bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of atmospheric pressure on the survival of photosynthetic microorganisms during simulations of ecopoesis
Authors: Thomas David J. , Eubanks L. Michelle , Rector Carl , Warrington Jaime , Todd Paul
Published: October 2008

Three cyanobacteria (Anabaenasp.,Plectonema boryanumandChroococcidiopsisCCMEE171) and an alga (Chlorella ellipsoidea) were grown under simulated martian ecopoesis conditions. A xenon arc lamp with a solar filter provided simulated martian sunlight, and temperature cycled diurnally from −80°C to 26°C. A Mars-like atmosphere of 100% CO2was provided at 50, 100, 300, 500 and 1000 mbar. The cyanobacteria and alga were inoculated into JSC Mars-1 soil simulant and exposed to each atmospheric pressure for five weeks. Survival and growth were determined via extractable chlorophyllaand total esterase (fluorescein diacetate hydrolysis) activity. Maximum survival occurred at 100 and 300 mbar. At 50, 500 and 1000 mbar, esterase activity was near zero, and extractable chlorophyllawas less than 10% of control samples. Overall, the cyanobacteria survived better than the alga. Low survival at 50 mbar was probably due to desiccation. Low survival at 500 and 1000 mbar may have been due to CO2toxicity.
Schwere Verhaltensstörung mit organischer Ursache
Authors: Meyer M.R. , Rüegger-Frey B. , Nikolic N. , Bopp-Kistler I.
Published: October 2008

Ein 65-jähriger Architekt wurde zur Abklärung einer rasch progredienten Demenz mit Verhaltensauffälligkeiten und zunehmender Einschränkung seiner Selbständigkeit zugewiesen. Klinisch imponierten Residuen abgelaufener zerebrovaskulärer Ereignisse, wobei das Schädel-MRI einen hämorrhagischen und einen ischämischen Infarkt sowie ausgedehnte subkortikale Hämosiderinablagerungen zeigte. Neuropsychologisch stand eine subkortikal-frontale Störung im Vordergrund. Der Fall illustriert die differentialdiagnostische Bedeutung der zerebralen Amyloidangiopathie als Ursache einer vaskulären Demenz und betont die Bedeutung der zerebralen Bildgebung bei der diagnostischen Einordnung eines vaskulären dementiellen Syndroms.
Reevaluation of magnetic chrons in the North Atlantic between 35°N and 47°N: Implications for the formation of the Azores Triple Junction and associated plateau
Authors: Luis J. F. , Miranda J. M.
Published: October 2008

In this paper we present a new magnetic compilation for an area of the North Atlantic located between 35°N and 47°N and up to anomaly 33r. We also present a strategy to pick magnetic isochrones and compute finite rotation poles. This technique is based on a continuous reduction to the pole technique and some basic assumptions regarding the direction of the remanent magnetization vector. A cost function that measures the misfit between interpreted and rotated isochrones and the systematic exploitation of the parameter space is used to compute the best set of finite Eulerian rotations for the chrons 5, 6, 6C, 11–12, 13, 18, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, and 33r. This set of chrons and poles is used to discuss the evolution of the North Atlantic close to Iberia and, in particular, the onset and early development of the Azores Triple Junction area. We show that the relative motion between the Eurasian and the African plates can be coherently described in terms of rigid plate kinematics, respecting both the anomalies shapes and the precise location of the main structural elements of the area: the Pico Fracture Zone, the East Azores Fracture Zone, and the Gloria Fault. We distinguish from the magnetic point of view two different areas of the Azores plateau: the South Azores domain where almost undisturbed NNW magnetic lineations can be found and the Azores domain close to the topographic highs and with no systematic magnetic stripping with the exception of a few recent lineations, probably Matuyama and Brunhes. We present an approximate reconstruction of the plate configuration after chron 18 to conclude that the attachment of Iberia to Eurasia was younger than previously thought (lower Miocene), triggering the formation of the Azores domain, in which stretching took place essentially in the last 20 Ma at an average rate of ∼3.8 mm/a, and progressively attaching the South Azores domain to the African plate by a northward progression of the triple junction.
Pathways and variability of the off‐equatorial undercurrents in the Atlantic Ocean
Authors: Hüttl‐Kabus Sabine , Böning Claus W.
Published: October 2008

The cold upwelling waters of the eastern tropical oceans not only interact with the atmospheric circulation via changing the sea surface temperatures but also influence the biological activity via affecting the nutrient and oxygen contents of the upwelling waters. While the sources of the equatorial upwelling associated with the Equatorial Undercurrent (EUC) have been studied extensively, the relevance of the northern and southern off‐equatorial undercurrents (NEUC, SEUC) for the off‐equatorial upwelling regions has remained unclear. In this study we use output from a high‐resolution, 1/12° model (FLAME) to investigate the mean pathways and variability of the off‐equatorial undercurrents (OEUCs) in the Atlantic. In particular, a calculation of Lagrangian trajectories helps to gain insight into the source waters of the OEUCs and their connection to the upwelling regions in the eastern tropical Atlantic. In the model solution the sources of both OEUCs belong almost exclusively to the Southern Hemisphere. The pathways of the source waters are found to be governed by strong recirculations between the different eastward and westward zonal currents because of intense eddy motions associated with the tropical instability wave activity. Whereas the SEUC is predominantly fed through the recirculation in the ocean interior, the NEUC is also fed by a weak inflow from the western boundary current. Investigation of the fate of the NEUC shows only a weak direct supply to the upwelling in the Guinea Dome and along the African coast but a significant contribution to the equatorial upwelling.
Estimation of global CO2 fluxes at regional scale using the maximum likelihood ensemble filter
Authors: Lokupitiya R. S. , Zupanski D. , Denning A. S. , Kawa S. R. , Gurney K. R. , Zupanski M.
Published: October 2008

