bluuebunny/crossref_metadata_2025_split huggingface dataset:
Splicing mutation in the fibrillin‐1 gene associated with neonatal Marfan syndrome and severe pulmonary emphysema with tracheobronchomalacia
Authors: Shinawi Marwan , Boileau Catherine , Brik Riva , Mandel Hanna , Bentur Lea 
Published: January 2005

AbstractNeonatal Marfan syndrome is an autosomal‐dominant connective tissue disease with unique clinical manifestations and mutations. We describe the clinical course of an infant with neonatal Marfan syndrome that had the novel IVS31‐2A > G splice site mutation in fibrillin‐1. This mutation affects the second base of the acceptor consensus splice site of intron 31, and probably leads to abnormal splicing events. The patient presented with respiratory distress and heart murmur in early neonatal life. Cardiac evaluation revealed pulmonic stenosis, atrioventricular regurgitation, and a dilated aortic root that were controlled by balloon dilatation of the pulmonic stenosis and medications for congestive heart failure. At age 3 months, he presented with severe respiratory distress caused by upper and lower airway obstruction. Imaging studies showed severe pulmonary emphysema, and a bronchoscopy demonstrated megatracheobronchomalacia, an unusual finding in this syndrome. Subsequently, the patient developed recurrent hyperinflation of the right and left lungs, with emphysematous changes and mediastinal shift. After discussing with his parents the grave prognosis for neonatal Marfan syndrome, he was discharged home with oxygen treatment and died at home at age 4.5 months. This case report demonstrates and discusses pulmonary involvement in neonatal Marfan syndrome and the difficult therapeutic challenges created by the severe cardiopulmonary abnormalities in this invariably fatal condition. Pediatr Pulmonol. 2005; 39:374–378. © 2005 Wiley‐Liss, Inc.
Receptor for advanced glycation end products (RAGE) and its ligand, amphoterin are overexpressed and associated with prostate cancer development
Authors: Ishiguro Hitoshi , Nakaigawa Noboru , Miyoshi Yasuhide , Fujinami Kiyoshi , Kubota Yoshinobu , Uemura Hiroji 
Published: January 2005

AbstractBACKGROUNDAdvanced glycation end products (AGE) are produced with normal aging. Recently, some reports indicated that the interaction between AGE and the cognate receptor (RAGE) has a role in cancer dependent.METHODSWe investigated RAGE and amphoterin mRNA expression in prostate cancer cell lines (DU145, PC‐3, and LNCaP cells), hormone‐refractory prostate cancer tissues, and paired untreated primary prostate cancer and normal prostate (including benign prostatic hypertrophy (BPH)) tissues using real‐time quantitative PCR. Moreover, to confirm the AGE–RAGE interaction in prostate cancer, DU145 cells stimulated with AGE–bovine serum albumin (AGE–BSA) were examined by in vitro matrigel assay, cell viability assay, MTT assay, reverse transcription‐polymerase chain reaction (RT‐PCR), and Western blot.RESULTSDU145 cells, a hormone‐independent prostate cancer cell line, showed the highest RAGE mRNA expression. Amphoterin mRNA was expressed in all three cell lines. In prostate tissues, untreated prostate cancer tissue and hormone‐refractory prostate cancer tissue showed higher RAGE and amphoterin mRNA expression than normal prostate tissue. The AGE–RAGE interaction induced the invasion and growth in DU145 cells stimulated with AGE–BSA.CONCLUSIONSThe AGE–RAGE interaction is important in prostate cancer development, and inhibition of this interaction has potential as a new molecular target for cancer therapy or prevention. © 2005 Wiley‐Liss, Inc.
Prediction of interfaces for oligomerizations of G‐protein coupled receptors
Authors: Nemoto Wataru , Toh Hiroyuki 
Published: January 2005

