bluuebunny/crossref_metadata_2025 huggingface dataset:
Patients with acute myeloid leukemia and an activating mutation in FLT3 respond to a small-molecule FLT3 tyrosine kinase inhibitor, PKC412
Authors: Stone Richard M. , DeAngelo Daniel J. , Klimek Virginia , Galinsky Ilene , Estey Eli , Nimer Stephen D. , Grandin Wilson , Lebwohl David , Wang Yanfeng , Cohen Pamela , Fox Edward A. , Neuberg Donna , Clark Jennifer , Gilliland D. Gary , Griffin James D.
Published: September 2004

Leukemic cells from 30% of patients with acute myeloid leukemia (AML) have an activating mutation in the FLT3 (fms-like tyrosine kinase) gene, which represents a target for drug therapy. We treated 20 patients, each with mutant FLT3 relapsed/refractory AML or high-grade myelodysplastic syndrome and not believed to be candidates for chemotherapy, with an FLT3 tyrosine kinase inhibitor, PKC412 (N-benzoylstaurosporine), at a dose of 75 mg 3 times daily by mouth. The drug was generally well tolerated, although 2 patients developed fatal pulmonary events of unclear etiology. The peripheral blast count decreased by 50% in 14 patients (70%). Seven patients (35%) experienced a greater than 2-log reduction in peripheral blast count for at least 4 weeks (median response duration, 13 weeks; range, 9-47 weeks); PKC412 reduced bone marrow blast counts by 50% in 6 patients (2 of these to < 5%). FLT3 autophosphorylation was inhibited in most of the Corresponding patients, indicating in vivo target inhibition at the dose schedule used in this study. PKC412 is an oral tyrosine kinase inhibitor with clinical activity in patients with AML whose blasts have an activating mutation of FLT3, suggesting potential use in combination with active agents, such as chemotherapy.
Heterologous expression of plant virus genes that suppress post-transcriptional gene silencing results in suppression of RNA interference in Drosophilacells
Authors: Reavy Brian , Dawson Sheila , Canto Tomas , MacFarlane Stuart A
Published: September 2004

Background

RNA interference (RNAi) in animals and post-transcriptional gene silencing (PTGS) in plants are related phenomena whose functions include the developmental regulation of gene expression and protection from transposable elements and viruses. Plant viruses respond by expressing suppressor proteins that interfere with the PTGS system.

Results

Here we demonstrate that both transient and constitutive expression of the Tobacco etch virus HC-Pro silencing suppressor protein, which inhibits the maintenance of PTGS in plants, prevents dsRNA-induced RNAi of a lacZ gene in cultured Drosophila cells. Northern blot analysis of the RNA present in Drosophila cells showed that HC-Pro prevented degradation of lacZ RNA during RNAi but that there was accumulation of the short (23nt) RNA species associated with RNAi. A mutant HC-Pro that does not suppress PTGS in plants also does not affect RNAi in Drosophila. Similarly, the Cucumber mosaic virus 2b protein, which inhibits the systemic spread of PTGS in plants, does not suppress RNAi in Drosophila cells. In addition, we have used the Drosophila system to demonstrate that the 16K cysteine-rich protein of Tobacco rattle virus, which previously had no known function, is a silencing suppressor protein.

Conclusion

These results indicate that at least part of the process of RNAi in Drosophila and PTGS in plants is conserved, and that plant virus silencing suppressor proteins may be useful tools to investigate the mechanism of RNAi.
Estimating blood vessel areas in ultrasound images using a deformable template model
Authors: Husby Oddvar , Rue Haåvard
Published: September 2004

We consider the problem of obtaining interval estimates of vessel areas from ultrasound images of cross sections through the carotid artery. Robust and automatic estimates of the cross sectional area is of medical interest and of help in diagnosing atherosclerosis, which is caused by plaque deposits in the carotid artery. We approach this problem by using a deformable template to model the blood vessel outline, and use recent developments in ultrasound science to model the likelihood. We demonstrate that by using an explicit model for the outline, we can easily adjust for an important feature in the data: strong edge reflections called specular reflection. The posterior is challenging to explore, and naive standard MCMC algorithms simply converge too slowly. To obtain an efficient MCMC algorithm we make extensive use of computational efficient Gaussian Markov random fields, and use various block sampling constructions that jointly update large parts of the model.
Bayesian analysis of extreme events with threshold estimation
Authors: Behrens Cibele N , Lopes Hedibert F , Gamerman Dani
Published: September 2004

The aim of this paper is to analyse extremal events using generalized Pareto distributions (GPD), considering explicitly the uncertainty about the threshold. Current practice empirically determines this quantity and proceeds by estimating the GPD parameters on the basis of data beyond it, discarding all the information available below the threshold. We introduce a mixture model that combines a parametric form for the center and a GPD for the tail of the distributions and uses all observations for inference about the unknown parameters from both distributions, the threshold included. Prior distributions for the parameters are indirectly obtained through experts quantiles elicitation. Posterior inference is available through Markov chain Monte Carlo methods. Simulations are carried out in order to analyse the performance of our proposed model under a wide range of scenarios. Those scenarios approximate realistic situations found in the literature. We also apply the proposed model to a real dataset, Nasdaq 100, an index of the financial market that presents many extreme events. Important issues such as predictive analysis and model selection are considered along with possible modeling extensions.
The CCCH tandem zinc-finger protein Zfp36l2 is crucial for female fertility and early embryonic development
Authors: Ramos Silvia B. V. , Stumpo Deborah J. , Kennington Elizabeth A. , Phillips Ruth S. , Bock Cheryl B. , Ribeiro-Neto Fernando , Blackshear Perry J.
Published: September 2004

