Machine-learning descriptor search on the density of states profile of bimetallic alloy systems and comparison with the d-band center theory.

In this study, the electronic density of states (DOSs) calculated with density functional theory (DFT) were analyzed by the machine-learning techniques. More than 400 pure metal and bimetallic alloy systems were calculated with DFT, and obtained the surface DOSs and the CH3 adsorption energy (Ead). By fitting the Gaussian functions to the DOS, multiple descriptors, such as the Gaussian peak positions, heights, and widths were extracted. Several regression methods, such as the least absolute shrinkage of selection operator (LASSO), random-forest, gradient-boosting, and extra-tree were used to find the relationship between these descriptors and the Ead. The results show that the energy position of the peaks in the d-projected DOS is the most important descriptor, in agreement with the previously known d-band center theory. It was also shown that the peak position in d-projected DOS improves the regression model in addition to the d-band center, since it reduces the regression error.

The Homeodomain-Leucine Zipper Subfamily I Contributes to Leaf Age- and Time-Dependent Resistance to Pathogens in Arabidopsis thaliana.

In Arabidopsis thaliana (Arabidopsis), nonhost resistance (NHR) is influenced by both leaf age and the moment of inoculation. While the circadian clock and photoperiod have been linked to the time-dependent regulation of NHR in Arabidopsis, the mechanism underlying leaf age-dependent NHR remains unclear. In this study, we investigated leaf age-dependent NHR to Pyricularia oryzae in Arabidopsis. Our findings revealed that this NHR type is regulated by both miR156-dependent and miR156-independent pathways. To identify the key players, we utilized rice-FOX Arabidopsis lines and identified the rice HD-Zip I OsHOX6 gene. Notably, OsHOX6 expression confers robust NHR to P. oryzae and Colletotrichum nymphaeae in Arabidopsis, with its effect being contingent upon leaf age. Moreover, we explored the role of AtHB7 and AtHB12, the Arabidopsis closest homologues of OsHOX6, by studying mutants and overexpressors in Arabidopsis-C. higginsianum interaction. AtHB7 and AtHB12 were found to contribute to both penetration resistance and post-penetration resistance to C. higginsianum in a leaf age- and time-dependent manner. These findings highlight the involvement of HD-Zip I AtHB7 and AtHB12, well-known regulators of development and abiotic stress responses, in biotic stress responses in Arabidopsis.

Magnetism in Nonplanar Zigzag Edge Termini of Graphene Nanoribbons.

Graphene nanoribbons (GNRs) and nanographenes synthesized by on-surface reactions using tailor-made molecular precursors offer an ideal playground for a study of magnetism towards nano-spintronics. Although the zigzag edge of GNRs has been known to host magnetism, the underlying metal substrates usually veil the edge-induced Kondo effect. Here, we report the on-surface synthesis of unprecedented, π-extended 7-armchair GNRs using 7-bromo-12-(10-bromoanthracen-9-yl)tetraphene as the precursor. Characterization by scanning tunneling microscopy/spectroscopy revealed unique rearrangement reactions leading to pentagon- or pentagon/heptagon-incorporated, nonplanar zigzag termini, which demonstrated Kondo resonances even on bare Au(111). Density functional theory calculations indicate that the nonplanar structure significantly reduces the interaction between the zigzag terminus and the Au(111) surface, leading to a recovery of the spin localization of the zigzag edge. Such a distortion of planar GNR structures offers a degree of freedom to control the magnetism on metal substrates.

Epidermal CCA1 and PMR5 contribute to nonhost resistance in Arabidopsis.