We use an ensemble‐based data assimilation method, known as the maximum likelihood ensemble filter (MLEF), which has been coupled with a global atmospheric transport model to estimate slowly varying biases of carbon surface fluxes. Carbon fluxes for this test consist of hourly gross primary production and ecosystem, respiration over land, and air‐sea gas exchange. Persistent multiplicative biases intended to represent incorrectly simulated biogeochemical or land‐management processes such as stand age, soil fertility, or coarse woody debris were estimated for 1 year at 10° longitude by 6° latitude spatial resolution and with an 8‐week time window. We tested the model using a pseudodata experiment with an existing observation network that includes flasks, aircraft profiles, and continuous measurements. Because of the underconstrained nature of the problem, strong covariance smoothing was applied in the first data assimilation cycle, and localization schemes have been introduced. Error covariance was propagated in subsequent cycles. The coupled model satisfactorily recovered the land biases in densely observed areas. Ocean biases, however, were poorly constrained by the atmospheric observations. Unlike in batch mode inversions, the MLEF has a capability of assimilating large observation vectors and hence is suitable for assimilating hourly continuous observations and satellite observations in the future. Uncertainty was reduced further in our pseudodata experiment than by previous batch methods because of the ability to assimilate a large observation vector. Propagation of spatial covariance and dynamic localization avoid the need for prescribed spatial patterns of error covariance centered at observation sites as in previous grid‐scale methods.
Effect of geomorphic channel restoration on streamflow and groundwater in a snowmelt‐dominated watershed
Authors: Tague Christina , Valentine Scott , Kotchen Matthew
Published: October 2008

Reengineering of stream channels is a common approach used to restore hydrologic function in degraded landscapes, but there has been little published research analyzing its effectiveness. A key challenge for impact assessment is disentangling the effects of restoration from climate variability. Trout Creek, near Lake Tahoe, California, was reengineered to reestablish hydrologic connectivity between the stream and its former floodplain. Gauges located above and below the site, along with groundwater well measurements, were used to analyze prerestoration and postrestoration hydrology. Results show that restoration has a seasonal impact with statistically significant increases in streamflow during the summer recession period and decreased groundwater table depths across a wide range of streamflow conditions. Paired gauges and statistical models that are robust to serial autocorrelation demonstrate a feasible approach for assessing hydrologic restoration in regions where climate patterns lead to substantial within‐year and between‐years variation in streamflow.
Time variations of δ15N of organic nitrogen in deep western subarctic Pacific sediment over the last 145 ka
Authors: Shigemitsu Masahito , Watanabe Yutaka W. , Narita Hisashi
Published: October 2008

We present δ15N data of organic nitrogen (δ15NON) from a deep western subarctic Pacific (WSAP) sediment core over the last 145 ka. To remove the effect of inorganic nitrogen (IN) on bulk nitrogen (BN), we used the contents of IN and BN, and the isotopic ratios of IN (δ15NIN) and BN (δ15NBN). The contribution of IN to BN was largest 59% and δ15NIN had lower values than δ15NBN. However, the large contributions of IN to BN and the distinct isotopic values did not largely change any variability associated with δ15NON in the δ15NBN. Thus, it is possible to use δ15NBN in carrying out paleoceanographic research with δ15N at least in the open WSAP. The δ15NON values have been affected by long‐term diagenesis making the values lower with depth in the sediment, but the values during less productive colder periods were generally lower compared to those during neighboring productive warmer periods. The results might indicate that δ15NON during the less productive colder periods (i.e., glacial periods) were lower than that during the productive warmer periods (i.e., interglacial periods). Previous studies have reported that the biological production in WSAP, where it is limited by iron at present, during glacial periods was at more reduced level than during interglacials despite there being more eolian dust supply during glacial periods. This indicates that the increase of biological production with enhanced iron supply derived from eolian dust during the glacial periods did not occur. If this is the case and alternatively the iron input from the subsurface layer to the surface‐mixed layer by ventilation process is more important as suggested by recent works, the variations in δ15NON would be explained by the variations in the Fe/NO3− ratio in the upwelled water. Although δ15NON has been affected by long‐term diagenesis in the sediment, the usage of this isotopic ratio provides new implication regarding the past ocean circulation in the open WSAP.
Regime shift in Indian summer monsoon climatological intraseasonal oscillations
Authors: Suhas E. , Goswami B. N.
Published: October 2008

