bluuebunny/crossref_metadata_2025 huggingface dataset:
Encoding and Decoding Spikes for Dynamic Stimuli
Authors: Natarajan Rama , Huys Quentin J. M. , Dayan Peter , Zemel Richard S.
Published: April 2008

Naturally occurring sensory stimuli are dynamic. In this letter, we consider how spiking neural populations might transmit information about continuous dynamic stimulus variables. The combination of simple encoders and temporal stimulus correlations leads to a code in which information is not readily available to downstream neurons. Here, we explore a complex encoder that is paired with a simple decoder that allows representation and manipulation of the dynamic information in neural systems. The encoder we present takes the form of a biologically plausible recurrent spiking neural network where the output population recodes its inputs to produce spikes that are independently decodeable. We show that this network can be learned in a supervised manner by a simple local learning rule.
Simultaneous Approximations of Polynomials and Derivatives and Their Applications to Neural Networks
Authors: Ito Yoshifusa
Published: April 2008

We have constructed one-hidden-layer neural networks capable of approximating polynomials and their derivatives simultaneously. Generally, optimizing neural network parameters to be trained at later steps of the BP training is more difficult than optimizing those to be trained at the first step. Taking into account this fact, we suppressed the number of parameters of the former type. We measure degree of approximation in both the uniform norm on compact sets and the Lp-norm on the whole space with respect to probability measures.
Understanding Parkinsonian Handwriting Through a Computational Model of Basal Ganglia
Authors: Gangadhar Garipelli , Joseph Denny , Chakravarthy V. Srinivasa
Published: April 2008

Handwriting in Parkinson's disease (PD) is typically characterized by micrographia, jagged line contour, and unusual fluctuations in pen tip velocity. Although PD handwriting features have been used for diagnostics, they are not based on a signaling model of basal ganglia (BG). In this letter, we present a computational model of handwriting generation that highlights the role of BG. When PD conditions like reduced dopamine and altered dynamics of the subthalamic nucleus and globus pallidus externa subsystems are simulated, the handwriting produced by the model manifested characteristic PD handwriting distortions like micrographia and velocity fluctuations. Our approach to PD modeling is in tune with the perspective that PD is a dynamic disease.
Normalization Enables Robust Validation of Disparity Estimates from Neural Populations
Authors: Tsang Eric K. C. , Shi Bertram E.
Published: April 2008

Binocular fusion takes place over a limited region smaller than one degree of visual angle (Panum's fusional area), which is on the order of the range of preferred disparities measured in populations of disparity-tuned neurons in the visual cortex. However, the actual range of binocular disparities encountered in natural scenes extends over tens of degrees. This discrepancy suggests that there must be a mechanism for detecting whether the stimulus disparity is inside or outside the range of the preferred disparities in the population. Here, we compare the efficacy of several features derived from the population responses of phase-tuned disparity energy neurons in differentiating between in-range and out-of-range disparities. Interestingly, some features that might be appealing at first glance, such as the average activation across the population and the difference between the peak and average responses, actually perform poorly. On the other hand, normalizing the difference between the peak and average responses results in a reliable indicator. Using a probabilistic model of the population responses, we improve classification accuracy by combining multiple features. A decision rule that combines the normalized peak to average difference and the peak location significantly improves performance over decision rules based on either measure in isolation. In addition, classifiers using normalized difference are also robust to mismatch between the image statistics assumed by the model and the actual image statistics.
Modified RAMS-Urban Canopy Model for Heat Island Simulation in Chongqing, China
Authors: Zhang Hongbin , Sato Naoki , Izumi Takeki , Hanaki Keisuke , Aramaki Toshiya
Published: April 2008

A single-layer urban canopy model was integrated into a nonhydrostatic meteorological model, the Regional Atmospheric Modeling System (RAMS). In the new model, called RAMS-Urban Canopy (RAMS-UC), anthropogenic heat emission was also considered. The model can be used to calculate radiation, heat, and water fluxes in an urban area, considering the geometric structure and thermodynamic characteristics of the urban canopy. The urban canopy was represented by normalized street canyons of infinite length, which were bordered by buildings on both sides. The urban region was covered by three types of surfaces: roof, wall, and road. Anthropogenic heat was emitted from these surfaces. Sensitivity tests between the original RAMS and the modified one were carried out by simulating the urban heat island (UHI) of Chongqing, located in an inland mountainous region in China. The results of the model were also compared with the observational data. It was found that the original model could not accurately simulate the UHI, in particular at night, whereas the accuracy was significantly improved in the RAMS-UC. The improvement is substantial even when anthropogenic heat emission is set to zero.
Impact of Domain Size on Modeled Ozone Forecast for the Northeastern United States
Authors: Lee Pius , Kang Daiwen , McQueen Jeff , Tsidulko Marina , Hart Mary , DiMego Geoff , Seaman Nelson , Davidson Paula
Published: April 2008

