Classification of Possible Finite-Time Singularities by Functional Renormalization

Starting from a representation of the early time evolution of a dynamical system in terms of the polynomial expression of some observable f (t) as a function of the time variable in some interval 0 < t < T, we investigate how to extrapolate/forecast in some optimal stability sense the future evolution of f(t) for time t>T. Using the functional renormalization of Yukalov and Gluzman, we offer a general classification of the possible regimes that can be defined based on the sole knowledge of the coefficients of a second-order polynomial representation of the dynamics. In particular, we investigate the conditions for the occurence of finite-time singularities from the structure of the time series, and quantify the critical time and the functional nature of the singularity when present. We also describe the regimes when a smooth extremum replaces the singularity and determine its position and amplitude. This extends previous works by (1) quantifying the stability of the functional renormalization method more accurately, (2) introducing new global constraints in terms of moments and (3) going beyond the ``mean-field'' approximation.Comment: Latex document of 18 pages + 7 ps figure

Wave-driven inner-shelf motions on the Oregon coast

Author Posting. © American Meteorological Society, 2009. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 39 (2009): 2942-2956, doi:10.1175/2009JPO4041.1.Recent work by S. Lentz et al. documents offshore transport in the inner shelf due to a wave-driven return flow associated with the Hasselmann wave stress (the Stokes–Coriolis force). This analysis is extended using observations from the central Oregon coast to identify the wave-driven return flow present and quantify the potential bias of wind-driven across-shelf exchange by unresolved wave-driven circulation. Using acoustic Doppler current profiler (ADCP) measurements at six stations, each in water depths of 13–15 m, observed depth-averaged, across-shelf velocities were generally correlated with theoretical estimates of the proposed return flow. During times of minimal wind forcing, across-shelf velocity profiles were vertically sheared, with stronger velocities near the top of the measured portion of the water column, and increased in magnitude with increasing significant wave height, consistent with circulation due to the Hasselmann wave stress. Yet velocity magnitudes and vertical shears were stronger than that predicted by linear wave theory, and more similar to the stratified “summer” velocity profiles described by S. Lentz et al. Additionally, substantial temporal and spatial variability of the wave-driven return flow was found, potentially due to changing wind and wave conditions as well as local bathymetric variability. Despite the wave-driven circulation found, subtracting estimates of the return flow from the observed across-shelf velocity had no significant effect on estimates of the across-shelf exchange due to along-shelf wind forcing at these water depths along the Oregon coast during summer.This work was performed with the Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO), funded primarily by the Gordon and Betty Moore Foundation and David and Lucile Packard Foundation. SL acknowledges support from NSF Ocean Science Grant #OCE-0548961. AK acknowledges support from the WHOI Coastal Ocean Institute Fellowship

Genome analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared t

Performance assessment of the database downscaled ocean waves (DOW) on Santa Catarina coast, South Brazil

ABSTRACT: This work presents a validation of wave parameters from the new sixty years Downscaled Ocean Waves (DOW) reanalysis database. This study compares quantiles of the Gumbel distribution of Hs (significant wave height) and Tp (peak period) from simulated data with an 11 months' time series obtained from a buoy moored seaward on the Santa Catarina coast. Analysis by means of Gumbel distribution quantiles allows more weight to be given to the highest values of the time series, which are especially important in design projects. The statistical parameters used to verify the fit between the measured and the modeled data included: RMSE, BIAS, Scatter Index and Pearson Correlation Coefficient. Mean direction (9m) validation was conducted qualitatively. The database showed good fit of the mean conditions, especially Hs which was well Reproduced by the wave model. Underestimation of Tp, related mainly to the low spatial and temporal resolution of wind data used to generate waves, highlights this general modeling problem. Based on calculated statistical parameters, DOW data were considered comparable to the values obtained by measurements; however, such data must be cautiously used for extreme events analysis and in areas of bimodal sea conditions, where major deficiencies in the database were observed.The authors are also thankful to the Brazilian government through the Ministério do Meio Ambiente (MMA) and the Agência Brasileira de Cooperação (ABC) for the financial support of this research (within the project Transference of Methodologies and Tools to Support the Brazilian Coastal Management)

How are podocytes affected in nail–patella syndrome?

