bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hepatocyte‐specific activation of NF‐κB does not aggravate chemical hepatocarcinogenesis in transgenic mice
Authors: Yau T‐O , Chan C‐F , Gee‐San Lam S , Cheung O‐F , Ching Y‐P , Jin D‐Y , Sham M‐H , Ng IOL 
Published: September 2008

AbstractThe NF‐κB signalling pathway plays important roles in liver organogenesis and carcinogenesis. Mouse embryos deficient in IKKβ die in mid‐gestation, due to excessive apoptosis of hepatoblasts. Although activation of the NF‐κB signalling pathway has been demonstrated in human hepatocellular carcinoma, the role of NF‐κB is controversial. Here, we have generated transgenic mice in which a constitutively active form of IKKβ was expressed in a hepatocyte‐specific manner. Using electrophoretic mobility shift assay, we documented increased NF‐κB activities and up‐regulated levels of NF‐κB downstream target genes, Bcl‐xL and STAT5, in the transgenic mouse livers. These results confirmed that the NF‐κB pathway was activated in the livers of the transgenic mice. However, there was no significant difference in tumour formation between transgenic and wild‐type mice up to an age of 50 weeks. When we treated the transgenic mice with the chemical carcinogen diethylnitrosamine (DEN), we observed no significant differences in the incidence and size of liver tumours formed in these mice with and without DEN treatment at 35 weeks of age, suggesting that the activated NF‐κB pathway in the livers of the transgenic mice did not enhance hepatocarcinogenesis. Interestingly, some of the transient transgenic embryos (E12.5) had abnormal excessive accumulation of nucleated red blood cells in their developing livers. In summary, NF‐κB activation in hepatocytes did not significantly affect chemical hepatocarcinogenesis. In addition, the TTR/IKKCA transgenic mice may serve as a useful model for studying the role of NF‐κB activation in hepatocarcinogenesis as well as inflammatory and metabolic diseases. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Frequency and clinical features of the JAK2 V617F mutation in pediatric patients with sporadic essential thrombocythemia
Authors: Nakatani Takuya , Imamura Toshihiko , Ishida Hiroyuki , Wakaizumi Katsuji , Yamamoto Tohru , Otabe Osamu , Ishigami Tsuyoshi , Adachi Souichi , Morimoto Akira 
Published: September 2008

AbstractBackgroundPediatric essential thrombocythemia (ET) is a rare and heterogenous disease entity. While several recent studies have focused on the role of the JAK2 V617F mutation in pediatric ET, the frequency of pediatric ET cases with this mutation and the associated clinical features remain unclear.ProcedureWe examined six childhood cases who had been diagnosed with ET according to WHO criteria (onset age: 0.2–14 years) for the presence of the JAK2 V617F mutation, MPLW515L mutation and JAK2 exon 12 mutations. Two sensitive PCR‐based methods were used for the JAK2 V617F genotyping. We also examined the expression of polycythemia rubra vera‐1 (PRV‐1), which is a diagnostic marker for clonal ET.ResultsWe found that three of the six cases had the JAK2 V617F mutation and that all six cases expressed PRV‐1 in their peripheral granulocytes. Neither MPL W515L mutation nor JAK2 exon 12 mutations was detected in the patients without JAK2 V617F mutation. The two patients who developed thrombocythemia during infancy were JAK2 V617F‐negative.ConclusionsThese findings suggest that the JAK2 V617F mutation is not rare in childhood sporadic ET cases, and that these cases might be older and myeloproliferative features. Pediatr Blood Cancer 2008;51:802–805. © 2008 Wiley‐Liss, Inc.
Identification of a novel mutation in DKC1 in dyskeratosis congenita
Authors: Kurnikova Maria , Shagina Irina , Khachatryan Lilia , Schagina Olga , Maschan Mikchail , Shagin Dmitriy 
Published: September 2008

AbstractDyskeratosis congenita (DC) is a rare congenital syndrome characterized by the triad of reticular skin pigmentation, nail dystrophy and mucosal leukoplakia, and the predisposition to bone marrow failure and malignancy. DC is genetically heterogeneous and X‐linked and autosomal forms of the disease exist. Here, we report the clinical description and mutation analysis of a Russian family with X‐linked DC. A novel mutation in DKC1 raised de novo in the maternal grandmother's gamete was found; this mutation is a 2 bp inversion in exon 3: NM_001363:c.166_167invCT (Leu56Ser). Pediatr Blood Cancer 2009;52:135–137. © 2008 Wiley‐Liss, Inc.
Using genetic algorithms to select most predictive protein features
Authors: Kernytsky Andrew , Rost Burkhard 
Published: September 2008