Using a high resolution daily rainfall data over Indian continent between 1951 and 2004, summer monsoon climatological intraseasonal oscillations (CISO) and its regime shift around mid seventies is investigated. Explaining 20% −40% of intraseasonal oscillation (ISO) amplitude, the summer monsoon CISO represents a significant predictable component of the monsoon ISOs. Indian monsoon CISO is characterized by a dominant northward propagating episode in both pre‐seventies (1951–75, pre75) and in the post‐seventies (1979–04, post79). The dominant episode starts in the beginning of July during pre75 in contrast to beginning of June during post79 period. We find that the IAV of the initial phase of both the first and the second ISO episodes worked in tandem with the changes in the northward propagation speed in producing the phase locking for the second episode during pre75 while for the first episode during post79. Change in northward propagation speed is shown to be consistent with changes in easterly vertical shear and meridional gradient of low level humidity during the two climate regimes.
Runaway relativistic electron avalanche seeding in the Earth's atmosphere
Authors: Carlson B. E. , Lehtinen N. G. , Inan U. S.
Published: October 2008

Relativistic runaway electron avalanches (RREAs) occur when relativistic electrons undergo avalanche multiplication when driven by electric fields. The RRE avalanche has been studied extensively, but existing results typically assume a rudimentary source of seed relativistic electrons. Here we focus on the seeding process and simulate effective seeding efficiencies for various seed particle types, energies, and geometries. Including known results from cosmic ray physics, we calculate total seed particle distributions and their statistical fluctuations and use the seeding efficiency results to determine the total number of effective RREA seed particles at various points in the atmosphere. The results indicate that effective seed flux is quite large with only moderate statistical fluctuations.
Wind forcing of the coastal circulation off north and northwest Iberia: Comparison of atmospheric models
Authors: Otero P. , Ruiz‐Villarreal M.
Published: October 2008

Comparisons between observed winds and winds from reanalysis (National Centers for Environmental Prediction (NCEP) Reanalysis 1 and 2) and forecast meteorological models (High‐Resolution Limited Area Model (HIRLAM)‐Agencia Estatal de Meteorologia 0.2° and Atmospheric Research Mesoscale Model version 5‐MeteoGalicia with 30 km and 10 km resolution) have been performed for the coastal region around northwest and north Iberia during a typical autumn downwelling period (September–December 2002). Observations at buoys and coastal stations and QuikSCAT‐derived winds were employed. The analyzed period was dominated by southerly and southwesterly winds associated to the passage of low‐pressure systems. Our results show that the westward component is higher on the north coast than on the west coast and that winds are intensified at the western north coast. In this situation, the performance is similar in all model products in general terms, but only HIRLAM represents the reduction of winds in the Cantabrian Sea and NCEP and MM5 overestimate the magnitude of south‐southwest winds. Spatial differences in winds are also obtained for upwelling favorable events, associated either with a high‐pressure system north from Iberia at the beginning of the autumn transition (northeasterly winds) or with conditions after the passage of a low‐pressure system (northwesterly winds). The existence of sea surface temperature (SST) gradients in the coastal region implies that higher‐resolution boundary SST products for meteorological models are necessary. Finally, the effect of these wind products on the coastal circulation was assessed with a 3‐D numerical simulation. Differences in the expansion/confinement of river plumes and the surface speed of the slope current are induced by differences in wind patterns over the shelf and slope area among atmospheric models.
Contribution of water vapor to observational estimates of longwave cloud radiative forcing
Authors: Sohn Byung‐Ju , Bennartz Ralf
Published: October 2008

It has been long recognized that cloud‐free regions are typically associated with drier air, whereas cloudy regions typically are associated with more moisture. Using Advanced Microwave Scanning Radiometer (AMSR‐E) passive microwave observations, we estimated the bias between water vapor path (WVP) of clear‐sky and all‐sky conditions. Furthermore, we assessed the impact of these biases on longwave cloud radiative forcing (CRF). Results indicate that, in a zonal mean sense, the difference between all‐sky and clear‐sky WVP estimates is around 2 mm, with highest values in the midlatitudes summer, where differences up to 7 mm occur. The corresponding CRF change forced by these WVP changes is about 2 W m−2 in a zonal mean sense. Highest values occur in the midlatitudes of the northern hemisphere in which a magnitude up to 6 W m−2 is shown. Over the convectively active regions, the WVP contributed CRF appears to be smaller than 5 W m−2, substantially smaller than the CRF contributed by upper tropospheric water vapor only, suggesting that a significant portion of satellite‐estimated CRF over the tropics is contributed by the redistribution of water vapor associated with convection development.
Diurnal cycle of the Oklahoma City urban heat island
Authors: Basara Jeffrey B. , Hall Peter K. , Schroeder Amanda J. , Illston Bradley G. , Nemunaitis Kodi L.
Published: October 2008

Between the dates of 28 June and 31 July 2003, the Joint Urban 2003 (JU2003) field project was conducted in Oklahoma City and was the largest urban dispersion experiment ever in North America. Because the focus of JU2003 was on atmospheric processes within the urban environment, an extremely dense network of instrumentation was deployed in and around the central business district (CBD) both prior to and during the field experiment. Among the variables collected were high‐resolution observations of air temperature from various instrument sources. Additional observations of air temperature were also collected at Oklahoma Mesonet stations in the rural areas surrounding Oklahoma City. Using an index value, the diurnal cycle of the urban heat island (UHI) for Oklahoma City, with respect to the surrounding rural terrain, was quantified. The results revealed a consistent mean nocturnal UHI greater than 1.5°C at both 2 and 9 m. However, observations at 2 m during JU2003 revealed a significant urban “cool” island during the convective portion of the day. The mean variability of temperature within the urban core of Oklahoma City increased significantly after sunrise, increased to a maximum near solar noon, and decreased following sunset. These results were inconsistent with the rural observations wherein the variability among sites was maximized during the nocturnal period. Finally, the vertical temperature gradient between 2 and 9 m demonstrated a clear and strong diurnal trend at the rural locations, whereas observations from the urban environment were nearly isothermal and consistent with near‐neutral conditions throughout JU2003.
Efficient calculation of intensity and polarization spectra in vertically inhomogeneous scattering and absorbing atmospheres
Authors: Hasekamp Otto P. , Butz André
Published: October 2008