Nail–patella syndrome is an autosomal-dominant hereditary disease named for dysplastic fingernails and toenails and hypoplastic or absent kneecaps evident in patients with the syndrome. Prognosis is determined by the nephropathy that develops in many such patients. Besides podocyte foot-process effacement, pathognomonic changes in the kidney comprise electron-lucent areas and fibrillar inclusions in the glomerular basement membrane. These characteristic symptoms are caused by mutations in the gene encoding the transcription factor LMX1B, a member of the LIM-homeodomain gene family. Comparable with the human syndrome, homozygous Lmx1b knockout mice lack patellae and suffer from severe podocyte damage. In contrast, however, podocin and the α3 and α4 chains of collagen IV are absent in the glomeruli of Lmx1b knockout mice. Further studies with podocyte-specific Lmx1b knockout mice have confirmed the importance of LMX1B in podocytes, as these mice apparently develop foot processes initially but lose them later on. We therefore conclude that LMX1B is essential for the development of metanephric precursor cells into podocytes and possibly also for maintaining the differentiation status of podocytes. LMX1B can serve as a model system to elucidate a genetic program in podocytes

Validation of T-Track® CMV to assess the functionality of cytomegalovirus-reactive cell-mediated immunity in hemodialysis patients

Background: Uncontrolled cytomegalovirus (CMV) replication in immunocompromised solid-organ transplant recipients is a clinically relevant issue and an indication of impaired CMV-specific cell-mediated immunity (CMI). Primary aim of this study was to assess the suitability of the immune monitoring tool T-Track (R) CMV to determine CMV-reactive CMI in a cohort of hemodialysis patients representative of patients eligible for renal transplantation. Positive and negative agreement of T-Track (R) CMV with CMV serology was examined in 124 hemodialysis patients, of whom 67 (54%) revealed a positive CMV serostatus. Secondary aim of the study was to evaluate T-Track (R) CMV performance against two unrelated CMV-specific CMI monitoring assays, QuantiFERON (R)-CMV and a cocktail of six class I iTAg (TM) MHC Tetramers. Results: Positive T-Track (R) CMV results were obtained in 90% (60/67) of CMV-seropositive hemodialysis patients. In comparison, 73% (45/62) and 77% (40/52) positive agreement with CMV serology was achieved using QuantiFERON (R)-CMV and iTAg (TM) MHC Tetramer. Positive T-Track (R) CMV responses in CMV-seropositive patients were dominated by pp65-reactive cells (58/67 [ 87%]), while IE-1-responsive cells contributed to an improved (87% to 90%) positive agreement of T-Track (R) CMV with CMV serology. Interestingly, T-Track (R) CMV, QuantiFERON (R)-CMV and iTAg (TM) MHC Tetramers showed 79% (45/57), 87% (48/55) and 93% (42/45) negative agreement with serology, respectively, and a strong inter-assay variability. Notably, T-Track (R) CMV was able to detect IE-1-reactive cells in blood samples of patients with a negative CMV serology, suggesting either a previous exposure to CMV that yielded a cellular but no humoral immune response, or TCR cross-reactivity with foreign antigens, both suggesting a possible protective immunity against CMV in these patients. Conclusion: T-Track (R) CMV is a highly sensitive assay, enabling the functional assessment of CMV-responsive cells in hemodialysis patients prior to renal transplantation. T-Track (R) CMV thus represents a valuable immune monitoring tool to identify candidate transplant recipients potentially at increased risk for CMV-related clinical complications

