Aircraft measurements of microphysical properties of subvisible cirrus in the tropical tropopause layer

International audienceSubvisible cirrus (SVC) clouds are often observed within the tropical tropopause layer (TTL). Some studies suggest that SVC has a significant impact on the earth radiation budget. The Costa Rica Aura Validation Experiment (CR-AVE) sponsored by the National Aeronautics and Space Administration (NASA) took place near San Jose, Costa Rica from 14 January?15 February 2006. The NASA WB-57F sampled SVC in the TTL from ?75°C to ?90°C with an improved set of cloud particle probes. The first digital images of ice particles in the TTL are compared with replicator images of ice particles collected in 1973 by a WB-57F in the TTL. The newer measurements reveal larger particles, on the order of 100 ?m compared with <50 ?m from the earlier measurements, and also different particle shapes. The 1973 particles were mainly columnar and trigonal, whereas the newer measurements are quasi-spherical and hexagonal plates. The WB-57F also measured very high water vapor contents with some instruments, up to 4 ppmv, and aerosols with mixed organics and sulfates. It is unknown whether these ambient conditions were present in the 1973 studies, and whether such conditions have an influence on particle shape and the development of the large particles. A companion paper (Jensen et al., 2008) presents crystal growth calculations that suggest that the high water vapor measurements are required to grow ice particles to the observed sizes of 100 ?m and larger

Nailfold Videocapillaroscopic Features and Other Clinical Risk Factors for Digital Ulcers in Systemic Sclerosis: A Multicenter, Prospective Cohort Study

OBJECTIVE: To identify nailfold videocapillaroscopic and other clinical risk factors for new digital ulcers (DUs) in a 6-month period in patients with systemic sclerosis (SSc), the videoCAPillaroscopy (CAP) study. METHODS: Overall 623 patients with SSc from 59 centers (14 countries) were stratified into two groups: "DU History" and "No-DU History". At enrollment, patients underwent detailed nailfold videocapillaroscopic evaluation and an assessment of demographics, DU status, and clinical and SSc characteristics. Risk factors for developing new DUs were assessed using univariable and multivariable logistic regression analyses. RESULTS: Of the "DU History" group (n = 468), 79.5% were female, the mean age was 54.0 ± 13.7 years, 59.8% had limited cutaneous SSc, and 22% developed a new DU during follow-up. The strongest risk factors for new DUs identified by multivariable logistic regression (MLR) in the "DU History" group included: mean number of capillaries/mm in the middle finger of the dominant hand, number of DUs (0, 1, 2, ≥3), and presence of critical digital ischemia. The receiver operating characteristic area under the curve (ROC-AUC) (95% confidence interval [CI]) of the final MLR model was 0.738 (0.681-0.795). Internal validation through bootstrap generated a ROC-AUC (95% CI) of 0.633 (0.510-0.756). CONCLUSION: This international, prospective study including detailed nailfold videocapillaroscopic evaluation and extensive clinical characterization of patients with SSc identified the mean number of capillaries/mm in the middle finger of the dominant hand, number of DUs and presence of critical digital ischemia at enrollment as risk factors for the development of new DUs. This article is protected by copyright. All rights reserved

