A photoelectron diffraction investigation of vanadyl phthalocyanine on Au(1 1 1)

Scanned-energy mode photoelectron diffraction using the O 1s and V 2p emission perpendicular to the surface has been used to investigate the orientation and internal conformation of vanadyl phthalocyanine (VOPc) adsorbed on Au(1 1 1). The results confirm earlier indications from scanning tunnelling microscopy that the Vdouble bond; length as m-dashO vanadyl bond points out of, and not into, the surface. The Vdouble bond; length as m-dashO bondlength is 1.60 ± 0.04 Å, not significantly different from its value in bulk crystalline VOPc. However, the V atom in the adsorbed molecule is almost coplanar with the surrounding N atoms and is thus pulled down into the approximately planar region defined by the N and C atoms by 0.52 (+0.14/−0.10) Å, relative to its location in crystalline VOPc. This change must be attributed to the bonding interaction between the molecule and the underlying metal surface

Depth profile of 10Be in the West Antarctic Ice Sheet Divide ice core

第2回極域科学シンポジウム　氷床コアセッション 11月16日（水） 国立極地研究所 2階大会議

The Keck Aperture Masking Experiment: spectro-interferometry of 3 Mira Variables from 1.1 to 3.8 microns

We present results from a spectro-interferometric study of the Miras o Cet, R Leo and W Hya obtained with the Keck Aperture Masking Experiment from 1998 Sep to 2002 Jul. The spectrally dispersed visibility data permit fitting with circularly symmetric brightness profiles such as a simple uniform disk. The stellar angular diameter obtained over up to ~ 450 spectral channels spaning the region 1.1-3.8 microns is presented. Use of a simple uniform disk brightness model facilitates comparison between epochs and with existing data and theoretical models. Strong size variations with wavelength were recorded for all stars, probing zones of H2O, CO, OH, and dust formation. Comparison with contemporaneous spectra extracted from our data show a strong anti-correlation between the observed angular diameter and flux. These variations consolidate the notion of a complex stellar atmosphere consisting of molecular shells with time-dependent densities and temperatures. Our findings are compared with existing data and pulsation models. The models were found to reproduce the functional form of the wavelength vs. angular diameter curve well, although some departures are noted in the 2.8-3.5 micron range.Comment: 10 pages, 10 figures Accepted to Ap

Adsorption structure of glycine on TiO2(1 1 0): a photoelectron diffraction determination

High-resolution core-level photoemission and scanned-energy mode photoelectron diffraction (PhD) of the O 1s and N 1s states have been used to investigate the interaction of glycine with the rutile TiO2(1 1 0) surface. Whilst there is clear evidence for the presence of the zwitterion View the MathML sourceCH2COO− with multilayer deposition, at low coverage only the deprotonated glycinate species, NH2CH2COO is present. Multiple-scattering simulations of the O 1s PhD data show the glycinate is bonded to the surface through the two carboxylate O atoms which occupy near-atop sites above the five-fold-coordinated surface Ti atoms, with a Ti–O bondlength of 2.12 ± 0.06 Å. Atomic hydrogen arising from the deprotonation is coadsorbed to form hydroxyl species at the bridging oxygen sites with an associated Ti–O bondlength of 2.01 ± 0.03 Å. Absence of any significant PhD modulations of the N 1s emission is consistent with the amino N atom not being involved in the surface bonding, unlike the case of glycinate on Cu(1 1 0) and Cu(1 0 0)

Pyomo - Optimization Modeling in Python

INFORMS Journal of Computing, November 2012The article of record as published may be located at http://dx.doi.org/10.1287/ijoc.2012.4.brIf a simple, intuitive tool for a task exists, the task is done more often, by more people. This basic principle is as true for gardening and gadgets, as it is for computation in operations research. The book, Pyomo { Optimization Modeling in Python, documents a simple, yet versatile tool for modeling and solving optimization problems

Quantitative adsorbate structure determination under catalytic reaction conditions

Current methods allow quantitative local structure determination of adsorbate geometries on surfaces in ultrahigh vacuum (UHV) but are incompatible with the higher pressures required for a steady-state catalytic reactions. Here we show that photoelectron diffraction can be used to determine the structure of the methoxy and formate reaction intermediates during the steady-state oxidation of methanol over Cu(110) by taking advantage of recent instrumental developments to allow near-ambient pressure x-ray photoelectron spectroscopy. The local methoxy site differs from that under static UHV conditions, attributed to the increased surface mobility and dynamic nature of the surface under reaction conditions

Large Differences in Small RNA Composition Between Human Biofluids.

