bluuebunny/crossref_metadata_2025_split huggingface dataset:
The androgen‐regulated type II serine protease TMPRSS2 is differentially expressed and mislocalized in prostate adenocarcinoma
Authors: Lucas JM , True L , Hawley S , Matsumura M , Morrissey C , Vessella R , Nelson PS 
Published: February 2008

AbstractTransmembrane serine protease 2 (TMPRSS2) is an androgen‐regulated member of the type two transmembrane protease (TTSP) family. Two other members of the TTSP family, matriptase and hepsin, are over‐expressed in prostate adenocarcinoma and mechanistically influence cancer cell invasion and metastasis. This study was performed to determine TMPRSS2 protein expression in primary and metastatic prostate cancers. We developed a monoclonal antibody capable of the sensitive and specific detection of TMPRSS2 protein. TMPRSS2 regulation by androgen and presence in seminal fluid was measured. TMPRSS2 localization and expression was evaluated in 415 cases of primary prostate cancer and 144 prostate cancer metastases by immunohistochemistry. We determined that TMPRSS2 protein expression is regulated by androgens and that TMPRSS2 is a component of the normal seminal fluid proteome. TMPRSS2 protein is abundantly expressed in the prostate, with low levels in the epithelia of the colon, stomach, epididymis and breast. Pancreatic acini, hepatic bile ducts, testicular Leydig cells and the kidney also express TMPRSS2. In the prostate, TMPRSS2 protein is specifically localized to the secretory epithelium, with enhanced expression in the plasma membrane orientated towards the ductal lumen. TMPRSS2 expression was significantly higher in both neoplastic prostate and in the epithelium of prostatic hyperplasia compared to normal epithelium (p < 0.01). TMPRSS2 expression was further elevated in higher Gleason grade cancers (patterns 4 and 5) compared to pattern 3 (p = 0.04). Furthermore, in most high‐grade cancers, TMPRSS2 was mislocalized, being expressed in the cytoplasm as well as in the cell membrane. Prostate cancer metastases also generally expressed high levels of TMPRSS2. In summary, the TMPRSS2 protease is expressed highly in primary and metastatic prostate cancers and is associated with tumour cell differentiation. Based on studies with the related proteins matriptase and hepsin, TMPRSS2 should be investigated for causal roles in prostate carcinogenesis. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Initial testing (stage 1) of a monoclonal antibody (SCH 717454) against the IGF‐1 receptor by the pediatric preclinical testing program
Authors: Kolb E. Anders , Gorlick Richard , Houghton Peter J. , Morton Christopher L. , Lock Richard , Carol Hernan , Reynolds C. Patrick , Maris John M. , Keir Stephen T. , Billups Catherine A. , Smith Malcolm A. 
Published: February 2008

AbstractBackgroundSCH 717454 (19D12) is a fully human antibody directed against the insulin‐like growth factor 1 receptor (IGF‐1R), which is implicated in the growth and metastatic phenotype of a broad range of malignancies. The activity of SCH 717454 was evaluated against the in vitro and in vivo panels of the Pediatric Preclinical Testing Program (PPTP).ProceduresSCH 717454 was tested against the PPTP in vitro panel at concentrations ranging from 0.01 to 100 nM and was tested against the PPTP in vivo panel at a dose of 0.5 mg per mouse administered twice weekly for 4 weeks via intraperitoneal injection.ResultsSCH 717454 was ineffective at retarding growth of cell lines in the in vitro panel. In vivo, SCH 717454 significantly increased event‐free survival in 20 of 35 (57%) solid tumor xenograft models with tumor regressions in one Ewing sarcoma model (complete response) and 2 osteosarcoma models (maintained complete responses). Using the time to event activity measure, SCH 717454 had intermediate (n = 9) or high (n = 1) activity against 31 evaluable solid tumor xenografts, including xenografts from the rhabdoid tumor, Ewing, rhabdomyosarcoma, glioblastoma, neuroblastoma, and osteosarcoma panels. SCH 717454 showed little activity against the 8 xenografts of the acute lymphoblastic leukemia panel.ConclusionsSCH 717454 demonstrated broad antitumor activity against the PPTP's in vivo solid tumor panels. Further characterization of the molecular predictors of response and of the activity of combinations of SCH 717454 with other anticancer agents are anticipated. Pediatr Blood Cancer 2008;50:1190–1197. © 2008 Wiley‐Liss, Inc.
Mycoplasma pneumoniae and atypical Stevens–Johnson syndrome in a hematopoietic stem cell transplant recipient
Authors: Birch Jennifer , Chamlin Sarah , Duerst Reggie , Jacobsohn David 
Published: February 2008

