Holes in the tundra: Invasive earthworms alter soil structure and moisture in tundra soils.

Human introductions have resulted in earthworms establishing in the Arctic, species known to cause cascading ecosystem change. However, few quantitative outdoor experiments have been performed that describe how these soil modifying earthworms are reshaping structures in tundra soils. In this study, we used three-dimensional (3-D) X-ray images of soil cores (approximately 10 cm diameter, 20 cm height, N = 48) to assess how earthworms (Aporrectodea sp. and Lumbricus sp.) affect soil structure and macropore networks in an outdoor mesocosm experiment that lasted four summers. Effects were assessed in both shrub-dominated (heath) and herb-dominated (meadow) tundra. Earthworms almost doubled the macroporosity in meadow soils and tripled macroporosity in heath. Interestingly, the fractal dimension of macropores decreased in response to earthworm burrowing in both systems, indicating that the presence of earthworms reduced the geometric complexity in comparison to other pore-generating processes active in the tundra. Observed effects on soil structure occurred along with a dramatically reduced soil moisture content, which was observed the first winter after earthworm introduction in the meadow. Our findings suggest that predictions of future changes in vegetation and soil carbon pools in the Arctic should include major impacts on soil properties that earthworms induce.

Observations of phase changes in monoolein during high viscous injection.

Serial crystallography of membrane proteins often employs high-viscosity injectors (HVIs) to deliver micrometre-sized crystals to the X-ray beam. Typically, the carrier medium is a lipidic cubic phase (LCP) media, which can also be used to nucleate and grow the crystals. However, despite the fact that the LCP is widely used with HVIs, the potential impact of the injection process on the LCP structure has not been reported and hence is not yet well understood. The self-assembled structure of the LCP can be affected by pressure, dehydration and temperature changes, all of which occur during continuous flow injection. These changes to the LCP structure may in turn impact the results of X-ray diffraction measurements from membrane protein crystals. To investigate the influence of HVIs on the structure of the LCP we conducted a study of the phase changes in monoolein/water and monoolein/buffer mixtures during continuous flow injection, at both atmospheric pressure and under vacuum. The reservoir pressure in the HVI was tracked to determine if there is any correlation with the phase behaviour of the LCP. The results indicated that, even though the reservoir pressure underwent (at times) significant variation, this did not appear to correlate with observed phase changes in the sample stream or correspond to shifts in the LCP lattice parameter. During vacuum injection, there was a three-way coexistence of the gyroid cubic phase, diamond cubic phase and lamellar phase. During injection at atmospheric pressure, the coexistence of a cubic phase and lamellar phase in the monoolein/water mixtures was also observed. The degree to which the lamellar phase is formed was found to be strongly dependent on the co-flowing gas conditions used to stabilize the LCP stream. A combination of laboratory-based optical polarization microscopy and simulation studies was used to investigate these observations.

Diffuse idiopathic skeletal hyperostosis in elderly Icelanders and its association with the metabolic syndrome: the AGES-Reykjavik Study.

Objective: To describe the prevalence of diffuse idiopathic skeletal hyperostosis (DISH) in a large population-based study of elderly Icelanders, with particular reference to weight-related factors and the metabolic syndrome.Method: The study population comprised 5321 participants aged 68-96 years (2276 males, mean ± sd age 76 ± 5 , and 3045 females, age 77 ± 6) from the AGES-Reykjavik Study. DISH diagnosis was based on computed tomography (CT) scans, and interpreted strictly by the Resnick criteria and additional suggestions for CT interpretation by Oudkerk et al. Radiology readings were taken by a radiology resident and sample readings by two experienced radiologists.Results: A diagnosis of DISH was made in 13.7% of males and 2.8% of females. There was no association with age, but a strong association was seen with the metabolic syndrome [odds ratio (OR) 2.12, 95% confidence interval (CI) 1.69-2.64, p = 3.9 × 10-11]. Among the components of the metabolic syndrome, the association with DISH was significant for the insulin resistance criterion (OR 1.66, 95% CI 1.32-2.01, p < 0.001) and the body mass index (BMI) criterion (OR 2.16, 95% CI 1.70-2.74, p < 0.001). Other weight-related variables (midlife BMI, weight, and abdominal circumference) showed similar associations.Conclusions: This study, which to our knowledge is the largest published study on the prevalence of DISH, shows an association with the metabolic syndrome, particularly with the insulin resistance and BMI criteria. This is analogous with previous reports linking DISH with metabolic causes. In this age category, we did not observe any increase in prevalence with age.