AbstractMany important characteristics of proteins such as biochemical activity and subcellular localization present a challenge to machine‐learning methods: it is often difficult to encode the appropriate input features at the residue level for the purpose of making a prediction for the entire protein. The problem is usually that the biophysics of the connection between a machine‐learning method's input (sequence feature) and its output (observed phenomenon to be predicted) remains unknown; in other words, we may only know that a certain protein is an enzyme (output) without knowing which region may contain the active site residues (input). The goal then becomes to dissect a protein into a vast set of sequence‐derived features and to correlate those features with the desired output. We introduce a framework that begins with a set of global sequence features and then vastly expands the feature space by generically encoding the coexistence of residue‐based features. It is this combination of individual features, that is the step from the fractions ofserineandburied(input space 20 + 2) to the fraction ofburied serine(input space 20 ☆ 2) that implicitly shifts the search space from global feature inputs to features that can capture very local evidence such as a the individual residues of a catalytic triad. The vast feature space created is explored by a genetic algorithm (GA) paired with neural networks and support vector machines. We find that the GA is critical for selecting combinations of features that are neither too general resulting in poor performance, nor too specific, leading to overtraining. The final framework manages to effectively sample a feature space that is far too large for exhaustive enumeration. We demonstrate the power of the concept by applying it to prediction of protein enzymatic activity. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA‐II from Sambucus nigra
Authors: Maveyraud Laurent , Niwa Hideaki , Guillet Valérie , Svergun Dmitri I. , Konarev Peter V. , Palmer Rex A. , Peumans Willy J. , Rougé Pierre , Van Damme Els J. M. , Reynolds Colin D. , Mourey Lionel 
Published: September 2008

AbstractBark of elderberry (Sambucus nigra) contains a galactose (Gal)/N‐acetylgalactosamine (GalNAc)‐specific lectin (SNA‐II) corresponding to slightly truncated B‐chains of a genuine Type‐II ribosome‐inactivating protein (Type‐II RIPs, SNA‐V), found in the same species. The three‐dimensional X‐ray structure of SNA‐II has been determined in two distinct crystal forms, hexagonal and tetragonal, at 1.90 Å and 1.35 Å, respectively. In both crystal forms, the SNA‐II molecule folds into two linked ββ‐trefoil domains, with an overall conformation similar to that of the B‐chains of ricin and other Type‐II RIPs. Glycosylation is observed at four sites along the polypeptide chain, accounting for 14 saccharide units. The high‐resolution structures of SNA‐II in complex with Gal and five Gal‐related saccharides (GalNAc, lactose, αα1‐methylgalactose, fucose, and the carcinoma‐specific Tn antigen) were determined at 1.55 Å resolution or better. Binding is observed in two saccharide‐binding sites for most of the sugars: a conserved aspartate residue interacts simultaneously with the O3 and O4 atoms of saccharides. In one of the binding sites, additional interactions with the protein involve the O6 atom. Analytical gel filtration, small angle X‐ray scattering studies and crystal packing analysis indicate that, although some oligomeric species are present, the monomeric species predominate in solution. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Sampling efficiency in explicit and implicit membrane environments studied by peptide folding simulations
Authors: Ulmschneider Jakob P. , Ulmschneider Martin B. 
Published: September 2008

AbstractEfficient exploration of the conformational space of peptides embedded in biological membranes is vital to extract converged thermodynamic and kinetic data from simulation studies. Recently developed implicit membrane models promise vast increases in sampling efficiency compared to explicit membrane simulations, allowing for ab initio structure prediction and functional studies. In this study, a previously developed implicit membrane model, based on the generalized Born method, is compared to an explicit di‐palmitoyl‐phosphatidyl‐choline lipid bilayer and an octane slab membrane mimic. The complete folding process of a synthetic 16‐residue peptide is compared using these three setups. Since the comparison requires the entire folding pathway to be captured, individual simulations ranged up to 3 μs of MD. A quantitative sampling comparison using a wide range of performance metrics reveals that the implicit membrane model is at least 2 orders of magnitude more efficient than the simplest explicit setups. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Interactions of different inhibitors with active‐site aspartyl residues of HIV‐1 protease and possible relevance to pepsin
Authors: Sayer Jane M. , Louis John M. 
Published: September 2008

