bluuebunny/crossref_metadata_2025 huggingface dataset:
The pathogenesis of Niemann–Pick type C disease: a role for autophagy?
Authors: Pacheco Chris D. , Lieberman Andrew P.
Published: September 2008

Niemann–Pick type C disease (NPC) is a sphingolipid-storage disorder that results from inherited deficiencies of intracellular lipid-trafficking proteins, and is characterised by an accumulation of cholesterol and glycosphingolipids in late endosomes and lysosomes. Patients with this disorder develop progressive neurological impairment that often begins in childhood, is ultimately fatal and is currently untreatable. How impaired lipid trafficking leads to neurodegeneration is largely unknown. Here we review NPC clinical features and biochemical defects, and discuss model systems used to study this disorder. Recent studies have established that NPC is associated with an induction of autophagy, a regulated and evolutionarily conserved process by which cytoplasmic proteins are sequestered within autophagosomes and targeted for degradation. This pathway enables recycling of limited or damaged macromolecules to promote cell survival. However, in other instances, robust activation of autophagy leads to cell stress and programmed cell death. We summarise evidence showing that autophagy induction and flux are increased in NPC by signalling through a complex of the class III phosphoinositide 3-kinase and beclin-1. We propose that an imbalance between induction and flux through the autophagic pathway contributes to cell stress and neuronal loss in NPC and related sphingolipid-storage disorders, and discuss potential therapeutic strategies for modulating activity of this pathway.
Gezielter Einsatz des Tumormarkers PSA
Authors: Kwiatkowski Maciej , Stieber Petra , Huber Andreas R. , Recker Franz
Published: September 2008

Tumormarker werden unter anderem in der Karzinom Früherkennung, Prognose, Behandlung und Beobachtung des Krankheitsverlaufes eingesetzt. Viele klinische Studien sind heutzutage ohne Einsatz der Tumormarker kaum denkbar. Da die Tumormarker in der klinischen Anwendung eine beschränkte Aussagekraft haben (beschränkte Sensitivität und/oder Spezifität), soll deren Einsatz gezielt erfolgen, d.h. in der klinischen Situation, wo der Nutzen am größten ist. Der am häufigsten benutzte Tumormarker ist das Prostata spezifische Antigen (PSA). Sein Einsatz reicht von der Vorsorge des Prostatakarzinoms bis hin zur Therapiekontrolle des hormonrefraktären Karzinoms. Bevor eine «PSA-Kaskade» im Rahmen der Prostatakrebsvorsorge ausgelöst wird, muss der Patient nicht nur über das Risiko Prostatakrebs, sondern auch über die evtl. Therapieschritte inklusive Nebenwirkungen informiert werden. Stimmt er einer Vorsorge zu, so ist die weitere bioptische Abklärung direkt ab einem PSA von 4.0 ng/ml oder auffälliger digital rektaler Untersuchung indiziert. Die früher beschriebene PSA-«Grauzone» 4–10 ng/ml mit abwartender Haltung ist nicht mehr gerechtfertigt. Ein erhöhter Anteil des freien PSA oberhalb des Cut-off 4.0 ng/ml darf nicht zu einer Protrahierung der Biopsie Indikation führen. Bei PSA zwischen 3.0 und 3.9 ng/ml und gleichzeitig einem Anteil des freien PSA unterhalb des Cut-off 12% ist eine Prostatabiopsie ebenfalls angezeigt. Die PSA-Verlaufskontrollen sind bei einer geschätzten Lebenserwartung über 10 Jahre sinnvoll und vom Ausgangs PSA Wert abhängig: bei PSA zwischen 2 und 3.9 ng/ml jährlich, zwischen 1.0 und 1.9 ng/ml 2-jährlich und unterhalb von 1.0 ng/ml 3-jährlich. Etwa 3–25% der initial entdeckten Karzinome in der Biopsie sind klinisch irrelevant und lassen sich durch Vorhersagemodelle mittels PSA, Gleason Score und Tumorbefall der Biopsien prätherapeutisch bestimmen. Zusammenfassend: «Nicht jedes früh erkannte Prostatakarzinom muss behandelt werden, aber das Behandlungsbedürftige muss früh erkannt werden!». Rund ein Drittel der primär mittels kompletter Prostatektomie oder Radiotherapie behandelten organbegrenzten Karzinome werden ein Rezidiv entwickeln. Lediglich ein Drittel dieser Männer wird jedoch eine klinische Symptomatik zeigen respektive tumorbedingt sterben. Hier ist die Verlaufskontrolle des PSA, insbesondere seine Verdopplungszeit, ein zukünftiger Parameter, die Patienten mit hohem Risiko einer klinischen Manifestation des Rezidivs zu isolieren.
Die Rolle des Labors in der Diagnostik und Verlaufskontrolle der Osteoporose
Authors: Kraenzlin Marius E. , Anliker Markus , Griesmacher Andrea
Published: September 2008

Die Osteoporose ist durch einen generalisierten und progredienten Knochensubstanzverlust charakterisiert, der zu einer erhöhten Brüchigkeit des Knochens führt, die sich (klinisch) im Auftreten von Frakturen äußert. Bei einigen Prozent der untersuchten Risikopatienten finden sich laborchemische Besonderheiten, die auf eine sekundäre Osteoporose hinweisen oder Besonderheiten der Diagnostik und Therapie nach sich ziehen. Ziel des Basislabors ist deshalb der weitgehende Ausschluss der wichtigsten sekundären Osteoporosen und differentialdiagnostisch in Frage kommenden anderen Osteopathien. Nach entsprechender Eingrenzung der Diagnose kann das Labor außerdem bei der Evaluation des Frakturrisikos und später bei der Verlaufs- und Therapiekontrolle hilfreich sein.
Monitoring von Immunsuppressiva
Authors: Rentsch Katharina M.
Published: September 2008