Characterization of Aerosol Hygroscopicity Over the Northeast Pacific Ocean: Impacts on Prediction of CCN and Stratocumulus Cloud Droplet Number Concentrations.

During the Marine Aerosol Cloud and Wildfire Study (MACAWS) in June and July of 2018, aerosol composition and cloud condensation nuclei (CCN) properties were measured over the N.E. Pacific to characterize the influence of aerosol hygroscopicity on predictions of ambient CCN and stratocumulus cloud droplet number concentrations (CDNC). Three vertical regions were characterized, corresponding to the marine boundary layer (MBL), an above-cloud organic aerosol layer (AC-OAL), and the free troposphere (FT) above the AC-OAL. The aerosol hygroscopicity parameter (κ) was calculated from CCN measurements (κ CCN) and bulk aerosol mass spectrometer (AMS) measurements (κ AMS). Within the MBL, measured hygroscopicities varied between values typical of both continental environments (~0.2) and remote marine locations (~0.7). For most flights, CCN closure was achieved within 20% in the MBL. For five of the seven flights, assuming a constant aerosol size distribution produced similar or better CCN closure than assuming a constant "marine" hygroscopicity (κ = 0.72). An aerosol-cloud parcel model was used to characterize the sensitivity of predicted stratocumulus CDNC to aerosol hygroscopicity, size distribution properties, and updraft velocity. Average CDNC sensitivity to accumulation mode aerosol hygroscopicity is 39% as large as the sensitivity to the geometric median diameter in this environment. Simulations suggest CDNC sensitivity to hygroscopicity is largest in marine stratocumulus with low updraft velocities (<0.2 m s-1), where accumulation mode particles are most relevant to CDNC, and in marine stratocumulus or cumulus with large updraft velocities (>0.6 m s-1), where hygroscopic properties of the Aitken mode dominate hygroscopicity sensitivity.

Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source.

Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7 keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 µm x 1.7 µm full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.

Efficient optimization method for finding minimum energy paths of magnetic transitions.

Efficient algorithms for the calculation of minimum energy paths of magnetic transitions are implemented within the geodesic nudged elastic band (GNEB) approach. While an objective function is not available for GNEB and a traditional line search can, therefore, not be performed, the use of limited memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) and conjugate gradient algorithms in conjunction with orthogonal spin optimization (OSO) approach is shown to greatly outperform the previously used velocity projection and dissipative Landau-Lifschitz dynamics optimization methods. The implementation makes use of energy weighted springs for the distribution of the discretization points along the path and this is found to improve performance significantly. The various methods are applied to several test problems using a Heisenberg-type Hamiltonian, extended in some cases to include Dzyaloshinskii-Moriya and exchange interactions beyond nearest neighbours. Minimum energy paths are found for magnetization reversals in a nano-island, collapse of skyrmions in two-dimensional layers and annihilation of a chiral bobber near the surface of a three-dimensional magnet. The LBFGS-OSO method is found to outperform the dynamics based approaches by up to a factor of 8 in some cases.

Quantitative 3D imaging parameters improve prediction of hip osteoarthritis outcome.

