Recovering hidden Bloch character: Unfolding Electrons, Phonons, and Slabs

For a quantum state, or classical harmonic normal mode, of a system of spatial periodicity "R", Bloch character is encoded in a wavevector "K". One can ask whether this state has partial Bloch character "k" corresponding to a finer scale of periodicity "r". Answering this is called "unfolding." A theorem is proven that yields a mathematically clear prescription for unfolding, by examining translational properties of the state, requiring no "reference states" or basis functions with the finer periodicity (r,k). A question then arises, how should one assign partial Bloch character to a state of a finite system? A slab, finite in one direction, is used as the example. Perpendicular components k_z of the wavevector are not explicitly defined, but may be hidden in the state (and eigenvector |i>.) A prescription for extracting k_z is offered and tested. An idealized silicon (111) surface is used as the example. Slab-unfolding reveals surface-localized states and resonances which were not evident from dispersion curves alone.Comment: 11 pages, 7 figure

Evidence-based rules from family practice to inform family practice; The learning healthcare system case study on urinary tract infections

Background: Analysis of encounter data relevant to the diagnostic process sourced from routine electronic medical record (EMR) databases represents a classic example of the concept of a learning healthcare system (LHS). By collecting International Classification of Primary Care (ICPC) coded EMR data as part of the Transition Project from Dutch and Maltese databases (using the EMR TransHIS), data mining algorithms can empirically quantify the relationships of all presenting reasons for encounter (RfEs) and recorded diagnostic outcomes. We have specifically looked at new episodes of care (EoC) for two urinary system infections: simple urinary tract infection (UTI, ICPC code: U71) and pyelonephritis (ICPC code: U70). Methods: Participating family doctors (FDs) recorded details of all their patient contacts in an EoC structure using the ICPC, including RfEs presented by the patient, and the FDs' diagnostic labels. The relationships between RfEs and episode titles were studied using probabilistic and data mining methods as part of the TRANSFoRm project. Results: The Dutch data indicated that the presence of RfE's "Cystitis/Urinary Tract Infection", "Dysuria", "Fear of UTI", "Urinary frequency/urgency", "Haematuria", "Urine symptom/complaint, other" are all strong, reliable, predictors for the diagnosis "Cystitis/Urinary Tract Infection". The Maltese data indicated that the presence of RfE's "Dysuria", "Urinary frequency/urgency", "Haematuria" are all strong, reliable, predictors for the diagnosis "Cystitis/Urinary Tract Infection". The Dutch data indicated that the presence of RfE's "Flank/axilla symptom/complaint", "Dysuria", "Fever", "Cystitis/Urinary Tract Infection", "Abdominal pain/cramps general" are all strong, reliable, predictors for the diagnosis "Pyelonephritis". The Maltese data set did not present any clinically and statistically significant predictors for pyelonephritis. Conclusions: We describe clinically and statistically significant diagnostic associations observed between UTIs and pyelonephritis presenting as a new problem in family practice, and all associated RfEs, and demonstrate that the significant diagnostic cues obtained are consistent with the literature. We conclude that it is possible to generate clinically meaningful diagnostic evidence from electronic sources of patient data

An Imprint of Molecular Cloud Magnetization in the Morphology of the Dust Polarized Emission

We describe a morphological imprint of magnetization found when considering the relative orientation of the magnetic field direction with respect to the density structures in simulated turbulent molecular clouds. This imprint was found using the Histogram of Relative Orientations (HRO): a new technique that utilizes the gradient to characterize the directionality of density and column density structures on multiple scales. We present results of the HRO analysis in three models of molecular clouds in which the initial magnetic field strength is varied, but an identical initial turbulent velocity field is introduced, which subsequently decays. The HRO analysis was applied to the simulated data cubes and mock-observations of the simulations produced by integrating the data cube along particular lines of sight. In the 3D analysis we describe the relative orientation of the magnetic field $\mathbf{B}$ with respect to the density structures, showing that: 1.The magnetic field shows a preferential orientation parallel to most of the density structures in the three simulated cubes. 2.The relative orientation changes from parallel to perpendicular in regions with density over a critical density $n_{T}$ in the highest magnetization case. 3.The change of relative orientation is largest for the highest magnetization and decreases in lower magnetization cases. This change in the relative orientation is also present in the projected maps. In conjunction with simulations HROs can be used to establish a link between the observed morphology in polarization maps and the physics included in simulations of molecular clouds.Comment: (16 pages, 11 figures, submitted to ApJ 05MAR2013, accepted 07JUL2013