AbstractThe importance of the active site region aspartyl residues 25 and 29 of the mature HIV‐1 protease (PR) for the binding of five clinical and three experimental protease inhibitors [symmetric cyclic urea inhibitor DMP323, nonhydrolyzable substrate analog (RPB) and the generic aspartic protease inhibitor acetyl‐pepstatin (Ac‐PEP)] was assessed by differential scanning calorimetry. ΔTm values, defined as the difference in Tm for a given protein in the presence and absence of inhibitor, for PR with DRV, ATV, SQV, RTV, APV, DMP323, RPB, and Ac‐PEP are 22.4, 20.8, 19.3, 15.6, 14.3, 14.7, 8.7, and 6.5°C, respectively. Binding of APV and Ac‐PEP is most sensitive to the D25N mutation, as shown by ΔTm ratios [ΔTm(PR)/ΔTm(PRD25N)] of 35.8 and 16.3, respectively, whereas binding of DMP323 and RPB (ΔTm ratios of 1–2) is least affected. Binding of the substrate‐like inhibitors RPB and Ac‐PEP is nearly abolished (ΔTm(PR)/ΔTm(PRD29N) ≥ 44) by the D29N mutation, whereas this mutation only moderately affects binding of the smaller inhibitors (ΔTm ratios of 1.4–2.2). Of the nine FDA‐approved clinical HIV‐1 protease inhibitors screened, APV, RTV, and DRV competitively inhibit porcine pepsin with Ki values of 0.3, 0.6, and 2.14 μM, respectively. DSC results were consistent with this relatively weak binding of APV (ΔTm 2.7°C) compared with the tight binding of Ac‐PEP (ΔTm ≥ 17°C). Comparison of superimposed structures of the PR/APV complex with those of PR/Ac‐PEP and pepsin/pepstatin A complexes suggests a role for Asp215, Asp32, and Ser219 in pepsin, equivalent to Asp25, Asp25′, and Asp29 in PR in the binding and stabilization of the pepsin/APV complex. Proteins 2009. Published 2008 Wiley‐Liss, Inc.
Thermoelectric power of nanoscale MnSi1.7 films
Authors: Hou Q. R. , Zhao W. , Chen Y. B. , He Y. J. 
Published: September 2008

AbstractMnSi1.7 bulk materials and thin films are usually p‐type. When the thickness of MnSi1.7 film is reduced to nanoscale, however, the carriers are p‐type around room temperature and transform to n‐type at high temperatures. The thermoelectric powers at room temperature and 633 K are 128 and –340 μV/K, respectively. A n‐type MnSi1.7 film with a thickness of about 14 nm is prepared. The thermoelectric power reaches to –967 μV/K at 483 K. From these data, the energy band gap is estimated as 0.93 eV, which is consistent with that obtained from the temperature dependence of the electrical resistivity measurements. The large thermoelectric power may be due to the increase in the electronic density of states and energy band gap in low‐dimensional semiconductors or hetero‐structures being formed. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Phase‐change memories
Authors: Lacaita Andrea L. , Wouters Dirk J. 
Published: September 2008

AbstractPhase Change Materials are adopted in optical data storage and are currently evolving to become the active material of a new viable non‐volatile memory technology which is expected to eventually replace no‐longer‐scaling Flash memory technologies. Phase‐Change Memories store their information as the material phase of a chalcogenide metal alloy (high‐resistive amorphous, respectively low‐resistive crystalline phase), the most important compound being Ge2Sb2Te5(GST). To give insight in this important evolution, the paper describes the different aspects of Phase‐Change Memories. It starts from basic operation principle and fundamental material properties (Sections 2 and 3). Vital to their operation are not only the vitrification and crystallization properties of the chalcogenide material, but also the phenomenon of electronic threshold switching enabling low‐voltage Joule heating in the amorphous phase. Understanding and modeling of these effects are described in Section 4. Cell concepts and integration technology aspects, including optimization schemes aimed at reducing the program current are covered in Section 5. Finally, the excellent reliability and scaling properties of Phase‐Change Memories are discussed in Sections 6 and 7. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Single dot spectroscopy on InAs/GaAs piezoelectric quantum dots
Authors: Dialynas G. E. , Chatzidimitriou N. , Kalliakos S. , Tsintzos S. , Savvidis P. G. , Hatzopoulos Z. , Pelekanos N. T. 
Published: September 2008

