Landau Damping and Coherent Structures in Narrow-Banded 1+1 Deep Water Gravity Waves

We study the nonlinear energy transfer around the peak of the spectrum of surface gravity waves by taking into account nonhomogeneous effects. In the narrow-banded approximation the kinetic equation resulting from a nonhomogeneous wave field is a Vlasov-Poisson type equation which includes at the same time the random version of the Benjamin-Feir instability and the Landau damping phenomenon. We analytically derive the values of the Phillips' constant $\alpha$ and the enhancement factor $\gamma$ for which the narrow-banded approximation of the JONSWAP spectrum is unstable. By performing numerical simulations of the nonlinear Schr\"{o}dinger equation we check the validity of the prediction of the related kinetic equation. We find that the effect of Landau damping is to suppress the formation of coherent structures. The problem of predicting freak waves is briefly discussed.Comment: 4 pages, 3 figure

Mechanistic insight into RET kinase inhibitors targeting the DFG-out conformation in RET-rearranged cancer

Oncogenic fusion events have been identified in a broad range of tumors. Among them, RET rearrangements represent distinct and potentially druggable targets that are recurrently found in lung adenocarcinomas. Here, we provide further evidence that current anti-RET drugs may not be potent enough to induce durable responses in such tumors. We report that potent inhibitors such as AD80 or ponatinib that stably bind in the DFG-out conformation of RET may overcome these limitations and selectively kill RET-rearranged tumors. Using chemical genomics in conjunction with phosphoproteomic analyses in RET-rearranged cells we identify the CCDC6-RETI788N mutation and drug-induced MAPK pathway reactivation as possible mechanisms, by which tumors may escape the activity of RET inhibitors. Our data provide mechanistic insight into the druggability of RET kinase fusions that may be of help for the development of effective therapies targeting such tumors

Trehalose-6-phosphate-mediated toxicity determines essentiality of OtsB2 in Mycobacterium tuberculosis in vitro and in mice

Trehalose biosynthesis is considered an attractive target for the development of antimicrobials against fungal, helminthic and bacterial pathogens including Mycobacterium tuberculosis. The most common biosynthetic route involves trehalose-6-phosphate (T6P) synthase OtsA and T6P phosphatase OtsB that generate trehalose from ADP/UDP-glucose and glucose-6-phosphate. In order to assess the drug target potential of T6P phosphatase, we generated a conditional mutant of M. tuberculosis allowing the regulated gene silencing of the T6P phosphatase gene otsB2. We found that otsB2 is essential for growth of M. tuberculosis in vitro as well as for the acute infection phase in mice following aerosol infection. By contrast, otsB2 is not essential for the chronic infection phase in mice, highlighting the substantial remodelling of trehalose metabolism during infection by M. tuberculosis. Blocking OtsB2 resulted in the accumulation of its substrate T6P, which appears to be toxic, leading to the self-poisoning of cells. Accordingly, blocking T6P production in a ΔotsA mutant abrogated otsB2 essentiality. T6P accumulation elicited a global upregulation of more than 800 genes, which might result from an increase in RNA stability implied by the enhanced neutralization of toxins exhibiting ribonuclease activity. Surprisingly, overlap with the stress response caused by the accumulation of another toxic sugar phosphate molecule, maltose-1-phosphate, was minimal. A genome-wide screen for synthetic lethal interactions with otsA identified numerous genes, revealing additional potential drug targets synergistic with OtsB2 suitable for combination therapies that would minimize the emergence of resistance to OtsB2 inhibitors

Metabolic Network for the Biosynthesis of Intra- and Extracellular alpha-Glucans Required for Virulence of Mycobacterium tuberculosis