This study investigates the impact of model domain extent and the specification of lateral boundary conditions on the forecast quality of air pollution constituents in a specific region of interest. A developmental version of the national Air Quality Forecast System (AQFS) has been used in this study. The AQFS is based on the NWS/NCEP Eta Model (recently renamed the North American Mesoscale Model) coupled with the U.S. Environmental Protection Agency Community Multiscale Air Quality (CMAQ) model. This coupled Eta–CMAQ modeling system provided experimental air quality forecasts for the northeastern region of the United States during the summers of 2003 and 2004. The initial forecast over the northeastern United States was approved for operational deployment in September 2004. The AQFS will provide forecast coverage for the entire United States in the near future. In a continuing program of phased development to extend the geographical coverage of the forecast, the developmental version of AQFS has undergone two domain expansions. Hereinafter, this “developmental” domain-expanded forecast system AQFS will be dubbed AQFS-β. The current study evaluates the performance of AQFS-β for the northeastern United States using three domain sizes. Quantitative comparisons of forecast results with compiled observation data from the U.S. Aerometric Information Retrieval Now (AIRNOW) network were performed for each model domain, and interdomain comparisons were made for the regions of overlap. Several forecast skill score measures have been employed. Based on the categorical statistical metric of the critical success index, the largest domain achieved the highest skill score. This conclusion should catapult the implementation of the largest domain to attain the best forecast performance whenever the operational resource and criteria permit.
Mesoscale Boundary Layer and Heat Flux Variations over Pack Ice–Covered Lake Erie
Authors: Gerbush Mathieu R. , Kristovich David A. R. , Laird Neil F.
Published: April 2008

The development of extensive pack ice fields on the Great Lakes significantly influences lake-effect storms and local airmass modification, as well as the regional hydrologic cycle and lake water levels. The evolution of the ice fields and their impacts on the atmospheric boundary layer complicates weather forecasters’ ability to accurately predict late-season lake-effect snows. The Great Lakes Ice Cover–Atmospheric Flux (GLICAF) experiment was conducted over Lake Erie during February 2004 to investigate the surface–atmosphere exchanges that occur over midlatitude ice-covered lakes. GLICAF observations taken by the University of Wyoming King Air on 26 February 2004 show a strong mesoscale thermal link between the lake surface and the overlying atmospheric boundary layer. Mesoscale atmospheric variations that developed over the lake in turn influenced heat exchanges with the surface. Boundary layer sensible and latent heat fluxes exhibited different relationships to variations in surface pack ice concentration. Turbulent sensible heat fluxes decreased nonlinearly with increases in underlying lake-surface ice concentration such that the largest decreases occurred when ice concentrations were greater than 70%. Latent heat fluxes tended to decrease linearly with increasing ice concentration and had a reduced correlation. Most current operational numerical weather prediction models use simple algorithms to represent the influence of heterogeneous ice cover on heat and moisture fluxes. The GLICAF findings from 26 February 2004 suggest that some currently used and planned approaches in numerical weather prediction models may significantly underestimate sensible heat fluxes in regions of high-concentration ice cover, leading to underpredictions of the local modification of air masses and lake-effect snows.
Finescale Diurnal Rainfall Statistics Refined from Eight Years of TRMM PR Data
Authors: Hirose Masafumi , Oki Riko , Shimizu Shuji , Kachi Misako , Higashiuwatoko Tomohiko
Published: April 2008

The adequacy of hourly rainfall sampling was examined in terms of the detection of diurnal variations using 8 yr (1998–2005) of data observed by the precipitation radar on the Tropical Rainfall Measuring Mission (TRMM) satellite. It was found that the monthly and hourly rain samples for each 0.2° grid point over the 8-yr period are composed of multiple precipitation systems. In this study, a “3-h-significant diurnal peak” was defined as the time of maximum rainfall with consecutive positive anomalies for more than 3 h. The fraction of the analyzed area with a 3-h-significant diurnal peak increased annually and accounted for 43% of the total global tropics at 0.2° resolution over the 8-yr period. The diurnal signature over Tibet and the Amazon showed a high degree of spatial uniformity (at >10° scale). The degree of similarity and locations of the regional diurnal characteristics are described in terms of seasonal variations and at multiple resolutions based on spatial uniformity. For example, uniform early-afternoon peaks generally appear over the coastal land and areas of high relief, whereas a seasonally invariant early-afternoon peak over the low-lying Amazon basin is recognized as a regional characteristic. In areas of coastal ocean, early-morning peaks appear in certain regions such as the area surrounding the so-called Maritime Continent and the area off the west coast of Mexico. These peaks are distinct from the global characteristics of late-morning rainfall maxima recorded over most coastal oceans and early-morning peaks recorded over open ocean. The results are also compared with those derived from TRMM Microwave Imager (TMI) data. In addition to obtaining a coherent signal, regional differences in the timing of maximum rainfall over the Tibetan Plateau were addressed; this discrepancy is attributed to limitations of the scattering algorithm used for TMI data in terms of detecting shallow convection and screening cold surfaces.
The Berry and Reinhardt Autoconversion Parameterization: A Digest
Authors: Gilmore Matthew S. , Straka Jerry M.
Published: April 2008