Nonhost resistance (NHR) is the most robust and durable resistance in plants, but its spatiotemporal regulation is poorly understood. The circadian clock functions in a tissue-specific manner and regulates individual physiological processes in plants. Using mutant and RNA-seq analyses, we revealed a role of CIRCADIAN CLOCK ASSOCIATED1 (CCA1) in tissue-specific and time-of-day-specific regulation of NHR to Pyricularia oryzae (syn. Magnaporthe oryzae) in Arabidopsis thaliana (Arabidopsis). Targeted perturbation of CCA1 function in epidermis compromised time-of-day-specific regulation of NHR to P. oryzae in Arabidopsis. RNA-seq analysis showed that P. oryzae inoculation alters the transcriptome in penetration 2 (pen2) plants and identified POWDERY MILDEW RESISTANCE 5 (PMR5) as a candidate gene of direct targets of CCA1. Time-of-day-specific penetration resistance to P. oryzae was reduced in Arabidopsis pen2 pmr5 mutant plants. These findings suggest that epidermal CCA1 and PMR5 contribute to the establishment of time-of-day-specific NHR to P. oryzae in Arabidopsis.

On-Surface Synthesis of Porphyrin-Complex Multi-Block Co-Oligomers by Defluorinative Coupling.

On-surface chemical reaction has become a very powerful technique to synthesize nanostructures by linking small molecules in the bottom-up approach. Given the fact that most reactants are simultaneously activated at certain temperatures, a sequential reaction in a controlled way has remained challenging. Here, we present an on-surface synthesis of multi-block co-oligomers from trifluoromethyl (CF3 ) substituted porphyrin metal complexes. The oligomerization on Au(111) is demonstrated with a combination of bond-resolved scanning probe microscopy and density functional theory (DFT) calculations. Even after the first oligomerization of single monomer unit, the termini of the oligomer keep the CF3 group, which can be used as a reactant for further coupling in a sequential order. Consequently, copper, cobalt, and palladium complexes of bisanthracene-fused porphyrin oligomers were linked with each other in a designed order.

Genetic Variations and Neuropathologic Features of Patients with PRKN Mutations.

BACKGROUND: Mutations in PRKN are the most common cause of autosomal recessive juvenile parkinsonism. The objective of this study was to investigate the association between genotype and pathology in patients with PRKN mutations. METHODS: We performed a sequence and copy number variation analysis of PRKN, mRNA transcripts, Parkin protein expression, and neuropathology in 8 autopsied patients. RESULTS: All the patients harbored biallelic PRKN mutations. Two patients were homozygous and heterozygous, respectively, for the missense mutation p.C431F. Seven patients had exon rearrangements, including 2 patients from a single family who harbored a homozygous deletion of exon 4, and 3 patients who carried a homozygous duplication of exons 6-7, a homozygous duplication of exons 10-11, and a heterozygous duplication of exons 2-4. In the other 2 patients, we found a compound heterozygous duplication of exon 2, deletion of exon 3, and a heterozygous duplication of exon 2. However, sequencing of cDNA prepared from mRNA revealed 2 different transcripts derived from triplication of exon 2 and deletion of exons 2-3 and from duplication of exons 2-4 and deletion of exons 3-4. Western blotting and immunohistochemistry revealed faint or no expression of Parkin in their brains. In the substantia nigra pars compacta, a subfield-specific pattern of neuronal loss and mild gliosis were evident. Lewy bodies were found in 3 patients. Peripheral sensory neuronopathy was a feature. CONCLUSIONS: Genomic and mRNA analysis is needed to identify the PRKN mutations. Variable mutations may result in no or little production of mature Parkin and the histopathologic features may be similar. © 2021 International Parkinson and Movement Disorder Society.

Theoretical prediction by DFT and experimental observation of heterocation-doping effects on hydrogen adsorption and migration over the CeO2(111) surface.

Hydrogen (H) atom adsorption and migration over the CeO2-based materials surface are of great importance because of its wide applications to catalytic reactions and electrochemical devices. Therefore, comprehensive knowledge for controlling the H atom adsorption and migration over CeO2-based materials is crucially important. For controlling H atom adsorption and migration, we investigated irreducible divalent, trivalent, and quadrivalent heterocation-doping effects on H atom adsorption and migration over the CeO2(111) surface using density functional theory (DFT) calculations. Results revealed that the electron-deficient lattice oxygen (Olat) and the flexible CeO2 matrix played key roles in strong adsorption of H atoms. Heterocations with smaller valence and smaller ionic radius induced the electron-deficient Olat. In addition, smaller cation doping enhanced the CeO2 matrix flexibility. Moreover, we confirmed the influence of H atom adsorption controlled by doping on surface proton migration (i.e. surface protonics) and catalytic reaction involving surface protonics (NH3 synthesis in an electric field). Results confirmed clear correlation between H atom adsorption energy and surface protonics.