The CCCH tandem zinc finger protein, Zfp36l2, like its better-known relative tristetraprolin (TTP), can decrease the stability of AU-rich element-containing transcripts in cell transfection studies; however, its physiological importance is unknown. We disrupted Zfp36l2 in mice,resulting in decreased expression of a truncated protein in which the N-terminal 29 amino acids had been deleted (ΔN-Zfp36l2). Mice derived from different clones of ES cells exhibited complete female infertility,despite evidence from embryo and ovary transplantation experiments that they could gestate and rear wild-type young. ΔN-Zfp36l2 females apparently cycled and ovulated normally, and their ova could be fertilized; however, the embryos did not progress beyond the two-cell stage of development. These mice represent a specific model of disruption of the earliest stages of embryogenesis, implicating Zfp36l2, a probable mRNA-binding and destabilizing protein, in the physiological control of female fertility at the level of early embryonic development. This newly identified biological role for Zfp36l2 may have implications for maternal mRNA turnover in normal embryogenesis, and conceivably could be involved in some cases of unexplained human female infertility.
Structure, isolation, composition and reconstitution of the neuronal fusion pore
Authors: Cho Won Jin , Jeremic Aleksandar , Rognlien Kathy T. , Zhvania Mzia G. , Lazrishvili Ilia , Tamar Bikashvili , Jena Bhanu P.
Published: August 2004

Neuronal communication is dependent on the fusion of 40–50 nm in diameter synaptic vesicles containing neurotransmitters, at the presynaptic membrane. Here we report for the first time at 5–8 Å resolution, the presence of 8–10 nm in diameter cup‐shaped neuronal fusion pores or porosomes at the presynaptic membrane, where synaptic vesicles dock and fuse to release neurotransmitters. The structure, isolation, composition, and functional reconstitution of porosomes present at the nerve terminal are described. These findings reveal the molecular mechanism of neurotransmitter release at the presynaptic membrane of nerve terminals.
Vesicle swelling regulates content expulsion during secretion
Authors: Kelly Marie L. , Cho Won Jin , Jeremic Aleksandar , Abu‐Hamdah Rania , Jena Bhanu P.
Published: August 2004

The involvement of secretory vesicle swelling has been proposed in secretion; however, little is known about its role. Using both the pancreatic acinar cell and neuronal model, we show secretory vesicle swelling in live cells. Our study reveals that vesicle swelling potentiates its fusion at the cell plasma membrane, and is required for expulsion of intravesicular contents. Since the extent of swelling is directly proportional to the amount of vesicular contents expelled, this provides cells with the ability to regulate release of secretory products. These direct observations of the requirement of secretory vesicle swelling in secretion, provides an understanding of the appearance of partially empty vesicles following the process.
Studying spatial and trophic interactions between capelin and cod using individual-based modelling
Authors: Huse Geir , Johansen Geir Odd , Bogstad Bjarte , Gjøsæter Harald
Published: August 2004

The objective of this study was to use spatially explicit individual-based models for simulating the movement, foraging, growth, and mortality of cod and capelin in the Barents Sea in order to identify general features in their migration patterns and the consumption of capelin by cod. The individual-based models are initiated from survey data run over 1 year and validated against survey information. Directed movement is based on a combination of movement vectors and temperature boundaries, and bioenergetics models are used to calculate growth. Capelin consumption by cod is calculated from local encounters between the species. For capelin, the best movement model can be summarized as: stay southwest of the 2.5°C and 4°C temperature front at 50-m depth for juvenile and mature individuals, respectively, in winter, and migrate northwards during summer, but do not pass the −1.5°C temperature front. The best cod model was to migrate south-southwest during winter and north-northeast during summer, within the temperature range 1°C to 8°C. The annual consumption estimates found here reflected the interannual and seasonal pattern from previous studies based on stomach samples, but were generally lower. Consumption estimates varied depending on the movement models, and the best movement model also produced the consumption estimate closest to that obtained in other studies. Introducing a simple rule stating that cod should move in a randomly selected direction when the local capelin density is zero increased the consumption estimate by 30%. This suggests that more emphasis needs to be put on exploring how behavioural rules in predators and prey affect their interactions. Even though there are some discrepancies between predictions and observations, the results achieved by the model with regard to spatial distribution, growth, and consumption are promising.
Behaviour of herring (Clupea harengus L.) towards an approaching autonomous underwater vehicle
Authors: Patel Ruben , Handegard Nils Olav , Godø Olav Rune
Published: August 2004

