A method to represent subgrid-scale updraft velocity in kilometer-scale models: Implication for aerosol activation

©2014. American Geophysical Union. All Rights Reserved. Updraft velocities strongly control the activation of aerosol particles or that component that act as cloud condensation nuclei (CCN). For kilometer-scale models, vertical motions are partially resolved but the subgrid-scale (SGS) contribution needs to be parametrized or constrained to properly represent the activation of CCNs. This study presents a method to estimate the missing SGS (or unresolved) contribution to vertical velocity variability in models with horizontal grid sizes up to ∼2 km. A framework based on Large Eddy Simulations (LES) and high-resolution aircraft observations of stratocumulus and shallow cumulus clouds has been developed and applied to output from the United Kingdom Met Office Unified Model (UM) operating at kilometer-scale resolutions in numerical weather prediction configuration. For a stratocumulus deck simulation, we show that the UM 1 km model underestimates significantly the variability of updraft velocity with an averaged cloud base standard deviation between 0.04 and 0.05 m s-1 compared to LES and aircraft estimates of 0.38 and 0.54 m s-1, respectively. Once the SGS variability is considered, the UM corrected averages are between 0.34 and 0.44 m s-1. Off-line calculations of CCN-activated fraction using an activation scheme have been performed to illustrate the implication of including the SGS vertical velocity. It suggests increased CCN-activated fraction from 0.52 to 0.89 (respectively, 0.10 to 0.54) for a clean (respectively, polluted) aerosol environment for simulations with a 1 km horizontal grid size. Our results highlight the importance of representing the SGS vertical velocity in kilometer-scale simulations of aerosol-cloud interactions. Key PointsWe seek to improve the aerosol activation behavior in kilometer-scale modelsA method to constrain the subgrid-scale updraft velocity is presentedWe highlight the potential implication for aerosol-cloud interactions modeling.This work was funded by the Natural Environment Research Council (NERC) Aerosol-Cloud Interactions—a Directed Programme to Reduce Uncertainty in Forcing (ACID-PRUF) programme, grant code NE/I020121/1. The authors thank the scientists, ground crew and aircrew of the FAAM BAe-146 and C-130 aircraft, who were instrumental in the collection of the data analyzed from the VOCALS-REx campaign. The C-130 data were provided by NCAR/EOL, under sponsorship of the National Science Foundation. http://data.eol. ucar.edu/. The FAAM BAe-146 is jointly funded by the UK Met Office and the Natural Environment Research Council. VOCALS was supported by the UK Met Office and NERC, the latter through grant NE/F019874/1

Overvaluation of shape and weight in adolescents with anorexia nervosa: does shape concern or weight concern matter more for treatment outcome?

BACKGROUND: Overvaluation of shape and weight is a key diagnostic feature of anorexia nervosa (AN); however, limited research has evaluated the clinical utility of differentiating between weight versus shape concerns. Understanding differences in these constructs may have important implications for AN treatment given the focus on weight regain. This study examined differences in treatment outcome between individuals whose primary concern was weight versus those whose primary concern was shape in a randomized controlled trial of treatment for adolescent AN. METHODS: Data were drawn from a two-site randomized controlled trial that compared family-based treatment and adolescent focused therapy for AN. Chi-square tests and logistic regression analyses were conducted. RESULTS: Thirty percent of participants presented with primary weight concern (n = 36; defined as endorsing higher Eating Disorder Examination (EDE) Weight Concern than Shape Concern subscale scores); 60 % presented with primary shape concern (n = 72; defined as endorsing higher EDE Shape Concern than Weight Concern scores). There were no significant differences between the two groups in remission status at the end of treatment. Treatment did not moderate the effect of group status on achieving remission. CONCLUSIONS: Results suggest that treatment outcomes are comparable between adolescents who enter treatment for AN with greater weight concerns and those who enter treatment with greater shape concerns. Therefore, treatment need not be adjusted based on primary weight or primary shape concerns

Review: ‘Gimme five’: future challenges in multiple sclerosis. ECTRIMS Lecture 2009

This article is based on the ECTRIMS lecture given at the 25th ECTRIMS meeting which was held in Düsseldorf, Germany, from 9 to 12 September 2009. Five challenges have been identified: (1) safeguarding the principles of medical ethics; (2) optimizing the risk/benefit ratio; (3) bridging the gap between multiple sclerosis and experimental autoimmune encephalitis; (4) promoting neuroprotection and repair; and (5) tailoring multiple sclerosis therapy to the individual patient. Each of these challenges will be discussed and placed in the context of current research into the pathogenesis and treatment of multiple sclerosis

