bluuebunny/crossref_metadata_2025 huggingface dataset:
Human P450 Microarrays for In Vitro Toxicity Analysis: Toward Complete Automation of Human Toxicology Screening
Authors: Lee Moo-Yeal , Clark Douglas S. , Dordick Jonathan S.
Published: December 2006

The development of a tool that can provide early-stage predictive toxicology data may accelerate the identification of safer drug candidates, and thereby improve the clinical progression of drug candidates to pharmaceuticals. Such a system would require an accurate and reliable technique that is amenable to the large number of drug candidates that must be screened in the lead discovery and optimization stages of drug development. A key component of predictive toxicology is the ability to harness the metabolite-generating capacity of human cytochromes P450, which are involved in first-pass drug metabolism function of the liver. We have miniaturized P450 catalysis into a microarray format consisting of up to 11,200 isolated P450 reactions, each in 5 nL sol-gel spots, on a single functionalized glass microscope-size biochip. This dramatic scale down from more conventional 96 and 384-well plate scales (at least a 1000-fold reduction in volume) did not adversely affect P450 catalytic activity. Based on the functionality of the P450-containing microarray, we developed the metabolizing enzyme toxicology assay Chip (MetaChip), which combines high-throughput P450 catalysis with cell-based screening on a microscale platform. Proof of concept was demonstrated using anticancer prodrugs cyclophosphamide and Tegafur, as well as the analgesic acetaminophen. The MetaChip may provide a high-throughput microscale alternative to currently used in vitro methods for human metabolism and toxicology screening.
Microfluidic 3-Dimensional Encapsulation System by Self-Assembling Peptide Hydrogel
Authors: Kim Minseok S. , Park Je-Kyun
Published: December 2006

This article describes a novel microfluidic 3-dimensional encapsulation method via the self-assembling peptide hydrogel. The microfluidic immobilization strategies using a peptide hydrogel have been designed for microfluidic cell-based assays, cocultures, and biomimetic micro blood vessels. A sol-gel transition peptide hydrogel, Puramatrix, is adopted for use in the microfluidic device fabricated by photolithography and a poly(dimethylsiloxane) replica molding process. The peptide hydrogel was hydrodynamically focused by sheath flows of distilled water and cell culture media, and gelled by diffusion of media. After being transitioned from a sol to gel phase, the fabricated scaffold in the middle of the main channel was not washed away via fluid flows. The diffused chemicals in a stripe-shaped peptide scaffold of microchannel formed a linear concentration gradient within the scaffold. Based on application in an in vivo-like 3-dimensional microenvironment, this microfluidic system could be applied to cocultures, angiological research, cytotoxicity tests, cell viability monitoring, and continuous dose-response assays as well as drug-drug interaction studies.
Alien species and other notable records from a rapid assessment survey of marinas on the south coast of England
Authors: Arenas F. , Bishop J.D.D , Carlton J.T. , Dyrynda P.J. , Farnham W.F. , Gonzalez D.J. , Jacobs M.W , Lambert C. , Lambert G. , Nielsen S.E. , Pederson J.A. , Porter J.S. , Ward S. , Wood C.A.
Published: December 2006

In September 2004, a rapid assessment survey for non-native species was conducted at 12 harbours along the south coast of England from East Sussex to Cornwall, focusing on communities of algae and invertebrates colonizing floating pontoons in marinas. Over 80 taxa each of algae and invertebrates were recorded, including 20 recognized non-native species. The southern hemisphere solitary ascidian Corella eumyota was recorded in the UK for the first time and was present at three sites. The colonial ascidian Botrylloides violaceus was also recorded as new to the UK, but was very widespread and has probably been present for a number of years but misidentified as the native congener B. leachi, which was infrequent. Other ascidians included Styela clava, introduced at Plymouth in the early 1950s, which was recorded at all locations visited, and Perophora japonica, which was found only at the Plymouth locality where it first occurred in the UK in 1999. The diverse algal flora included nine alien species previously recorded in the British Isles. Range extensions and population increases were noted for the kelp Undaria pinnatifida and the bryozoan Tricellaria inopinata, both first recorded in UK waters during the 1990s. The widespread occurrence of another non-native bryozoan, Bugula neritina, appears significant, since in earlier times this was known in UK waters predominantly from artificially heated docks. The results of this survey indicate that dock pontoon systems in southern England are significant reservoirs of non-native species dispersed by vessels and other means. The proliferation of these structures is therefore of conservation importance. The new UK records highlight the need for periodic monitoring of ports for non-native species.
Evidence for benthic body size miniaturization in the deep sea
Authors: Kaariainen Janne I. , Bett Brian J.
Published: December 2006

