bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of UHF path loss for forest environments
Authors: Blaunstein N. , Kovacs I. Z. , Ben‐Shimol Y. , Bach Andersen J. , Katz D. , Eggers P. C. F. , Giladi R. , Olesen K.
Published: June 2003

We describe radio wave propagation within terrain with vegetation, based on the measurements performed in a forested areas using low transmitter (TX) and receiver (RX) antenna elevations. We continue to investigate 3‐D statistical multiparametric model of radio wave propagation above the rough terrain with some modifications made to describe multiple scattering of the signal field from randomly distributed trees, as phase screens, that model the random structure of trees with the rough surfaces and the irregular structure of branches and leaves, and other roughnesses placed on the ground surface. The scattering effects of trees and roughnesses are considered using a statistical description of an array of randomly distributed screens placed on a rough terrain. At the same time, an empirical short‐range path loss model which is based on measurements carried out in typical forested areas in Denmark is considered. Comparison between results obtained from the statistical and the empirical models and those obtained from examination of the experimental data, as well as with the results of other existing models, is presented. It is shown that both models predict the exponential field intensity decay with the wide range of the power law index variations (from ‐2.5 to ‐4.3) with accuracy ±6 dB with respect to experimental data and which is better than that obtained from other existing theoretical models.
Determination of plasmaspheric electron density profile by a stochastic approach
Authors: Goto Y. , Kasahara Y. , Sato T.
Published: June 2003

The determination of plasmaspheric electron density profiles has been attempted using a stochastic approach, using Omega signals observed on the Akebono satellite. Since the wave normal directions and delay times of Omega signals can be theoretically calculated by ray tracing under an appropriate electron density model, the density profile can be estimated by fitting the calculated directions and times to the observed values. In the present paper, we introduce a flexible model and a novel algorithm in the fitting method, taking into account the stochastic factors of the density distribution and wave propagation. The stochastic representations of directions and times enable us to separately estimate the effects of the ionosphere and the plasmasphere. The validity of the proposed method is examined using observational data collected during the recovery phase of a magnetic storm. In another example, an estimation of the asymmetry of the plasmasphere is attempted.
L‐band sea surface emissivity: Preliminary results of the WISE‐2000 campaign and its application to salinity retrieval in the SMOS mission
Authors: Camps A. , Corbella I. , Vall‐llossera M. , Duffo N. , Torres F. , Villarino R. , Enrique L. , Miranda J. , Julbé F. , Font J. , Julià A. , Gabarró C. , Etchetto J. , Boutin J. , Weill A. , Caselles V. , Rubio E. , Wursteisen P. , Berger M. , Martín‐Neira M.
Published: June 2003

Soil moisture and ocean salinity at surface level can be measured by passive microwave remote sensing at L‐band. To provide global coverage data of soil moisture and ocean salinity with three‐day revisit time, the Earth Explorer Opportunity Mission SMOS (Soil Moisture and Ocean Salinity) was selected by ESA (European Space Agency) in May 1999. SMOS' single payload is a Y‐shaped 2‐D aperture synthesis interferometric radiometer called MIRAS (Microwave Imaging Radiometer by Aperture Synthesis). SMOS presents some particular imaging peculiarities: variation of incidence and azimuth angles, different radiometric sensitivity and accuracy at each direction (pixels), and geometric polarization mixing. Therefore, the accuracy of the geophysical parameter retrieval depends on the knowledge of the angular dependence of the emissivity over a wide range of incidence and azimuth angles. The accuracy of the sea surface salinity retrievals depends on our capability to correct the wind‐induced variation of the brightness temperatures. To better understand wind effects, ESA sponsored the WInd and Salinity Experiment 2000 (WISE‐2000) from November 15, 2000, to January 16, 2001, in the Casablanca oil rig, at 40 km off the coast of Tarragona (Spain). This paper is divided into two parts. First, it presents the derived sensitivities of the brightness temperatures at vertical and horizontal polarizations with wind speed, and compares to Hollinger's measurements and numerical simulations. Second, these results are applied to the SMOS sea surface salinity (SSS) retrieval problem for different tracks within the swath. It is shown that, except for low SSS and sea surface temperature (SST), the retrieved SSS has a RMS error of approximately 1 psu in one satellite pass.
Physically based statistical integration of TRMM microwave measurements for precipitation profiling
Authors: Di Michele Sabatino , Marzano Frank S. , Mugnai Alberto , Tassa Alessandra , Poiares Baptista José Pedro V.
Published: June 2003

