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

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

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

Bethe-Peierls approximation and the inverse Ising model

We apply the Bethe-Peierls approximation to the problem of the inverse Ising model and show how the linear response relation leads to a simple method to reconstruct couplings and fields of the Ising model. This reconstruction is exact on tree graphs, yet its computational expense is comparable to other mean-field methods. We compare the performance of this method to the independent-pair, naive mean- field, Thouless-Anderson-Palmer approximations, the Sessak-Monasson expansion, and susceptibility propagation in the Cayley tree, SK-model and random graph with fixed connectivity. At low temperatures, Bethe reconstruction outperforms all these methods, while at high temperatures it is comparable to the best method available so far (Sessak-Monasson). The relationship between Bethe reconstruction and other mean- field methods is discussed

Fatal poisonings in Oslo: a one-year observational study

<p>Abstract</p> <p>Background</p> <p>Acute poisonings are common and are treated at different levels of the health care system. Since most fatal poisonings occur outside hospital, these must be included when studying characteristics of such deaths. The pattern of toxic agents differs between fatal and non-fatal poisonings. By including all poisoning episodes, cause-fatality rates can be calculated.</p> <p>Methods</p> <p>Fatal and non-fatal acute poisonings in subjects aged ≥16 years in Oslo (428 198 inhabitants) were included consecutively in an observational multi-centre study including the ambulance services, the Oslo Emergency Ward (outpatient clinic), and hospitals, as well as medico-legal autopsies from 1st April 2003 to 31st March 2004. Characteristics of fatal poisonings were examined, and a comparison of toxic agents was made between fatal and non-fatal acute poisoning.</p> <p>Results</p> <p>In Oslo, during the one-year period studied, 103 subjects aged ≥16 years died of acute poisoning. The annual mortality rate was 24 per 100 000. The male-female ratio was 2:1, and the mean age was 44 years (range 19-86 years). In 92 cases (89%), death occurred outside hospital. The main toxic agents were opiates or opioids (65% of cases), followed by ethanol (9%), tricyclic anti-depressants (TCAs) (4%), benzodiazepines (4%), and zopiclone (4%). Seventy-one (69%) were evaluated as accidental deaths and 32 (31%) as suicides. In 70% of all cases, and in 34% of suicides, the deceased was classified as drug or alcohol dependent. When compared with the 2981 non-fatal acute poisonings registered during the study period, the case fatality rate was 3% (95% C.I., 0.03-0.04). Methanol, TCAs, and antihistamines had the highest case fatality rates; 33% (95% C.I., 0.008-0.91), 14% (95% C.I., 0.04-0.33), and 10% (95% C.I., 0.02-0.27), respectively.</p> <p>Conclusions</p> <p>Three per cent of all acute poisonings were fatal, and nine out of ten deaths by acute poisonings occurred outside hospital. Two-thirds were evaluated as accidental deaths. Although case fatality rates were highest for methanol, TCAs, and antihistamines, most deaths were caused by opiates or opioids.</p

Predictors of Shoulder Pain and Disability Index (SPADI) and work status after 1 year in patients with subacromial shoulder pain

<p>Abstract</p> <p>Background</p> <p>Shoulder pain is a common complaint in primary health care and has an unfavourable outcome in many patients. The objectives were to identify predictors for pain and disability (SPADI) and work status in patients with subacromial shoulder pain.</p> <p>Methods</p> <p>Secondary analyses of data from a randomized clinical controlled trial were performed. Outcome measures were the absolute values of the combined Shoulder Pain and Disability Index (SPADI) and work status 1 year after treatment with supervised exercises (SE) or radial extracorporeal shockwave therapy (rESWT). Predictors of outcome were investigated using multiple linear regression (SPADI) and logistic regression (work status).</p> <p>Results</p> <p>104 patients were included. Low education (≤ 12 years), previous shoulder pain, and a high baseline SPADI score predicted poor results with these variables explaining 29.9% of the variance in SPADI score at 1 year. Low education and poor self-reported health status predicted a work status of "not working": Odds Ratio, OR = 4.3(95% CI (1.3 to 14.9)), p = 0.02 for education, and OR = 1.06 (95% CI (1.0 to 1.1)), p = 0.001 for self-reported health status, respectively. Adjustments for age, gender, and treatment group were performed, but did not change the results.</p> <p>Conclusion</p> <p>Education was the most consistent predictor of pain and disability, and work status at 1 year follow-up. Also, baseline SPADI score, previous shoulder pain and self-reported health status predicted outcome.</p> <p>Trial registration</p> <p>Clinical trials NCT00653081</p

Co-evolution of Structures and Controllers for Neubot Underwater Modular Robots

This article presents the first results of a project in underwater modular robotics, called Neubots. The goals of the projects are to explore, following Von Neumann’s ideas, potential mechanisms underlying self-organization and self-replication. We briefly explain the design features of the module units. We then present simulation results of the artificial co-evolution of body structures and neural controllers for locomotion. The neural controllers are inspired from the central pattern generators underlying locomotion in vertebrate animals. They are composed of multiple neural oscillators which are connected together by a specific type of coupling called synaptic spreading. The co-evolution of body and controller leads to interesting robots capable of efficient swimming. Interesting features of the neural controllers include the possibility to modulate the speed of locomotion by varying simple input signals, the robustness against perturbations, and the distributed nature of the controllers which makes them well suited for modular robotics

3D diffractive imaging of nanoparticle ensembles using an X-ray laser

We report the 3D structure determination of gold nanoparticles (AuNPs) by X-ray single particle imaging (SPI). Around 10 million diffraction patterns from gold nanoparticles were measured in less than 100 hours of beam time, more than 100 times the amount of data in any single prior SPI experiment, using the new capabilities of the European X-ray free electron laser which allow measurements of 1500 frames per second. A classification and structural sorting method was developed to disentangle the heterogeneity of the particles and to obtain a resolution of better than 3 nm. With these new experimental and analytical developments, we have entered a new era for the SPI method and the path towards close-to-atomic resolution imaging of biomolecules is apparent