The simplified version of the Berry and Reinhardt parameterization used for initiating rain from cloud droplets is presented and is compared with 12 other versions of itself from the literature. Many of the versions that appear to be different from each other can be brought into agreement with the original parameterization by making the same assumptions: a mean diameter based upon mass or volume and distribution shape parameters chosen to give the same cloud mass relative variance as the original Berry and Reinhardt parameterization. However, there are differences in how authors have chosen to parameterize the cloud number concentration sink and rain number concentration source, and those choices, along with model limitations, have important impacts on rain development within the scheme. These differences among versions are shown to have important time-integrated feedbacks upon the developing initial rain distribution. Three of 12 implementations of the bulk scheme are shown to be able to reproduce the original Berry and Reinhardt bin-model solutions very well, and about 6 of 12 do poorly.
Statistical Characteristics of Raindrop Size Distribution in Southwest Monsoon Season
Authors: Kirankumar N. V. P. , Rao T. Narayana , Radhakrishna B. , Rao D. Narayana
Published: April 2008

Raindrop size distribution (DSD) parameters are retrieved from dual-frequency (UHF and VHF) wind profiler measurements made at Gadanki, India, in a summer monsoon season. The convoluted UHF spectra are first corrected for vertical air motion and spectral broadening (using VHF measurements) and later are used for deriving DSD parameters. Two distinctly different case studies, a mesoscale convective system and a pure stratiform precipitation system, have been considered for a detailed study. DSD parameters obtained in these case studies reveal systematic variations of DSD from case to case and also from one rain regime to another within the same precipitating system. A statistical study has been carried out using the profiler data collected during the passage of 16 rain events. The retrieved DSD profiles are divided into separate rain regimes (stratiform and convection), based on reflectivity, to examine salient microphysical characteristics and the vertical variability of DSD in different precipitation regimes. The distribution of DSD parameters is, in general, wider in the convective rain regime than in the stratiform regime, particularly below 2.4 km. The vertical variation of the gamma parameter distribution in the stratiform rain regime is minimal, indicating that the microphysical processes (growth and decay), which alter the rain DSD, may be in equilibrium. On the other hand, the distribution in the convective rain regime appears to be more complex, with the mean profile of the shape parameter varying significantly with height. The observed vertical variability of the gamma parameters and the median volume diameter in the convective rain regime is attributed to two major microphysical processes: evaporation and breakup. The role of other processes, like drop sorting and collision–coalescence, in altering the DSD parameters is also discussed. The present statistics, representing continental monsoon rainfall, are compared with the existing statistics at Darwin, Australia, and the results are discussed in light of DSD differences in oceanic and continental monsoon precipitation.
Comparison of Hurricane Return Levels Using Historical and Geological Records
Authors: Elsner James B. , Jagger Thomas H. , Liu Kam-biu
Published: April 2008

Hurricane return levels estimated using historical and geological information are quantitatively compared for Lake Shelby, Alabama. The minimum return level of overwash events recorded in sediment cores is estimated using a modern analog (Hurricane Ivan of 2004) to be 54 m s−1 (105 kt) for a return period of 318 yr based on 11 events over 3500 yr. The expected return level of rare hurricanes in the observed records (1851–2005) at this location and for this return period is estimated using a parametric statistical model and a maximum likelihood procedure to be 73 m s−1 (141 kt), with a lower bound on the 95% confidence interval of 64 m s−1 (124 kt). Results are not significantly different if data are taken from the shorter 1880–2005 period. Thus, the estimated sensitivity of Lake Shelby to overwash events is consistent with the historical record given the model. In fact, assuming the past is similar to the present, the sensitivity of the site to overwash events as estimated from the model is likely more accurately set at 64 m s−1.
Spectral Retrieval of Latent Heating Profiles from TRMM PR Data. Part III: Estimating Apparent Moisture Sink Profiles over Tropical Oceans
Authors: Shige Shoichi , Takayabu Yukari N. , Tao Wei-Kuo
Published: April 2008

The spectral latent heating (SLH) algorithm was developed to estimate apparent heat source (Q1) profiles for the Tropical Rainfall Measuring Mission (TRMM) precipitation radar (PR) in Parts I and II of this study. In this paper, the SLH algorithm is used to estimate apparent moisture sink (Q2) profiles. The procedure of Q2 retrieval is the same as that of heating retrieval except for using the Q2 profile lookup tables derived from numerical simulations of tropical cloud systems from the Tropical Ocean and Global Atmosphere (TOGA) Coupled Ocean–Atmosphere Response Experiment (COARE) utilizing a cloud-resolving model (CRM). The Q2 profiles were reconstructed from CRM-simulated parameters with the COARE table and then compared with CRM-simulated “true” Q2 profiles, which were computed directly from the water vapor equation in the model. The consistency check indicates that discrepancies between the SLH-reconstructed and CRM-simulated profiles for Q2, especially at low levels, are larger than those for Q1 and are attributable to moistening for the nonprecipitating region that SLH cannot reconstruct. Nevertheless, the SLH-reconstructed total Q2 profiles are in good agreement with the CRM-simulated ones. The SLH algorithm was applied to PR data, and the results were compared with Q2 profiles derived from the budget study. Although discrepancies between the SLH-retrieved and sounding-based profiles for Q2 for the South China Sea Monsoon Experiment (SCSMEX) are larger than those for heating, key features of the vertical profiles agree well. The SLH algorithm can also estimate differences of Q2 between the western Pacific Ocean and the Atlantic Ocean, consistent with the results from the budget study.
Performance and Uncertainty of CNR1 Net Radiometers during a One-Year Field Comparison
Authors: Michel Dominik , Philipona Rolf , Ruckstuhl Christian , Vogt Roland , Vuilleumier Laurent
Published: April 2008