Mycobacterium tuberculosis synthesizes intra- and extracellular alpha-glucans that were believed to originate from separate pathways. The extracellular glucose polymer is the main constituent of the mycobacterial capsule that is thought to be involved in immune evasion and virulence. However, the role of the alpha-glucan capsule in pathogenesis has remained enigmatic due to an incomplete understanding of alpha-glucan biosynthetic pathways preventing the generation of capsule-deficient mutants. Three separate and potentially redundant pathways had been implicated in alpha-glucan biosynthesis in mycobacteria: the GlgC-GlgA, the Rv3032 and the TreS-Pep2-GlgE pathways. We now show that alpha-glucan in mycobacteria is exclusively assembled intracellularly utilizing the building block alpha-maltose-1-phosphate as the substrate for the maltosyltransferase GlgE, with subsequent branching of the polymer by the branching enzyme GlgB. Some alpha-glucan is exported to form the alpha-glucan capsule. There is an unexpected convergence of the TreS-Pep2 and GlgC-GlgA pathways that both generate alpha-maltose-1-phosphate. While the TreS-Pep2 route from trehalose was already known, we have now established that GlgA forms this phosphosugar from ADP-glucose and glucose 1-phosphate 1000-fold more efficiently than its hitherto described glycogen synthase activity. The two routes are connected by the common precursor ADPglucose, allowing compensatory flux from one route to the other. Having elucidated this unexpected configuration of the metabolic pathways underlying alpha-glucan biosynthesis in mycobacteria, an M. tuberculosis double mutant devoid of alpha-glucan could be constructed, showing a direct link between the GlgE pathway, alpha-glucan biosynthesis and virulence in a mouse infection model

Spatially valid data of atmospheric deposition of heavy metals and nitrogen derived by moss surveys for pollution risk assessments of ecosystems

For analysing element input into ecosystems and associated risks due to atmospheric deposition, element concentrations in moss provide complementary and time-integrated data at high spatial resolution every 5 years since 1990. The paper reviews (1) minimum sample sizes needed for reliable, statistical estimation of mean values at four different spatial scales (European and national level as well as landscape-specific level covering Europe and single countries); (2) trends of heavy metal (HM) and nitrogen (N) concentrations in moss in Europe (1990–2010); (3) correlations between concentrations of HM in moss and soil specimens collected across Norway (1990–2010); and (4) canopy drip-induced site-specific variation of N concentration in moss sampled in seven European countries (1990–2013). While the minimum sample sizes on the European and national level were achieved without exception, for some ecological land classes and elements, the coverage with sampling sites should be improved. The decline in emission and subsequent atmospheric deposition of HM across Europe has resulted in decreasing HM concentrations in moss between 1990 and 2010. In contrast, hardly any changes were observed for N in moss between 2005, when N was included into the survey for the first time, and 2010. In Norway, both, the moss and the soil survey data sets, were correlated, indicating a decrease of HM concentrations in moss and soil. At the site level, the average N deposition inside of forests was almost three times higher than the average N deposition outside of forests

Modelling and mapping heavy metal and nitrogen concentrations in moss in 2010 throughout Europe by applying Random Forests models

Objective: This study explores the statistical relations between the concentration of nine heavy metals(HM) (arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), mercury (Hg), nickel (Ni), lead (Pb),vanadium (V), zinc (Zn)), and nitrogen (N) in moss and potential explanatory variables (predictors)which were then used for mapping spatial patterns across Europe. Based on moss specimens collected in 2010 throughout Europe, the statistical relation between a set of potential predictors (such as the atmospheric deposition calculated by use of two chemical transport models (CTM), distance from emission sources, density of different land uses, population density, elevation, precipitation, clay content of soils) and concentrations of HMs and nitrogen (N) in moss (response variables) were evaluated by the use of Random Forests (RF) and Classification and Regression Trees (CART). Four spatial scales were regarded: Europe as a whole, ecological land classes covering Europe, single countries participating in the European Moss Survey (EMS), and moss species at sampling sites. Spatial patterns were estimated by applying a series of RF models on data on potential predictors covering Europe. Statistical values and resulting maps were used to investigate to what extent the models are specific for countries, units of the Ecological Land Classification of Europe (ELCE), and moss species. Results: Land use, atmospheric deposition and distance to technical emission sources mainly influence the element concentration in moss. The explanatory power of calculated RF models varies according to elements measured in moss specimens, country, ecological land class, and moss species. Measured and predicted medians of element concentrations agree fairly well while minima and maxima show considerable differences. The European maps derived from the RF models provide smoothed surfaces of element concentrations (As, Cd, Cr, Cu, N, Ni, Pb, Hg, V, Zn), each explained by a multivariate RF model and verified by CART, and thereby more information than the dot maps depicting the spatial patterns of measured values. Conclusions: RF is an eligible method identifying and ranking boundary conditions of element concentrations in moss and related mapping including the influence of the environmental factors