The benthic body size miniaturization hypothesis states that deep-sea communities are dominated by organisms of smaller body size, although some field studies have produced contradictory results. Using appropriate sample sets, this study tests this hypothesis by contrasting the benthic communities of the Fladen Ground (North Sea, 150 m) and the Faroe–Shetland Channel (1600 m). Samples were collected for large (500 μm) and small macrofauna (250–355 μm), meiofauna (45 μm) as well as an intermediate sized ‘mesofauna’ (180 μm) to ensure comprehensive coverage of the full meio- and macro-faunal body size-range. The body size structure of the benthos was compared using two methods. The more widely used average individual biomass method involves dividing the total sample biomass by sample abundance. Additionally, body size accumulation curves were constructed by assigning all specimens into a logarithmic size-class and then plotting the cumulative percentage of individuals present in each size-class. The results seem to support the hypothesis that the deep-sea environment is a small organism habitat. Although these findings only represent two locations, the overall body size accumulation curves clearly display a statistically significant shift towards smaller body sizes at the deeper site. The magnitude of the effect is appreciable with median metazoan body size reducing from 14.3 μg wet weight in the Fladen Ground to 3.8 μg wet weight in the Faroe–Shetland Channel. The average individual biomass measurements are shown to be of limited value and can lead to potentially misleading conclusions if the underlying size structure is not analysed in detail.
Reproductive biology of Alvinocaris muricola (Decapoda: Caridea: Alvinocarididae) from cold seeps in the Congo Basin
Authors: Ramirez-Llodra Eva , Segonzac Michel
Published: December 2006

The caridean shrimp Alvinocaris muricola has been observed forming high density populations over mussel beds on the giant pockmark cold seep site Regab in the Gulf of Guinea at 3150 m depth. Samples were collected using the ROV Victor 6000, a beam trawl and a TV grab from two sites. The specimens were sexed and measured for population structure analysis. In one sample the sex ratio was 1:1, but the other sample had a sex ratio significantly biased towards females. The maximum size of females is larger than males. A sub-sample was used for gametogenesis and fecundity analysis. The oogenesis and spermatogenesis of A. muricola is characteristic of caridean shrimps. The oogonia proliferate from the germinal epithelium and develop into previtellogenic oocytes that migrate to the growth zone. Vitellogenesis starts at 80–100 μm oocyte size and the developing oocytes are surrounded by a monolayer of accessory cells. The maximum oocyte size was 515 μm. There was no evidence of synchrony in oocyte development, with all oocyte stages present in all ovaries analysed. However, seasonal sampling would be necessary to confirm the lack of seasonality in reproduction. In males, the sperm develops in sperm sacs in the testis. As in all caridean shrimp, the broods of A. muricola are held on the pleopods P11 to P14. Total fecundity was related to female size and ranged between 1432 and 5798 embryos. Within a brood all embryos are at the same stage of development, but three different stages were identified in different females, with no clear seasonal trend. The embryos were small, with mean dimensions of 0.66×0.55 mm, suggesting planktotrophic larvae and a potential extended larval development.
PCR–RFLP analysis of mitochondrial DNA for identification of Rutilus rutilus caspicus populations on the southern coast of the Caspian Sea, Iran
Authors: Rezvani Sohrab , Eimanifar Amin , Aghili Reza , Laloei Faramarz
Published: December 2006

Genetic analysis using restriction fragment length polymorphisms (RFLPs) of cytochrome b in mtDNA was made to clarify genetic variations among two Iranian Rutilus rutilus caspicus populations of commercial importance from the southern coast of the Caspian Sea. Polymorphism was detected using six restriction enzymes and a total of six composite haplotypes were identified. Four haplotypes were rare occurring only once in two regions (west and east of the southern Caspian Sea). Nucleotide and haplotype diversities were higher in the south-west region of the Caspian Sea (π=3.43%, h=23.3).The nucleotide divergence between the two populations was low (0.064%). The test for heterogeneity of composite haplotype frequencies gave no significant outcome for all samples (χ2=0.137, P≤0.05). The results indicate that significant attention should be paid to the genetic characterization of R. rutilus caspicus populations for conservation of their genetic pools and aquaculture policies at the coastlines of the Caspian Sea.
Development and early life history behaviour of aquarium reared Syngnathus acus (Pisces: Syngnathidae)
Authors: Silva K. , Monteiro N.M , Almada V.C. , Vieira M.N.
Published: December 2006

Some notes on development and early life history behaviour of aquarium-reared Syngnathus acus are presented and compared with other syngnathid species, namely S. abaster. Implications in population dynamics and connectivity are discussed.
EXTREMAL WEIGHTED PATH LENGTHS IN RANDOM BINARY SEARCH TREES
Authors: Aguech Rafik , Lasmar Nabil , Mahmoud Hosam
Published: December 2006

We consider weighted path lengths to the extremal leaves in a random
binary search tree. When linearly scaled, the weighted path length to the
minimal label has Dickman's infinitely divisible distribution as a
limit. By contrast, the weighted path length to the maximal label needs to
be centered and scaled to converge to a standard normal variate in
distribution. The exercise shows that path lengths associated with
different ranks exhibit different behaviors depending on the rank.
However, the majority of the ranks have a weighted path length with
average behavior similar to that of the weighted path to the maximal
node.
Efficient Ambiguity Search Technique Using Separated Decision Variables
Authors: Kee Changdon , Kim Doyoon , Jang Jaegyu
Published: December 2006

In this paper, we propose new separated decision variables that are derived by directly using the normal distribution of each measurement error and allowing substitution of the chi-square variable of the conventional method. In the derivation of the proposed decision variables, we considered not only the related mathematical model, but also the additional unmodelled properties of GPS measurements. Using the sequential pseudo-moving-average technique, we developed a method that easily obtains the combined results of multiple epochs. To verify our proposed algorithm, we analysed its performance using real data and compared the results with those of the conventional method. Our proposed approach performs better than the conventional approach, and effectively reduces computational effort by approximately 60%. Our results demonstrate that our method achieves a solution that is as reliable as the conventional technique, while reducing the time required to only 15% of that required by the conventional technique.
The Importance of Importance
Authors: Brinker J.K. , Aitken Harris J. , Guyitt B. , Dozois D.J.A.
Published: December 2006

