bluuebunny/crossref_metadata_2025_split huggingface dataset:
Centrosome‐, chromosomal‐passenger‐ and cell‐cycle‐associated mRNAs are differentially regulated in the development of sporadic colorectal cancer
Authors: Gerlach Ulrike , Kayser Gian , Walch Axel , Hopt Ulrich , Schulte‐Mönting Jürgen , Werner Martin , Lassmann Silke 
Published: January 2006

AbstractDysregulation of the centrosome complex and chromosomal segregation has been associated with aneuploid cells and aggressive solid tumours, but the relevance of this mechanism to the adenoma–carcinoma sequence of sporadic colorectal cancer (sCRC), especially tumours showing chromosomal instability (CIN), is still unknown. In a series of matching normal epithelial cells (n = 41), dysplastic cells (n = 18), and invasive carcinoma cells (n = 41) from cases with sCRC, mRNA levels of the centrosomal kinase Aurora‐A/STK15 and the chromosomal passenger‐ and cell cycle‐associated molecules Incenp, Survivin, Mad‐2, and Cyclin‐D1 were therefore measured with specific reference to the type of genetic instability. Compared with normal epithelium, significant up‐regulation of mRNAs was already present for Aurora‐A/STK15 (p = 0.0313) in dysplastic cells and for all investigated markers in invasive carcinoma. Whereas Aurora‐A/STK15 mRNA levels were similarly up‐regulated in dysplastic and invasive carcinoma cells (p = 0.0797), Survivin (p = 0.0046) and Cyclin‐D1 (p = 0.0017) mRNA levels increased from dysplastic to invasive carcinoma cells. In carcinomas, Incenp mRNA correlated with T category (p = 0.0149), and Survivin (p = 0.0382) and Cyclin‐D1 (p = 0.0185) were associated with tumour differentiation. Importantly, a significantly higher (p = 0.0419) fold‐change of Aurora‐A/STK15 mRNA (p = 0.0419), but not Incenp, Survivin, Mad‐2 or Cyclin‐D1, was observed in sCRC cases with CIN (n = 29) when compared with tumours showing microsatellite instability (MIN, n = 10). The present data are the first to show an early increase of the centrosomal kinase Aurora‐A/STK15 in the adenoma–carcinoma sequence of sCRC. The regulation of this kinase differs in CIN‐ and MIN‐type sCRCs and the pattern of changes is different from those of the cell‐cycle‐associated markers Survivin, Mad‐2, and Cyclin‐D1. This reinforces the concept of preferential dysregulation of the centrosome complex in CIN‐type (aneuploid), compared with MIN‐type, sporadic colorectal cancers and may influence the response to and efficiency of novel therapeutics targeting Aurora kinases. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Potential biomarkers for ischemic heart damage identified in mitochondrial proteins by comparative proteomics
Authors: Kim Nari , Lee Youngsuk , Kim Hyungkyu , Joo Hyun , Youm Jae Boum , Park Won Sun , Warda Mohamad , Cuong Dang Van , Han Jin 
Published: January 2006

AbstractWe used proteomics to detect regional differences in protein expression levels from mitochondrial fractions of control, ischemia–reperfusion (IR), and ischemic preconditioned (IPC) rabbit hearts. Using 2‐DE, we identified 25 mitochondrial proteins that were differentially expressed in the IR heart compared with the control and IPC hearts. For three of the spots, the expression patterns were confirmed by Western blotting analysis. These proteins included 3‐hydroxybutyrate dehydrogenase, prohibitin, 2‐oxoglutarate dehydrogenase, adenosine triphosphate synthases, the reduced form of nicotinamide adenine dinucleotide (NADH) oxidoreductase, translation elongation factor, actin alpha, malate dehydrogenase, NADH dehydrogenase, pyruvate dehydrogenase and the voltage‐dependent anion channel. Interestingly, most of these proteins are associated with the mitochondrial respiratory chain and energy metabolism. The successful use of multiple techniques, including 2‐DE, MALDI‐TOF‐MS and Western blotting analysis demonstrates that proteomic analysis provides appropriate means for identifying cardiac markers for detection of ischemia‐induced cardiac injury.
Entropy capacity determines protein folding
Authors: Galzitskaya Oxana V. , Garbuzynskiy Sergiy O. 
Published: January 2006