BHPR research: qualitative1. Complex reasoning determines patients' perception of outcome following foot surgery in rheumatoid arhtritis

Background: Foot surgery is common in patients with RA but research into surgical outcomes is limited and conceptually flawed as current outcome measures lack face validity: to date no one has asked patients what is important to them. This study aimed to determine which factors are important to patients when evaluating the success of foot surgery in RA Methods: Semi structured interviews of RA patients who had undergone foot surgery were conducted and transcribed verbatim. Thematic analysis of interviews was conducted to explore issues that were important to patients. Results: 11 RA patients (9 ♂, mean age 59, dis dur = 22yrs, mean of 3 yrs post op) with mixed experiences of foot surgery were interviewed. Patients interpreted outcome in respect to a multitude of factors, frequently positive change in one aspect contrasted with negative opinions about another. Overall, four major themes emerged. Function: Functional ability & participation in valued activities were very important to patients. Walking ability was a key concern but patients interpreted levels of activity in light of other aspects of their disease, reflecting on change in functional ability more than overall level. Positive feelings of improved mobility were often moderated by negative self perception ("I mean, I still walk like a waddling duck”). Appearance: Appearance was important to almost all patients but perhaps the most complex theme of all. Physical appearance, foot shape, and footwear were closely interlinked, yet patients saw these as distinct separate concepts. Patients need to legitimize these feelings was clear and they frequently entered into a defensive repertoire ("it's not cosmetic surgery; it's something that's more important than that, you know?”). Clinician opinion: Surgeons' post operative evaluation of the procedure was very influential. The impact of this appraisal continued to affect patients' lasting impression irrespective of how the outcome compared to their initial goals ("when he'd done it ... he said that hasn't worked as good as he'd wanted to ... but the pain has gone”). Pain: Whilst pain was important to almost all patients, it appeared to be less important than the other themes. Pain was predominately raised when it influenced other themes, such as function; many still felt the need to legitimize their foot pain in order for health professionals to take it seriously ("in the end I went to my GP because it had happened a few times and I went to an orthopaedic surgeon who was quite dismissive of it, it was like what are you complaining about”). Conclusions: Patients interpret the outcome of foot surgery using a multitude of interrelated factors, particularly functional ability, appearance and surgeons' appraisal of the procedure. While pain was often noted, this appeared less important than other factors in the overall outcome of the surgery. Future research into foot surgery should incorporate the complexity of how patients determine their outcome Disclosure statement: All authors have declared no conflicts of interes

Costlets: A Generalized Approach to Cost Functions for Automated Optimization of IMRT Treatment Plans

We present the creation and use of a generalized cost function methodology based on costlets for automated optimization for conformal and intensity modulated radiotherapy treatment plans. In our approach, cost functions are created by combining clinically relevant “costlets”. Each costlet is created by the user, using an “evaluator” of the plan or dose distribution which is incorporated into a function or “modifier” to create an individual costlet. Dose statistics, dose-volume points, biological model results, non-dosimetric parameters, and any other information can be converted into a costlet. A wide variety of different types of costlets can be used concurrently. Individual costlet changes affect not only the results for that structure, but also all the other structures in the plan (e.g., a change in a normal tissue costlet can have large effects on target volume results as well as the normal tissue). Effective cost functions can be created from combinations of dose-based costlets, dose-volume costlets, biological model costlets, and other parameters. Generalized cost functions based on costlets have been demonstrated, and show potential for allowing input of numerous clinical issues into the optimization process, thereby helping to achieve clinically useful optimized plans. In this paper, we describe and illustrate the use of the costlets in an automated planning system developed and used clinically at the University of Michigan Medical Center. We place particular emphasis on the flexibility of the system, and its ability to discover a variety of plans making various trade-offs between clinical goals of the treatment that may be difficult to meet simultaneously.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47484/1/11081_2005_Article_2066.pd