and traits studied. A longitudinal examination shows fluctuating ancestral diversity, still predominantly European Ancestry (88% in 2017) with 72% of discoveries from participants recruited from three countries (US, UK, Iceland). US agencies, primarily NIH, fund 85% and women are less often senior authors. We generate a unique GWAS H-Index and reveal a tight social network of prominent authors and frequently used data sets. We conclude with 10 evidence-based policy recommendations for scientists, research bodies, funders, and editors.
Stereochemical inversion as a route to improved biophysical properties of therapeutic peptides exemplified by glucagon
Authors: Mroz Piotr A. , Perez-Tilve Diego , Mayer John P. , DiMarchi Richard D. 
Published: December 2018

AbstractPeptides and small proteins are attractive therapeutic candidates due to their inherent selectivity and limited off-target effects. Unfortunately, their potential is often hindered by unfavorable physicochemical properties. This is particularly true in the case of glucagon, a peptide indispensable in the treatment of life-threatening hypoglycemia. Glucagon displays extremely low solubility in physiological buffers and suffers chemical degradation when the pH is adjusted in either direction. Here we systematically examine site-specific stereochemical inversion as a means to enhance aqueous solubility and stability, yet not diminish bio-potency or pharmacodynamics. We report several analogs that maintain full biological activity with substantially increased aqueous solubility, and resistance to fibrillation. We conclude that d-amino acids offer an attractive option for biophysical optimization of therapeutic peptides.
Unveiling the n→π* interactions in dipeptides
Authors: León I. , Alonso E. R. , Cabezas C. , Mata S. , Alonso J. L. 
Published: December 2018

AbstractNumerous studies have suggested that the n→π* interactions between carbonyls could contribute significantly to the stability of proteins. Nevertheless, their evaluation is challenging because of the solvent environment or crystal packing forces in solids. Here we study the rotational spectrum of HGlyProOH dipeptide, a very common sequence found in collagen, the most abundant protein in vertebrates, in isolated conditions. Three different structures are unequivocally characterized in the gas phase. Interestingly, the most abundant structure is stabilized by an n→π* interaction and adopts the same conformation as is found in crystalline collagen. This observation serves to support the importance of the n→π* interactions between carbonyl groups.