AbstractSearch and study of the general principles that govern kinetics and thermodynamics of protein folding generate a new insight into the factors controlling this process. Here, based on the known experimental data and using theoretical modeling of protein folding, we demonstrate that there exists an optimal relationship between the average conformational entropy and the average energy of contacts per residue—that is, an entropy capacity—for fast protein folding. Statistical analysis of conformational entropy and number of contacts per residue for 5829 protein structures from four general structural classes (all‐α, all‐β, α/β, α+β) demonstrates that each class of proteins has its own class‐specific average number of contacts (class α/β has the largest number of contacts) and average conformational entropy per residue (class all‐α has the largest number of rotatable angles ϕ, ψ, and χ per residue). These class‐specific features determine the folding rates: α proteins are the fastest folding proteins, then follow β and α+β proteins, and finally α/β proteins are the slowest ones. Our result is in agreement with the experimental folding rates for 60 proteins. This suggests that structural and sequence properties are important determinants of protein folding rates. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Electron band structure and optical properties of InN and related alloys
Authors: Alexandrov D. , Butcher S. , Tansley T. 
Published: January 2006

AbstractNew metric system called electron metric system having basic metric constant is introduced. The connection between the electron metric system and the external metric system is defined. The symmetry relationships of the multinary semiconductor compound alloys are defined according to the electron metric system. The basic metric constant is found on the basis of diatomic tetrahedral cell. The electron wave vector in the new system is found and the electron energy states are determined. It is shown correlation between them in the multinary crystal. LCAO electron band structures of Inx Al1–x N and of Inx Ga1–x N are presented. The phenomenon tunnel optical absorption is investigated in Inx Al1–x N, in Inx Ga1–x N, in InN containing oxygen and in non‐stoichiometric InN. It is found the optical absorption edges begin in energies 0.2–1.62 eV that are lower than the energy band gaps due to this phenomenon. Existence of excitons of the structure is shown in these semiconductors and it is found that the peaks of the PL spectra correspond to annihilation energies of these excitons that change in interval 0.5–1.01 eV. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
RF plasma sources for III‐nitrides growth: influence of operating conditions and device geometry on active species production and InN film properties
Authors: Anderson P. A. , Reeves R. J. , Durbin S. M. 
Published: January 2006

AbstractThe optical emission from an RF inductively coupled plasma source has been monitored at various flow rates and RF powers in the spectral range of 500–900 nm. It was found that low powers and high flow rates resulted in emission from the 1st‐positive series of excited molecular nitrogen dominating the spectrum relative to atomic nitrogen. Growth of InN on GaN showed improved electrical properties when the molecular species dominated the spectrum. In contrast, growth of InN on (111) yttrium stabilised zirconia (YSZ) was found to yield films of similar electrical properties at different plasma operating conditions. Reflection high energy electron diffraction (RHEED) patterns were used to monitor the a ‐lattice constant during growth. Films grown on GaN with higher relative atomic flux were found to relax within the first several nm of growth, whereas films grown with higher molecular nitrogen species did not fully relax until approximately 50 nm of growth. These observations suggest that the active nitrogen species plays a significant role in determining how strain is accommodated during InN epitaxy. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Characterization of crystallographic properties and defects via X‐ray microdiffraction in GaN (0001) layers
Authors: Barabash R. I. , Barabash O. M. , Ice G. E. , Roder C. , Figge S. , Einfeldt S. , Hommel D. , Katona T. M. , Speck J. S. , DenBaars S. P. , Davis R. F. 
Published: January 2006

AbstractIntrinsic stresses due to lattice mismatch, high densities of threading dislocations, and extrinsic stresses resulting from the mismatch in the coefficients of thermal expansion, are present in almost all III‐Nitride heterostructures. Stress relaxation in the GaN layers occurs in conventional, cantilever (CE) and in pendeo‐epitaxial (PE) films via the formation of additional misfit dislocations, domain boundaries, elastic strain and wing tilt. Polychromatic X‐ray microdiffraction, high resolution monochromatic X‐ray diffraction and SEM analysis have been used to determine the crystallographic properties, misfit dislocations distribution and crystallographic tilts in uncoalesced GaN layers grown by PE and CE. The crystallographic tilt between the GaN(0001) and Si(111) planes was detected in the CE grown samples on Si(111). In contrast there was no tilt between GaN(0001) and SiC(0001) planes in PE grown samples. The wings are tilted upward for both the PE and CE grown uncoalesced GaN layers. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Stoichiometry effects and the Moss–Burstein effect for InN
Authors: Butcher K. S. A. , Hirshy H. , Perks R. M. , Wintrebert‐Fouquet M. , Chen P. P‐T. 
Published: January 2006