Manipulation of CO adsorption over Me1/CeO2 by heterocation doping: Key roles of single-atom adsorption energy.

The performance of metal atoms chemically bonded to oxide supports cannot be explained solely by the intrinsic properties of the metals such as the d-band center. Herein, we present an in-depth study of the correlation between metal-oxide interactions and the properties of the supported metal using CO adsorption on Me1 (Fe1, Co1, and Ni1) loaded over CeO2 (111) doped with divalent (Ca, Sr, and Ba), trivalent (Al, Ga, Sc, Y, and La), and quadrivalent (Hf and Zr) heterocations. CO adsorption over Me1 is strongly dependent on the binding energies of Me1. Two factors led to this trend. First, the extent of the Me1-surface oxygen (Me1-O) bond relaxation during CO adsorption played a key role. Second, the d-band center shifted drastically because of charge transfer to the oxides. The shift is related to the oxophilicity of metals. Adsorption energies of Me1 over oxides include the contributions of the factors described above. Therefore, we can predict the activities of Me1 using the strength of anchoring by oxide supports. Results show that smaller ionic radii of the doped heterocations were associated with more tightly bound Me1. This finding sheds light on the possibility of heterocation-doping manipulating the reactivity of the Me1 catalyst based on theoretical predictions.

Photoperiod Following Inoculation of Arabidopsis with Pyricularia oryzae (syn. Magnaporthe oryzae) Influences on the Plant-Pathogen Interaction.

In plant-pathogen interactions, a proper light environment affects the establishment of defense responses in plants. In our previous experiments, we found that nonhost resistance (NHR) to Pyricularia oryzae Cav. in Arabidopsis thaliana (L.) Heynh. (Arabidopsis), in diurnal conditions, varies with the inoculation time. Moreover, we indicated that the circadian clock plays an important role in regulating time-of-day differences in NHR to P. oryzae in Arabidopsis. However, the involvement of photoperiod in regulating NHR was still not understood. To determine the photoperiod role, we performed the experiments in continuous light and darkness during the early Arabidopsis-P. oryzae interaction. We found that the light period after the inoculation in the evening enhanced the resistance to penetration. However, the dark period after the inoculation in the morning suppressed the penetration resistance. Furthermore, the genetic analysis indicated that jasmonic acid, reactive oxygen species, and tryptophan-derived metabolite(s) contribute to the photoperiod regulation of NHR in Arabidopsis. The present results denote that photoperiod plays an important role in regulating time-of-day differences in NHR to P. oryzae in Arabidopsis.

Heteroatom doping effects on interaction of H2O and CeO2 (111) surfaces studied using density functional theory: Key roles of ionic radius and dispersion.

Understanding heteroatom doping effects on the interaction between H2O and cerium oxide (ceria, CeO2) surfaces is crucially important for elucidating heterogeneous catalytic reactions of CeO2-based oxides. Surfaces of CeO2 (111) doped with quadrivalent (Ti, Zr), trivalent (Al, Ga, Sc, Y, La), or divalent (Ca, Sr, Ba) cations are investigated using density functional theory (DFT) calculations modified for onsite Coulomb interactions (DFT + U). Trivalent (except for Al) and divalent cation doping induces the formation of intrinsic oxygen vacancy (Ovac), which is backfilled easily by H2O. Partially OH-terminated surfaces are formed. Furthermore, dissociative adsorption of H2O is simulated on the OH terminated surfaces (for trivalent or divalent cation doped models) and pure surfaces (for Al and quadrivalent cation doped surfaces). The ionic radius is crucially important. In fact, H2O dissociates spontaneously on the small cations. Although a slight change is induced by doping as for the H2O adsorption energy at Ce sites, the H2O dissociative adsorption at Ce sites is well-assisted by dopants with a smaller ionic radius. In terms of the amount of promoted Ce sites, the arrangement of dopant sites is also fundamentally important.