Das Therapeutic Monitoring der Immunsuppressiva nimmt eine wichtige Rolle in der Überwachung von transplantierten Patienten und immer mehr auch bei Patienten mit Autoimmunkrankheiten ein. Die Analysenmethoden die heute eingesetzt werden, sind Immunoassays und chromatographische Methoden, vor allem Hochdruckflüssigkeitschromatographie gekoppelt an die Massenspektrometrie (LC-MS/MS). Währenddem bei den meisten Immunsuppressiva Talspiegel bestimmt werden, sind es beim Ciclosporin auch die Maximal- oder C2-Spiegel, die eine bessere Korrelation mit der Wirkung zeigen. Die Bestimmung der Talspiegel der Mycophenolsäure sollte besser durch die Bestimmung der Fläche unter der Konzentrations-Zeit-Kurve (AUC) ersetzt werden, die allerdings mehrere Blutentnahmen erfordert. Alle Immunoassays zeigen mehr oder weniger ausgeprägt Kreuzreaktionen entweder mit den Metaboliten oder mit strukturell ähnlichen Verbindungen (Sirolimus und Everolimus), währenddem die chromatographischen Methoden gezielt nur die Muttersubstanz bestimmen. Dies muss bei der Interpretation der Messresultate berücksichtigt werden.
Model experiments on snow and ice thermodynamics in the Arctic Ocean with CHINARE 2003 data
Authors: Cheng Bin , Zhang Zhanhai , Vihma Timo , Johansson Milla , Bian Lingen , Li Zhijun , Wu Huiding
Published: September 2008

Snow and ice thermodynamics over the Arctic Ocean were simulated applying a one‐dimensional model. A number of numerical experiments in synoptic (10 days in early autumn) and seasonal (May–September) scales were carried out to investigate the impact of external forcing, snow physics, and the model resolution: the number of layers in both snow and ice ranged from 3 to 40. The model forcing was based on in situ observations carried out in 2003 during the Chinese National Arctic Research Expedition (CHINARE) as well as on forecasts and analyses of the European Centre for Medium‐Range Weather Forecasts (ECMWF) and the National Centers for Environmental Prediction (NCEP)/National Center for Atmospheric Research (NCAR). The model results were compared against the results of the ECMWF and NCEP/NCAR sea ice schemes. The ECMWF operational precipitation forecasts yielded realistic seasonal snowfall, while the precipitation in NCEP/NCAR reanalysis was unrealistically large. A good result on snow thickness evolution also strongly depended on the accuracy of modeled snowmelt. A time‐dependent surface albedo parameterization was critical for the seasonal evolution of snow and ice thickness. Application of 15–20 model levels in snow and ice is recommended as it (1) ensured good reproduction of the vertical snow/ice temperature profile also when solar radiation was large, (2) decreased the sensitivity of snow and ice mass balance to changes in surface albedo, (3) enabled the calculation of subsurface melting of snow and ice, and (4) reasonably reproduced the superimposed ice formation and onset of ice melt. In autumn, however, the accuracy of atmospheric forcing was more important than the model resolution.
Inference of optical properties from radiation profiles within melting landfast sea ice
Authors: Ehn J. K. , Papakyriakou T. N. , Barber D. G.
Published: September 2008

Vertical in‐ice spectral radiation profiles were measured within melting 1.5‐ to 1.7‐m‐thick landfast sea ice in western Hudson Bay on 25 April 2005. Because the surface ice was subject to extensive melting and refreezing, the sea ice had fractioned into two main types, i.e., areas of more reflective white ice and less reflective blue ice. The shortwave albedo was about 0.69 for white ice and 0.47 for bare blue ice. The corresponding shortwave transmittance through the ice cover was about 0.02 and 0.09, respectively. The inherent optical properties of the sea ice were inferred by tying the input and output of radiative transfer simulations to the radiation profiles and the ice physical properties, as well as to the irradiance measurements above and below the ice cover. To explain observed spectral albedo and transmittance simultaneously, the ice/snow above the interior ice was divided into three layers on the basis of the following observations: snow (white ice) or a thin soot containing layer (blue ice), drained ice above and saturated ice below the waterline. Similarly, the bottom portion was divided on the basis of the presence of a living ice algae layer adjacent to the seawater interface and a layer extending 30 cm above the bottom containing mostly detrital matter. The interior of the ice, i.e., roughly 20–40 cm from boundaries, was well‐represented by a single layer of pure sea ice as the radiation field was nearly asymptotic and the absorption spectra showed little evidence of impurities. Representative values for the scattering coefficient ranged 600–800 m−1, with a Henyey‐Greenstein asymmetry parameter of 0.995. Observations within white ice suggest that about 40% of the energy responsible of the internal melting was provided directly by shortwave radiation, while the rest is due to heat conduction.
Halving of the northern wetland CH4 source by a large Icelandic volcanic eruption
Authors: Gauci Vincent , Blake Stephen , Stevenson David S. , Highwood Eleanor J.
Published: September 2008