The reaction of schooling wintering herring (Clupea harengus L.) in Ofotfjord in northern Norway is studied when approached by an autonomous underwater vehicle (AUV) with electrical propulsion. The reaction of herring is recorded running the AUV in the beam of the mother vessel's 38-kHz echosounder and in more detail with an onboard 120-kHz echosounder. The results indicate an insignificant reaction of herring to the approaching AUV, although some variations were observed depending on the experimental set-up. Technical uncertainty in the recordings close to the AUV transducer creates some ambiguity in the results. No reaction could be identified from the ship's sounder when the AUV passed under the vessel. Processing of the onboard echosounder data suggests a mean avoidance distance of 8.0 m in these experiments. In a realistic autonomous survey situation it is assumed that the AUV can approach as closely as 5–10 m to herring schools without affecting the acoustic observation, which makes it a potentially useful platform for hydroacoustic research and survey. More systematic studies are needed to precisely define the threshold reaction distance to the AUV, and the work should be conducted with transducers on a more silent platform than RV “Johan Hjort”, which was used in this study.
Ultrasonic tracking reveals multiple behavioural modes of snapper (Pagrus auratus) in a temperate no-take marine reserve
Authors: Egli D.P. , Babcock R.C.
Published: August 2004

Interactions between marine reserve populations and non-reserve populations of exploited fishes have generally been modelled using simplistic assumptions about behaviour. Consequently, there is a recognized need for better information on fish movement behaviour at the appropriate spatial scales to generate more realistic interaction models. Automated ultrasonic tracking of marine fish, applied in this study, offers the potential to continuously track individuals for periods of up to several years within the study area. Snapper (Pagrus auratus) (FL: 33–68 cm) were surgically implanted with individually coded ultrasonic transmitters to monitor their movement within the Cape Rodney to Okakari Point Marine Reserve in northeast New Zealand from October 2001 to September 2002. The range of movement patterns observed includes some fish resident for the entire tracking period, while others were more mobile. Of the latter group, some fish left the array permanently while others returned after up to 83 days of continuous absence. Nearly all fish showed some level of site fidelity for varying periods of the time they were tracked. Fish activity peaked in the summer, when highest densities are known to occur. Results suggest that snapper behaviour is variable, and that patterns of habitat utilization vary between fish and also seasonally. Such a complex range of behaviours may be a key component for achieving desirable outcomes for both conservation and fisheries in marine reserves.
Role of Ca2+‐independent phospholipase A2 and n−3 polyunsaturated fatty acid docosahexaenoic acid in prostanoid production in brain: perspectives for protection in neuroinflammation
Authors: Strokin Mikhail , Sergeeva Marina , Reiser Georg
Published: August 2004

Various diseases of the central nervous system are characterized by induction of inflammatory events, which involve formation of prostaglandins. Production of prostaglandins is regulated by activity of phospholipases A2 and cyclooxygenases. These enzymes release the prostaglandin precursor, the n−6 polyunsaturated fatty acid, arachidonic acid and oxidize it into prostaglandin H2. Docosahexaenoic acid, which belongs to the n−3 class of polyunsaturated fatty acids, was shown to reduce production of prostaglandins after in vivo and in vitro administration. Nevertheless, the fact that in brain tissue cellular phospholipids naturally have a uniquely high content of docosahexaenoic acid was ignored so far in studies of prostaglandin formation in brain tissue. We consider the following possibilities: docosahexaenoic acid might attenuate production of prostaglandins by direct inhibition of cyclooxygenases. Such inhibition was found with the isolated enzyme. Another possibility, which has been already shown is reduction of expression of inducible cyclooxygenase‐2. Additionally, we propose that docosahexaenoic acid could influence intracellular Ca2+ signaling, which results in changes of activity of Ca2+‐dependent phospholipase A2, hence reducing the amount of arachidonic acid available for prostaglandin production. Astrocytes, the main type of glial cells in the brain control the release of arachidonic acid, docosahexaenoic acid and the formation of prostaglandins. Our recently obtained data revealed that the release of arachidonic and docosahexaenoic acids in astrocytes is controlled by different isoforms of phospholipase A2, i.e. Ca2+‐dependent phospholipase A2 and Ca2+‐independent phospholipase A2, respectively. Moreover, the release of arachidonic and docosahexaenoic acids is differently regulated through Ca2+‐ and cAMP‐dependent signal transduction pathways. Based on analysis of the current literature and our own data we put forward the hypothesis that Ca2+‐independent phospholipase A2 and docosahexaenoic acid are promising targets for treatment of inflammatory related disorders in brain. We suggest that Ca2+‐independent phospholipase A2 and docosahexaenoic acid might be crucially involved in brain‐specific regulation of prostaglandins.
Selective changes in expression of different nicotinic receptor subtypes in brain and adrenal glands of mice carrying human mutated gene for APP or over‐expressing human acetylcholinestrase
Authors: Mousavi Malahat , Bednar Ivan , Nordberg Agneta
Published: August 2004

In this study, we investigated regulatory mechanisms and plasticity of the nicotinic acetylcholine receptors (nAChRs) in the brain and adrenal glands of two transgenic mice models over‐expressing human β‐amyloid precursor protein (APPSWETg) and human AChE enzyme (hAChE‐Tg), respectively. All animals were studied at 3 months of age. Binding studies showed higher 125I‐α‐bungarotoxin (α7 nAChRs) and 3H‐epibatidine (α3 and α4 nAChRs) binding in the brain cortex and adrenal glands of hAChE‐Tg mice compared to control mice. The APPSWETg mice showed a significantly lower relative level for the α4 mRNA in the brain cortex as well as a lower level of α3 mRNA, and higher level of α7 mRNA in the adrenal glands compared to control mice. A higher relative mRNA level of α3 and α4 nAChRs was observed in the brain as well as of α3 and α7 nAChRs in the adrenal glands of hAChE‐Tg mice compared to control mice.