A statistical methodology to combine measurements from space‐borne microwave radar and radiometers is proposed. The approach is fairly general, even though the combination technique is here tailored for the two instruments onboard the Tropical Rainfall Measuring Mission (TRMM) satellite specifically devoted to rainfall measurements, that is, the Precipitation Radar (PR) and the TRMM Microwave Imager (TMI). Two combined retrieval algorithms are proposed, both derived from the previously developed Bayesian algorithm for microwave‐based precipitation retrieval from passive sensors (BAMPR‐P), which is based on a Bayesian inversion method and is trained by a modeled cloud radiation database. The first combined technique, called BAMPR‐C (BAMPR combined), operates in the narrower common swath aiming at exploiting the simultaneous measurements of PR and TMI instruments. Within BAMPR‐C the hydrometeor profiles, retrieved from TMI, are used as a constraint for the PR‐based inversion: this two step cascade allows us to overcome the difficulty to take into account the different scan geometries of TMI and PR. The second combined technique is called BAMPR‐B (BAMPR broadening) and aims at improving the TMI‐only retrieval outside the common swath. In this approach, first optimal retrieved profiles are generated by reversing the order of the previous two steps of BAMPR‐C cascade within the common swath. Then the resulting profile data set and the corresponding TMI brightness temperatures are used to define the cloud radiation database to be employed outside the common swath for the TMI‐only retrieval, achieving the so‐called radar swath synthetic broadening. Numerical internal tests, using simulated data, are illustrated to quantify the features of the proposed synergetic algorithms. Finally, an application to measured TRMM data for a selected case study (hurricane Bonnie on August 1998) is shown and discussed.
Electromagnetic field of a vertical electric dipole on the spherical conductor covered with a dielectric layer
Authors: Pan Wei‐Yan , Zhang Hong‐Qi
Published: June 2003

The expressions of the electromagnetic field induced by a vertical electric dipole on the spherical conductor covered with a dielectric layer have been obtained. The calculation shows that the trapped surface wave may be efficiently excited by a vertical electric dipole on the surface of the dielectric layer when the thickness of the dielectric layer is larger than a certain value which depends on the operating frequency and the dielectric permittivity. This conclusion coincides with that of the field excited by a vertical electric dipole on the planar conductor covered with a dielectric layer.
Rift asymmetry and continental uplift
Authors: Doglioni Carlo , Carminati Eugenio , Bonatti Enrico
Published: June 2003

The topography of ocean ridges and rifts show a distinct asymmetry. The eastern sides of the East Pacific Rise, the Mid‐Atlantic Ridge, and the NW Indian Ridge are, on average, 100–300 m more elevated than the conjugate flank to the west. The asymmetry is maintained when bathymetry is plotted versus the square root of crustal age. A comparable topographic asymmetry occurs in the Red Sea and Baikal rifts where the “eastern” continental shoulders are more elevated. We suggest that depleted and lighter asthenosphere generated below the ocean ridge was shifted “eastward” relative to the lithosphere, determining a density deficit below the eastern flank. The eastward migration of the lighter Atlantic asthenosphere below the African continent could eventually have contributed to the anomalous postrift uplift of Africa. This model suggests that the “westward” drift of the lithosphere relative to the underlying mantle might be a global phenomenon.
Dynamics of channel bifurcations in noncohesive sediments
Authors: Federici Bianca , Paola Chris
Published: June 2003

Braided rivers produce flow confluences and divergences (diffluences) in roughly equal numbers, but braided river research has focused mainly on confluences. Divergences, however, are of equal importance dynamically: they are sites of formation of central bars and the development of flow divisions that can steer the flow toward one part of the braided network or another. In a series of experiments on flow in isolated, well‐defined bifurcations, we found that although a central bar always develops, the divided flow may continue to flow on both sides of the bar (“stable” bifurcation) or may eventually be forced entirely to one side of the bar or the other (“unstable” bifurcation). We found that an unstable bifurcation forms when the flow field is characterized by both a low Shields stress and a nonuniform incoming flow. We also found that divergences with erodible banks tend to an equilibrium configuration that depends mainly on the widening ratio of the channel.
Sensitivity analysis of aquifer parameter estimations based on the Laplace equation with linearized boundary conditions
Authors: Szilagyi Jozsef
Published: June 2003

Estimates of aquifer parameters, saturated hydraulic conductivity, and drainable porosity were obtained by an analytical solution of the two‐dimensional Laplace equation with linearized boundary conditions and were compared to prescribed parameters in a finite element model that simulated drainage of a coupled system of unsaturated/saturated flow. Boundary conditions prerequisite for the analytical solution were systematically relaxed during numerical experiments to see how the resulting aquifer‐parameter estimates deteriorate if (1) correct aquifer geometry values are used and (2) aquifer geometry is imprecisely estimated. Sensitivity of aquifer parameter estimation to imprecise saturated thickness and groundwater profile information was also performed at the watershed scale. The analysis supports the robustness of the saturated hydraulic conductivity and drainable porosity estimates in all cases considered, at both field and catchment scales, with the only exception being the drainable porosity for sand where a significant flux‐exchange between the vadose and phreatic zones during drawdown results in both modeled and estimated effective drainable porosities significantly larger than traditionally expected.
Production, storage, and output of particulate organic carbon: Waipaoa River basin, New Zealand
Authors: Gomez Basil , Trustrum N. A. , Hicks D. M. , Rogers K. M. , Page M. J. , Tate K. R.
Published: June 2003

We compute the particulate organic carbon (POC) yield of the Waipaoa River, New Zealand, using sediment rating curves in conjunction with measurements of the carbon content of the suspended sediment. To ascertain the source of the carbon and the extent to which the POC flux is tied to different erosion processes, we determined the stable isotopic carbon composition (δ13C) and carbon to nitrogen (C/N) ratio of weathered bedrock, soil, and regolith. Most POC is derived from suspended sediment generated by gully erosion (incision into weathered bedrock), supplemented by landsliding during extreme events. The specific yield of POC from the headwaters (drainage area 1580 km2) is 55 g m−2 yr−1, which is very high by global standards and by comparison with other turbid steep‐land rivers. The annual loss to floodplain storage is ∼4% (3.6 Kt) of the mean annual POC yield (86.7 Kt). Thus the Waipaoa River is a very effective conduit for transporting POC to the ocean.
Numerical models for mixing corrosion in natural and artificial karst environments
Authors: Kaufmann Georg
Published: June 2003