Northern temperate and high‐latitude wetlands are a major source of the greenhouse gas methane (CH4). Here, we estimate the sensitivity in the strength of this source to the effects of large Icelandic volcanic eruptions such as the Laki eruption of 1783–1784. We applied spatially explicit modeled sulfate aerosol and S deposition fields from a Laki eruption simulation to a climate‐sensitive model of CH4 emissions from wetlands. We estimate that the combined influence on climate and S deposition from the Laki eruption halved the output of CH4 from wetlands north of 30°N for the first 12 months following the eruption. The largest short‐term component responsible for the CH4 suppression is the aerosol‐influenced surface cooling, although the effect of large‐scale S deposition on CH4 emissions provides a longer‐term suppressive effect on emissions. Together, we estimate this combination of processes to result in an annual suppression of ∼20 Tg CH4 in the year of the eruption and two subsequent years. Further, the impact of the eruption on atmospheric CH4 concentration extends beyond the likely duration of suppressed emission. The modeled effect of this large Icelandic eruption is consistent with ice core records of atmospheric CH4 concentrations at the time and is equivalent, in size, to the current estimated suppressive effect of industrially derived S pollution on the global wetland CH4 source.
Lattice‐Boltzmann modeling of contaminant degradation by chemotactic bacteria: Exploring the formation and movement of bacterial bands
Authors: Long Wei , Hilpert Markus
Published: September 2008

We developed a three‐dimensional Lattice‐Boltzmann (LB) model to simulate the biodegradation of a dissolved substrate, toward which bacteria exhibit chemotaxis. The model was verified by comparing simulations to capillary assay experiments performed elsewhere. In these assays, a capillary containing an aqueous solution, with initially uniformly distributed dissolved naphthalene, was dipped into a reservoir containing Pseudomonas putida, a microorganism that exhibits chemotaxis to naphthalene. These experiments were also performed with additional glass beads present in the capillary and reservoir. The simulations show that a fraction of the bacteria separates from the reservoir to form a band that moves with constant speed into the capillary while metabolizing the naphthalene. We also used the LB model to explore band formation in a porous medium under groundwater flow conditions. If a bacterial slug is injected, two bacterial bands form; one moves upstream and the other moves downstream. The magnitudes of the two band velocities, as measured relative to the pore water velocity, are identical. Bacteria injected in excess are advected downstream in a fluid parcel containing no substrate. Our simulations suggest that the bioremediation of a contaminant plume in groundwater can potentially be enhanced by the injection of chemotactic bacteria. We also derived a correlation that predicts the number of bacteria in a band that separates from a semi‐infinite bacterial slug in a domain containing substrate that is initially uniformly distributed. This correlation allows estimation of the optimal number of bacteria that needs to be added to a substrate‐filled domain, such that the number of bacteria in the band is maximum while simultaneously avoiding the injection of excess bacteria that do not make it into the band.
Probabilistic description of grain resistance from simultaneous flow field and grain motion measurements
Authors: Bottacin‐Busolin Andrea , Tait Simon J. , Marion Andrea , Chegini Amir , Tregnaghi Matteo
Published: September 2008

Experiments were carried out using a mobile gravel bed placed in a tilting flume with a modified particle image velocimetry (PIV) system. Individual grain movements were surveyed using data from time series of images. Near‐bed velocity flow field measurements were made simultaneously above the same area of the sediment surface by applying cross‐correlation techniques to the collected plan view images. Statistics of grain motions were collected through a semiautomatic procedure. Significant changes in the flow field were observed in the proximity of the entrained or deposited particles. A strong correlation is shown between the changes in the local streamwise and lateral velocity and the movement of the grains. The theory of Grass is revisited and developed based on the experimental results. The probability distribution of individual grain resistance has been derived from the statistics of the near‐bed velocity field and of the entrainment risk.
Streamflow distribution of non–point source nitrogen export from urban‐rural catchments in the Chesapeake Bay watershed
Authors: Shields Catherine A. , Band Lawrence E. , Law Neely , Groffman Peter M. , Kaushal Sujay S. , Savvas Katerina , Fisher Gary T. , Belt Kenneth T.
Published: September 2008

Nitrogen (N) export from urban and urbanizing watersheds is a major contributor to water quality degradation and eutrophication of receiving water bodies. Methods to reduce N exports using best management practices (BMP) have targeted both source reduction and hydrologic flow path retention. Stream restoration is a BMP targeted to multiple purposes but includes increasing flow path retention to improve water quality. As restorations are typically most effective at lower discharge rates with longer residence times, distribution of N load by stream discharge is a significant influence on catchment nitrogen retention. We explore impacts of urbanization on magnitude and export flow distribution of nitrogen along an urban‐rural gradient in a set of catchments studied by the Baltimore Ecosystem Study (BES). We test the hypotheses that N export magnitude increases and cumulative N export shifts to higher, less frequent discharge with catchment urbanization. We find that increasing development in watersheds is associated with shifts in nitrogen export toward higher discharge, while total magnitude of export does not show as strong a trend. Forested reference, low‐density suburban, and agricultural catchments export most of the total nitrogen (TN) and nitrate (NO3−) loads at relatively low flows. More urbanized sites export TN and NO3− at higher and less frequent flows. The greatest annual loads of nitrogen are from less developed agricultural and low‐density residential (suburban/exurban) areas; the latter is the most rapidly growing land use in expanding metropolitan areas. A simple statistical model relating export distribution metrics to impervious surface area is then used to extrapolate parameters of the N export distribution across the Gwynns Falls watershed in Baltimore County. This spatial extrapolation has potential applications as a tool for predictive mapping of variations in export distribution and targeting stream channel restoration efforts at the watershed scale.
Electron impact ionization: A new parameterization for 100 eV to 1 MeV electrons
Authors: Fang Xiaohua , Randall Cora E. , Lummerzheim Dirk , Solomon Stanley C. , Mills Michael J. , Marsh Daniel R. , Jackman Charles H. , Wang Wenbin , Lu Gang
Published: September 2008