AbstractSeveral lines of biochemical and pharmacological evidence have suggested that some G‐protein‐coupled receptors (GPCRs) form homo oligomers, hetero oligomers or both. The GPCRs oligomerizations are considered to be related to signal transduction and some diseases. Therefore, an accurate prediction of the residues that interact upon oligomerization interface would further our understanding of signal transduction and the diseases in which GPCRs are involved. One of the complications for such a prediction is that the interfaces differ with the subtypes, even within the same GPCR family. Focusing on the distribution of residues conserved on the molecular surface in a particular subtype, we developed a new method to predict the interface for the GPCR oligomers, and applied it to several subtypes of known GPCRs to check the sensitivity. Subsequently, we found that predicted interfaces of rhodopsin, D2 dopamine receptor and β2 adrenergic receptor agreed with the experimentally suggested interfaces, despite difference in the interface region among the three subtypes. Moreover, a highly conserved residue detected from the D2 dopamine receptor corresponded to a residue involved in a missense change found in the large family of myoclonus dystonia. Our observation suggests the possibility that the disease is caused by the disorder of the oligomerization, although the molecular mechanism of the disease has not been revealed yet. The benefits and the pitfalls of the new method will be discussed, based on the results of the applications. Proteins 2005. © 2004 Wiley‐Liss, Inc.
Parametric oscillation in semiconductor microcavities: nonlinear and quantum effects
Authors: Karr J. Ph. , Baas A. , Romanelli M. , Bramati A. , Giacobino E. 
Published: January 2005

AbstractWe report the observation of optical bistability in a semiconductor microcavity pumped at the “magic angle” above the parametric oscillation threshold. Experimental evidence is given in the form of a hysteresis cycle of the nonlinear emission as a function of the pump intensity. A model analogous to those developped for triply resonant Optical Parametric Oscillators (OPO) is in good agreement with the experimental findings. In the second part, we study the potential application of the parametric oscillation regime to quantum optics. The quantum correlations between the emitted “signal” and “idler” beams are computed. We show that very strong quantum correlations between the signal and idler polaritons can be achieved. However the quantum effects in the outgoing light fields are strongly reduced due to the large mismatch in the coupling of the signal and idler polaritons to the external photons. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Giant light absorption by plasmons in a nanoporous metal film
Authors: Teperik T. V. , Popov V. V. , García de Abajo F. J. 
Published: January 2005

AbstractWe have calculated the light absorption spectra of a metal film containing a hexagonal two‐dimensional lattice of spherical nano‐voids. It is shown that giant resonant absorption of light occurs at the plasma resonance of the void lattice in the visible when the void‐to‐surface distance and the inter‐void spacing are thinner than the skin depth. The maximum absorbance, at plasma resonance, is shown to be 50%. This phenomenon occurs when the void‐to‐surface distance has a specific value, which ensures optimal coupling of plasmons in the voids to the external light. We have found a physical criterion for the optimal coupling, which reads that the radiative broadening of the plasma resonance must be equal to its dissipative broadening in order to produce maximum light absorption at the resonance. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Closely spaced external standard: a universal method of achieving 5 ppm mass accuracy over the entire MALDI plate in axial matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry
Authors: Moskovets Eugene , Chen Hsuan‐Shen , Pashkova Anna , Rejtar Tomas , Andreev Viktor , Karger Barry L. 
Published: January 2005

AbstractClose deposition of the sample and external standard was used in axial matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) to achieve mass accuracy equivalent to that obtained with an internal standard across the entire MALDI plate. In this work, the sample and external standard were deposited by continuous deposition in separate traces, each approximately 200 μm wide. The dependence of the mass accuracy on the distance between the sample and standard traces was determined across a MALDI target plate with dimensions of 57.5 mm × 57.0 mm by varying the gap between the traces from 100 μm to 4 mm. During acquisition, two adjacent traces were alternately irradiated with a 200‐Hz laser, such that the peaks in the resulting mass spectra combined the sample and external standard. Ion suppression was not observed even when the peptide concentrations in the two traces differed by more than two orders of magnitude. The five peaks from the external standard trace were used in a four‐term mass calibration of the masses of the sample trace. The average accuracy across the whole plate with this method was 5 ppm when peaks of the sample trace had signal‐to‐noise ratios of at least 30 and the gap between the traces was approximately 100 μm. This approach was applied to determining peptide masses of a reversed‐phase liquid chromatographic (LC) separation of a tryptic digest of β‐galactosidase deposited as a long serpentine trace across the MALDI plate, with accuracy comparable to that obtainable using internal calibration. In addition, the eluent from reversed‐phase LC separation of a strong cation‐exchange fraction containing tryptic peptides from a yeast lysate along with the closely placed external standard was deposited on the MALDI plate. The data obtained in the MS and MS/MS modes on a MALDI‐TOF/TOF mass spectrometer were combined and used in database searching with MASCOT. Since the significant score is a function of mass accuracy in the MS mode, database searching with high mass accuracy reduced the number of false positives and also added peptides which otherwise would have been eliminated at lower mass accuracy (false negatives). Copyright © 2003 John Wiley & Sons, Ltd.
Improvement of electron capture efficiency by resonant excitation
Authors: Mormann Michael , Peter‐Katalinić Jasna 
Published: January 2005