AbstractStevens–Johnson syndrome (SJS) is not typically reported following hematopoietic stem cell transplant (HSCT). The most severe form of SJS, which is toxic epidermal necrolysis (TEN) has been reported following HSCT, albeit very rarely. We describe a case of Mycoplasma‐associated SJS following HSCT. While this association is commonly reported in previously healthy children, it has not been reported in patients following HSCT. Pediatr Blood Cancer 2008;50:1278–1279. © 2008 Wiley‐Liss, Inc.
Descriptive epidemiology of childhood Langerhans cell histiocytosis in France, 2000–2004
Authors: Guyot‐Goubin Aurélie , Donadieu Jean , Barkaoui Mohamed , Bellec Stéphanie , Thomas Caroline , Clavel Jacqueline 
Published: February 2008

AbstractIntroductionChildhood Langerhans cell histiocytosis (LCH) is a rare and poorly understood multisystemic disease. The French National Registry of Childhood Hematopoietic Malignancies (NRCH) has recorded LCH cases of all subtypes since 2000. The present study describes the data on LCH collected on a national scale over a 5‐year period.Materials and MethodsThe cases were children aged less than 15 years, diagnosed with LCH of any type between 2000 and 2004, and residing in mainland France at the time of diagnosis. Completeness was evaluated by capture–recapture after cross‐checking against the database compiled by the French Langerhans Cell Histiocytosis Study Group.ResultsTwo hundred fifty‐eight cases of LCH were registered. The completeness of the NRCH was estimated to be 97%. The annual incidence rate was 4.6/106 children aged less than 15 years and the sex ratio was 1.2. Bone and skin were the most commonly involved organs at diagnosis. The incidence rate decreased with age from 15.3/106 before 1 year to 2.0/106 after 10 years. The disease was mainly unifocal (2.6/106) and rarely disseminated (0.6/106), but disseminated forms predominated in infants. The overall 2‐year survival rate was 99% (95%CI: [97; 100]). About 30% of the LCH cases were enrolled in a clinical trial at first onset. No case was treated by radiotherapy.ConclusionThis study evidenced the main features of LCH incidence in the overall population and was consistent with previous studies. The NRCH thus appears to be a very promising tool for further elucidation of LCH. Pediatr Blood Cancer 2008;51:71–75. © 2008 Wiley‐Liss, Inc.
A New Concept to Characterize Nonspherical Particles from Multi‐wavelength Depolarization Ratios Based on T‐matrix Computation
Authors: Somekawa Toshihiro , Yamanaka Chihiro , Fujita Masayuki , Galvez Maria Cecillia 
Published: February 2008

AbstractA new concept to derive particle information from depolarization ratios obtained by a simultaneous three‐wavelength depolarization lidar was presented. This new data treatment utilized the wavelength dependence of the ratio of the polarization components in the scattering light based on T‐matrix computation. The results showed that calculated three‐wavelength depolarization ratios can be used to characterize particle sizes of ice particles. Assessing the mixing of spherical and nonspherical aerosols, the presented method successfully reproduced the lidar data in real.
Influence of the germline sequence on the thermodynamic stability and fibrillogenicity of human lambda 6 light chains
Authors: del Pozo Yauner Luis , Ortiz Ernesto , Sánchez Rosalba , Sánchez‐López Rosana , Güereca Leopoldo , Murphy Charles L. , Allen Amy , Wall Jonathan S. , Fernández‐Velasco D. Alejandro , Solomon Alan , Becerril Baltazar 
Published: February 2008