Net radiation flux in correlation with surface energy budget, snowmelt, glacier ice balance, and forest or agricultural flux exchange investigations is measured in numerous field experiments. Instrument costs and energy consumption versus performance and uncertainty of net radiation instruments has been widely discussed. Here the authors analyze and show performance and uncertainty of two Kipp and Zonen CNR1 net radiometers, which were compared to high standard reference radiation instruments measuring individual shortwave and longwave downward and upward flux components. The intercomparison was aimed at investigating the performance of the radiometers under different climatological conditions and was made over one year at the midlatitude Baseline Surface Radiation Network (BSRN) station in Payerne, Switzerland (490 MSL). Of the two CNR1 radiometers tested, one was installed in a ventilation and heating system, whereas the other was mounted without ventilation and heating. Uncertainties of the different flux components were found to be larger for shortwave than longwave radiation and larger for downward than upward components. Using the single sensitivity coefficient provided by the manufacturer, which for CNR1 radiometers conditions using all four sensors, rather large root-mean-square differences between 2 and 14 W m−2 were measured for the individual components for hourly averages and between 2 and 12 W m−2 for daily averages. The authors then performed a field calibration, comparing each individual sensor to the reference instrument for one particular day. With the individual field calibration the uncertainty of hourly averages was reduced significantly for all components of the ventilated and heated instrument. For the unventilated CNR1 uncertainties could not be reduced significantly for all sensors. The total net radiation uncertainty of both CNR1 is rather large with up to 26% on daily averages (∼10 W m−2) for the original sensitivity coefficients and without field calibration. Only with the field calibration and for the ventilated and heated CNR1 net radiometer is an uncertainty of 10% of the daily totals of total net radiation reached, as claimed by the manufacturer.
Satellite Estimates and Shipboard Observations of Downward Radiative Fluxes at the Ocean Surface
Authors: Guo G. , Coakley J. A.
Published: April 2008

Clouds and the Earth’s Radiant Energy System (CERES) uses a suite of instruments on the Terra and Aqua satellites combined with analyzed weather data and information on surface conditions to estimate surface radiative fluxes. CERES estimates for the Terra satellite were compared with measurements of the surface radiative fluxes collected with the research vessels (RVs) Wecoma and Thomas G. Thompson radiometers for cruises off the Oregon coast undertaken during 2000–03. To assess the shipboard measurements, the radiometer observations were analyzed to identify cloud-free conditions characterized by ∼1–2 h of relatively stable radiative fluxes. Fluxes for the cloud-free conditions were compared with those calculated using profiles of temperature and humidity from analyzed meteorological fields for the times and locations of the measurements and broadband radiative transfer models. For summertime conditions along the Oregon coast, and assuming a marine aerosol having 0.55-μm optical depth of 0.05, modeled and observed values of the shortwave flux agreed to within 1%–2%. Similar comparisons for the downward cloud-free longwave flux were within 1%–3%. This agreement also held for the CERES surface radiative flux estimates with CERES cloud-free fields of view for ocean scenes within 50 km of the ship being compared with 30-min averages of the shipboard measurements centered on the times of the Terra overpass. Using the CERES observations to identify cloud-free conditions for the Wecoma revealed that in some cases the shipboard measurements of the shortwave flux varied erratically. Criteria were adopted to avoid such behavior, yielding periods in which the surface radiative fluxes were reasonably stable for a range of cloud-free and cloudy conditions. With the criteria applied, the absolute magnitude of the mean differences between the shipboard measurements and the CERES estimates for the downward shortwave flux were within 2%, with RMS differences less than 6% within each month of CERES–shipboard matchups. The absolute magnitude of the mean differences for the downward longwave flux was less than 2%, with RMS differences less than 5%.
Dependence of Land Surface Albedo on Solar Zenith Angle: Observations and Model Parameterization
Authors: Yang Fanglin , Mitchell Kenneth , Hou Yu-Tai , Dai Yongjiu , Zeng Xubin , Wang Zhuo , Liang Xin-Zhong
Published: April 2008

