bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomics of MUC1‐containing lipid rafts from plasma membranes and exosomes of human breast carcinoma cells MCF‐7
Authors: Staubach Simon , Razawi Hanieh , Hanisch Franz‐Georg 
Published: May 2009

AbstractApically expressed human MUC1 is known to become endocytosed and either to re‐enter the secretory pathway for recycling to the plasma membrane or to be exported by the cells via the formation of multi‐vesicular bodies and the release of exosomes. By using recombinant fusion‐tagged MUC1 as a bait protein we followed an anti‐myc affinity‐based approach for isolating subpopulations of lipid rafts from the plasma membranes and exosomes of MCF‐7 breast cancer cells. MUC1+ lipid rafts were not only found to contain genuine raft proteins (flotillin‐1, prohibitin, G protein, annexin A2), but also raft‐associated proteins linking these to the cytoskeleton (ezrin/villin‐2, profilin II, HSP27, γ‐actin, β‐actin) or proteins in complexes with raft proteins, including the bait protein (HSP60, HSP70). Major overlaps were revealed for the subproteomes of plasma membranous and exosomal lipid raft preparations, indicating that MUC1 is sorted into subpopulations of rafts for its trafficking via flotillin‐dependent pathways and export via exosomes.
Generally detected proteins in comparative proteomics – A matter of cellular stress response?
Authors: Wang Ping , Bouwman Freek G. , Mariman Edwin C. M. 
Published: May 2009

AbstractThe specificity of proteins identified by proteomics as biomarkers for defined conditions or as components of biological processes and pathways is crucial. We critically reviewed differentially expressed proteins from comparative proteomic studies identified by 2‐DE followed by MS, especially with MALDI technique. Based on 66 of those studies, a list of 44 proteins is presented as generally detected proteins regardless of species, in vivo or in vitro conditions, tissues and organs, and experimental objective. Similarly, a list of 28 generally detected protein families is presented. The enriched functions linked to these generally detected proteins reveal that there are some common biological features beyond the technical limitations. Cellular stress response can be the universal reason as to why these proteins are generally expressed differentially. Using those proteins as biomarkers for cellular processes other than stress response should be done with caution. In future proteomic studies more profound approaches should be applied to look beyond these proteins to find specific biomarkers. Our results are discussed in relation to a recent viewpoint publication by Petrak et al. [Proteomics 2008, 8, 1744–1749].
Distinct contractile and cytoskeletal protein patterns in the Antarctic midge are elicited by desiccation and rehydration
Authors: Li Aiqing , Benoit Joshua B. , Lopez‐Martinez Giancarlo , Elnitsky Michael A. , Lee Richard E. , Denlinger David L. 
Published: May 2009

AbstractDesiccation presents a major challenge for the Antarctic midge, Belgica antarctica. In this study, we use proteomic profiling to evaluate protein changes in the larvae elicited by dehydration and rehydration. Larvae were desiccated at 75% relative humidity (RH) for 12 h to achieve a body water loss of 35%, approximately half of the water that can be lost before the larvae succumb to dehydration. To evaluate the rehydration response, larvae were first desiccated, then rehydrated for 6 h at 100% RH and then in water for 6 h. Controls were held continuously at 100% RH. Protein analysis was performed using 2‐DE and nanoscale capillary LC/MS/MS. Twenty‐four identified proteins changed in abundance in response to desiccation: 16 were more abundant and 8 were less abundant; 84% of these proteins were contractile or cytoskeletal proteins. Thirteen rehydration‐regulated proteins were identified: 8 were more abundant and 5 were less abundant, and 69% of these proteins were also contractile or cytoskeletal proteins. Additional proteins responsive to desiccation and rehydration were involved in functions including stress responses, energy metabolism, protein synthesis, glucogenesis and membrane transport. We conclude that the major protein responses elicited by both desiccation and rehydration are linked to body contraction and cytoskeleton rearrangements.
Molecular dynamics simulations and functional characterization of the interactions of the PAR2 ectodomain with factor VIIa
Authors: Zhang Qing , Petersen Helle H. , Ostergaard Henrik , Ruf Wolfram , Olson Arthur J. 
Published: May 2009