Different nicotinic receptor plasticity is revealed in the brain cortex and adrenal glands in two transgenic mice models with different underlying pathophysiological mechanisms. Deposition of β‐amyloid (Aβ) may impair neurotransmitter activity in brain as well as in the adrenal gland.
Turning the heterogeneous into homogeneous: studies on selectively isolated GABAergic interneuron subsets
Authors: Berghuis Paul , Dobszay Marton B. , Ibanez Raquel Martin , Ernfors Patrik , Harkany Tibor
Published: August 2004

The amazing morphological and electrophysiological diversity of cortical GABAergic interneurons subserves the broad diversity of processes these cells modulate in neuronal networks. Until recently, interneuron development and functions have been extensively studied in heterogeneous in vitro and in vivo systems containing both excitatory and inhibitory components. However, mechanisms of interneuron specification during development, key signaling mechanisms controlling the establishment of particular inhibitory neuron subsets, and the spatial and temporal regulation of their integration in neuronal microcircuits remain poorly understood. Selective isolation of particular interneuron subsets may significantly extend our knowledge on the scenario of neurochemical and electrophysiological specification of developing interneurons, identification of signaling cues directing their axon growth, and principles of their anterograde and retrograde synaptic communication with other cell types. Here, we show that selective isolation of perisomatic inhibitory cells containing either parvalbumin or cholecystokinin reveals major differences in the temporal dynamics of their functional differentiation, and their dependence on target‐derived signals like brain‐derived neurotrophic factor and endocannabinoids. In addition, we discuss therapeutic prospects of modulating increased excitatory output in the hippocampus and subthalamic nucleus by re‐adjusting the inhibitory control of principal cells.
Neuronal trauma model: in search of Thanatos
Authors: Cole Kasie , Perez‐Polo J. Regino
Published: August 2004

Trauma to the nervous system triggers responses that include oxidative stress due to the generation of reactive oxygen species (ROS). DNA is a major macromolecular target of ROS, and ROS‐induced DNA strand breaks activate poly(ADP‐ribose)polymerase‐1 (PARP‐1). Upon activation PARP‐1 uses NAD+ as a substrate to catalyze the transfer of ADP‐ribose subunits to a host of nuclear proteins. In the face of extensive DNA strand breaks, PARP‐1 activation can lead to depletion of intracellular NAD(P)(H) pools, large decreases in ATP, that threaten cell survival. Accordingly, inhibition of PARP‐1 activity after acute oxidative injury has been shown to increase cell survival. When NGF‐differentiated PC12 cells, an in vitro neuronal model, are exposed to H2O2 there is increased synthesis of poly ADP‐ribose and decreases in intracellular NAD(P)(H) and ATP. Addition of the chemical PARP inhibitor 3‐aminobenzamide (AB) prior to H2O2 exposure blocks the synthesis of poly ADP‐ribose and maintains intracellular NAD(P)(H) and ATP levels. H2O2 injury is characterized by an immediate, necrotic cell death 2 h after injury and a delayed apoptotic‐like death 12–24 h after injury. This apoptotic‐like death is characterized by apoptotic membrane changes and apoptotic DNA fragmentation but is not associated with measurable caspase‐3 activity. AB delays cell death beyond 24 h and increases cell survival by ∼25%. This protective effect is accompanied by significantly decreased necrosis and the apoptotic‐like death associated with H2O2 exposure. AB also restores caspase‐3 which can be attributed to the activation of the upstream activator of caspase‐3, caspase‐9. Thus, the maintenance of intracellular ATP levels associated with PARP‐1 inhibition shifts cell death from necrosis to apoptosis and from apoptosis to cell survival. Furthermore, the shift from necrosis to apoptosis may be explained, in part, by an energy‐dependent activation of caspase‐9.
Chemistry of burning the forest floor during the FROSTFIRE experimental burn, interior Alaska, 1999
Authors: Harden J. W. , Neff J. C. , Sandberg D. V. , Turetsky M. R. , Ottmar R. , Gleixner G. , Fries T. L. , Manies K. L.
Published: August 2004

Wildfires represent one of the most common disturbances in boreal regions, and have the potential to reduce C, N, and Hg stocks in soils while contributing to atmospheric emissions. Organic soil layers of the forest floor were sampled before and after the FROSTFIRE experimental burn in interior Alaska, and were analyzed for bulk density, major and trace elements, and organic compounds. Concentrations of carbon, nutrients, and several major and trace elements were significantly altered by the burn. Emissions of C, N, and Hg, estimated from chemical mass balance equations using Fe, Al, and Si as stable constituents, indicated that 500 to 900 g C and up to 0 to 4 × 10−4 g Hg/m2 were lost from the site. Calculations of nitrogen loss range from −4 to +6 g/m2 but were highly variable (standard deviation 19), with some samples showing increased N concentrations post‐burn potentially from canopy ash. Noncombustible major nutrients such as Ca and K also were inherited from canopy ash. Thermogravimetry indicates a loss of thermally labile C and increase of lignin‐like C in char and ash relative to unburned counterparts. Overall, atmospheric impacts of boreal fires include large emissions of C, N and Hg that vary greatly as a function of severe fire weather and its access to deep organic layers rich in C, N, and Hg. In terrestrial systems, burning rearranges the vertical distribution of nutrients in fuels and soils, the proximity of nutrients and permafrost to surface biota, and the chemical composition of soil including its nutrient and organic constituents, all of which impact C cycling.
Influence of ionosphere conductivity on the ring current
Authors: Ebihara Y. , Fok M.‐C. , Wolf R. A. , Immel T. J. , Moore T. E.
Published: August 2004