We present a new parameterization of the altitude profile of the ionization rate in the Earth's atmosphere due to precipitating energetic electrons. Precipitating electrons are assumed to have a Maxwellian energy distribution and an isotropic pitch angle distribution above the atmosphere. In this study, two electron transport models (whose validity has been verified by observations) are employed to calculate the ionization rate, to which we have fit our new parameterization. To derive a new parameterization, we follow a similar scheme to that of Roble and Ridley (1987) but take into account further functional dependence on the incident electron energy. As a result, the new method presented in this paper provides a highly improved prediction for electron impact in a significantly extended energy range from 100 eV to 1 MeV, spanning 4 orders of magnitude. Note that we have neglected the contribution of bremsstrahlung X rays generated by energetic electrons, which are mostly important below 50 km altitude. The comparison of parameterization results with model calculations shows that the errors generally fall well within ±5% in both the altitude‐integrated total ionization rate and the peak value. The altitude profile as a whole is also accurately predicted, with errors in the altitudes of the peak and e‐folding ionization rates significantly less than 5 km. The proposed new parameterization method with high accuracy is thus ready to be implemented into global models to assess the electron impact on the ionosphere and the atmosphere.
Metastatic cell detection using a phage‐peptide‐modified light‐addressable potentiometric sensor
Authors: Zhang Hongkai , Li Xin , Bai Yunpeng , Niu Ruifang , Jia Yunfang , Zhang Cuizhu , Zhang Lin , Feng Xizeng , Cao Youjia
Published: September 2008

Detection of metastatic cells is clinically demanded to diagnose metastasis in the early stage and access the therapeutic response to anticancer drugs. We applied phage display technology to cultured cells with different metastasis potentials and obtained four metastasis‐associated peptides. The association between peptides and metastatic cells was validated by ELISA as well as biosensor studies. The selected phage‐peptides not only bound SW620, the metastatic cell against which the peptides were screened, but were also able to capture breast cancer cells of high metastasis. The phage‐peptide‐modified LAPS (light‐addressable potentiometric sensor) was able to distinguish metastatic cells from non‐metastatic cells and detect as few as 100 metastatic cells per ml of blood. Thus LAPS modified with specific phage‐peptides may be developed to provide a new diagnostic approach that can aid the treatment of cancer.
Antibacterial and antioxidant activity of the secondary metabolites from in vitro cultures of the Alice sundew (Drosera aliciae)
Authors: Krolicka Aleksandra , Szpitter Anna , Maciag Monika , Biskup Edyta , Gilgenast Ewelina , Romanik Grazyna , Kaminski Marian , Wegrzyn Grzegorz , Lojkowska Ewa
Published: September 2008

The objective of the present study was to evaluate the antioxidant as well as the antibacterial properties of secondary metabolites obtained from Drosera aliciae (Alice sundew) plants grown in vitro and to examine the mechanism of their antimicrobial action. Bactericidal activity of extracts from D. aliciae, as well as pure ramentaceone (naphthoquinone), which is present in this plant, were examined against human pathogenic strains of micro‐organisms that are both resistant and susceptible to antibiotics. A chloroform extract proved to be more effective than a methanol preparation against all of the tested strains, except for Pseudomonas aeruginosa isolates. The lowest minimal‐bactericidal‐concentration value was in the case of Staphylococcus aureus (25–50 mg fresh weight·ml−1). The influence of D. aliciae extracts and ramentaceone on the synthesis of DNA, RNA or proteins in cultures of Enterococcus faecalis was estimated by measurement of the incorporation of the radioactively labelled precursors [3H]thymidine, [3H]uridine or [3H]leucine respectively. The methanol extract of D. aliciae, except for a moderate effect on DNA synthesis, had no influence on RNA and protein synthesis. The chloroform preparation caused about a 75% decrease in [3H]uridine incorporation in comparison with the control after 60 min and a significant diminution in DNA and protein synthesis (44 and 30% respectively). Ramentaceone also decreased DNA and RNA synthesis, but less efficiently than did the chloroform extract, and it caused no changes in [3H]leucine incorporation. The methanol extract from D. aliciae proved to be an effective antioxidant in both the DPPH (2,2‐diphenyl‐10‐picrylhydrazyl free radical) and the FRAP (ferric reducing antioxidant power) assay, with the activities exceeding those of well‐known antioxidants, namely the flavonoids. The chloroform extract and ramentaceone showed no antioxidative properties.
Characterization of the activity and folding of the glutathione transferase fromEscherichia coliand the roles of residues Cys10 and His106
Authors: Wang Xin-Yu , Zhang Zai-Rong , Perrett Sarah
Published: September 2008

GSTs (glutathione transferases) are an important class of enzymes involved in cellular detoxification. GSTs are found in all classes of organisms and are implicated in resistance towards drugs, pesticides, herbicides and antibiotics. The activity, structure and folding, particularly of eukaryotic GSTs, have therefore been widely studied. The crystal structure of EGST (GST from Escherichia coli) was reported around 10 years ago and it suggested Cys10 and His106 as potential catalytic residues. However, the role of these residues in catalysis has not been further investigated, nor have the folding properties of the protein been described. In the present study we investigated the contributions of residues Cys10 and His106 to the activity and stability of EGST. We found that EGST shows a complex equilibrium unfolding profile, involving a population of at least two partially folded intermediates, one of which is dimeric. Mutation of residues Cys10 and His106 leads to stabilization of the protein and affects the apparent steady-state kinetic parameters for enzyme catalysis. The results suggest that the imidazole ring of His106 plays an important role in the catalytic mechanism of the enzyme, whereas Cys10 is involved in binding of the substrate, glutathione. Engineering of the Cys10 site can be used to increase both the stability and GST activity of EGST. However, in addition to GST activity, we discovered that EGST also possesses thiol:disulfide oxidoreductase activity, for which the residue Cys10 plays an essential role. Further, tryptophan quenching experiments indicate that a mixed disulfide is formed between the free thiol group of Cys10 and the substrate, glutathione.
Arabidopsis thaliana GLX2-1 contains a dinuclear metal binding site, but is not a glyoxalase 2
Authors: Limphong Pattraranee , Crowder Michael W. , Bennett Brian , Makaroff Christopher A.
Published: September 2008