AbstractSignaling of the tissue factor‐FVIIa complex regulates angiogenesis, tumor growth, and inflammation. TF‐FVIIa triggers cell signaling events by cleavage of protease activated receptor (PAR2) at the Arg36‐Ser37 scissile bond. The recognition of PAR2 by the FVIIa protease domain is poorly understood. We perform molecular modeling and dynamics simulations to derive the PAR2‐FVIIa interactions. Docking of the PAR2 Arg36‐Ser37 scissile bond to the S1 site and subsequent molecular dynamics leads to interactions of the PAR2 ectodomain with P and P′ sites of the FVIIa catalytic cleft as well as to electrostatic interactions between a stably folded region of PAR2 and a cluster of basic residues remote from the catalytic cleft of FVIIa. To address the functional significance of this interaction for PAR2 cleavage, we employed two antibodies with epitopes previously mapped to this cluster of basic residues. Although these antibodies do not block the catalytic cleft, both antibodies completely abrogated PAR2 activation by TF‐FVIIa. Our simulations indicate a conformation of the PAR2 ectodomain that limits the cleavage site to no more than 33 Å from its membrane proximal residue. Since the active site of FVIIa in the TF‐FVIIa complex is ∼75 Å above the membrane, cleavage of the folded conformation of PAR2 would require tilting of the TF‐FVIIa complex toward the membrane, indicating that additional cellular factors may be required to properly align the scissile bond of PAR2 with TF‐FVIIa. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Molecular determinants of the pKa values of Asp and Glu residues in staphylococcal nuclease
Authors: Castañeda Carlos A. , Fitch Carolyn A. , Majumdar Ananya , Khangulov Victor , Schlessman Jamie L. , García‐Moreno Bertrand E. 
Published: May 2009

AbstractPrior computational studies of the acid‐unfolding behavior of staphylococcal nuclease (SNase) suggest that the pKa values of its carboxylic groups are difficult to reproduce with electrostatics calculations with continuum methods. To examine the molecular determinants of the pKa values of carboxylic groups in SNase, the pKa values of all 20 Asp and Glu residues were measured with multidimensional and multinuclear NMR spectroscopy in an acid insensitive variant of SNase. The crystal structure of the protein was obtained to describe the microenvironments of the carboxylic groups. Fourteen Asp and Glu residues titrate with relatively normal pKa values that are depressed by less than 1.1 units relative to the normal pKa of Asp and Glu in water. Only six residues have pKa values shifted by more than 1.5 units. Asp‐21 has an unusually high pKa of 6.5, which is probably the result of interactions with other carboxylic groups at the active site. The most perturbed pKa values appear to be governed by hydrogen bonding and not by Coulomb interactions. The pKa values calculated with standard continuum electrostatics methods applied to static structures are more depressed than the measured values because Coulomb effects are exaggerated in the calculations. The problems persist even when the protein is treated with the dielectric constant of water. This can be interpreted to imply that structural relaxation is an important determinant of the pKa values; however, no major pH‐sensitive conformational reorganization of the backbone was detected using NMR spectroscopy. Proteins 2009. © 2009 Wiley‐Liss, Inc.
The α‐particle excited scintillation response of YAG:Ce thin films grown by liquid phase epitaxy
Authors: Prusa Petr , Nikl Martin , Mares Jiri A. , Kucera Miroslav , Nitsch Karel , Beitlerova Alena 
Published: May 2009

AbstractY3Al5O12:Ce (YAG:Ce) thin films were grown from PbO‐, BaO‐, and MoO3‐based fluxes using the liquid phase epitaxy (LPE) method. Photoelectron yield, its time dependence within 0.5–10 μs shaping time, and energy resolution of these samples were measured under α‐particle excitation. For comparison a sample of the Czochralski grown bulk YAG:Ce single crystal was measured as well. Photoelectron yield values of samples grown from the BaO‐based flux were found superior to other LPE films and comparable with that of the bulk single crystal. The same is valid also for the time dependence of photoelectron yield. Obtained results are discussed taking into account the influence of the flux and technology used. Additionally, α particle energy deposition in very thin films is modelled and discussed. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Up‐conversion mechanisms in Er3+ doped YbAG crystals
Authors: Kaczkan Marcin , Borowska Maja , Malinowski Michał , Łukasiewicz Tadeusz , Kołodziejak Katarzyna 
Published: May 2009