Using the Comprehensive Ring Current Model (CRCM), which self‐consistently solves the kinetic equation of ring current protons and the closure of the electric current between the magnetosphere and ionosphere, we have studied how different changes in the ionospheric conductivity affect the strength of the ring current. The conductivity for F10.7 = 250 × 104 Janskys (Jy) (solar maximum condition) results in a ring current that is about 29% stronger than for F10.7 = 70 × 104 Jy (solar minimum condition). The conductivity at equinox results in a ring current that is about 5% stronger than at solstice because the two‐hemisphere height‐integrated conductivities at equinox are higher than at solstice. This would be a new mechanism for explaining the semiannual variation of Dst. Simulation with a realistic auroral conductivity estimated from the Imager for Magnetopause‐to‐Aurora Global Exploration (IMAGE)/Far Ultraviolet Imager (FUV) auroral imager data reveals the fact that auroral brightenings do not significantly change the intensity of the ring current. The overshielding condition is found to be produced when the auroral conductivity decreases abruptly near the Dst minimum, triggering a rapid decay of the ring current. The ring current is shown to be influenced not only by the interplanetary magnetic field and the solar wind but also by solar radiation and morphological features of the auroral electron precipitation as well.
Euxinia and primary production in Late Cretaceous eastern equatorial Atlantic surface waters fostered orbitally driven formation of marine black shales
Authors: Wagner Thomas , Sinninghe Damsté Jaap S. , Hofmann Peter , Beckmann Britta
Published: August 2004

Oceanic anoxic events (OAE) in the Cretaceous represent major perturbations in the global climate and ocean system characterized by widespread deposition of organic carbon in the ocean. The causes and effects of these events are poorly constrained, mainly because of the lack of high‐resolution marine records. Here we report the distribution of molecular markers from a millennial‐scale record of Coniacian‐Santonian black shale (OAE‐3) from Ocean Drilling Program Site 959 in the Deep Ivorian Basin in the eastern equatorial Atlantic. Highly branched isoprenoids and alkenone‐derived organic compounds indicate that diatoms and calcareous nanoplankton were important primary producers. Changes in redox sensitive trace metal accumulation and biomarkers of green sulfur bacteria provide evidence for extreme variations in redox conditions, with intervals of lower photic zone euxinia (PZE). Accordingly, oxygen in the Coniacian‐Santonian tropical Atlantic was absent as during the Cenomanian‐Turonian boundary OAE‐2 but over more restricted geographic area and more limited time intervals. We hypothesize that PZE was a common phenomenon typical in large areas of tropical continental margins. These conditions fostered sequestration of atmospheric CO2 and thus helped cause the positive excursion in δ13C of carbonate documented in higher latitude marine records.
Mixed convection and density‐dependent seawater circulation in coastal aquifers
Authors: Smith Anthony J.
Published: August 2004

Density‐dependent circulation of seawater in coastal aquifers results in submarine groundwater discharge (SGD) across the seabed that is a mixture of terrestrial groundwater and former marine water. In this study, the controls of the relative amount of seawater to freshwater in SGD were investigated numerically using the FEFLOW and SUTRA codes. It was found that the key controls could be expressed in the form of a single nondimensional recirculation number that incorporates the combined effects of free convection, forced convection, and hydrodynamic dispersion on convective overturn within the coastal salt wedge. Anisotropy effects were incorporated into the recirculation number with limited success based on the principle of equivalent isotropic hydraulic conductivity. The type of boundary condition employed along the seabed was shown to be important. Convective overturn was substantially increased if backward dispersion of salt into the aquifer from along the outflowing portion of the seabed boundary was prevented. Overall, the results demonstrated a strong dependence of convective overturn on the aquifer dispersivities, suggesting that results from numerical simulations are problematic to apply to real aquifer systems that typically exhibit uncertain, scale‐dependent dispersion properties.
Quantification of seismic scattering in situ with the conversion log method: A study from the KTB super‐deep drill hole
Authors: Beilecke Thies , Rabbel Wolfgang
Published: August 2004

The “conversion log” is a new approach to quantify seismic scattering in situ in terms of PS conversion in transmission along a vertical seismic profile (VSP): The amount of converted seismic energy is determined by slant‐stacking and plotted as a function of depth, thus forming a borehole log of seismic conversion. We investigated seismic scattering of crystalline crust at the Continental Deep Drilling Site (KTB) in southern Germany where detailed knowledge exists of crustal parameters down to 9 km depth. In 1999 a deep VSP was acquired in the KTB main borehole. The experiment yielded high quality seismic data in terms of signal bandwidth, signal‐to‐noise ratio and stability of the source signal. The seismic data show varying levels of PS conversion along the borehole. The dip of layering and foliation is about 45° to 75° along the KTB drill hole. Under these conditions the conversion amplitudes depend only weakly on the angle between the incident seismic wave and the impedance contrast surface. The conversion log method was used to quantify energy loss by forward scattering. Field data were compared with finite‐difference computations and with petrological and structural borehole information. It turned out that only 10–50% of PS forward scattering originates from conversion at lithological interfaces and structural complexity whereas 90–50% is due to velocity heterogeneity caused by fractures. The conversion log is correlated with the depth function of fracture density, and it is inversely correlated with the depth function of chlorite content, that seems to ‘heal’ the influence of cracks and fissures.
Local time effects in satellite estimates of electromagnetic induction transfer functions
Authors: Balasis Georgios , Egbert Gary D. , Maus Stefan
Published: August 2004