AbstractLight chain‐associated amyloidosis is a fatal disease characterized by the aggregation and pathologic deposition of monoclonal light chain‐related fragments as amyloid fibrils in organs or tissues throughout the body. Notably, it has been observed that proteins encoded by the λ variable light chain (VL) gene segment 6a are invariably associated with amyloid deposition; however, the contribution of the gene to this phenomenon has not been established. In this regard, we have determined the thermodynamic stability and kinetics of in vitro fibrillogenesis of a recombinant (r) VLprotein, designated 6aJL2, which contains the predicted sequences encoded by the 6a and JL2 germline genes. Additionally, we studied a 6a mutant (6aJL2‐Arg25Gly), that is present in ∼25% of all amyloid‐associated λ6 light chains. Remarkably, the wild‐type 6aJL2 protein was more stable than were all known amyloidogenic κ and λ light chains for which stability parameters are available; more importantly, it was even more so (and less fibrillogenic) than the only clinically proven nonamyloidogenic λ6 protein, Jto. Conversely, the mutated 6aJL2‐R25G molecule was considerably less stable and more fibrillogenic than was the native 6aJL2. Our data indicate that the propensity of λ6 light chains to form amyloid can not be attributed to thermodynamic instability of the germline‐encoded Vλ6 domain, but rather, is dependent on sequence alterations that render such proteins amyloidogenic. Proteins 2008. © 2008 Wiley‐Liss, Inc.
PSLDoc: Protein subcellular localization prediction based on gapped‐dipeptides and probabilistic latent semantic analysis
Authors: Chang Jia‐Ming , Su Emily Chia‐Yu , Lo Allan , Chiu Hua‐Sheng , Sung Ting‐Yi , Hsu Wen‐Lian 
Published: February 2008

AbstractPrediction of protein subcellular localization (PSL) is important for genome annotation, protein function prediction, and drug discovery. Many computational approaches for PSL prediction based on protein sequences have been proposed in recent years for Gram‐negative bacteria. We present PSLDoc, a method based on gapped‐dipeptides and probabilistic latent semantic analysis (PLSA) to solve this problem. A protein is considered as a term string composed by gapped‐dipeptides, which are defined as any two residues separated by one or more positions. The weighting scheme of gapped‐dipeptides is calculated according to a position specific score matrix, which includes sequence evolutionary information. Then, PLSA is applied for feature reduction, and reduced vectors are input to five one‐versus‐rest support vector machine classifiers. The localization site with the highest probability is assigned as the final prediction. It has been reported that there is a strong correlation between sequence homology and subcellular localization (Nair and Rost, Protein Sci 2002;11:2836–2847; Yu et al., Proteins 2006;64:643–651). To properly evaluate the performance of PSLDoc, a target protein can be classified into low‐ or high‐homology data sets. PSLDoc's overall accuracy of low‐ and high‐homology data sets reaches 86.84% and 98.21%, respectively, and it compares favorably with that of CELLO II (Yu et al., Proteins 2006;64:643–651). In addition, we set a confidence threshold to achieve a high precision at specified levels of recall rates. When the confidence threshold is set at 0.7, PSLDoc achieves 97.89% in precision which is considerably better than that of PSORTb v.2.0 (Gardy et al., Bioinformatics 2005;21:617–623). Our approach demonstrates that the specific feature representation for proteins can be successfully applied to the prediction of protein subcellular localization and improves prediction accuracy. Besides, because of the generality of the representation, our method can be extended to eukaryotic proteomes in the future. The web server of PSLDoc is publicly available at http://bio‐cluster.iis.sinica.edu.tw/∼bioapp/PSLDoc/. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Mutant bovine odorant‐binding protein: Temperature affects the protein stability and dynamics as revealed by infrared spectroscopy and molecular dynamics simulations
Authors: Marabotti Anna , Lefèvre Thierry , Staiano Maria , Crescenzo Roberta , Varriale Antonio , Rossi Mosè , Pézolet Michel , D'Auria Sabato 
Published: February 2008

AbstractBovine odorant‐binding protein (bOBP), a member of the lipocalin family, presents the so‐called 3D “domain‐swapped” protein structure. In fact, in solution, it appears as a dimer in which each monomer is composed by the classical lipocalin fold, with a central β‐barrel followed by a stretch of residues and the α‐helix domain protruding out of the barrel and crossing the dimer interface. Recently, a deswapped mutant form of bOBP was obtained, in which a Gly residue was inserted after position 121 and the two residues in position 64 and 156 were replaced by Cys residues for restoring the disulfide bridge common to the lipocalin family. In this work, we used Fourier transform infrared spectroscopy and molecular dynamics simulations to investigate the effect of temperature on the structural stability and conformational dynamics of the mutant bOBP. The spectroscopic and molecular simulation data pointed out that the hydrophobic regions of the protein matrix appear to be an important factor for the protein stability and integrity. In addition, it was also found that the mutant bOBP is significantly stabilized by the binding of the ligand, which may have an impact on the biological function of bOBP. The obtained results will allow for a better use of this protein as probe for the design of advanced protein‐based biosensors for the detection of compounds used in the fabrication of explosive powders. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Apo‐parvalbumin as an intrinsically disordered protein
Authors: Permyakov Sergei E. , Bakunts Anush G. , Denesyuk Alexander I. , Knyazeva Ekaterina L. , Uversky Vladimir N. , Permyakov Eugene A. 
Published: February 2008