We present a method for the efficient calculation of moderate‐ and high‐resolution spectra of intensity and polarization in absorption bands. This linear‐k method explicitly accounts for the vertical distribution of the absorption optical thickness by using a linear approximation. It can be applied to any radiative transfer model that calculates the intensity (vector) and its derivatives with respect to the absorption optical thickness in different altitude layers of the model atmosphere. For the three spectral windows of the Orbiting Carbon Observatory (OCO), the error on the modeled intensity introduced by the linear‐k method is below 0.13% for the O2‐A band, below 0.06% in the weak CO2 band, and below 0.12% for the strong CO2 band, for an aerosol type dominated by coarse mode particles with an aerosol optical thickness (AOT) of 0.3 at the O2‐A band (the maximum AOT for which OCO retrievals are intended to be performed), and a typical aerosol height distribution with most aerosols located in the boundary layer. For these accuracies the computational effort is reduced by two orders of magnitude compared to line‐by‐line calculations. A sensitivity study with synthetic OCO measurements shows that the linear‐k method introduces a small error of 0.025–0.20 ppm on the retrieved profile weighted mean CO2 mixing ratio, for a boundary layer dominated aerosol distribution, and 0.050–0.50 ppm for an elevated aerosol layer between 5 and 6 km. In most cases the error is considerably smaller than the retrieval noise.
Venus Express observations of an atypically distant bow shock during the passage of an interplanetary coronal mass ejection
Authors: Zhang T. L. , Pope S. , Balikhin M. , Russell C. T. , Jian L. K. , Volwerk M. , Delva M. , Baumjohann W. , Wang C. , Cao J. B. , Gedalin M. , Glassmeier K.‐H. , Kudela K.
Published: October 2008

On 10–11 September 2006 the Venus Express magnetometer detected a very strong Interplanetary Coronal Mass Ejection (ICME) event with an average field about 2 times higher than that of a typical ICME at 0.72 AU. While the effective obstacle to the solar wind is compressed to a smaller dimension during this ICME event, the bow shock is located far upstream of its nominal location. The observed shocks are weak and appear very dynamic. The location of the shock crossing can be found all along the Venus Express trajectory, which has an apocenter of 12 RV. We attribute the atypical distant bow shock location as an effect of the extremely low Mach number during the ICME.
Lack of MD‐2 expression in human corneal epithelial cells is an underlying mechanism of lipopolysaccharide (LPS) unresponsiveness
Authors: Zhang Jing , Kumar Ashok , Wheater Michelle , Yu Fu‐Shin X
Published: October 2008

In the present study we tested the responsiveness of human corneal epithelial cells (HCECs) and corneal fibroblasts to lipopolysaccharide (LPS), a Toll‐like receptor (TLR) 4 ligand. Purified Pseudomonas aeruginosa LPS was used to stimulate telomerase‐immortalized HCECs (HUCL) and stromal fibroblast (THK) cell lines. Exposure of cells to LPS induced a time‐dependent activation of NF‐κB in THK but not in HUCL cells, as assessed by an increase in IκB‐α phosphorylation and degradation. Concomitant with NF‐κB activation, LPS‐treated THK cells, but not HUCL cells, produced a significantly larger number of cytokines than control untreated cells. A cell surface biotinylation assay revealed that HUCL cells express TLR4 intracellularly, whereas TLR5 is expressed on the cell surface. Furthermore, reverse transcriptase‐PCR analysis revealed that HUCL and primary HCECs, in contrast to THK cells, do not express myeloid differentiation (MD)‐2. Thus, our results demonstrate that the LPS unresponsiveness of HCECs might be due to deficient expression of MD‐2, an essential component for LPS‐TLR4 signaling.
Covalent immobilization of tobacco‐etch‐virus NIa protease: a useful tool for cleavage of the histidine tag of recombinant proteins
Authors: Puhl Ana Cristina , Giacomini Cecilia , Irazoqui Gabriela , Batista‐Viera Francisco , Villarino Andrea , Terenzi Hernán
Published: October 2008

Addition of tags [such as His (histidine) tags] is extremely helpful for the affinity purification of recombinant proteins. In several cases, these tags must be removed before performing functional and structural studies. The enzyme most frequently used to cleave tags of recombinant proteins is the TEV‐protease (tobacco‐etch‐virus NIa protease). The continuous production of this enzyme in soluble form is quite an expensive process and not easily accessible to many laboratories. Thus an interesting alternative is the use of TEV‐protease in an immobilized form, which may be reutilized several times. The main objective of the present study was to obtain a TEV‐protease in an immobilized form, by covalent immobilization on to solid supports through selective use of different amino acid residues, lysine or cysteine. High protein immobilization yields (75–97%) were obtained with both strategies. The TEV‐protease immobilized through its exposed cysteine thiol groups maintained its ability for cleaving a 20 kDa substrate. While the activity of the immobilized TEV‐protease maintained only 30% of the activity of the enzyme in soluble form, its stability at 4 °C was improved three times. Moreover, this enzyme could be reutilized in at least five cycles of cleavage without loss of performance. The present results indicate that the use of a TEV‐protease in an immobilized form is a potentially useful tool for the cleavage of His tags of recombinant proteins and may be useful for reducing the cost of the total process of cleavage.
Cytoplasmic signalling by the c‐Abl tyrosine kinase in normal and cancer cells
Authors: Sirvent Audrey , Benistant Christine , Roche Serge
Published: October 2008