The current satellite magnetic missions offer new opportunities to determine the electrical conductivity of the Earth. However, satellites are nearly stationary in local time and therefore sample the inducing and induced fields quite differently than geomagnetic observatories, which rotate with the Earth. We show that estimates of induction transfer functions obtained from CHAMP magnetic data under the traditional symmetric magnetospheric ring current source (Y10) assumption depend systematically on local time, suggesting that source fields contain also a coherent non‐axisymmetric component. An extended magnetospheric source model that incorporates a coherent non‐axisymmetric quadrupole (Y21), and allows for Earth rotation qualitatively explains the observations.
Discrepancies in the prediction of solar wind using potential field source surface model: An investigation of possible sources
Authors: Poduval Bala , Zhao Xue Pu
Published: August 2004

An inverse correlation has been found to exist between the magnetic flux tube expansion factor (FTE) at the source surface and the solar wind speed (SWS) observed at Earth, which has been made use of in the prediction of solar wind speed near the Earth with reasonable accuracy. However, the correlation between FTE and the solar wind speed at Earth is not always consistently high, and the discrepancies between the observed and predicted SWS are quite significant. There are several factors causing this discrepancy. The present work is an investigation of such factors and an estimation of error caused by them. We found that the number of multipole components included in the spherical harmonic expansion in the potential field source surface model, Nmax, has tremendous influence on the location of photospheric foot points of coronal features as well as the computation of FTE. Another important factor is the transit time of solar wind used in the inverse mapping. Approximate values of this parameter that are currently being used can lead to significant errors in the predicted solar wind speed. We also present a detailed discussion on the importance of considering interaction between slow and fast solar wind streams in the inverse mapping technique.
Predicting the ionospheric F layer using neural networks
Authors: McKinnell Lee‐Anne , Poole Allon W. V.
Published: August 2004

A new neural network (NN) based ionospheric model for the bottomside electron density profile over Grahamstown, South Africa (33.3°S, 26.5°E) has been developed and is referred to as the LAM model. This paper discusses the development of the F layer contribution to the LAM model. Archived data from the Grahamstown ionospheric station have been presented to various NNs, which have been trained to predict the parameters required to produce an electron density profile. Since the dataset was only made up of Grahamstown data, the model is currently a single station model. The input space designed for the F layer contribution to the LAM model consisted of various combinations of the following parameters: day number (DN), hour (HR), a measure of the solar activity, and a measure of the magnetic activity. The solar activity input was represented by a 2‐month running mean value of the sunspot number (R2), while the magnetic activity variable was represented by either a 24‐hour or 48‐hour running mean of the magnetic ak value (A8 or A16). The outputs from the NNs were the peak parameters and Chebyshev coefficients required to describe the shape and location of the F profile. This paper also discusses how NNs have been employed to provide an effective mechanism for determining the probability of the existence of an F1 layer. An F1 layer can exist in one of the following three states; F1 exists, no F1, or F1 exists in L condition state. A special NN was trained to provide the probability of F1 layer existence in each of these states. An L algorithm is applied to determine the shape and location of the profile under L condition state. In addition, a smoothing technique was designed to deal with discontinuities across the F1‐F2 boundary. It is shown that the NN‐based LAM model can successfully predict descriptions for the shape and location of the average profile for a given input set, and, in addition, that NNs can be employed to provide solutions to previously difficult prediction tasks such as the probability of F1 layer existence.
Earthquake source scaling and self‐similarity estimation from stacking P and S spectra
Authors: Prieto Germán A. , Shearer Peter M. , Vernon Frank L. , Kilb Debi
Published: August 2004

We study the scaling relationships of source parameters and the self‐similarity of earthquake spectra by analyzing a cluster of over 400 small earthquakes (ML = 0.5 to 3.4) recorded by the Anza seismic network in southern California. We compute P, S, and preevent noise spectra from each seismogram using a multitaper technique and approximate source and receiver terms by iteratively stacking the spectra. To estimate scaling relationships, we average the spectra in size bins based on their relative moment. We correct for attenuation by using the smallest moment bin as an empirical Green's function (EGF) for the stacked spectra in the larger moment bins. The shapes of the log spectra agree within their estimated uncertainties after shifting along the ω−3 line expected for self‐similarity of the source spectra. We also estimate corner frequencies and radiated energy from the relative source spectra using a simple source model. The ratio between radiated seismic energy and seismic moment (proportional to apparent stress) is nearly constant with increasing moment over the magnitude range of our EGF‐corrected data (ML = 1.8 to 3.4). Corner frequencies vary inversely as the cube root of moment, as expected from the observed self‐similarity in the spectra. The ratio between P and S corner frequencies is observed to be 1.6 ± 0.2. We obtain values for absolute moment and energy by calibrating our results to local magnitudes for these earthquakes. This yields a S to P energy ratio of 9 ± 1.5 and a value of apparent stress of about 1 MPa.
Analyses of the spring dust storm frequency of northern China in relation to antecedent and concurrent wind, precipitation, vegetation, and soil moisture conditions
Authors: Liu Xiaodong , Yin Zhi‐Yong , Zhang Xiaoye , Yang Xuchao
Published: August 2004