Extracellular microRNAs (miRNAs) and other small RNAs are implicated in cellular communication and may be useful as disease biomarkers. We systematically compared small RNAs in 12 human biofluid types using RNA sequencing (RNA-seq). miRNAs and tRNA-derived RNAs (tDRs) accounted for the majority of mapped reads in all biofluids, but the ratio of miRNA to tDR reads varied from 72 in plasma to 0.004 in bile. miRNA levels were highly correlated across all biofluids, but levels of some miRNAs differed markedly between biofluids. tDR populations differed extensively between biofluids. Y RNA fragments were seen in all biofluids and accounted for >10% of reads in blood plasma, serum, and cerebrospinal fluid (CSF). Reads mapping exclusively to Piwi-interacting RNAs (piRNAs) were very rare, except in seminal plasma. These results demonstrate extensive differences in small RNAs between human biofluids and provide a useful resource for investigating extracellular RNA biology and developing biomarkers

Direct calculation of the hard-sphere crystal/melt interfacial free energy

We present a direct calculation by molecular-dynamics computer simulation of the crystal/melt interfacial free energy, $\gamma$, for a system of hard spheres of diameter $\sigma$. The calculation is performed by thermodynamic integration along a reversible path defined by cleaving, using specially constructed movable hard-sphere walls, separate bulk crystal and fluid systems, which are then merged to form an interface. We find the interfacial free energy to be slightly anisotropic with $\gamma$ = 0.62$\pm 0.01$, 0.64$\pm 0.01$ and 0.58$\pm 0.01 k_BT/\sigma^2$ for the (100), (110) and (111) fcc crystal/fluid interfaces, respectively. These values are consistent with earlier density functional calculations and recent experiments measuring the crystal nucleation rates from colloidal fluids of polystyrene spheres that have been interpreted [Marr and Gast, Langmuir {\bf 10}, 1348 (1994)] to give an estimate of $\gamma$ for the hard-sphere system of $0.55 \pm 0.02 k_BT/\sigma^2$, slightly lower than the directly determined value reported here.Comment: 4 pages, 4 figures, submitted to Physical Review Letter

Photoelectron diffraction investigation of the structure of the clean TiO2(110)(1×1) surface

The surface relaxations of the rutile TiO2(110)(1×1) clean surface have been determined by O 1 s and Ti 2p3∕2 scanned-energy mode photoelectron diffraction. The results are in excellent agreement with recent low-energy electron diffraction (LEED) and medium energy ion scattering (MEIS) results, but in conflict with the results of some earlier investigations including one by surface x-ray diffraction. In particular, the bridging O atoms at the surface are found to relax outward, rather than inward, relative to the underlying bulk. Combined with the recent LEED and MEIS results, a consistent picture of the structure of this surface is provided. While the results of the most recent theoretical total-energy calculations are qualitatively consistent with this experimental consensus, significant quantitative differences remain

Synthetic data of simulated microcalcification clusters to train and explain deep learning detection models in contrast-enhanced mammography

Deep learning (DL) models can be trained on contrast-enhanced mammography (CEM) images to detect and classify lesions in the breast. As they often put more emphasis on the masses enhanced in the recombined image, they can fail in recognizing microcalcification clusters since these are hardly enhanced and are mainly visible in the (processed) lowenergy image. Therefore, we developed a method to create synthetic data with simulated microcalcification clusters to be used for data augmentation and explainability studies when training DL models. At first 3-dimensional voxel models of simulated microcalcification clusters based on descriptors of the shape and structure were constructed. In a set of 500 simulated microcalcification clusters the range of the size and of the number of microcalcifications per cluster followed the distribution of real clusters. The insertion of these clusters in real images of non-delineated CEM cases was evaluated by radiologists. The realism score was acceptable for single view applications. Radiologists could more easily categorize synthetic clusters into benign versus malignant than real clusters. In a second phase of the work, the role of synthetic data for training and/or explaining DL models was explored. A Mask R-CNN model was trained with synthetic CEM images containing microcalcification clusters. After a training run of 100 epochs the model was found to overfit on a training set of 192 images. In an evaluation with multiple test sets, it was found that this high level of sensitivity was due to the model being capable of recognizing the image rather than the cluster. Synthetic data could be applied for more tests, such as the impact of particular features in both background and lesion models