Osteoarthritis is an increasingly important health problem for which the main treatment remains joint replacement. Therapy developments have been hampered by a lack of biomarkers that can reliably predict disease, while 2D radiographs interpreted by human observers are still the gold standard for clinical trial imaging assessment. We propose a 3D approach using computed tomography-a fast, readily available clinical technique-that can be applied in the assessment of osteoarthritis using a new quantitative 3D analysis technique called joint space mapping (JSM). We demonstrate the application of JSM at the hip in 263 healthy older adults from the AGES-Reykjavík cohort, examining relationships between 3D joint space width, 3D joint shape, and future joint replacement. Using JSM, statistical shape modelling, and statistical parametric mapping, we show an 18% improvement in prediction of joint replacement using 3D metrics combined with radiographic Kellgren & Lawrence grade (AUC 0.86) over the existing 2D FDA-approved gold standard of minimum 2D joint space width (AUC 0.73). We also show that assessment of joint asymmetry can reveal significant differences between individuals destined for joint replacement versus controls at regions of the joint that are not captured by radiographs. This technique is immediately implementable with standard imaging technologies.

Phase stability and electronic structure of iridium metal at the megabar range.

The 5d transition metals have attracted specific interest for high-pressure studies due to their extraordinary stability and intriguing electronic properties. In particular, iridium metal has been proposed to exhibit a recently discovered pressure-induced electronic transition, the so-called core-level crossing transition at the lowest pressure among all the 5d transition metals. Here, we report an experimental structural characterization of iridium by x-ray probes sensitive to both long- and short-range order in matter. Synchrotron-based powder x-ray diffraction results highlight a large stability range (up to 1.4 Mbar) of the low-pressure phase. The compressibility behaviour was characterized by an accurate determination of the pressure-volume equation of state, with a bulk modulus of 339(3) GPa and its derivative of 5.3(1). X-ray absorption spectroscopy, which probes the local structure and the empty density of electronic states above the Fermi level, was also utilized. The remarkable agreement observed between experimental and calculated spectra validates the reliability of theoretical predictions of the pressure dependence of the electronic structure of iridium in the studied interval of compressions.

Femtosecond phase-transition in hard x-ray excited bismuth.

The evolution of bismuth crystal structure upon excitation of its A1g phonon has been intensely studied with short pulse optical lasers. Here we present the first-time observation of a hard x-ray induced ultrafast phase transition in a bismuth single crystal at high intensities (~1014 W/cm2). The lattice evolution was followed using a recently demonstrated x-ray single-shot probing setup. The time evolution of the (111) Bragg peak intensity showed strong dependence on the excitation fluence. After exposure to a sufficiently intense x-ray pulse, the peak intensity dropped to zero within 300 fs, i.e. faster than one oscillation period of the A1g mode at room temperature. Our analysis indicates a nonthermal origin of a lattice disordering process, and excludes interpretations based on electron-ion equilibration process, or on thermodynamic heating process leading to plasma formation.

Towards a patient-specific estimation of intra-operative femoral fracture risk.

Total Hip Arthroplasty requires pre-surgical evaluation between un-cemented and cemented prostheses. A Patient with intra-operative periprosthetic fracture and another with a successful outcome were recruited, and their finite element models were constructed by processing CT data, assuming elastic-plastic behavior of the bone as function of the local density. To resemble the insertion of the prosthesis into the femur, a fictitious thermal dilatation is applied to the broach volume. Strain-based fracture risk factor is estimated, depicting results in terms of the total mechanical strain expressed using a simple "traffic lights" color code to provide immediate, concise, and intelligible pre-operative information to surgeons.

Biological treatment in ankylosing spondylitis in the Nordic countries during 2010-2016: a collaboration between five biological registries.