In an effort to probe the structure and function of a predicted mitochondrial glyoxalase 2, GLX2-1, from Arabidopsis thaliana, GLX2-1 was cloned, overexpressed, purified and characterized using metal analyses, kinetics, and UV–visible, EPR, and 1H-NMR spectroscopies. The purified enzyme was purple and contained substoichiometric amounts of iron and zinc; however, metal-binding studies reveal that GLX2-1 can bind nearly two equivalents of either iron or zinc and that the most stable analogue of GLX2-1 is the iron-containing form. UV–visible spectra of the purified enzyme suggest the presence of Fe(II) in the protein, but the Fe(II) can be oxidized over time or by the addition of metal ions to the protein. EPR spectra revealed the presence of an anti-ferromagnetically-coupled Fe(III)Fe(II) centre and the presence of a protein-bound high-spin Fe(III) centre, perhaps as part of a FeZn centre. No paramagnetically shifted peaks were observed in 1H-NMR spectra of the GLX2-1 analogues, suggesting low amounts of the paramagnetic, anti-ferromagnetically coupled centre. Steady-state kinetic studies with several thiolester substrates indicate that GLX2-1 is not a GLX2. In contrast with all of the other GLX2 proteins characterized, GLX2-1 contains an arginine in place of one of the metal-binding histidine residues at position 246. In order to evaluate further whether Arg246 binds metal, the R246L mutant was prepared. The metal binding results are very similar to those of native GLX2-1, suggesting that a different amino acid is recruited as a metal-binding ligand. These results demonstrate that Arabidopsis GLX2-1 is a novel member of the metallo-β-lactamase superfamily.
When expressed in yeast, mammalian mitogen-activated protein kinases lose proper regulation and become spontaneously phosphorylated
Authors: Levin-Salomon Vered , Maayan Inbal , Avrahami-Moyal Liat , Marbach Irit , Livnah Oded , Engelberg David
Published: September 2008

MAPKs (mitogen-activated protein kinases) are key components in cell signalling pathways. Under optimal growth conditions, their activity is kept off, but in response to stimulation it is dramatically evoked. Because of the high degree of evolutionary conservation at the levels of sequence and mode of activation, MAPKs are believed to share similar regulatory mechanisms in all eukaryotes and to be functionally substitutable between them. To assess the reliability of this notion, we systematically analysed the activity, regulation and phenotypic effects of mammalian MAPKs in yeast. Unexpectedly, all mammalian MAPKs tested were spontaneously phosphorylated in yeast. JNKs (c-Jun N-terminal kinases) lost their phosphorylation in pbs2Δ cells, but p38s and ERKs (extracellular-signal-regulated kinases) maintained their spontaneous phosphorylation even in pbs2Δste7Δmkk1Δmkk2Δ cells. Kinase-dead variants of ERKs and p38s were phosphorylated in strains lacking a single MEK (MAPK/ERK kinase), but not in pbs2Δste7Δmkk1Δmkk2Δ cells. Thus, in yeast, p38 and ERKs are phosphorylated via a combined mechanism of autophosphorylation and MEK-mediated phosphorylation (any MEK). We further addressed the mechanism allowing mammalian MAPKs to exploit yeast MEKs in the absence of any activating signal. We suggest that mammalian MAPKs lost during evolution a C-terminal region that exists in some yeast MAPKs. Indeed, removal of this region from Hog1 and Mpk1 rendered them spontaneously and highly phosphorylated. It implies that MAPKs possess an efficient inherent autoposphorylation capability that is suppressed in yeast MAPKs via a C-terminal domain and in mammalian MAPKs via as yet unknown means.
Long-Term Outcome of Endonasal Endoscopic Skull Base Reconstruction with Nasal Turbinate Graft
Authors: Altuwaijri Mohammed A , Ayad Heshmat , El-Sharnoby Mohamed M , El-Banhawy Omar A , Halaka Ahmed N
Published: September 2008