CCA1 and LHY contribute to nonhost resistance to Pyricularia oryzae (syn. Magnaporthe oryzae) in Arabidopsis thaliana.

The circadian clock enables plants to adapt to their environment and control numerous physiological processes, including plant-pathogen interactions. However, it is unknown if the circadian clock controls nonhost resistance (NHR) in plants. To find out, we analyzed microarray data with the web-based tool DIURNAL to reveal that NHR-related genes show rhythmic expression patterns in the absence of a pathogen challenge. Our clock mutant analyses found that cca1-1 lhy-11 double mutant showed compromised NHR to Pyricularia oryzae, suggesting that two components of the circadian clock, CCA1 and LHY, are involved in regulating penetration resistance in Arabidopsis thaliana. By analyzing pen2 double mutants, we revealed that CCA1 contributes to time-of-day-dependent penetration resistance as a positive regulator and that LHY regulates post-penetration resistance as a positive regulator. Taken together, our results suggest that the circadian clock regulates the time-of-day-dependent NHR to P. oryzae and thus enables A. thaliana to counteract pathogen attacks.Abbreviations: EE: evening element; ETI: effector-triggered immunity; NHR: nonhost resistance; PAMP: pathogen-associated molecular pattern; PTI: PAMP-triggered immunity; SAR: systemic acquired resistance.

Reaction energy benchmarks of hydrocarbon combustion by Gaussian basis and plane wave basis approaches.

The reaction energies of 275 elementary reactions from the hydrocarbon combustion model GRI-Mech 3.0 were evaluated by electronic structure calculations using both localized Gaussian basis and plane wave basis sets. In the Gaussian basis calculations, the d-polarization function on C, N, and O elements reduces the mean absolute deviation (MAD) from the experimental value by 53%, a significant improvement in computational accuracy. In the plane wave basis calculation using different exchange-correlation (XC) functionals, the MAD values were 0.316-0.426 eV when non-hybrid type XC functionals such as RPBE, PBE, PW91, revPBE, and PBEsol were used. On the other hand, hybrid functionals like B3LYP and HSE06 reduced the MAD values significantly down to 0.182 and 0.233 eV, respectively. The B3LYP results have 49% less MAD compared to the PBE results. These demonstrated the strong advantage of the hybrid functional for calculating gas-phase reaction energies. The present comprehensive benchmarks will be crucial for future microkinetics as well as machine learning studies on the catalytic reactions. © 2019 Wiley Periodicals, Inc.

Machine learning prediction of coordination energies for alkali group elements in battery electrolyte solvents.

We combined a data science-driven method with quantum chemistry calculations, and applied it to the battery electrolyte problem. We performed quantum chemistry calculations on the coordination energy (Ecoord) of five alkali metal ions (Li, Na, K, Rb, and Cs) to electrolyte solvent, which is intimately related to ion transfer at the electrolyte/electrode interface. Three regression methods, namely, multiple linear regression (MLR), least absolute shrinkage and selection operator (LASSO), and exhaustive search with linear regression (ES-LiR), were employed to find the relationship between Ecoord and descriptors. Descriptors include both ion and solvent properties, such as the radius of metal ions or the atomic charge of solvent molecules. Our results clearly indicate that the ionic radius and atomic charge of the oxygen atom that is connected to the metal ion are the most important descriptors. Good prediction accuracy for Ecoord of 0.127 eV was obtained using ES-LiR, meaning that we can predict Ecoord for any alkali ion without performing quantum chemistry calculations for ion-solvent pairs. Further improvement in the prediction accuracy was made by applying the exhaustive search with Gaussian process, which yields 0.016 eV for the prediction accuracy of Ecoord.

SOBIR1 and AGB1 independently contribute to nonhost resistance to Pyricularia oryzae (syn. Magnaporthe oryzae) in Arabidopsis thaliana.