OBJECTIVES: Large-scale observational cohorts may be used to study the effectiveness and rare side effects of biological disease-modifying anti-rheumatic drugs (bDMARDs) in ankylosing spondylitis (AS), but may be hampered by differences in baseline characteristics and disease activity across countries. We aimed to explore the research infrastructure in the five Nordic countries regarding bDMARD treatment in AS. METHOD: This observational cohort study was based on data from biological registries in Denmark (DANBIO), Sweden (SRQ/ARTIS), Finland (ROB-FIN), Norway (NOR-DMARD), and Iceland (ICEBIO). Data were collected for the years 2010-2016. Registry coverage, registry inventory (patient characteristics, disease activity measures), and national guidelines for bDMARD prescription in AS were described per country. Incident (first line) and prevalent bDMARD use per capita, country, and year were calculated. In AS patients who started first line bDMARDs during 2010-2016 (n = 4392), baseline characteristics and disease activity measures were retrieved. RESULTS: Registry coverage of bDMARD-treated patients ranged from 60% to 95%. All registries included extensive prospectively collected data at patient level. Guidelines regarding choice of first line drug and prescription patterns varied across countries. During the period 2010-2016 prevalent bDMARD use increased (p < 0.001), whereas incident use tended to decrease (p for trend < 0.004), with large national variations (e.g. 2016 incidence: Iceland 10.7/100 000, Finland 1.7/100 000). Baseline characteristics were similar regarding C-reactive protein, but differed for other variables, including the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) (range 3.5-6.3) and Ankylosing Spondylitis Disease Activity Score (ASDAS) (2.7-3.8) (both p < 0.0001). CONCLUSION: Collaboration across the five Nordic biological registries regarding bDMARD use in AS is feasible but national differences in coverage, prescription patterns, and patient characteristics must be taken into account depending on the scientific question.

Ultrafast nonthermal heating of water initiated by an X-ray Free-Electron Laser.

The bright ultrafast pulses of X-ray Free-Electron Lasers allow investigation into the structure of matter under extreme conditions. We have used single pulses to ionize and probe water as it undergoes a phase transition from liquid to plasma. We report changes in the structure of liquid water on a femtosecond time scale when irradiated by single 6.86 keV X-ray pulses of more than 106 J/cm2 These observations are supported by simulations based on molecular dynamics and plasma dynamics of a water system that is rapidly ionized and driven out of equilibrium. This exotic ionic and disordered state with the density of a liquid is suggested to be structurally different from a neutral thermally disordered state.

Reproducibility of single protein explosions induced by X-ray lasers.

Single particle imaging (SPI) using X-ray pulses has become increasingly attainable with the advent of high-intensity free electron lasers. Eliminating the need for crystallized samples enables structural studies of molecules previously inaccessible by conventional crystallography. While this emerging technique already demonstrates substantial promise, some obstacles need to be overcome before SPI can reach its full potential. One such problem is determining the spatial orientation of the sample at the time of X-ray interaction. Existing solutions rely on diffraction data and are computationally demanding and sensitive to noise. In this in silico study, we explore the possibility of aiding these methods by mapping the ion distribution as the sample undergoes a Coulomb explosion following the intense ionization. By detecting the ions ejected from the fragmented sample, the orientation of the original sample should be possible to determine. Knowledge of the orientation has been shown earlier to be of substantial advantage in the reconstruction of the original structure. 150 explosions of each of twelve separate systems - four polypeptides with different amounts of surface bound water - were simulated with molecular dynamics (MD) and the average angular distribution of carbon and sulfur ions was investigated independently. The results show that the explosion maps are reproducible in both cases, supporting the idea that orientation information is preserved. Additional water seems to restrict the carbon ion trajectories further through a shielding mechanism, making the maps more distinct. For sulfurs, water has no significant impact on the trajectories, likely due to their higher mass and greater ionization cross section, indicating that they could be of particular interest. Based on these findings, we conclude that explosion data can aid spatial orientation in SPI experiments and could substantially improve the capabilities of the novel technique.

Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission.

Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000 pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser. Plasma emission spectra are simulated for systems exposed to high-intensity femtosecond pulses, for both protein crystals and the liquid carrier systems that are used for sample delivery. The thermal radiation from the glowing plasma gives a strong background in the XUV region that depends on the intensity of the pulse, around the emission lines from light elements (carbon, nitrogen, oxygen). Sample hits can be reliably distinguished from the carrier liquid based on the characteristic emission lines from heavier elements present only in the sample, such as sulfur. For buffer systems with sulfur present, selenomethionine substitution is suggested, where the selenium emission lines could be used both as an indication of a hit and as an aid in phasing and structural reconstruction of the protein.

Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex.

A multiscale density functional theory-quantum mechanics/molecular mechanics (DFT-QM/MM) scheme is presented, based on an efficient electrostatic coupling between the electronic density obtained from a grid-based projector augmented wave (GPAW) implementation of density functional theory and a classical potential energy function. The scheme is implemented in a general fashion and can be used with various choices for the descriptions of the QM or MM regions. Tests on H2O clusters, ranging from dimer to decamer show that no systematic energy errors are introduced by the coupling that exceeds the differences in the QM and MM descriptions. Over 1 ns of liquid water, Born-Oppenheimer QM/MM molecular dynamics (MD) are sampled combining 10 parallel simulations, showing consistent liquid water structure over the QM/MM border. The method is applied in extensive parallel MD simulations of an aqueous solution of the diplatinum [Pt2(P2O5H2)4]4- complex (PtPOP), spanning a total time period of roughly half a nanosecond. An average Pt-Pt distance deviating only 0.01 Å from experimental results, and a ground-state Pt-Pt oscillation frequency deviating by <2% from experimental results were obtained. The simulations highlight a remarkable harmonicity of the Pt-Pt oscillation, while also showing clear signs of Pt-H hydrogen bonding and directional coordination of water molecules along the Pt-Pt axis of the complex.

Atomic Scale Formation Mechanism of Edge Dislocation Relieving Lattice Strain in a GeSi overlayer on Si(001).

Understanding how edge misfit dislocations (MDs) form in a GeSi/Si(001) film has been a long standing issue. The challenge is to find a mechanism accounting for the presence of these dislocations at the interface since they are not mobile and cannot nucleate at the surface and glide towards the interface. Furthermore, experiments can hardly detect the nucleation and early stages of growth because of the short time scale involved. Here we present the first semi-quantitative atomistic calculation of the formation of edge dislocations in such films. We use a global optimization method and density functional theory calculations, combined with computations using potential energy functions to identify the best mechanisms. We show that those previously suggested are relevant only for a low film strain and we propose a new mechanism which accounts for the formation of edge dislocations at high film strain. In this one, a 60° MD nucleates as a "split" half-loop with two branches gliding on different planes. One branch belongs to the glide plane of a complementary 60° MD and therefore strongly favors the formation of the complementary MD which is immediately combined with the first MD to form an edge MD.

Sewage sludge as fertiliser - environmental assessment of storage and land application options.

Sewage sludge (SS) contains beneficial plant nutrients and organic matter, and therefore application of SS on agricultural land helps close nutrient loops. However, spreading operations are restricted to certain seasons and hence the SS needs to be stored. Storage and land application of SS are both potential sources of greenhouse gases and ammonia, leading to global warming, acidification and eutrophication. Covering the stored SS, treating it with urea and choosing the correct time for land application all have the potential to reduce emissions from the system. Using life cycle assessment (LCA), this study compares storage and land application options of SS in terms of global warming potential (GWP), acidification potential, eutrophication potential and primary energy use. The system with covered storage has the lowest impact of all categories. Systems with autumn application are preferable to spring application for all impact categories but, when nitrate leaching is considered, spring application is preferable in terms of eutrophication and primary energy use and, for some SS treatments, GWP. Ammonia addition reduces nitrous oxide and ammonia emissions during storage, but increases these emissions after land application. Storage duration has a large impact on GWP, while amount of chemical nitrogen fertiliser substituted has a large impact on primary energy use.

Physiological changes associated with routine nursing procedures in critically ill are common: an observational pilot study.