Overshadowing depends on cue and reinforcement sensitivity but not schizotypy

There is evidence for impaired selective learning mechanisms in individuals high in schizotypy. Overshadowing provides a direct test of selective learning based on cue salience and has previously been reported to be impaired in relation to schizotypy scores. The present study tested for overshadowing using food allergy and Lego construction task variants. Both variants used the same number of conditioned stimulus (CS) cues and the same number of learning trials. CS cues were trained in compound pairs or in isolation and overshadowing was subsequently tested on trials followed by negative versus positive outcomes. Participants also completed the O-LIFE to measure schizotypy and BIS-BAS scales to measure reinforcement sensitivity. Learning was demonstrated for both cue variants; however overshadowing emerged only in the Lego variant and only on the trials followed by the negative outcome. Contrary to expectations, there was no evidence for any relationship between overshadowing and O-LIFE scores. However, there was evidence of a positive relationship between overshadowing and BAS-Drive as well as a negative relationship with BIS-Anxiety, for the trials followed by the positive outcome in the food allergy variant. These results suggest that the development of overshadowing depends on cue and reinforcement sensitivity, but not necessarily on schizotypy

FRA2 is a STAT5 target gene regulated by IL-2 in human CD4 T cells

Signal transducers and activators of transcription 5(STAT5) are cytokine induced signaling proteins, which regulate key immunological processes, such as tolerance induction, maintenance of homeostasis, and CD4 T-effector cell differentiation. In this study, transcriptional targets of STAT5 in CD4 T cells were studied by Chromatin Immunoprecipitation (ChIP). Genomic mapping of the sites cloned and identified in this study revealed the striking observation that the majority of STAT5-binding sites mapped to intergenic (>50 kb upstream) or intronic, rather than promoter proximal regions. Of the 105 STAT5 responsive binding sites identified, 94% contained the canonical (IFN-γ activation site) GAS motifs. A number of putative target genes identified here are associated with tumor biology. Here, we identified Fos-related antigen 2 (FRA2) as a transcriptional target of IL-2 regulated STAT5. FRA2 is a basic -leucine zipper (bZIP) motif 'Fos' family transcription factor that is part of the AP-1 transcription factor complex and is also known to play a critical role in the progression of human tumours and more recently as a determinant of T cell plasticity. The binding site mapped to an internal intron within the FRA2 gene. The epigenetic architecture of FRA2, characterizes a transcriptionally active promoter as indicated by enrichment for histone methylation marks H3K4me1, H3K4me2, H3K4me3, and transcription/elongation associated marks H2BK5me1 and H4K20me1. FRA2 is regulated by IL-2 in activated CD4 T cells. Consistently, STAT5 bound to GAS sequence in the internal intron of FRA2 and reporter gene assays confirmed IL-2 induced STAT5 binding and transcriptional activation. Furthermore, addition of JAK3 inhibitor (R333) or Daclizumab inhibited the induction in TCR stimulated cells. Taken together, our data suggest that FRA2 is a novel STAT5 target gene, regulated by IL-2 in activated CD4 T cells

Drift and mixing under the ocean surface : a coherent one-dimensional description with application to unstratified conditions

Author Posting. © American Geophysical Union, 2006. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 111 (2006): C03016, doi:10.1029/2005JC003004.Waves have many effects on near-surface dynamics: Breaking waves enhance mixing, waves are associated with a Lagrangian mean drift (the Stokes drift), waves act on the mean flow by creating Langmuir circulations and a return flow opposite to the Stokes drift, and, last but not least, waves modify the atmospheric surface roughness. A realistic ocean model is proposed to embrace all these aspects, focusing on near-surface mixing and surface drift associated with the wind and generated waves. The model is based on the generalized Lagrangian mean that separates the momentum into a wave pseudomomentum and a quasi-Eulerian momentum. A wave spectrum with a reasonably high frequency range is used to compute the Stokes drift. A turbulent closure scheme based on a single evolution equation for the turbulent kinetic energy includes the mixing due to breaking wave effects and wave-turbulence interactions. The roughness length of the closure scheme is adjusted using observations of turbulent kinetic energy near the surface. The model is applied to unstratified and horizontally uniform conditions, showing good agreement with observations of strongly mixed quasi-Eulerian currents near the surface when waves are developed. Model results suggest that a strong surface shear persists in the drift current because of the Stokes drift contribution. In the present model the surface drift only reaches 1.5% of the wind speed. It is argued that stratification and the properties of drifting objects may lead to a supplementary drift as large as 1% of the wind speed