Inverse Ising inference using all the data

We show that a method based on logistic regression, using all the data, solves the inverse Ising problem far better than mean-field calculations relying only on sample pairwise correlation functions, while still computationally feasible for hundreds of nodes. The largest improvement in reconstruction occurs for strong interactions. Using two examples, a diluted Sherrington-Kirkpatrick model and a two-dimensional lattice, we also show that interaction topologies can be recovered from few samples with good accuracy and that the use of $l_1$-regularization is beneficial in this process, pushing inference abilities further into low-temperature regimes.Comment: 5 pages, 2 figures. Accepted versio

Outpatient treatment of acute poisonings in Oslo: poisoning pattern, factors associated with hospitalization, and mortality

<p>Abstract</p> <p>Background</p> <p>Most patients with acute poisoning are treated as outpatients worldwide. In Oslo, these patients are treated in a physician-led outpatient clinic with limited diagnostic and treatment resources, which reduces both the costs and emergency department overcrowding. We describe the poisoning patterns, treatment, mortality, factors associated with hospitalization and follow-up at this Emergency Medical Agency (EMA, "Oslo Legevakt"), and we evaluate the safety of this current practice.</p> <p>Methods</p> <p>All acute poisonings in adults (> or = 16 years) treated at the EMA during one year (April 2008 to April 2009) were included consecutively in an observational study design. The treating physicians completed a standardized form comprising information needed to address the study's aims. Multivariate logistic regression analysis was used to identify the factors associated with hospitalization.</p> <p>Results</p> <p>There were 2348 contacts for 1856 individuals; 1157 (62%) were male, and the median age was 34 years. The most frequent main toxic agents were ethanol (43%), opioids (22%) and CO or fire smoke (10%). The physicians classified 73% as accidental overdoses with substances of abuse taken for recreational purposes, 15% as other accidents (self-inflicted or other) and 11% as suicide attempts. Most (91%) patients were treated with observation only. The median observation time until discharge was 3.8 hours. No patient developed sequelae or died at the EMA. Seventeen per cent were hospitalized. Gamma-hydroxybutyric acid, respiratory depression, paracetamol, reduced consciousness and suicidal intention were factors associated with hospitalization. Forty-eight per cent were discharged without referral to follow-up. The one-month mortality was 0.6%. Of the nine deaths, five were by new accidental overdose with substances of abuse.</p> <p>Conclusions</p> <p>More than twice as many patients were treated at the EMA compared with all hospitals in Oslo. Despite more than a doubling of the annual number of poisoned patients treated at the EMA since 2003, there was no mortality or sequelae, indicating that the current practice is safe. Thus, most low- to intermediate-acuity poisonings can be treated safely without the need to access hospital resources. Although the short-term mortality was low, more follow-up of patients with substance abuse should be encouraged.</p

The dynamical background of polar mesosphere winter echoes from simultaneous EISCAT and ESRAD observations

On 30 October 2004 during a strong solar proton event, layers of enhanced backscatter from altitudes between 55 and 75km have been observed by both ESRAD (52MHz) and the EISCAT VHF (224MHz) radars. These echoes have earlier been termed Polar Mesosphere Winter Echoes, PMWE. After considering the morphology of the layers and their relation to observed atmospheric waves, we conclude that the radars have likely seen the same phenomenon even though the radars&apos; scattering volumes are located about 220km apart and that the most long-lasting layer is likely associated with wind-shear in an inertio-gravity wave. An ion-chemistry model is used to determine parameters necessary to relate wind-shear induced turbulent energy dissipation rates to radar backscatter. The model is verified by comparison with electron density profiles measured by the EISCAT VHF radar. Observed radar signal strengths are found to be 2-3 orders of magnitude stronger than the maximum which can be expected from neutral turbulence alone, assuming that previously published results relating radar signal scatter to turbulence parameters, and turbulence parameters to wind shear, are correct. The possibility remains that some additional or alternative mechanism may be involved in producing PMWE, such as layers of charged dust/smoke particles or large cluster ions

The Bethe approximation for solving the inverse Ising problem: a comparison with other inference methods

The inverse Ising problem consists in inferring the coupling constants of an Ising model given the correlation matrix. The fastest methods for solving this problem are based on mean-field approximations, but which one performs better in the general case is still not completely clear. In the first part of this work, I summarize the formulas for several mean- field approximations and I derive new analytical expressions for the Bethe approximation, which allow to solve the inverse Ising problem without running the Susceptibility Propagation algorithm (thus avoiding the lack of convergence). In the second part, I compare the accuracy of different mean field approximations on several models (diluted ferromagnets and spin glasses) defined on random graphs and regular lattices, showing which one is in general more effective. A simple improvement over these approximations is proposed. Also a fundamental limitation is found in using methods based on TAP and Bethe approximations in presence of an external field.Comment: v3: strongly revised version with new methods and results, 25 pages, 21 figure

Cryptotomography: reconstructing 3D Fourier intensities from randomly oriented single-shot diffraction patterns

