MtsslWizard: In Silico Spin-Labeling and Generation of Distance Distributions in PyMOL

MtsslWizard is a computer program, which operates as a plugin for the PyMOL molecular graphics system. MtsslWizard estimates distances between spin labels on proteins quickly with user-configurable options through a simple graphical interface. In default mode, the program searches for ensembles of possible MTSSL conformations that do not clash with a static model of the protein. Once conformations are assigned, distance distributions between two or more ensembles are calculated, displayed, and can be exported to other software. The program’s use is evaluated in a number of challenging test cases and its strengths and weaknesses evaluated. The benefits of the program are its accuracy and simplicity

Clear-air turbulence trends over the North Atlantic in high-resolution climate models

Clear-air turbulence (CAT) has a large impact on the aviation sector. Our current understanding of how CAT may increase with climate change in future is largely based on simulations from CMIP3 and CMIP5 global climate models (GCMs). However, these models have now been superseded by high-resolution CMIP6 GCMs, which for the first time have grid lengths at which individual turbulence patches may start to be resolved. Here we use a multi-model approach to quantify projected moderate CAT changes over the North Atlantic using CMIP6 models. The influence of the model resolution on CAT projections is analysed. Twenty-one CAT diagnostics are used, in order to represent uncertainties in CAT production mechanisms. Each diagnostic responds differently in time, but the majority display an increase in moderate CAT between 1950 and 2050. Although winter is historically the most turbulent season, there is strong multi-model agreement that autumn and summer will have the greatest overall relative increase in CAT frequency. By 2050, summers are projected to become as turbulent as 1950 winters and autumns. The global-mean seasonal near-surface temperature is used as a comparative metric. For every 1 °C of global near-surface warming, autumn, winter, spring, and summer are projected to have an average of 14%, 9%, 9%, and 14% more moderate CAT, respectively. Our results confirm that the aviation sector should prepare for a more turbulent future

Comparison of the biotypes of Yersinia enterocolitica isolated from pigs, cattle and sheep at slaughter and from humans with yersiniosis in Great Britain during 1999-2000

Aims: To investigate the relationship between livestock carriage of Yersinia enterocolitica and human disease. The biotypes/serotypes of strains recovered from the faeces of pigs, cattle and sheep at slaughter during a national survey in Great Britain in 1999-2000, were compared with those of strains isolated from human cases of yersiniosis during the same period. Methods and Results: The faecal carriage of Y. enterocolitica by cattle, sheep and pigs at slaughter was 6.3, 10.7 and 26.1%, respectively. Yersinia enterocolitica biotype (BT) 1a was the most frequently isolated biotype from livestock (58%) and was the predominant biotype (53%) isolated from human cases over the same period. The main recognized pathogenic Y. enterocolitica biotype isolated from livestock was BT3 (O:5,27) (35% of sheep, 22% of pigs and 4% of cattle) but this biotype was not detected in any of the human isolates investigated. The major pathogenic biotypes of strains isolated from humans were BT3 (O:9) (24%) and BT4 (O:3) (19%) whereas of the veterinary isolates investigated, only pigs (11%) carried BT3 (O:9) strains. Conclusions: Because of significant overlaps in phenotypes of the veterinary and human strains it is not possible to comment on the correlation between host and pathogenicity, especially of biotype 1a. Significance and Impact of the Study: The data suggest that further investigations using methods with greater discriminatory power are required. However the data also suggests that pigs may be the primary reservoir for human pathogenic Y. enterocolitica infection

Quantum Communication with Phantom Photons

We show that quantum information may be transferred between atoms in different locations by using ``phantom photons'': the atoms are coupled through electromagnetic fields, but the corresponding field modes do not have to be fully populated. In the case where atoms are placed inside optical cavities, errors in quantum information processing due to photon absorption inside the cavity are diminished in this way. This effect persists up to intercavity distances of about a meter for the current levels of cavity losses, and may be useful for distributed quantum computing.Comment: 6 pages RevTex, 4 eps figures included. Revised calculation with more details about mode structure calculation and the introduction of losse

How important are post-tropical cyclones for European windstorm risk?

Post-tropical cyclones (PTCs) extend many hazards associated with tropical cyclones (TCs) to the mid-latitudes. Despite recent high-impact cases affecting Europe such as Ophelia, little research has been done to characterize the risk of PTCs. Here we compare the climatologies and intensity distributions of mid-latitude cyclones (MLCs) and PTCs in the North Atlantic and Europe by tracking cyclones in the ERA5 reanalysis. Considering hurricane-season cyclones impacting Northern Europe, PTCs show a significantly higher mean maximum intensity than MLCs, but make only a small contribution to total windstorm risk. Our results show that a disproportionately large fraction of high-intensity cyclones impacting Europe during hurricane season are PTCs. The fraction of PTCs impacting N Europe with storm-force (>25ms-1) winds is approximately ten times higher than for MLCs. Less than 1% of cyclones impacting Northern Europe are identified to be PTCs. This rises to 8.8% when considering cyclones which impact with storm-force winds

Using Long-Duration Static Stretch Training to Counteract Strength and Flexibility Deficits in Moderately Trained Participants