On the degrees of freedom of a semi-Riemannian metric

A semi-Riemannian metric in a n-manifold has n(n-1)/2 degrees of freedom, i.e. as many as the number of components of a differential 2-form. We prove that any semi-Riemannian metric can be obtained as a deformation of a constant curvature metric, this deformation being parametrized by a 2-for

Anomalous Nuclear Quantum Effects in Ice

One striking anomaly of water ice has been largely neglected and never explained. Replacing hydrogen ($^1$H) by deuterium ($^2$H) causes ice to expand, whereas the "normal" isotope effect is volume contraction with increased mass. Furthermore, the anomaly increases with temperature $T$, even though a normal isotope shift should decrease with $T$ and vanish when $T$ is high enough to use classical nuclear motions. In this study, we show that these effects are very well described by {\it ab initio} density functional theory. Our theoretical modeling explains these anomalies, and allows us to predict and to experimentally confirm a counter effect, namely that replacement of $^{16}$O by $^{18}$O causes a normal lattice contraction.Comment: 5 pages, 3 figure

Socioeconomic Differences in Dietary Patterns in an East African Country: Evidence from the Republic of Seychelles.

In high income countries, low socioeconomic status (SES) is related to unhealthier dietary patterns, while evidence on the social patterning of diet in low and middle income countries is scarce. In this study, we assess dietary patterns in the general population of a middle income country in the African region, the Republic of Seychelles, and examine their distribution according to educational level and income. Data was drawn from two independent national surveys conducted in the Seychelles among adults aged 25-64 years in 2004 (n = 1236) and 2013 (n = 1240). Dietary patterns were assessed by principal component analysis (PCA). Educational level and income were used as SES indicators. Data from both surveys were combined as no interaction was found between SES and year. Three dietary patterns were identified: "snacks and drinks", "fruit and vegetables" and "fish and rice". No significant associations were found between SES and the "snacks and drinks" pattern. Low vs. high SES individuals had lower adherence to the "fruit and vegetables" pattern [prevalence ratio (95% CI) 0.71 (0.60-0.83)] but a higher adherence to the traditional "fish and rice" pattern [1.58 (1.32-1.88)]. Income modified the association between education and the "fish and rice" pattern (p = 0.02), whereby low income individuals had a higher adherence to this pattern in both educational groups. Low SES individuals have a lower consumption of fruit and vegetables, but a higher consumption of traditional foods like fish and rice. The Seychelles may be at a degenerative diseases stage of the nutrition transition

Antibody-Antigen Binding Interface Analysis in the Big Data Era

Antibodies have become the Swiss Army tool for molecular biology and nanotechnology. Their outstanding ability to specifically recognise molecular antigens allows their use in many different applications from medicine to the industry. Moreover, the improvement of conventional structural biology techniques (e.g., X-ray, NMR) as well as the emergence of new ones (e.g., Cryo-EM), have permitted in the last years a notable increase of resolved antibody-antigen structures. This offers a unique opportunity to perform an exhaustive structural analysis of antibody-antigen interfaces by employing the large amount of data available nowadays. To leverage this factor, different geometric as well as chemical descriptors were evaluated to perform a comprehensive characterization

Variational finite-difference representation of the kinetic energy operator

A potential disadvantage of real-space-grid electronic structure methods is the lack of a variational principle and the concomitant increase of total energy with grid refinement. We show that the origin of this feature is the systematic underestimation of the kinetic energy by the finite difference representation of the Laplacian operator. We present an alternative representation that provides a rigorous upper bound estimate of the true kinetic energy and we illustrate its properties with a harmonic oscillator potential. For a more realistic application, we study the convergence of the total energy of bulk silicon using a real-space-grid density-functional code and employing both the conventional and the alternative representations of the kinetic energy operator.Comment: 3 pages, 3 figures, 1 table. To appear in Phys. Rev. B. Contribution for the 10th anniversary of the eprint serve