This study examined the relationship between importance ratings of positive and negative personal attributes and depressed mood. Undergraduate psychology students (n = 115) completed the Beck Depression Inventory-II and made self-referential ratings on several adjectives. Participants subsequently indicated how important it was for them to possess or fail to exhibit each of these traits. The results demonstrated that the perceived lack of important positive traits was related to increased depressed mood whereas not exhibiting important negative traits was associated with less depressed mood. Moreover, depressed mood was related to the degree to which respondents were certain about their endorsement of the traits. The implications of these results are discussed.
Spatial and temporal distribution of Trichodesmium blooms in the world's oceans
Authors: Westberry Toby K. , Siegel David A.
Published: December 2006

Nitrogen fixing organisms, such as the cyanobacterium Trichodesmium, directly affect the oceanic nutrient inventory through the addition of new nitrogen to the ocean ecosystem and therefore have an important role in the strength and functioning of the biological carbon pump. Nonetheless, little is known about the distribution of Trichodesmium beyond limited shipboard observations. Even less is known about the occurrence and characteristics of very intense, transient blooms of this organism that have been observed historically throughout the world oceans. A new method for discriminating the occurrence of blooms from satellite ocean color data is used here to make the first global maps of Trichodesmium bloom occurrence and to examine their spatial and temporal distribution. As expected, Trichodesmium blooms are rare, occurring <5–10% of the time over most of the tropical and subtropical oceans for the time period examined (1998–2003). Areas of greatest persistence are found in the eastern tropical Pacific and the Arabian Sea, and reach recurrence levels of >30%. Many of the retrieved patterns are consistent with previously reported blooms, though differences exist. A strong seasonal cycle is observed in the Indian Ocean, probably related to monsoonal forcing, with weaker seasonal changes elsewhere. Estimated global nitrogen fixation rates by Trichodesmium blooms is ∼42 Tg N yr−1 which is biogeochemically significant on regional and global scales. Further, an estimate of the rate of Trichodesmium nitrogen fixation under nonbloom conditions is an additional ∼20 Tg N yr−1 suggesting that Trichodesmium is likely the dominant organism in the global ocean new nitrogen budget.
Origin and mechanical significance of foliated cataclastic rocks in the cores of crustal‐scale faults: Examples from the Median Tectonic Line, Japan
Authors: Jefferies S. P. , Holdsworth R. E. , Shimamoto T. , Takagi H. , Lloyd G. E. , Spiers C. J.
Published: December 2006

The Median Tectonic Line (MTL) is Japan's largest onshore fault and has been active since the mid‐Cretaceous. Foliated cataclastic fault rocks are exceptionally well exposed in the fault core at Anko, Nagano Prefecture. Following an early phase of mylonitization and exhumation during left‐lateral shearing, brittle fracture and cataclasis occurred leading to the development of centimeter‐ to submillimeter‐spaced, fault zone parallel fracture systems. These fracture systems established an initial architectural hierarchy that influenced the subsequent development of foliated cataclasites and gouge. Initially, fracture systems coalesced to form interconnected zones of fine‐grained ultracataclasite. Fluid influx at the onset of grain‐scale brittle deformation led to precipitation of fibrous chlorite within the ultracataclasites, ultimately leading to the development of an interconnected network of foliated, phyllosilicate‐rich cataclasites and gouges in the core of the MTL. The brittle reduction of grain size and ingress of a chemically active fluid phase simultaneously promoted reaction softening and diffusive mass transfer in the foliated ultracataclasites, leading to rate‐dependent “frictional‐viscous” flow at sub‐Byerlee friction values. Associated weakening is indicated by the preferential localization of deformation within the ultracataclasites. A protracted sequence of carbonate mineralization and cementation events is also recognized during the fault rock evolution and suggests episodic periods of fluid overpressuring. A crustal‐scale fault zone model is proposed, suggesting that the foliated cataclasites/gouges are weak in the long term and represent shallower crustal equivalents of phyllonitic fault rocks exposed in more deeply exhumed fault zones, including other parts of the MTL.
Enhanced mixing and reaction through flow focusing in heterogeneous porous media
Authors: Werth Charles J. , Cirpka Olaf A. , Grathwohl Peter
Published: December 2006

Transverse dispersion across adjacent streamlines can control the amount of mixing and reaction between one or more contaminants and a limiting substrate along the fringes of groundwater plumes. Streamlines in groundwater converge and diverge in heterogeneous porous media, depending on the permeability distribution. When flow is focused in a high‐permeability zone, the distance required for a solute to cross a given number of streamlines decreases, and the time allowed for mixing and reaction is reduced. Because the first effect outweighs the latter, the overall result is an enhancement of transverse mixing and reaction. Here we develop a conceptual model of heterogeneous two‐dimensional structures facilitating flow focusing. We use the conceptual model to develop simple analytical expressions quantifying the extent to which mixing and reaction are enhanced when flow focusing occurs and compare these to results of numerical simulations. Significant enhancement of transverse mixing and reaction by flow focusing is observed; for the cases considered, flow focusing enhances the amount of reaction by a factor ranging from 1.8 to 11.9. The relatively simple analytical expressions demonstrate that the fraction of the domain height made up by high‐permeability inclusions, the fraction of flow that passes through the inclusions, and the fringe bypassing of inclusions determine the amount of mixing and reaction enhancement for the permeability distributions considered. These results partially explain why field‐scale dispersivities are larger than laboratory derived dispersivities, where homogeneous and isotropic sediments are typically used. Further work is needed to verify the theoretical results presented here with laboratory and field experiments and to expand the relatively simple analytical expressions to consider more heterogeneous three‐dimensional permeability fields.
Compositional variability in a cold‐water scleractinian, Lophelia pertusa: New insights into “vital effects”
Authors: Cohen Anne L. , Gaetani Glenn A. , Lundälv Tomas , Corliss Bruce H. , George Robert Y.
Published: December 2006