AbstractWe report on single dot spectroscopy of InAs/GaAs quantum dots grown by molecular beam epitaxy along the polar (211)B direction. Unlike the (001) dots, in the (211)B dots we have systematically observed large blue shifts of the biexciton lines with respect to the excitonic ones. This is attributed to the strong piezoelectric field present inside the polar dots. In order to better interpret our results, we performed preliminary photoluminesence studies under the influence of an external electric field, which showed large Stark shifts of the quantum dot ensemble. From the analysis of these results, we deduced that the piezoelectric field in the (211)B InAs/GaAs quantum dots is as large as 800kV/cm, which is consistent with the large anti‐binding energies of bi‐excitons observed in this system. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Efficient infrared emission from patterned thin metal films on a Si photonic crystal
Authors: Theodoni P. , Vamvakas V. Em. , Speliotis Th. , Chatzichristidi M. , Bayiati P. , Raptis I. , Papanikolaou N. 
Published: September 2008

AbstractWe study the infrared optical response of periodically patterned thin metal films on a Si photonic crystal using Fourier‐transform infrared spectroscopy and full electrodynamic calculations. Thin metallic films on top of Si substrate were patterned using optical lithography; furthermore the Si substrate was etched, using the metal as a mask. The structures have a narrow band absorption spectrum for wavelengths close to the lattice constant of the patterning. Both Al and Au films gave similar infrared response. Our results can be explained by multiple scattering electrodynamic simulations. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
All‐organic optocouplers based on polymer light‐emitting diodes and photodetectors
Authors: Stathopoulos N. A. , Palilis L. C. , Vasilopoulou M. , Botsialas A. , Falaras P. , Argitis P. 
Published: September 2008

AbstractIn this work, we demonstrate all organic flexible polymeric optocouplers by utilizing a donor‐acceptor bulk heterojunction polymer photodetector (PD) as the output unit and a polymer light‐emitting diode (PLED) as the input unit. The input unit is a single‐layer PLED on a glass or a plastic (PET) substrate utilizing a green emitting polyfluorene‐benzothiadiazole copolymer in the active layer. The output unit is a single‐layer PD on a glass substrate utilizing a P3HT:PCBM(1:1 by weight) blend, where P3HT is regioregular poly(3‐hexylthiophene) and PCBM is (6,6)‐phenyl‐C61‐butyric acid methyl ester. The electroluminescence spectrum of the PLED peaks at 530 nm and covers a spectral range that coincides quite well with the PD absorption spectrum (between 450 and 650 nm). The current density transfer ratio reaches 0.012% for an optocoupler that operates at 0 V and 15 V for the PD and PLED, respectively. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
New modes of FFT impedance spectroscopy applied to semiconductor pore etching and materials characterization
Authors: Carstensen J. , Foca E. , Keipert S. , Föll H. , Leisner M. , Cojocaru A. 
Published: September 2008

AbstractA systematic approach for the application of fast Fourier transform (FFT) impedance spectroscopy to semiconductor photo‐electrochemistry is given. In particular, photo‐impedance spectroscopy in two novel modes is used in conjunction with conventional current–voltage impedance spectroscopy, and applied to some aspects of pore etching in InP and Si as well as to the characterization of multicrystalline Si or other solar cell material. The technique, applicable in situ with high time resolution, employs optimized hardware and software, extensive mathematical modeling of carrier transport, and the numerical implementation of fast parameter extraction algorithms. The complete system with a fully integrated impedance spectrometer delivers a wealth of new data including key parameters of pore etching. Examples given include the in situ tracking of the fast switch‐over between pore growth modes in InP as well as following a pore etching process over long time scales in Si. FFT impedance spectroscopy in the novel back side illumination mode, in combination with the conventional mode, allows not only some active control of macropore etching in n‐type Si by supplying crucial real‐time data like the valence of the dissolution process and the pore depth, but also provides new fundamental insights into the electrochemical processes occurring at the (porous) electrode. FFT photo‐impedance spectroscopy in the front side illumination mode used in conjunction with a scanned laser beam allows fast local measurements of all semiconductor parameters relevant for solar cell applications, like doping concentration, minority carrier lifetime, diffusion constant, or surface recombination velocity with high spatial resolution; this is demonstrated for large multicrystalline Si wafers. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Growth and electrical characterization of thin conductive Au nanoparticle chains on oxidized Si substrates between electrodes for sensor applications
Authors: Zoy A. , Nassiopoulou A. G. 
Published: September 2008