Rice blast caused by Pyricularia oryzae (syn. Magnaporthe oryzae) is a disease devastating to rice. We have studied the Arabidopsis-P. oryzae pathosystem as a model system for nonhost resistance (NHR) and found that SOBIR1, but not BAK1, is a positive regulator of NHR to P. oryzae in Arabidopsis. AGB1 is also involved in NHR. However, the genetic interactions between SOBIR1, BAK1, and AGB1 are uncharacterized. In this study, we delineated the genetic interactions between SOBIR1, BAK1, and AGB1 in NHR to P. oryzae in Arabidopsis and found SOBIR1 and AGB1 independently control NHR to P. oryzae in Arabidopsis pen2-1 mutant plants. Furthermore, XLG2, but not TMM, has a positive role in penetration resistance to P. oryzae in Arabidopsis pen2-1 mutant plants. Our study characterized genetic interactions in Arabidopsis NHR. Abbreviations: PRR: pattern recognition receptor, RLK: receptor-like kinase, RLP: receptor-like protein, BAK1: BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED RECEPTOR KINASE 1, BIR1: BAK1-INTERACTING RECEPTOR-LIKE KINASE 1, SOBIR1: SUPPRESSOR OF BIR1-1-1, AGB1: ARABIDOPSIS G PROTEIN ß-SUBUNIT 1, XLG2: EXTRA-LARGE G PROTEIN 2.

Interplay of mutual electric and magnetic couplings between three-dimensional split-ring resonators.

We experimentally and theoretically study the interplay between capacitive electric and inductive magnetic couplings in infrared metamaterials consisting of densely-packed three-dimensional (3D) meta-atoms. The meta-atom is made of metal-stress-driven assembled 3D split-ring resonators to exhibit strong bi-anisotropy, where electric and magnetic resonances occur simultaneously. By varying the spatial arrangement of the arrayed meta-atoms, the mutual coupling between meta-atoms dramatically modifies their mode profiles and resultant spectral responses. The corresponding numerical simulations evidently retrieved current densities and magnetic field strengths, as well as the transmittance, to reveal the important resonant behavior in the coupled meta-atom systems. We conclude that the mutual electric coupling between the neighboring meta-atoms plays a crucial role to the scattering behaviors of the bi-anisotropic metamaterials.

Characteristics of spinopelvic alignment in Parkinson's disease: Comparison with adult spinal deformity.

PURPOSE: The characteristics and pathogenesis of spinopelvic alignment in Parkinsons's disease (PD) patients-including differences compared to non-PD subjects and their relationships with the severity of PD-have not been clarified. The aim of this study was to investigate the characteristics of spinopelvic alignment in patients with PD. METHODS: Forty-eight PD patients complaining of chronic low back pain were included (PD group). The PD condition, determined using the Hoehn and Yahr (H&Y) stage and Unified Parkinson Disease Rating Scale (UPDRS) score; radiographic spinopelvic alignment; lumbar range of motion (ROM); and low back pain-related quality of life assessments were evaluated. Fifty age- and sex-matched patients with adult spinal deformities were included as controls (ASD group). RESULTS: The spinopelvic alignments of the PD/ASD groups demonstrated sagittal vertical axes of 120.9/106.3 mm and pelvic incidences of 49.7/52.9°, with no significant differences. Conversely, there were significant differences in the thoracic kyphosis (TK; 27.6/16.7°), lumbar lordosis (-22.7/-7.9°), and pelvic tilt (25.3/34.4°) (all, p < 0.05). With regard to correlations with the PD condition, the H&Y stage demonstrated significant correlations with the sagittal vertical axis, thoracolumbar kyphosis, and lumbar ROM (all, p < 0.05), and the UPDRS score tended to correlate with the TK and thoracolumbar kyphosis (both, p < 0.01). CONCLUSION: Characteristic spinal conditions in PD exist, with progressed PD condition causing stooped posture with increased thoracic or thoracolumbar kyphosis and decreased lumbar ROM; moreover, global sagittal malalignment progresses without sufficient compensatory mechanisms such as loss of TK and pelvic retroversion.