A Pan-African Convection-Permitting Regional Climate Simulation with the Met Office Unified Model: CP4-Africa

This is the final version. Available on open access from the American Meteorological Society via the DOI in this recordA convection-permitting multiyear regional climate simulation using the Met Office Unified Model has been run for the first time on an Africa-wide domain. The model has been run as part of the Future Climate for Africa (FCFA) Improving Model Processes for African Climate (IMPALA) project, and its configuration, domain, and forcing data are described here in detail. The model [Pan-African Convection-Permitting Regional Climate Simulation with the Met Office UM (CP4-Africa)] uses a 4.5-km horizontal grid spacing at the equator and is run without a convection parameterization, nested within a global atmospheric model driven by observations at the sea surface, which does include a convection scheme. An additional regional simulation, with identical resolution and physical parameterizations to the global model, but with the domain, land surface, and aerosol climatologies of CP4-Africa, has been run to aid in the understanding of the differences between the CP4-Africa and global model, in particular to isolate the impact of the convection parameterization and resolution. The effect of enforcing moisture conservation in CP4-Africa is described and its impact on reducing extreme precipitation values is assessed. Preliminary results from the first five years of the CP4-Africa simulation show substantial improvements in JJA average rainfall compared to the parameterized convection models, with most notably a reduction in the persistent dry bias in West Africa, giving an indication of the benefits to be gained from running a convection-permitting simulation over the whole African continent.Natural Environment Research Council (NERC

Core Site-Moiety Maps Reveal Inhibitors and Binding Mechanisms of Orthologous Proteins by Screening Compound Libraries

Members of protein families often share conserved structural subsites for interaction with chemically similar moieties despite low sequence identity. We propose a core site-moiety map of multiple proteins (called CoreSiMMap) to discover inhibitors and mechanisms by profiling subsite-moiety interactions of immense screening compounds. The consensus anchor, the subsite-moiety interactions with statistical significance, of a CoreSiMMap can be regarded as a “hot spot” that represents the conserved binding environments involved in biological functions. Here, we derive the CoreSiMMap with six consensus anchors and identify six inhibitors (IC50<8.0 µM) of shikimate kinases (SKs) of Mycobacterium tuberculosis and Helicobacter pylori from the NCI database (236,962 compounds). Studies of site-directed mutagenesis and analogues reveal that these conserved interacting residues and moieties contribute to pocket-moiety interaction spots and biological functions. These results reveal that our multi-target screening strategy and the CoreSiMMap can increase the accuracy of screening in the identification of novel inhibitors and subsite-moiety environments for elucidating the binding mechanisms of targets

The publication of ethically uncertain research: attitudes and practices of journal editors

<p>Abstract</p> <p>Background</p> <p>Publication of ethically uncertain research occurs despite well-published guidelines set forth in documents such as the Declaration of Helsinki. Such guidelines exist to aide editorial staff in making decisions regarding ethical acceptability of manuscripts submitted for publication, yet examples of ethically suspect and uncertain publication exist. Our objective was to survey journal editors regarding practices and attitudes surrounding such dilemmas.</p> <p>Methods</p> <p>The Editor-in-chief of each of the 103 English-language journals from the 2005 Abridged Index Medicus list publishing original research were asked to complete a survey sent to them by email between September-December 2007.</p> <p>Results</p> <p>A response rate of 33% (n = 34) was obtained from the survey. 18% (n = 6) of respondents had published ethically uncertain or suspect research within the last 10 years. 85% (n = 29) of respondents stated they would always reject ethically uncertain articles submitted for publication on ethical grounds alone. 12% (n = 4) of respondents stated they would approach each submission on a case-by-case basis. 3% (n = 1) stated they would be likely to publish such research, but only with accompanying editorial. Only 38% (n = 13) give reviewers explicit instruction to reject submissions on ethical grounds if found wanting.</p> <p>Conclusions</p> <p>Editorial compliance with the Declaration of Helsinki in rejecting research that is conducted unethically was difficult to ascertain because of a poor response rate despite multiple attempts using different modalities. Of those who did respond, the majority do reject ethically suspect research but few explicitly advise reviewers to do so. In this study editors did not take advantage of the opportunity to describe their support for the rejection of the publication of unethical research.</p

Impact Factor: outdated artefact or stepping-stone to journal certification?