The enlargement of initially small fractures in a karst aquifer by chemical dissolution is studied. Flow in the aquifer is driven by head differences between sinks and resurgences, and flow depends on the permeability of small fissures and fractures in the aquifer. Enlargement of fractures is controlled by the chemical composition of the recharge, as water undersaturated with respect to calcite is able to dissolve material from the fracture walls. As fractures are enlarged with time, permeability within the aquifer increases significantly, and flow becomes very heterogeneous. Two different processes are considered: enlargement due to normal corrosion, where water is undersaturated with respect to calcite, and enlargement due to mixing corrosion, where two solutions saturated with respect to calcite but with different carbon dioxide concentrations mix and the resulting solution becomes undersaturated again. The importance of mixing corrosion is discussed for two boundary conditions: A natural karst aquifer is modeled with fixed recharge boundary conditions representing sinking streams, and an artificial karst aquifer is simulated with fixed head boundary conditions representing a reservoir. In both cases, mixing corrosion is important, especially if recharge is characterized by an almost saturated chemistry. Mixing corrosion significantly changes the evolving passage pattern, as dissolution due to mixing of solutions is possible deep in the aquifer. Mixing corrosion also reduces breakthrough times of the aquifer and can result in dramatic leakage underneath dam sites, even if the impounded water is almost saturated with respect to calcite.
Study of pollutant washoff from small impervious experimental plots
Authors: Vaze J. , Chiew Francis H. S.
Published: June 2003

An understanding of the pollutant washoff process in urban catchments is essential to develop appropriate models for estimating storm water pollutant washoff loads. This paper investigates the relative importance of the raindrop and runoff energies in the pollutant washoff process by carrying out field and laboratory experiments. Two similar test surfaces are used, with simulated rainfall allowed to fall directly onto one surface, while insect screens are placed above the other surface to remove the rainfall energy. The results indicate that both the turbulence created by falling raindrops and the shear stress imparted by surface runoff are important in loosening the surface particles and suspending them in water, making them available for washoff. The energy of falling raindrops in detaching the surface pollutants is very important at the start of an event and is less dominant as the availability of easily detachable and transportable fractions of the surface pollutant decreases over the storm. Analyses of data from the experimental runs and from actual catchments also suggest that meaningful characteristic curves that relate event total suspended solids (TSS) and total phosphorus (TP) loads to storm durations for specific rainfall intensities can be developed from the experimental data.
An end to the “rain ratio” reign?
Authors: Ridgwell Andy J.
Published: June 2003

One of the most elegant mechanisms forwarded for late Quaternary atmospheric CO2 variability concerns the sensitivity of calcium carbonate preservation in deep ocean sediments to the relative delivery rates of calcium carbonate and particulate organic carbon (the CaCO3:POC “rain ratio”). It was implicitly assumed that any change in the CaCO3:POC rain ratio of biogenic material produced in the surface ocean will be communicated directly to the sediments. This would allow relatively subtle shifts in ecosystem composition to affect sedimentary CaCO3 preservation (and thus atmospheric CO2). However, recent research into the controls on the transport of POC to depth suggests that the rain ratio “seen” by the sediments may instead be buffered against any perturbation occurring at the surface. This casts doubt on the viability of hypotheses envisaging ecological changes as a means of accounting for the observed glacial‐interglacial CO2 signal.
Sensitivity of northern hemisphere surface climate to simulation of the stratospheric polar vortex
Authors: Norton W. A.
Published: June 2003

A sensitivity experiment has been performed with a stratosphere‐resolving GCM where the mean state and variability of the stratosphere have been altered. It is shown that this has a significant effect on the mean and variability of wintertime northern hemisphere surface climate. In particular it is shown that the stratosphere strongly contributes to the persistence of the surface Arctic Oscillation at lags of 10–25 days. This confirms the importance of the stratosphere on surface climate that has been inferred by recent studies examining the Arctic Oscillation in reanalysis datasets.
Increasing background ozone during spring on the west coast of North America
Authors: Jaffe Daniel , Price Heather , Parrish David , Goldstein Allen , Harris Joyce
Published: June 2003

Using a 15‐year record of O3 from Lassen Volcanic National Park, a rural elevated site in northern California, data from two aircraft campaigns conducted in 1984 and 2002 over the eastern North Pacific, and observations spanning 18 years from five U.S. west coast, marine boundary layer sites, we show that O3 in air arriving from the Eastern Pacific in spring has increased by approximately 10 ppbv, i.e. 30% from the mid 1980s to the present. This positive trend in O3 correlates with the increasing trend in global nitrogen oxide emissions, which is especially pronounced in Asia. As spring is the season of strongest transport of Asian emissions to the Pacific, we conclude that the emission trend is the most likely cause of the O3 trend.
Suprathermal electron isotropy in high‐beta solar wind and its role in heat flux dropouts
Authors: Crooker N. U. , Larson D. E. , Kahler S. W. , Lamassa S. M. , Spence H. E.
Published: June 2003