Formation of large (?100 ?m) ice crystals near the tropical tropopause

International audienceRecent high-altitude aircraft measurements with in situ imaging instruments indicated the presence of relatively large (?100 ?m length), thin (aspect ratios of ?6:1 or larger) hexagonal plate ice crystals near the tropical tropopause in very low concentrations (?1). These crystals were not produced by deep convection or aggregation. We use simple growth-sedimentation calculations as well as detailed cloud simulations to evaluate the conditions required to grow the large crystals. Uncertainties in crystal aspect ratio leave a range of possibilities, which could be constrained by knowledge of the water vapor concentration in the air where the crystal growth occurred. Unfortunately, water vapor measurements made in the cloud formation region near the tropopause with different instruments ranged from 3 ppmv). On the other hand, if the crystal aspect ratios are quite a bit larger (?10:1), then H2O concentrations toward the low end of the measurement range (?2?2.5 ppmv) would suffice to grow the large crystals. Gravity-wave driven temperature and vertical wind perturbations only slightly modify the H2O concentrations needed to grow the crystals. We find that it would not be possible to grow the large crystals with water concentrations less than 2 ppmv, even with assumptions of a very high aspect ratio of 15 and steady upward motion of 2 cm s?1 to loft the crystals in the tropopause region. These calculations would seem to imply that the measurements indicating water vapor concentrations less than 2 ppmv are implausible, but we cannot rule out the possibility that higher humidity prevailed upstream of the aircraft measurements and the air was dehydrated by the cloud formation. Simulations of the cloud formation with a detailed model indicate that homogeneous freezing should generate ice concentrations larger than the observed concencentrations (20 L?1), and even concentrations as low as 20 L?1 should have depleted the vapor in excess of saturation and prevented growth of large crystals. It seems likely that the large crystals resulted from ice nucleation on effective heterogeneous nuclei at low ice supersaturations. Improvements in our understanding of detailed cloud microphysical processes require resolution of the water vapor measurement discrepancies in these very cold, dry regions of the atmosphere

Genomic and Proteomic Analyses of the Fungus Arthrobotrys oligospora Provide Insights into Nematode-Trap Formation

Nematode-trapping fungi are “carnivorous” and attack their hosts using specialized trapping devices. The morphological development of these traps is the key indicator of their switch from saprophytic to predacious lifestyles. Here, the genome of the nematode-trapping fungus Arthrobotrys oligospora Fres. (ATCC24927) was reported. The genome contains 40.07 Mb assembled sequence with 11,479 predicted genes. Comparative analysis showed that A. oligospora shared many more genes with pathogenic fungi than with non-pathogenic fungi. Specifically, compared to several sequenced ascomycete fungi, the A. oligospora genome has a larger number of pathogenicity-related genes in the subtilisin, cellulase, cellobiohydrolase, and pectinesterase gene families. Searching against the pathogen-host interaction gene database identified 398 homologous genes involved in pathogenicity in other fungi. The analysis of repetitive sequences provided evidence for repeat-induced point mutations in A. oligospora. Proteomic and quantitative PCR (qPCR) analyses revealed that 90 genes were significantly up-regulated at the early stage of trap-formation by nematode extracts and most of these genes were involved in translation, amino acid metabolism, carbohydrate metabolism, cell wall and membrane biogenesis. Based on the combined genomic, proteomic and qPCR data, a model for the formation of nematode trapping device in this fungus was proposed. In this model, multiple fungal signal transduction pathways are activated by its nematode prey to further regulate downstream genes associated with diverse cellular processes such as energy metabolism, biosynthesis of the cell wall and adhesive proteins, cell division, glycerol accumulation and peroxisome biogenesis. This study will facilitate the identification of pathogenicity-related genes and provide a broad foundation for understanding the molecular and evolutionary mechanisms underlying fungi-nematodes interactions

Pharmacokinetic-Pharmacodynamic Modeling in Pediatric Drug Development, and the Importance of Standardized Scaling of Clearance.

Pharmacokinetic/pharmacodynamic (PKPD) modeling is important in the design and conduct of clinical pharmacology research in children. During drug development, PKPD modeling and simulation should underpin rational trial design and facilitate extrapolation to investigate efficacy and safety. The application of PKPD modeling to optimize dosing recommendations and therapeutic drug monitoring is also increasing, and PKPD model-based dose individualization will become a core feature of personalized medicine. Following extensive progress on pediatric PK modeling, a greater emphasis now needs to be placed on PD modeling to understand age-related changes in drug effects. This paper discusses the principles of PKPD modeling in the context of pediatric drug development, summarizing how important PK parameters, such as clearance (CL), are scaled with size and age, and highlights a standardized method for CL scaling in children. One standard scaling method would facilitate comparison of PK parameters across multiple studies, thus increasing the utility of existing PK models and facilitating optimal design of new studies

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field