Many sports injuries result in surgery and prolonged periods of immobilization, which may lead to significant atrophy accompanied by loss of maximal strength and range of motion and, therefore, a weak-leg/strong-leg ratio (as an imbalance index ∆ ) lower than 1. Consequently, there are common rehabilitation programs that aim to enhance maximal strength, muscle thickness and flexibility; however, the literature demonstrates existing strength imbalances after weeks of rehabilitation. Since no study has previously been conducted to investigate the effects of long-duration static stretch training to treat muscular imbalances, the present research aims to determine the possibility of counteracting imbalances in maximal strength and range of motion. Thirty-nine athletic participants with significant calf muscle imbalances in maximal strength and range of motion were divided into an intervention group (one-hour daily plantar flexors static stretching of the weaker leg for six weeks) and a control group to evaluate the effects on maximal strength and range of motion with extended and bent knee joint. Results show significant increases in maximal strength (d = 0.84–1.61, p < 0.001–0.005) and range of motion (d = 0.92–1.49, p < 0.001–0.002) following six weeks of static stretching. Group * time effects ( p < 0.001–0.004, η² = 0.22–0.55) revealed ∆ changes in the intervention group from 0.87 to 1.03 for maximal strength and from 0.92 to 1.11 in range of motion. The results provide evidence for the use of six weeks of daily, one hour stretching to counteract muscular imbalances. Related research in clinical settings after surgery is suggested

How interactions between tropical depressions and western disturbances affect heavy precipitation in South Asia

Interactions over South Asia between tropical depressions (TDs) and extratropical storms known as western disturbances (WDs) are known to cause extreme precipitation events, including those responsible for the 2013 floods over northern India. In this study, existing databases of WD and TD tracks are used to identify potential WD–TD interactions from 1979–2015; these are filtered according to proximity and intensity, leaving 59 cases which form the basis of this paper. Synoptic charts, vorticity budgets, and moisture trajectory analyses are employed to identify and elucidate common interaction types among these cases. Two broad families of interaction emerge. Firstly, a dynamical coupling of the WD and TD, whereby either the upper- and lower-level vortices superpose (a vortex merger), or the TD is intensified as it passes into the entrance region of a jet streak associated with the WD (a jet-streak excitation). Secondly, a moisture exchange between the WD and TD, whereby either anomalous moisture is advected from the TD to the WD, resulting in anomalous precipitation near the WD (a TD-to-WD moisture exchange), or anomalous moisture is advected from the WD to the TD (a WD-to-TD moisture exchange). Interactions are most common in the post-monsoon period as the subtropical jet, which brings WDs to the subcontinent, returns south; there is a smaller peak in May and June, driven by monsoon onset vortices. Precipitation is heaviest in dynamically-coupled interactions, particularly jet–streak excitations. Criteria for automated identification of interaction types are proposed, and schematics for each type are presented to highlight key mechanisms

Unravelling the Mechanism of Summer Monsoon Rainfall Modes over the West Coast of India using Model Simulations

A transition from a predominantly offshore to an onshore rainfall phase over the west coast of India was simulated using three one-way nested domains with 12-, 4-, and 1.33-km horizontal grid spacing in the Weather Research and Forecasting model. The mechanism of offshore-onshore rainfall oscillation and the orographic effects of the Western Ghats are studied. A convective parameterization scheme was employed only in the 12-km domain. A trough extending offshore from the west coast facilitates offshore rainfall. This trough is absent during the onshore phase, and rainfall occurs over the coast mainly via orographic uplift by the Western Ghats. The model overestimates rainfall over the Western Ghats at all resolutions as it consistently underestimates the boundary layer stratification along the coast. Weaker stratification weakens the blocking effect of the Western Ghats, resulting in anomalous deep convection and rainfall over its windward slopes. The 4- and 1.33-km domains simulate the offshore-to-onshore transition of rainfall but fail to capture a sufficient contrast in rainfall between land and sea compared to observations. The 12-km domain produces light rainfall, anchored along the coast, throughout the simulation period, and hence gravely underestimates the offshore rainfall. The offshore rainfall persisted in the 4- and 1.33-km domains in a sensitivity experiment in which the Western Ghats were flattened. This suggests that orographic effects do not significantly influence offshore rainfall. In another experiment, the convective parameterization scheme in the 12-km domain was turned off. This experiment simulated the offshore and onshore rainfall phases correctly to some extent but the rainfall intensity was unrealistically high. Thus, a model with a horizontal grid spacing of O(∼ 1 km), in which convection evolves explicitly, is desired for simulating the west coast rainfall variations. However, improvements in the representation of boundary layer processes are needed to capture the land-sea contrast

Historical variability and lifecycles of North Atlantic midlatitude cyclones originating in the tropics

North Atlantic tropical and post‐tropical cyclones impact midlatitude regions, but the inhomogeneous observational record of the latter stages of tropical cyclones precludes many climatological analyses. The frequency of tropical‐origin storms basin‐wide is projected to increase under anthropogenic climate change, so establishing confidence in our knowledge of their historical variability and lifecycles—against which climate model simulations may be evaluated—is important. We used a Lagrangian feature‐tracking algorithm to identify tropical cyclones that impacted Northeast North America and Europe in seven global reanalysis datasets, distinguishing systems that retained warm‐core structures or underwent warm seclusion from those that underwent extratropical transition, acquiring cold‐core, frontal structures. Over the last four decades, ∼25 % and ∼10 % of tropical‐origin cyclones made landfall across Northeast North America and Europe, respectively, as warm‐core systems, with, on average, higher wind speeds than cold‐core systems. Historical warm‐ and cold‐core landfalls also exhibit distinct tracks, likely responding to differing steering flow and midlatitude conditions