c‐Abl is a non‐receptor tyrosine kinase which is localized both in the nucleus and cytoplasm, and is involved in the regulation of cell growth, survival and morphogenesis. Although c‐Abl nuclear function has been extensively studied, recent data also indicate an important role in cytoplasmic signalling through mitogenic and adhesive receptors. Here, we review the mechanisms by which growth factors promote cytoplasmic c‐Abl activation and signalling and its function in the induction of DNA synthesis, changes in cell morphology and receptor endocytosis. The importance of de‐regulated c‐Abl cytoplasmic signalling in solid tumours is also discussed.
Increased levels of superoxide and H2O2 mediate the differential susceptibility of cancer cells versus normal cells to glucose deprivation
Authors: Aykin-Burns Nùkhet , Ahmad Iman M. , Zhu Yueming , Oberley Larry W. , Spitz Douglas R.
Published: October 2008

Cancer cells, relative to normal cells, demonstrate increased sensitivity to glucose-deprivation-induced cytotoxicity. To determine whether oxidative stress mediated by O2•− and hydroperoxides contributed to the differential susceptibility of human epithelial cancer cells to glucose deprivation, the oxidation of DHE (dihydroethidine; for O2•−) and CDCFH2 [5- (and 6-)carboxy-2′,7′-dichlorodihydrofluorescein diacetate; for hydroperoxides] was measured in human colon and breast cancer cells (HT29, HCT116, SW480 and MB231) and compared with that in normal human cells [FHC cells, 33Co cells and HMECs (human mammary epithelial cells)]. Cancer cells showed significant increases in DHE (2–20-fold) and CDCFH2 (1.8–10-fold) oxidation, relative to normal cells, that were more pronounced in the presence of the mitochondrial electron-transport-chain blocker, antimycin A. Furthermore, HCT116 and MB231 cells were more susceptible to glucose-deprivation-induced cytotoxicity and oxidative stress, relative to 33Co cells and HMECs. HT29 cells were also more susceptible to 2DG (2-deoxyglucose)-induced cytotoxicity, relative to FHC cells. Overexpression of manganese SOD (superoxide dismutase) and mitochondrially targeted catalase significantly protected HCT116 and MB231 cells from glucose-deprivation-induced cytotoxicity and oxidative stress and also protected HT29 cells from 2DG-induced cytotoxicity. These results show that cancer cells (relative to normal cells) demonstrate increased steady-state levels of ROS (reactive oxygen species; i.e. O2•− and H2O2) that contribute to differential susceptibility to glucose-deprivation-induced cytotoxicity and oxidative stress. These studies support the hypotheses that cancer cells increase glucose metabolism to compensate for excess metabolic production of ROS and that inhibition of glucose and hydroperoxide metabolism may provide a biochemical target for selectively enhancing cytotoxicity and oxidative stress in human cancer cells.
Characterization of SCaMC-3-like/slc25a41, a novel calcium-independent mitochondrial ATP-Mg/Pi carrier
Authors: Traba Javier , Satrústegui Jorgina , del Arco Araceli
Published: October 2008

The SCaMCs (small calcium-binding mitochondrial carriers) constitute a subfamily of mitochondrial carriers responsible for the ATP-Mg/Pi exchange with at least three paralogues in vertebrates. SCaMC members are proteins with two functional domains, the C-terminal transporter domain and the N-terminal domain which harbours calcium-binding EF-hands and faces the intermembrane space. In the present study, we have characterized a shortened fourth paralogue, SCaMC-3L (SCaMC-3-like; also named slc25a41), which lacks the calcium-binding N-terminal extension. SCaMC-3L orthologues are found exclusively in mammals, showing approx. 60% identity to the C-terminal half of SCaMC-3, its closest paralogue. In mammalian genomes, SCaMC-3 and SCaMC-3L genes are adjacent on the same chromosome, forming a head-to-tail tandem array, and show identical exon–intron boundaries, indicating that SCaMC-3L could have arisen from an SCaMC-3 ancestor by a partial duplication event which occurred prior to mammalian radiation. Expression and functional data suggest that, following the duplication event, SCaMC-3L has acquired more restrictive functions. Unlike the broadly expressed longer SCaMCs, mouse SCaMC-3L shows a limited expression pattern; it is preferentially expressed in testis and, at lower levels, in brain. SCaMC-3L transport activity was studied in yeast deficient in Sal1p, the calcium-dependent mitochondrial ATP-Mg/Pi carrier, co-expressing SCaMC-3L and mitochondrial-targeted luciferase, and it was found to perform ATP-Mg/Pi exchange, in a similar manner to Sal1p or other ATP-Mg/Pi carriers. However, metabolite transport through SCaMC-3L is calcium-independent, representing a novel mechanism involved in adenine nucleotide transport across the inner mitochondrial membrane, different to ADP/ATP translocases or long SCaMC paralogues.
Netropsin improves survival from endotoxaemia by disrupting HMGA1 binding to the NOS2 promoter
Authors: Grant Marianne A. , Baron Rebecca M. , Macias Alvaro A. , Layne Matthew D. , Perrella Mark A. , Rigby Alan C.
Published: October 2008

