Ab Initio Calculation of Impurity Effects in Copper Oxide Materials

We describe a method for calculating, within density functional theory, the electronic structure associated with typical defects which substitute for Cu in the CuO2 planes of high-Tc superconducting materials. The focus is primarily on Bi2Sr2CaCu2O8, the material on which most STM measurements of impurity resonances in the superconducting state have been performed. The magnitudes of the effective potentials found for Zn, Ni and vacancies on the in-plane Cu sites in this host material are remarkably consistent with phenomenological fits of potential scattering models to STM resonance energies. The effective potential ranges are quite short, of order 1 A with weak long range tails, in contrast to some current models of extended potentials which attempt to fit STM data. For the case of Zn and Cu vacancies, the effective potentials are strongly repulsive, and states on the impurity site near the Fermi level are simply removed. The local density of states (LDOS) just above the impurity is nevertheless found to be a maximum in the case of Zn and a local minimum in case of the vacancy, in agreement with experiment. The Zn and Cu vacancy patterns are explained as due to the long-range tails of the effective impurity potential at the sample surface. The case of Ni is richer due to the Ni atom's strong hybridization with states near the Fermi level; in particular, the short range part of the potential is attractive, and the LDOS is found to vary rapidly with distance from the surface and from the impurity site. We propose that the current controversy surrounding the observed STM patterns can be resolved by properly accounting for the effective impurity potentials and wave-functions near the cuprate surface. Other aspects of the impurity states for all three species are discussed.Comment: 37 pp. pdf including figures, submitted to Phys. Rev.

Divergent drivers of leaf trait variation within species, among species, and among functional groups.

Understanding variation in leaf functional traits-including rates of photosynthesis and respiration and concentrations of nitrogen and phosphorus-is a fundamental challenge in plant ecophysiology. When expressed per unit leaf area, these traits typically increase with leaf mass per area (LMA) within species but are roughly independent of LMA across the global flora. LMA is determined by mass components with different biological functions, including photosynthetic mass that largely determines metabolic rates and contains most nitrogen and phosphorus, and structural mass that affects toughness and leaf lifespan (LL). A possible explanation for the contrasting trait relationships is that most LMA variation within species is associated with variation in photosynthetic mass, whereas most LMA variation across the global flora is associated with variation in structural mass. This hypothesis leads to the predictions that (i) gas exchange rates and nutrient concentrations per unit leaf area should increase strongly with LMA across species assemblages with low LL variance but should increase weakly with LMA across species assemblages with high LL variance and that (ii) controlling for LL variation should increase the strength of the above LMA relationships. We present analyses of intra- and interspecific trait variation from three tropical forest sites and interspecific analyses within functional groups in a global dataset that are consistent with the above predictions. Our analysis suggests that the qualitatively different trait relationships exhibited by different leaf assemblages can be understood by considering the degree to which photosynthetic and structural mass components contribute to LMA variation in a given assemblage

Chemical Properties from Graph Neural Network-Predicted Electron Densities

According to density functional theory, any chemical property can be inferred from the electron density, making it the most informative attribute of an atomic structure. In this work, we demonstrate the use of established physical methods to obtain important chemical properties from model-predicted electron densities. We introduce graph neural network architectural choices that provide physically relevant and useful electron density predictions. Despite not training to predict atomic charges, the model is able to predict atomic charges with an order of magnitude lower error than a sum of atomic charge densities. Similarly, the model predicts dipole moments with half the error of the sum of atomic charge densities method. We demonstrate that larger data sets lead to more useful predictions in these tasks. These results pave the way for an alternative path in atomistic machine learning, where data-driven approaches and existing physical methods are used in tandem to obtain a variety of chemical properties in an explainable and self-consistent manner

A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method

<p>Abstract</p> <p>Background</p> <p>The Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating biological information in a concise manner. A lack of software tools for the notation restricts wider usage of the notation. Development of software is facilitated by a more detailed specification regarding software requirements than has previously existed for the MIM notation.</p> <p>Results</p> <p>A formal implementation of the MIM notation was developed based on a core set of previously defined glyphs. This implementation provides a detailed specification of the properties of the elements of the MIM notation. Building upon this specification, a machine-readable format is provided as a standardized mechanism for the storage and exchange of MIM diagrams. This new format is accompanied by a Java-based application programming interface to help software developers to integrate MIM support into software projects. A validation mechanism is also provided to determine whether MIM datasets are in accordance with syntax rules provided by the new specification.</p> <p>Conclusions</p> <p>The work presented here provides key foundational components to promote software development for the MIM notation. These components will speed up the development of interoperable tools supporting the MIM notation and will aid in the translation of data stored in MIM diagrams to other standardized formats. Several projects utilizing this implementation of the notation are outlined herein. The MIM specification is available as an additional file to this publication. Source code, libraries, documentation, and examples are available at <url>http://discover.nci.nih.gov/mim</url>.</p

Predicate Abstraction for Linked Data Structures

We present Alias Refinement Types (ART), a new approach to the verification of correctness properties of linked data structures. While there are many techniques for checking that a heap-manipulating program adheres to its specification, they often require that the programmer annotate the behavior of each procedure, for example, in the form of loop invariants and pre- and post-conditions. Predicate abstraction would be an attractive abstract domain for performing invariant inference, existing techniques are not able to reason about the heap with enough precision to verify functional properties of data structure manipulating programs. In this paper, we propose a technique that lifts predicate abstraction to the heap by factoring the analysis of data structures into two orthogonal components: (1) Alias Types, which reason about the physical shape of heap structures, and (2) Refinement Types, which use simple predicates from an SMT decidable theory to capture the logical or semantic properties of the structures. We prove ART sound by translating types into separation logic assertions, thus translating typing derivations in ART into separation logic proofs. We evaluate ART by implementing a tool that performs type inference for an imperative language, and empirically show, using a suite of data-structure benchmarks, that ART requires only 21% of the annotations needed by other state-of-the-art verification techniques