AbstractWe examine the Moss–Burstein effect for InN and demonstrate an independent method for determing its magnitude for high carrier concentration material. Consequently it is shown that the extent of the Moss–Burstein effect is less than 0.72 eV for a high carrier concentration sample with a 1.88 eV absorption edge. Early results are also provided for high band‐gap low carrier concentration InN films that can be grown reprodcibly, vindicating the work of early groups in the field. The role of stoichiometry is examined in relation to point defects that appear to be common to many forms of InN. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Surface band bending at nominally undoped and Mg‐doped InN by Auger Electron Spectroscopy
Authors: Cimalla V. , Niebelschütz M. , Ecke G. , Lebedev V. , Ambacher O. , Himmerlich M. , Krischok S. , Schaefer J. A. , Lu H. , Schaff W. J. 
Published: January 2006

AbstractNon intentionally doped and Mg‐doped InN layers were analyzed by sputter depth profiling in an Auger electron spectroscopy (AES) equipment and by Ultra‐violet photoelectron spectroscopy (UPS). On the surface of both types of layers a high concentration of oxygen and a strong accumulation of electrons was observed, however, in contrast to the undoped layers the conductivity profile of Mg doped InN shows a strong discontinuity close to the surface. The depth of this discontinuity strongly depends on the oxygen concentration. The energy shift of the InMNN peak was estimated during the depth profiling in order to obtain information about the position of the Fermi level. In the bulk of the Mg‐doped InN the InMNN peak shift of about 0.15 eV demonstrates the influence of the Mg on the Fermi level, while the surface is clearly n‐type. A strong shift of the Fermi level close to the surface was observed, which might be attributed to the formation of In2O3. By the combination of AES and UPS a model for the band bending is proposed, which demonstrates that Mg doping indeed can compensate the n‐type conductivity in the bulk and is therefore a prospective candidate to achieve p‐type doping in InN. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Detailed analysis of the dielectric function for wurtzite InN and In‐rich InAlN alloys
Authors: Goldhahn R. , Schley P. , Winzer A. T. , Gobsch G. , Cimalla V. , Ambacher O. , Rakel M. , Cobet C. , Esser N. , Lu H. , Schaff W. J. 
Published: January 2006

AbstractA detailed analysis of the dielectric function (DF) for wurtzite InN as well as for In‐rich InAlN alloys is presented. The experimental data, covering the energy range from 0.72 up to 9.5 eV, were obtained by ellipsometric studies of an (11&2macr;0) a‐plane InN film and low carrier density (0001) c‐plane films. Model calculations of the imaginary part of the DF around the band gap provide direct insight how to determine the energetic position of the Fermi energy from the experimental results. Then, taking into account both, band gap renormalization and Burstein–Moss shift, the values of the gaps at zero carrier density are calculated. The dependence of the InAlN band gap on the alloy composition is described by a bowing parameter of 4.0 eV. The a‐plane film exhibits a characteristic optical anisotropy below 1 eV which is attributed to the polarization dependence of transition probabilities from the three valence bands at the Γ point of the Brillouin zone into the conduction band. The splitting of 25 meV between the absorption edges for the two polarization directions can be well explained by a crystal field energy of 19 (24) meV if a calculated spin–orbit energy of 13 (5) meV is assumed. All results emphasize a band gap value of wurtzite InN of about 0.68 eV. By fitting the third derivatives of the dielectric function up to 9.5 eV we determine the compositional dependences of the transition energies for at least three critical points of the band structure. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effects of Si doping position on the emission energy and recombination dynamics of GaN/AlGaN multiple quantum wells
Authors: Haratizadeh Hamid , Monemar Bo , Amano Hiroshi 
Published: January 2006