AbstractUp‐conversion phenomena leading to the red, green and violet emissions in erbium doped ytterbium‐aluminum garnet (YbAG) are investigated. Absorption and emission spectra and luminescence dynamics from various excited states of YbAG:Er3+ were registered. The low temperature absorption spectra were used to determine Stark levels energies of Er3+ ion in the investigated host. Emissions from the high lying excited states 2G9/2, 4S3/2 and 4F9/2 of Er3+ were characterized under pulsed multi‐photon IR excitation in the region of wavelength corresponding to the strong 2F7/2 → 2F5/2 absorption transition of Yb3+ ions. Using the rate equations formalism the dynamics of the observed emissions were modeled. From the comparison of the measured and calculated decays the energy transfer rates between Yb3+ and Er3+ ions were evaluated. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Reinvestigation of the Fe, Cu and Cr valences in (FeCu)Cr2S4 spinels
Authors: Taubitz Christian , Kuepper Karsten , Raekers Michael , Galakhov Vadim R. , Felea Viorel , Tsurkan Vladimir , Neumann Manfred 
Published: May 2009

AbstractThe valence states of Fe, Cu, and Cr ions in single crystalline Fe1–x Cux Cr2S4 have been studied using X‐ray photoelectron spectroscopy (XPS), X‐ray absorption spectroscopy (XAS) and X‐ray magnetic circular dichroism (XMCD). XPS measurements of compositions x = 0.2, 0.5, 0.6, and 0.9 indicate that the Cu and Cr ions remain mainly in the same valence state over the whole substitution range. XAS, XPS and XMCD investigations of Fe0.5Cu0.5Cr2S4 reveal a sample and preparation dependence of the Cu and Fe spectra. The comparison of the Cu 2p XAS spectrum with a literature measurement shows a change in the amount of Cu2+ explained by the appearance of an additional Cu2+ phase, possibly due to oxidation on the surface. XAS, XPS and XMCD spectra of Fe show a Fe3+ impurity phase present in air‐treated Fe0.5Cu0.5Cr2S4, especially in powdered samples. The lines related to trivalent Fe are found to disappear completely after cleaning the samples in‐situ and only the lines attributed to divalent Fe remain. Since many experimental methods rely on powdered samples and measure in air or in low vacuum, these findings provide an explanation for the differing results concerning the Fe valence obtained by these methods. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Spin‐coupling and hyperfine interaction of the nitrogen donors in 6H‐SiC
Authors: Savchenko Dariya V. , Kalabukhova Ekaterina N. , Kiselev Vitalii S. , Hoentsch Joachim , Pöppl Andreas 
Published: May 2009

AbstractThe X‐, Q‐band field‐sweep electron spin echo (FS ESE) study of n‐type 6H‐SiC wafers shows besides the well known hyperfine (hf) triplet lines of14N on two quasi‐cubic (Nc1, Nc2) and hexagonal (Nh) sites additional triplet lines (Nx) of comparatively low intensity with ag‐tensor of about the average value of the Nc2and Nhspectrum at 4.2 K. The Nxtriplet has half of the hf splitting with respect to the nitrogen residing at cubic sites Nc2. Pulsed electron nuclear double resonance (ENDOR) measurements performed on the NxEPR triplet line demonstrate that there is an efficient spin‐coupling between Nhand Nxnitrogen related centers. The Nxtriplet lines were attributed to distant donor Nc–Nhpairs between nitrogen atoms residing at quasi‐cubic and hexagonal sites having a total electron spinS= 1, which were found before in n‐type 4H‐SiC. Based on Q‐band FS ESE and X‐band pulsed ENDOR measurements the values of the hf interaction for Nc1, Nc2were reassigned with respect to the assignment accepted hitherto.The super hyperfine (shf) interaction with neighboring atoms of nitrogen on the quasi‐cubic lattice sites was studied by FS ESE and pulsed ENDOR. The new shf lines due to29Si and13C atoms with large shf interaction which were not observed previously were found in nitrogen FS ESE and ENDOR spectra. One of them, with the largest shf splitting (23.12 MHz), were attributed to the29Si atoms along thec‐axis in nearest‐neighbor positions of nitrogen on the quasi‐cubic sites which unambiguously confirms that nitrogen substitute carbon lattice site in 6H‐SiC. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Characteristics of Gastric Cancer with Esophageal Invasion and Aspects of Surgical Treatment
Authors: Wakatsuki Kohei , Takayama Tomoyoshi , Ueno Masato , Matsumoto Sohei , Enomoto Koji , Tanaka Tetsuya , Nakajima Yoshiyuki 
Published: May 2009