AbstractA novel pulse sequence improving the efficiency for electron capture dissociation (ECD) of an unmodified Fourier transform ion cyclotron resonance (FTICR) mass spectrometer by more than an order of magnitude is presented. Commercially available FTICR instruments are usually equipped with a filament‐based electron source producing an electron beam that has a rather small cross section. An ideal overlap between the rotating ion cloud and the electron beam appears to be a prerequisite for a high ECD efficiency. A reduced interception of the ion cloud and the electron beam is probably due to the contribution of the magnetron motion to the trajectory of the ions, resulting in a precession about the z‐axis of the instrument. By increasing the kinetic energy and therefore increasing the cyclotron radii of the precursor ions by resonant excitation, the overlap of the rotating ion cloud with the electron beam is improved. By use of this protocol the efficiency of electron capture is substantially increased and consequently the acquisition time of ECD spectra is reduced significantly. The capability of resonant excitation of the precursor ions during the irradiation with electrons is demonstrated for standard peptides. This approach is particularly valuable for analysis and characterization of O‐glycosylated peptides. In addition to amino acid sequence information, the attachment site of the labile glycan moiety is determined, and also radical‐site‐induced fragmentations of the glycosidic bonds are observed. Copyright © 2003 John Wiley & Sons, Ltd.
Probing cell chemistry with time‐of‐flight secondary ion mass spectrometry: development and exploitation of instrumentation for studies of frozen‐hydrated biological material
Authors: Cliff Ben , Lockyer Nicholas , Jungnickel Harald , Stephens Gill , Vickerman John C. 
Published: January 2005

AbstractImaging static secondary ion mass spectrometry (SIMS) offers a powerful method of obtaining molecular information from biological systems with good spatial resolution. However, the technique needs further development to make it suitable for routine analysis of cells. We report here the development of a new freeze‐facture device to facilitate the manipulation and analysis of biological cell material, with the cell chemistry preserved intact by rapid freezing. We illustrate performance characteristics with high‐contrast images of freeze‐fractured, frozen‐hydrated liposomes with the drug clofazamine constrained within the lipid bilayer providing a marker to determine the fracture plane across the liposome structure. By monitoring and imaging clofazamine on the surface of yeast cells in the frozen‐hydrated state, and demonstrating its absence within molecular information from a cell fractured to reveal the cell ultrastructure, we demonstrate that the molecule does not penetrate the cell wall. Copyright © 2003 John Wiley & Sons, Ltd.
Targeted lipidomics using electron capture atmospheric pressure chemical ionization mass spectrometry
Authors: Lee Seon Hwa , Williams Michelle V. , DuBois Raymond N. , Blair Ian A. 
Published: January 2005

AbstractThere is an increasing need to be able to conduct quantitative lipidomics analyses as a complement to proteomics studies. The highest specificity for proteomics analysis can be obtained using methodology based on electrospray ionization (ESI) or atmospheric pressure chemical ionization (APCI) coupled with liquid chromatography/tandem mass spectrometry (LC/MS/MS). For lipidomics analysis it is often necessary to be able to separate enantiomers and regioisomers. This can be very challenging when using methodology based on conventional reversed‐phase chromatography. Normal‐phase chromatography using chiral columns can provide dramatic improvements in the resolution of enantiomers and regioisomers. However, conventional ESI‐ and APCI‐MS/MS has limited sensitivity, which makes it difficult to conduct studies in cell culture systems where only trace amounts of non‐esterified bioactive lipids are present. The use of electron capture APCI‐MS/MS overcomes this problem. Enantiomers and regioisomers of diverse bioactive lipids can be quantified using stable isotope dilution methodology coupled with normal‐phase chiral chromatography and electron capture APCI‐MS/MS. This methodology has allowed a lipidomics profile from rat epithelial cells maintained in culture to be delineated and allowed the effect of a non‐selective lipoxygenase inhibitor to be assessed. Copyright © 2003 John Wiley & Sons, Ltd.
Fast liquid chromatography coupled to electrospray tandem mass spectrometry peptide sequencing for cross‐species protein identification
Authors: Witters Erwin , Laukens Kris , Deckers Peter , Dongen Walter Van , Esmans Eddy , Onckelen Harry Van 
Published: January 2005