Objective: To study the long-term outcome of endonasal endoscopic skull base reconstruction with nasal turbinate tissue free graft. Patients and Methods: This study included 55 consecutive patients who underwent endonasal endoscopic skull base reconstruction with nasal turbinate graft and were available for follow-up. They were 30 patients with pituitary adenomas, 20 with cerebrospinal fluid (CSF) rhinorrhea of different etiologies, three with meningoencephalocele, and two with skull base meningiomas. Autologous nasal turbinate tissue materials were used in reconstructing the skull base defect. Clinical follow-up with endoscopic nasal examination was done routinely 1, 3, 6, and 12 months after surgery. Computed tomography and magnetic resonance imaging were performed when indicated. The follow-up period ranged from 6 months to 8 years. Results: There were no major operative or postoperative complications. Nasal turbinate graft was effective in sealing of intraoperative CSF leak, obliteration of dead space, and anatomic reconstruction of the skull base. There was no evidence of graft migration or inflammatory changes. Starting from 3 months after surgery to the rest of the follow-up period, endonasal endoscopic view of the site of duraplasty showed that: with small skull base defect (less than 5 mm), there was neither dural pulsation nor prolapse; with moderate-sized defect (5 to 10 mm), there was dural pulsation without prolapse; with larger defect (> 10 mm), there was dural pulsation and prolapse. These finding were constant regardless of the etiology of the lesion and the reconstruction material used. Conclusions: This long-term study demonstrated the efficacy of nasal turbinate graft in sealing of CSF leak without any delayed complications. Other rigid materials may be considered in reconstruction of large skull base defect (more than 10 mm) to prevent dural prolapse and herniation. For any future endonasal procedure for those patients, who had previous endonasal endoscopic duraplasty, the surgeons should be fully aware of the state of duraplasty (e.g., dural prolapse) to avoid any intraoperative complication (e.g., penetration of the prolapsed dura during nasal packing).
Viscoelastic properties of room temperature ionic liquids
Authors: Makino Wataru , Kishikawa Ryoko , Mizoshiri Makoto , Takeda Shinichi , Yao Makoto
Published: September 2008

The sound absorption coefficient α and sound velocity νS have been measured for 1-alkyl-3-methylimidazolium hexafluorophosphate [Cnmim]PF6, with n=8,6,4 and 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide [C4 mim]TFSI, at the frequencies of 11.3, 34.9, and 57.7MHz in the temperature range from 293to393K. From the obtained α and available viscosity data, [Cnmim]PF6 with large n proves to be no longer Newtonian liquids at room temperatures. Applying a Maxwell viscoelastic model with the elastic modulus G of a spring and the shear coefficient γ of a dashpot to the experimental frequency dependence of α, one finds that G is insensitive to n, while the relaxation time τ(=γ∕G), which is on the order of nanoseconds, does depend on n.
Synthesis and optical properties of ZnO and carbon nanotube based coaxial heterostructures
Authors: Kim D. S. , Lee S.-M. , Scholz R. , Knez M. , Gösele U. , Fallert J. , Kalt H. , Zacharias M.
Published: September 2008

Carbon nanotubes and ZnO based functional coaxial heterostructured nanotubes have been fabricated by using atomic layer deposition. An irregular structured shell composed of ZnO nanocrystals was deposited on pristine nanotubes, while a highly defined ZnO shell was deposited on the tubes after its functionalization with Al2O3. Photoluminescence measurements of the ZnO shell on Al2O3/nanotube show a broad green band emission, whereas the shell grown on the bare nanotube shows a band shifted to the orange spectral range.
Characterization of hydrogen absorption/desorption states on lithium-carbon-hydrogen system by neutron diffraction
Authors: Miyaoka Hiroki , Itoh Keiji , Fukunaga Toshiharu , Ichikawa Takayuki , Kojima Yoshitsugu , Fuji Hironobu
Published: September 2008

The nanostructural hydrogenated graphite (CnanoHx) was synthesized from graphite by ball milling under hydrogen (H2) atmosphere. In this product, characteristic hydrogenated states in the form of polarized hydrocarbon groups (CH, CH2, and CH3) are realized in the nanoscale. By synthesizing the composite of CnanoHx and lithium hydride (LiH), known as the LiCH system, hydrogen was desorbed at 350°C, which is a lower temperature compared to the decomposition temperature of each component. It is considered that this hydrogen desorption would be induced by destabilization of each hydrogen absorbed state due to an interaction between the polarized CH groups in CnanoHx and LiH. Therefore, in order to understand the hydrogen absorption/desorption mechanism of the LiCH system, it is an important issue to investigate the change in the CH groups during hydrogen absorption/desorption reactions in the composite. The correlations among atoms contained in this composite are examined by neutron diffraction measurements, where the protium/deuterium (H/D) isotopic substitution was used to clarify the location of hydrogen atoms in this composite. Some CD and LiD correlations are found from the radial distribution function [RDF(r)] obtained by the neutron diffraction for the CnanoDx and LiD composite. After dehydrogenation, CC triple bond and LiC bond, ascribed to lithium carbide (Li2C2), are observed. Furthermore, the RDF(r) corresponding to rehydrogenated composite indicates the presence of not only the LiD correlation but also the CD one.
Transverse laser-induced thermoelectric voltages in tilted La2−xSrxCuO4 thin films
Authors: Xiong F. , Zhang H. , Jiang Z. M. , Zhang P. X.
Published: September 2008

The transverse laser-induced thermoelectric voltages in the tilted La2−xSrxCuO4 (LSCO) thin films are observed for the first time. The detected signals are demonstrated to originate from the anisotropy of thermoelectric power and depend on the Sr-doping level drastically. The largest voltage is observed in the LSCO films at x=0.15 under the irradiation of different lasers with the wavelength in the spectrum range from infrared to ultraviolet. The dependence of the signals on Sr-doping content is associated with a two dimensional charge transport behavior in LSCO films near the optimum doping content.
Two-trap model for low voltage stress-induced leakage current in ultrathin SiON dielectrics
Authors: Nicollian Paul E. , Krishnan Anand T. , Reddy Vijay K.
Published: September 2008