The inducible form of nitric oxide synthase (NOS2) plays an important role in sepsis incurred as a result of infection with Gram-negative bacteria that elaborate endotoxin. The HMGA1 (high-mobility group A1) architectural transcription factor facilitates NOS2 induction by binding a specific AT-rich Oct (octamer) sequence in the core NOS2 promoter via AT-hook motifs. The small-molecule MGB (minor-groove binder) netropsin selectively targets AT-rich DNA sequences and can interfere with transcription factor binding. We therefore hypothesized that netropsin would improve survival from murine endotoxaemia by attenuating NOS2 induction through interference with HMGA1 DNA binding to the core NOS2 promoter. Netropsin improved survival from endotoxaemia in wild-type mice, yet not in NOS2-deficient mice, supporting an important role for NOS2 in the beneficial effects of MGB administration. Netropsin significantly attenuated NOS2 promoter activity in macrophage transient transfection studies and the AT-rich HMGA1 DNA-binding site was critical for this effect. EMSAs (electrophoretic mobility-shift assays) demonstrated that netropsin interferes with HMGA1 NOS2 promoter binding and NMR spectroscopy was undertaken to characterize this disruption. Chemical shift perturbation analysis identified that netropsin effectively competes both HMGA1 DNA-binding AT-hooks from the AT-rich NOS2 promoter sequence. Furthermore, NOESY data identified direct molecular interactions between netropsin and A/T base pairs within the NOS2 promoter HMGA1-binding site. Finally, we determined a structure of the netropsin/NOS2 promoter Oct site complex from molecular modelling and dynamics calculations. These findings represent important steps toward refined structure-based ligand design of novel compounds for therapeutic benefit that can selectively target key regulatory regions within genes that are important for the development of critical illness.
Price Comparison between Innovator and Generic Medicines Sold by Community Pharmacies in the State of Penang, Malaysia
Authors: Shafie Asrul Akmal , Hassali Mohamed Azmi
Published: October 2008

Generic medicines play a key role in the affordability of pharmaceuticals. This study aims to compare price and to document the actual savings that can be achieved if generics are used by consumers in the state of Penang, Malaysia. This is a cross-sectional pilot study on the price of innovator and generic medicines for the 20 most-used medications in Malaysia. Upon consent, 20 retail pharmacies were conveniently selected. A pre-validated data collection form was used to collect their selling price from the community pharmacist. The analysis was limited to medicines in the same dosage form and dose. Those still under patent protection or combined with other active ingredients were excluded from the study. This study found that most innovator drugs are 27–90 per cent more expensive than generics. Some generic drugs are, however, more expensive than their innovator counterparts (40 per cent higher). Some locally produced generics are also more expensive than foreign products. The current findings suggest that consumers can save up to 90 per cent of the cost of their medication by using generic products. Further investigation is needed to explore the causality of the observed differences in price of products in order to increase their accessibility to the general population.
Phase transitions and isothermal equations of state of epsilon hexanitrohexaazaisowurtzitane (CL-20)
Authors: Gump Jared C. , Peiris Suhithi M.
Published: October 2008

The phase stability of epsilon hexanitrohexaazaisowurtzitane at high pressure and temperature was investigated using synchrotron angle-dispersive x-ray diffraction experiments. The samples were compressed at room temperature using a Merrill–Bassett diamond anvil cell. For high-temperature compression experiments a hydrothermal diamond anvil cell developed by Bassett was used. Pressures and temperatures of around 5 GPa and 175 °C, respectively, were achieved. The epsilon phase was determined to be stable under ambient pressure to a temperature of 120 °C. A phase transition to the gamma phase was seen at 125 °C and the gamma phase remained stable until thermal decomposition above 150 °C. Pressure-volume data for the epsilon phase at ambient and 75 °C were fitted to the Birch–Murnaghan formalism to obtain isothermal equations of state.
Level distributions, partition functions, and rates of chirality changing processes for the torsional mode around O–O bonds
Authors: Bitencourt Ana C. P. , Ragni Mirco , Maciel Glauciete S. , Aquilanti Vincenzo , Prudente Frederico V.
Published: October 2008

In view of the particular attention recently devoted to hindered rotations, we have tested reduced kinetic energy operators to study the torsional mode around the O–O bond for H2O2 and for a series of its derivatives (HOOCl, HOOCN, HOOF, HOONO, HOOMe, HOOEt, MeOOMe, ClOOCl, FOOCl, FOOF, and FOONO), for which we had previously determined potential energy profiles along the dihedral ROOR′ angle [R,R′=H,F,Cl,CN,NO,Me (=CH3), Et (=C2H5)]. We have calculated level distributions as a function of temperature and partition functions for all systems. Specifically, for the H2O2 system we have used two procedures for the reduction in the kinetic energy operator to that of a rigid-rotor-like one and the calculated partition functions are compared with previous work. Quantum partition functions are evaluated both by quantum level state sums and by simple classical approximations. A semiclassical approach, using a linear approximation of the classical path and a quadratic Feynman–Hibbs approximation of Feynman path integral, introduced in previous work and here applied to the torsional mode, is shown to greatly improve the classical approximations. Further improvement is obtained by the explicit introduction of the dependence of the moment of inertia from the torsional angle. These results permit one to discuss the characteristic time for chirality changes for the investigated molecules either by quantum mechanical tunneling (dominating at low temperatures) or by transition state theory (expected to provide an estimate of racemization rates in the high energy limit).
Dynamics of a stretched nonlinear polymer chain
Authors: Febbo M. , Milchev A. , Rostiashvili V. , Dimitrov D. , Vilgis T. A.
Published: October 2008