We reconstructed the 3D Fourier intensity distribution of mono-disperse prolate nano-particles using single-shot 2D coherent diffraction patterns collected at DESY's FLASH facility when a bright, coherent, ultrafast X-ray pulse intercepted individual particles of random, unmeasured orientations. This first experimental demonstration of cryptotomography extended the Expansion-Maximization-Compression (EMC) framework to accommodate unmeasured fluctuations in photon fluence and loss of data due to saturation or background scatter. This work is an important step towards realizing single-shot diffraction imaging of single biomolecules.Comment: 4 pages, 4 figure

Subacromial ultrasound guided or systemic steroid injection for rotator cuff disease: randomised double blind study

Objective To compare the effectiveness of ultrasound guided corticosteroid injection in the subacromial bursa with systemic corticosteroid injection in patients with rotator cuff disease

A 20-year prospective study of mortality and causes of death among hospitalized opioid addicts in Oslo

<p>Abstract</p> <p>Background</p> <p>To study mortality rate and causes of death among all hospitalized opioid addicts treated for self-poisoning or admitted for voluntary detoxification in Oslo between 1980 and 1981, and to compare their mortality to that of the general population.</p> <p>Methods</p> <p>A prospective cohort study was conducted on 185 opioid addicts from all medical departments in Oslo who were treated for either self-poisoning (<it>n </it>= 93, 1980), voluntary detoxification (<it>n </it>= 75, 1980/1981) or both (<it>n </it>= 17). Their median age was 24 years; with a range from 16 to 41, and 53% were males. All deaths that had occurred by the end of 2000 were identified from the Central Population Register. Causes of death were obtained from Statistics Norway. Standardized mortality ratios (SMRs) were computed for mortality, in general, and in particular, for different causes of death.</p> <p>Results</p> <p>During a period of 20 years, 70 opioid addicts died (37.8%), with a standardized mortality ratio (SMR) equal to 23.6 (95% CI, 18.7–29.9). The SMR remained high during the whole period, ranging from 32.4 in the first five-year period, to 13.4 in the last five-year period. There were no significant differences in SMR between self-poisonings and those admitted for voluntarily detoxification. The registered causes of death were accidents (11.4%), suicide (7.1%), cancer (4.3%), cardiovascular disease (2.9%), other violent deaths (2.9%), other diseases (71.4%). Among the 50 deaths classified as other diseases, the category "drug dependence" was listed in the vast majority of cases (37 deaths, 52.9% of the total). SMRs increased significantly for all causes of death, with the other diseases group having the highest SMR; 65.8 (95% CI, 49.9–86.9). The SMR was 5.4 (95% CI, 1.3–21.5) for cardiovascular diseases, and 4.3 (95% CI, 1.4–13.5) for cancer. The SMR was 13.2 (95% CI, 6.6–26.4) for accidents, 10.7 (95% CI, 4.5–25.8) for suicides, and 28.6 (95% CI, 7.1–114.4) for other violent deaths.</p> <p>Conclusion</p> <p>The risk of death among opioid addicts was significantly higher for all causes of death compared with the general population, implying a poor prognosis over a 20-year period for this young patient group.</p

Run-Time Interoperability Between Neuronal Network Simulators Based on the MUSIC Framework

MUSIC is a standard API allowing large scale neuron simulators to exchange data within a parallel computer during runtime. A pilot implementation of this API has been released as open source. We provide experiences from the implementation of MUSIC interfaces for two neuronal network simulators of different kinds, NEST and MOOSE. A multi-simulation of a cortico-striatal network model involving both simulators is performed, demonstrating how MUSIC can promote inter-operability between models written for different simulators and how these can be re-used to build a larger model system. Benchmarks show that the MUSIC pilot implementation provides efficient data transfer in a cluster computer with good scaling. We conclude that MUSIC fulfills the design goal that it should be simple to adapt existing simulators to use MUSIC. In addition, since the MUSIC API enforces independence of the applications, the multi-simulation could be built from pluggable component modules without adaptation of the components to each other in terms of simulation time-step or topology of connections between the modules

Three-Dimensional Reconstruction of the Giant Mimivirus Particle with an X-Ray Free-Electron Laser

Citation: Ekeberg, T., Svenda, M., Abergel, C., Maia, F., Seltzer, V., Claverie, J. M., . . . Hajdu, J. (2015). Three-Dimensional Reconstruction of the Giant Mimivirus Particle with an X-Ray Free-Electron Laser. Physical Review Letters, 114(9), 6. doi:10.1103/PhysRevLett.114.098102We present a proof-of-concept three-dimensional reconstruction of the giant mimivirus particle from experimentally measured diffraction patterns from an x-ray free-electron laser. Three-dimensional imaging requires the assembly of many two-dimensional patterns into an internally consistent Fourier volume. Since each particle is randomly oriented when exposed to the x-ray pulse, relative orientations have to be retrieved from the diffraction data alone. We achieve this with a modified version of the expand, maximize and compress algorithm and validate our result using new methods.Additional Authors: Andersson, I.;Loh, N. D.;Martin, A. V.;Chapman, H.;Bostedt, C.;Bozek, J. D.;Ferguson, K. R.;Krzywinski, J.;Epp, S. W.;Rolles, D.;Rudenko, A.;Hartmann, R.;Kimmel, N.;Hajdu, J