This study examines the dependence of surface albedo on solar zenith angle (SZA) over snow-free land surfaces using the intensive observations of surface shortwave fluxes made by the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) Program and the National Oceanic and Atmospheric Administration Surface Radiation Budget Network (SURFRAD) in 1997–2005. Results are used to evaluate the National Centers for Environmental Prediction (NCEP) Global Forecast Systems (GFS) parameterization and several new parameterizations derived from the Moderate Resolution Imaging Spectroradiometer (MODIS) products. The influence of clouds on surface albedo and the albedo difference between morning and afternoon observations are also investigated. A new approach is taken to partition the observed upward flux so that the direct-beam and diffuse albedos can be separately computed. The study focused first on the ARM Southern Great Plains Central Facility site. It is found that the diffuse albedo prescribed in the NCEP GFS matched closely with the observations. The direct-beam albedo parameterized in the GFS is largely underestimated at all SZAs. The parameterizations derived from the MODIS product underestimated the direct-beam albedo at large SZAs and slightly overestimated it at small SZAs. Similar results are obtained from the analyses of observations at other stations. It is also found that the morning and afternoon dependencies of direct-beam albedo on SZA differ among the stations. Attempts are made to improve numerical model algorithms that parameterize the direct-beam albedo as a product of the direct-beam albedo at SZA = 60° (or the diffuse albedo), which varies with surface type or geographical location and/or season, and a function that depends only on SZA. A method is presented for computing the direct-beam albedos over these snow-free land points without referring to a particular land-cover classification scheme, which often differs from model to model.
Inclusion of a Drag Approach in the Town Energy Balance (TEB) Scheme: Offline 1D Evaluation in a Street Canyon
Authors: Hamdi R. , Masson V.
Published: April 2008

The Town Energy Balance module bridges the micro- and mesoscale and simulates local-scale urban surface energy balance for use in mesoscale meteorological models. Previous offline evaluations show that this urban module is able to simulate in good behavior road, wall, and roof temperatures and to correctly partition radiation forcing into turbulent and storage heat fluxes. However, to improve prediction of the meteorological fields inside the street canyon, a new version has been developed, following the methodology described in a companion paper by Masson and Seity. It resolves the surface boundary layer inside and above urban canopy by introducing a drag force approach to account for the vertical effects of buildings. This new version is tested offline, with one-dimensional simulation, in a street canyon using atmospheric and radiation data recorded at the top of a 30-m-high tower as the upper boundary conditions. Results are compared with simulations using the original single-layer version of the Town Energy Balance module on one hand and with measurements within and above a street canyon on the other hand. Measurements were obtained during the intensive observation period of the Basel Urban Boundary Layer Experiment. Results show that this new version produces profiles of wind speed, friction velocity, turbulent kinetic energy, turbulent heat flux, and potential temperature that are more consistent with observations than with the single-layer version. Furthermore, this new version can still be easily coupled to mesoscale meteorological models.
Barotropic Regeneration of Upper-Level Synoptic Disturbances in Different Configurations of the Zonal Weather Regime
Authors: Rivière Gwendal
Published: April 2008

Barotropic dynamics of upper-tropospheric midlatitude disturbances evolving in different configurations of the zonal weather regime (i.e., in different zonal-like large-scale flows) were studied using observational analyses and barotropic model experiments.

The contraction stage of upper-level disturbances that follows their elongation stage leads to an increase of eddy kinetic energy that is called the barotropic regeneration process in this text. This barotropic mechanism is studied through notions of barotropic critical regions (BtCRs) and effective deformation that have been introduced in a previous paper. The effective deformation field is equal to the difference between the square of the large-scale deformation magnitude and the square of the large-scale vorticity. Regions where the effective deformation is positive correspond to regions where the large-scale flow tends to strongly stretch synoptic disturbances. A BtCR is an area separating two large-scale regions of positive effective deformation, one located upstream and on the south side of the jet and the other downstream and on the north side. Such a region presents a discontinuity in the orientation of the dilatation axes and is a potential area where the barotropic regeneration process may occur.

Winter days presenting a zonal weather regime in the 40-yr ECMWF Re-Analysis dataset are decomposed, via a partitioning algorithm, into different configurations of the effective deformation field at 300 hPa. A six-cluster partition is obtained. Composite maps of the barotropic generation rate for each cluster exhibit a succession of negative and positive values on both sides of the BtCRs. It confirms statistically that the barotropic regeneration mechanism occurs preferentially about BtCRs.

Numerical experiments using a forced barotropic model on the sphere are performed. Each experiment consists of adding a synoptic-scale perturbation to one of the zonal-like jet configurations found in observations, which is kept fixed with time. The combined effects of the effective deformation and nonlinearities are shown to be crucial to reproduce the barotropic regeneration process about BtCRs.
Asymmetry of Daily Temperature Records
Authors: Ashkenazy Yosef , Feliks Yizhak , Gildor Hezi , Tziperman Eli
Published: April 2008

The authors study the NCEP–NCAR reanalysis temperature records and find that surface daily mean temperature cools rapidly and warms gradually at the midlatitudes (around 40°N and 40°S). This “asymmetry” is partially related to the midlatitude cyclone activity, in which cold fronts are significantly faster and steeper than warm fronts, and to intrusions of cold air. The gradual warming may be attributed also to the radiative relaxation to average atmospheric conditions after the passage of cold fronts or other intrusions of cold air. At the high latitudes there is an opposite asymmetry with rapid warming and gradual cooling; this asymmetry may be attributed to the radiative relaxation to average cold atmospheric conditions after the passage of warm fronts or intrusions of warm air.
The Ocean–Land–Atmosphere Model (OLAM). Part II: Formulation and Tests of the Nonhydrostatic Dynamic Core
Authors: Walko Robert L. , Avissar Roni
Published: April 2008