We analyzed Sr/Ca and Mg/Ca ratios in the thecal wall of Lophelia pertusa, a cold‐water coral, using SIMS ion microprobe techniques. The wall grows by simultaneous upward extension and outward thickening. Compositional variability displays similar trends along the upward and outward growth axes. Sr/Ca and Mg/Ca ratios oscillate systematically and inversely. The sensitivity of Lophelia Sr/Ca ratios to the annual temperature cycle (−0.18 mmol · mol−1/°C) is twice as strong as that exhibited by tropical reef corals, and four times as strong as the temperature dependence of Sr/Ca ratios of abiogenic aragonites precipitated experimentally from seawater. A comparison of the skeletal composition of Lophelia with results from precipitation calculations carried out using experimentally determined partition coefficients suggests that both temperature‐dependent element partitioning and seasonal changes in the mass fraction of aragonite precipitated from the calcifying fluid influence the composition of Lophelia skeleton. Results from calculations that combine these effects reproduce both the exaggerated amplitude of the Sr/Ca and Mg/Ca oscillations and the inverse relationship between Sr/Ca and Mg/Ca ratios.
Earthquake magnitude estimation from peak amplitudes of very early seismic signals on strong motion records
Authors: Zollo Aldo , Lancieri Maria , Nielsen Stefan
Published: December 2006

We show that the low‐pass filtered, peak amplitudes of initial P‐ and S‐wave seismic signals recorded in the vicinity of an occurring earthquake source correlates with the earthquake magnitude and may be used for real‐time estimation of the event size in seismic early warning applications. The earthquake size can be therefore estimated using only a couple of seconds of signal from the P‐ or S‐wave onsets, i.e. while the rupture itself is still propagating and rupture dimension is far from complete. We argue that dynamic stress release and/or slip duration on the fault in the very early stage of seismic fracture, scales both with the observed peak amplitude and with the elastic energy available for fracture propagation. The probability that a fracture grows to a larger size should scale with the energy initially available.
Coexistence of structure I and II gas hydrates in Lake Baikal suggesting gas sources from microbial and thermogenic origin
Authors: Kida Masato , Khlystov Oleg , Zemskaya Tamara , Takahashi Nobuo , Minami Hirotsugu , Sakagami Hirotoshi , Krylov Alexey , Hachikubo Akihiro , Yamashita Satoshi , Shoji Hitoshi , Poort Jeffrey , Naudts Lieven
Published: December 2006

We report the field observation of hydrate deposits of different crystal structures in the same cores of a mud volcano in the Kukuy Canyon. We link those deposits to chemical fractionation during gas hydrate crystallization. Gas composition and crystallographic analyses of hydrate samples reveal involvement of two distinct gas source types in gas hydrate formation at present or in the past: microbial (methane) and thermogenic (methane and ethane) gas types. The clathrate structure II, observed for the first time in fresh water sediments, is believed to be formed by higher mixing of thermogenic gas.
On the physical explanation of the Perkins instability
Authors: Zhou Qina , Mathews John D.
Published: December 2006

Perkins' instability theory (1973) provides a reasonable theoretical explanation for the midlatitude ionospheric spread‐F phenomenon. Although his derivation process and model are correct, the physical explanation provided can be improved. In this paper a plasma motion‐balanced view of the Perkins instability is provided as an improvement to the Perkins force‐balanced explanation. We derive the growth rate equation with neutral wind present and show that the new approach yields the same growth rate equation given by Perkins (1973) when the neutral wind is zero. Additionally, a new mathematical approach yields the same result and identifies the source term of the instability.
Magnetic helicity and flux tube dynamics in the solar convection zone: Comparisons between observation and theory
Authors: Nandy Dibyendu
Published: December 2006