The relationships between the spring (March–May) dust storm frequency (DSF) of northern China, gridded precipitation based on gauge observations, wind velocity at different geopotential heights, satellite‐measured land vegetation index, and grid box soil moisture data during 1982–2001 are examined using correlation analysis and singular value decomposition methods. The results show that the spring DSF time series has strong positive correlations with the upwind wind velocity but strong negative correlations with the antecedent summer (June–August) and annual (June of the prior year to May of the current year) precipitation and soil moisture anomalies, as well as with the spring vegetation condition across a region running northeast‐southwest from the northeast China and China‐Mongolia border to the Taklimakan Desert. This region has been identified as the major source of dust emission in northern China. The results suggest that the summer rainfall anomaly over an extensive area close to the China‐Mongolia border is the primary factor that determines the local soil moisture condition in the summer and then the vegetation condition in the following spring through persistence of the soil moisture, eventually determining the variation pattern of the spring DSF in northern China.
Temporal changes in North Atlantic circulation constrained by planktonic foraminiferal shell weights
Authors: Barker Stephen , Kiefer Thorsten , Elderfield Henry
Published: August 2004

Records of planktonic foraminiferal shell weights for Globigerina bulloides, covering Termination I from four proximal sites at waters depths from 1150 to 4045 m in the northeast Atlantic, demonstrate the influence of dissolution superimposed upon initial shell weight variability. Records of shell weight, unaffected by dissolution, may be used as a reference for interpreting deeper records in terms of preservation history. Combining records of planktonic shell weight (and benthic δ13C) from shallow and deep sites suggests that maximum oceanic stratification and incursion of southern sourced deep waters in the North Atlantic occurred at about 18–20 ka, defining the glacial mode of Atlantic circulation. Reduced stratification and enhanced preservation in deeper waters reflect conditions during Heinrich event 1. A state similar to the modern mode of Atlantic circulation was attained by about 10 ka.
Deposition and mobilization of clay colloids in unsaturated porous media
Authors: Gao Bin , Saiers James E. , Ryan Joseph N.
Published: August 2004

We report results on the effects of porewater pH and transients in porewater flow on the deposition and mobilization of colloid‐sized clay particles within unsaturated sand columns. The deposition rates of illite under steady‐flow conditions were essentially independent of pH, while the deposition rates of kaolinite nearly doubled as the pH decreased from 7.4 to 4.6. Mobilization of kaolinite colloids was slow or negligible under steady‐flow conditions; however, transients in porewater flow induced rapid colloid release. A model that accounts for rate‐limited deposition reactions and that links colloid mobilization to variations in moisture content and porewater velocity describes the effluent colloid concentrations measured during the steady‐flow and transient‐flow stages of the column experiments. On the basis of these results we infer that the effects of pH on clay‐colloid deposition depend on the mineralogy of the clay colloids and that perturbations in flow are critical in mobilizing clay colloids within the vadose zone.
A coplanar waveguide permeameter for studying high-frequency properties of soft magnetic materials
Authors: Ding Y. , Klemmer T. J. , Crawford T. M.
Published: September 2004

The high-frequency relative permeability of thin permalloy films was measured in the frequency and time domain using a microwave coplanar waveguide (CPW). Frequency domain measurements using a loop permeameter were performed for comparison. The Fourier transform of the time domain measurement, and the frequency domain measurement on the CPW agree closely, both showing a higher-frequency secondary resonance peak which is not seen with the loop measurement. This resonance likely arises from the lowest-order perpendicular standing spin wave mode of the permalloy film.
Incorporation of a single His residue by rational design enables thiol-ester hydrolysis by human glutathione transferase A1-1
Authors: Hederos Sofia , Broo Kerstin S. , Jakobsson Emma , Kleywegt Gerard J. , Mannervik Bengt , Baltzer Lars
Published: August 2004

A strategy for rational enzyme design is reported and illustrated by the engineering of a protein catalyst for thiol-ester hydrolysis. Five mutants of human glutathione (GSH; γ-Glu-Cys-Gly) transferase A1-1 were designed in the search for a catalyst and to provide a set of proteins from which the reaction mechanism could be elucidated. The single mutant A216H catalyzed the hydrolysis of the
S
-benzoyl ester of GSH under turnover conditions with a
k
cat
/
K
M
of 156 M
–1
·min
–1
, and a catalytic proficiency of >10
7
M
–1
when compared with the first-order rate constant of the uncatalyzed reaction. The wild-type enzyme did not hydrolyze the substrate, and thus, the introduction of a single histidine residue transformed the wild-type enzyme into a turnover system for thiol-ester hydrolysis. By kinetic analysis of single, double, and triple mutants, as well as from studies of reaction products, it was established that the enzyme A216H catalyzes the hydrolysis of the thiol-ester substrate by a mechanism that includes an acyl intermediate at the side chain of Y9. Kinetic measurements and the crystal structure of the A216H GSH complex provided compelling evidence that H216 acts as a general-base catalyst. The introduction of a single His residue into human GSH transferase A1-1 created an unprecedented enzymatic function, suggesting a strategy that may be of broad applicability in the design of new enzymes. The protein catalyst has the hallmarks of a native enzyme and is expected to catalyze various hydrolytic, as well as transesterification, reactions.
Thermally oxidised sunflower-seed oil increases liver and serum peroxidation and modifies lipoprotein composition in rats
Authors: Garrido-Polonio Carmen , García-Linares M. Carmen , García-Arias M. Trinidad , López-Varela Sara , García-Fernández M. Camino , Terpstra Antonius H. M. , Sánchez-Muniz Francisco J.
Published: August 2004