The dynamic core of the Ocean–Land–Atmosphere Model (OLAM), which is a new global model that is partly based on the Regional Atmospheric Modeling System (RAMS), is described and tested. OLAM adopts many features of its predecessor, but its dynamic core is new and incorporates a global geodesic grid with triangular mesh cells and a finite-volume discretization of the nonhydrostatic compressible Navier–Stokes equations. The spatial discretization of horizontal momentum is based on a C-staggered grid and uses a method that has not been previously applied in atmospheric modeling. The temporal discretization uses a unique form of time splitting that enforces consistency of advecting mass flux among all conservation equations. OLAM grid levels are horizontal, and topography is represented by the shaved-cell method. Aspects of the shaved-cell method that pertain to the OLAM discretization on the triangular mesh are described, and a method of conserving momentum in shaved cells on a C-staggered grid is presented.

The dynamic core was tested in simulations with multiple vertical model levels and significant vertical motion. The tests include an idealized global circulation simulation, a cold density current, and mountain-wave flow over an orographic barrier, all of which are well-known standard benchmark experiments. OLAM gave acceptable results in all tests, demonstrating that its dynamic core produces accurate and robust solutions.
Sense of Futility
Authors: Van Houtte Mieke , Stevens Peter A. J.
Published: April 2008

It is often reported that delinquency and school misconduct are more prevalent among students in lower academic tracks. This article examines the relationship between school type (general vs. technical/vocational) and self-reported school misconduct, considering simultaneously two recurrent explanations: the students' self-esteem and “strain theory.” Through a multilevel analysis, we assess the explanatory value of self-esteem, the sense of futility, and a school's overall culture of futility in this relationship. Data on 6,373 students from 44 Flemish schools gathered in the 2004-2005 academic year show that technical/ vocational students report higher levels of school misconduct. The association between school type and self-reported misconduct cannot be attributed to the students' self-esteem. Their sense of futility, however, proves to be wholly responsible for the relationship. The culture of futility at a school, on the other hand, does not seem to be related to misconduct.
The Blessing of a Wounded Patriarch: Genesis 27.1-40
Authors: Sylva Dennis
Published: April 2008

The interrelation of the characterization of Isaac in Gen. 27.1-40, his blessing in 27.28-29, and the narrative past constructed for him in the non-Priestly material addresses a number of questions that have persisted about the evaluation of this blessing and its relation to the divine blessings promised to the patriarchs. The present study argues that the character of Isaac restricts and deforms the blessings that are the leitmotif of the patriarchal narrative. The thesis is articulated in dialogue with current source-critical scholarship on the Pentateuch and presents a stratum of biblical material whose conception of Isaac and his blessing is at odds with subsequent inner-biblical and post-biblical mainstream interpretations. Perspectives derived from the nexus of character, blessing, and narrative 'history' are germane for understanding the oracle to Rebekah (25.23) and the different uses of niphal and hithpael verbs in discrete passages on the nations' participation in the patriarchal blessings.
The Mediation of Suffering and the Vision of a Cosmopolitan Public
Authors: Chouliaraki Lilie
Published: April 2008

In this article, the author argues that if researchers wish to move toward a “global village” with cosmopolitan values, then they need to examine critically the discourses and practices by which global information flows invite the individual spectator to be a public actor in the contexts of her or his everyday life. In the light of empirical analysis, the author presents a hierarchical typology of news stories on distant suffering that consists of adventure, emergency, and ecstatic news, and she examines the two broad ethical norms that inform these types of news: communitarianism and cosmopolitanism. The possibility for cosmopolitanism, the author concludes, lies importantly (but not exclusively) in the ways in which television tells the stories of suffering, inviting audiences to care for and act on conditions of human existence that go beyond their own communities of belonging.
Elevated protein tyrosine phosphatase activity provokes Eph/ephrin-facilitated adhesion of pre-B leukemia cells
Authors: Wimmer-Kleikamp Sabine H. , Nievergall Eva , Gegenbauer Kristina , Adikari Samantha , Mansour Mariam , Yeadon Trina , Boyd Andrew W. , Patani Neill R. , Lackmann Martin
Published: April 2008

