Effect of quantum nuclear motion on hydrogen bonding

This work considers how the properties of hydrogen bonded complexes, D-H....A, are modified by the quantum motion of the shared proton. Using a simple two-diabatic state model Hamiltonian, the analysis of the symmetric case, where the donor (D) and acceptor (A) have the same proton affinity, is carried out. For quantitative comparisons, a parametrization specific to the O-H....O complexes is used. The vibrational energy levels of the one-dimensional ground state adiabatic potential of the model are used to make quantitative comparisons with a vast body of condensed phase data, spanning a donor-acceptor separation (R) range of about 2.4-3.0 A, i.e., from strong to weak bonds. The position of the proton and its longitudinal vibrational frequency, along with the isotope effects in both are discussed. An analysis of the secondary geometric isotope effects, using a simple extension of the two-state model, yields an improved agreement of the predicted variation with R of frequency isotope effects. The role of the bending modes in also considered: their quantum effects compete with those of the stretching mode for certain ranges of H-bond strengths. In spite of the economy in the parametrization of the model used, it offers key insights into the defining features of H-bonds, and semi-quantitatively captures several experimental trends.Comment: 12 pages, 8 figures. Notation clarified. Revised figure including the effect of bending vibrations on secondary geometric isotope effect. Final version, accepted for publication in Journal of Chemical Physic

An evaluation of machine-learning for predicting phenotype: studies in yeast, rice, and wheat

Abstract: In phenotype prediction the physical characteristics of an organism are predicted from knowledge of its genotype and environment. Such studies, often called genome-wide association studies, are of the highest societal importance, as they are of central importance to medicine, crop-breeding, etc. We investigated three phenotype prediction problems: one simple and clean (yeast), and the other two complex and real-world (rice and wheat). We compared standard machine learning methods; elastic net, ridge regression, lasso regression, random forest, gradient boosting machines (GBM), and support vector machines (SVM), with two state-of-the-art classical statistical genetics methods; genomic BLUP and a two-step sequential method based on linear regression. Additionally, using the clean yeast data, we investigated how performance varied with the complexity of the biological mechanism, the amount of observational noise, the number of examples, the amount of missing data, and the use of different data representations. We found that for almost all the phenotypes considered, standard machine learning methods outperformed the methods from classical statistical genetics. On the yeast problem, the most successful method was GBM, followed by lasso regression, and the two statistical genetics methods; with greater mechanistic complexity GBM was best, while in simpler cases lasso was superior. In the wheat and rice studies the best two methods were SVM and BLUP. The most robust method in the presence of noise, missing data, etc. was random forests. The classical statistical genetics method of genomic BLUP was found to perform well on problems where there was population structure. This suggests that standard machine learning methods need to be refined to include population structure information when this is present. We conclude that the application of machine learning methods to phenotype prediction problems holds great promise, but that determining which methods is likely to perform well on any given problem is elusive and non-trivial

Quantum oscillations in the parent pnictide BaFe2_2As2_2 : itinerant electrons in the reconstructed state

We report quantum oscillation measurements that enable the direct observation of the Fermi surface of the low temperature ground state of \ba122. From these measurements we characterize the low energy excitations, revealing that the Fermi surface is reconstructed in the antiferromagnetic state, but leaving itinerant electrons in its wake. The present measurements are consistent with a conventional band folding picture of the antiferromagnetic ground state, placing important limits on the topology and size of the Fermi surface.Comment: 5 pages, 3 figure

Mixed valency in cerium oxide crystallographic phases: Determination of valence of the different cerium sites by the bond valence method

We have applied the bond valence method to cerium oxides to determine the oxidation states of the Ce ion at the various site symmetries of the crystals. The crystals studied include cerium dioxide and the two sesquioxides along with some selected intermediate phases which are crystallographically well characterized. Our results indicate that cerium dioxide has a mixed-valence ground state with an f-electron population on the Ce site of 0.27 while both the A- and C-sesquioxides have a nearly pure f^1 configuration. The Ce sites in most of the intermediate oxides have non-integral valences. Furthermore, many of these valences are different from the values predicted from a naive consideration of the stoichiometric valence of the compound

Intravenous lipid emulsion and dexmedetomidine for treatment of feline permethrin intoxication: A report from 4 cases

Four cases of feline permethrin intoxication are described. The cause of intoxication is the application of canine permethrin spot-on product (Advantix®, Bayer) by the owners. Principal clinical guidelines recommends the use of anticonvulsant drugs to treat seizures or neurological symptoms after initial stabilization and dermal decontamination. The use of lipid emulsion had an increasing interest in the last decade for treatment of toxicosis caused by lipophylic drugs as reported in human and in veterinary medical practices. All cats presented in this study, were treated with intravenous lipid emulsion (ILE) at variable dosages, and dexmedetomidine was also administered by intravenous way. No adverse reaction such as thrombophlebitis, overload circulation or others was noticed during and after administration of ILE. Dexmedetomidine was proved to be helpful in tranquillizing the cats. All cats were discharged in good condition faster than other cases treated without their use

Double filtration plasmapheresis in a dog with multiple myeloma and hyperviscosity syndrome