AbstractUsing a parallel microcolumn switching liquid chromatography set‐up coupled to a quadrupole time‐of‐flight mass spectrometer, a rapid liquid chromatography/mass spectrometric (LC/MS) protein identification method is presented. Without prior sample clean‐up up to 300 protein digest samples a day can be processed. Using data‐directed acquisition, up to 10 fragmentation analyses for each protein sample can be acquired in the same chromatographic run that can be used for database searching. Using internal peptide sequence information, protein databases and the various nucleic acid databases can both be queried for cross‐species identification of the protein sample. The method was evaluated and put into force to generate data for a tobacco cell culture protein database. Copyright © 2003 John Wiley & Sons, Ltd.
Matrix‐assisted laser desorption/ionization analysis of lipids and high molecular weight hydrocarbons with lithium 2,5‐dihydroxybenzoate matrix
Authors: Cvačka Josef , Svatoš Aleš 
Published: January 2005

AbstractLithium 2,5‐dihydroxybenzoate (LiDHB) is shown to be a very effective matrix for matrix‐assisted laser desorption/ionization (MALDI) analysis of nonpolar long‐chain lipids, hydrocarbons and polymers. Under standard desorption and ionization conditions using a conventional nitrogen UV laser (337 nm), hydrocarbons (C24–C40), diverse lipids (triglycerides, diglycerides, wax esters from leaves) and saturated polymers are effectively lithiated providing [M+Li]+ ions. The formation of lithiated hydrocarbons is not accompanied by an elimination of hydrogen or other fragmentation reactions and, due to the relatively simple isotopic distribution of lithium, seems to be more useable for analysis of hydrocarbon mixtures than the previously used silver cationization agents. The mass calibration can be conveniently performed either externally or internally using poly(ethylene glycol) commercial standards. Copyright © 2003 John Wiley & Sons, Ltd.
Determination of phosphorylation sites in lipooligosaccharides from Pseudoalteromonas haloplanktis TAC 125 grown at 15°C and 25°C by nano‐electrospray ionization quadrupole time‐of‐flight tandem mass spectrometry
Authors: Ummarino S. , Corsaro M. M. , Lanzetta R. , Parrilli M. , Peter‐Katalinić J. 
Published: January 2005

AbstractLipooligosaccharides (LOSs) are macromolecules present on the external cellular membrane of Gram‐negative bacteria, structurally made of two distinct regions, lipid A and Core. By varying their growth temperature, bacteria such as psychrophiles change the phosphorylation distribution of the LOSs produced. The level of phosphorylation and the phosphate group positions in LOSs produced by the extremophile psychrophilic bacterium Pseudoalteromonas haloplanktis TAC 125, grown at 15°C and 25°C, were investigated by nano‐electrospray ionization quadrupole time‐of‐flight mass spectrometry (nanoESI‐QTOF‐MS) and tandem mass spectrometry (MS/MS). The samples, obtained by phenol/chloroform/petroleum ether (PCP) extraction of dried cells, were treated with hydrazine at 37°C in order to reduce the heterogeneity by removal of the ester‐linked fatty acid moieties. The molecular ion distributions in these LOS fractions were investigated in negative ion mode. Based on these data it was postulated that the sample grown at 25°C contained four phosphate groups while that at 15°C contained three. In order to determine phosphorylation sites in sugar chains, the samples were submitted to low collision energy MS/MS for sequencing. In the sample with three phosphates, one was found to be linked to the tetrasaccharide Core region, more precisely to position C‐4 of the Kdo unit. The two remaining phosphate groups were both linked to the 2‐acylamide‐2‐deoxy‐D‐glucopyranose of the lipid A moiety, and two possible distributions could be postulated on the basis of the fragmentation pattern obtained; in the first case both phosphate groups are linked as a pyrophosphate moiety to position C‐1 of the proximal glucosamine (reducing residue), while in the second case one phosphate is linked to position C‐1 of the proximal glucosamine and the other to position C‐4′ of the distal glucosamine (non‐reducing residue). This distribution was also found in the lipid A moiety of the tetraphosphorylated sample grown at 25°C, which bears two phosphate groups on the Core region, one on position C‐4 of the Kdo and the other on position C‐7 or C‐8 of the same residue. The phosphate locations were derived from the intra‐ring cleavage ions of sugar moieties in the LOSs obtained by an optimized CID procedure using negative ion QTOF‐MS/MS. Copyright © 2003 John Wiley & Sons, Ltd.
Proteome analysis of conditioned medium from cultured adult hippocampal progenitors
Authors: Dahl Annika , Eriksson Peter S , Persson Anders I , Karlsson Gosta , Davidsson Pia , Ekman Rolf , Westman‐Brinkmalm Ann 
Published: January 2005