Peroxidation of LDL and other lipoproteins is thought to play a central role in atherogenesis. Dietary thermally oxidised oils may increase atherogenic risk in consumers by increasing their oxidative status. The present paper compares the effects of two diets containing unused sunflower-seed oil (US) or sunflower-seed oil repeatedly used in frying (FS) (both 15 g/100 g diet) on weight gain, food efficiency ratio, serum lipid levels and lipoprotein composition, and the content of thiobarbituric acid-reactive substances (TBARS) in the liver, serum, and lipoproteins in growing Wistar rats. After sixty potato fryings the FS contained 27·7 g polar material/100 g oil and 16·6 g oligomers/100 g oil. The FS-fed rats had a significantly lower weight gain and food efficiency ratio. Liver-TBARS increased due to the consumption of the highly altered oil and showed a significant linear relationship (allr<0·68;P>0·002) with the ingestion of thermally oxidised compounds. Serum-, VLDL-, LDL- and HDL-TBARS were significantly higher in the FS-fed rats (allP>0·001). Concentrations of serum total and non-esterified cholesterol and phospholipids were significantly higher in the FS-fed rats (P>0·05,P>0·05, andP>0·001, respectively). Serum triacylglycerol concentrations did not vary between the two dietary groups. Total and esterified cholesterol and phospholipid levels increased significantly in the HDL fraction (P>0·05,P>0·05, andP>0·001, respectively) of the FS-fed rats. HDL-cholesterol and HDL-phospholipids were significantly correlated with liver-TBARS (r<0·747;P>0·0001), VLDL-TBARS (r<0·642;P>0·003), LDL-TBARS (r<0·475;P>0·04), and HDL-TBARS (r<0·787;P>0·0001). The data suggest that the rat increases HDL as a protecting mechanism against the peroxidative stress induced by the consumption of a diet containing the thermally oxidised oil.
Studies on the bioavailability of the provitamin A carotenoid, β-carotene, using human exfoliated colonic epithelial cells
Authors: Gireesh T. , Nair P. P. , Sudhakaran P. R.
Published: August 2004

The possibility of using exfoliated colonic epithelial cells for assessing the bioavailability of β-carotene was examined. Analysis of exfoliated colonic epithelial cells showed the presence of β-carotene and vitamin A. The β-carotene content was significantly lower in cells from stool samples of subjects on a β-carotene-poor diet than those receiving a single dose of a β-carotene supplement. Colonic epithelial cells isolated from stool samples collected daily during a wash-out period while the subjects were on a β-carotene-poor diet showed a steady decrease in β-carotene content, reaching the lowest value on day 7. Kinetic analysis showed that a single dose of a β-carotene supplement in the form of spirulina (Spirulina platensis) or agathi (Sesbania grandiflora) after the wash-out period caused an increase in the β-carotene content after a lag period of 5–7 d, but the vitamin A levels during these periods were not significantly affected. Analysis of plasma β-carotene concentration also showed similar changes, which correlated with those of exfoliated colonic cells. A relationship between the β-carotene content of the diet and that of the colonic epithelial cells suggests that analysis of the β-carotene content in exfoliated human colonic epithelial cells is a useful non-invasive method to assess the bioavailability of provitamin A β-carotene.
Effects of dietary sunflower seeds on rumen protozoa and growth of lambs
Authors: Ivan M. , Mir P. S. , Mir Z. , Entz T. , He M. L. , McAllister T. A.
Published: August 2004

Linoleic acid-rich sunflower-seed supplements (SSS) were used in two experiments (experiment 1, high-concentrate diets; experiment 2, high-forage diets) to study effects on rumen protozoa and the growth of lambs. Both experiments consisted of four treatments, two with a low-protein diet (120 g/kg) and two with a high-protein diet (160 g/kg). For both diets, one treatment was without (control) and one with the SSS (140 g/kg dietary DM). The lambs were fed ad libitum for 70 and 140 d in experiments 1 and 2, respectively. Thereafter, the digestibility of organic matter (OM), acid-detergent fibre and neutral-detergent fibre were determined for each diet with four lambs, and then all lambs were slaughtered and rumen fluid samples were collected and analysed. The results showed substantial decreases (P<0·001) or total elimination of protozoa in the rumen fluid of the SSS-receiving lambs. In the first experiment the SSS also decreased (P<0·05) feed intake, but an increase in average daily gain (P<0·06) resulted in an improved (P<0·05) feed:gain ratio. Also, the SSS increased (P<0·05) the digestibility of fibre. In the second experiment the SSS decreased (P<0·05) the OM digestibility, feed intake and growth of lambs. It was concluded that the use of sunflower-seed supplementation in high-concentrate diets of ruminants reduces rumen fauna, resulting in savings on dietary protein supplements and an increased digestion of feed.