Signaling by Eph receptors and cell-surface ephrin ligands modulates adhesive cell properties and thereby coordinates cell movement and positioning in normal and oncogenic development. While cell contact–dependent Eph activation frequently leads to cell-cell repulsion, also the diametrically opposite response, cell-cell adhesion, is a probable outcome. However, the molecular principles regulating such disparate functions have remained controversial. We have examined cell-biologic mechanisms underlying this switch by analyzing ephrin-A5–induced cell-morphologic changes of EphA3-positive LK63 pre-B acute lymphoblastic leukemia cells. Their exposure to ephrin-A5 surfaces leads to a rapid conversion from a suspended/nonpolarized to an adherent/polarized cell type, a transition that relies on EphA3 functions operating in the absence of Eph-kinase signaling. Cell morphology change and adhesion of LK63 cells are effectively attenuated by endogenous protein tyrosine phosphatase (PTP) activity, whereby PTP inhibition and productive EphA3-phosphotyrosine signaling reverse the phenotype to nonadherent cells with a condensed cytoskeleton. Our findings suggest that Eph-associated PTP activities not only control receptor phosphorylation levels, but as a result switch the response to ephrin contact from repulsion to adhesion, which may play a role in the pathology of hematopoietic tumors.
The RGS gene loco is essential for male reproductive system differentiation in Drosophila melanogaster
Authors: McGurk Leeanne , Pathirana Stephen , Rothwell Kathleen , Trimbuch Thorsten , Colombini Paolo , Yu Fengwei , Chia William , Bownes Mary
Published: April 2008

Background

The loco gene encodes several different isoforms of a regulator of G-protein signalling. These different isoforms of LOCO are part of a pathway enabling cells to respond to external signals. LOCO is known to be required at various developmental stages including neuroblast division, glial cell formation and oogenesis. Less is known about LOCO and its involvement in male development therefore to gain further insight into the role of LOCO in development we carried out a genetic screen and analysed males with reduced fertility.

Results

We identified a number of lethal loco mutants and four semi-lethal lines, which generate males with reduced fertility. We have identified a fifth loco transcript and show that it is differentially expressed in developing pupae. We have characterised the expression pattern of all loco transcripts during pupal development in the adult testes, both in wild type and loco mutant strains. In addition we also show that there are various G-protein α subunits expressed in the testis all of which may be potential binding partners of LOCO.

Conclusion

We propose that the male sterility in the new loco mutants result from a failure of accurate morphogenesis of the adult reproductive system during metamorphosis, we propose that this is due to a loss of expression of loco c3. Thus, we conclude that specific isoforms of loco are required for the differentiation of the male gonad and genital disc.
Spatial distribution of transcript changes in the maize primary root elongation zone at low water potential
Authors: Spollen William G , Tao Wenjing , Valliyodan Babu , Chen Kegui , Hejlek Lindsey G , Kim Jong-Joo , LeNoble Mary E , Zhu Jinming , Bohnert Hans J , Henderson David , Schachtman Daniel P , Davis Georgia E , Springer Gordon K , Sharp Robert E , Nguyen Henry T
Published: April 2008

Background

Previous work showed that the maize primary root adapts to low Ψw (-1.6 MPa) by maintaining longitudinal expansion in the apical 3 mm (region 1), whereas in the adjacent 4 mm (region 2) longitudinal expansion reaches a maximum in well-watered roots but is progressively inhibited at low Ψw. To identify mechanisms that determine these responses to low Ψw, transcript expression was profiled in these regions of water-stressed and well-watered roots. In addition, comparison between region 2 of water-stressed roots and the zone of growth deceleration in well-watered roots (region 3) distinguished stress-responsive genes in region 2 from those involved in cell maturation.

Results

Responses of gene expression to water stress in regions 1 and 2 were largely distinct. The largest functional categories of differentially expressed transcripts were reactive oxygen species and carbon metabolism in region 1, and membrane transport in region 2. Transcripts controlling sucrose hydrolysis distinguished well-watered and water-stressed states (invertase vs. sucrose synthase), and changes in expression of transcripts for starch synthesis indicated further alteration in carbon metabolism under water deficit. A role for inositols in the stress response was suggested, as was control of proline metabolism. Increased expression of transcripts for wall-loosening proteins in region 1, and for elements of ABA and ethylene signaling were also indicated in the response to water deficit.

Conclusion

The analysis indicates that fundamentally different signaling and metabolic response mechanisms are involved in the response to water stress in different regions of the maize primary root elongation zone.
Interaction between the C-terminal region of human myelin basic protein and calmodulin: analysis of complex formation and solution structure
Authors: Majava Viivi , Petoukhov Maxim V , Hayashi Nobuhiro , Pirilä Päivi , Svergun Dmitri I , Kursula Petri
Published: April 2008

Background

The myelin sheath is a multilamellar membrane structure wrapped around the axon, enabling the saltatory conduction of nerve impulses in vertebrates. Myelin basic protein, one of the most abundant myelin-specific proteins, is an intrinsically disordered protein that has been shown to bind calmodulin. In this study, we focus on a 19-mer synthetic peptide from the predicted calmodulin-binding segment near the C-terminus of human myelin basic protein.

Results

The interaction of native human myelin basic protein with calmodulin was confirmed by affinity chromatography. The binding of the myelin basic protein peptide to calmodulin was tested with isothermal titration calorimetry (ITC) in different temperatures, and Kd was observed to be in the low μM range, as previously observed for full-length myelin basic protein. Surface plasmon resonance showed that the peptide bound to calmodulin, and binding was accompanied by a conformational change; furthermore, gel filtration chromatography indicated a decrease in the hydrodynamic radius of calmodulin in the presence of the peptide. NMR spectroscopy was used to map the binding area to reside mainly within the hydrophobic pocket of the C-terminal lobe of calmodulin. The solution structure obtained by small-angle X-ray scattering indicates binding of the myelin basic protein peptide into the interlobal groove of calmodulin, while calmodulin remains in an extended conformation.