Stress-induced leakage current is a useful probe of the buildup of trap states created by the electrical stress of ultrathin dielectric films. The generation of both bulk and interface traps can affect the current-voltage characteristics. It has been shown that trap assisted tunneling through interface traps is the dominant transport mechanism below 3.5 nm thickness when the poststress leakage is sensed in the off state. However, there is some ambiguity in the literature regarding whether traps at one or both of the contact interfaces are involved in the tunneling process. In this work, we show that for n-channel metal-oxide-semiconductor (NMOS) devices, the off-state (VG<0 V) gate current of electrically stressed ultrathin SiON dielectrics senses a two-trap tunneling process that involves interface states at both anode and cathode interfaces. In aggregate, five peaks due to tunneling via interface traps are observed in the poststress I-V characteristics of ultrathin NMOS SiON dielectrics.
Molecular dynamics study on the influence of quencher concentration on the reaction rate for ionic systems
Authors: Litniewski Marek
Published: September 2008

The influence of concentrations of reagents on the rate of reaction: A+B→C+B for low density equimolar mixtures of spherically symmetric ions immersed in the Brownian medium has been investigated by performing large scale molecular dynamics simulations. The Coulomb potential of ion-ion interactions is truncated at the cutoff distance large enough to make the kinetics of the reaction independent of its value. The simulations have been performed at conditions close to that for quenching reactions for fluophores. One of the simulation results is that the excess in the rate coefficient Δk is always positive and converges to a constant value which is two to three orders in magnitude higher than that for the soft spheres immersed in the Brownian medium [Litniewski, J. Chem. Phys. 124, 114502 (2006)]. Δk is approximately proportional to c however, if the concentration is high, positive deviations [O(c2)] are noticeable. The simulation results are compared with simple model that bases on the superposition approximation. The model predicts most of the properties of Δk. The predicted values are about 30%–40% lower than that from the simulations.
Quasiparticle energy spectra of alkali-metal clusters: All-electron first-principles calculations
Authors: Noguchi Yoshifumi , Ishii Soh , Ohno Kaoru , Sasaki Taizo
Published: September 2008

A good approximation to the one-electron self-energy operator in the calculation of quasiparticle energy spectra including the first ionization potential (IP) and electron affinity (EA) is to expand it as a simple product of a one-particle Green’s function G and a dynamically screened Coulomb interaction W, namely, GW approximation. We developed a spin-polarized version of the all-electron GW approach and applied it to the first-principles calculation of quasiparticle energy spectra of alkali-metal clusters (Nan and Kn, n=1–8). Our all-electron mixed basis approach, in which wave functions are expressed as a linear combination of numerical atomic orbitals and plane waves, enables us to compare the absolute values of the singly (or highest) occupied molecular orbital and the lowest unoccupied molecular orbital levels with available experimental IPs and EAs. The agreements with the corresponding experimental values are fairly good. Comparing with the non-spin-polarized results of Na2n and K2n (n=1–4), we discuss the effect of spin polarization as well as the cluster size dependence of IPs or EAs.
Dynamic carrier lifetime imaging of silicon wafers using an infrared-camera-based approach
Authors: Ramspeck K. , Reissenweber S. , Schmidt J. , Bothe K. , Brendel R.
Published: September 2008

We present a calibration-free dynamic infrared carrier lifetime mapping technique, yielding images of the carrier lifetime of multicrystalline silicon wafers within seconds. Images of the infrared emission of the sample under test are taken directly after switching on a monochromatic illumination source and after steady-state conditions have been established in the sample. Making use of the proportionality between the infrared emission and the free carrier density inside the sample, the carrier lifetime is calculated from the signal ratio of these two images by an analytical method. We achieve an excellent agreement when comparing our results with carrier lifetime mappings obtained by the microwave-detected photoconductance decay technique.
Design and development of detector signal conditioning electronics for SST-1 Thomson scattering system
Authors: Thakar Aruna , Kumar Ajai , Thomas Jinto , Chavda Chhaya
Published: September 2008

An IR enhanced thermoelectrically cooled Si-avalanche photodiode (Si-APD) module is used for detection of scattered photons from plasma electrons. Present design of signal conditioning electronics for the APD has fast (50MHz) and slow (500kHz) channels to measure scattered and plasma background light, respectively. We report design analysis for different stages and their performance. The performance of fast channel is analyzed for two different group delays, speed, linearity, and its cross-talk with slow channel. Temperature dependence of APD’s responsivity is studied in the wavelength range of 900–1060nm. A minimum detection of ∼25 photoelectrons (with S∕N=1) in the range of 5to25°C is achieved at an APD gain of 75 in the present design.
Carrier-phonon interaction in small cross-sectional silicon nanowires
Authors: Buin A. K. , Verma A. , Anantram M. P.
Published: September 2008

Using first-order perturbation theory and deformation potential approximation, the interaction of electrons and holes with acoustic and optical phonons is investigated in silicon nanowires (SiNWs) with different diameters and crystallographic axis orientations. The electronic band structures for [110] and [100] SiNWs are obtained from a sp3d5s∗ tight-binding scheme, while a continuum model is assumed for phonon dispersion. The influence of confined and bulk phonons on carrier transport is investigated.
Polar orientation of a pendant anionic chromophore in thick layer-by-layer self-assembled polymeric films
Authors: Garg Akhilesh , Davis Richey M. , Durak Cemil , Heflin James R. , Gibson Harry W.
Published: September 2008