AbstractRecently defined family of intrinsically disordered proteins (IDP) includes proteins lacking rigid tertiary structure meanwhile fulfilling essential biological functions. Here we show that apo‐state of pike parvalbumin (α‐ and β‐isoforms, pI 5.0 and 4.2, respectively) belongs to the family of IDP, which is in accord with theoretical predictions. Parvalbumin (PA) is a 12‐kDa calcium‐binding protein involved into regulation of relaxation of fast muscles. Differential scanning calorimetry measurements of metal‐depleted form of PA revealed the absence of any thermally induced transitions with measurable denaturation enthalpy along with elevated specific heat capacity, implying the lack of rigid tertiary structure and exposure of hydrophobic protein groups to the solvent. Calcium removal from the PAs causes more than 10‐fold increase in fluorescence intensity of hydrophobic probe bis‐ANS and is accompanied by a decrease in α‐helical content and a marked increase in mobility of aromatic residues environment, as judged by circular dichroism spectroscopy (CD). Guanidinium chloride‐induced unfolding of the apo‐parvalbumins monitored by CD showed the lack of fixed tertiary structure. Theoretical estimation of energetics of the charge–charge interactions in the PAs indicated their pronounced destabilization upon calcium removal, which is in line with sequence‐based predictions of disordered protein chain regions. Far‐UV CD studies of apo‐α‐PA revealed hallmarks of cold denaturation of the protein at temperatures below 20°C. Moreover, a cooperative thermal denaturation transition with mid‐temperature at 10–15°C is revealed by near‐UV CD for both PAs. The absence of detectable enthalpy change in this temperature region suggests continuous nature of the transition. Overall, the theoretical and experimental data obtained show that PA in apo‐state is essentially disordered nevertheless demonstrates complex denaturation behavior. The native rigid tertiary structure of PA is attained upon association of one (α‐PA) or two (β‐PA) calcium ions per protein molecule, as follows from calorimetric and calcium titration data. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Early timing and new combinations to increase the efficacy of neonicotinoid–entomopathogenic nematode (Rhabditida: Heterorhabditidae) combinations against white grubs (Coleoptera: Scarabaeidae)
Authors: Koppenhöfer Albrecht M , Fuzy Eugene M 
Published: February 2008

AbstractBACKGROUND: An investigation was carried out to determine whether new neonicotinoid–nematode combinations and earlier applications against younger larval stages could increase the efficacy of synergistic neonicotinoid–entomopathogenic nematode combinations against white grubs.RESULTS: In the laboratory, combinations of the neonicotinoids imidacloprid and clothianidin and the nematodes Heterorhabditis bacteriophora Poinar and H. zealandica Poinar against third instars were compared. In Anomala orientalis (Waterhouse) and Popillia japonica Newman, H. bacteriophora–imidacloprid combinations showed the most consistent synergism but did not cause significantly higher mortality than H. zealandica–imidacloprid combinations. In Cyclocephala borealis Arrow, there was no clear trend as to which combinations caused the most consistent synergism, but H. zealandica–imidacloprid combinations tended to cause the highest mortalities. In the laboratory, imidacloprid–H. bacteriophora combinations provided more consistent synergism against third‐instar than against second‐instar A. orientalis, but mortality was higher in second instars. In field experiments, imidacloprid–H. bacteriophora combinations against A. orientalis and P. japonica provided more consistent synergism when applied in mid‐September but more consistent control when applied in late August.CONCLUSIONS: Imidacloprid is a better synergist for entomopathogenic nematodes than clothianidin. Imidacloprid–nematode combinations are more effective against second instars than against third instars, allowing rate reductions of both agents to make this approach more competitive with full‐rate applications of neonicotinoid alone. Copyright © 2008 Society of Chemical Industry
Effect of indium‐doped interlayer on the strain relief in GaN films grown on Si(111)
Authors: Wu Jiejun , Zhao Lubing , Zhang Guoyi , Liu Xianglin , Zhu Qinsheng , Wang Zhanguo , Jia Quanjie , Guo Liping , Hu Tiandou 
Published: February 2008