Magnetic helicity, a conserved topological parameter in ideal MHD systems, conditions close to which are realized in the solar plasma, is intimately connected to the creation and subsequent dynamics of magnetic flux tubes in the solar interior. It can therefore be used as a tool to probe such dynamics. In this paper we show how photospheric observations of magnetic helicity of isolated magnetic flux tubes, manifested as the twist and writhe of solar active regions, can constrain the creation and dynamics of flux tubes in the solar convection zone and the nature of convective turbulence itself. We analyze the observed latitudinal distribution of twists in photospheric active regions, derived from solar vector magnetograms, in the largest such sample studied till‐date. We confirm and put additional constraints on the hemispheric twist helicity trend and find that the dispersion in the active region twist distribution is latitude‐independent, implying that the amplitude of turbulent fluctuations does not vary with latitude in the convection zone. Our data set also shows that the amplitude and dispersion of twist decreases with increasing magnetic size of active regions, supporting the conclusion that larger flux tubes are less affected by turbulence. Among the various theoretical models that have been proposed till‐date to explain the origin of twist, our observations best match the Σ effect model, which invokes helical turbulent buffeting of rising flux tubes as the mechanism for twist creation. Finally, we complement our analysis of twists with past observations of tilts in solar active regions and tie them in with theoretical modeling studies, to build up a comprehensive picture of the dynamics of twisted magnetic flux tubes throughout the solar convection zone. This general framework, binding together theory and observations, suggests that flux tubes have a wide range of twists in the solar convection zone, with some as high as to make them susceptible to the kink instability mechanism that results in the formation of δ spot or non‐Hale active regions.
Alfvén vortex filaments observed in magnetosheath downstream of a quasi‐perpendicular bow shock
Authors: Alexandrova O. , Mangeney A. , Maksimovic M. , Cornilleau‐Wehrlin N. , Bosqued J.‐M. , André M.
Published: December 2006

Magnetic field fluctuations in the frequency range [0.02–12.5] Hz are studied with the four Cluster satellites in the Earth magnetosheath downstream of a quasi‐perpendicular bow shock. The turbulent spectrum presents a spectral break accompanied by a broad maximum usually interpreted as due to Alfvén ion cyclotron waves. In this paper we establish that this spectral knee corresponds to space‐localized coherent magnetic structures in the form of Alfvén vortices. The Alfvén vortex is a nonlinear cylindrical Alfvén wave, quasi‐parallel to the mean magnetic field B0 and propagating in a plane perpendicular to B0. In this plane the observed vortices are localized within 20c/ωpi. The frequent observations of such structures indicate their stability in the plasma. Therefore the Alfvén vortices can be an important element in the magnetosheath turbulence. The possible origins of these vortices, such as a strong turbulence or the filamentation instability of an Alfvén wave, are discussed.
Overview of the Opportunity Mars Exploration Rover Mission to Meridiani Planum: Eagle Crater to Purgatory Ripple
Authors: Squyres S. W. , Arvidson R. E. , Bollen D. , Bell J. F. , Brückner J. , Cabrol N. A. , Calvin W. M. , Carr M. H. , Christensen P. R. , Clark B. C. , Crumpler L. , Des Marais D. J. , d'Uston C. , Economou T. , Farmer J. , Farrand W. H. , Folkner W. , Gellert R. , Glotch T. D. , Golombek M. , Gorevan S. , Grant J. A. , Greeley R. , Grotzinger J. , Herkenhoff K. E. , Hviid S. , Johnson J. R. , Klingelhöfer G. , Knoll A. H. , Landis G. , Lemmon M. , Li R. , Madsen M. B. , Malin M. C. , McLennan S. M. , McSween H. Y. , Ming D. W. , Moersch J. , Morris R. V. , Parker T. , Rice J. W. , Richter L. , Rieder R. , Schröder C. , Sims M. , Smith M. , Smith P. , Soderblom L. A. , Sullivan R. , Tosca N. J. , Wänke H. , Wdowiak T. , Wolff M. , Yen A.
Published: December 2006

The Mars Exploration Rover Opportunity touched down at Meridiani Planum in January 2004 and since then has been conducting observations with the Athena science payload. The rover has traversed more than 5 km, carrying out the first outcrop‐scale investigation of sedimentary rocks on Mars. The rocks of Meridiani Planum are sandstones formed by eolian and aqueous reworking of sand grains that are composed of mixed fine‐grained siliciclastics and sulfates. The siliciclastic fraction was produced by chemical alteration of a precursor basalt. The sulfates are dominantly Mg‐sulfates and also include Ca‐sulfates and jarosite. The stratigraphic section observed to date is dominated by eolian bedforms, with subaqueous current ripples exposed near the top of the section. After deposition, interaction with groundwater produced a range of diagenetic features, notably the hematite‐rich concretions known as “blueberries.” The bedrock at Meridiani is highly friable and has undergone substantial erosion by wind‐transported basaltic sand. This sand, along with concretions and concretion fragments eroded from the rock, makes up a soil cover that thinly and discontinuously buries the bedrock. The soil surface exhibits both ancient and active wind ripples that record past and present wind directions. Loose rocks on the soil surface are rare and include both impact ejecta and meteorites. While Opportunity's results show that liquid water was once present at Meridiani Planum below and occasionally at the surface, the environmental conditions recorded were dominantly arid, acidic, and oxidizing and would have posed some significant challenges to the origin of life.
Mdm2 targets the p53 transcription cofactor JMY for degradation
Authors: Coutts Amanda S , Boulahbel Houda , Graham Anne , La Thangue Nicholas B
Published: December 2006

We define here a new mechanism through which Mdm2 (mouse double minute 2) regulates p53 activity, by targeting the p53 transcription cofactor JMY. DNA damage causes an increase in JMY protein, and, in a similar manner, small molecule inhibitors of Mdm2 activity induce JMY in unperturbed cells. At a mechanistic level, Mdm2 regulation of JMY requires the Mdm2 RING (really interesting new gene) finger, which promotes the ubiquitin‐dependent degradation of JMY. However, regulation of JMY occurs independently of the p53‐binding domain in Mdm2 and p53 activity. These results define a new functional relationship between the p53 cofactor JMY and Mdm2, and indicate that transcription cofactors that facilitate p53 activity are important targets for Mdm2 in suppressing the p53 response.
The human GINS complex binds to and specifically stimulates human DNA polymerase α‐primase
Authors: De Falco Mariarosaria , Ferrari Elena , De Felice Mariarita , Rossi Mosè , Hübscher Ulrich , Pisani Francesca M
Published: December 2006

