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

Recent Results from MICE on Multiple Coulomb Scattering and Energy Loss

Multiple coulomb scattering and energy loss are well known phenomena experienced by charged particles as they traverse a material. However, from recent measurements by the MuScat collaboration, it is known that the available simulation codes (GEANT4, for example) overestimate the scattering of muons in low Z materials. This is of particular interest to the Muon Ionization Cooling Experiment (MICE) collaboration which has the goal of measuring the reduction of the emittance of a muon beam induced by energy loss in low Z absorbers. MICE took data without magnetic field suitable for multiple scattering measurements in the fall of 2015 with the absorber vessel filled with Xenon and in the spring of 2016 using a lithium hydride absorber. The scattering data are compared with the predictions of various models, including the default GEANT4 model. In the fall of 2016 MICE took data with magnetic fields on and measured the energy loss of muons in a lithium hydride absorber. These data are also compared with model predictions and with the Bethe-Bloch formula

Recent Results from MICE on Multiple Coulomb Scattering and Energy Loss

Multiple coulomb scattering and energy loss are well known phenomena experienced by charged particles as they traverse a material. However, from recent measurements by the MuScat collaboration, it is known that the available simulation codes (GEANT4, for example) overestimate the scattering of muons in low Z materials. This is of particular interest to the Muon Ionization Cooling Experiment (MICE) collaboration which has the goal of measuring the reduction of the emittance of a muon beam induced by energy loss in low Z absorbers. MICE took data without magnetic field suitable for multiple scattering measurements in the fall of 2015 with the absorber vessel filled with Xenon and in the spring of 2016 using a lithium hydride absorber. The scattering data are compared with the predictions of various models, including the default GEANT4 model. In the fall of 2016 MICE took data with magnetic fields on and measured the energy loss of muons in a lithium hydride absorber. These data are also compared with model predictions and with the Bethe-Bloch formula

Aviram-Ratner rectifying mechanism for DNA base pair sequencing through graphene nanogaps

We demonstrate that biological molecules such as Watson-Crick DNA base pairs can behave as biological Aviram-Ratner electrical rectifiers because of the spatial separation and weak hydrogen bonding between the nucleobases. We have performed a parallel computational implementation of the ab-initio non-equilibrium Green's function (NEGF) theory to determine the electrical response of graphene---base-pair---graphene junctions. The results show an asymmetric (rectifying) current-voltage response for the Cytosine-Guanine base pair adsorbed on a graphene nanogap. In sharp contrast we find a symmetric response for the Thymine-Adenine case. We propose applying the asymmetry of the current-voltage response as a sensing criterion to the technological challenge of rapid DNA sequencing via graphene nanogaps

Assessing the capability of in silico mutation protocols for predicting the finite temperature conformation of amino acids

Mutation protocols are a key tool in computational biophysics for modelling unknown side chain conformations. In particular, these protocols are used to generate the starting structures for molecular dynamics simulations. The accuracy of the initial side chain and backbone placement is crucial to obtain a stable and quickly converging simulation. In this work, we assessed the performance of several mutation protocols in predicting the most probable conformer observed in finite temperature molecular dynamics simulations for a set of protein-peptide crystals differing only by single-point mutations in the peptide sequence. Our results show that several programs which predict well the crystal conformations fail to predict the most probable finite temperature configuration. Methods relying on backbone-dependent rotamer libraries have, in general, a better performance, but even the best protocol fails in predicting approximately 30% of the mutations

Toroidal magnetized iron neutrino detector for a neutrino factory

A neutrino factory has unparalleled physics reach for the discovery and measurement of CP violation in the neutrino sector. A far detector for a neutrino factory must have good charge identification with excellent background rejection and a large mass. An elegant solution is to construct a magnetized iron neutrino detector (MIND) along the lines of MINOS, where iron plates provide a toroidal magnetic field and scintillator planes provide 3D space points. In this paper, the current status of a simulation of a toroidal MIND for a neutrino factory is discussed in light of the recent measurements of large θ13. The response and performance using the 10 GeV neutrino factory configuration are presented. It is shown that this setup has equivalent δCP reach to a MIND with a dipole field and is sensitive to the discovery of CP violation over 85% of the values of δCP

Structural relaxations in electronically excited poly(para-phenylene)

Structural relaxations in electronically excited poly(para-phenylene) are studied using many-body perturbation theory and density-functional-theory methods. A sophisticated description of the electron-hole interaction is required to describe the energies of the excitonic states, but we show that the structural relaxations associated with exciton formation can be obtained quite accurately within a constrained density-functional-theory approach. We find that the structural relaxations in the low-energy excitonic states extend over about 8 monomers, leading to an energy reduction of 0.22 eV and a Stokes shift of 0.40 eV.Comment: 4 pages, 3 figure

Damping mechanisms for oscillations in solar prominences

Small amplitude oscillations are a commonly observed feature in prominences/filaments. These oscillations appear to be of local nature, are associated to the fine structure of prominence plasmas, and simultaneous flows and counterflows are also present. The existing observational evidence reveals that small amplitude oscillations, after excited, are damped in short spatial and temporal scales by some as yet not well determined physical mechanism(s). Commonly, these oscillations have been interpreted in terms of linear magnetohydrodynamic (MHD) waves, and this paper reviews the theoretical damping mechanisms that have been recently put forward in order to explain the observed attenuation scales. These mechanisms include thermal effects, through non-adiabatic processes, mass flows, resonant damping in non-uniform media, and partial ionization effects. The relevance of each mechanism is assessed by comparing the spatial and time scales produced by each of them with those obtained from observations. Also, the application of the latest theoretical results to perform prominence seismology is discussed, aiming to determine physical parameters in prominence plasmas that are difficult to measure by direct means.Comment: 36 pages, 16 figures, Space Science Reviews (accepted

Thermally stimulated H emission and diffusion in hydrogenated amorphous silicon

We report first principles ab initio density functional calculations of hydrogen dynam- ics in hydrogenated amorphous silicon. Thermal motion of the host Si atoms drives H diffusion, as we demonstrate by direct simulation and explain with simple models. Si-Si bond centers and Si ring centers are local energy minima as expected. We also describe a new mechanism for break- ing Si-H bonds to release free atomic H into the network: a fluctuation bond center detachment (FBCD) assisted diffusion. H dynamics in a-Si:H is dominated by structural fluctuations intrinsic to the amorphous phase not present in the crystal.Comment: 4 pages, 5 figures, In press EPL (Jun. 2007