AbstractCrack‐free GaN films have been achieved by inserting an In‐doped low‐temperature (LT) AlGaN interlayer grown on silicon by metalorganic chemical vapor deposition. The relationship between lattice constants c and a obtained by X‐ray diffraction analysis shows that indium doping interlayer can reduce the stress in GaN layers. The stress in GaN decreases with increasing trimethylindium (TMIn) during interlayer growth. Moreover, for a smaller TMIn flow, the stress in GaN decreases dramatically when In acts as a surfactant to improve the crystallinity of the AlGaN interlayer, and for a larger TMIn flow, the stress will increase again. The decreased stress leads to smoother surfaces and fewer cracks for GaN layers by using an In‐doped interlayer than by using an undoped interlayer. In doping has been found to enhance the lateral growth and reduce the growth rate of the c face. It can explain the strain relief and cracks reduction in GaN films. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Enhancement of nonlinear optical properties of Au–TiO2 granular composite with high percolation threshold
Authors: Zhou Z. K. , Li M. , Su X. R. , Zhai Y. Y. , Song H. , Han J. B. , Hao Z. H. 
Published: February 2008

AbstractTwo series of Au–TiO2 composite films with Au percola‐ tion threshold qC of 0.34 and 0.82 were prepared by using sputtering technique at the pressure of 5.0 × 10–2 and 8.0 × 10–2 Torr, respectively. As qC increases from 0.34 to 0.82, the plasmon resonant absorption of the composite films near qC shifts from about 700 nm to 760 nm, and the maximal second harmonic generation (SHG) intensity increases by 20%, the maximal nonlinear absorption coefficient increases from –3.0 × 104 cm/GW to 1.7 × 105 cm/GW, and the maximal nonlinear refraction index increases from a very small value to –2.6 cm2/GW. The large second‐ and third‐order optical nonlinearity of the Au–TiO2 composite films with high qC is attributed to the high density of Au particle in the nonconductive film and the strong local field enhancement caused by the surface plasmon resonant absorption. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Influence of thermal annealing treatment in oxygen atmosphere on grain boundary chemistry and non‐ohmic properties of SnO2·MnO polycrystalline semiconductors
Authors: Orlandi M. O. , Bueno P. R. , Longo E. 
Published: February 2008

AbstractThe present work studied the influence of thermal treatment in oxygen rich atmosphere on heterogeneous junctions in Mn‐doped SnO2 polycrystalline system presenting varistor behavior. The samples were prepared by conventional oxide mixture methodology, and were submitted to heat treatment in oxygen rich atmosphere at 900 °C for 2 h. The samples were characterized by X‐ray diffraction, scanning electron microscopy, dc and ac electrical measurements. The results showed that there is an evident relationship between the microstructure heterogeneity and non‐ohmic electrical properties. It was found that for this SnO2·MnO‐based varistor system the heat treatment in oxygen rich atmosphere does not necessarily increase the varistors' properties, which was related to the decrease in the grain boundary resistance. The results are compared with Co‐doped SnO2 varistors and ZnO based varistors. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Nonlinear electrical characteristics of semi‐insulating GaAs
Authors: Kurt H. Y. , Sadiq Y. , Salamov B. G. 
Published: February 2008

AbstractNonlinear electrical transport processes in a semiconductor‐gas discharge structure with semi‐insulating GaAs are studied for a wide range of gas pressures, interelectrode distances and different diameters of the photocathode areas. A primary destabilization of homogeneous state observed in a planar dc‐driven structure is due to nonlinear transport properties of GaAs photocathode. GaAs samples present N‐shaped negative differential conductivity under high‐electric fields and the presence of the deep electronic levels of defects, the so‐called EL2 centers, gives rise to the N‐type‐NDC of the material, as a consequence, to low‐frequency oscillations in current when a dc voltage of a high enough magnitude is applied to a GaAs photocathode. It is important to note that we have experimentally investigated the above‐mentioned nonlinear electrical characteristics of GaAs by a new‐suggested method and our experimental findings are obviously in good agreement with estimated results reported by other independent authors. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
High resolution measurement of the thermal expansion coefficient of semiconductor multilayer lateral nanostructures
Authors: Brüser B. , Panzner T. , Grigorian S. , Grenzer J. , Zorn M. , Zeimer U. , Pietsch U. 
Published: February 2008

AbstractWe measured the thermal expansion coefficient (TEC) of a vertically stacked multi‐quantum‐well (MQW) structure buried under a thick GaAs top layer before and after lateral patterning of the GaAs top layer. After patterning the TEC of the whole MQW structure differs from that of the planar structure by about 20%. Based on calculations in terms of methods of finite elements the effect is explained by the influence of the strain field originating from the bottom edges of the etched nanostructure. Due to the long range nature of this strain field the strain release within the individual quantum wells changes as a function from the distance from the valley. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)