Conclusion

Taken together, our results give a detailed structural insight into the interaction of calmodulin with a C-terminal segment of a major myelin protein, the myelin basic protein. The used 19-mer peptide interacts mainly with the C-terminal lobe of calmodulin, and a conformational change accompanies binding, suggesting a novel mode of calmodulin-target protein interaction. Calmodulin does not collapse and wrap around the peptide tightly; instead, it remains in an extended conformation in the solution structure. The observed affinity can be physiologically relevant, given the high abundance of both binding partners in the nervous system.
Mosquito larvicidal activities of Solanum villosum berry extract against the dengue vector Stegomyia aegypti
Authors: Chowdhury Nandita , Ghosh Anupam , Chandra Goutam
Published: April 2008

Background

Vector control is facing a threat due to the emergence of resistance to synthetic insecticides. Insecticides of botanical origin may serve as suitable alternative biocontrol techniques in the future. Although several plants have been reported for mosquitocidal activity, only a few botanicals have moved from the laboratory to field use, because they are poorly characterized, in most cases active principals are not determined and most of the works are restricted to preliminary screening. Solanum villosum is a common weed distributed in many parts of India with medicinal properties, but the larvicidal activity of this plant has not been reported so far.

Methods

Aqueous and polar/non-polar solvent extract of fresh, mature, green berries of S. villosum was tested against Stegomyia aegypti, a common vector of dengue fever. A phytochemical analysis of chloroform:methanol extract was performed to search for the active toxic ingredient. The lethal concentration was determined (log probit analysis) and compared with Malathion. The chemical nature of the active substance was also evaluated following ultraviolet-visual (UV-Vis) and infrared (IR) analysis.

Results

In a 72 hour bioassay experiment with the aqueous extract, the highest mortality was recorded in 0.5% extract. When the mortality of different solvent extracts was compared, the maximum (p < 0.05) mortality was recorded at a concentration of 50 ppm of chloroform:methanol extract (1:1, v/v). The larvicidal activity was lower when compared with the chemical insecticide, Malathion (p < 0.05). Results of regression analysis revealed that the mortality rate (Y) was positively correlated with the period of exposure (X) and the log probit analysis (95% confidence level) recorded lowest value (5.97 ppm) at 72 hours of exposure. Phytochemical analysis of the chlororm:methanol extract reported the presence of many bioactive phytochemicals. Two toxic compounds were detected having R
f = 0.82 (70% and 73.33% mortality in 24 and 48 hours, respectively) and R
f = 0.95 (40% and 50% mortality in 24 and 48 hours, respectively). IR analysis provided preliminary information about the steroidal nature of the active ingredient.

Conclusion

S. villosum offers promise as potential bio control agent against S. aegypti particularly in its markedly larvicidal effect. The extract or isolated bioactive phytochemical could be used in stagnant water bodies for the control of mosquitoes acting as vector for many communicable diseases.
A case of spotted fever group rickettsiosis imported into the United Kingdom and treated with ciprofloxacin: a case report
Authors: Rashid Rifat , Pasqualotto Alessandro C , Denning David W
Published: April 2008

Introduction

Spotted fever group rickettsioses are an interesting group of infections, which are increasing in incidence worldwide.

Case presentation

Here we describe an imported case to the United Kingdom occurring in a patient who had recently visited Kruger National Park in South Africa – a highly endemic area for Rickettsia infections. Initial treatment with doxycycline failed but the patient made a prompt recovery after commencement of ciprofloxacin.

Conclusion

This finding raises the possibility that there are resistant strains of Rickettsia present.
Centrosome separation driven by actin-microfilaments during mitosis is mediated by centrosome-associated tyrosine-phosphorylated cortactin
Authors: Wang Wenqi , Chen Luyun , Ding Yubo , Jin Jing , Liao Kan
Published: April 2008

The regulation of protein tyrosine phosphorylation is an important aspect during the cell cycle. From G2-M transition to mitotic anaphase, phosphorylation of Tyr421, Tyr466 and Tyr482 of cortactin, an actin-filament associated protein, is dramatically induced. The phosphorylated cortactin is almost exclusively associated with centrosomes or spindle poles during mitosis. At G2-M transition prior to the breakdown of the nuclear envelope, two duplicated centrosomes migrate towards opposite ends of the nucleus to form the spindle poles. This centrosome-separation process and also the start of mitosis are inhibited or delayed by the depolymerization of actin filaments. Also inhibited is the separation of centrosomes when a truncated form of cortactin is expressed, whose C-terminus contains the tyrosine phosphorylation region but lacks the actin-binding domains. We introduced mutations at the tyrosine phosphorylation sites in the truncated C-terminus of cortactin and found that the C-terminus could no longer interfere with centrosome separation process. Our study shows that, cortactin phosphorylated at Tyr421, Tyr466 and Tyr482 mediates the actin-filament-driven centrosome separation at G2-M transition by providing a bridge between the centrosome and actin-filaments.