Time variations in plasma beta and a parameter which measures isotropy in suprathermal electron pitch angle distributions show a remarkably close correspondence throughout the solar wind. The finding implies that high‐beta plasma, with its multiple magnetic holes and sharp field and plasma gradients, is conducive to electron pitch‐angle scattering, which reduces heat flux from the Sun without field‐line disconnection. Thus the finding impacts our understanding of signatures we use to determine magnetic topology in the heliosphere.
Simultaneous observation of the electron acceleration and ion deceleration in the dayside high‐latitude auroral region
Authors: Tanaka H. , Saito Y. , Ishii S. , Asamura K. , Mukai T.
Published: June 2003

SS‐520‐2 sounding rocket flew through the dayside high‐latitude auroral region in the vicinity of the cusp. One of the science instruments LEP‐ESA/ISA simultaneously observed electron acceleration and ion deceleration when inverted‐V type electron precipitations were observed. The correspondence between the electron acceleration energy and the ion deceleration energy clearly indicated the existence of the quasi‐static field‐aligned potential drop above the sounding rocket. Moreover, ion deceleration started 9.5 seconds later than electron acceleration. By considering a simple temporal model that field‐aligned potential drop gradually grew in 10 seconds at 4200 km altitude region, we have succeeded in explaining the observed characteristics of the electron acceleration and ion deceleration.
Radiative Absorption Capability of Asian Dust with Black Carbon Contamination
Authors: Chou Charles C.‐K. , Chen Tze‐Kuang , Huang Shu‐Hui , Liu Shaw C.
Published: June 2003

Radiative forcing by mineral dust is one of the major uncertainties in assessing the impact of aerosols on the climate. Coagulation and condensation of pollutants on dust particles can further complicate the problem by altering their optical properties. During four Asian dust events in the spring 2002, concentration and size distribution of aerosols were measured in Taipei, Taiwan. Black carbon (BC), organic carbon (OC) and optical properties of the dust aerosols were measured. We found that both the mass specific absorption efficiency and imaginary refractive index of the aerosols decreased significantly during the dust events because of reduced black carbon concentrations. In addition the black carbon in aerosols was found to have significantly higher absorption efficiency than that adopted in current climate models. We suggest that the higher absorption efficiency is due to the formation of an internal mixture of BC and other particulate matter.
Parallel bands of seismicity at the Mid‐Atlantic Ridge, 12–14°N
Authors: Escartín Javier , Smith Deborah K. , Cannat Mathilde
Published: June 2003

Seismicity distribution along the Mid‐Atlantic Ridge (MAR), monitored with the Autonomous Underwater Hydrophone (AUH) array, shows a band of seismicity ∼70 km west of the axis between ∼11.9°N and 14.2°N. Available focal mechanisms at the off‐axis seismic band show extension directions consistent with the accommodation of the North‐American (NA) and South‐American (SA) relative plate motion. Axial seismicity shows a gap at ∼14°N, coinciding with the 14°N hotspot‐like region, and the focal mechanisms near this region are consistent with spreading of the African (AF) and the NA or SA plates. We speculate that the triple junction between the AF, NA and SA plates is close to the 14°N seismic gap. The westward continuation of the NA‐SA plate boundary is unconstrained, but could initiate at ∼13°N, at the south end of the off‐axis seismic band, or be diffuse between ∼12°N and ∼15°N.
The fate of mercury species in a sub‐arctic snowpack during snowmelt
Authors: Dommergue Aurélien , Ferrari Christophe P. , Gauchard Pierre‐Alexis , Boutron Claude F. , Poissant Laurier , Pilote Martin , Jitaru Petru , Adams Freddy C.
Published: June 2003

An extensive mercury study was conducted in April 2002 prior to and during the annual melting of a snowpack in a sub‐arctic site along the Hudson Bay (Canada). Gas‐phase measurements show that the snowmelt coincides with an elemental mercury (Hg°) pulse in the snowpack air far above ambient levels. Additional measurements of inorganic mercury (Hg2+) and methylmercury (MeHg+) in snow pits, in surface snow and in a meltwater sample clearly reveal that most of Hg is removed from the snow during the first days of snowmelt. We estimate that gas‐phase exchanges contribute poorly to remove Hg from the snowpack; consequently during a snowmelt day more than 90% of Hg present in the snow surface is likely released with the meltwater. In arctic areas, where Hg accumulates at an accelerated rate in the snow surfaces [Lu et al., 2001] during mercury depletion events (MDE), the discharge of this toxic and bio‐accumulating pollutant in water systems could be a threat to ecosystems and local indigenous populations.
Cyclic rapid warming on centennial‐scale revealed by a 2650‐year stalagmite record of warm season temperature
Authors: Tan Ming , Liu Tungsheng , Hou Juzhi , Qin Xiaoguang , Zhang Hucai , Li Tieying
Published: June 2003

A 2650‐year (BC665‐AD1985) warm season (MJJA: May, June, July, August) temperature reconstruction is derived from a correlation between thickness variations in annual layers of a stalagmite from Shihua Cave, Beijing, China and instrumental meteorological records. Observations of soil CO2 and drip water suggest that the temperature signal is amplified by the soil‐organism‐CO2 system and recorded by the annual layer series. Our reconstruction reveals that centennial‐scale rapid warming occurred repeatedly following multicentenial cooling trends during the last millennia. These results correlate with different records from the Northern Hemisphere, indicating that the periodic alternation between cool and warm periods on a sub‐millennial scale had a sub‐hemispherical influence.
Layering in the wall rock of Valles Marineris: intrusive and extrusive magmatism
Authors: Williams Jean‐Pierre , Paige David A. , Manning Craig E.
Published: June 2003

