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

Physical distress is associated with cardiovascular events in a high risk population of elderly men

Background Self-reported health perceptions such as physical distress and quality of life are suggested independent predictors of mortality and morbidity in patients with established cardiovascular disease. This study examined the associations between these factors and three years incidence of cardiovascular events in a population of elderly men with long term hyperlipidemia. Methods We studied observational data in a cohort of 433 men aged 64–76 years from a prospective, 2 × 2 factorial designed, three-year interventional trial. Information of classical risk factors was obtained and the following questionnaires were administered at baseline: Hospital Anxiety and Depression Scale, Physical Symptom Distress Index and Life Satisfaction Index. The occurrence of cardiovascular death, myocardial infarction, cerebrovascular incidences and peripheral arterial disease were registered throughout the study period. Continuous data with skewed distribution was split into tertiles. Hazard ratios (HR) were calculated from Cox regression analyses to assess the associations between physical distress, quality of life and cardiovascular events. Results After three years, 49 cardiovascular events were registered, with similar incidence among subjects with and without established cardiovascular disease. In multivariate analyses adjusted for age, smoking, systolic blood pressure, serum glucose, HADS-anxiety and treatment-intervention, physical distress was positively associated (HR 3.1, 95% CI 1.2 – 7.9 for 3rd versus 1st tertile) and quality of life negatively associated (HR 2.6, 95% CI 1.1–5.8 for 3rd versus 1st tertile) with cardiovascular events. The association remained statistically significant only for physical distress (hazard ratio 2.8 95% CI 1.2 – 6.8, p < 0.05) when both variables were evaluated in the same model. Conclusion Physical distress, but not quality of life, was independently associated with increased risk of cardiovascular events in an observational study of elderly men predominantly without established cardiovascular disease. Trial Registration Trial registration: NCT0076401

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

Principal Milk Components in Buffalo, Holstein Cross, Indigenous Cattle and Red Chittagong Cattle from Bangladesh

The aim of the present study was to get a total physical and chemical characterization and comparison of the principal components in Bangladeshi buffalo (B), Holstein cross (HX), Indigenous cattle (IC) and Red Chittagong Cattle (RCC) milk. Protein and casein (CN) composition and type, casein micellar size (CMS), naturally occurring peptides, free amino acids, fat, milk fat globule size (MFGS), fatty acid composition, carbohydrates, total and individual minerals were analyzed. These components are related to technological and nutritional properties of milk. Consequently, they are important for the dairy industry and in the animal feeding and breeding strategies. Considerable variation in most of the principal components of milk were observed among the animals. The milk of RCC and IC contained higher protein, CN, β-CN, whey protein, lactose, total mineral and P. They were more or less similar in most of the all other components. The B milk was found higher in CN number, in the content of αs2-, κ-CN and α-lactalbumin, free amino acids, unsaturated fatty acids, Ca and Ca:P. The B milk was also lower in β-lactoglobulin content and had the largest CMS and MFGS. Proportion of CN to whey protein was lower in HX milk and this milk was found higher in β-lactoglobulin and naturally occuring peptides. Considering the results obtained including the ratio of αs1-, αs2-, β- and κ-CN, B and RCC milk showed best data both from nutritional and technological aspects

Imaging single cells in a beam of live cyanobacteria with an X-ray laser

There exists a conspicuous gap of knowledge about the organization of life at mesoscopic levels. Ultra-fast coherent diffractive imaging with X-ray free-electron lasers can probe structures at the relevant length scales and may reach sub-nanometer resolution on micron-sized living cells. Here we show that we can introduce a beam of aerosolised cyanobacteria into the focus of the Linac Coherent Light Source and record diffraction patterns from individual living cells at very low noise levels and at high hit ratios. We obtain two-dimensional projection images directly from the diffraction patterns, and present the results as synthetic X-ray Nomarski images calculated from the complex-valued reconstructions. We further demonstrate that it is possible to record diffraction data to nanometer resolution on live cells with X-ray lasers. Extension to sub-nanometer resolution is within reach, although improvements in pulse parameters and X-ray area detectors will be necessary to unlock this potential

The relationship between sales of SSRI, TCA and suicide rates in the Nordic countries

<p>Abstract</p> <p>Background</p> <p>In the period 1990-2006, strong and almost equivalent increases in sales figures of selective serotonin re-uptake inhibitors (SSRIs) were observed in all Nordic countries. The sales figures of tricyclic antidepressants (TCAs) dropped in Norway and Sweden in the nineties. After 2000, sales figures of TCAs have been almost constant in all Nordic countries. The potentially toxic effect of TCAs in overdose was an important reason for replacing TCAs with SSRIs when treating depression. We studied whether the rapid increase in sales of SSRIs and the corresponding decline in TCAs in the period 1990-98 were associated with a decline in suicide rates.</p> <p>Methods</p> <p>Aggregated suicide rates for the period 1975-2006 in four Nordic countries (Denmark, Finland, Norway and Sweden) were obtained from the national causes-of-death registries. The sales figures of antidepressants were provided from the wholesale registers in each of the Nordic countries. Data were analysed using Fisher's exact test and Pearson's correlation coefficient.</p> <p>Results</p> <p>There was no statistical association (P = 1.0) between the increase of sales figures of SSRIs and the decline in suicide rates. There was no statistical association (P = 1.0) between the decrease in the sale figures of TCAs and change in suicide rates either.</p> <p>Conclusions</p> <p>We found no evidence for the rapid increase in use of SSRIs and the corresponding decline in sales of TCAs being associated with a decline in the suicide rates in the Nordic countries in the period 1990-98. We did not find any inverse relationship between the increase in sales of SSRIs and declining suicide rates in four Nordic countries.</p

A data set from flash X-ray imaging of carboxysomes

Citation: Hantke, M. F., Hasse, D., Ekeberg, T., John, K., Svenda, M., Loh, D., . . . Maia, F. R. N. C. (2016). A data set from flash X-ray imaging of carboxysomes. Scientific Data, 3. doi:10.1038/sdata.2016.61Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere

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