A 12 year old, 38 kg, mix-breed, intact male dog presented with a 20 day history of clinical signs consistent with hyperviscosity syndrome secondary to multiple myeloma. The dog received three double filtration plasmapheresis treatments on day 0, 7 and 22 after presentation. A significant (p<0.05) reduction in serum total protein, alpha-2 and gamma globulins was found following each treatment. These reductions were accompanied by a complete resolution, although temporary, of the clinical signs of hyperviscosity syndrome. The present study reported for the first time the use of double filtration plasmapheresis to reduce clinical signs of hyperviscosity syndrome in a dog with multiple myeloma

Line Emission from an Accretion Disk around a Black hole: Effects of Disk Structure

The observed iron K-alpha fluorescence lines in Seyfert-1 galaxies provide strong evidence for an accretion disk near a supermassive black hole as a source of the line emission. These lines serve as powerful probes for examining the structure of inner regions of accretion disks. Previous studies of line emission have considered geometrically thin disks only, where the gas moves along geodesics in the equatorial plane of a black hole. Here we extend this work to consider effects on line profiles from finite disk thickness, radial accretion flow and turbulence. We adopt the Novikov and Thorne (1973) solution, and find that within this framework, turbulent broadening is the dominant new effect. The most prominent change in the skewed, double-horned line profiles is a substantial reduction in the maximum flux at both red and blue peaks. The effect is most pronounced when the inclination angle is large, and when the accretion rate is high. Thus, the effects discussed here may be important for future detailed modeling of high quality observational data.Comment: 21 pages including 8 figures; LaTeX; ApJ format; accepted by ApJ; short results of this paper appeared before as a conference proceedings (astro-ph/9711214

Holographic Renormalization for z=2 Lifshitz Space-Times from AdS

Lifshitz space-times with critical exponent z=2 can be obtained by dimensional reduction of Schroedinger space-times with critical exponent z=0. The latter space-times are asymptotically AdS solutions of AdS gravity coupled to an axion-dilaton system and can be uplifted to solutions of type IIB supergravity. This basic observation is used to perform holographic renormalization for 4-dimensional asymptotically z=2 locally Lifshitz space-times by Scherk-Schwarz dimensional reduction of the corresponding problem of holographic renormalization for 5-dimensional asymptotically locally AdS space-times coupled to an axion-dilaton system. We can thus define and characterize a 4-dimensional asymptotically locally z=2 Lifshitz space-time in terms of 5-dimensional AdS boundary data. In this setup the 4-dimensional structure of the Fefferman-Graham expansion and the structure of the counterterm action, including the scale anomaly, will be discussed. We find that for asymptotically locally z=2 Lifshitz space-times obtained in this way there are two anomalies each with their own associated nonzero central charge. Both anomalies follow from the Scherk--Schwarz dimensional reduction of the 5-dimensional conformal anomaly of AdS gravity coupled to an axion-dilaton system. Together they make up an action that is of the Horava-Lifshitz type with nonzero potential term for z=2 conformal gravity.Comment: 32 pages, v2: modified discussion of the central charge

Dinosaur tracks from the Kilmaluag Formation (Bathonian, Middle Jurassic) of Score Bay, Isle of Skye, Scotland, UK

Tracks of a juvenile theropod dinosaur with footprint lengths of between 2 and 9 cm as well as adults of the same ichnospecies with footprints of about 15–25 cm in length were found in the Bathonian (Middle Jurassic) Kilmaluag Formation of Score Bay, northwestern Trotternish Peninsula, Isle of Skye, Scotland, UK. Two footprint sizes occur together on the same bedding plane in the central portion of Score Bay, both in situ and on loose blocks. Another horizon containing footprints above this was also identified. The footprints from the lowest horizon were produced in a desiccated silty mud that was covered with sand. A close association of both adults and juveniles with similar travel direction indicated by the footprints may suggest post-hatching care in theropod dinosaurs. Other footprints, produced on a rippled sandy substrate, have been found on the slightly higher bedding plane at this locality. Loose blocks found 130 m to the northeast in the central part of Score Bay have not been correlated with any in situ sediments, but were preserved in a similar manner to those from the higher bedding plane. These tracks represent the youngest dinosaur remains yet found in Scotland

The effect of dissipative corona on the structure and stability of cold optically thick accretion disks at high accretion rates

The vertical structure of optically thick accretion disks is investigated in the two-zone approximation. The disk is divided into an underlying disk and a corona, where the latter is defined as the upper surface layers for which the effective optical depth is unity. It is found that a significant part of the accretion flow (or dissipation rate) can take place in the corona if the scale height of the magnetic field is larger than that of the disk. The presence of such a dissipative corona leads to a modification in the topology of local disk solutions. For example, these solutions are found from local stability analysis to be both secularly and thermally stable, for accretion rates which are a factor $\approx$ four higher than those inferred from the stability of standard disk solutions. Thus, the applicability of optically thick disks with dissipative coronas are not as restrictive as disks without such coronas and can provide an attractive explanation for the origin of the soft spectral component observed in black hole X-ray binary systems.Comment: Accepted for publication in Ap