AbstractWe report results from detailed optical spectroscopy from MOCVD grown GaN/Al0.07Ga0.93N multiple quantum wells (MQWs). Effects of Si doping position on the emission energy and recombination dynamics were studied by means of photoluminescence (PL) and time‐resolved PL measurements. The samples were Si doped with the same level but different position of the dopant layer. Only the sample doped in the well shows the MQW emission redshifted compare to the GaN bandgap. The redshift is attributed to the self‐energy shift of the electron states due to the correlated motion of the electrons exposed to the fluctuating potential of the donor ions. At low temperature the PL decay time of the sample doped in the well by a factor of two is longer than for the barrier doped case. The difference is explained by the effect of interplay of free carriers and ions on the screening of the polarization field in these doped structures. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
InGaN(0001) alloys grown in the entire composition range by plasma assisted molecular beam epitaxy
Authors: Iliopoulos E. , Georgakilas A. , Dimakis E. , Adikimenakis A. , Tsagaraki K. , Androulidaki M. , Pelekanos N. T. 
Published: January 2006

AbstractIndium gallium nitride alloy (0001) films in the entire composition range were grown heteroepitaxially by radio‐frequency plasma assisted molecular beam epitaxy on Ga‐polarity GaN(0001)/Al2O3 substrates. A growth approach based on low substrate temperatures and near‐stoichiometric growth conditions was followed. Under these conditions incorporation efficiency of indium atoms was equal to one. X‐ray diffraction data reveal that phase separation phenomena were effectively suppressed. As the indium mole fraction increased, a tendency of the strain state of the films to change from compressive to tensile was observed. This was attributed to growth through nucleation and coalescence of three‐dimensional InGaN islands with high lattice mismatch on GaN(0001). (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quantitative electron microscopy of InN–GaN alloys
Authors: Bartel T. , Jinschek J. R. , Freitag B. , Specht P. , Kisielowski C. 
Published: January 2006

AbstractTime series of high‐resolution lattice images are examined to probe for possible alterations of the indium distribution in GaN/InxGa1–xN/GaN quantum well structures during electron irradiation with energies of 150 kV and 800 kV. By comparison with theory it is reasoned that sample preparation, microscope stability, and chosen acceleration voltages are essential factors that determine the reliability of the results. If considered, it is shown that for relevant time scales of <2 minutes and current densities of 20–40 A/cm2 no measurable alteration of the initial element distribution occurs. A quantitative method is highlighted for the characterization of existing indium fluctuations that are concentration dependent. Consistency between measurements from lattice images, Z‐contrast images, and local band gap measurements support our conclusion. It is argued that the formation of such indium clusters is driven by strain‐dependent spinodal decomposition. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Photoluminescence of n‐InN with low electron concentrations
Authors: Klochikhin Albert , Davydov Valery , Emtsev Vadim , Sakharov Alexey , Kapitonov Vladimir , Andreev Boris , Lu Hai , Schaff William J. 
Published: January 2006

AbstractPhotoluminescence (PL) of n‐InN grown by molecular beam epitaxy with Hall concentrations from 3.6 × 1017 to 1.0 × 1018 cm–3 demonstrates new features as compared with that of the samples of previous generation which are characterized by a higher carrier concentration. The striking dependences of PL spectra on carrier concentration, temperature, and excitation density give evidences of a fast energy relaxation rate of photoholes and their equilibrium distribution over localized states. The well resolved structure consisting of three peaks was observed in the PL spectra of these samples in the energy interval from 0.50 to 0.67 eV at liquid helium and nitrogen temperatures. We attributed one of two low‐energy features of the spectra to the recombination of degenerate electrons with the holes trapped by deep acceptors with a binding energy of Eda = 0.050–0.055 eV and the other one is attributable to the LO‐phonon replica of this band. The higher‐energy PL peak is considered as a complex band formed by two mechanisms. The first one is related to the transitions of electrons to the states of shallow acceptors with a binding energy of Esh = 0.005–0.010 eV and/or to the states of Urbach tail populated by photoholes. The second mechanism contributing to this band is the band‐to‐band recombination of free holes and electrons. Relative intensities of two higher‐energy PL peaks were found to be strongly dependent on temperature and excitation power. At room temperature, the band‐to‐band recombination of free holes and electrons dominates in PL. Experimental results on PL and absorption are described by the model calculations under the assumptions of the band gap equal to 0.665–0.670 eV at zero temperature and zero carrier concentration and the non‐parabolic conduction band with the effective mass at Γ‐point equal to 0.07 of free electron mass. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Mass flow and reaction analysis of the growth of GaN by HVPE
Authors: Kempisty P. , Grzegory I. , Boćkowski M. , Krukowski S. , Łucznik B. , Pastuszka B. , Porowski S. 
Published: January 2006