The eukaryotic GINS complex has an essential role in the initiation and elongation phases of genome duplication. It is composed of four paralogous subunits—Sld5, Psf1, Psf2 and Psf3—which are ubiquitous and evolutionarily conserved in eukaryotic organisms. Here, we report the biochemical characterization of the human GINS complex (hGINS). The four hGINS subunits were coexpressed in Escherichia coli in a highly soluble form and purified as a complex. hGINS was shown to interact directly with the heterodimeric human DNA primase, by using either surface plasmon resonance measurements or by immunoprecipitation experiments carried out with anti‐hGINS antibodies. The DNA polymerase α‐primase synthetic activity was specifically stimulated by hGINS on various primed DNA templates. The significance of these findings is discussed in view of the molecular dynamics at the human replication fork.
Ginkgo biloba leaf extract (EGb 761) diminishes adriamycin‐induced hyperlipidaemic nephrotoxicity in rats: association with nitric oxide production
Authors: Abd‐Ellah Mohamed F. , Mariee Amr D.
Published: December 2006

The aim of this experimental study was to investigate the effect of a standardized preparation of Ginkgo biloba extract (EGb 761) on the hyperlipidaemic nephrotoxicity and oxidative stress induced by a single intravenous injection (5 mg/kg) of adriamycin. EGb 761 was received daily thereafter by a gavage at the dose of 100 mg/kg for 35 consecutive days. EGb 761 administration significantly attenuated adriamycin‐induced renal dysfunction, as assessed by measuring serum lipid profile, serum total protein, serum urea and Ccr (creatinine clearance). Furthermore, urinary excretions of protein and NAG (N‐acetyl‐β‐D‐glucosaminidase; a marker of renal tubular injury) were significantly inhibited following EGb 761 administration. EGb 761 supplementation significantly prevented the generation of TBARS (thiobarbituric acid‐reacting substances) with a marked improvement in terms of GSH content and activity of antioxidant enzymes in the kidney homogenate. Moreover, EGb 761 treatment significantly reduced both renal‐tissue and urine total NO (nitric oxide) levels. The results suggest that the protective potential of EGb 761 in the prevention of adriamycin‐induced hyperlipidaemic nephrotoxicity in rats was associated with the decrease in the oxidative stress and the total NO levels of renal tissues. Likewise, the present study demonstrates the ability of EGb 761 to reduce the hyperlipidaemia and proteinuria associated with this nephropathy, which might be beneficial to enhance the therapeutic index of adriamycin.
Erythropoietic and anti‐obesity effects of Garcinia cambogia (bitter kola) in Wistar rats
Authors: Oluyemi Kayode Alaba , Omotuyi Idowu O. , Jimoh Olusegun R. , Adesanya Olamide A. , Saalu Chia L. , Josiah Sunday J.
Published: December 2006

The anti‐obesity and erythropoietic effects of crude ethanolic extracts of Garcinia cambogia (bitter kola) seeds on Wistar rats (Rattus norvegicus) were investigated. The rats were divided into three dosage groups: A (0 mg/kg of body weight), B (200 mg/kg) and C (400 mg/kg). Weight changes, plasma lipoprotein levels and the lipid profile of the liver, gastrointestinal system and adipose tissue were monitored as indices for anti‐obesity, while the RBC (red blood cell) count (assessed by using a haemocytometer) was monitored as a measure of erythropoiesis. The extract was administered by gavage for 5 weeks. The results for each test group was compared statistically with those for the control (P<0.05). Analysis of the results showed a significant increase in RBC counts in both test groups and a decrease in weights of experimental animals. There was a dose‐dependent decrease in the plasma level of very‐low‐density lipoprotein and a dose‐dependent increase in the level of chylomicrons. There was a slight, but significant, decrease in the level of high‐density lipoprotein and a significant increase in the level of LDL (low‐density lipoprotein). There was significant dose‐dependent decrease in the TAG (triacylglycerol) pool of adipose tissue and the liver of the test groups, but a significant increase in the TAG pool of the gastrointestinal system. The increase in the TAG pool of the gastrointestinal system is possibly compensatory. The results therefore confirm that ethanolic extracts of G. cambogia seeds have both haematologically enhancing and anti‐obesity effects. The decrease in the high‐density‐lipoprotein level and an increase in the LDL level may play an important role in cardiovascular disease.
Targeting and localized signalling by small GTPases
Authors: ten Klooster Jean Paul , Hordijk Peter L.
Published: December 2006