AbstractIt is known that proliferation and survival of neural stem/progenitor cells in vitro not only depend on exogenous factors, but also on autocrine factors secreted into the conditioned medium. It is also well known that the identification of bioactive proteins secreted into the conditioned medium poses a substantial challenge. Recently, neural stem/progenitor cells were shown to secrete a survival factor, cystatin C, into the conditioned medium. Here, we demonstrate an approach to identify other low molecular weight proteins in conditioned medium from cultured adult rat hippocampal progenitor cells. A combination of preparative two‐dimensional gel electrophoresis (2‐DE) and mass spectrometry was utilized in the analysis. We were able to identify a number of proteins, which include Rho‐guanine nucleotide dissociation inhibitor 1, phosphatidylethanolamine binding protein (PEBP), also termed Raf‐1 kinase interacting protein, polyubiquitin, immunophilin FK506 binding protein 12 (FKBP12) and cystatin C. The presence of PEBP and FKBP12 in conditioned medium was confirmed immunologically. All nestin‐positive progenitor cells showed immunoreactivity for antibodies against PEBP and FKBP12. To our knowledge we are the first to use this preparative proteomic approach to search for stem cell factors in conditioned medium. The method could be used to identify novel bioactive proteins secreted by stem/progenitor cells in vitro. Identification of bioactive proteins in vitro is of potential importance for the understanding of the regulatory mechanisms of the cells in vivo. Copyright © 2003 John Wiley & Sons, Ltd.
Micro-structure and Lagrangian statistics
of the scalar field with a mean gradient in
isotropic turbulence
Authors: BRETHOUWER G. , HUNT J. C. R. , NIEUWSTADT F. T. M. 
Published: January 2005

This paper presents an analysis and numerical study of the relations between the
small-scale velocity and scalar fields in fully developed isotropic turbulence with
random forcing of the large scales and with an imposed constant mean scalar
gradient. Simulations have been performed for a range of Reynolds numbers from
Reλ = 22 to 130 and Schmidt numbers from Sc = 1/25 to 144.The simulations show that for all values of Sc [ges ] 0.1 steep scalar gradients are
concentrated in intermittently distributed sheet-like structures with a thickness approximately equal to the Batchelor length scale η/Sc½ with η the Kolmogorov length
scale. We observe that these sheets or cliffs are preferentially aligned perpendicular
to the direction of the mean scalar gradient. Due to this preferential orientation of
the cliffs the small-scale scalar field is anisotropic and this is an example of direct
coupling between the large- and small-scale fluctuations in a turbulent field. The
numerical simulations also show that the steep cliffs are formed by straining motions
that compress the scalar field along the imposed mean scalar gradient in a very short
time period, proportional to the Kolmogorov time scale. This is valid for the whole
range of Sc. The generation of these concentration gradients is amplified by rotation
of the scalar gradient in the direction of compressive strain. The combination of high
strain rate and the alignment results in a large increase of the scalar gradient and
therefore in a large scalar dissipation rate.These results of our numerical study are discussed in the context of experimental
results (Warhaft 2000) and kinematic simulations (Holzer & Siggia 1994). The theoretical arguments developed here follow from earlier work of Batchelor & Townsend
(1956), Betchov (1956) and Dresselhaus & Tabor (1991).