AbstractHVPE growth in horizontal flow reactor has been analysed using finite element calculations and molecular estimates of the reaction rates. Finite element code FIDAP (commercially available from Fluent Inc.) has been used to calculate the flow pattern in the reactor. In the first approximation it was assumed that the flow pattern is weekly dependent on the temperature distribution in the reactor. It was also assumed that the volume reaction rates can be approximated by temperature independent reaction constants. The HCl + Ga(l) reaction rate has been estimated using ideal gas approximation for HCl vapour.The degree of HCl to GaCl conversion was obtained in function of the pressure, flow velocity and geometry of the reactor. The conversion dependence on the sticking coefficient of HCl on liquid Ga surface was analysed. It is shown that for the typical design of the reactor, high conversion rates were observed, even for the sticking coefficient as low as 0.001. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Full‐potential study of d‐electrons effects on the electronic structure of wurtzite and zinc‐blende InN
Authors: Litimein F. , Bouhafs B. , Ruterana P. 
Published: January 2006

AbstractIn this paper, we focus on the role played by the relativistic and d‐electron effects on the electronic structure of both wurtzite (α‐InN), as well as the zinc‐blende (β‐InN) modifications of indium nitride. Here we perform all‐electron full‐potential linearized‐augmented plane‐wave calculations with spin–orbit interaction. The In 4d electrons are treated both as core and as valence electrons. We compare the performance of the local‐density approximation (LDA), the generalized gradient approximation (GGA) and the recently proposed non‐empirical meta‐generalized gradient approximation (Meta‐GGA) in calculations of the structural and electronic properties of InN. Band structures, densities of states, orbital‐resolved densities of states, charge densities and ionicity factors are analyzed in great detail. The calculated values of the energy gaps, bandwidths, spin–orbit and crystal‐field splittings and the correct band degeneracies are compared to experimental and/or ab‐initio results. The role played by relativistic effects and meta‐GGA functional on the band structure is discussed. For the structural properties meta‐GGA is more accurate and gives the best description of InN. We found that several features of α‐InN resemble those of β‐InN. Most of the calculated band parameters, of band gaps, total valence bandwidths for α‐InN are close to those of β‐InN to within 1%. The charges distributions have similar features meaning that this material has the same ionicity factor in both structures even when In 4d states were treated both as core and as valence electrons. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
III‐Nitrides semiconductor compounds for microwave devices
Authors: di Forte‐Poisson M. A. , Magis M. , Sarazin N. , Tordjman M. , di Persio J. 
Published: January 2006

AbstractThis paper reports on the LP‐MOCVD growth optimisation of GaAlN/GaN heterostructures grown on sapphire and silicon carbide substrates for HEMT applications, and on the device performances obtained with these structures. The devices performances related to the GaAlN/GaN HEMT structures grown on sapphire and silicon carbide have confirmed the high potentiality of GaN and related alloys for high power microwave transistors. Load–Pull measurements performed at 2 GHz on devices related to GaAlN/GaN/Al2O3 HEMT structures, have shown a remarkably high output power density (4.4 W/mm) and absolute power level (3.2 W for 1 mm devices). These power level results for devices on sapphire substrates measured on wafer, are well in agreement with the international state of the art.Devices related to GaAlN/GaN/SiC HEMT structures have been measured at 10 GHz using a load pull system. They exhibited a CW output power in excess of 6.2 W/mm for a gate length of 0.25 µm and an absolute CW power level of 60 W (22 mm development). On the other hand, the GaAlN/InGaN/GaN double heterostructure, in which the channel layer is made of InGaN instead of GaN, is expected to significantly enhance device performance due to a stronger carrier confinement and a higher two‐dimensional electron gas (2DEG) density at the interface in comparison with an GaAlN/GaN single heterostructure. Simin et al. have demonstrated GaInN channel devices with RF output powers as high as 4.3 W/mm in CW mode [2]. Recently, HEMT devices based on InAlN/GaN lattice‐matched heterostructures exhibiting very promising RF performances have been reported (4.1 W/mm at 2 GHz) [3]. These different heterostructures used for HEMT devices are compared to the conventional GaAlN/GaN heterostructure in term of device results. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)