Polarized cellular responses, for example, cell migration, require the co‐ordinated assembly of signalling complexes at a particular subcellular location, such as the leading edge of cells. Small GTPases of the Ras superfamily play central roles in many (polarized) responses to growth factors, chemokines or integrin ligands. These small GTPases are functionally distinct, yet remarkably homologous in their primary sequence and especially in their effector domains. Therefore it has long been unclear how GTPase signalling specificity is regulated. Small GTPases carry a lipid anchor, in the context of a hypervariable region, which mediates membrane association. However, whereas the lipid has long been proposed to be the critical regulator of subcellular GTPase targeting, there is now increasing evidence that specific protein—protein interactions are important as well. This review discusses recent findings on GTPase targeting and proposes a revised model for GTPase signalling. In this model, the hypervariable domain acts in conjunction with the lipid tail to target the GTPase to specific membrane‐associated protein complexes. Here, local GTPase activation occurs, leading to subsequent exposure of the effector domain, binding to effector proteins and the initiation of downstream signalling.
Correction of apparent finite size effects in the area per lipid of lipid membranes simulations
Authors: Herce Henry D. , Garcia Angel E.
Published: December 2006

Molecular dynamics simulations of lipids bilayers have reported that the average area per lipid increases with the size of the simulated unit cell under constant temperature, pressure, and number of molecules. Here we show that the cause of this finite size effect are artifacts associated with the heat bath coupling. This can be corrected by coupling individually each degree of freedom to the heat bath, instead of coupling globally the system. We present the results of the investigation on three aspects of molecular dynamics simulations and their effect on the computed average area per lipid: (I) the accuracy in the computation of electrostatic interactions, the energy, and the virial, (II) long range Lennard-Jones interactions for systems with symmetry in one plane, and (III) thermodynamic baths. We show that the average area per lipid remains constant for simulations of systems containing 32, 64, and 256 lipids.
Spectra of the liquid cluster surface thermal fluctuations
Authors: Zhukhovitskii D. I.
Published: December 2006

Classification of cluster particles is proposed that introduces three particle types: the internal particles, surface particles, and virtual chains of particles. Thermal fluctuations of a surface passing through the surface particles of a Lennard-Jones liquid cluster are studied using a molecular dynamics simulation. It is shown that for large clusters, the Fourier spectral amplitude of these fluctuations decays faster than 1∕q, where q is the wave number. The frequency Fourier spectrum shows an overdamped system behavior, which is the evidence for the absence of thermal capillary waves for clusters comprising less than 105 particles. The time-averaged cluster density profile is given by an error function with the width parameter diverging as the logarithm of the cluster size.
Electrostatic interactions in dissipative particle dynamics using the Ewald sums
Authors: González-Melchor Minerva , Mayoral Estela , Velázquez María Eugenia , Alejandre José
Published: December 2006

The electrostatic interactions in dissipative particle dynamics (DPD) simulations are calculated using the standard Ewald [Ann. Phys. 64, 253 (1921)] sum method. Charge distributions on DPD particles are included to prevent artificial ionic pair formation. This proposal is an alternative method to that introduced recently by Groot [J. Chem. Phys. 118, 11265 (2003)] where the electrostatic field was solved locally on a lattice. The Ewald method is applied to study a bulk electrolyte and polyelectrolyte-surfactant solutions. The structure of the fluid is analyzed through the radial distribution function between charged particles. The results are in good agreement with those reported by Groot for the same systems. We also calculated the radius of gyration of a polyelectrolyte in salt solution as a function of solution pH and degree of ionization of the chain. The radius of gyration increases with the net charge of the polymer in agreement with the trend found in static light scattering experiments of polystyrene sulfonate solutions.
Electrical measurement of carrier population modulation by two-color coherent control
Authors: Wahlstrand J. K. , Pipis J. A. , Roos P. A. , Cundiff S. T. , Smith R. P.
Published: December 2006

Two-color quantum interference control in a semiconductor results in a charge current or a modulation of the carrier population depending on the phase shift between an optical wave and its second harmonic. Population control requires certain polarizations for the two colors with respect to the crystal axes. The authors present results of an electrical measurement of quantum interference control of charge carrier population in (111) oriented GaAs. The dependence of the population control signal on power, light polarization, bias, and laser spot position is studied.
Three-dimensional phase-contrast imaging of single floating cells
Authors: Kobayashi Hiroaki , Ishimaru Ichirou , Yasokawa Toshiki , Ishizaki Katsumi , Kuriyama Shigeki , Masaki Tsutomu , Nakai Seiji , Takegawa Kaoru , Tanaka Naotaka
Published: December 2006

A three-dimensional phase-contrast imaging technique that does not involve fluorescent labeling has been developed for observing floating cells. In this method, a single floating cell is made to rotate and images are acquired at several orientations of the cell using a phase-contrast microscope. From these two-dimensional phase-contrast images, three-dimensional cross-sectional images are obtained using the conventional computed tomography algorithm. This proposed method enabled successful rotation of a floating cell (a breast cancer cell line) and reconstruction of three-dimensional phase-contrast images. In these reconstructed three-dimensional images, the distribution of cell organelles is obtained and the cell nucleus is clearly distinguishable.
Electron bunch acceleration in an inverse free-electron laser with a helical magnetic wiggler and axial guide field
Authors: Mirzanejhad Saeed , Sohbatzadeh Farshad , Asri Mehdi , Toosi Ershad Sadeghi
Published: December 2006