High‐resolution images of the walls exposed in Valles Marineris reveal variations in appearance and degree of layering indicating various lithologies comprise the Tharsis plateau. The layered wall rock has been proposed to result from effusive flood basalt volcanism or interbedded sediments and volcanics. We present observations of unlayered rock that indicate layering extends to a greater depth in the western half of Valles Marineris and is confined to the Tharsis plateau, a region of thickened, uplifted crust resulting from prolonged intrusive activity. Consistent with this view, we propose that the observed layering may be a manifestation of intrusive rocks resulting from crystal fractionation of intruded basaltic magmas. Terrestrial layered plutons provide analogs for comparison such as those of the North Atlantic Igneous Province (NAIP) a large igneous province associated with crustal rifting and exposures of thick sequences of layered flood basalts and intruded layered cumulates.
Detection of ionospheric perturbations using a dense GPS array in Southern California
Authors: Calais E. , Haase J. S. , Minster J. B.
Published: June 2003

We present observations of high‐frequency ionospheric perturbations detected using Global Positioning System (GPS) data from the Southern California Integrated GPS Network (SCIGN), a densely spaced GPS array of about 250 stations centered on the Los Angeles area. We show examples of perturbations with 3–10 minute periods that may result from coupling between the ionosphere and neutral gravity waves generated in the lower atmosphere. Although the signal‐to‐noise ratio of the perturbations is relatively small, we show how multi‐station array processing techniques can take advantage of the high spatial density of the measurements and the coherence of the signal over a region the size of the SCIGN to considerably improve the detection capability.
Kava-Kava
Authors: Loew Dieter , Gaus Wilhelm
Published: June 2003

Ein kalter wässriger Auszug aus Kava-Kava-Wurzelstock wird seit Jahrhunderten traditionell wegen seiner angst- und aggressionslösenden Wirkung auf den Inseln des Pazifiks in vernünftigen Mengen ohne hepatotoxische Wirkungen getrunken. Im Verteilungsmuster der Kavapyrone sind wässriger und industriell hergestellter ethanolischer und acetonischer Auszug vergleichbar. In klinisch-pharmakologischen Studien unterscheiden sich Kava-Extrakte im Wirkprofil von den Benzodiazepinen. Klinischen Studien, die nach GCP-Richtlinien durchgeführt wurden, belegen die Wirksamkeit ausreichend. Nach Auswertung der berichteten hepatotoxischen Fälle ist das im Widerruf mit Sofortvollzug seitens des BfArM aufgeführte Risiko nicht nachvollziehbar, weshalb die Kommission E klare Empfehlungen zur Anwendung von Kava-Kava-Extrakten ausgesprochen hat.
Reset of human neocortical oscillations during a working memory task
Authors: Rizzuto D. S. , Madsen J. R. , Bromfield E. B. , Schulze-Bonhage A. , Seelig D. , Aschenbrenner-Scheibe R. , Kahana M. J.
Published: June 2003

Both amplitude and phase of rhythmic slow-wave electroencephalographic activity are physiological correlates of learning and memory in rodents. In humans, oscillatory amplitude has been shown to correlate with memory; however, the role of oscillatory phase in human memory is unknown. We recorded intracranial electroencephalogram from human cortical and hippocampal areas while subjects performed a short-term recognition memory task. On each trial, a series of four list items was presented followed by a memory probe. We found agreement across trials of the phase of oscillations in the 7- to 16-Hz range after randomly timed stimulus events, evidence that these events either caused a phase shift in the underlying oscillation or initiated a new oscillation. Phase locking in this frequency range was not generally associated with increased poststimulus power, suggesting that stimulus events reset the phase of ongoing oscillations. Different stimulus classes selectively modulated this phase reset effect, with topographically distinct sets of recording sites exhibiting preferential reset to either probe items or to list items. These findings implicate the reset of brain oscillations in human working memory.
Synthetic small molecules that control stem cell fate
Authors: Ding Sheng , Wu Tom Y. H. , Brinker Achim , Peters Eric C. , Hur Wooyoung , Gray Nathanael S. , Schultz Peter G.
Published: June 2003

In an attempt to better understand and control the processes that regulate stem cell fate, we have set out to identify small molecules that induce neuronal differentiation in embryonic stem cells (ESCs). A high-throughput phenotypic cell-based screen of kinase-directed combinatorial libraries led to the discovery of TWS119, a 4,6-disubstituted pyrrolopyrimidine that can induce neurogenesis in murine ESCs. The target of TWS119 was shown to be glycogen synthase kinase-3β (GSK-3β) by both affinity-based and biochemical methods. This study provides evidence that GSK-3β is involved in the induction of mammalian neurogenesis in ESCs. This and such other molecules are likely to provide insights into the molecular mechanisms that control stem cell fate, and may ultimately be useful to
in vivo
stem cell biology and therapy.
Genera of the human lineage
Authors: Cela-Conde Camilo J. , Ayala Francisco J.
Published: June 2003