A review of Garfield's journal impact factor and its specific implementation as the Thomson Reuters Impact Factor reveals several weaknesses in this commonly-used indicator of journal standing. Key limitations include the mismatch between citing and cited documents, the deceptive display of three decimals that belies the real precision, and the absence of confidence intervals. These are minor issues that are easily amended and should be corrected, but more substantive improvements are needed. There are indications that the scientific community seeks and needs better certification of journal procedures to improve the quality of published science. Comprehensive certification of editorial and review procedures could help ensure adequate procedures to detect duplicate and fraudulent submissions.Comment: 25 pages, 12 figures, 6 table

The use of phylogeny to interpret cross-cultural patterns in plant use and guide medicinal plant discovery: an example from Pterocarpus (Leguminosae)

The study of traditional knowledge of medicinal plants has led to discoveries that have helped combat diseases and improve healthcare. However, the development of quantitative measures that can assist our quest for new medicinal plants has not greatly advanced in recent years. Phylogenetic tools have entered many scientific fields in the last two decades to provide explanatory power, but have been overlooked in ethnomedicinal studies. Several studies show that medicinal properties are not randomly distributed in plant phylogenies, suggesting that phylogeny shapes ethnobotanical use. Nevertheless, empirical studies that explicitly combine ethnobotanical and phylogenetic information are scarce.In this study, we borrowed tools from community ecology phylogenetics to quantify significance of phylogenetic signal in medicinal properties in plants and identify nodes on phylogenies with high bioscreening potential. To do this, we produced an ethnomedicinal review from extensive literature research and a multi-locus phylogenetic hypothesis for the pantropical genus Pterocarpus (Leguminosae: Papilionoideae). We demonstrate that species used to treat a certain conditions, such as malaria, are significantly phylogenetically clumped and we highlight nodes in the phylogeny that are significantly overabundant in species used to treat certain conditions. These cross-cultural patterns in ethnomedicinal usage in Pterocarpus are interpreted in the light of phylogenetic relationships.This study provides techniques that enable the application of phylogenies in bioscreening, but also sheds light on the processes that shape cross-cultural ethnomedicinal patterns. This community phylogenetic approach demonstrates that similar ethnobotanical uses can arise in parallel in different areas where related plants are available. With a vast amount of ethnomedicinal and phylogenetic information available, we predict that this field, after further refinement of the techniques, will expand into similar research areas, such as pest management or the search for bioactive plant-based compounds

Pharmacokinetic Modeling of an Induction Regimen for In Vivo Combined Testing of Novel Drugs against Pediatric Acute Lymphoblastic Leukemia Xenografts

Current regimens for induction therapy of pediatric acute lymphoblastic leukemia (ALL), or for re-induction post relapse, use a combination of vincristine (VCR), a glucocorticoid, and l-asparaginase (ASP) with or without an anthracycline. With cure rates now approximately 80%, robust pre-clinical models are necessary to prioritize active new drugs for clinical trials in relapsed/refractory patients, and the ability of these models to predict synergy/antagonism with established therapy is an essential attribute. In this study, we report optimization of an induction-type regimen by combining VCR, dexamethasone (DEX) and ASP (VXL) against ALL xenograft models established from patient biopsies in immune-deficient mice. We demonstrate that the VXL combination was synergistic in vitro against leukemia cell lines as well as in vivo against ALL xenografts. In vivo, VXL treatment caused delays in progression of individual xenografts ranging from 22 to >146 days. The median progression delay of xenografts derived from long-term surviving patients was 2-fold greater than that of xenografts derived from patients who died of their disease. Pharmacokinetic analysis revealed that systemic DEX exposure in mice increased 2-fold when administered in combination with VCR and ASP, consistent with clinical findings, which may contribute to the observed synergy between the 3 drugs. Finally, as proof-of-principle we tested the in vivo efficacy of combining VXL with either the Bcl-2/Bcl-xL/Bcl-w inhibitor, ABT-737, or arsenic trioxide to provide evidence of a robust in vivo platform to prioritize new drugs for clinical trials in children with relapsed/refractory ALL