SOBIR1 contributes to non-host resistance to Magnaporthe oryzae in Arabidopsis.

The rate of entry of Magnaporthe oryzae into Arabidopsis pen2 sobir1 plants was significantly higher than that into pen2 plants. The length of the infection hyphae in pen2 sobir1 plants was significantly longer than that in pen2 plants. These results suggest that SOBIR1 is involved in both penetration and post-penetration resistance to M. oryzae in Arabidopsis.

ERECTA contributes to non-host resistance to Magnaporthe oryzae in Arabidopsis.

ERECTA controls both developmental processes and disease resistance in Arabidopsis. We investigated the function of ERECTA in non-host resistance to Magnaporthe oryzae in Arabidopsis. In the pen2 er mutant, penetration resistance and post-penetration resistance to M. oryzae were compromised. These results suggest that ERECTA is involved in both penetration and post-penetration resistance to M. oryzae in Arabidopsis.

Optical transmission between III-V chips on Si using photonic wire bonding.

Photonic wire bonding (PWB) was used to achieve flexible chip-scale optical interconnection as a kind of 3D-freeform polymer waveguide based on the two-photon polymerization of SU-8. First, the fabrication conditions of PWB were determined for the two-photon absorption process, and the coupling structure between PWB and III-V optical components was numerically simulated in order to obtain high coupling efficiency. Then, using PWB, chip-to-chip optical transmission was realized between laser and detector chips located on a common Si substrate. We fabricated a 2.5-µm-wide PWB with 1:3 aspect ratio between two optical chips of 140-µm gap and achieved a connection loss of approximately 10 dB.

Molecular structure and internal rotation of CF3 group of methyl trifluoroacetate: gas electron diffraction, microwave spectroscopy, and quantum chemical calculation studies.

The molecular structure of methyl trifluoroacetate (CF3COOCH3) has been determined by gas electron diffraction (GED), microwave spectroscopy (MW), and quantum chemical calculations (QC). QC study provides the optimized geometries and force constants of the molecule. They were used to estimate the structural model for GED study and to calculate the vibrational corrections for GED and MW data. In addition, potential energy curves for the internal rotations of CF3 and CH3 groups have been calculated for anti (dihedral angle of α(CCOC) is 180°) and syn (α(CCOC) = 0°) conformers of methyl trifluoroacetate. Both the GED and MW data revealed the existence of the anti conformer. Molecular constants determined by MW are A0 = 3613.4(3) MHz, B0 = 1521.146(8) MHz, C0 = 1332.264(9) MHz, ΔJ = 0.09(2) kHz, and ΔJK = 0.23(6) kHz. The GED data were well-reproduced by the analysis in which a large-amplitude motion of the CF3 group was taken into account. The barrier of the internal rotation of the CF3 group was determined to be V3 = 2.3(4) kJ mol(-1), where V3 is the potential coefficient of the assumed potential function, V(ϕ) = (V3/2)(1 - cos 3ϕ), and ϕ is a rotational angle for the CF3 group. The values of geometrical parameters (re structure) of the anti conformer of CF3COOCH3 are r((O═)C-O) = 1.326(6) Å, r(O-CH3) = 1.421(4) Å, r(C-H(in-plane)) = 1.083(14) Å, r(C-H(out-of-plane)) = 1.087(14) Å, r(C═O) = 1.190(7) Å, r(C-C) = 1.533(4) Å, r(C-F(in-plane)) = 1.319(4) Å, r(C-F(out-of-plane)) = 1.320(6) Å, ∠COC = 116.3(5)°, ∠OCH(in-plane) = 105.2° (fixed), ∠OCH(out-of-plane) = 110.0° (fixed), ∠O═CC = 123.7° (fixed), ∠O-CC = 111.2(5)°, ∠OCO = 125.2(5)°, ∠CCF = 110.1(3)°, and OCCF (out-of-plane dihedral angles) = ± 121.5(1)°. Numbers in parentheses are three times the standard deviations of the data fit.