Human fossils dated between 3.5 and nearly 7 million years old discovered during the last 8 years have been assigned to as many as four new genera of the family Hominidae:
Ardipithecus, Orrorin, Kenyanthropus,
and
Sahelanthropus.
These specimens are described as having morphological traits that justify placing them in the family Hominidae while creating a new genus for the classification of each. The discovery of these fossils pushed backward by >2 million years the date of the oldest hominids known. Only two or three hominid genera,
Australopithecus, Paranthropus,
and
Homo,
had been previously accepted, with
Paranthropus
considered a subgenus of
Australopithecus
by some authors. Two questions arise from the classification of the newly discovered fossils: (
i
) Should each one of these specimens be placed in the family Hominidae? (
ii
) Are these specimens sufficiently distinct to justify the creation of four new genera? The answers depend, in turn, on the concepts of what is a hominid and how the genus category is defined. These specimens seem to possess a sufficient number of morphological traits to be placed in the Hominidae. However, the nature of the morphological evidence and the adaptation-rooted concept of what a genus is do not justify the establishment of four new genera. We propose a classification that includes four well defined genera:
Praeanthropus, Ardipithecus, Australopithecus,
and
Homo,
plus one tentative
incertae sedis
genus:
Sahelanthropus.
A lupus-like syndrome develops in mice lacking the Ro 60-kDa protein, a major lupus autoantigen
Authors: Xue Dahai , Shi Hong , Smith James D. , Chen Xinguo , Noe Dennis A. , Cedervall Tommy , Yang Derek D. , Eynon Elizabeth , Brash Douglas E. , Kashgarian Michael , Flavell Richard A. , Wolin Sandra L.
Published: June 2003

Antibodies against a conserved RNA-binding protein, the Ro 60-kDa autoantigen, occur in 24–60% of all patients with systemic lupus erythematosus. Anti-Ro antibodies are correlated with photosensitivity and cutaneous lesions in these patients and with neonatal lupus, a syndrome in which mothers with anti-Ro antibodies give birth to children with complete congenital heart block and photosensitive skin lesions. In higher eukaryotes, the Ro protein binds small RNAs of unknown function known as Y RNAs. Because the Ro protein also binds misfolded 5S rRNA precursors, it is proposed to function in a quality-control pathway for ribosome biogenesis. Consistent with a role in the recognition or repair of intracellular damage, an orthologue of Ro in the radiation-resistant eubacteriumDeinococcus radioduranscontributes to survival of this bacterium after UV irradiation. Here, we show that mice lacking the Ro protein develop an autoimmune syndrome characterized by anti-ribosome antibodies, anti-chromatin antibodies, and glomerulonephritis. Moreover, in one strain background,Ro–/–mice display increased sensitivity to irradiation with UV light. Thus, one function of this major human autoantigen may be to protect against autoantibody development, possibly by sequestering defective ribonucleoproteins from immune surveillance. Furthermore, the finding that mice lacking the Ro protein are photosensitive suggests that loss of Ro function could contribute to the photosensitivity associated with anti-Ro antibodies in humans.
Nanobacteria-like calcite single crystals at the surface of the Tataouine meteorite
Authors: Benzerara Karim , Menguy Nicolas , Guyot François , Dominici Christian , Gillet Philippe
Published: June 2003

Nanobacteria-like objects evidenced at the surface of the orthopyroxenes of the Tataouine meteorite in South Tunisia have been studied by scanning and transmission electron microscopies. A method of micromanipulation has been developed to ensure that exactly the same objects were studied by both methods. We have shown that the nanobacteria-like objects are spatially correlated with filaments of microorganisms that colonized the surface of the meteoritic pyroxene during its 70 years of residence in the aridic Tataouine soil. Depressions of a few micrometers in depth are observed in the pyroxene below the carbonates, indicating preferential dissolution of the pyroxene and calcite precipitation at these locations. The nanobacteria-like small rods that constitute calcium carbonate rosettes are well crystallized calcite single crystals surrounded by a thin amorphous layer of carbonate composition that smoothes the crystal edges and induces rounded shapes. Those morphologies are unusual for calcite single crystals observed in natural samples. A survey of recent literature suggests that the intervention of organic compounds derived from biological activity is likely in their formation.
Transglutaminase 2-/-mice reveal a phagocytosis-associated crosstalk between macrophages and apoptotic cells
Authors: Szondy Zsuzsa , Sarang Zsolt , Molnár Péter , Németh Tamás , Piacentini Mauro , Mastroberardino Pier Giorgio , Falasca Laura , Aeschlimann Daniel , Kovács Judit , Kiss Ildikó , Szegezdi Éva , Lakos Gabriella , Rajnavölgyi Éva , Birckbichler Paul J. , Melino Gerry , Fésüs László
Published: June 2003

Tissue transglutaminase (TGase2) is a protein-crosslinking enzyme known to be associated with thein vivoapoptosis program. Here we report that apoptosis could be induced in TGase2-/-mice; however, the clearance of apoptotic cells was defective during the involution of thymus elicited by dexamethasone, anti-CD3 antibody, or γ-irradiation, and in the liver after induced hyperplasia. The lack of TGase2 prevented the production of active transforming growth factor-β1 in macrophages exposed to apoptotic cells, which is required for the up-regulation of TGase2 in the thymusin vivo, for accelerating deletion of CD4+CD8+ cells and for efficient phagocytosis of apoptotic bodies. The deficiency is associated with the development of splenomegaly, autoantibodies, and immune complex glomerulonephritis in TGase2-/-mice. These findings have broad implications not only for diseases linked to inflammation and autoimmunity but also for understanding the interrelationship between the apoptosis and phagocytosis process.
The terminal nucleotide of the Mu genome controls catalysis of DNA strand transfer
Authors: Goldhaber-Gordon Ilana , Early Michael H. , Baker Tania A.
Published: June 2003