BACKGROUND: Nursing procedures that are routinely performed in the intensive care unit (ICU) are assumed to have minimal side effects. However, these procedures may sometimes cause physiological changes that negatively affect the patient. We hypothesized that physiological changes associated with routine nursing procedures in the ICU are common. METHODS: A clinical observational study of 16 critically ill patients in a nine-bed mixed university hospital ICU. All nursing procedures were observed, and physiological data were collected and subsequently analyzed. Minor physiological changes were defined as minimal changes in respiratory or circulatory variables, and major physiological changes were marked as hyper/hypotension, bradycardia/tachycardia, bradypnea/tachypnea, ventilatory distress, and peripheral blood oxygen desaturation. RESULTS: In the 16 patients, 668 procedures generated 158 major and 692 minor physiological changes during 187 observational hours. The most common procedure was patient position change, which also generated the majority of the physiological changes. The most common major physiological changes were blood oxygen desaturation, ventilatory distress, and hypotension, and the most common minor changes were arterial pressure alteration, coughing, and increase in respiratory rate. CONCLUSION: In this pilot study, we examined physiological changes in connection with all regular routine nursing procedures in the ICU. We found that physiological changes were common and sometimes severe.

Quality of greywater treated in biochar filter and risk assessment of gastroenteritis due to household exposure during maintenance and irrigation.

AIM: This study evaluated treatment of greywater (GW) by a biochar filter in Jordan and assessed the annual risks of infection (Pi-annual ), annual risk of disease (Pd-annual ) and disease burden (in disability-adjusted life years; DALYs) of gastroenteritis caused by Salmonella spp. and rotavirus due to ingestion of GW during system maintenance and consumption of green onions irrigated with treated and nontreated GW. METHODS AND RESULTS: The biochar filter efficiently removed 93% of biochemical oxygen demand (BOD5 ) and 85% of solids, while removal of Escherichia coli was insignificant. Treatment of GW decreased the median Pd-annual due to ingestion of GW from 1·39 × 10-2 to 6·0 × 10-3 for Salmonella spp. but did not affect Pd-annual caused by rotavirus (9·73 × 10-1 to 1·0). Consumption of onions irrigated with treated GW had a median Pd-annual of 1·25 × 10-9 to 1·2 × 10-8 for Salmonella spp. and 4·96 × 10-4 to 4·37 × 10-3 for rotavirus infection, which was 99·9 and 90% lower, respectively, than the risk when consuming onions irrigated with nontreated GW. The highest risks of gastrointestinal disease were thus associated mainly with direct ingestion of GW when maintaining the system. CONCLUSIONS: Garden produce irrigated with GW treated in biochar filter did not display intolerable risks of rotavirus-based gastroenteritis during summer season in the study area given that the produce is harvested 1 to 2 days, and washed, before consumption. SIGNIFICANCE AND IMPACT OF THE STUDY: This study contributes to scientific-based knowledge on the suitability of biochar filters for onsite greywater treatment and confirms the microbial safety of recycling treated greywater for garden irrigation.

Activation of Complement Following Total Hip Replacement.

The aim of this study was to investigate whether complement activation, via the classical and alternative pathways, occurs following a cemented total hip replacement (THR) surgery due to osteoarthritis. Blood samples were collected systematically from 12 patients - six male and six women, with a median age of 75 (range: 59-90 years) - preoperatively, 6 h post-operatively and on the first, second and third post-operative day. Total function of classical (CH50) and alternative pathways (AH50) was evaluated, along with the determination of serum concentrations of the complement proteins C3, C4, C3d, the soluble terminal complement complex (sTCC) sC5b-9, as well as C-reactive protein (CRP) and albumin. Measurements of CRP and albumin levels elucidated a marked inflammatory response following the operation. The CH50, AH50 and C3 and C4 levels were significantly lower 6 h after the surgery compared with the preoperative levels, but elevated above the preoperative levels during the following 3 days. The complement activation product C3d levels increased continually during the whole observation period, from 13.5 AU/ml (range: 8-19 AU/ml) preoperative to 20 AU/ml (range: 12-34 AU/ml) on the third post-operative day. Furthermore, we observed an increase in the sC5b-9 levels between the preoperative and the third post-operative day. These results demonstrate a significant activation of the complement system following cemented THR. Further studies are needed to elucidate the time frame and the pathogenic role of this observed complement activation.