Multilayer films with up to 600 bilayers and 740 nm thickness were fabricated using the alternating deposition of poly(allylamine hydrochloride) and poly{1-[p-(3′-carboxy-4′- hydroxyphenylazo)benzenesulfonamido]-1,2-ethandiyl} on glass substrates. Linear relationships for absorbance, thickness, and the square root of the second harmonic intensity versus the number of bilayers demonstrates that the films have long range polar order and optical homogeneity. The deposition conditions (i.e., pH of the solutions, solvent quality, deposition and rinsing times) are critical variables in fabricating layer-by-layer thick films that exhibit long range polar orientation of chromophores. The ability to fabricate noncentrosymmetric films on the order of a micron thick with bulk second order nonlinear optical responses is crucial because it enables the development of nonlinear optical waveguide devices such as electro-optic modulators.
Why are ionic liquid ions mainly associated in water? A Car–Parrinello study of 1-ethyl-3-methyl-imidazolium chloride water mixture
Authors: Spickermann C. , Thar J. , Lehmann S. B. C. , Zahn S. , Hunger J. , Buchner R. , Hunt P. A. , Welton T. , Kirchner B.
Published: September 2008

In this study we present the results of a first principles molecular dynamics simulation of a single 1-ethyl-3-methyl-imidazolium chloride [C2C1im][Cl] ion pair dissolved in 60 water molecules. We observe a preference of the in plane chloride coordination with respect to the cation ring plane as compared to the energetic slightly more demanding on top coordination. Evaluation of the different radial distribution functions demonstrates that the structure of the hydration shell around the ion pair differs significantly from bulk water and that no true ion pair dissociation in terms of completely autonomous solvation shells takes place on the timescale of the simulation. In addition, dipole moment distributions of the solvent in distinct solvation shells around different functional parts of the [C2C1im][Cl] ion pair are calculated from maximally localized Wannier functions. The analysis of these distributions gives evidence for a depolarization of water molecules close to the hydrophobic parts of the cation as well as close to the anion. Examination of the angular distribution of different OH(H2O)–X angles in turn shows a linear coordination of chloride accompanied by a tangential orientation of water molecules around the hydrophobic groups, being a typical feature of hydrophobic hydration. Based on these orientational aspects, a structural model for the obvious preference of ion pair association is developed, which justifies the associating behavior of solvated [C2C1im][Cl] ions in terms of an energetically favorable interface between the solvation shells of the anion and the hydrophobic parts of the cation.
Misfit point defects at the epitaxial Lu2O3/(111)Si interface revealed by electron spin resonance
Authors: Stesmans A. , Somers P. , Afanas’ev V. V. , Tian W. , Edge L. F. , Schlom D. G.
Published: September 2008

Electron spin resonance study on heteroepitaxial Si/insulator structures obtained through the growth of epi-Lu2O3 films on (111)Si (∼4.5 % mismatched) by reactive molecular beam epitaxy indicates the presence in the as-grown state of interfacial Pb defects (∼5×1011 cm−2) with an unpaired sp3 Si dangling bond (DB) along the [111] sample normal, prototypical of the standard thermal (111)Si/SiO2 interface. The defects, with density remaining unchanged to anneal in vacuum up to temperatures of Tan∼420 °C, directly reveal the nonperfect pseudoepitaxial nature of the interface, laid down in electrically detrimental interface traps. These are suggested to be interfacial Si DBs related to Si misfit dislocations. Alarmingly, defect passivation by standard anneal treatments in H2 fall short. For higher Tan, the interface deteriorates to “standard” Si/SiO2 properties, with an attendant appearance of EX centers indicating SiO2 growth. Above Tan∼1000 °C, the interface disintegrates altogether.
Formation of nanocavities in dielectrics: A self-consistent modeling
Authors: Mézel C. , Hallo L. , Bourgeade A. , Hébert D. , Tikhonchuk V. T. , Chimier B. , Nkonga B. , Schurtz G. , Travaillé G.
Published: September 2008

Tight focusing of a subpicosecond laser pulse in transparent dielectrics is an efficient way to release laser energy and to produce plasma. A micro-explosion results in a submicrometer cavity formation if the deposited laser energy exceeds a threshold. A self-consistent model is developed that describes this process. The energy deposition is described by a full set of Maxwell’s equations in the three-dimensional geometry and it accounts for nonlinear propagation phenomena in the femtosecond time scale. The calculated energy deposition is transferred to a hydrodynamic code that describes the cavity formation. Numerical simulations show that cavity size in silica depends strongly on the latent heat of sublimation. An equation of state is developed and introduced into the hydrodynamic model that takes into account the influence of such material parameters as the binding energy, the bulk modulus, and the Grüneisen coefficient. The cavity and shock-affected region sizes are compared to experimental data. This comparison suggests that laser micro-explosions might allow to tune the parameters of equations of state in the domain of phase transitions in a cold dense matter.
Spin reorientation in Al/Metglas 2605S2/Al trilayers induced by magnetoelastic effect
Authors: Moscon P. S. , Passamani E. C. , Larica C. , Takeuchi A. Y. , Sánchez F. H. , Zélis P. Mendoza , Baggio-Saitovitch Elisa
Published: September 2008

Mössbauer spectroscopy, in a broad temperature interval of 12–425 K, has been applied to investigate the spin reorientation dynamics caused by the temperature induced magnetoelastic effect on Al(x μm)/Metglas 2605S2 (20 μm)/Al(x μm) trilayers (x=0; 2.5; 5 and 20). It was found that the angle between the average sample magnetization and gamma ray direction (perpendicular to the sample plane) depends on the Al layer thickness. For temperatures smaller than 260 K, saturation of spin reorientation, which can be controlled by adjusting the Al thickness, was reached for Al thicknesses larger than and equal to 5 μm. For a 20 μm Al thickness, changes in the F57e atom spin and charge densities have also been observed. A simple spin model has been proposed to describe qualitatively the spin reorientation effect as well as the influence of the Al thickness on the spin reorientation sensitivity.