Members of the transposase/retroviral-integrase superfamily use a single active site to perform at least two reactions during transposition of a DNA transposon or a retroviral cDNA. They hydrolyze a DNA sequence at the end of the mobile DNA and then join this DNA end to a target DNA (a reaction called DNA strand transfer). Critical to understanding the mechanism of recombination is elucidating how these distinct reactions are orchestrated by the same active site. Here we find that DNA substrates terminating in a dideoxynucleotide allow Mu transposase to hydrolyze a target DNA, combining aspects of both natural reactions. Analyses of the sequence preferences for target hydrolysis and of the structure of the cleaved product indicate that this reaction is promoted by the active site in the conformation that normally promotes DNA strand transfer. Dissecting the DNA requirements for target hydrolysis reveals that the ribose of the last nucleotide of the Mu DNA activates transposase's catalytic potential, even when this residue is not a direct chemical participant. These findings provide insight into the molecular mechanism insuring that DNA strand transfer ordinarily occurs rather than inappropriate DNA cleavage. The required presence of the terminal nucleotide in the transposase active site creates a great advantage for the attached 3′OH to serve as nucleophile.
Function and glycosylation of plant-derived antiviral monoclonal antibody
Authors: Ko Kisung , Tekoah Yoram , Rudd Pauline M. , Harvey David J. , Dwek Raymond A. , Spitsin Sergei , Hanlon Cathleen A. , Rupprecht Charles , Dietzschold Bernhard , Golovkin Maxim , Koprowski Hilary
Published: June 2003

Plant genetic engineering led to the production of plant-derived mAb (mAbP), which provides a safe and economically feasible alternative to the current methods of antibody production in animal systems. In this study, the heavy and light chains of human anti-rabies mAb were expressed and assembledin plantaunder the control of two strong constitutive promoters. An alfalfa mosaic virus untranslated leader sequence and Lys-Asp-Glu-Leu (KDEL) endoplasmic reticulum retention signal were linked at the N and C terminus of the heavy chain, respectively. mAbPwas as effective at neutralizing the activity of the rabies virus as the mammalian-derived antibody (mAbM) or human rabies Ig (HRIG). The mAbPcontained mainly oligomannose type N-glycans (90%) and had no potentially antigenic α(1,3)-linked fucose residues. mAbPhad a shorter half-life than mAbM. The mAbPwas as efficient as HRIG for post-exposure prophylaxis against rabies virus in hamsters, indicating that differences in N-glycosylation do not affect the efficacy of the antibody in this model.
Modeling of DNA microarray data by using physical properties of hybridization
Authors: Held G. A. , Grinstein G. , Tu Y.
Published: June 2003

A method of analyzing DNA microarray data based on the physical modeling of hybridization is presented. We demonstrate, in experimental data, a correlation between observed hybridization intensity and calculated free energy of hybridization. Then, combining hybridization rate equations, calculated free energies of hybridization, and microarray data for known target concentrations, we construct an algorithm to compute transcript concentration levels from microarray data. We also develop a method for eliminating outlying data points identified by our algorithm. We test the efficacy of these methods by comparing our results with an existing statistical algorithm, as well as by performing a cross-validation test on our model.
Nutrient loading and consumers: Agents of change in open-coast macrophyte assemblages
Authors: Nielsen Karina J.
Published: June 2003

Human activities are significantly altering nutrient regimes and the abundance of consumers in coastal ecosystems. A field experiment in an open-coast, upwelling ecosystem showed that small increases in nutrients increased the biomass and evenness of tide pool macrophytes where consumer abundance and nutrient loading rates were low. Consumers, when abundant, had negative effects on the diversity and biomass of macrophytes. Nutrient loading increases and consumers are less abundant and efficient as wave exposure increases along open coastlines. Experimentally reversing the natural state of nutrient supply and consumer pressure at a wave-protected site to match wave-exposed sites caused the structure of the macrophyte assemblage to converge on that found naturally in wave-exposed pools. The increases in evenness and abundance were driven by increases in structurally complex functional groups. In contrast, increased nutrient loading in semienclosed marine or estuarine ecosystems is typically associated with declines in macrophyte diversity because of increases in structurally simple and opportunistic functional groups. If nutrient concentration of upwelled waters changes with climatic warming or increasing frequency of El Niños, as predicted by some climate models, these results suggest that macrophyte abundance and evenness along wave-swept open-coasts will also change. Macrophytes represent a significant fraction of continental shelf production and provide important habitat for many marine species. The combined effects of shifting nutrient regimes and overexploitation of consumers may have unexpected consequences for the structure and functioning of open-coast communities.
High-resolution structure of RNase P protein from
Thermotoga maritima
Authors: Kazantsev Alexei V. , Krivenko Angelika A. , Harrington Daniel J. , Carter Richard J. , Holbrook Stephen R. , Adams Paul D. , Pace Norman R.
Published: June 2003