AbstractCitrate‐stabilized colloid Au nanoparticles with an average diameter of 40 nm have been assembled in nanoparticle chains between microelectrodes on oxidized V‐groove‐etched Si surfaces by the technique of dielectrophoresis. Chain formation was investigated as a function of electrodes configuration and the amplitude and frequency of the applied electric field. Conductive thin (∼100‐200 nm thick) single and multiple Au nanoparticle chains, with a length in the range of 1 to 10 µm, were preferentially formed on V‐groove lines between the electrodes. Electrical characterization by temperature‐dependent current‐voltage measurements showed that the Au nanoparticle chains exhibit ohmic conductivity with a resistance in the range of few Ω to few kΩ, depending on the distance between electrodes and the configuration of the Au nanoparticles in the structure. On the contrary, 5 nm diameter tiopronin‐stabilized Au NPs chains exhibited nearest‐ neighbour hopping conductivity and non‐linear thermally‐activated I‐V characteristics. We also tested nanogap formation in the chains by an applied pulse of electric current, in view of applying the nanoparticle chains in the tracing of chemical or biological molecules. The conductive thin Au nanoparticle chains, with or without nanogaps, are interesting building blocks for different sensor devices. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Theoretical study of electronic spectra of [Pt3(μ‐CO)3(CO)3] (n = 3–5) complexes
Authors: Mendizabal Fernando , Burgos Darwin , Olea‐Azar Claudio 
Published: September 2008

AbstractThe platinum‐platinum attraction and the spectroscopic properties of [Pt3(μ‐CO)3(CO)3] (n = 3–5) were studied at the PBE level. Theoretical calculations are in agreement with experimental geometries. The absorption spectra of these platinum complexes were calculated by the single excitation time‐dependent (TD) density functional method. All complexes showed MLCT transitions interrelated with the intertriangular complexes. The values obtained at the PBE level are in agreement with the experimental color range. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Molecular parameters of tetraatomic carbonyls X2CO and XYCO (X, Y = H, F, Cl) in the ground and lowest excited electronic states, part 1: A test ofab initiomethods
Authors: Bokarev Sergey I. , Dolgov Evgeny K. , Bataev Vadim A. , Godunov Igor A. 
Published: September 2008

AbstractGeometrical parameters of tetraatomic carbonyl molecules X2CO and XYCO (X, Y = H, F, Cl) in the ground (S0) and lowest excited singlet (S1) and triplet (T1) electronic states as well as values of barriers to inversion inS1andT1states andS1←S0andT1←S0adiabatic transition energies were systematically investigated by means of various quantum‐chemical techniques. The following methods were tested: HF, MP2, CIS, CISD, CCSD, EOM‐CCSD, CCSD(T), CR‐EOM‐CCSD(T), CASSCF, MR‐MP2, CASPT2, CASPT3, NEVPT2, MR‐CISD, and MR‐AQCC within cc‐pVTZ and cc‐pVQZ basis sets. The accuracy of quantum‐chemical methods was estimated in comparison with experimental data and rather accurate structures of excited electronic states were obtained. MP2 and CASPT2 methods appeared to be the most efficient and CCSD(T), CR‐EOM‐CCSD(T), and MR‐AQCC the most accurate. It was found that at equilibrium all the molecules under study are nonplanar inS1andT1electronic states with CO out‐of‐plane angle ranging from 34° (H2CO,S1) to 52° (F2CO,T1), and height of barrier to inversion varying from 300 (H2CO,S1) to 11,000 (F2CO,T1) cm−1. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Tribophyiscal scaling effects in friction and wear of polymers on small‐ and large‐scale tests
Authors: Samyn P. , Schoukens G. 
Published: September 2008

AbstractCoefficients of friction and wear rates for polyacetal and polytetrafluoroethylene are measured on small‐scale cylinder‐on‐plate tests and large‐scale flat‐on‐flat tests. Three models for extrapolation between small‐ and large‐scale test results, which are based on experimental parameters, are presented: (i) one single mechanical parameter (normal load), (ii) the contact‐pressure–sliding‐velocity model (temperature limit), and (iii) a macroscopic geometry model. The last model is most extensively evaluated and considers thermal effects, sample geometry and contact conditions. After correction for the thermal sliding regime and viscoelastic deformation, the coefficients of friction can be extrapolated while the wear rates are more sensitive to the contact situation. High‐temperature tests on small scale are not representative for high‐load tests on large scale. Besides mechanical effects such as stress concentrations and debris mobility, variations in polymer structure under sliding (formation of rigid amorphous phase) and chemical interactions (wear debris polymerisation) also change with testing scale. The latter effects are explicitly illustrated from spectroscopic measurements on the worn surfaces. Copyright © 2008 John Wiley & Sons, Ltd.