AbstractBackgroundGastric cancer with esophageal invasion (GCE) is a disease of poor prognosis, and issues pertaining to surgical treatment still remain unresolved. Particularly problematic areas in GCE cases include the need for lower mediastinal lymph node (MSLN) dissection, the most effective surgical approach, and the optimal extent of the esophageal resection. In this study, we evaluate the characteristics of GCE and investigate aspects of surgical treatment.MethodsSixty‐five patients with GCE were surgically treated in our department from 1990 to 2007. Fifty‐two patients with M0 were evaluated for clinicopathological factors, disease recurrence pattern, and prognosis, and 47 patients with R0 resection were evaluated for operative factors.ResultsPatients with MSLN metastasis had significantly poor prognosis. The survival rate significantly differed among patients depending on T‐factor, LN metastasis, MSLN metastasis, and lymphatic vessel invasion, but operative factors were not significant prognostic factors. Multivariate analysis indicated that T‐factor and MSLN metastasis were independent prognostic factors. The peritoneum was the site of the highest recurrence rate (26.9%), followed by the liver (9.6%). Peritoneal recurrence correlated with T‐factor and lymphatic vessel invasion and liver recurrence correlated with MSLN metastasis.ConclusionsIt seems that radical MSLN dissection and extended esophageal resection by thoracotomy have little therapeutic purpose for Siewert Types II or III tumors in GCE if the length of esophageal resection is within 6 cm. Patients with GCE have a poorer prognosis than those with common gastric cancer, and early detection and multimodal treatments for distant metastases are vital for ameliorating clinical outcome in patients with GCE.
Dangerously few liaisons: a review of mate‐finding Allee effects
Authors: Gascoigne Joanna , Berec Ludek , Gregory Stephen , Courchamp Franck 
Published: May 2009

AbstractIn this paper, we review mate‐finding Allee effects from ecological and evolutionary points of view. We define ‘mate‐finding’ as mate searching in mobile animals, and also as the meeting of gametes for sessile animals and plants (pollination). We consider related issues such as mate quality and choice, sperm limitation and physiological stimulation of reproduction by conspecifics, as well as discussing the role of demographic stochasticity in generating mate‐finding Allee effects. We consider the role of component Allee effects due to mate‐finding in generating demographic Allee effects (at the population level). Compelling evidence for demographic Allee effects due to mate‐finding (as well as via other mechanisms) is still limited, due to difficulties in censusing rare populations or a failure to identify underlying mechanisms, but also because of fitness trade‐offs, population spatial structure and metapopulation dynamics, and because the strength of component Allee effects may vary in time and space. Mate‐finding Allee effects act on individual fitness and are thus susceptible to change via natural selection. We believe it is useful to distinguish two routes by which evolution can act to mitigate mate‐finding Allee effects. The first is evolution of characteristics such as calls, pheromones, hermaphroditism, etc. which make mate‐finding more efficient at low density, thus eliminating the Allee effect. Such adaptations are very abundant in the natural world, and may have arisen to avoid Allee effects, although other hypotheses are also possible. The second route is to avoid low density via adaptations such as permanent or periodic aggregation. In this case, the Allee effect is still present, but its effects are avoided. These two strategies may have different consequences in a world where many populations are being artificially reduced to low density: in the first case, population growth rate can be maintained, while in the second case, the mechanism to avoid Allee effects has been destroyed. It is therefore in these latter populations that we predict the greatest evidence for mate‐finding Allee effects and associated demographic consequences. This idea is supported by the existing empirical evidence for demographic Allee effects. Given a strong effect that mate‐finding appears to have on individual fitness, we support the continuing quest to find connections between component mate‐finding Allee effects (individual reproductive fitness) and the demographic consequences. There are many reasons why such studies are difficult, but it is important, particularly given the increasing number of populations and species of conservation concern, that the ecological community understands more about how widespread demographic Allee effects really are, and why.
Extracorporeal membrane oxygenation in a patient with propionic acidaemia: a therapeutic option for cardiac failure
Authors: Mizuguchi K. , Hoshino H. , Nagasawa T. , Kubota M. 
Published: May 2009