The structure of RNase P protein from the hyperthermophilic bacterium
Thermotoga maritima
was determined at 1.2-Å resolution by using x-ray crystallography. This protein structure is from an ancestral-type RNase P and bears remarkable similarity to the recently determined structures of RNase P proteins from bacteria that have the distinct,
Bacillus
type of RNase P. These two types of protein span the extent of bacterial RNase P diversity, so the results generalize the structure of the bacterial RNase P protein. The broad phylogenetic conservation of structure and distribution of potential RNA-binding elements in the RNase P proteins indicate that all of these homologous proteins bind to their cognate RNAs primarily by interaction with the phylogenetically conserved core of the RNA. The protein is found to dimerize through an extensive, well-ordered interface. This dimerization may reflect a mechanism of thermal stability of the protein before assembly with the RNA moiety of the holoenzyme.
TSG101 interaction with HRS mediates endosomal trafficking and receptor down-regulation
Authors: Lu Quan , Hope Lila Weiqiao , Brasch Michael , Reinhard Christoph , Cohen Stanley N.
Published: June 2003

Down-regulation of mitogenic signaling in mammalian cells relies in part on endosomal trafficking of activated receptors into lysosomes, where the receptors are degraded. These events are mediated by ubiquitination of the endosomal cargo and its consequent sorting into multivesicular bodies that form at the surfaces of late endosomes. Tumor susceptibility gene 101 (
tsg101
) recently was found to be centrally involved in this process. Here we report that TSG101 interacts with hepatocyte growth factor-regulated tyrosine kinase substrate (HRS), an early endosomal protein, and that disruption of this interaction impedes endosomal trafficking and endocytosis-mediated degradation of mitogenic receptors. TSG101/HRS interaction occurs between a ubiquitin-binding domain of TSG101 and two distinct proline-rich regions of HRS, and is modulated by a C-terminal TSG101 sequence that resembles a motif targeted in HRS. Mutational perturbation of TSG101/HRS interaction prevented delivery of epidermal growth factor receptor (EGFR) to late endosomes, resulted in the cellular accumulation of ubiquitinated EGFR in early endosomes, and inhibited ligand-induced down-regulation of EGFR. Our results reveal the TSG101 interaction with HRS as a crucial step in endocytic down-regulation of mitogenic signaling and suggest a role for this interaction in linking the functions of early and late endosomes.
The evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes
Authors: Jiang Yong , Doolittle Russell F.
Published: June 2003

The blood coagulation scheme for the puffer fish,
Fugu rubripes
, has been reconstructed on the basis of orthologs of genes for mammalian blood clotting factors being present in its genome. As expected, clotting follows the same fundamental pattern as has been observed in other vertebrates, even though genes for some clotting factors found in mammals are absent and some others are present in more than one gene copy. All told, 26 different proteins involved in clotting or fibrinolysis were searched against the puffer fish genome. Of these, orthologs were found for 21. Genes for the ``contact system'' factors (factor XI, factor XII, and prekallikrein) could not be identified. On the other hand, two genes were found for factor IX and four for factor VII. It was evident that not all four factor VII genes are functional, essential active-site residues having been replaced in two of them. A search of the genome of a urochordate, the sea squirt,
Ciona intestinalis
, did not turn up any genuine orthologs for these 26 factors, although paralogs and/or constituent domains were evident for virtually all of them.
Expression of utrophin A mRNA correlates with the oxidative capacity of skeletal muscle fiber types and is regulated by calcineurin/NFAT signaling
Authors: Chakkalakal Joe V. , Stocksley Mark A. , Harrison Mary-Ann , Angus Lindsay M. , Deschênes-Furry Julie , St-Pierre Simon , Megeney Lynn A. , Chin Eva R. , Michel Robin N. , Jasmin Bernard J.
Published: June 2003

Utrophin levels have recently been shown to be more abundant in slow vs. fast muscles, but the nature of the molecular events underlying this difference remains to be fully elucidated. Here, we determined whether this difference is due to the expression of utrophin A or B, and examined whether transcriptional regulatory mechanisms are also involved. Immunofluorescence experiments revealed that slower fibers contain significantly more utrophin A in extrasynaptic regions as compared with fast fibers. Single-fiber RT-PCR analysis demonstrated that expression of utrophin A transcripts correlates with the oxidative capacity of muscle fibers, with cells expressing myosin heavy chain I and IIa demonstrating the highest levels. Functional muscle overload, which stimulates expression of a slower, more oxidative phenotype, induced a significant increase in utrophin A mRNA levels. Because calcineurin has been implicated in controlling this slower, high oxidative myofiber program, we examined expression of utrophin A transcripts in muscles having altered calcineurin activity. Calcineurin inhibition resulted in an 80% decrease in utrophin A mRNA levels. Conversely, muscles from transgenic mice expressing an active form of calcineurin displayed higher levels of utrophin A transcripts. Electrophoretic mobility shift and supershift assays revealed the presence of a nuclear factor of activated T cells (NFAT) binding site in the utrophin A promoter. Transfection and direct gene transfer studies showed that active forms of calcineurin or nuclear NFATc1 transactivate the utrophin A promoter. Together, these results indicate that expression of utrophin A is related to the oxidative capacity of muscle fibers, and implicate calcineurin and its effector NFAT in this mechanism.