We study the relaxation dynamics of a coarse-grained polymer chain at different degrees of stretching by both analytical means and numerical simulations. The macromolecule is modeled as a string of beads, connected by anharmonic springs, subject to a tensile force applied at the end monomer of the chain while the other end is fixed at the origin of coordinates. The impact of bond nonlinearity on the relaxation dynamics of the polymer at different degrees of stretching is treated analytically within the Gaussian self-consistent (GSC) approach and then compared to simulation results derived from two different methods: Monte Carlo (MC) and Molecular Dynamics (MD). At low and medium degrees of chain elongation we find good agreement between GSC predictions and the MC simulations. However, for strongly stretched chains, the MD method, which takes into account inertial effects, reveals two important aspects of the nonlinear interaction between monomers: (i) a coupling and energy transfer between the damped, oscillatory normal modes of the chain and (ii) the appearance of nonvanishing contributions of a continuum of frequencies around the characteristic modes in the power spectrum of the normal mode correlation functions.
Structure and thermal fluctuation of one-dimensional AgO chains on Ag(110) surfaces studied with density functional theory and Monte Carlo simulations
Authors: Nakai Ikuyo , Matsumoto Yoshiyasu , Takagi Noriaki , Okazaki Susumu
Published: October 2008

The structures of continuous and truncated AgO chains on Ag(110) surfaces are studied by using density functional theory (DFT) calculations and the thermal fluctuations of truncated chains are simulated by using the Monte Carlo method. Although it is known that oxygen elimination by CO from one-dimensional AgO chains takes place exclusively at chain ends when the chains keep a linear structure at low temperatures, the structure of chain ends has been unexplored. The DFT calculations reveal that oxygen-terminated chains are more stable than silver-terminated ones and have an enhanced density of states near the Fermi level at the terminal oxygen, which is consistent with scanning tunneling microscope (STM) observations. The Monte Carlo simulations with pairwise interactions between AgO units reproduce characteristic features observed in STM studies, including the existence of an onset temperature for the chain fluctuations and the oxygen-coverage dependence of average chain length. The onset temperature, on one hand, is largely controlled by attractive interactions in the direction parallel to chain growth. On the other hand, the spatial distribution of fragmented AgO chains depends strongly on repulsive interactions in the direction perpendicular to chains. In particular, the repulsive interactions ranging ten units of the lattice constant in the direction perpendicular to the AgO chains are essential to mimic STM observations, where fragmented chains almost keep the mutual distance inherent to the (n×1)-O phase even under thermal fluctuations.
Topological defects in antiferromagnetically coupled multilayers with perpendicular anisotropy
Authors: Kiselev N. S. , Rößler U. K. , Bogdanov A. N. , Hellwig O.
Published: October 2008

A rich variety of specific multidomain textures recently observed in antiferromagnetically coupled multilayers with perpendicular anisotropy include regular (equilibrium) multidomain states as well as different types of topological magnetic defects. Within a phenomenological theory we have classified and analyzed the possible magnetic defects in the antiferromagnetic ground state and determine their structures. The calculated magnetic phase diagrams show the existent regions for all types of magnetic defects. Experimental investigations of the remanent states (observed after different magnetic prehistory) in [Co/Pt]/Ru multilayers with wedged Co layers reveal a corresponding succession of different magnetic defect domain types.
Influence of alkanethiol self-assembled monolayers with various tail groups on structural and dynamic properties of water films
Authors: Yang An-Cheng , Weng Cheng-I
Published: October 2008

Molecular dynamics simulations are performed to investigate the structural and dynamic properties of a water layer lying on a clean Au(111) surface and on alkanethiol self-assembled monolayers (SAMs) with three different tail groups: methyl, carboxyl, and hydroxyl. The effects of these functional groups on the local structure of the water are quantified by analyzing the reduced density profiles of the oxygen and hydrogen atoms, the average number of hydrogen bonds, and the distribution of the OH bond angle, respectively. Meanwhile, the dynamic properties of the water layer are evaluated by analyzing the diffusion coefficients of the water molecules in the xy-plane and z-direction. The simulation results indicate that in both the hydrophobic and the hydrophilic alkanethiol SAMs, the formation of a two-layer water structure is suppressed. And the water molecules can approach the SAMs composed of hydroxyl tails most closely and SAMs composed of methyl tails furthest. Due to the existence of hydrogen bonds between water molecules and hydrophilic alkanethiol SAMs, the distribution of water molecules is more uniform than that in the hydrophobic interface. Meanwhile, the water-water hydrogen bond network weakens. Furthermore, the mobility of the water molecules in the hydrophilic interface is reduced more significantly than in the hydrophobic interface. The results developed in this study yield detailed insights into the microscopic interfacial phenomena.
Thermodynamic and kinetic supercooling of liquid in a wedge pore
Authors: Nowak Dominika , Heuberger Manfred , Zäch Michael , Christenson Hugo K.
Published: October 2008