SummaryWe report a Japanese girl affected with a neonatal‐onset form of propionic acidaemia (PA). She developed severe metabolic crisis after dehydration at 2 years of age. Bradycardia with complete atrioventricular block responded to haemodiafiltration, but severe cardiac failure was refractory to inotropic treatment. She was diagnosed with acute cardiac dysfunction caused by PA‐induced metabolic crisis. Extracorporeal membrane oxygenation (ECMO), a technique for providing mechanical circulatory support, was required. This is the first case report of a PA patient who recovered from a life‐threatening metabolic crisis with cardiac failure by ECMO. Cardiac failure may be a cause of death, but it is occasionally an under‐recognized complication. Mitochondrial dysfunction in the myocardium due to propionyl‐CoA could contribute to the pathomechanism of cardiac complications of PA. We believe that ECMO should be attempted in PA patients with cardiac failure, in addition to haemodiafiltration and other therapeutic measures, because doing so may lead to the recovery of cardiac dysfunction, as was evident in our patient. In conclusion, prompt investigations and management of cardiac complications should be performed immediately during PA‐induced metabolic crises.
Crystalline Gaq3Nanostructures: Preparation, Thermal Property and Spectroscopy Characterization
Authors: Yu Ya-Wen , Cho Chun-Pei , Perng Tsong-Pyng 
Published: May 2009

Abstract
Crystalline Gaq31-D nanostructures and nanospheres could be fabricated by thermal evaporation under cold trap. The influences of the key process parameters on formation of the nanostructures were also investigated. It has been demonstrated that the morphology and dimension of the nanostructures were mainly controlled by working temperature and working pressure. One-dimensional nanostructures were fabricated at a lower working temperature, whereas nanospheres were formed at a higher working temperature. Larger nanospheres could be obtained when a higher working pressure was applied. The XRD, FTIR, and NMR analyses evidenced that the nanostructures mainly consisted of δ-phase Gaq3. Their DSC trace revealed two small exothermic peaks in addition to the melting endotherm. The one in lower temperature region was ascribed to a transition from δ to β phase, while another in higher temperature region could be identified as a transition from β to δ phase. All the crystalline nanostructures show similar PL spectra due to absence of quantum confinement effect. They also exhibited a spectral blue shift because of a looser interligand spacing and reduced orbital overlap in their δ-phase molecular structures.
Tin Oxide Nanowires: The Influence of Trap States on Ultrafast Carrier Relaxation
Authors: Othonos Andreas , Zervos Matthew , Tsokkou Demetra 
Published: May 2009

Abstract
We have studied the optical properties and carrier dynamics in SnO2nanowires (NWs) with an average radius of 50 nm that were grown via the vapor–liquid solid method. Transient differential absorption measurements have been employed to investigate the ultrafast relaxation dynamics of photogenerated carriers in the SnO2NWs. Steady state transmission measurements revealed that the band gap of these NWs is 3.77 eV and contains two broad absorption bands. The first is located below the band edge (shallow traps) and the second near the center of the band gap (deep traps). Both of these absorption bands seem to play a crucial role in the relaxation of the photogenerated carriers. Time resolved measurements suggest that the photogenerated carriers take a few picoseconds to move into the shallow trap states whereas they take ~70 ps to move from the shallow to the deep trap states. Furthermore the recombination process of electrons in these trap states with holes in the valence band takes ~2 ns. Auger recombination appears to be important at the highest fluence used in this study (500 μJ/cm2); however, it has negligible effect for fluences below 50 μJ/cm2. The Auger coefficient for the SnO2NWs was estimated to be 7.5 ± 2.5 × 10−31 cm6/s.
Field Emission Properties and Fabrication of CdS Nanotube Arrays
Authors: Qian Xuemin , Liu Huibiao , Guo Yanbing , Zhu Shiqun , Song Yinglin , Li Yuliang 
Published: May 2009

Abstract
A large area arrays (ca. 40 cm2) of CdS nanotube on silicon wafer are successfully fabricated by the method of layer-by-layer deposition cycle. The wall thicknesses of CdS nanotubes are tuned by controlling the times of layer-by-layer deposition cycle. The field emission (FE) properties of CdS nanotube arrays are investigated for the first time. The arrays of CdS nanotube with thin wall exhibit better FE properties, a lower turn-on field, and a higher field enhancement factor than that of the arrays of CdS nanotube with thick wall, for which the ratio of length to the wall thickness of the CdS nanotubes have played an important role. With increasing the wall thickness of CdS nanotube, the enhancement factorβ decreases and the values of turn-on field and threshold field increase.