A randomised controlled trial to assess the effectiveness of a single session of nurse administered massage for short term relief of chronic non-malignant pain

Background: Massage is increasingly used to manage chronic pain but its benefit has not been clearly established. The aim of the study is to determine the effectiveness of a single session of nurse-administered massage for the short term relief of chronic non-malignant pain and anxiety. Methods: A randomised controlled trial design was used, in which the patients were assigned to a massage or control group. The massage group received a 15 minute manual massage and the control group a 15 minute visit to talk about their pain. Adult patients attending a pain relief unit with a diagnosis of chronic pain whose pain was described as moderate or severe were eligible for the study. An observer blind to the patients' treatment group carried out assessments immediately before (baseline), after treatment and 1, 2, 3 and 4 hours later. Pain was assessed using 100 mm visual analogue scale and the McGill Pain Questionnaire. Pain Relief was assessed using a five point verbal rating scale. Anxiety was assessed with the Spielberger short form State-Trait Anxiety Inventory. Results: 101 patients were randomised and evaluated, 50 in the massage and 51 in the control group. There were no statistically significant differences between the groups at baseline interview. Patients in the massage but not the control group had significantly less pain compared to baseline immediately after and one hour post treatment. 95% confidence interval for the difference in mean pain reduction at one hour post treatment between the massage and control groups is 5.47 mm to 24.70 mm. Patients in the massage but not the control group had a statistically significant reduction in anxiety compared to baseline immediately after and at 1 hour post treatment. Conclusion: Massage is effective in the short term for chronic pain of moderate to severe intensity

Stroke Severity Predicted by Aortic Atheroma Detected by Ultra-Fast and Cardiac-Gated Chest Tomography†

Background and Purpose: The presence of aortic atherosclerosis is an independent risk factor for secondary stroke. The present study was designed to have an initial exploration of the correlation between the load and extent of aortic atheroma (AA) and initial stroke severity or clinical outcome 3 months after stroke. Methods: Cardiac-gated chest tomography (CGCT) was used to detect and measure AA in patients with acute ischemic stroke as shown by our group in prior prospective studies and this is part four sub-exploratory study of the same cohort. The National Institute of Health Stroke Scale (NIHSS) was used to assess the initial stroke severity, and the modified Rankin Scale (mRS) was used to assess 3-month outcome. Results: Thirty-two patients underwent CGCT for evaluation of AA, and 21 were found to have AA. AA was more prevalent in patient with NIHSS >6 (14/17 versus 7/15, p-value 0.03). Applying the multiple logistic regression and propensity score adjustment (using the propensity of having AA given the baseline features as covariates) showed a non-significant trend that AA is three times more likely to be associated with NIHSS >6 (p = 0.08, OR 3.08, 95% CI 0.94–13.52). There was no evidence of association of AA with 3-month functional outcome (mRS): 11/14 (78.6%) mRS >1 had AA, and 10/18 (55.5%) of those with mRS ≤1 had AA (p = 0.27). Conclusion: In our current study with limited sample number and exploratory nature, the presence of AA on CGCT with acute ischemic stroke patients may be associated with worse neurological deficit at presentation. There was no evidence of association with 3-month functional outcome using the mRS

Lunar impact basins: New data for the nearside northern high latitudes and eastern limb from the second Galileo flyby

During the December 1992 Galileo Earth/Moon encounter the northern half of the nearside, the eastern limb, and parts of the western farside of the Moon were illuminated and in view, a geometry that was complementary to the first lunar encounter in December, 1990, which obtained images of the western limb and eastern farside. The Galileo Solid State Imaging System (SSI) obtained multispectral images for these regions during the second encounter and color ratio composite images were compiled using combinations of band ratios chosen on the basis of telescopic spectra and laboratory spectra of lunar samples. Ratios of images taken at 0.41 and 0.76 micron are sensitive to changes in the slope in the visible portion of the spectrum, and ratios of 0.99 and 0.76 micron relate to the strength of near-infrared absorptions due to iron-rich mafic minerals (0.76/0.99 ratio) such as olivine and pyroxene. Results of the analyses of the compositional diversity of the crust, maria, and Copernican craters are presented elsewhere. Primary objectives for lunar basin analysis for the second encounter include analysis of: the north polar region and the Humboldtianum basin; the characteristics of the Imbrium basin along its northern border and the symmetry of associated deposits; the origin of light plains north of Mare Frigoris and associated with several other basins; the nature and significance of pre-basin substrate; the utilization of the stereo capability to assess subtle basis structure; the identification of previously unrecognized ancient basins; basin deposits and structure for limb and farside basins; and assessment of evidence for proposed ancient basins. These data and results will be applied to addressing general problems of evaluation of the nature and origin of basin deposits, investigation of mode of ejecta emplacement and ejecta mixing, analysis of the origin of light plains deposits, analysis of basin deposit symmetry/asymmetry, investigation of basin depth of excavation and crustal stratigraphy, and assessment of models for basin formation and evolution. Here we discuss some preliminary results concerning lunar impact basins, their deposits, and prebasin substrates, using the same approaches that we employed for the Orientale and South Pole-Aitken basins using the data from the first encounter