Electron bunch acceleration by a laser pulse having Gaussian radial and temporal profiles of intensity has been studied numerically in a static helical magnetic wiggler in vacuum. The main electron bunch parameters for simulations are 10MeV initial energy with 0.1% longitudinal energy spread, 1mm mrad rms transverse emittance, and 3×1012cm−3 density. It is shown that the radial Gaussian profile can decrease the acceleration gradient compared with that of the plane-wave approximation due to the reduction of electron-pulse interaction area. In order to collimate electron bunch and overcome the decreasing of the acceleration gradient, an external axial magnetic field is used. The importance of the electron initial phase with respect to laser pulse is considered, and some appropriate values are found. Finally, acceleration of a femtosecond (fs) microbunch with an optimum appropriate initial phase is considered, which leads to a nearly monoenergetic microbunch and an acceleration gradient of about ≈0.2GeV∕m.
Space-charge limiting currents in magnetically focused intense relativistic beams with an ion channel
Authors: Li Jianqing , Mo Yuanlong
Published: December 2006

The intense relativistic beam propagation through the drift tube filled with background plasma is investigated. The self-consistent differential equations, which describe the laminar-flow equilibria state in magnetically focused relativistic beams with an ion channel, are presented. By solving these equations using the Runge-Kutta method, the azimuthal velocity, the axial velocity, and the electron beam density, which are functions of radial position, can be calculated. Then the space-charge limiting current and the externally applied magnetic field can be obtained for solid beams and hollow beams. In the case of plasma fill, the axial velocity of the laminar flow is a nonuniform radial profile. The simulated results show that the background plasma can increase the space-charge limiting current, reduce the externally applied magnetic field, and improve the electron beam propagation through the drift tube.
Transition of window breakdown from vacuum multipactor discharge to rf plasma
Authors: Kim H. C. , Verboncoeur J. P.
Published: December 2006

In high-power microwave systems, the transition of window breakdown from single surface vacuum multipactor discharge to rf plasma with increasing gas pressure is investigated using particle-in-cell simulations. An intermediate pressure regime where multipactor discharge and rf plasma coexist was found. The pressure range where the multipactor can be maintained is summarized in the plot of the secondary electron emission yield as a function of the gas pressure. As the gas pressure increases, electron-neutral collisions prevail against secondary electron emissions and the electron energy probability function changes from the bi-Maxwellian at low pressures to Druyvesteyn at high pressures as a result of the change in electron heating and cooling processes. The discharge formation time in argon, neon, and xenon is shown for different gas pressures. Different scaling laws in the discharge formation time are presented at low and high pressures, respectively.
Permanent luminescent micropatterns photoinduced by low-power ultraviolet irradiation in lithium fluoride
Authors: Vincenti Maria Aurora , Almaviva Salvatore , Montereali Rosa Maria , Kalinowski Hypolito José , Nogueira Rogério Nunes
Published: December 2006

The permanent recording of regularly spaced, periodic, light-emitting submicrometric structures in gamma-ray irradiated LiF crystals has been obtained by low-power illumination with a continuous laser at 244nm in a standard phase mask interferometer used for Bragg gratings registration in optical fibers. Selective bleaching of primary F electronic defects and aggregate F2 laser active color centers has been identified as the mechanism responsible of photoinduced spatial modulation of absorption and photoemission properties. The results look promising for the realization of micropatterns with refractive index and gain modulation on scale comparable with the optical wavelengths to easily integrate with miniaturized LiF-based structures.
High efficiency 90° bending metal heterowaveguides for nanophotonic integration
Authors: Chen Lin , Wang Bing , Wang Guo Ping
Published: December 2006

The propagation properties of surface plasmon polaritons (SPPs) along metal heterowaveguide (MHWG)-constructed bending nanowaveguides are investigated by finite-difference time-domain simulation. The results reveal that SPPs can pass through 90° sharp bending MHWGs with higher than 90% propagation efficiency. Further numerical demonstrations of the bending MHWGs in splitters and Mach-Zehnder interferometers imply that MHWGs may find significant applications in highly integrated nanophotonic networks.
Dependence of photocurrent in single-crystalline boron nanobelts on atmosphere
Authors: Kirihara Kazuhiro , Kawaguchi Kenji , Shimizu Yoshiki , Sasaki Takeshi , Koshizaki Naoto , Soga Kohei , Kimura Kaoru
Published: December 2006

This letter describes the dependence of photocurrent of single-crystalline boron nanobelts on the atmosphere. In ambient air, slow photoresponse under blue light illumination was observed. Rise and decay times exceeded three days. The magnitude of photoresponse in ambient air and oxygen was greater than that in hydrogen and argon atmospheres. In vacuum, a photoresistivity effect consisting of the continuous decrease of conductance under blue light illumination was observed. Variation of band bending of the nanobelt surface by adsorption or desorption of oxygen and water molecules appeared to switch the photoconduction on and off by the respective trapping and recombination of photoexcited carriers at the nanobelt core and surface.
Optimized dielectric properties of SrTiO3:Nb∕SrTiO3 (001) films for high field effect charge densities
Authors: Cai Xiuyu , Frisbie C. Daniel , Leighton C.
Published: December 2006

The authors report the growth, structural and electrical characterizations of SrTiO3 films deposited on conductive SrTiO3:Nb (001) substrates by high pressure reactive rf magnetron sputtering. Optimized deposition parameters yield smooth epitaxial layers of high crystalline perfection with a room temperature dielectric constant ∼200 (for a thickness of 1150Å). The breakdown fields in SrTiO3:Nb∕SrTiO3∕Ag capacitors are consistent with induced charge densities >1×1014cm−2 for both holes and electrons, making these films ideal for high charge density field effect devices.