Cyclohexane allowed to capillary condense from vapor in an annular wedge pore of mica in a surface force apparatus (SFA) remains liquid down to at least 14K below the bulk melting-point Tm. This is an example of supercooling of a liquid due to confinement, like melting-point depression in porous media. In the wedge pore, however, the supercooled liquid is in equilibrium with vapor, and the amount of liquid (and thereby the radius of curvature r of the liquid-vapor interface) depends on the surface tension γLV of the liquid, not the interfacial tension between the solid and liquid. At coexistence r is inversely proportional to the temperature depression ΔT below Tm, in accordance with a recently proposed model [P. Barber, T. Asakawa, and H. K. Christenson, J. Phys. Chem. C 111, 2141 (2007)]. We have now extended this model to include effects due to the temperature dependence of both the surface tension and the enthalpy of melting. The predictions of the improved model have been quantitatively verified in experiments using both a Mark IV SFA and an extended surface force apparatus (eSFA). The three-layer interferometer formed by the two opposing, backsilvered mica surfaces in a SFA was analyzed by conventional means (Mark IV) and by fast spectral correlation of up to 40 fringes (eSFA). We discuss the absence of freezing in the outermost region of the wedge pore down to 14K below Tm and attribute it to nonequilibrium (kinetic) supercooling, whereas the inner region of the condensate is thermodynamically supercooled.
Light emission properties and mechanism of low-temperature prepared amorphous SiNX films. II. Defect states electroluminescence
Authors: Wang M. , Huang J. , Yuan Z. , Anopchenko A. , Li D. , Yang D. , Pavesi L.
Published: October 2008

In this paper, we present a room-temperature electroluminescence (EL) study of amorphous nonstoichiometric silicon nitride (SiNX) films. The light-emitting device is formed by an ITO/SiNX/p-type silicon structure. EL shows a yellowish broad emission spectrum with a power efficiency of 10−6. The EL peak energy depends on the bias voltage rather than on the silicon content in SiNX. By fitting the current-voltage characteristic with existing models, we found that under high voltages the Poole–Frenkel hole conduction is the main carrier transport mechanism in these devices. Injected electrons are captured by silicon dangling bonds (K center) and recombine with holes, which are localized in valence band tail states. Unbalanced hole and electron injection and nonradiative recombination are the main constraints on the EL efficiency of SiNX.
Two definitions of the hopping time in a confined fluid of finite particles
Authors: Kalinay Pavol , Percus Jerome K.
Published: October 2008

We consider a fluid of hard disks diffusing in a flat long narrow channel of width approaching from above the doubled diameter of the disks. In this limit, the disks can pass their neighbors only rarely, in a mean hopping time growing to infinity, so the disks start by diffusing anomalously. We study the hopping time, which is the crucial parameter of the theory describing the subsequent transition to normal diffusion. We show that two different definitions of this quantity, based either on the mean first passage time calculated from solution of the Fick–Jacobs equation, or coming from transition state theory, are incompatible. They have different physical interpretation and also, they give different dependencies of the hopping time on the width of the channel.
Model for hydrogen bubbles and connection to roughness of etched surfaces
Authors: Hynninen Teemu , Gosálvez Miguel A.
Published: October 2008

We analyze the stability of bubbles in the slow growth—small contact angle approximation both numerically and analytically. Dependence is derived between the contact angle and the maximum bubble size. The connection to hydrogen bubble induced roughness of etched surfaces is discussed.
Generalization of the Gibbs–Kelvin–Köhler and Ostwald–Freundlich equations for a liquid film on a soluble nanoparticle
Authors: Shchekin A. K. , Rusanov A. I.
Published: October 2008

A derivation of chemical equilibrium equations for a spherical thin film of solution around a soluble solid nanoparticle is presented. The equations obtained generalize the Gibbs–Kelvin–Köhler and Ostwald–Freundlich equations for a soluble particle immersed in the bulk phase. The generalized equations describe the dependence of the chemical potentials of a condensate and dissolved nanoparticle matter in the thin solution film, the condensate saturated pressure, and the solubility of the nanoparticle matter on the film thickness, and the nanoparticle size with account of the disjoining pressure of the liquid film.
Resonant third harmonic generation in a laser produced thin foil plasma
Authors: Kaur Sukhdeep , Sharma A. K.
Published: October 2008

An analytical model is developed for third harmonic generation (THG) efficiency from a high-density inhomogeneous plasma produced by laser irradiation of a thin metallic film. The laser suffers strong reflection from the critical layer. The superposition of forward and backward waves creates a quasistatic density ripple of wave number 2k and a second harmonic density ripple at 2ω, 4k, where ω and k are the frequency and wave number of the laser. The density ripple couples with the oscillatory electron velocity at ω, k to produce a nonlinear current at 3ω, 5k driving a resonant third harmonic radiation in the region where 5k=k3 and k3 is the wave number at 3ω frequency. As the density scale length of the plasma is increased, the efficiency of THG increases. The same behavior is reproduced in two particle in cell simulation by launching a laser in a rippled density underdense plasma of phase-matched density and a ripple period of half-laser wavelength.